Publications

Karlina, R. ; Lutter, D. ; Miok, V. ; Fischer, D.S. ; Altun, I. ; Schöttl, T. ; Schorpp, K.K. ; Israel, A. ; Cero, C. ; Johnson, J.W. ; Kapser-Fischer, I. ; Böttcher, A. ; Keipert, S. ; Feuchtinger, A. ; Graf, E. ; Strom, T.M. ; Walch, A.K. ; Lickert, H. ; Walzthoeni, T. ; Heinig, M. ; Theis, F.J. ; García-Cáceres, C. ; Cypess, A.M. ; Ussar, S.

Identification and characterization of distinct brown adipocyte subtypes in C57BL/6J mice.

Life Sci. All. 4:e202000924 (2021)

Wörheide, M. ; Krumsiek, J. ; Kastenmüller, G. ; Arnold, M.

Multi-omics integration in biomedical research – A metabolomics-centric review.

Anal. Chim. Acta 1141, 144-162 (2021)

Efendiyev, M.A. ; Vougalter, V.

Solvability in the sense of sequences for some fourth order non-Fredholm operators.

J. Differ. Equations 271, 280-300 (2021)

Fuetterer, C. ; Augustin, T. ; Fuchs, C.

Adapted single-cell consensus clustering (adaSC3).

Adv. Data Anal. Classif., accepted (2020)

Litviňuková, M. ; Talavera-López, C. ; Maatz, H. ; Reichart, D. ; Worth, C.L. ; Lindberg, E.L. ; Kanda, M. ; Polanski, K. ; Heinig, M. ; Lee, M. ; Nadelmann, E.R. ; Roberts, K. ; Tuck, L. ; Fasouli, E.S. ; DeLaughter, D.M. ; McDonough, B. ; Wakimoto, H. ; Gorham, J.M. ; Samari, S. ; Mahbubani, K.T. ; Saeb-Parsy, K. ; Patone, G. ; Boyle, J.J. ; Zhang, H. ; Viveiros, A. ; Oudit, G.Y. ; Bayraktar, O.A. ; Seidman, J.G. ; Seidman, C.E. ; Noseda, M. ; Hubner, N. ; Teichmann, S.A.

Cells of the adult human heart.

Nature 588, 466-472 (2020)

Kranich, J. ; Chlis, N.-K. ; Rausch, L. ; Latha, A. ; Schifferer, M. ; Kurz, T. ; Foltyn-Arfa Kia, A. ; Simons, M. ; Theis, F.J. ; Brocker, T.

In vivo identification of apoptotic and extracellular vesicle-bound live cells using image-based deep learning.

J. Extra. Vesicles 9:1792683 (2020)

Matek, C. ; Spiekermann, K. ; Marr, C.

Zytomorphologische Diagnostik mithilfe von künstlicher Intelligenz (KI).

Tumordiagnos. Ther. 41, 666-668 (2020)

Baloni, P. ; Funk, C.C. ; Yan, J. ; Yurkovich, J.T. ; Kueider-Paisley, A. ; Nho, K. ; Heinken, A. ; Jia, W. ; MahmoudianDehkordi, S. ; Louie, G. ; Saykin, A.J. ; Arnold, M. ; Kastenmüller, G. ; Griffiths, W.J. ; Thiele, I. ; Kaddurah-Daouk, R. ; Price, N.D.

Metabolic network analysis reveals altered bile acid synthesis and metabolism in Alzheimer's Disease.

Cell Rep. Med. 1:100138 (2020)

Lupperger, V. ; Marr, C. ; Chapouton, P.

Reoccurring neural stem cell divisions in the adult zebrafish telencephalon are sufficient for the emergence of aggregated spatiotemporal patterns.

PLoS Biol. 18:e3000708 (2020)

Peschel, S. ; Müller, C. ; von Mutius, E. ; Boulesteix, A.L. ; Depner, M.

NetCoMi: Network construction and comparison for microbiome data in R.

Brief. Bioinform., accepted (2020)

Langenau, J. ; Oluwagbemigun, K. ; Brachem, C. ; Lieb, W. ; di Giuseppe, R. ; Artati, A. ; Kastenmüller, G. ; Weinhold, L. ; Schmid, M. ; Nöthlings, U.

Blood metabolomic profiling confirms and identifies biomarkers of food intake.

Metabolites 10:468 (2020)

Faquih, T. ; van Smeden, M. ; Luo, J. ; le Cessie, S. ; Kastenmüller, G. ; Krumsiek, J. ; Noordam, R. ; van Heemst, D. ; Rosendaal, F.R. ; van Hylckama Vlieg, A. ; Willems van Dijk, K. ; Mook-Kanamori, D.O.

A workflow for missing values imputation of untargeted metabolomics data.

Metabolites 10, 1-23:E486 (2020)

Chlis, N.-K. ; Karlas, A. ; Fasoula, N.-A. ; Kallmayer, M. ; Eckstein, H.H. ; Theis, F.J. ; Ntziachristos, V. ; Marr, C.

A sparse deep learning approach for automatic segmentation of human vasculature in multispectral optoacoustic tomography.

Photoacoustics 20:100203 (2020)

Philipp, J. ; Le Gleut, R. ; von Toerne, C. ; Subedi, P. ; Azimzadeh, O. ; Atkinson, M.J. ; Tapio, S.

Radiation response of human cardiac endothelial cells reveals a central role of the CGAS-sting pathway in the development of inflammation.

Proteomes 8:30 (2020)

Kappelmann, N. ; Arloth, J. ; Georgakis, M.K. ; Czamara, D. ; Rost, N. ; Ligthart, S. ; Khandaker, G.M. ; Binder, E.B.

Dissecting the association between inflammation, metabolic dysregulation, and specific depressive symptoms. A genetic correlation and 2-sample mendelian randomization study.

JAMA psychiatry, accepted (2020)

zu Castell, W. ; Schrenk, H.

Computing the adaptive cycle.

Sci. Rep. 10:18175 (2020)

Filbir, F. ; Liehr, L.

Phase distortion by linear signal transforms.

Front. App. Math. Stat. 6:556585 (2020)

Goba, I. ; Goricanec, D. ; Schum, D. ; Hillenbrand, M. ; Plückthun, A. ; Hagn, F.

Probing the conformation states of neurotensin receptor 1 variants by NMR site-directed methyl labeling.

ChemBioChem, accepted (2020)

Chlis, N.-K. ; Rausch, L. ; Brocker, T. ; Kranich, J. ; Theis, F.J.

Predicting single-cell gene expression profiles of imaging flow cytometry data with machine learning.

Nucleic Acids Res. 48, 11335-11346 (2020)

Pieschner, S. ; Fuchs, C.

Bayesian inference for diffusion processes: Using higher-order approximations for transition densities.

R. Soc. Open Sci. 7:200270 (2020)

Hofmeister, B.T. ; Denkena, J. ; Colomé-Tatché, M. ; Shahryary, Y. ; Hazarika, R. ; Grimwood, J. ; Mamidi, S. ; Jenkins, J. ; Grabowski, P.P. ; Sreedasyam, A. ; Shu, S. ; Barry, K. ; Lail, K. ; Adam, C. ; Lipzen, A. ; Sorek, R. ; Kudrna, D. ; Talag, J. ; Wing, R. ; Hall, D.W. ; Jacobsen, D. ; Tuskan, G.A. ; Schmutz, J. ; Johannes, F. ; Schmitz, R.J.

A genome assembly and the somatic genetic and epigenetic mutation rate in a wild long-lived perennial Populus trichocarpa.

Genome Biol. 21:259 (2020)

Shahryary, Y. ; Symeonidi, A. ; Hazarika, R.R. ; Denkena, J. ; Mubeen, T. ; Hofmeister, B. ; Van Gurp, T. ; Colomé-Tatché, M. ; Verhoeven, K.J.F. ; Tuskan, G. ; Schmitz, R.J. ; Johannes, F.

AlphaBeta: Computational inference of epimutation rates and spectra from high-throughput DNA methylation data in plants.

Genome Biol. 21:33023650 (2020)

Benedetti, E. ; Pučić-Baković, M. ; Keser, T. ; Gerstner, N. ; Büyüközkan, M. ; Štambuk, T. ; Selman, M.H.J. ; Rudan, I. ; Polašek, O. ; Hayward, C. ; Al-Amin, H. ; Suhre, K. ; Kastenmüller, G. ; Lauc, G. ; Krumsiek, J.

A strategy to incorporate prior knowledge into correlation network cutoff selection.

Nat. Commun. 11:5153 (2020)

Sieberts, S.K. ; Perumal, T.M. ; Carrasquillo, M.M. ; Allen, M. ; Reddy, J.S. ; Hoffman, G.E. ; Dang, K.K. ; Calley, J. ; Ebert, P.J. ; Eddy, J. ; Wang, X. ; Greenwood, A.K. ; Mostafavi, S. ; Omberg, L. ; Peters, M.A. ; Logsdon, B.A. ; de Jager, P.L. ; Ertekin-Taner, N. ; Mangravite, L.M. ; The AMP-AD Consortium (Arnold, M.)

Large eQTL meta-analysis reveals differing patterns between cerebral cortical and cerebellar brain regions.

Sci. Data 7:340 (2020)

Fischer, C.A, ; Besora-Casals, L. ; Rolland, S.G. ; Haeussler, S. ; Singh, K. ; Duchen, M. ; Conradt, B. ; Marr, C.

MitoSegNet: Easy-to-use deep learning segmentation for analyzing mitochondrial morphology.

iScience 23:101601 (2020)

Holmberg, O. ; Köhler, N. ; Martins, T. ; Siedlecki, J. ; Herold, T. ; Keidel, L. ; Asani, B. ; Schiefelbein, J. ; Priglinger, S. ; Kortuem, K.U. ; Theis, F.J.

Self-supervised retinal thickness prediction enables deep learning from unlabelled data to boost classification of diabetic retinopathy.

Nat. Mach. Intell. 2, 719-726 (2020)

Jiang, D. ; Christ, S. ; Correa-Gallegos, D. ; Ramesh, P. ; Kalgudde Gopal, S. ; Wannemacher, J. ; Mayr, C. ; Lupperger, V. ; Yu, Q. ; Ye, H. ; Mück-Häusl, M. ; Rajendran, V. ; Wan, L. ; Liu, J. ; Mirastschijski, U. ; Volz, T. ; Marr, C. ; Schiller, H. B. ; Rinkevich, Y.

Injury triggers fascia fibroblast collective cell migration to drive scar formation through N-cadherin.

Nat. Commun. 11:5653 (2020)

Conlon, T.M. ; John-Schuster, G. ; Heide, D. ; Pfister, D. ; Lehmann, M. ; Hu, Y. ; Ertüz, Z. ; López, M.A. ; Ansari, M. ; Strunz, M. ; Mayr, C. ; Ciminieri, C. ; Costa, R. ; Kohlhepp, M.S. ; Guillot, A. ; Güneş, G. ; Jeridi, A. ; Funk, M.C. ; Beroshvili, G. ; Prokosch, S. ; Hetzer, J. ; Verleden, S.E. ; Alsafadi, H.N. ; Lindner, M. ; Burgstaller, G. ; Becker, L. ; Irmler, M. ; Dudek, M. ; Janzen, J. ; Goffin, E. ; Gosens, R. ; Knolle, P. ; Pirotte, B. ; Stöger, T. ; Beckers, J. ; Wagner, D.E. ; Singh, I. ; Theis, F.J. ; Hrabě de Angelis, M. ; O’Connor, T. ; Tacke, F. ; Boutros, M. ; Dejardin, E. ; Eickelberg, O. ; Schiller, H. B. ; Königshoff, M. ; Heikenwalder, M. ; Yildirim, A.Ö.

Inhibition of LTβR signalling activates WNT-induced regeneration in lung.

Nature 588, 151–156 (2020)

Huynh, K. ; Lim, W.L.F. ; Giles, C. ; Jayawardana, K.S. ; Salim, A. ; Mellett, N.A. ; Smith, A.A.T. ; Olshansky, G. ; Drew, B.G. ; Chatterjee, P. ; Martins, I. ; Laws, S.M. ; Bush, A.I. ; Rowe, C.C. ; Villemagne, V.L. ; Ames, D. ; Masters, C.L. ; Arnold, M. ; Nho, K. ; Saykin, A.J. ; Baillie, R. ; Han, X. ; Kaddurah-Daouk, R. ; Meikle, P.J.

Concordant peripheral lipidome signatures in two large clinical studies of Alzheimer’s disease.

Nat. Commun. 11:5698 (2020)

Ebert, K. ; Zwingenberger, G. ; Barbaria, E. ; Keller, S. ; Heck, C. ; Arnold, R. ; Hollerieth, V. ; Mattes, J. ; Geffers, R. ; Raimundez-Alvarez, E. ; Hasenauer, J. ; Luber, B.

Determining the effects of trastuzumab, cetuximab and afatinib by phosphoprotein, gene expression and phenotypic analysis in gastric cancer cell lines.

BMC Cancer 20:1039 (2020)

Ayestaran, I. ; Galhoz, A. ; Spiegel, E ; Sidders, B. ; Dry, J.R. ; Dondelinger, F. ; Bender, A. ; McDermott, U. ; Iorio, F. ; Menden, M.

Identification of intrinsic drug resistance and its biomarkers in high-throughput pharmacogenomic and CRISPR screens.

Patterns 1:100065 (2020)

Dorigatti, E. ; Schubert, B.

Graph-theoretical formulation of the generalized epitope-based vaccine design problem.

PLoS Comput. Biol. 16:e1008237 (2020)

Stadler, E. ; Müller, J.

Analyzing plasmid segregation: Existence and stability of the eigensolution in a non-compact case.

Discrete Contin. Dyn. Syst.-Ser. B 25, 4127-4164 (2020)

Krautenbacher, N. ; Kabesch, M. ; Horak, E. ; Braun-Fahrländer, C. ; Genuneit, J. ; Boznanski, A. ; von Mutius, E. ; Theis, F.J. ; Fuchs, C. ; Ege, M.J. ; GABRIELA, PASTURE study groups

Asthma in farm children is more determined by genetic polymorphisms and in non-farm children by environmental factors.

Pediatr. Allergy Immunol., accepted (2020)

Grech, V. ; Scherb, H.

COVID-19: Mathematical estimation of delay to deaths in relation to upsurges in positive rates.

Early Hum. Dev., accepted (2020)

Forstner, A. ; Krahmer, F. ; Melnyk, O. ; Sissouno, N.

Well-conditioned ptychograpic imaging via lost subspace completion.

Inverse Probl. 36:105009 (2020)

Rajewsky, N. ; Almouzni, G. ; Gorski, S.A. ; Aerts, S. ; Amit, I. ; Bertero, M.G. ; Bock, C. ; Bredenoord, A.L. ; Cavalli, G. ; Chiocca, S. ; Clevers, H. ; de Strooper, B. ; Eggert, A. ; Ellenberg, J. ; Fernández, X.M. ; Figlerowicz, M. ; Gasser, S.M. ; Hubner, N. ; Kjems, J. ; Knoblich, J.A. ; Krabbe, G. ; Lichter, P. ; Linnarsson, S. ; Marine, J.C. ; Marioni, J. ; Marti-Renom, M.A. ; Netea, M.G. ; Nickel, D. ; Nollmann, M. ; Novak, H.R. ; Parkinson, H. ; Piccolo, S. ; Pinheiro, I. ; Pombo, A. ; Popp, C. ; Reik, W. ; Roman-Roman, S. ; Rosenstiel, P. ; Schultze, J.L. ; Stegle, O. ; Tanay, A. ; Testa, G. ; Thanos, D. ; Theis, F.J. ; Torres-Padilla, M.E. ; Valencia, A. ; Vallot, C. ; van Oudenaarden, A. ; Vidal, M. ; Voet, T. ; LifeTime Community (Schiller, H. B.) ; LifeTime Community (Ziegler, A.-G.)

LifeTime and improving European healthcare through cell-based interceptive medicine.

Nature, accepted (2020)

Lasser, R. ; Obermaier, J.

Weighted shift operators, orthogonal polynomials and chain sequences.

Acta Sci. Math. 86, 331-342 (2020)

Wang, J. ; Wei, R. ; Xie, G. ; Arnold, M. ; Kueider-Paisley, A. ; Louie, G. ; Mahmoudian Dehkordi, S. ; Blach, C. ; Baillie, R. ; Han, X. ; de Jager, P.L. ; Bennett, D.A. ; Kaddurah-Daouk, R. ; Jia, W.

Peripheral serum metabolomic profiles inform central cognitive impairment.

Sci. Rep. 10:14059 (2020)

Fischer, D.S. ; Wu, Y. ; Schubert, B. ; Theis, F.J.

Predicting antigen specificity of single T cells based on TCR CDR3 regions.

Mol. Syst. Biol. 16:e9416 (2020)

Huang, J. ; Huth, C. ; Covic, M. ; Troll, M. ; Adam, J. ; Zukunft, S. ; Prehn, C. ; Wang, L. ; Nano, J. ; Scheerer, M.F. ; Neschen, S. ; Kastenmüller, G. ; Suhre, K. ; Laxy, M. ; Schliess, F. ; Gieger, C. ; Adamski, J. ; Hrabě de Angelis, M. ; Peters, A. ; Wang-Sattler, R.

Machine learning approaches reveal metabolic signatures of incident chronic kidney disease in individuals with prediabetes and type 2 diabetes.

Diabetes 69, 2756-2765 (2020)

Strunz, M. ; Simon, L. ; Ansari, M. ; Kathiriya, J.J. ; Angelidis, I. ; Mayr, C. ; Tsidiridis, G. ; Lange, M. ; Mattner, L. ; Yee, M. ; Ogar, P. ; Sengupta, A. ; Kukhtevich, I. ; Schneider, R. ; Zhao, Z. ; Voss, C. ; Stöger, T. ; Neumann, J.H.L. ; Hilgendorff, A. ; Behr, J. ; O'Reilly, M. ; Lehmann, M. ; Burgstaller, G. ; Königshoff, M. ; Chapman, H.A. ; Theis, F.J. ; Schiller, H. B.

Alveolar regeneration through a Krt8+transitional stem cell state that persists in human lung fibrosis.

Nat. Commun. 11:3559 (2020)

Spriewald, S. ; Stadler, E. ; Hense, B.A. ; Münch, P.C. ; McHardy, A.C. ; Weiss, A.S. ; Obeng, N. ; Müller, J. ; Stecher, B.

Evolutionary stabilization of cooperative toxin production through a bacterium-plasmid-phage interplay.

mBio 11:e00912-20 (2020)

Schmiester, L. ; Weindl, D. ; Hasenauer, J.

Parameterization of mechanistic models from qualitative data using an efficient optimal scaling approach.

J. Math. Biol. 81, 603–623 (2020)

Storath, M. ; Weinmann, A.

Wavelet sparse regularization for manifold-valued data.

Multiscale Model. Simul. 18, 674-706 (2020)

Kling, M.A. ; Goodenowe, D.B. ; Senanayake, V. ; MahmoudianDehkordi, S. ; Arnold, M. ; Massaro, T.J. ; Baillie, R. ; Han, X. ; Leung, Y.Y. ; Saykin, A.J. ; Nho, K. ; Kueider-Paisley, A. ; Tenenbaum, J.D. ; Wang, L.S. ; Shaw, L.M. ; Trojanowski, J.Q. ; Kaddurah-Daouk, R.F.

Circulating ethanolamine plasmalogen indices in Alzheimer's disease: Relation to diagnosis, cognition, and CSF tau.

Alzheimers Dement. 16, 1234-1247 (2020)

Ostaszewski, M. ; Mazein, A. ; Gillespie, M.E. ; Kuperstein, I. ; Niarakis, A. ; Hermjakob, H. ; Pico, A.R. ; Willighagen, E.L. ; Evelo, C.T. ; Hasenauer, J. ; Schreiber, F. ; Dräger, A. ; Demir, E. ; Wolkenhauer, O. ; Furlong, L.I. ; Barillot, E. ; Dopazo, J. ; Orta-Resendiz, A. ; Messina, F. ; Valencia, A. ; Funahashi, A. ; Kitano, H. ; Auffray, C. ; Balling, R. ; Schneider, R.

Author Correction: COVID-19 Disease Map, building a computational repository of SARS-CoV-2 virus-host interaction mechanisms (Scientific Data, (2020), 7, 1, (136), 10.1038/s41597-020-0477-8).

Sci. Data 7:247 (2020)

Behzadi, S. ; Müller, N.S. ; Plant, C. ; Böhm, C.

Clustering of mixed-type data considering concept hierarchies: Problem specification and algorithm.

Int. J. Data Sci. Anal. 10, 233–248 (2020)

Bergen, V. ; Lange, M. ; Peidli, S. ; Wolf, F.A. ; Theis, F.J.

Generalizing RNA velocity to transient cell states through dynamical modeling.

Nat. Biotechnol., accepted (2020)

Scherb, H. ; Hayashi, K.

Spatiotemporal association of low birth weight with Cs-137 deposition at the prefecture level in Japan after the Fukushima nuclear power plant accidents: An analytical-ecologic epidemiological study.

Environ. Health 19:82 (2020)

Beyerlein, A. ; Lack, N. ; Maier, W.

Associations of area-level deprivation with adverse obstetric and perinatal outcomes in Bavaria, Germany: Results from a cross-sectional study.

PLoS ONE 15:e0236020 (2020)

Noordam, R. ; van Heemst, D. ; Suhre, K. ; Krumsiek, J. ; Mook-Kanamori, D.O.

Proteome-wide assessment of diabetes mellitus in Qatari identifies IGFBP-2 as a risk factor already with early glycaemic disturbances.

Arch. Biochem. Biophys. 689:108476 (2020)

Combettes, P.L. ; Müller, C.

Regression models for compositional data: General log-contrast formulations, proximal optimization, and microbiome data applications.

Stat. Biosci., accepted (2020)

Schälte, Y. ; Hasenauer, J.

Efficient exact inference for dynamical systems with noisy measurements using sequential approximate Bayesian computation.

Bioinformatics 36, 1, 551-559 (2020)

Juárez-Saldivar, A. ; Schroeder, M. ; Salentin, S. ; Haupt, V.J. ; Saavedra, E. ; Vázquez, C. ; Reyes-Espinosa, F. ; Herrera-Mayorga, V. ; Villalobos-Rocha, J.C. ; Garcia Perez, C. ; Campillo, N.E. ; Rivera, G.

Computational drug repositioning for chagas disease using protein-ligand interaction profiling.

Int. J. Mol. Sci. 21:4270 (2020)

Benedetti, E. ; Gerstner, N. ; Pučić-Baković, M. ; Keser, T. ; Reiding, K.R. ; Ruhaak, L.R. ; Štambuk, T. ; Selman, M.H.J. ; Rudan, I. ; Polašek, O. ; Hayward, C. ; Beekman, M. ; Slagboom, E. ; Wuhrer, M. ; Dunlop, M.G. ; Lauc, G. ; Krumsiek, J.

Systematic evaluation of normalization methods for glycomics data based on performance of network inference.

Metabolites 10:271 (2020)

Stegelmann, F. ; Wille, K. ; Busen, H. ; Fuchs, C. ; Schauer, S. ; Sadjadian, P. ; Becker, T. ; Kolatzki, V. ; Döhner, H. ; Stadler, R. ; Döhner, K. ; Griesshammer, M.

Significant association of cutaneous adverse events with hydroxyurea: Results from a prospective non-interventional study inBCR-ABL1-negative myeloproliferative neoplasms (MPN)-on behalf of the German Study Group-MPN.

Leukemia, accepted (2020)

Haimerl, P. ; Bernhardt, U. ; Schindela, S. ; Henkel, F. ; Lechner, A. ; Zissler, U.M. ; Pastor, X. ; Thomas, D. ; Cecil, A. ; Ge, Y. ; Haid, M. ; Prehn, C. ; Tokarz, J. ; Heinig, M. ; Adamski, J. ; Schmidt-Weber, C.B. ; Chaker, A. ; Esser-von Bieren, J.

Inflammatory macrophage memory in nonsteroidal anti-inflammatory drug–exacerbated respiratory disease.

J. Allergy Clin. Immunol., accepted (2020)

Radon, K. ; Saathoff, E. ; Pritsch, M. ; Guggenbühl Noller, J.M. ; Kroidl, I. ; Olbrich, L. ; Thiel, V. ; Diefenbach, M. ; Riess, F. ; Förster, F. ; Theis, F.J. ; Wieser, A. ; Hoelscher, M. ; the KoCo19 collaboration group (Hasenauer, J. ; Castelletti, N. ; Zeggini, E. ; Laxy, M. ; Leidl, R. ; Schwettmann, L.) ; the KoCo19 collaboration group (Fuchs, C.)

Protocol of a population-based prospective COVID-19 cohort study Munich, Germany (KoCo19).

BMC Public Health 20:1036 (2020)

Naulaerts, S. ; Menden, M. ; Ballester, P.J.

Concise polygenic models for cancer-specific identification of drug-sensitive tumors from their multi-omics profiles.

Biomolecules 10:963 (2020)

Höllbacher, B. ; Balazs, K. ; Heinig, M. ; Uhlenhaut, N.H.

Seq-ing answers: Current data integration approaches to uncover mechanisms of transcriptional regulation.

Comp. Struc. Biotech. J. 18, 1330-1341 (2020)

Müller, J.B. ; Geyer, P.E. ; Colaço, A.R. ; Treit, P.V. ; Strauss, M.T. ; Oroshi, M. ; Doll, S. ; Virreira Winter, S. ; Bader, J.M. ; Koehler, N. ; Theis, F.J. ; Santos, A. ; Mann, M.

The proteome landscape of the kingdoms of life.

Nature, accepted (2020)

Banga, J. ; Frappart, L. ; Hasenauer, J. ; Herault, Y. ; Jonkers, J. ; Koubi, D. ; Lange, B. ; Lines, G.T. ; Plouidou, A. ; Rinner, O.

Predictive modeling, applied to genetically engineered mouse models of breast or lung cancer, provides insights into major oncogenic pathways.

Cancer Res. 80, 35-35 (2020)

Hulstaert, E. ; Morlion, A. ; Cobos, F.A. ; Verniers, K. ; Nuytens, J. ; Eynde, E.V. ; Yigit, N. ; Anckaert, J. ; Geerts, A. ; Hindryckx, P. ; Jacques, P. ; Brusselle, G. ; Bracke, K. ; Maes, T. ; Malfait, T. ; Derveaux, T. ; Ninclaus, V. ; Van Cauwenbergh, C. ; Roelens, K. ; Roets, E. ; Hemelsoet, D. ; Tilleman, K. ; Brochez, L. ; Kuersten, S. ; Simon, L. ; Karg, S. ; Nohammer, C. ; Kautzky-Willers, A. ; Leutner, M. ; Slaby, O. ; Schroth, G. ; Vandesompele, J. ; Mestdagh, P.

Charting extracellular transcriptomes in The Human Biofluid RNA Atlas.

Clin. Cancer Res. 26, 33-34 (2020)

Radzikowska, U. ; Ding, M. ; Tan, G. ; Zhakparov, D. ; Peng, Y. ; Wawrzyniak, P. ; Wang, M. ; Li, S. ; Morita, H. ; Altunbulakli, C. ; Reiger, M. ; Neumann, A.U. ; Lunjani, N. ; Traidl-Hoffmann, C. ; Nadeau, K. ; O'Mahony, L. ; Akdis, C.A. ; Sokolowska, M.

Distribution of ACE2, CD147, CD26, and other SARS-CoV-2 associated molecules in tissues and immune cells in health and in asthma, COPD, obesity, hypertension, and COVID-19 risk factors.

Allergy 75, 2829-2845 (2020)

Bheda, P. ; Aguilar-Gomez, D. ; Becker, N.B. ; Becker, J. ; Stavrou, E. ; Kukhtevich, I. ; Höfer, T. ; Maerkl, S. ; Charvin, G. ; Marr, C. ; Kirmizis, A. ; Schneider, R.

Single-cell tracing dissects regulation of maintenance and inheritance of transcriptional reinduction memory.

Mol. Cell 78, 915-925 (2020)

Yang, M. ; Jaaks, P. ; Dry, J. ; Garnett, M. ; Menden, M. ; Saez-Rodriguez, J.

Stratification and prediction of drug synergy based on target functional similarity.

NPJ Syst. Biol. Appl. 6:16 (2020)

Becker, M. ; Noll-Puchta, H. ; Amend, D. ; Nolte, F. ; Fuchs, C. ; Jeremias, I. ; Braun, C.J.

CLUE: A bioinformatic and wet-lab pipeline for multiplexed cloning of custom sgRNA libraries.

Nucleic Acids Res. 48:e78 (2020)

Ostaszewski, M. ; Mazein, A. ; Gillespie, M.E. ; Kuperstein, I. ; Niarakis, A. ; Hermjakob, H. ; Pico, A.R. ; Willighagen, E.L. ; Evelo, C.T. ; Hasenauer, J. ; Schreiber, F. ; Dräger, A. ; Demir, E. ; Wolkenhauer, O. ; Furlong, L.I. ; Barillot, E. ; Dopazo, J. ; Orta-Resendiz, A. ; Messina, F. ; Valencia, A. ; Funahashi, A. ; Kitano, H. ; Auffray, C. ; Balling, R. ; Schneider, R.

COVID-19 Disease Map, building a computational repository of SARS-CoV-2 virus-host interaction mechanisms.

Sci. Data 7:136 (2020)

Filbir, F. ; Occorsio, D. ; Themistoclakis, W.

Approximation of finite Hilbert and Hadamard transforms by using equally spaced nodes.

Mathematics 8:542 (2020)

Matek, C. ; Schwarz, S. ; Spiekermann, K. ; Marr, C.

Abstract: Recognition of AML blast cells in a curated single-cell dataset of leukocyte morphologies using deep convolutional neural networks.

In: Bildverarbeitung für die Medizin 2020. 2020. 53-54 (Inf. aktuell)

Herkt, C.E. ; Caffrey, B.E. ; Surmann, K. ; Blankenburg, S. ; Gesell Salazar, M. ; Jung, A.L. ; Herbel, S.M. ; Hoffmann, K. ; Schulte, L.N. ; Chen, W. ; Sittka-Stark, A. ; Völker, U. ; Vingron, M. ; Marsico, A. ; Bertrams, W. ; Schmeck, B.

A miRNA network controls Legionella pneumophila replication in human macrophages via LGALS8 and MX1.

mBio 11:e03155-19 (2020)

Ziegler, C.G.K. ; Allon, S.J. ; Nyquist, S.K. ; Mbano, I.M. ; Miao, V.N. ; Tzouanas, C.N. ; Cao, Y. ; Yousif, A.S. ; Bals, J. ; Hauser, B.M. ; Feldman, J. ; Muus, C. ; Wadsworth, M.H. ; Kazer, S.W. ; Hughes, T.K. ; Doran, B. ; Gatter, G.J. ; Vukovic, M. ; Taliaferro, F. ; Mead, B.E. ; Guo, Z. ; Wang, J.P. ; Gras, D. ; Plaisant, M. ; Ansari, M. ; Angelidis, I. ; Adler, H. ; Sucre, J.M.S. ; Taylor, C.J. ; Lin, B. ; Waghray, A. ; Mitsialis, V. ; Dwyer, D.F. ; Buchheit, K.M. ; Boyce, J.A. ; Barrett, N.A. ; Laidlaw, T.M. ; Carroll, S.L. ; Colonna, L. ; Tkachev, V. ; Peterson, C.W. ; Yu, A. ; Zheng, H.B. ; Gideon, H.P. ; Winchell, C.G. ; Lin, P.L. ; Bingle, C.D. ; Snapper, S.B. ; Kropski, J.A. ; Theis, F.J. ; Schiller, H. B. ; Zaragosi, L.E. ; Barbry, P. ; Leslie, A. ; Kiem, H.P. ; Flynn, J.L. ; Fortune, S.M. ; Berger, B. ; Finberg, R.W. ; Kean, L.S. ; Garber, M. ; Schmidt, A.G. ; Lingwood, D. ; Shalek, A.K. ; Ordovas-Montanes, J.

SARS-CoV-2 receptor ACE2 is an interferon-stimulated gene in human airway epithelial cells and is detected in specific cell subsets across tissues.

Cell 181, 1016-1035 (2020)

Solovey, M. ; Scialdone, A.

COMUNET: A tool to explore and visualize intercellular communication.

Bioinformatics 36, 4296-4300 (2020)

Schuh, L. ; Saint-Antoine, M. ; Sanford, E.M. ; Emert, B.L. ; Singh, A. ; Marr, C. ; Raj, A. ; Goyal, Y.

Gene networks with transcriptional bursting recapitulate rare transient coordinated high expression states in cancer.

Cell Syst. 10, 363-378.e12 (2020)

Lopez Garcia, A. ; Tran, V. ; Alic, A.S. ; Caballer, M. ; Plasencia, I.C. ; Costantini, A. ; Dlugolinsky, S. ; Duma, D.C. ; Donvito, G. ; Gomes, J. ; Heredia Cacha, I. ; De Lucas, J.M. ; Ito, K. ; Kozlov, V.Y. ; Nguyen, G. ; Orviz Fernandez, P. ; Sustr, Z. ; Wolniewicz, P. ; Antonacci, M. ; zu Castell, W. ; David, M. ; Hardt, M. ; Lloret Iglesias, L. ; Molto, G. ; Plociennik, M.

A cloud-based framework for machine learning workloads and applications.

IEEE Access 8, 18681-18692 (2020)

Efendiyev, M.A. ; Otani, M. ; Eberl, H.J.

Mathematical analysis of a PDE-ode coupled model of mitochondrial swelling with degenerate calcium ion diffusion.

SIAM J. Math. Anal. 52, 543-569 (2020)

Deering, K. ; Spiegel, E. ; Quaisser, C. ; Nowak, D. ; Rakete, S. ; Garí, M. ; Bose-O'Reilly, S.

Exposure assessment of toxic metals and organochlorine pesticides among employees of a natural history museum.

Environ. Res. 184:109271 (2020)

Rondina, M.T. ; Voora, D. ; Simon, L. ; Schwertz, H. ; Harper, J.F. ; Lee, O. ; Bhatlekar, S.C. ; Li, Q. ; Eustes, A.S. ; Montenont, E. ; Campbell, R.A. ; Tolley, N.D. ; Kosaka, Y. ; Weyrich, A.S. ; Bray, P.F. ; Rowley, J.W.

Longitudinal RNA-Seq analysis of the reeatability of gene expression and splicing in human platelets identifies a platelet SELP splice QTL.

Circ. Res. 126, 501-516 (2020)

Sachs, S. ; Bastidas-Ponce, A. ; Tritschler, S. ; Bakhti, M. ; Böttcher, A. ; Sánchez-Garrido, M.A. ; Tarquis Medina, M. ; Kleinert, M. ; Fischer, K. ; Jall, S. ; Harger, A. ; Bader, E. ; Roscioni, S. ; Ussar, S. ; Feuchtinger, A. ; Yesildag, B. ; Neelakandhan, A. ; Jensen, C.B. ; Cornu, M. ; Yang, B. ; Finan, B. ; DiMarchi, R.D. ; Tschöp, M.H. ; Theis, F.J. ; Hofmann, S.M. ; Müller, T.D. ; Lickert, H.

Author Correction: Targeted pharmacological therapy restores β-cell function for diabetes remission (Nature Metabolism, (2020), 2, 2, (192-209), 10.1038/s42255-020-0171-3).

Nat. Metab. 2, 380 (2020)

Jiang, D. ; Ramesh, P. ; Christ, S. ; Correa-Gallegos, D. ; Gopal, S.K. ; Yu, Q. ; Lupperger, V. ; Marr, C. ; Rinkevich, Y.

Scar formation is driven by N-cadherin dependent collective fibroblast migration.

Wound Repair Regen. 28, A16-A16 (2020)

Chouvarine, P. ; Giera, M. ; Kastenmüller, G. ; Artati, A. ; Adamski, J. ; Bertram, H. ; Hansmann, G.

Trans-right ventricle and transpulmonary metabolite gradients in human pulmonary arterial hypertension.

Heart 106, 1332-1341 (2020)

Kozak, E.L. ; Palit, S. ; Miranda Rodriguez, J.R. ; Janjic, A. ; Böttcher, A. ; Lickert, H. ; Enard, W. ; Theis, F.J. ; López-Schier, H.

Epithelial planar bipolarity emerges from Notch-mediated asymmetric inhibition of Emx2.

Curr. Biol. 30, 1142-1151 (2020)

Efendiyev, M.A. ; Vougalter, V.

Solivability of some integro-differential equations with drift.

Osaka J. Math. 57, 247-265 (2020)

Lähnemann, D. ; Köster, J. ; Szczurek, E. ; McCarthy, D.J. ; Hicks, S.C. ; Robinson, M.D. ; Vallejos, C.A. ; Campbell, K.R. ; Beerenwinkel, N. ; Mahfouz, A. ; Pinello, L. ; Skums, P. ; Stamatakis, A. ; Attolini, C.S.O. ; Aparicio, S. ; Baaijens, J. ; Balvert, M. ; Barbanson, B.d. ; Cappuccio, A. ; Corleone, G. ; Dutilh, B.E. ; Florescu, M. ; Guryev, V. ; Holmer, R. ; Jahn, K. ; Lobo, T.J. ; Keizer, E.M. ; Khatri, I. ; Kielbasa, S.M. ; Korbel, J.O. ; Kozlov, A.M. ; Kuo, T.H. ; Lelieveldt, B.P.F. ; Mandoiu, I.I. ; Marioni, J.C. ; Marschall, T. ; Mölder, F. ; Niknejad, A. ; Raczkowski, L. ; Reinders, M. ; Ridder, J.d. ; Saliba, A.E. ; Somarakis, A. ; Stegle, O. ; Theis, F.J. ; Yang, H. ; Zelikovsky, A. ; McHardy, A.C. ; Raphael, B.J. ; Shah, S.P. ; Schönhuth, A.

Eleven grand challenges in single-cell data science.

Genome Biol. 21:31 (2020)

Strunz, M. ; Simon, L. ; Ansari, M. ; Mattner, L. ; Angelidis, I. ; Mayr, C. ; Kathiriya, J. ; Yee, M. ; Ogar, P. ; Voss, C. ; Stöger, T. ; Kukhtevich, I. ; Schneider, R. ; Lehmann, M. ; Koenigshoff, M. ; Burgstaller, G. ; O'Reilly, M. ; Chapman, H. ; Theis, F.J. ; Schiller, H. B.

Fate trajectory modeling reveals convergence of airway derived progenitors and AT2 cells on transient KRT8+alveolar cell state during lung regeneration.

Wound Repair Regen. 28, A7-A7 (2020)

Arnold, M. ; Nho, K. ; Kueider-Paisley, A. ; Massaro, T. ; Huynh, K. ; Brauner, B. ; MahmoudianDehkordi, S. ; Louie, G. ; Moseley, M.A. ; Thompson, J.W. ; St John-Williams, L. ; Tenenbaum, J.D. ; Blach, C. ; Chang, R. ; Brinton, R.D. ; Baillie, R. ; Han, X. ; Trojanowski, J.Q. ; Shaw, L.M. ; Martins, R. ; Weiner, M.W. ; Trushina, E. ; Toledo, J.B. ; Meikle, P.J. ; Bennett, D.A. ; Krumsiek, J. ; Doraiswamy, P.M. ; Saykin, A.J. ; Kaddurah-Daouk, R. ; Kastenmüller, G.

Sex and APOE ε4 genotype modify the Alzheimer’s disease serum metabolome.

Nat. Commun. 11:1148 (2020)

van der Wijst, M. ; de Vries, D.H. ; Groot, H.E. ; Trynka, G. ; Hon, C.C. ; Bonder, M.J. ; Stegle, O. ; Nawijn, M.C. ; Idaghdour, Y. ; van der Harst, P. ; Ye, C.J. ; Powell, J. ; Theis, F.J. ; Mahfouz, A. ; Heinig, M. ; Franke, L.

The single-cell eQTLGen consortium.

eLife 9:e52155 (2020)

Nag, A. ; Kurushima, Y. ; Bowyer, R.C.E. ; Wells, P.M. ; Weiss, S. ; Pietzner, M. ; Kocher, T. ; Raffler, J. ; Völker, U. ; Mangino, M. ; Spector, T.D. ; Milburn, M.V. ; Kastenmüller, G. ; Mohney, R.P. ; Suhre, K. ; Menni, C. ; Steves, C.J.

Genome-wide scan identifies novel genetic loci regulating salivary metabolite levels.

Hum. Mol. Genet. 29, 864-875 (2020)

Combettes, P.L. ; Müller, C.

Perspective maximum likelihood-type estimation via proximal decomposition.

Electron. J. Statist. 14, 207-238 (2020)

Otto, L. ; Budde, K. ; Kastenmüller, G. ; Kaul, A. ; Völker, U. ; Völzke, H. ; Adamski, J. ; Kühn, J.P. ; Krumsiek, J. ; Artati, A. ; Nauck, M. ; Friedrich, N. ; Pietzner, M.

Associations between adipose tissue volume and small molecules in plasma and urine among asymptomatic subjects from the general population.

Sci. Rep. 10:1487 (2020)

Angerer, P. ; Fischer, D.S. ; Theis, F.J. ; Scialdone, A. ; Marr, C.

Automatic identification of relevant genes from low-dimensional embeddings of single-cell RNA-seq data.

Bioinformatics 36, 4291-4295 (2020)

Schlosser, P. ; Li, Y. ; Sekula, P. ; Raffler, J. ; Grundner-Culemann, F. ; Pietzner, M. ; Cheng, Y. ; Wuttke, M. ; Steinbrenner, I. ; Schultheiss, U.T. ; Kotsis, F. ; Kacprowski, T. ; Forer, L. ; Hausknecht, B. ; Ekici, A.B. ; Nauck, M. ; Völker, U. ; Walz, G. ; Oefner, P.J. ; Kronenberg, F. ; Mohney, R.P. ; Köttgen, M. ; Suhre, K. ; Eckardt, K.U. ; Kastenmüller, G. ; Köttgen, A.

Genetic studies of urinary metabolites illuminate mechanisms of detoxification and excretion in humans.

Nat. Genet. 52, 167-176 (2020)

Alabert, C. ; Loos, C. ; Voelker-Albert, M. ; Graziano, S. ; Forné, I. ; Reveron-Gomez, N. ; Schuh, L. ; Hasenauer, J. ; Marr, C. ; Imhof, A. ; Groth, A.

Domain model explains propagation dynamics and stability of histone H3K27 and H3K36 methylation landscapes.

Cell Rep. 30, 1223-1234 (2020)

Haffner, I. ; Schierle, K. ; Maier, D. ; Geier, B. ; Raimundez, E. ; Hasenauer, J. ; Luber, B. ; Kretzschmar, A.K. ; von Weikersthal, L.F. ; Ahlborn, M. ; Riera, J. ; Rau, B. ; Siegler, G. ; Fuxius, S. ; Decker, T. ; Wittekind, C. ; Lordick, F.

Treatment of HER2 positive advanced gastric cancer: Deviations in HER2 results and its impact on survival.

Oncol. Res. Treat. 43, 65-65 (2020)

Schukken, K.M. ; Lin, Y.-C. ; Bakker, P.L. ; Schubert, M. ; Preuss, S.F. ; Simon, J.E. ; van den Bos, H. ; Storchova, Z. ; Colomé-Tatché, M. ; Bastians, H. ; Spierings, D.C. ; Foijer, F.

Altering microtubule dynamics is synergistically toxic with spindle assembly checkpoint inhibition.

Life Sci. All. 3:e201900499 (2020)

Raimundez-Alvarez, E. ; Keller, S. ; Ebert, K. ; Hug, S. ; Theis, F.J. ; Maier, D. ; Luber, B. ; Hasenauer, J.

Model-based analysis of response and resistance factors of cetuximab treatment in gastric cancer cell lines.

PLoS Comput. Biol. 16:e1007147 (2020)

Trivedi, A. ; Mehrotra, A. ; Baum, C.E. ; Lewis, B. ; Basuroy, T. ; Blomquist, T. ; Trumbly, R. ; Filipp, F.V. ; Setaluri, V. ; de la Serna, I.L.

Bromodomain and extra-terminal domain (BET) proteins regulate melanocyte differentiation.

Epigenetics Chromatin 13:14 (2020)

Dwyer, D.B. ; Kalman, J.L. ; Budde, M. ; Kambeitz, J. ; Ruef, A. ; Antonucci, L.A. ; Kambeitz-Ilankovic, L. ; Hasan, A. ; Kondofersky, I. ; Anderson-Schmidt, H. ; Gade, K. ; Reich-Erkelenz, D. ; Adorjan, K. ; Senner, F. ; Schaupp, S. ; Andlauer, T.F.M. ; Comes, A.L. ; Schulte, E.C. ; Klöhn-Saghatolislam, F. ; Gryaznova, A. ; Hake, M. ; Bartholdi, K. ; Flatau-Nagel, L. ; Reitt, M. ; Quast, S. ; Stegmaier, S. ; Meyers, M. ; Emons, B. ; Haußleiter, I.S. ; Juckel, G. ; Nieratschker, V. ; Dannlowski, U. ; Yoshida, T. ; Schmauß, M. ; Zimmermann, J. ; Reimer, J. ; Wiltfang, J. ; Reininghaus, E. ; Anghelescu, I.G. ; Arolt, V. ; Baune, B.T. ; Konrad, C. ; Thiel, A. ; Fallgatter, A.J. ; Figge, C. ; von Hagen, M. ; Koller, M. ; Lang, F.U. ; Wigand, M.E. ; Becker, T. ; Jäger, M. ; Dietrich, D.E. ; Scherk, H. ; Spitzer, C. ; Folkerts, H. ; Witt, S.H. ; Degenhardt, F. ; Forstner, A.J. ; Rietschel, M. ; Nöthen, M.M. ; Müller, N.S. ; Papiol, S. ; Heilbronner, U. ; Falkai, P. ; Schulze, T.G. ; Koutsouleris, N.

An investigation of psychosis subgroups with prognostic validation and exploration of genetic underpinnings: The PsyCourse study.

JAMA psychiatry 77, 523-533 (2020)

Ricci, W.A. ; Lu, Z. ; Ji, L. ; Marand, A.P. ; Ethridge, C.L. ; Murphy, N.G. ; Noshay, J.M. ; Galli, M. ; Mejía-Guerra, M.K. ; Colomé-Tatché, M. ; Johannes, F. ; Rowley, M.J. ; Corces, V.G. ; Zhai, J. ; Scanlon, M.J. ; Buckler, E.S. ; Gallavotti, A. ; Springer, N.M. ; Schmitz, R.J. ; Zhang, X.

Author Correction: Widespread long-range cis-regulatory elements in the maize genome.

Nat. Plants 6:328 (2020)

Arloth, J. ; Eraslan, G. ; Andlauer, T.F.M. ; Martins, J. ; Iurato, S. ; Kühnel, B. ; Waldenberger, M. ; Frank, J. ; Gold, R. ; Hemmer, B. ; Luessi, F. ; Nischwitz, S. ; Paul, F. ; Wiendl, H. ; Gieger, C. ; Heilmann-Heimbach, S. ; Kacprowski, T. ; Laudes, M. ; Meitinger, T. ; Peters, A. ; Rawal, R. ; Strauch, K. ; Lucae, S. ; Müller-Myhsok, B. ; Rietschel, M. ; Theis, F.J. ; Binder, E.B. ; Müller, N.S.

DeepWAS: Multivariate genotype-phenotype associations by directly integrating regulatory information using deep learning.

PLoS Comput. Biol. 16:e1007616 (2020)

Schranner, D. ; Kastenmüller, G. ; Schönfelder, M. ; Römisch-Margl, W. ; Wackerhage, H.

Metabolite concentration changes in humans after a bout of exercise: A systematic review of exercise metabolomics studies.

Sports Med. Open 6:11 (2020)

Okolie, A. ; Müller, J.

Exact and approximate formulas for contact tracing on random trees.

Math. Biosci. 321:108320 (2020)

Sachs, S. ; Bastidas-Ponce, A. ; Tritschler, S. ; Bakhti, M. ; Böttcher, A. ; Sánchez-Garrido, M.A. ; Tarquis Medina, M. ; Kleinert, M. ; Fischer, K. ; Jall, S. ; Harger, A. ; Bader, E. ; Roscioni, S. ; Ussar, S. ; Feuchtinger, A. ; Yesildag, B. ; Neelakandhan, A. ; Jensen, C.B. ; Cornu, M. ; Yang, B. ; Finan, B. ; DiMarchi, R.D. ; Tschöp, M.H. ; Theis, F.J. ; Hofmann, S.M. ; Müller, T.D. ; Lickert, H.

Targeted pharmacological therapy restores β-cell function for diabetes remission.

Nat. Metab. 2, 192-209 (2020)

Hoksza, D. ; Gawron, P. ; Ostaszewski, M. ; Hasenauer, J. ; Schneider, R.

Closing the gap between formats for storing layout information in systems biology.

Brief. Bioinform., accepted (2020)

Loos, C. ; Hasenauer, J.

Robust calibration of hierarchical population models for heterogeneous cell populations.

J. Theor. Biol. 488:110118 (2020)

Sissouno, N. ; Boßmann, F. ; Filbir, F. ; Iwen, M. ; Kahnt, M. ; Saab, R. ; Schroer, C. ; zu Castell, W.

A direct solver for the phase retrieval problem in ptychographic imaging.

Math. Comput. Simul. 176, 292-300 (2020)

Kiefer, L. ; Storath, M. ; Weinmann, A.

An efficient algorithm for the piecewise affine-linear Mumford-Shah model based on a Taylor jet splitting.

IEEE Trans. Image Process. 29, 921-933 (2020)

Schubert, M. ; Colomé-Tatché, M. ; Foijer, F.

Gene networks in cancer are biased by aneuploidies and sample impurities.

Biochim. Biophys. Acta-Gene Regul. Mech. 1863:194444 (2020)

Cordero-Martínez, J. ; Flores-Alonso, J.C. ; Aguirre-Alvarado, C. ; Oviedo, N. ; Alcántara-Farfán, V. ; Garcia Perez, C. ; Bermúdez-Ruiz, K.F. ; Jiménez-Gutiérrez, G.E. ; Rodríguez-Páez, L.

Influence of Echeveria gibbiflora DC aqueous crude extract on mouse sperm energy metabolism and calcium-dependent channels.

J. Ethnopharmacol. 248, accepted (2020)

Schmiester, L. ; Schälte, Y. ; Fröhlich, F. ; Hasenauer, J. ; Weindl, D.

Efficient parameterization of large-scale dynamic models based on relative measurements.

Bioinformatics 36, 594-602 (2020)

Guala, D. ; Ogris, C. ; Müller, N.S. ; Sonnhammer, E.L.L.

Genome-wide functional association networks: Background, data & state-of-the-art resources.

Brief. Bioinform. 21, 1224-1237 (2020)

Hoksza, D. ; Gawron, P. ; Ostaszewski, M. ; Hasenauer, J. ; Schneider, R.

Closing the gap between formats for storing layout information in systems biology.

Brief. Bioinform. 21, 1249-1260 (2020)

Förster, K. ; Ertl-Wagner, B. ; Ehrhardt, H. ; Busen, H. ; Sass, S. ; Pomschar, A. ; Naehrlich, L. ; Schulze, A. ; Flemmer, A.W. ; Hübener, C. ; Eickelberg, O. ; Theis, F.J. ; Dietrich, O. ; Hilgendorff, A.

Altered relaxation times in MRI indicate bronchopulmonary dysplasia.

Thorax 75, 184-187 (2020)

Pitea, A. ; Kondofersky, I. ; Sass, S. ; Theis, F.J. ; Müller, N.S. ; Unger, K.

Copy number aberrations from Affymetrix SNP 6.0 genotyping data-how accurate are commonly used prediction approaches?

Brief. Bioinform. 21, 272-281 (2020)

Melnyk, O. ; Filbir, F. ; Krahmer, F.

Phase retrieval from local correlation measurements with fixed shift length.

In: (Mathematics in Imaging 2019, 24–27 June 2019, Munich, Germany). 2019. ( ; Part F158-MATH 2019)

Melnyk, O. ; Filbir, F. ; Krahmer, F.

Phase retrieval from local correlation measurements with fixed shift length.

In: (13th International Conference on Sampling Theory and Applications, SampTA 2019, 8-12 July 2019, Bordeaux, France). 2019.:9030967

Lines, G.T. ; Paszkowski, L. ; Schmiester, L. ; Weindl, D. ; Stapor, P. ; Hasenauer, J.

Efficient computation of steady states in large-scale ODE models of biochemical reaction networks.

IFAC PapersOnline 52, 32-37 (2019)

Kapfer, E.M. ; Stapor, P. ; Hasenauer, J.

Challenges in the calibration of large-scale ordinary differential equation models.

IFAC PapersOnline 52, 58-64 (2019)

Villaverde, A.F. ; Raimundez-Alvarez, E. ; Hasenauer, J.

A comparison of methods for quantifying prediction uncertainty in systems biology.

IFAC PapersOnline 52, 45-51 (2019)

Wang, D. ; Stapor, P. ; Hasenauer, J.

Dirac mixture distributions for the approximation of mixed effects models.

IFAC PapersOnline 52, 200-206 (2019)

Lee, J. ; Ahmidi, N. ; Srinivasan, R. ; Alejo, D. ; Dinatale, J. ; Schena, S. ; Whitman, G. ; Sussman, M. ; Shpitser, I.

Finding predictors and causes of cardiac surgery ICU readmission using machine learning and causal inference.

Eur. Heart J. 40, 3575-3575 (2019)

Gutiérrez-Reyes, E. ; García-Segundo, C. ; García-Valenzuela, A. ; Ortega, R. ; Buj, C. ; Filbir, F.

Heat transport considerations in the mathematical analysis of the photoacoustic and photothermal effects.

J. Phys. Commun. 3:085007 (2019)

Sterr, M. ; Aliluev, A. ; Tritschler, S. ; Cernilogar, F.M. ; Irmler, M. ; Beckers, J. ; Schotta, G. ; Böttcher, A. ; Lickert, H.

Gradual pioneer factor expression resolves enteroendocrine lineage recruitment from intestinal stem cells.

Poster: Intestinal organoids - from stem cells to metabolism and microbiome interactions, 29 September 2019, Kopenhagen. (2019)

Cartis, C. ; Gould, N.I.M. ; Lange, M.

On monotonic estimates of the norm of the minimizers of regularized quadratic functions in Krylov spaces.

BIT Num. Math., accepted (2019)

Cruceanu, C. ; Dony, L. ; Kontira, A.C. ; Fischer, D.S. ; Roeh, S. ; DiGiaimo, R. ; Cappello, S. ; Theis, F.J. ; Binder, E.B.

Brain organoids as models of the developing human brain: deciphering the molecular signature of prenatal stress.

Eur. Neuropsychopharmacol. 29, S7-S8 (2019)

Argelaguet, R. ; Clark, S.J. ; Mohammed, H. ; Stapel, L.C. ; Krueger, C. ; Kapourani, C.A. ; Imaz-Rosshandler, I. ; Lohoff, T. ; Xiang, Y. ; Hanna, C.W. ; Smallwood, S. ; Ibarra-Soria, X. ; Buettner, F. ; Sanguinetti, G. ; Xie, W. ; Krueger, F. ; Göttgens, B. ; Rugg-Gunn, P.J. ; Kelsey, G. ; Dean, W. ; Nichols, J. ; Stegle, O. ; Marioni, J.C. ; Reik, W.

Multi-omics profiling of mouse gastrulation at single-cell resolution.

Nature 576, 487-491 (2019)

Porubsky, D. ; Sanders, A.D. ; Taudt, A. ; Colomé-Tatché, M. ; Lansdorp, P.M. ; Guryev, V.

breakpointR: An R/Bioconductor package to localize strand state changes in Strand-seq data.

Bioinformatics, accepted (2019)

Filipp, F.V.

Opportunities for artificial intelligence in advancing precision medicine.

Curr. Genet. Med. Rep. 7, 208-213 (2019)

Tsepilov, Y.A. ; Sharapov, S.Z. ; Zaytseva, O.O. ; Krumsiek, J. ; Prehn, C. ; Adamski, J. ; Kastenmüller, G. ; Wang-Sattler, R. ; Strauch, K. ; Gieger, C. ; Aulchenko, Y.S.

A network-based conditional genetic association analysis of the human metabolome (vol 7, gij137, 2018).

GigaScience 8:giz162 (2019)

Guo, T. ; Luna, A. ; Rajapakse, V.N. ; Koh, C.C. ; Wu, Z. ; Liu, W. ; Sun, Y. ; Gao, H. ; Menden, M. ; Xu, C. ; Calzone, L. ; Martignetti, L. ; Auwerx, C. ; Buljan, M. ; Banaei-Esfahani, A. ; Ori, A. ; Iskar, M. ; Gillet, L. ; Bi, R. ; Zhang, J. ; Zhang, H. ; Yu, C. ; Zhong, Q. ; Varma, S. ; Schmitt, U. ; Qiu, P. ; Zhang, Q. ; Zhu, Y. ; Wild, P.J. ; Garnett, M.J. ; Bork, P. ; Beck, M. ; Liu, K. ; Saez-Rodriguez, J. ; Elloumi, F. ; Reinhold, W.C. ; Sander, C. ; Pommier, Y. ; Aebersold, R.

Quantitative proteome landscape of the NCI-60 cancer cell lines.

iScience 21, 664-680 (2019)

Frank, U. ; Kublik, S. ; Mayer, D. ; Engel, M. ; Schloter, M. ; Durner, J. ; Gaupels, F.

A T-DNA mutant screen that combines high-throughput phenotyping with the efficient identification of mutated genes by targeted genome sequencing.

BMC Plant Biol. 19:539 (2019)

Loos, C. ; Hasenauer, J.

Mathematical modeling of variability in intracellular signaling.

Curr. Opin. Syst. Biol. 16, 17-24 (2019)

Lauffer, F. ; Jargosch, M. ; Baghin, V. ; Krause, L. ; Kempf, W. ; Absmaier-Kijak, M. ; Morelli, M. ; Madonna, S. ; Marsais, F. ; Lepescheux, L. ; Albanesi, C. ; Müller, N.S. ; Theis, F.J. ; Schmidt-Weber, C.B. ; Eyerich, S. ; Biedermann, T. ; Vandeghinste, N. ; Steidl, S. ; Eyerich, K.

IL-17C amplifies epithelial inflammation in human psoriasis and atopic eczema.

J. Eur. Acad. Dermatol. Venereol., accepted (2019)

Thomas, J. ; Küpper, M. ; Batra, R. ; Jargosch, M. ; Atenhan, A. ; Baghin, V. ; Krause, L. ; Lauffer, F. ; Biedermann, T. ; Theis, F.J. ; Eyerich, K. ; Schmidt-Weber, C.B. ; Eyerich, S. ; Garzorz-Stark, N.

Is the humoral immunity dispensable for the pathogenesis of psoriasis? (vol 33, pg 115, 2019).

J. Eur. Acad. Dermatol. Venereol. 33, 2380-2380 (2019)

Theis, F.J. ; Ludwig, T.

Munich School for Data Science (MUDS) – Eine Graduiertenschule für Data Science in München.

Inf.-Spektrum, accepted (2019)

Ricci, W.A. ; Lu, Z. ; Ji, L. ; Marand, A.P. ; Ethridge, C.L. ; Murphy, N.G. ; Noshay, J.M. ; Galli, M. ; Mejía-Guerra, M.K. ; Colomé-Tatché, M. ; Johannes, F. ; Rowley, M.J. ; Corces, V.G. ; Zhai, J. ; Scanlon, M.J. ; Buckler, E.S. ; Gallavotti, A. ; Springer, N.M. ; Schmitz, R.J. ; Zhang, X.

Widespread long-range cis-regulatory elements in the maize genome.

Nat. Plants 5, 1237-1249 (2019)

Peng, T. ; Boxberg, M. ; Weichert, W. ; Navab, N. ; Marr, C.

Multi-task learning of a deep K-nearest neighbour network for histopathological image classification and retrieval.

Lecture Notes Comp. Sci. 11764 LNCS, 676-684 (2019)

Sadafi, A. ; Koehler, N. ; Makhro, A. ; Bogdanova, A. ; Navab, N. ; Marr, C. ; Peng, T.

Multiclass deep active learning for detecting red blood cell subtypes in brightfield microscopy.

Lecture Notes Comp. Sci. 11764 LNCS, 685-693 (2019)

Matek, C. ; Schwarz, S. ; Spiekermann, K. ; Marr, C.

Human-level recognition of blast cells in acute myeloid leukemia with convolutional neural networks.

Nat. Mach. Intell. 1, 538-544 (2019)

Sethunath, V. ; Hu, H. ; de Angelis, C. ; Veeraraghavan, J. ; Qin, L. ; Wang, N. ; Simon, L. ; Wang, T. ; Fu, X. ; Nardone, A. ; Pereira, R. ; Nanda, S. ; Griffith, O.L. ; Tsimelzon, A. ; Shaw, C. ; Chamness, G.C. ; Reis-Filho, J.S. ; Weigelt, B. ; Heiser, L.M. ; Hilsenbeck, S.G. ; Huang, S. ; Rimawi, M.F. ; Gray, J.W. ; Osborne, C.K. ; Schiff, R.

Targeting the mevalonate pathway to overcome acquired anti-HER2 treatment resistance in breast cancer.

Mol. Cancer Res. 17, 2318-2330 (2019)

Brown, P. ; RELISH Consortium (Filipp, F.V.) ; RELISH Consortium (Roobol, M.J.) ; Zhou, Y.

Large expert-curated database for benchmarking document similarity detection in biomedical literature search.

Database 2019, 1-67 (2019)

Quagliarini, F. ; Mir, A.A. ; Balazs, K. ; Wierer, M. ; Dyar, K.A. ; Jouffe, C. ; Makris, K. ; Hawe, J. ; Heinig, M. ; Filipp, F.V. ; Barish, G.D. ; Uhlenhaut, N.H.

Cistromic reprogramming of the diurnal glucocorticoid hormone response by high-fat diet.

Mol. Cell 76, 531-545.e5 (2019)

Sellinger, T. ; Müller, J. ; Hösel, V. ; Tellier, A.

Are the better cooperators dormant or quiescent?

Math. Biosci. 318, accepted (2019)

Jankowska, A. ; Polańska, K. ; Koch, H.M. ; Pälmke, C. ; Waszkowska, M. ; Stańczak, A. ; Wesołowska, E. ; Hanke, W. ; Bose-O'Reilly, S. ; Calamandrei, G. ; Garí, M.

Phthalate exposure and neurodevelopmental outcomes in early school age children from Poland.

Environ. Res. 179:108829 (2019)

Holmberg, O. ; Kortuem, K.U. ; Koehler, N. ; Theis, F.J.

Predicting retinal thickness from fundus images across modalities using deep learning.

Invest. Ophthalmol. Vis. Sci. 60 (2019)

Hanna, C.W. ; Pérez-Palacios, R. ; Gahurova, L. ; Schubert, M. ; Krueger, F. ; Biggins, L. ; Andrews, S. ; Colomé-Tatché, M. ; Bourc'his, D. ; Dean, W. ; Kelsey, G.

Endogenous retroviral insertions drive non-canonical imprinting in extra-embryonic tissues.

Genome Biol. 20:225 (2019)

Hibbah, E.H. ; El Maroufy, H. ; Fuchs, C. ; Ziad, T.

An MCMC computational approach for a continuous time state-dependent regime switching diffusion process.

J. Appl. Stat., accepted (2019)

Sorg, T. ; Herault, Y. ; Jonkers, J. ; Ploubidou, A. ; Frappart, L. ; Hasenauer, J. ; Banga, J. ; Rinner, O. ; Naumova, V. ; Koubi, D. ; Lange, B.

Generation of the Cancer Pathway Prototype - a platform for predictive cancer pathway modeling.

Eur. J. Hum. Genet. 27, 571-572 (2019)

Garí, M. ; Grimalt, J.O. ; Vizcaino, E. ; Tardón, A. ; Fernández-Somoano, A.

Mother-child transfer rates of organohalogen compounds up to four years of age.

Environ. Int. 133:105241 (2019)

Esposito, M. ; Hennersperger, C. ; Göbl, R. ; Demaret, L. ; Storath, M. ; Navab, N. ; Baust, M. ; Weinmann, A.

Total variation regularization of pose signals with an application to 3D freehand ultrasound.

IEEE Trans. Med. Imaging 38, 2245-2258 (2019)

Böttcher, A. ; Tritschler, S. ; Yang, K. ; Theis, F.J. ; Lickert, H. ; Wolf, E. ; Kemter, E.

Studying in vivo beta cell maturation in pigs by scRNAseq.

Xenotransplantation 26 (2019)

Arloth, J. ; Eraslan, G. ; Andlauer, T. ; Gieger, C. ; Gold, R. ; Heilmann-Heimbach, S. ; Kacprowski, T. ; Meitinger, T. ; Laudes, M. ; Luessi, F. ; Müller-Myhsok, B. ; Nischwitz, S. ; Peters, A. ; Paul, F. ; Rawal, R. ; Strauch, K. ; Wiendl, H. ; Hemmer, B. ; Theis, F.J. ; Binder, E. ; Müller, N.S.

Identification of functionally relevant genetic variants associated with multiple sclerosis using deep learning.

Mult. Scler. J. 25, 906-907 (2019)

Gestaut, D. ; Roh, S.H. ; Ma, B. ; Pintile, G. ; Joachimiak, L. ; Leitner, A. ; Walzotheini, T. ; Aebersold, R. ; Chiu, W. ; Frydman, J.

The chaperonin TRIC/CCT associates with prefoldin through a conserved electrostatic interface essential for cellular proteostasis.

Protein Sci. 28, 44-44 (2019)

Johnson, R.K. ; Vanderlinden, L. ; DeFelice, B.C. ; Kechris, K. ; Uusitalo, U. ; Fiehn, O. ; Sontag, M. ; Crume, T. ; Beyerlein, A. ; Lernmark, Å. ; Toppari, J. ; Ziegler, A.-G. ; She, J.X. ; Hagopian, W. ; Rewers, M. ; Akolkar, B. ; Krischer, J. ; Virtanen, S.M. ; Norris, J.M. ; Teddy Study Group

Sci. Rep. 9:14819 (2019)

Kimura, R.H. ; Wang, L. ; Shen, B. ; Huo, L. ; Tummers, W. ; Filipp, F.V. ; Guo, H.H. ; Haywood, T. ; Abou-Elkacem, L. ; Baratto, L. ; Habte, F. ; Devulapally, R. ; Witney, T.H. ; Cheng, Y. ; Tikole, S. ; Chakraborti, S. ; Nix, J. ; Bonagura, C.A. ; Hatami, N. ; Mooney, J.J. ; Desai, T. ; Turner, S. ; Gaster, R.S. ; Otte, A. ; Visser, B.C. ; Poultsides, G.A. ; Norton, J. ; Park, W. ; Stolowitz, M. ; Lau, K. ; Yang, E. ; Natarajan, A. ; Ilovich, O. ; Srinivas, S. ; Srinivasan, A. ; Paulmurugan, R. ; Willmann, J. ; Chin, F.T. ; Cheng, Z. ; Iagaru, A. ; Li, F. ; Gambhir, S.S.

Evaluation of integrin αvβ₆ cystine knot PET tracers to detect cancer and idiopathic pulmonary fibrosis.

Nat. Commun. 10:4673 (2019)

Waibel, D.J.E. ; Tiemann, U. ; Lupperger, V. ; Semb, H. ; Marr, C.

In-silico staining from bright-field and fluorescent images using deep learning.

In:. 2019. 184-186 (Lecture Notes Comp. Sci. ; 11729 LNCS)

Schneider, M. ; Wang, L. ; Marr, C.

Evaluation of domain adaptation approaches for robust classification of heterogeneous biological data sets.

Lecture Notes Comp. Sci. 11728 LNCS, 673-686 (2019)

Keshava, N. ; Toh, T.S. ; Yuan, H. ; Yang, B. ; Menden, M. ; Wang, D.

Defining subpopulations of differential drug response to reveal novel target populations.

NPJ Syst. Biol. Appl. 5:36 (2019)

Schulte-Sasse, R. ; Budach, S. ; Hnisz, D. ; Marsico, A.

Graph convolutional networks improve the prediction of cancer driver genes.

Lecture Notes Comp. Sci. 11731 LNCS, 658-668 (2019)

Tetko, I.V. ; Theis, F.J. ; Karpov, P. ; Kůrková, V.

Preface.

Lecture Notes Comp. Sci. 11731 LNCS, v-vii (2019)

Mishra, M. ; Schmitt, S. ; Zischka, H. ; Strasser, M. ; Navab, N. ; Marr, C. ; Peng, T.

Quantifying structural heterogeneity of healthy and cancerous mitochondria using a combined segmentation and classification USK-net.

Lecture Notes Comp. Sci. 11731 LNCS, 289-298 (2019)

Rausch, L. ; Kranich, J. ; Chlis, N.-K. ; Schifferer, M. ; Simons, M. ; Theis, F.J. ; Brocker, T.

Analysis of EV-decorated CD8+T cells during viral infection.

Eur. J. Immunol. 49, 88-88 (2019)

Musumeci, A. ; Lutz, K. ; Dursun, E. ; Sie, C. ; Ziegenhain, C. ; Bagnoli, J. ; Luecken, M. ; Korn, T. ; Enard, W. ; Theis, F.J. ; Krug, A.

Identification of a DC precursor population with pDC and cDC potential responding to endosomal TLR stimulation with increased pDC output.

Eur. J. Immunol. 49, 48-48 (2019)

Bakhti, M. ; Scheibner, K. ; Tritschler, S. ; Bastidas-Ponce, A. ; Tarquis-Medina, M. ; Theis, F.J. ; Lickert, H.

Establishment of a high-resolution 3D modeling system for studying pancreatic epithelial cell biology in vitro.

Mol. Metab. 30, 16-29 (2019)

Kiefer, L. ; Weinmann, A.

Smoothing for signals with discontinuities using higher order Mumford-Shah models.

Numer. Math. 143, 423-460 (2019)

Thomas, J. ; Quaranta, M. ; Krause, L. ; Atenhan, A. ; Buters, J.T.M. ; Ohnmacht, C. ; de Jong, R.J. ; Schmidt-Weber, C.B. ; Eyerich, S.

FOXO4 and AHR control a stress-induced immune-mediated host protection via secretion of IL-22.

Eur. J. Immunol. 49, 282-283 (2019)

Haimerl, P. ; Bernhard, U. ; Chaker, A.M. ; Zissler, U.M. ; Pastor, X. ; Cecil, A. ; Schindela, S. ; Prehn, C. ; Schmidt-Weber, C.B. ; Esser-von Bieren, J.

Lipid metabolism and macrophage activation are broadly dysregulated in aspirin-exacerbated respiratory disease.

Eur. J. Immunol. 49, 200-200 (2019)

Tetko, I.V. ; Theis, F.J. ; Karpov, P. ; Kůrková, V.

Preface.

Lecture Notes Comp. Sci. 11727 LNCS, v-vii (2019)

Tetko, I.V. ; Theis, F.J. ; Karpov, P. ; Kůrková, V.

Preface.

Lecture Notes Comp. Sci. 11728 LNCS, v-vii (2019)

Tetko, I.V. ; Theis, F.J. ; Karpov, P. ; Kůrková, V.

Preface.

Lecture Notes Comp. Sci. 11729 LNCS, v-vii (2019)

Vlot, A.H.C. ; Aniceto, N. ; Menden, M. ; Ulrich-Merzenich, G. ; Bender, A.

Applying synergy metrics to combination screening data: Agreements, disagreements and pitfalls.

Drug Discov. Today 24, 2286-2298 (2019)

Miller, M. ; Sabrautzki, S. ; Beyerlein, A. ; Brielmeier, M.

Combining fish and environmental PCR for diagnostics of diseased laboratory zebrafish in recirculating systems.

PLoS ONE 14:e0222360 (2019)

Scherb, H. ; Grech, V.

Trends in births and the birth sex ratio in the vicinity of the Mainz research reactor in Germany.

Early Hum. Dev. 141, accepted (2019)

List, M. ; Alcaraz, N. ; Batra, R.

De novo pathway-based classification of breast cancer subtypes.

In: Protein-Protein Interaction Networks. 2019. 201-213 (Methods Mol. Biol. ; 2074)

Yamamoto, H. ; Hayashi, K. ; Scherb, H.

Association between the detection rate of thyroid cancer and the external radiation dose-rate after the nuclear power plant accidents in Fukushima, Japan.

Medicine (Baltimore) 98:e17165 (2019)

Wang, X. ; Efendiyev, M.A. ; Lutscher, F.

How spatial heterogeneity affects transient behavior in reaction-diffusion systems for ecological interactions?

Bull. Math. Biol. 81, 3889-3917 (2019)

Altenbuchinger, M. ; Zacharias, H.U. ; Solbrig, S. ; Schäfer, A. ; Büyüközkan, M. ; Schultheiß, U.T. ; Kotsis, F. ; Köttgen, A. ; Spang, R. ; Oefner, P.J. ; Krumsiek, J. ; Gronwald, W.

A multi-source data integration approach reveals novel associations between metabolites and renal outcomes in the German Chronic Kidney Disease study.

Sci. Rep. 9:13954 (2019)

Mameishvili, E. ; Serafimidis, I. ; Iwaszkiewicz, S. ; Lesche, M. ; Reinhardt, S. ; Bölicke, N. ; Büttner, M. ; Stellas, D. ; Papadimitropoulou, A. ; Szabolcs, M. ; Anastassiadis, K. ; Dahl, A. ; Theis, F.J. ; Efstratiadis, A. ; Gavalas, A.

Aldh1b1 expression defines progenitor cells in the adult pancreas and is required for Kras-induced pancreatic cancer.

Proc. Natl. Acad. Sci. U.S.A. 116, 20679-20688 (2019)

Ashuach, T. ; Fischer, D.S. ; Kreimer, A. ; Ahituv, N. ; Theis, F.J. ; Yosef, N.

MPRAnalyze: Statistical framework for massively parallel reporter assays.

Genome Biol. 20:183 (2019)

Czamara, D. ; Eraslan, G. ; Lahti, J. ; Figueiredo, A.S. ; Girchenko, P. ; Lahti-Pulkkinen, M. ; Hämäläinen, E. ; Kajantie, E. ; Laivuori, H. ; Villa, P. ; Reynolds, R. ; Müller, N.S. ; Theis, F.J. ; Räikkönen, K. ; Binder, E.

Genotype, prenatal environment or both-what shapes the newborn´s epigenome?

Eur. Neuropsychopharmacol. 29, 1037-1037 (2019)

Schaupp, S. ; Budde, M. ; Kondofersky, I. ; Papiol, S. ; Heilbronner, U. ; Gade, K. ; Anderson-Schmidt, H. ; Kalman, J. ; Senner, F. ; Andlauer, T.F.M. ; Rietschel, M. ; Degenhardt, F. ; Müller, N.S. ; Theis, F.J. ; Schulze, T.

Polygenic risk score analysis of trajectories of cognitive performance in psychiatric patients.

Eur. Neuropsychopharmacol. 29, 1161-1161 (2019)

Schulte, E. ; Kondofersky, I. ; Budde, M. ; Adorjan, K. ; Aldinger, F. ; Anderson-Schmidt, H. ; Gade, K. ; Heilbronner, U. ; Kalman, J. ; Papiol, S. ; Theis, F.J. ; Falkai, P. ; Müller, N.S. ; Schulze, T.G.

Polygenic burden analysis of longitudinal clusters of psychopathological features in a cross-diagnostic group of individuals with severe mental illness.

Eur. Neuropsychopharmacol. 29, 1257-1258 (2019)

Comes, A. ; Adorjan, K. ; Andlauer, T. ; Budde, M. ; Degenhardt, F. ; Forstner, A.J. ; Gade, K. ; Heilbronner, U. ; Kalman, J. ; Kondofersky, I. ; Papiol, S. ; Senner, F. ; Sivalingam, S. ; Falkai, P. ; Schulze, T.

The role of environmental stress and DNA methylation in the longitudinal course of bipolar disorder.

Eur. Neuropsychopharmacol. 29, 1300-1301 (2019)

Weberpals, J. ; Becker, T. ; Schmich, F. ; Ruettinger, D. ; Theis, F.J. ; Bauer-Mehren, A.

Deep learning-based propensity score computation: Cohort study in second line treated advanced non-small cell lung cancer (aNSCLC) patients.

Pharmacoepidemiol. Drug Saf. 28, 585-586 (2019)

Aliee, H. ; Khosravi, F. ; Teich, J.

Efficient treatment of uncertainty in system reliability analysis using importance measures.

49th Annual IEEE/IFIP International Conference on Dependable Systems and Networks (DSN), 76-87 (2019)

Jankowska, A. ; Polańska, K. ; Hanke, W. ; Wesołowska, E. ; Ligocka, D. ; Waszkowska, M. ; Stańczak, A. ; Tartaglione, A.M. ; Mirabella, F. ; Chiarotti, F. ; Garí, M. ; Calamandrei, G.

Prenatal and early postnatal phthalate exposure and child neurodevelopment at age of 7 years – Polish Mother and Child Cohort.

Environ. Res. 177, accepted (2019)

Sorg, A.-L. ; von Kries, R. ; Klemme, M. ; Gerstl, L. ; Weinberger, R. ; Beyerlein, A. ; Lack, N. ; Felderhoff-Müser, U. ; Dzietko, M.

Risk factors for perinatal arterial ischaemic stroke: A large case–control study.

Dev. Med. Child. Neurol., accepted (2019)

Tirier, S.M. ; Park, J. ; Preußer, F. ; Amrhein, L. ; Gu, Z. ; Steiger, S. ; Mallm, J.P. ; Krieger, T. ; Waschow, M. ; Eismann, B. ; Gut, M. ; Gut, I.G. ; Rippe, K. ; Schlesner, M. ; Theis, F.J. ; Fuchs, C. ; Ball, C.R. ; Glimm, H. ; Conrad, C.

Pheno-seq - linking visual features and gene expression in 3D cell culture systems.

Sci. Rep. 9:12367 (2019)

Lotfollahi, M. ; Wolf, F.A. ; Theis, F.J.

scGen predicts single-cell perturbation responses.

Nat. Methods 16, 715-721 (2019)

Uzbas, F. ; Opperer, F. ; Sönmezer, C. ; Shaposhnikov, D. ; Sass, S. ; Krendl, C. ; Angerer, P. ; Theis, F.J. ; Müller, N.S. ; Drukker, M.

BART-Seq: cost-effective massively parallelized targeted sequencing for genomics, transcriptomics, and single-cell analysis.

Genome Biol. 20:155 (2019)

Provençal, N. ; Arloth, J. ; Cattaneo, A. ; Anacker, C. ; Cattane, N. ; Wiechmann, T. ; Röh, S. ; Ködel, M. ; Klengel, T. ; Czamara, D. ; Müller, N.S. ; Lahti, J. ; Räikkönen, K. ; Pariante, C.M. ; Binder, E.B.

Glucocorticoid exposure during hippocampal neurogenesis primes future stress response by inducing changes in DNA methylation.

Proc. Natl. Acad. Sci. U.S.A. 117, 23280-23285 (2019)

Scherb, H. ; Kusmierz, R. ; Voigt, K.

Secondary sex ratio and trends in the associated gender-specific births near nuclear facilities in France and Germany: Update of birth counts.

Reprod. Toxicol. 89, 159-167 (2019)

Caicedo, J.C. ; Roth, J. ; Goodman, A. ; Becker, T. ; Karhohs, K.W. ; Broisin, M. ; Molnar, C. ; McQuin, C. ; Singh, S. ; Theis, F.J. ; Carpenter, A.E.

Evaluation of deep learning strategies for nucleus segmentation in fluorescence images.

Cytometry A 95, 952-965 (2019)

Müller, J. ; Spriewald, S. ; Stecher, B. ; Stadler, E. ; Fuchs, T.M.

Evolutionary stability of salmonella competition with the gut microbiota: How the environment fosters heterogeneity in exploitative and interference competition.

J. Mol. Biol. 431, 4732-4748 (2019)

Patil, S. ; Heuser, C. ; de Almeida, G.P. ; Theis, F.J. ; Zielinski, C.E.

Meeting the challenges of high-dimensional single-cell data analysis in immunology.

Front. Immunol. 10:1515 (2019)

Erhard, F. ; Baptista, M.A.P. ; Krammer, T. ; Hennig, T. ; Lange, M. ; Arampatzi, P. ; Jürges, C.S. ; Theis, F.J. ; Saliba, A.-E. ; Dölken, L.

scSLAM-seq reveals core features of transcription dynamics in single cells.

Nature 571, 419-423 (2019)

Hawe, J. ; Theis, F.J. ; Heinig, M.

Inferring interaction networks from multi-omics data.

Front. Genet. 10, accepted (2019)

Tritschler, S. ; Büttner, M. ; Fischer, D.S. ; Lange, M. ; Bergen, V. ; Lickert, H. ; Theis, F.J.

Concepts and limitations for learning developmental trajectories from single cell genomics.

Development 146, accepted (2019)

Luecken, M. ; Theis, F.J.

Current best practices in single-cell RNA-seq analysis: A tutorial.

Mol. Syst. Biol. 15:e8746 (2019)

Vieira Braga, F.A. ; Kar, G. ; Berg, M. ; Carpaij, O.A. ; Polanski, K. ; Simon, L. ; Brouwer, S. ; Gomes, T. ; Hesse, L. ; Jiang, J. ; Fasouli, E.S. ; Efremova, M. ; Vento-Tormo, R. ; Talavera-López, C. ; Jonker, M.R. ; Affleck, K. ; Palit, S. ; Strzelecka, P.M. ; Firth, H.V. ; Mahbubani, K.T. ; Cvejic, A. ; Meyer, K.B. ; Saeb-Parsy, K. ; Luinge, M. ; Brandsma, C.A. ; Timens, W. ; Angelidis, I. ; Strunz, M. ; Koppelman, G.H. ; van Oosterhout, A.J. ; Schiller, H. B. ; Theis, F.J. ; van den Berge, M. ; Nawijn, M.C. ; Teichmann, S.A.

A cellular census of human lungs identifies novel cell states in health and in asthma.

Nat. Med. 25, 1153-1163 (2019)

Menden, M. ; Wang, D. ; Mason, M.J. ; Szalai, B. ; Bulusu, K.C. ; Guan, Y. ; Yu, T. ; Kang, J. ; Jeon, M. ; Wolfinger, R. ; Nguyen, T. ; Zaslavskiy, M. ; Jang, I.S. ; Ghazoui, Z. ; Ahsen, M.E. ; Vogel, R. ; Neto, E.C. ; Norman, T. ; Tang, E.K.Y. ; Garnett, M.J. ; Veroli, G.Y.D. ; Fawell, S. ; Stolovitzky, G. ; Guinney, J. ; Dry, J.R. ; Saez-Rodriguez, J. ; AstraZeneca-Sanger Drug Combination DREAM Consortium (Kurz, C.F.)

Community assessment to advance computational prediction of cancer drug combinations in a pharmacogenomic screen.

Nat. Commun. 10:2674 (2019)

Czamara, D. ; Eraslan, G. ; Page, C.M. ; Lahti, J. ; Lahti-Pulkkinen, M. ; Hämäläinen, E. ; Kajantie, E. ; Laivuori, H. ; Villa, P.M. ; Reynolds, R.M. ; Nystad, W. ; Håberg, S.E. ; London, S.J. ; O'Donnell, K.J. ; Garg, E. ; Meaney, M.J. ; Entringer, S. ; Wadhwa, P.D. ; Buss, C. ; Jones, M.J. ; Lin, D.T.S. ; MacIsaac, J.L. ; Kobor, M.S. ; Koen, N. ; Zar, H.J. ; Koenen, K.C. ; Dalvie, S. ; Stein, D.J. ; Kondofersky, I. ; Müller, N.S. ; Theis, F.J. ; Räikkönen, K. ; Binder, E.B.

Integrated analysis of environmental and genetic influences on cord blood DNA methylation in new-borns.

Nat. Commun. 10:2548 (2019)

Quell, J. ; Römisch-Margl, W. ; Haid, M. ; Krumsiek, J. ; Skurk, T. ; Halama, A. ; Stephan, N. ; Adamski, J. ; Hauner, H. ; Mook-Kanamori, D.O. ; Mohney, R.P. ; Daniel, H. ; Suhre, K. ; Kastenmüller, G.

Characterization of bulk phosphatidylcholine compositions in human plasma using side-chain resolving lipidomics.

Metabolites 9:109 (2019)

Wintergerst, L. ; Selmansberger, M. ; Maihoefer, C. ; Schuettrumpf, L. ; Walch, A.K. ; Wilke, C. ; Pitea, A. ; Woischke, C. ; Baumeister, P. ; Kirchner, T. ; Belka, C. ; Ganswindt, U. ; Zitzelsberger, H. ; Unger, K. ; Hess, J.

A 16q24.3 4-gene mRNA signature predicts outcome in radio(chemo)therapy-treated head and neck squamous cell carcinoma.

Strahlenther. Onkol. 195, S24-S25 (2019)

Ntini, E. ; Marsico, A.

Functional impacts of non-coding RNA processing on enhancer activity and target gene expression.

J. Mol. Cell Biol. 11, 868-879 (2019)

Bastidas-Ponce, A. ; Tritschler, S. ; Dony, L. ; Scheibner, K. ; Tarquis-Medina, M. ; Salinno, C. ; Schirge, S. ; Burtscher, I. ; Böttcher, A. ; Theis, F.J. ; Lickert, H. ; Bakhti, M.

Comprehensive single cell mRNA profiling reveals a detailed roadmap for pancreatic endocrinogenesis.

Development 146:dev173849 (2019)

Thiel, D. ; Conrad, N.D. ; Ntini, E. ; Peschutter, R.X. ; Siebert, H. ; Marsico, A.

Identifying lncRNA-mediated regulatory modules via ChIA-PET network analysis.

BMC Bioinformatics 20:292 (2019)

Theis, F.J. ; Lickert, H.

A map of beta-cell differentiation.

Nature 569, 342-343 (2019)

Scherb, H. ; Mori, K. ; Hayashi, K.

Comment on 'Perinatal mortality after the Fukushima accident'.

J. Radiol. Prot. 39, 647-649 (2019)

Wiechmann, T. ; Röh, S. ; Sauer, S. ; Czamara, D. ; Arloth, J. ; Ködel, M. ; Beintner, M. ; Knop, L. ; Menke, A. ; Binder, E.B. ; Provençal, N.

Identification of dynamic glucocorticoid-induced methylation changes at the FKBP5 locus.

Clin. Epigenet. 11:83 (2019)

Matejka, K. ; Stückler, F. ; Salomon, M. ; Ensenauer, R. ; Reischl, E. ; Hoerburger, L. ; Grallert, H. ; Kastenmüller, G. ; Peters, A. ; Daniel, H. ; Krumsiek, J. ; Theis, F.J. ; Hauner, H. ; Laumen, H.

Dynamic modelling of an ACADS genotype in fatty acid oxidation - Application of cellular models for the analysis of common genetic variants.

PLoS ONE 14:e0216110 (2019)

Filipp, F.V. ; Li, C. ; Boiko, A.D.

CD271 is a molecular switch with divergent roles in melanoma and melanocyte development.

Sci. Rep. 9:7696 (2019)

Zannas, A.S. ; Jia, M. ; Hafner, K. ; Baumert, J.J. ; Wiechmann, T. ; Pape, J.C. ; Arloth, J. ; Ködel, M. ; Martinelli, S. ; Roitman, M. ; Röh, S. ; Haehle, A. ; Emeny, R.T. ; Iurato, S. ; Carrillo-Roa, T. ; Lahti, J. ; Räikkönen, K. ; Eriksson, J.G. ; Drake, A.J. ; Waldenberger, M. ; Wahl, S. ; Kunze, S. ; Lucae, S. ; Bradley, B. ; Gieger, C. ; Hausch, F. ; Smith, A.K. ; Ressler, K.J. ; Müller-Myhsok, B. ; Ladwig, K.-H. ; Rein, T. ; Gassen, N.C. ; Binder, E.B.

Epigenetic upregulation of FKBP5 by aging and stress contributes to NF-kappa B-driven inflammation and cardiovascular risk.

Proc. Natl. Acad. Sci. U.S.A. 166, 11370-11379 (2019)

Pellegrino, J. ; Shahjahanpour, A. ; Lukauskas, S. ; Olayo Alarcon, R. ; Ramakrishnan, A. ; Colomé-Tatché, M. ; Schneider, R.

Glucose starvation in Huh7 cells triggers a transcriptional memory.

Poster: CSH meeting: mechanisms of metabolic signaling, 14 May 2019, Cold Spring Harbour, NY, USA. (2019)

Hawe, J. ; Lehne, B. ; Waldenberger, M. ; Gieger, C. ; Chambers, J. ; Heinig, M.

Reconstructing regulatory networks from multi-omics data using prior information.

Poster: RECOMB 2019, 4-8 May 2019, Washington D.C.. (2019)

Bressin, A. ; Schulte-Sasse, R. ; Figini, D. ; Urdaneta, E.C. ; Beckmann, B.M. ; Marsico, A.

TriPepSVM: De novo prediction of RNA-binding proteins based on short amino acid motifs.

Nucleic Acids Res. 47, 4406-4417 (2019)

Schiller, H. B. ; Montoro, D.T. ; Simon, L. ; Rawlins, E.L. ; Meyer, K.B. ; Strunz, M. ; Vieira Braga, F. ; Timens, W. ; Koppelman, G.H. ; Budinger, G.R.S. ; Burgess, J.K. ; van den Berge, M. ; Theis, F.J. ; Regev, A. ; Kaminski, N. ; Rajagopal, J. ; Teichmann, S.A. ; Misharin, A.V. ; Nawijn, M.C.

The Human Lung Cell Atlas: A high-resolution reference map of the human lung in health and disease.

Am. J. Respir. Cell Mol. Biol. 61, 31-41 (2019)

Behzadi, S. ; Müller, N.S. ; Plant, C. ; Böhm, C.

Clustering of mixed-type data considering concept hierarchies.

Lecture Notes Comp. Sci. 11439 LNAI, 555-573 (2019)

Laimighofer, M. ; Lickert, R. ; Fuerst, R. ; Theis, F.J. ; Winkler, C. ; Bonifacio, E. ; Ziegler, A.-G. ; Krumsiek, J.

Common patterns of gene regulation associated with Cesarean section and the development of islet autoimmunity - indications of immune cell activation.

Sci. Rep. 9:6250 (2019)

Garí, M. ; Koch, H.M. ; Pälmke, C. ; Jankowska, A. ; Wesołowska, E. ; Hanke, W. ; Nowak, D. ; Bose-O'Reilly, S. ; Polańska, K.

Determinants of phthalate exposure and risk assessment in children from Poland.

Environ. Int. 127, 742-753 (2019)

Eraslan, G. ; Avsec, Ž. ; Gagneur, J. ; Theis, F.J.

Deep learning: New computational modelling techniques for genomics.

Nat. Rev. Genet. 20, 389-403 (2019)

Shah, R. ; Singh, S.J. ; Eddy, K. ; Filipp, F.V. ; Chen, S.

Concurrent targeting of glutaminolysis and metabotropic glutamate receptor 1 (GRM1) reduces glutamate bioavailability in GRM1(+) melanoma.

Cancer Res. 79, 1799-1809 (2019)

Hösel, V. ; Müller, J. ; Tellier, A.

Universality of neutral models: Decision process in politics.

Palg. Comm. 5:14 (2019)

Gestaut, D. ; Roh, S.H. ; Ma, B. ; Pintilie, G. ; Joachimiak, L.A. ; Leitner, A. ; Walzthoeni, T. ; Aebersold, R. ; Chiu, H. ; Frydman, J.

The chaperonin TRiC/CCT associates with prefoldin through a conserved electrostatic interface essential for cellular proteostasis.

Cell 177, 751-765.e15 (2019)

Fischer, D.S. ; Fiedler, A. ; Kernfeld, E.M. ; Genga, R.M.J. ; Bastidas-Ponce, A. ; Bakhti, M. ; Lickert, H. ; Hasenauer, J. ; Maehr, R. ; Theis, F.J.

Inferring population dynamics from single-cell RNA-sequencing time series data.

Nat. Biotechnol. 37, 461-468 (2019)

Krautenbacher, N. ; Flach, N. ; Böck, A. ; Laubhahn, K. ; Laimighofer, M. ; Theis, F.J. ; Ankerst, D.P. ; Fuchs, C. ; Schaub, B.

A strategy for high-dimensional multivariable analysis classifies childhood asthma phenotypes from genetic, immunological, and environmental factors.

Allergy 74, 1364-1373 (2019)

Zacharias, H.U. ; Altenbuchinger, M. ; Schultheiss, U.T. ; Samol, C. ; Kotsis, F. ; Poguntke, I. ; Sekula, P. ; Krumsiek, J. ; Köttgen, A. ; Spang, R. ; Oefner, P.J. ; Gronwald, W.

A novel metabolic signature to predict the requirement of dialysis or renal transplantation in patients with chronic kidney disease.

J. Proteome Res. 18, 1796–1805 (2019)

Spiegel, E ; Kneib, T. ; Otto-Sobotka, F.

Spatio-temporal expectile regression models.

Stat. Model. 20, 386-409 (2019)

Wang, R. ; Thomas, J. ; Batra, R. ; Biedermann, T. ; Theis, F.J. ; Eyerich, S. ; Eyerich, K.

CD23 is a biomarker of clinical response to IgE-specific immunoadsorption in patients with severe atopic eczema.

Exp. Dermatol. 28, E29-E30 (2019)

Jiang, D. ; Christ, S. ; Gallegos, D.C. ; Ramesh, P. ; Gopal, S.K. ; Yu, Q. ; Mayr, C. ; Lupperger, V. ; Liu, J. ; Marr, C. ; Schiller, H. B. ; Rinkevich, Y.

Visualizing scar development in living tissues reveals the collective migration of fibroblasts mediated by N-cadherin.

Exp. Dermatol. 28, E13-E13 (2019)

Thomas, J. ; Quaranta, M. ; Krause, L. ; Atenhan, A. ; Buters, J.T.M. ; Ohnmacht, C. ; de Jong, R.J. ; Schmidt-Weber, C.B. ; Eyerich, S.

Foxo4 and AHR control a stress-induced immune-mediated host protection via secretion of IL-22.

Exp. Dermatol. 28, E76-E77 (2019)

Reyes-Espinosa, F. ; Juárez-Saldivar, A. ; Palos, I. ; Herrera-Mayorga, V. ; Garcia Perez, C. ; Rivera, G.

In silico analysis of homologous heterodimers of cruzipain-chagasin from structural models built by homology.

Int. J. Mol. Sci. 20:1320 (2019)

Wolf, F.A. ; Hamey, F.K. ; Plass, M. ; Solana, J. ; Dahlin, J.S. ; Göttgens, B. ; Rajewsky, N. ; Simon, L. ; Theis, F.J.

PAGA: Graph abstraction reconciles clustering with trajectory inference through a topology preserving map of single cells.

Genome Biol. 20:59 (2019)

Li, C. ; Nguyen, V. ; Clark, K.N. ; Zahed, T. ; Sharkas, S. ; Filipp, F.V. ; Boiko, A.D.

Down-regulation of FZD3 receptor suppresses growth and metastasis of human melanoma independently of canonical WNT signaling.

Proc. Natl. Acad. Sci. U.S.A. 116, 4548-4557 (2019)

Münch, K. ; Münch, R. ; Biedendieck, R. ; Jahn, D. ; Müller, J.

Evolutionary model for the unequal segregation of high copy plasmids.

PLoS Comput. Biol. 15:e1006724 (2019)

El Omari, M. ; El Maroufy, H. ; Fuchs, C.

Non parametric estimation for fractional diffusion processes with random effects.

Statistics 53, 753-769 (2019)

Sinzger, M. ; Vanhoefer, J. ; Loos, C. ; Hasenauer, J.

Comparison of null models for combination drug therapy reveals Hand model as biochemically most plausible.

Sci. Rep. 9:3002 (2019)

Fröhlich, F. ; Reiser, A. ; Fink, L. ; Woschée, D. ; Ligon, T. ; Theis, F.J. ; Rädler, J.O. ; Hasenauer, J.

Publisher Correction: Multi-experiment nonlinear mixed effectmodeling of single-cell translation kinetics after transfection.

NPJ Syst. Biol. Appl. 5:11 (2019)

Akagi, G. ; Melchionna, S.

Porous medium equation with a blow-up nonlinearity and a non-decreasing constraint.

Non. diff. equat. app. 26:10 (2019)

Villaverde, A.F. ; Fröhlich, F. ; Weindl, D. ; Hasenauer, J. ; Banga, J.R.

Benchmarking optimization methods for parameter estimation in large kinetic models.

Bioinformatics 35, 830-838 (2019)

Hass, H. ; Loos, C. ; Raimundez-Alvarez, E. ; Timmer, J. ; Hasenauer, J. ; Kreutz, C.

Benchmark problems for dynamic modeling of intracellular processes.

Bioinformatics 35, 3073-3082 (2019)

Meehan, M.T. ; Cocks, D.G. ; Müller, J. ; McBryde, E.S.

Global stability properties of a class of renewal epidemic models.

J. Math. Biol. 78, 1713-1725 (2019)

Angelidis, I. ; Simon, L. ; Fernandez, I.E. ; Strunz, M. ; Mayr, C. ; Greiffo, F.R. ; Tsitsiridis, G. ; Ansari, M. ; Graf, E. ; Strom, T.M. ; Nagendran, M. ; Desai, T. ; Eickelberg, O. ; Mann, M. ; Theis, F.J. ; Schiller, H. B.

An atlas of the aging lung mapped by single cell transcriptomics and deep tissue proteomics.

Nat. Commun. 10:963 (2019)

Dony, L. ; He, F. ; Stumpf, M.P.H.

Parametric and non-parametric gradient matching for network inference: A comparison.

BMC Bioinformatics 20:52 (2019)

Sheng, X. ; Nenseth, H.Z. ; Qu, S. ; Kuzu, O.F. ; Frahnow, T. ; Simon, L. ; Greene, S. ; Zeng, Q. ; Fazli, L. ; Rennie, P.S. ; Mills, I.G. ; Danielsen, H. ; Theis, F.J. ; Patterson, J.B. ; Jin, Y. ; Saatcioglu, F.

IRE1α-XBP1s pathway promotes prostate cancer by activating c-MYC signaling.

Nat. Commun. 10:323 (2019)

Hippich, M. ; Beyerlein, A. ; Hagopian, W.A. ; Krischer, J.P. ; Vehik, K. ; Knoop, J. ; Winker, C. ; Toppari, J. ; Lernmark, Å. ; Rewers, M.J. ; Steck, A.K. ; She, J.X. ; Akolkar, B. ; Robertson, C.C. ; Onengut-Gumuscu, S. ; Rich, S.S. ; Bonifacio, E. ; Ziegler, A.-G. ; The Teddy Study Group

Genetic contribution to the divergence in type 1 diabetes risk between children from the general population and children from affected families.

Diabetes 68, 847-857 (2019)

zu Castell, W. ; Lüttge, U. ; Matyssek, R.

Gaia-A holobiont-like system emerging from interaction.

In: Emergence and Modularity in Life Sciences. 2019. 255-279

Eraslan, G. ; Simon, L. ; Mircea, M. ; Müller, N.S. ; Theis, F.J.

Single-cell RNA-seq denoising using a deep count autoencoder.

Nat. Commun. 10:390 (2019)

Kaderali, L. ; Theis, F.J. ; Ganusov, V.V. ; Ciupe, S.M. ; Mehr, R. ; Ribeiro, R.M. ; Hernandez-Vargas, E.A.

Editorial: Integrative computational systems biology approaches in immunology and medicine.

Front. Microbiol. 9:3338 (2019)

Berrar, D. ; Dubitzky, W.

Should significance testing be abandoned in machine learning?

Int. J. Data Sci. Anal. 7, 247-257 (2019)

Fröhlich, F. ; Loos, C. ; Hasenauer, J.

Scalable inference of ordinary differential equation models of biochemical processes.

Methods Mol. Biol. 1883, 385-422 (2019)

Büttner, M. ; Miao, Z. ; Wolf, F.A. ; Teichmann, S.A. ; Theis, F.J.

A test metric for assessing single-cell RNA-seq batch correction.

Nat. Methods 16, 43-49 (2019)

Yang, J. ; Busen, H. ; Scherb, H. ; Hürkamp, K. ; Guo, Q. ; Tschiersch, J.

Modeling of radon exhalation from soil influenced by environmental parameters.

Sci. Total Environ. 656, 1304-1311 (2019)

van den Bos, H. ; Bakker, B. ; Taudt, A. ; Guryev, V. ; Colomé-Tatché, M. ; Lansdorp, P.M. ; Foijer, F. ; Spierings, D.C.J.

Quantification of aneuploidy in mammalian systems.

Methods Mol. Biol. 1896, 159-190 (2019)

Akagi, G. ; Kimura, M.

Unidirectional evolution equations of diffusion type.

J. Differ. Equations 266, 1-43 (2019)

Berrar, D. ; Lopes, P. ; Davis, J. ; Dubitzky, W.

Guest editorial: Special issue on machine learning for soccer.

Mach. Learn. 108, 1-7 (2019)

Tischler, J. ; Gruhn, W.H. ; Reid, J. ; Allgeyer, E. ; Buettner, F. ; Marr, C. ; Theis, F.J. ; Simons, B.D. ; Wernisch, L. ; Surani, M.A.

Metabolic regulation of pluripotency and germ cell fate through alpha-ketoglutarate.

EMBO J. 38:e99518 (2019)

Berrar, D. ; Lopes, P. ; Dubitzky, W.

Incorporating domain knowledge in machine learning for soccer outcome prediction.

Mach. Learn. 108, 97-126 (2019)

Wille, K. ; Sadjadian, P. ; Becker, T. ; Kolatzki, V. ; Horstmann, A. ; Fuchs, C. ; Griesshammer, M.

High risk of recurrent venous thromboembolism in BCR-ABL-negative myeloproliferative neoplasms after termination of anticoagulation.

Ann. Hematol. 98, 93-100 (2019)

Do, K.T. ; Rasp, D.J.N.P. ; Kastenmüller, G. ; Suhre, K. ; Krumsiek, J.

MoDentify: Phenotype-driven module identification in metabolomics networks at different resolutions.

Bioinformatics 35, 532-534 (2019)

Boiger, R. ; Fiedler, A. ; Hasenauer, J. ; Kaltenbacher, B.

Continuous analogue to iterative optimization for PDE-constrained inverse problems.

Inverse Prob. Sci. Eng. 27, 710-734 (2019)

Dubitzky, W. ; Lopes, P. ; Davis, J. ; Berrar, D.

The Open International Soccer Database for machine learning.

Mach. Learn. 108, 9-28 (2019)

Thomas, J. ; Küpper, M. ; Batra, R. ; Jargosch, M. ; Atenhan, A. ; Baghin, V. ; Krause, L. ; Lauffer, F. ; Biedermann, T. ; Theis, F.J. ; Eyerich, K. ; Eyerich, S. ; Garzorz-Stark, N.

Is the humoral immunity dispensable for the pathogenesis of psoriasis?

J. Eur. Acad. Dermatol. Venereol. 33, 115-122 (2019)

Ostaszewski, M. ; Gebel, S. ; Kuperstein, I. ; Mazein, A. ; Zinovyev, A. ; Dogrusoz, U. ; Hasenauer, J. ; Fleming, R.M.T. ; Le Novère, N. ; Gawron, P. ; Ligon, T. ; Niarakis, A. ; Nickerson, D.A. ; Weindl, D. ; Balling, R. ; Barillot, E. ; Auffray, C. ; Schneider, R.

Community-driven roadmap for integrated disease maps.

Brief. Bioinform. 20, 659-670 (2019)

Lordick, F. ; Haffner, I. ; Luber, B. ; Maier, D. ; Raimundez, E. ; Hasenauer, J. ; Kretzschmar, A.K. ; von Weikersthal, L.F. ; Ahlborn, M. ; Knorrenschild, J.R. ; Siegler, G. ; Rau, B. ; Fuxius, S. ; Decker, T. ; Schierle, K. ; Wittekind, C.

Heterogeneity of HER2 expression in gastric cancer (GC) leads to high deviation rates between local and central testing and hampers efficacy of anti-HER2 therapy: Survival results from the VARIANZ study.

Cancer Res. 78 (2018)

Wierling, C. ; Herault, Y. ; Jonkers, J. ; Ploubidou, A. ; Frappart, L. ; Hasenauer, J. ; Banga, J.R. ; Rinner, O. ; Naumova, V. ; Koubi, D. ; Lange, B.

CanPathPro-development of a platform for predictive pathway modelling using genetically engineered mouse models.

Cancer Res. 78 (2018)

Backofen, R. ; Costa, F. ; Theis, F.J. ; Marr, C. ; Preusse, M. ; Becker, C. ; Saunders, S. ; Palme, K. ; Dovzhenko, O.

MicroRNA as an integral part of cell communication: Regularized target prediction and network prediction.

In: Lecture Notes in Bioengineerin. 2018. 85-100

Müller, N.S. ; Sass, S. ; Offermann, B. ; Singh, A. ; Knauer, S. ; Schüttler, A. ; Minardi, J.N. ; Theis, F.J. ; Busch, H. ; Boerries, M.

Information theoretic concepts to unravel cell–cell communication.

In: Lecture Notes in Bioengineering. 2018. 115-136

Kyncl, M. ; Bast, L. ; Henkel, L. ; Theis, F.J. ; Oostendorp, R.A.J. ; Marr, C. ; Goetze, K.S.

Data driven computational modeling of hematopoiesis in myelodysplastic syndromes unveils differences in hematopoietic stem cell kinetics compared to age-matched healthy controls.

Blood 132 (2018)

Efendiyev, M.A.

Mathematical modeling of mitochondrial swelling.

Math. Model. of Mitochondrial Swelling. 2018. 1-223

Kindt-Dunjko, A. ; Foerster, K. ; Flemmer, A. ; Oak, P. ; Pomschar, A. ; Ertl-Wagner, B. ; Krumsiek, J. ; Hilgendorff, A.

Late Breaking Abstract - Protein signature stratifies severity of chronic lung disease in preterms after birth.

Eur. Respir. J. 52 (2018)

Hross, S. ; Theis, F.J. ; Sixt, M. ; Hasenauer, J.

Mechanistic description of spatial processes using integrative modelling of noise-corrupted imaging data.

J. R. Soc. Interface 15:20180600 (2018)

Chatzopoulou, E.I. ; Raharja-Liu, P. ; Murschhauser, A. ; Sekhavati, F. ; Buggenthin, F. ; Vollmar, A.M. ; Marr, C. ; Rädler, J.O.

A single-cell micro-trench platform for automatic monitoring of cell division and apoptosis after chemotherapeutic drug administration.

Sci. Rep. 8:18042 (2018)

Bast, L. ; Calzolari, F. ; Strasser, M. ; Hasenauer, J. ; Theis, F.J. ; Ninkovic, J. ; Marr, C.

Increasing neural stem cell division asymmetry and quiescence are predicted to contribute to the age-related decline in neurogenesis.

Cell Rep. 25, 3231-3240.e8 (2018)

Fröhlich, F. ; Reiser, A. ; Fink, L. ; Woschée, D. ; Ligon, T. ; Theis, F.J. ; Rädler, J.O. ; Hasenauer, J.

Multi-experiment nonlinear mixed effect modeling of single-cell translation kinetics after transfection.

NPJ Syst. Biol. Appl. 5 (2018)

Thomas, J. ; Wang, R. ; Batra, R. ; Theis, F.J. ; Eyerich, S. ; Zink, A. ; Eyerich, K.

CD23 is a biomarker of clinical response to IgE-specific immunoadsorption in patients with severe atopic eczema.

Exp. Dermatol. 27, 26-27 (2018)

Fröhlich, F. ; Kessler, T. ; Weindl, D. ; Shadrin, A. ; Schmiester, L. ; Hache, H. ; Muradyan, A. ; Schütte, M. ; Lim, J.H. ; Heinig, M. ; Theis, F.J. ; Lehrach, H. ; Wierling, C. ; Lange, B. ; Hasenauer, J.

Efficient parameter estimation enables the prediction of drug response using a mechanistic pan-cancer pathway model.

Cell Syst. 7, 567-579 (2018)

Zanardo, M. ; Rosselli, R. ; Meneghesso, A. ; Sablok, G. ; Stevanato, P. ; Engel, M. ; Altissimo, A. ; Peserico, L. ; Dezuani, V. ; Concheri, G. ; Schloter, M. ; Squartini, A.

Response of bacterial communities upon application of different innovative organic fertilizers in a greenhouse experiment using low-nutrient soil cultivated with cynodon dactylon.

Soil Syst. 2:52 (2018)

Foerster, K. ; Ertl-Wagner, B. ; Sass, S. ; Stoecklein, S. ; Schoeppe, F. ; Dietrich, O. ; Pomschar, A. ; Schulze, A. ; Huebener, C. ; Theis, F.J. ; Ehrhardt, H. ; Flemmer, A. ; Hilgendorff, A.

Quantitative MRI measurements to detect pulmonary hypertension in bronchopulomnary dysplasia.

Am. J. Respir. Crit. Care Med. 197 (2018)

Foerster, K. ; Sass, S. ; Pomschar, A. ; Ehrhardt, H. ; Naehrlich, L. ; Schulze, A. ; Flemmer, A. ; Huebener, C. ; Eickelberg, O. ; Theis, F.J. ; Dietrich, O. ; Ertl-Wagner, B. ; Hilgendorff, A.

Diagnosis of bronchopulmonary dysplasia using magnetic resonance imaging analysis.

Am. J. Respir. Crit. Care Med. 197 (2018)

Nawijn, M.C. ; Rajagopal, J. ; Koppelman, G.H. ; van den Berge, M. ; Rose-Zerilli, M.J. ; Holloway, J.W. ; Schultze, J.L. ; Barbry, P. ; Teichmann, S.A. ; Prabhakar, S. ; Theis, F.J. ; Schiller, H. B.

The human lung cell atlas: A comprehensive reference map for all cell types in the healthy human lung.

Am. J. Respir. Crit. Care Med. 197 (2018)

Fischer, D.S. ; Theis, F.J. ; Yosef, N.

Impulse model-based differential expression analysis of time course sequencing data.

Nucleic Acids Res. 46:e119 (2018)

Adriaens, M.E. ; Lodder, E.M. ; Moreno-Moral, A. ; Silhavý, J. ; Heinig, M. ; Glinge, C. ; Belterman, C. ; Wolswinkel, R. ; Petretto, E. ; Pravenec, M. ; Remme, C.A. ; Bezzina, C.R.

Systems genetics approaches in rat identify novel genes and gene networks associated with cardiac conduction.

J. Am. Heart Assoc. 7:e009243 (2018)

Tsepilov, Y.A. ; Sharapov, S.Z. ; Zaytseva, O.O. ; Krumsiek, J. ; Prehn, C. ; Adamski, J. ; Kastenmüller, G. ; Wang-Sattler, R. ; Strauch, K. ; Gieger, C. ; Aulchenko, Y.S.

A network-based conditional genetic association analysis of the human metabolome.

GigaScience 7, accepted (2018)

Neelakantan, D. ; Zhou, H. ; Oliphant, M.U.J. ; Zhang, X. ; Simon, L. ; Henke, D.M. ; Shaw, C.A. ; Wu, M.F. ; Hilsenbeck, S.G. ; White, L.D. ; Lewis, M.T. ; Ford, H.L.

EMT cells increase breast cancer metastasis via paracrine GLI activation in neighbouring tumour cells (vol 8, 15773, 2017).

Nat. Commun. 9:4720 (2018)

Akagi, G. ; Schimperna, G. ; Segatti, A. ; Spinolo, L.

Quantitative estimates on localized finite differences for the fractional poisson problem, and applications to regularity and spectral stability.

Commun. Math. Sci. 16, 913-961 (2018)

Neschen, S. ; Wu, M. ; Fuchs, C. ; Kondofersky, I. ; Theis, F.J. ; Hrabě de Angelis, M. ; Häring, H.-U. ; Sartorius, T.

Impact of brain fatty acid signaling on peripheral insulin action in mice.

Exp. Clin. Endocrinol. Diabet. 126, 20-29 (2018)

Efendiyev, M.A.

The Case of p-laplacian operator.

In: (Symmetrization and Stabilization of Solutions of Nonlinear Elliptic Equations). 2018. 225-252 (Fields Inst. Monogr. ; 36)

Efendiyev, M.A.

Preliminaries.

In: (Symmetrization and Stabilization of Solutions of Nonlinear Elliptic Equations). 2018. 1-70 (Fields Inst. Monogr. ; 36)

Efendiyev, M.A.

Symmetry and attractors: The case N ≤ 3.

In: Symmetrization and Stabilization of Solutions of Nonlinear Elliptic Equations. 2018. 163-175 (Fields Inst. Monogr. ; 36)

Efendiyev, M.A.

Symmetry and attractors.

In: Symmetrization and Stabilization of Solutions of Nonlinear Elliptic Equations. 2018. 187-198 (Fields Inst. Monogr. ; 36)

Efendiyev, M.A.

Trajectory dynamical systems and their attractors.

In: Symmetrization and Stabilization of Solutions of Nonlinear Elliptic Equations. 2018. 71-162 (Fields Inst. Monogr. ; 36)

Efendiyev, M.A.

Symmetry and attractors: The case N ≤ 4.

In: Symmetrization and Stabilization of Solutions of Nonlinear Elliptic Equations. 2018. 177-186 (Fields Inst. Monogr. ; 36)

Efendiyev, M.A.

Symmetry and attractors: Arbitrary dimension.

In: Symmetrization and Stabilization of Solutions of Nonlinear Elliptic Equations. 2018. 199-224 (Fields Inst. Monogr. ; 36)

Efendiyev, M.A.

Symmetrization and stabilization of solutions of nonlinear elliptic equations.

In: Symmetrization and Stabilization of Solutions of Nonlinear Elliptic Equations. 2018. 1-258 (Fields Inst. Monogr. ; 36)

Haffner, I. ; Luber, B. ; Maier, D. ; Geier, B. ; Raimundez-Alvarez, E. ; Hasenhauer, J. ; Kretzschmar, A.K. ; von Weikersthal, F.L. ; Ahlborn, M. ; Knorrenschild, R.J. ; Rau, B. ; Siegler, G. ; Fuxius, S. ; Decker, T. ; Schierle, K. ; Wittekind, C. ; Lordick, F.

Determination of HER2 in Gastric Cancer (GC) is still challenging: high deviation rates between local and central pathologies and its impact on survival.

Oncol. Res. Treat. 41, 240-240 (2018)

Endesfelder, D. ; zu Castell, W. ; Bonifacio, E. ; Rewers, M. ; Hagopian, W.A. ; She, J.X. ; Lernmark, A. ; Toppari, J. ; Vehik, K. ; Williams, A.J.K. ; Yu, L. ; Akolkar, B. ; Krischer, J.P. ; Ziegler, A.-G. ; Achenbach, P.

Time-resolved autoantibody profiling facilitates stratification of preclinical type 1 diabetes in children.

Diabetes 68, 119-130 (2018)

Martinez-Corral, R. ; Raimundez-Alvarez, E. ; Lin, Y. ; Elowitz, M.B. ; Garcia-Ojalvo, J.

Self-amplifying pulsatile protein dynamics without positive feedback.

Cell Syst. 7, 453-462 (2018)

Schälte, Y. ; Stapor, P. ; Hasenauer, J.

Evaluation of derivative-free optimizers for parameter estimation in systems biology.

IFAC PapersOnline 51, 98-101 (2018)

Bredies, K. ; Holler, M. ; Storath, M. ; Weinmann, A.

Total generalized variation for manifold-valued data.

SIAM J. Imaging Sci. 11, 1785-1848 (2018)

Efendiyev, M.A. ; van Brunt, B. ; Zaidi, A.A. ; Shah, T.H.

Asymmetric cell division with stochastic growth rate. Dedicated to the memory of the late Spartak Agamirzayev.

Math. Meth. Appl. Sci. 41, 8059-8069 (2018)

Wintergerst, L. ; Selmansberger, M. ; Maihoefer, C. ; Schüttrumpf, L. ; Walch, A.K. ; Wilke, C. ; Pitea, A. ; Woischke, C. ; Baumeister, P. ; Kirchner, T. ; Belka, C. ; Ganswindt, U. ; Zitzelsberger, H. ; Unger, K. ; Hess, J.

A prognostic mRNA expression signature of four 16q24.3 genes in radio(chemo)therapy-treated head and neck squamous cell carcinoma (HNSCC).

Mol. Oncol., accepted (2018)

Kindt, A. ; Liebisch, G. ; Clavel, T. ; Haller, D. ; Hörmannsperger, G. ; Yoon, H. ; Kolmeder, D. ; Sigruener, A. ; Krautbauer, S. ; Seeliger, C. ; Ganzha, A. ; Schweizer, S. ; Morisset, R. ; Strowig, T. ; Daniel, H. ; Helm, D. ; Küster, B. ; Krumsiek, J. ; Ecker, J.R.

The gut microbiota promotes hepatic fatty acid desaturation and elongation in mice.

Nat. Commun. 9:3760 (2018)

Do, K.T. ; Wahl, S. ; Raffler, J. ; Molnos, S. ; Laimighofer, M. ; Adamski, J. ; Suhre, K. ; Strauch, K. ; Peters, A. ; Gieger, C. ; Langenberg, C. ; Stewart, I.D. ; Theis, F.J. ; Grallert, H. ; Kastenmüller, G. ; Krumsiek, J.

Characterization of missing values in untargeted MS-based metabolomics data and evaluation of missing data handling strategies.

Metabolomics 14:128 (2018)

Feigelman, J ; Weindl, D. ; Theis, F.J. ; Marr, C. ; Hasenauer, J.

LNA++: Linear noise approximation with first and second order sensitivities.

In: Lecture Notes in Computer Science (16th International Conference on Computational Methods in Systems Biology, 12-14 September 2018, Brno; Czech Republic). 2018. 300-306 ( ; 11095 LNBI)

Herder, C. ; Kannenberg, J.M. ; Carstensen-Kirberg, M. ; Strom, A. ; Boenhof, G.J. ; Rathmann, W. ; Huth, C. ; Koenig, W. ; Heier, M. ; Krumsiek, J. ; Peters, A. ; Meisinger, C. ; Roden, M. ; Thorand, B. ; Ziegler, D.

A systemic inflammatory signature reflecting crosstalk between innate and adaptive immunity is associated with polyneuropathy: KORA F4/FF4 Study.

Diabetologia 61, S467-S467 (2018)

Zacharias, H.U. ; Altenbuchinger, M. ; Gronwald, W.

Statistical analysis of NMR metabolic fingerprints: Established methods and recent advances.

Metabolites 8:47 (2018)

Krause, L. ; Brockow, K. ; Theis, F.J. ; Schmidt-Weber, C.B. ; Müller, N.S. ; Eyerich, S.

Mathematical concepts and their challenges in predicting severity of atopic eczema patients.

Allergy 73, 731-731 (2018)

Jargosch, M. ; Lauffer, F. ; Paetzold, K. ; Krause, L. ; Garzorz-Stark, N. ; Schmidt-Weber, C.B. ; Eyerich, S. ; Eyerich, K.

Necroptosis as special type of cell death in inflammatory skin diseases.

Allergy 73, 731-731 (2018)

Thomas, J. ; Kuepper, M.K. ; Batra, R. ; Jargosch, M. ; Atenhan, A. ; Baghin, V. ; Krause, L. ; Lauffer, F. ; Biedermann, T. ; Theis, F.J. ; Schmidt-Weber, C.B. ; Eyerich, K. ; Eyerich, S. ; Garzorz-Stark, N.

The role of humoral immunity in the pathogenesis of psoriasis.

Allergy 73, 732-733 (2018)

Herder, C. ; Kannenberg, J.M. ; Carstensen-Kirberg, M. ; Strom, A. ; Bönhof, G.J. ; Rathmann, W. ; Huth, C. ; Koenig, W. ; Heier, M. ; Krumsiek, J. ; Peters, A. ; Meisinger, C. ; Roden, M. ; Thorand, B. ; Ziegler, D.

A systemic inflammatory signature reflecting crosstalk between innate and adaptive immunity is associated with polyneuropathy: KORA F4/FF4 Study.

Diabetes 67, 2434-2442 (2018)

Jarasch, A. ; Glaser, A. ; Häring, H.-U. ; Roden, M. ; Schürmann, A. ; Solimena, M. ; Theis, F.J. ; Tschöp, M.H. ; Wess, G. ; Hrabě de Angelis, M.

Mit Big Data zur personalisierten Diabetesprävention.

Diabetologe 14, 486-492 (2018)

Beatson, R.K. ; zu Castell, W.

Thinplate splines on the sphere.

Symmetry Integr. Geom. Methods Appl. 14:083 (2018)

Stapor, P. ; Fröhlich, F. ; Hasenauer, J.

Optimization and profile calculation of ODE models using second order adjoint sensitivity analysis.

Bioinformatics 34, 151-159 (2018)

Ballnus, B. ; Schaper, S. ; Theis, F.J. ; Hasenauer, J.

Bayesian parameter estimation for biochemical reaction networks using region-based adaptive parallel tempering.

Bioinformatics 34, 494-501 (2018)

Fortun, D. ; Storath, M. ; Rickert, D. ; Weinmann, A. ; Unser, M.

Fast piecewise-affine motion estimation without segmentation.

IEEE Trans. Image Process. 27, 5612-5624 (2018)

Kriegel, F. ; Matek, C. ; Dršata, T. ; Kulenkampff, K. ; Tschirpke, S. ; Zacharias, M. ; Lankaš, F. ; Lipfert, J.

The temperature dependence of the helical twist of DNA.

Nucleic Acids Res. 46, 7998-8009 (2018)

Pietzner, M. ; Budde, K. ; Homuth, G. ; Kastenmüller, G. ; Henning, A.-K. ; Artati, A. ; Krumsiek, J. ; Völzke, H. ; Adamski, J. ; Lerch, M.M. ; Kühn, J.P. ; Nauck, M. ; Friedrich, N.

Hepatic steatosis is associates with adverse molecular signatures in subjects without diabetes.

J. Clin. Endocrinol. Metab. 103, 3856-3868 (2018)

Hertel, J. ; Rotter, M. ; Frenzel, S. ; Zacharias, H.U. ; Krumsiek, J. ; Rathkolb, B. ; Hrabě de Angelis, M. ; Rabstein, S. ; Pallapies, D. ; Brüning, T. ; Grabe, H.J. ; Wang-Sattler, R.

Dilution correction for dynamically influenced urinary analyte data.

Anal. Chim. Acta 1032, 18-31 (2018)

Akagi, G. ; Efendiyev, M.A.

Allen-Cahn equation with strong irreversibility.

Euro. J. of Applied Mathematics 30, 707-755 (2018)

Akagi, G. ; Melchionna, S.

Elliptic-regularization of nonpotential perturbations of doubly-nonlinear flows of nonconvex energies: A variational approach.

J. Convex Anal. 25:861-898 (2018)

Loos, C. ; Krause, S. ; Hasenauer, J.

Hierarchical optimization for the efficient parametrization of ODE models.

Bioinformatics 34, 4266-4273 (2018)

Vollmar, C. ; Stredl, I. ; Heinig, M. ; Noachtar, S. ; Rémi, J.

Unilateral temporal interictal epileptiform discharges correctly predict the epileptogenic zone in lesional temporal lobe epilepsy.

Epilepsia 59, 1577-1582 (2018)

Pitchika, A. ; Jolink, M. ; Winkler, C. ; Hummel, S. ; Hummel, N. ; Krumsiek, J. ; Kastenmüller, G. ; Raab, J. ; Kordonouri, O. ; Ziegler, A.-G. ; Beyerlein, A.

Associations of maternal type 1 diabetes with childhood adiposity and metabolic health in the offspring: A prospective cohort study.

Diabetologia 61, 2319–2332 (2018)

Colomé-Tatché, M. ; Theis, F.J.

Statistical single cell multi-omics integration.

Curr. Opin. Syst. Biol. 7, 54-59 (2018)

Argelaguet, R. ; Velten, B. ; Arnol, D. ; Dietrich, S. ; Zenz, T. ; Marioni, J.C. ; Buettner, F. ; Huber, W. ; Stegle, O.

Multi-Omics Factor Analysis-a framework for unsupervised integration of multi-omics data sets.

Mol. Syst. Biol. 14:e8124 (2018)

Strasser, M. ; Hoppe, P.S. ; Loeffler, D. ; Kokkaliaris, K.D. ; Schroeder, T. ; Theis, F.J. ; Marr, C.

Lineage marker synchrony in hematopoietic genealogies refutes the PU.1/GATA1 toggle switch paradigm.

Nat. Commun. 9:2697 (2018)

Heinrich, L. ; Müller, J. ; Tellier, A. ; Živković, D.

Effects of population- and seed bank size fluctuations on neutral evolution and efficacy of natural selection.

Theor. Popul. Biol. 123, 45-69 (2018)

Jalalimanesh, A. ; Kuttler, C. ; García-Contreras, R. ; Pérez-Velázquez, J.

An agent-based model to study selection of Pseudomonas aeruginosa quorum sensing by pyocyanin: A multidisciplinary perspective on bacterial communication.

In: Quantitative Models for Microscopic to Macroscopic Biological Macromolecules and Tissues. 2018. 133-147

Baghin, V. ; Lauffer, F. ; Garzorz-Stark, N. ; Krause, L. ; Jargosch, M. ; Eyerich, S. ; Eyerich, K.

Predictive models for the natural course of atopic dermatitis in childhood based on serum parameters and clinical attributes.

Exp. Dermatol. 27, E17-E17 (2018)

Castañeda-Tamez, P. ; Ramírez-Peris, J. ; Pérez-Velázquez, J. ; Kuttler, C. ; Jalalimanesh, A. ; Saucedo-Mora, M.A. ; Jiménez-Cortés, J.G. ; Maeda, T. ; González, Y. ; Tomás, M. ; Wood, T.K. ; García-Contreras, R.

Pyocyanin restricts social cheating in Pseudomonas aeruginosa.

Front. Microbiol. 9:1348 (2018)

Taudt, A. ; Roquis, D. ; Vidalis, A. ; Wardenaar, R. ; Johannes, F. ; Colomé-Tatché, M.

METHimpute: Imputation-guided construction of complete methylomes from WGBS data.

BMC Genomics 19:444 (2018)

Zannas, A.S. ; Arloth, J. ; Carrillo-Roa, T. ; Iurato, S. ; Roeh, S. ; Ressler, K.J. ; Nemeroff, C.B. ; Smith, A.K. ; Bradley, B. ; Heim, C. ; Menke, A. ; Lange, J.F. ; Brueckl, T. ; Ising, M. ; Wray, N.R. ; Erhardt, A. ; Binder, E.B. ; Mehta, D.

Correction: Lifetime stress accelerates epigenetic aging in an urban, African American cohort: Relevance of glucocorticoid signaling [Genome Biol., 16, 1, (2015) (266)] DOI: 10.1186/s13059-015-0828-5.

Genome Biol. 19:61 (2018)

Iqbal, K. ; Dietrich, S. ; Wittenbecher, C. ; Krumsiek, J. ; Kühn, T. ; Lacruz, M.E. ; Kluttig, A. ; Prehn, C. ; Adamski, J. ; von Bergen, M. ; Kaaks, R. ; Schulze, M.B. ; Boeing, H. ; Floegel, A.

Comparison of metabolite networks from four German population-based studies.

Int. J. Epidemiol. 47, 2070-2081 (2018)

Isensee, J. ; Kaufholz, M. ; Knape, M.J. ; Hasenauer, J. ; Hammerich, H. ; Gonczarowska-Jorge, H. ; Zahedi, R.P. ; Schwede, F. ; Herberg, F.W. ; Hucho, T.

PKA-RII subunit phosphorylation precedes activation by cAMP and regulates activity termination.

J. Cell Biol. 217, 2167-2184 (2018)

Simon, L. ; Karg, S. ; Westermann, A.J. ; Engel, M. ; Elbehery, A.H.A. ; Hense, B.A. ; Heinig, M. ; Deng, L. ; Theis, F.J.

MetaMap: An atlas of metatranscriptomic reads in human disease-related RNA-seq data.

GigaScience 7, 1-8 (2018)

Hastreiter, S. ; Skylaki, S. ; Loeffler, D. ; Reimann, A. ; Hilsenbeck, O. ; Hoppe, P.S. ; Coutu, D.L. ; Kokkaliaris, K.D. ; Schwarzfischer, M. ; Anastassiadis, K. ; Theis, F.J. ; Schroeder, T.

Inductive and selective effects of GSK3 and MEK inhibition on nanog heterogeneity in embryonic stem cells.

Stem Cell Rep. 10, 58-69 (2018)

Klinger, E. ; Rickert, D. ; Hasenauer, J.

pyABC: Distributed, likelihood-free inference.

Bioinformatics 34, 3591-3593 (2018)

Ghasemi, M. ; Hense, B.A. ; Eberl, H.J. ; Kuttler, C.

Simulation-based exploration of quorum sensing triggered resistance of biofilms to antibiotics.

Bull. Math. Biol. 80, 1736-1775 (2018)

Plass, M. ; Solana, J. ; Wolf, F.A. ; Ayoub, S. ; Misios, A. ; Glažar, P. ; Obermayer, B. ; Theis, F.J. ; Kocks, C. ; Rajewsky, N.

Cell type atlas and lineage tree of a whole complex animal by single-cell transcriptomics.

Science 360:eaaq1723 (2018)

Viader Llargues, O. ; Lupperger, V. ; Pola-Morell, L. ; Marr, C. ; López-Schier, H.

Live cell-lineage tracing and machine learning reveal patterns of organ regeneration.

eLife 7:e30823 (2018)

Matek, C. ; Marr, C. ; Spiekermann, K.

Digital cytomorphology: Deep learning on an image data set of cell morphologies in acute myeloid leukemia.

In: (Workshop on Bildverarbeitung fur die Medizin, 11-13 March 2018, Erlangen). 2018. 10-10

Heinig, M.

Using gene expression to annotate cardiovascular GWAS loci.

Front. Cardiovasc. Med. 5:59 (2018)

Jargosch, M. ; Lauffer, F. ; Paetzold, K. ; Krause, L. ; Garzorz-Stark, N. ; Biedermann, T. ; Eyerich, S. ; Eyerich, K.

Necroptosis as special type of cell death in inflammatory skin diseases.

J. Invest. Dermatol. 138, S116-S116 (2018)

Haghverdi, L. ; Lun, A.T.L. ; Morgan, M.D. ; Marioni, J.C.

Batch effects in single-cell RNA-sequencing data are corrected by matching mutual nearest neighbors.

Nat. Biotechnol. 36, 421-427 (2018)

Erb, W. ; Weinmann, A. ; Ahlborg, M. ; Brandt, C. ; Bringout, G. ; Buzug, T.M. ; Frikel, J. ; Kaethner, C. ; Knopp, T. ; Maerz, T. ; Moeddel, M. ; Storath, M. ; Weber, A.

Mathematical analysis of the 1D model and reconstruction schemes for magnetic particle imaging.

Inverse Probl. 34:055012 (2018)

Bonifacio, E. ; Beyerlein, A. ; Hippich, M. ; Winkler, C. ; Vehik, K. ; Weedon, M.N. ; Laimighofer, M. ; Hattersley, A.T. ; Krumsiek, J. ; Frohnert, B.I. ; Steck, A.K. ; Hagopian, W.A. ; Krischer, J.P. ; Lernmark, A. ; Rewers, M.J. ; She, J.X. ; Toppari, J. ; Akolkar, B. ; Oram, R.A. ; Rich, S.S. ; Ziegler, A.-G.

Genetic scores to stratify risk of developing multiple islet autoantibodies and type 1 diabetes: A prospective study in children.

PLoS Med. 15:e1002548 (2018)

Beyerlein, A. ; Lack, N. ; von Kries, R.

No further improvement in pregnancy-related outcomes in the offspring of mothers with pre-gestational diabetes in Bavaria, Germany, between 2001 and 2016.

Diabetic Med. 35, 1420-1424 (2018)

von Neubeck, B. ; Gondi, G. ; Riganti, C. ; Pan, C. ; Parra Damas, A. ; Scherb, H. ; Ertürk, A. ; Zeidler, R.

An inhibitory antibody targeting carbonic anhydrase XII abrogates chemoresistance and significantly reduces lung metastases in an orthotopic breast cancer model in vivo.

Int. J. Cancer 143, 2065-2075 (2018)

Hege, M.A. ; Veit, R. ; Krumsiek, J. ; Kullmann, S. ; Heni, M. ; Rogers, P.J. ; Brunstrom, J.M. ; Fritsche, A. ; Preissl, H.

Eating less or more - Mindset induced changes in neural correlates of pre-meal planning.

Appetite 125, 492-501 (2018)

Apweiler, R. ; Beissbarth, T. ; Berthold, M.R. ; Blüthgen, N. ; Burmeister, Y. ; Dammann, O. ; Deutsch, A.J. ; Feuerhake, F. ; Franke, A. ; Hasenauer, J. ; Hoffmann, S. ; Höfer, T. ; Jansen, P.L.M. ; Kaderali, L. ; Klingmüller, U. ; Koch, I. ; Kohlbacher, O. ; Kuepfer, L. ; Lammert, F. ; Maier, D. ; Pfeifer, N. ; Radde, N. ; Rehm, M. ; Roeder, I. ; Saez-Rodriguez, J. ; Sax, U. ; Schmeck, B.T. ; Schuppert, A. ; Seilheimer, B. ; Theis, F.J. ; Vera, J. ; Wolkenhauer, O.

Whither systems medicine?

Exp. Mol. Med. 50:e453 (2018)

Dehmel, S. ; Nathan, P. ; Bartel, S. ; El-Mehrie, N. ; Scherb, H. ; Milger, K. ; John-Schuster, G. ; Yildirim, A.Ö. ; Hyklema, M. ; Irmler, M. ; Beckers, J. ; Schaub, B. ; Eickelberg, O. ; Krauss-Etschmann, S.

Intrauterine smoke exposure deregulates lung function, pulmonary transcriptomes, and in particular insulin-like growth factor (IGF)-1 in a sex-specific manner.

Sci. Rep. 8:7547 (2018)

Loos, C. ; Möller, K. ; Fröhlich, F. ; Hucho, T. ; Hasenauer, J.

A hierarchical, data-driven approach to modeling single-cell populations predicts latent causes of cell-to-cell variability.

Cell Syst. 6, 593-603.e13 (2018)

Heykants, M. ; Scherb, H. ; Michel, G. ; Mahabir, E.

Influence of polygamous versus monogamous mating on embryo production in four different strains of mice after superovulatory treatment.

Theriogenology 114, 85-94 (2018)

Pera, B. ; Krumsiek, J. ; Assouline, S.E. ; Marullo, R. ; Patel, J. ; Phillip, J.M. ; Román, L. ; Mann, K.K. ; Cerchietti, L.

Metabolomic profiling reveals cellular reprogramming of B-cell lymphoma by a lysine deacetylase inhibitor through the choline pathway.

EBioMedicine 28, 80-89 (2018)

Gabryś, H.S. ; Buettner, F. ; Sterzing, F. ; Hauswald, H. ; Bangert, M.

Design and selection of machine learning methods using radiomics and dosiomics for normal tissue complication probability modeling of xerostomia.

Front. Oncol. 8:35 (2018)

Lauffer, F. ; Jargosch, M. ; Krause, L. ; Garzorz-Stark, N. ; Franz, R. ; Roenneberg, S. ; Böhner, A. ; Müller, N.S. ; Theis, F.J. ; Schmidt-Weber, C.B. ; Biedermann, T. ; Eyerich, S. ; Eyerich, K.

Type I immune response induces keratinocyte necroptosis and is associated with interface dermatitis.

J. Invest. Dermatol., accepted (2018)

Wahl, A. ; van den Akker, E. ; Klaric, L. ; Štambuk, J. ; Benedetti, E. ; Plomp, R. ; Razdorov, G. ; Trbojević-Akmačić, I. ; Deelen, J. ; van Heemst, D. ; Eline Slagboom, P. ; Vučković, F. ; Grallert, H. ; Krumsiek, J. ; Strauch, K. ; Peters, A. ; Meitinger, T. ; Hayward, C. ; Wuhrer, M. ; Beekman, M. ; Lauc, G. ; Gieger, C.

Genome-wide association study on immunoglobulin G glycosylation patterns.

Front. Immunol. 9:277 (2018)

Lange, T. ; Budde, K. ; Homuth, G. ; Kastenmüller, G. ; Artati, A. ; Krumsiek, J. ; Völzke, H. ; Adamski, J. ; Petersmann, A. ; Völker, U. ; Nauck, M. ; Friedrich, N. ; Pietzner, M.

Comprehensive metabolic profiling reveals a lipid-rich fingerprint of free thyroxine far beyond classic parameters.

J. Clin. Endocrinol. Metab. 103, 2050-2060 (2018)

Hanna, C.W. ; Taudt, A. ; Huang, J. ; Gahurova, L. ; Kranz, A. ; Andrews, S. ; Dean, W. ; Stewart, A.F. ; Colomé-Tatché, M. ; Kelsey, G.

MLL2 conveys transcription-independent H3K4 trimethylation in oocytes.

Nat. Struct. Mol. Biol. 25, 73-82 (2018)

Benedetti, E. ; Pučić-Baković, M. ; Keser, T. ; Wahl, A. ; Hassinen, A. ; Yang, J.Y. ; Liu, L. ; Trbojević-Akmačić, I. ; Razdorov, G. ; Štambuk, J. ; Klarić, L. ; Ugrina, I. ; Selman, M.H.J. ; Wuhrer, M. ; Rudan, I. ; Polasek, O. ; Hayward, C. ; Grallert, H. ; Strauch, K. ; Peters, A. ; Meitinger, T. ; Gieger, C. ; Vilaj, M. ; Boons, G.J. ; Moremen, K.W. ; Ovchinnikova, T. ; Bovin, N. ; Kellokumpu, S. ; Theis, F.J. ; Lauc, G. ; Krumsiek, J.

Erratum: Publisher Correction: Network inference from glycoproteomics data reveals new reactions in the IgG glycosylation pathway (Nature communications (2017) 8 1 (1483)).

Nat. Commun. 9:706 (2018)

Matek, C. ; Marr, C. ; Spiekermann, K.

Computer-aided morphological classification of blood cells relevant in Acute Myeloid Leukemia.

Oncol. Res. Treat. 41, 197-197 (2018)

Lordick, F. ; Haffner, I. ; Luber, B. ; Maier, D. ; Geier, B. ; Raimundez-Alvarez, E. ; Hasenauer, J. ; Kretzschmar, A.K. ; von Weikersthal, L.F. ; Ahlborn, M. ; Riera, J. ; Rau, B. ; Siegler, G. ; Fuxius, S. ; Decker, T. ; Schierle, K. ; Wittekind, C.

High Deviation rates between local and central HER2 assessment and survival with anti-HER2-therapy in advanced Gastric Cancer (GC): Results from the VARIANZ study.

Oncol. Res. Treat. 41, 191-191 (2018)

Wolf, F.A. ; Angerer, P. ; Theis, F.J.

SCANPY: Large-scale single-cell gene expression data analysis.

Genome Biol. 19:15 (2018)

Stirm, L. ; Huypens, P. ; Sass, S. ; Batra, R. ; Fritsche, L. ; Brucker, S. ; Abele, H. ; Hennige, A.M. ; Theis, F.J. ; Beckers, J. ; Hrabě de Angelis, M. ; Fritsche, A. ; Häring, H.-U. ; Staiger, H.

Maternal whole blood cell miRNA-340 is elevated in gestational diabetes and inversely regulated by glucose and insulin.

Sci. Rep. 8:1366 (2018)

Kiechle, M. ; Storath, M. ; Weinmann, A. ; Kleinsteuber, M.

Model-based learning of local image features for unsupervised texture segmentation.

IEEE Trans. Image Process. 27, 1994-2007 (2018)

Storath, M. ; Weinmann, A.

Fast median filtering for phase or orientation data.

IEEE Trans. Pattern Anal. Mach. Intell. 40, 639-652 (2018)

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An integrative disease-relevant multi-omics analysis to predict risk for stress-related psychiatric disorders.

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Ecological plant epigenetics: Evidence from model and non-model species, and the way forward.

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EMT cells increase breast cancer metastasis via paracrine GLI activation in neighbouring tumour cells.

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Does age really matter? Radiotherapy in elderly patients with glioblastoma, the Munich experience.

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Identification of a plasma miRNA biomarker-signature for allergic asthma: A translational approach.

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Comprehensive benchmarking of Markov chain Monte Carlo methods for dynamical systems.

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Rapid genome-wide recruitment of RNA polymerase II drives transcription, splicing, and translation events during T cell responses.

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2d cross-omics integrated enrichment analysis of human and mice COPD lungs reveal novel pathological mechanisms of disease progression.

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Pulmonary microRNA profiles identify involvement of Creb1 and Sec14l3 in bronchial epithelial changes in allergic asthma.

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Discrimination of pulmonary changes in neonatal chronic lung disease by a new Mri score.

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N-acyl taurines and acylcarnitines cause an imbalance in insulin synthesis and secretion provoking β cell dysfunction in type 2 diabetes.

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The quest for novel biomarkers in early diagnosis of diabetic neuropathy.

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Sex-specific metabolic profiles of androgens and its main binding protein SHBG in a middle aged population without diabetes.

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Predicting gene expression in massively parallel reporter assays: A comparative study.

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Calcium-regulatory proteins as modulators of chemotherapy in human neuroblastoma.

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Characterization of multiple B cell subsets in peripheral blood and skin biopsies of psoriasis patients identifies a correlation of plasma and regulatory B cells and disease severity.

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The imiquimod model as a model for psoriasis and/or eczema in humans?

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Interface dermatitis shows a distinctive molecular signature independent from individual disease background.

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CgCorrect: A method to correct for confounding cell-cell variation due to cell growth in single-cell transcriptomics.

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Mathematical analysis of an in vivo model of mitochondrial swelling.

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Transcriptome-wide co-expression analysis identifies LRRC2 as a novel mediator of mitochondrial and cardiac function.

PLoS ONE 12:e0170458 (2017)

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fastER: A user-friendly tool for ultrafast and robust cell segmentation in large-scale microscopy.

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On the stability of a space vehicle riding on an intense laser beam.

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Parameter estimation for dynamical systems with discrete events and logical operations.

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Scalable parameter estimation for genome-scale biochemical reaction networks.

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Robust parameter estimation for dynamical systems from outlier-corrupted data.

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A DREAM challenge to build prediction models for short-term discontinuation of docetaxel in metastatic castration-resistant prostate cancer.

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Prediction of overall survival for patients with metastatic castration-resistant prostate cancer: Development of a prognostic model through a crowdsourced challenge with open clinical trial data.

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Peptide serum markers in islet autoantibody-positive children.

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Effects of stressful events in France (1968) and Japan (1995) on the sex ratio at birth.

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TALEN/CRISPR-mediated engineering of a promoterless anti-viral RNAi hairpin into an endogenous miRNA locus.

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Environmental and mucosal microbiota and their role in childhood asthma.

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Signatures of Dobzhansky-Muller Incompatibilities in the genomes of recombinant inbred lines.

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LSC Abstract – Early biomarkers indicating the development of neonatal chronic lung disease defined by clinical and imaging parameters.

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Lactation is associated with altered metabolomic signatures in women with gestational diabetes.

Diabetologia 59, S187-S187 (2016)

Stirm, L. ; Huypens, P. ; Sass, S. ; Fritsche, L. ; Fritsche, A. ; Beckers, J. ; Hrabě de Angelis, M. ; Staiger, H. ; Häring, H.-U.

miRNA signatures in maternal whole blood cells of women with gestational diabetes.

Diabetologia 59, S47-S47 (2016)

Zierer, J. ; Pallister, T. ; Tsai, P.C. ; Krumsiek, J. ; Bell, J.T. ; Lauc, G. ; Spector, T.D. ; Menni, C. ; Kastenmüller, G.

Exploring the molecular basis of age-related disease comorbidities using a multi-omics graphical model.

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Characterization of rare, dormant, and therapy-resistant cells in acute lymphoblastic leukemia.

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Integration based profile likelihood calculation for PDE constrained parameter estimation problems.

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Searching for drug targets - Are Solute Carrier (SLC) transport proteins a promising target on human naive and activated CD4+T cells.

Allergy 71, 223-224 (2016)

Espinoza, J.A. ; Jabeen, S. ; Batra, R. ; Papaleo, E. ; Haakensen, V. ; Timmermans Wielenga, V. ; Talman, M.L.M. ; Brunner, N. ; Børresen-Dale, A.L. ; Gromov, P. ; Helland, Å. ; Kristensen, V.N. ; Gromova, I.

Cytokine profiling of tumor interstitial fluid of the breast and its relationship with lymphocyte infiltration and clinicopathological characteristics.

OncoImmunology 5:e1248015 (2016)

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Inhibition of fat cell differentiation in 3T3-L1 pre-adipocytes by all-trans retinoic acid: Integrative analysis of transcriptomic and phenotypic data.

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Epigenetic germline inheritance of diet-induced obesity and insulin resistance.

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Luber, B. ; Keller, S. ; Zwingenberger, G. ; Ebert, K. ; Maier, D. ; Geier, B. ; Theis, F.J. ; Hasenauer, J. ; Huge, S. ; Meyer-Hermann, M. ; Dehghany, J. ; Walch, A.K. ; Aichler, M. ; Lordick, F. ; Haffner, I.

Identification of predictive response and resistance factors to targeted therapy in gastric cancer using a systems medicine approach.

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Large-scale modeling of cancer signaling: Mechanistic modeling meets Big Data.

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Nuss, A.M. ; Schuster, F. ; Roselius, L. ; Klein, J. ; Bücker, R. ; Herbst, K. ; Heroven, A.K. ; Pisano, F. ; Wittmann, C. ; Münch, R. ; Müller, J. ; Jahn, D. ; Dersch, P.

A precise temperature-responsive bistable switch controlling yersinia virulence.

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Quantitative comparison of competing PDE models for Pomlp dynamics in fission yeast.

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Oncogenic Kras promotes early pancreatic carcinogenesis by perpetuating elements of natural inflammatory response.

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Abstract 1945: Identification of a miRNA/mRNA network driving non-small cell lung cancer (NSCLC) dissemination.

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Einzigartige Zellen: Computerbasierte Methoden verbessern die Einzelzell-Analyse.

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Parameter estimation and uncertainty quantification for image based systems biology.

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Introducing a stable bootstrap validation framework for reliable genomic signature extraction.

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Analysis of cell lineage trees by exact bayesian inference identifies negative autoregulation of nanog in mouse embryonic stem cells.

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CORALINA: A universal method for the generation of gRNA libraries for CRISPR-based screening.

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Characterization of multiple B cell subsets in peripheral blood of psoriasis patients identifies a correlation of plasma and regulatory B cells with disease severity.

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A distinct molecular signature of interface dermatitis as determined by gene expression analysis combined with disease independent histological phenotyping.

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München, Technische Universität, Fakultät für Medizin, Diss., 2016, 131 S.

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Identification of new cell surface targets on human T helper cells.

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München, Technische Universität, Fakultät für Mathematik, Diss., 2016, 178 S.

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Embedding metabolism into the omics landscape: Integrated analysis of metabolomics, transcriptomics and proteomics data from cellular to organ level.

München, Technische Universität, Fakultät Wissenschaftszentrum Weihenstephan, Diss., 2016, 201 S.

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München, Technische Universität, Fakultät für Mathematik, Diss., 2016, 171 S.

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A novel approach for the analysis of longitudinal profiles reveals delayed progression to type 1 diabetes in a subgroup of multiple-islet-autoantibody-positive children.

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Much, D. ; Beyerlein, A. ; Kindt, A. ; Krumsiek, J. ; Stückler, F. ; Rossbauer, M. ; Hofelich, A. ; Wiesenäcker, D. ; Hivner, S. ; Herbst, M. ; Römisch-Margl, W. ; Prehn, C. ; Adamski, J. ; Kastenmüller, G. ; Theis, F.J. ; Ziegler, A.-G. ; Hummel, S.

Lactation is associated with altered metabolomic signatures in women with gestational diabetes.

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Hilsenbeck, O. ; Schwarzfischer, M. ; Skylaki, S. ; Schauberger, B. ; Hoppe, P.S. ; Loeffler, D. ; Kokkaliaris, K.D. ; Hastreiter, S. ; Skylaki, E. ; Filipczyk, A. ; Strasser, M. ; Buggenthin, F. ; Feigelman, J. ; Krumsiek, J. ; van den Berg, A.J. ; Endele, M. ; Etzrodt, M. ; Marr, C. ; Theis, F.J. ; Schroeder, T.

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Early myeloid lineage choice is not initiated by random PU.1 to GATA1 protein ratios.

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Single-cell whole genome sequencing reveals no evidence for common aneuploidy in normal and Alzheimer's disease neurons.

Genome Biol. 17:116 (2016)

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Combined tensor fitting and TV regularization in diffusion tensor imaging based on a Riemannian manifold approach.

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A force-sensitive organoid assay to quantify regenerative potential of single primary human mammary cells.

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Principles of microRNA regulation revealed through modeling microRNA expression quantitative trait loci.

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Comparison of cox model methods in a low-dimensional setting with few events.

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Subramanian, D.R. ; Gupta, S. ; Burggraf, D. ; vom Silberberg, S. ; Heimbeck, I. ; Heiss-Neumann, M.S. ; Haeussinger, K. ; Newby, C. ; Hargadon, B. ; Raj, V. ; Singh, D. ; Kolsum, U. ; Hofer, T.P. ; Al-Shair, K. ; Luetzen, N. ; Prasse, A. ; Müller-Quernheim, J. ; Benea, G. ; Leprotti, S. ; Boschetto, P. ; Gorecka, D. ; Nowinski, A. ; Oniszh, K. ; zu Castell, W. ; Hagen, M. ; Barta, I. ; Döme, B. ; Strausz, J. ; Greulich, T. ; Vogelmeier, C. ; Koczulla, A.R. ; Gut, I. ; Hohlfeld, J. ; Welte, T. ; Lavae-Mokhtari, M. ; Ziegler-Heitbrock, L. ; Brightling, C. ; Parr, D.G.

Emphysema- and airway-dominant COPD phenotypes defined by standardised quantitative computed tomography.

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A novel molecular disease classifier for psoriasis and eczema.

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Taudt, A. ; Colomé-Tatché, M. ; Johannes, F.

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Parameter estimation for outlier corrupted data.

München, Technische Universität, Mathematische Fakultät, Master-Thesis, 2016, 61 S.

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Epigenetic signatures of environmental factors in children with familial risk for type 1 diabetes.

München, Ludwig-Maximilians-Universität & Technische Universität, Bioinformatik, Bachelor-Thesis, 2016, 57 S.

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A computational model to predict severity of atopic eczema from 30 serum proteins.

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Dragoi, D. ; Krattenmacher, A. ; Mishra, V.K. ; Schmidt, J. ; Kloos, U. ; Meixner, L.K. ; Hauck, S.M. ; Buggenthin, F. ; Schwartz, D. ; Marr, C. ; Johnsen, S.A. ; Scheel, C.

Twist1 induces distinct cell states depending on TGFBR1-activation.

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Effects of multiple but low pesticide loads on aquatic fungal communities colonizing leaf litter.

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Nitrogen fertilization affects bacteria utilizing plant-derived carbon in the rhizosphere of beech seedlings.

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Gut immunity and type 1 diabetes: A mélange of microbes, diet, and host interactions?

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Analysis of CFSE time-series data using division-, age- and label-structured population models.

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Single-cell gene expression profiling and cell state dynamics: Collecting data, correlating data points and connecting the dots.

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Towards a functional hypothesis relating anti-islet cell autoimmunity to the dietary impact on microbial communities and butyrate production.

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MEMO - multi-experiment mixture model analysis of censored data.

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Inferring catalysis in biological systems.

IET Syst. Biol. 10, 210-218 (2016)

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Stochastic and deterministic methods for the analysis of Nanog dynamics in mouse embryonic stem cells.

München, Technische Universität, Fakultät für Mathematik, Diss., 2016, 194 S.

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A second order non-smooth variational model for restoring manifold-valued images.

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Minimization and estimation of the variance of prediction errors for cross-validation designs.

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Analysis of the complete genome sequence of the archaeon Pyrococcus chitonophagus DSM 10152 (formerly Thermococcus chitonophagus).

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Exact algorithms for L¹-TV regularization of real-valued or circle-valued signals.

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Metabolomics reveals effects of maternal smoking on endogenous metabolites from lipid metabolism in cord blood of newborns.

Metabolomics 12:76 (2016)

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Organic contamination versus mineral properties: Competing selective forces shaping bacterial community assembly in aquifer sediments.

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de Oliveira, K.A. ; Kaergel, E. ; Heinig, M. ; Fontaine, J.F. ; Patone, G. ; Muro, E.M. ; Mathas, S. ; Hummel, M. ; Andrade-Navarro, M.A. ; Hubner, N. ; Scheidereit, C.

A roadmap of constitutive NF-κB activity in Hodgkin lymphoma: Dominant roles of p50 and p52 revealed by genome-wide analyses.

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miTALOS v2: Analyzing tissue specific microRNA function.

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CERENA: ChEmical REaction Network Analyzer - a toolbox for the simulation and analysis of stochastic chemical kinetics.

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Jung, B. ; Padula, D. ; Burtscher, I. ; Landerer, C. ; Lutter, D. ; Theis, F.J. ; Messias, A.C. ; Geerlof, A. ; Sattler, M. ; Kremmer, E. ; Boldt, K. ; Ueffing, M. ; Lickert, H.

Pitchfork and Gprasp2 target smoothened to the primary cilium for Hedgehog pathway activation.

PLoS ONE 11:e0149477 (2016)

Stojcheva, N. ; Schechtmann, G. ; Sass, S. ; Roth, P. ; Florea, A.M. ; Stefanski, A. ; Stühler, K. ; Wolter, M. ; Müller, N.S. ; Theis, F.J. ; Weller, M.G. ; Reifenberger, G. ; Happold, C.

MicroRNA-138 promotes acquired alkylator resistance in glioblastoma by targeting the Bcl-2-interacting mediator BIM.

Oncotarget 7, 12937-12950 (2016)

Scherb, H. ; Kusmierz, R. ; Voigt, K.

Human sex ratio at birth and residential proximity to nuclear facilities in France.

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Hahn, K.R. ; Massopust, P. ; Prigarin, S.M.

A new method to measure complexity in binary or weighted networks and applications to functional connectivity in the human brain.

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Bergmann, R. ; Weinmann, A.

A second-order TV-type approach for inpainting and denoising higher dimensional combined cyclic and vector space data.

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Masukume, G. ; Grech, V. ; Scherb, H.

Reply: Analysis of the sex ratio at birth in South Africa increased 9 months after the 2010 FIFA World Cup.

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Mund, A. ; Kuttler, C. ; Pérez-Velázquez, J. ; Hense, B.A.

An age-dependent model to analyse the evolutionary stability of bacterial quorum sensing.

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Combinatorial histone acetylation patterns are generated by motif-specific reactions.

Cell Syst. 2, 49-58 (2016)

Schulte, E.C. ; Altmaier, E. ; Berger, H.S. ; Do, K.T. ; Kastenmüller, G. ; Wahl, S. ; Adamski, J. ; Peters, A. ; Krumsiek, J. ; Suhre, K. ; Haslinger, B. ; Ceballos-Baumann, A. ; Gieger, C. ; Winkelmann, J.

Alterations in lipid and inositol metabolisms in two dopaminergic disorders.

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Weinmann, A. ; Demaret, L. ; Storath, M.

Mumford-Shah and Potts regularization for manifold-valued data.

J. Math. Imaging Vis. 55, 428-445 (2016)

Blasi, T. ; Hennig, H. ; Summers, H.D. ; Theis, F.J. ; Cerveira, J. ; Patterson, J.O. ; Davies, D. ; Filby, A. ; Carpenter, A.E. ; Rees, P.

Label-free cell cycle analysis for high-throughput imaging flow cytometry.

Nat. Commun. 7:10256 (2016)

Bergkemper, F. ; Schöler, A. ; Engel, M. ; Lang, F. ; Krüger, J. ; Schloter, M. ; Schulz, S.

Phosphorus depletion in forest soils shapes bacterial communities towards phosphorus recycling systems.

Environ. Microbiol. 18, 1988-2000 (2016)

Hug, S. ; Schmidl, D. ; Li, W.B. ; Greiter, M. ; Theis, F.J.

Bayesian model selection methods and their application to biological ODE systems.

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Massopust, P.

On local fractal functions in Besov and Triebel-Lizorkin spaces.

J. Math. Anal. Appl. 436, 393-407 (2016)

Angerer, P. ; Haghverdi, L. ; Büttner, M. ; Theis, F.J. ; Marr, C. ; Buettner, F.

Destiny: Diffusion maps for large-scale single-cell data in R.

Bioinformatics 32, 1241-1243 (2016)

Liebscher, V.

The relation of spatial and tensor product of Arveson systems - the random set point of view.

Infin. Dimens. Anal. Quantum Probab. Relat. Top. 18, accepted (2016)

Scherb, H. ; Grech, V. ; Kusmierz, R. ; Voigt, K.

Letter to the editor "Radiation and Environmental Biophysics" : Comment on "Sex ratio at birth: scenario from normal- and high-level natural radiation areas of Kerala coast in south-west India" by Koya PK, Jaikrishan G, Sudheer KR, Andrews VJ, Madhusoodhanan M, Jagadeesan CK, Das B. Radiat Environ Biophys. 2015 Sep 5 [Epub ahead of print].

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Willmann, S. ; Müller, N.S. ; Engert, S. ; Sterr, M. ; Burtscher, I. ; Raducanu, A. ; Irmler, M. ; Beckers, J. ; Sass, S. ; Theis, F.J. ; Lickert, H.

The global gene expression profile of the secondary transition during pancreatic development.

Mech. Dev. 139, 51-64 (2016)

Feng, L. ; Zhang, X. ; Wu, J. ; Efendiyev, M.A.

Necessary conditions for positivity-preserving property of reaction-diffusion systems with delay.

Electron. J. Qual. Theory Differ. Equations 13, 1-7 (2016)

Kunis, S. ; Peter, T. ; Römer, T. ; von der Ohe, U.

A multivariate generalization of Prony's method.

Linear Algebra Appl. 490, 31-47 (2016)

Scherb, H. ; Kusmierz, R. ; Sigler, M. ; Voigt, K.

Modeling human genetic radiation risks around nuclear facilities in Germany and five neighboring countries: A sex ratio study.

Environ. Modell. Softw. 79, 343-353 (2016)

Zissler, U.M. ; Chaker, A. ; Effner, R. ; Ulrich, M. ; Guerth, F. ; Piontek, G. ; Dietz, K. ; Regn, M. ; Knapp, B. ; Theis, F.J. ; Heine, H. ; Suttner, K. ; Schmidt-Weber, C.B.

Interleukin-4 and interferon-γ orchestrate an epithelial polarization in the airways.

Mucosal Immunol. 9, 917-926 (2016)

Conlon, T.M. ; Bartel, J. ; Ballweg, K. ; Günter, S. ; Prehn, C. ; Krumsiek, J. ; Meiners, S. ; Theis, F.J. ; Adamski, J. ; Eickelberg, O. ; Yildirim, A.Ö.

Metabolomics screening identifies reduced L-carnitine to be associated with progressive emphysema.

Clin. Sci. 130, 273-287 (2016)

Sekula, P. ; Goek, O.N. ; Quaye, L. ; Barrios, C. ; Levey, A.S. ; Römisch-Margl, W. ; Menni, C. ; Yet, I. ; Gieger, C. ; Inker, L.A. ; Adamski, J. ; Gronwald, W. ; Illig, T. ; Dettmer, K. ; Krumsiek, J. ; Oefner, P.J. ; Valdes, A.M. ; Meisinger, C. ; Coresh, J. ; Spector, T.D. ; Mohney, R.P. ; Suhre, K. ; Kastenmüller, G. ; Köttgen, A.

A metabolome-wide association study of kidney function and disease in the general population.

J. Am. Soc. Nephrol. 27, 1175-1188 (2016)

Miettinen, J. ; Illner, K. ; Nordhausen, K. ; Oja, H. ; Taskinen, S. ; Theis, F.J.

Separation of uncorrelated stationary time series using autocovariance matrices.

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zu Castell, W. ; Fleischmann, F. ; Heger, T. ; Matyssek, R.

Shaping theoretic foundations of holobiont-like systems.

Prog. Bot. 77, 219-244 (2016)

Kong, B. ; Wu, W. ; Cheng, T. ; Schlitter, A.M. ; Qian, C. ; Bruns, P. ; Jian, Z. ; Jager, C. ; Regel, I. ; Raulefs, S. ; Behler, N. ; Irmler, M. ; Beckers, J. ; Friess, H. ; Erkan, M. ; Siveke, J.T. ; Tannapfel, A. ; Hahn, S.A. ; Theis, F.J. ; Esposito, I. ; Kleeff, J. ; Michalski, C.W.

A subset of metastatic pancreatic ductal adenocarcinomas depends quantitatively on oncogenic Kras/Mek/Erk-induced hyperactive mTOR signalling.

Gut 65, 647-657 (2016)

van der Graaf, A. ; Wardenaar, R. ; Neumann, D.A. ; Taudt, A. ; Shaw, R.G. ; Jansen, R.C. ; Schmitz, R.J. ; Colomé-Tatché, M. ; Johannes, F.

Rate, spectrum, and evolutionary dynamics of spontaneous epimutations.

Proc. Natl. Acad. Sci. U.S.A. 112, 6676-6681 (2015)

Bartel, S. ; Schulz, N. ; Schamberger, A.C. ; Alessandrini, F. ; Pagel, P. ; Theis, F.J. ; Milger, K. ; Nößner, E. ; Stick, S.M. ; Kicic, A. ; Eickelberg, O. ; Freishtat, R.J. ; Krauss-Etschmann, S.

SEC14-like 3 is decreased in airway ciliated cells in experimental and paediatric asthma.

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Massopust, P. ; Zayed, A.I.

On the invalidity of fourier series expansions of fractional order.

Fractional Calc. Appl. Anal. 18, 1507-1517 (2015)

Zannas, A.S. ; Arloth, J. ; Carrillo-Roa, T. ; Iurato, S. ; Röh, S. ; Ressler, K.J. ; Nemeroff, C.B. ; Smith, A.K. ; Bradley, B. ; Heim, C. ; Menke, A. ; Lange, J.F. ; Brückl, T. ; Ising, M. ; Wray, N.R. ; Erhardt, A. ; Binder, E.B. ; Mehta, D.

Lifetime stress accelerates epigenetic aging in an urban, African American cohort: Relevance of glucocorticoid signaling.

Genome Biol. 16:266 (2015)

Schröder, K.

Error estimates for approximate operator inversion via Kernel-based methods.

Lecture Notes Comp. Sci. 9213, 399-413 (2015)

Zweng, M. ; Fallavollita, P. ; Demirci, S. ; Kowarschik, M. ; Navab, N. ; Mateus, D.

Automatic guide-wire detection for neurointerventions using low-rank sparse matrix decomposition and denoising.

Lecture Notes Comp. Sci. 9365, 114-123 (2015)

Stavropoulou, F. ; Müller, J.

Parametrization of random vectors in polynomial chaos expansions via optimal transportation.

SIAM J. Sci. Comput. 37, A2535-A2557 (2015)

Akagi, G. ; Schimperna, G. ; Segatti, A.

Fractional Cahn-Hilliard, Allen-Cahn and porous medium equations.

J. Differ. Equations 261, 2935-2985 (2015)

Frank, U. ; Zhao, F. ; El-Kelish, A. ; Heller, W. ; Braun, P. ; Durner, J. ; Winkler, J.B. ; Engel, M. ; Pfeifer, M. ; von Toerne, C. ; Hauck, S.M. ; Oeder, S. ; Traidl-Hoffmann, C. ; Ernst, D.

Ragweed (Ambrosia artemisiifolia): How does Ambrosia pollen react to different air pollution? A systems biology approach.

Allergy 70, 128 (2015)

Graessel, A. ; Hauck, S.M. ; von Toerne, C. ; Kloppmann, E. ; Goldberg, T. ; Koppensteiner, H. ; Schindler, M. ; Knapp, B. ; Krause, L. ; Kremmer, E. ; Blank, S. ; Schmidt-Weber, C.B. ; Suttner, K.

Identification of new cell surface proteins on human naive CD4⁺ T-cells potentially involved in the early T-cell activation.

Allergy 70, 104 (2015)

Ehler, M. ; Filbir, F.

Wavelet frames to optimally learn functions on diffusion measure spaces.

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Obermaier, J.

On convergence and absolute convergence of Fourier series with respect to orthogonal polynomials.

Bull. Math. Anal. Appl. 7, 1-10 (2015)

Ringler, J.

Tracking cell lineage to analyse anti-cancer drug resistance development in an agent based model.

München, Technische Universität, Fakultät für Mathematik, Bachelor-Thesis, 2015, 75 S.

Weck, S.

Identification of protein biomarkers for early detection of neonatal chronic lung disease in preterm infants.

München, Ludwig-Maximilians-Universität & Technische Universität, Bioinformatik, Bachelor-Thesis, 2015, 41 S.

Sass, S. ; Pitea, A. ; Unger, K. ; Hess, J. ; Müller, N.S. ; Theis, F.J.

MicroRNA-target network inference and local network enrichment analysis identify two microRNA clusters with distinct functions in head and neck squamous cell carcinoma.

Int. J. Mol. Sci. 16, 30204-30222 (2015)

Kovac, M. ; Blattmann, C. ; Ribi, S. ; Smida, J. ; Müller, N.S. ; Engert, F. ; Castro-Giner, F. ; Weischenfeldt, J. ; Kovacova, M. ; Krieg, A. ; Andreou, D. ; Tunn, P.U. ; Dürr, H.R. ; Rechl, H.P. ; Schaser, K.D. ; Melcher, I. ; Burdach, S. ; Kulozik, A. ; Specht, K. ; Heinimann, K. ; Fulda, S. ; Bielack, S. ; Jundt, G. ; Tomlinson, I. ; Korbel, J.O. ; Nathrath, M. ; Baumhoer, D.

Exome sequencing of osteosarcoma reveals mutation signatures reminiscent of BRCA deficiency.

Nat. Commun. 6:8940 (2015)

Peter, L. ; Pauly, O. ; Chatelain, P. ; Mateus, D. ; Navab, N.

Scale-adaptive forest training via an efficient feature sampling scheme.

Lecture Notes Comp. Sci. 9349, 637-644 (2015)

Rinck, A.

Molecular and computational characterization of microRNA/target interactions.

München, Technische Universität, Fakultät für Medizin, Diss., 2015, 201 S.

Hohm, K. ; Storath, M. ; Weinmann, A.

An algorithmic framework for Mumford-Shah regularization of inverse problems in imaging.

Inverse Probl. 31:115011 (2015)

Baust, M. ; Demaret, L. ; Storath, M. ; Navab, N. ; Weinmann, A.

Total variation regularization of shape signals.

Proc. IEEE Inst. Electr. Electron. Eng., 2075-2083 (2015)

Görner, T.

Spherical mean values : Efficient computation by Fourier techniques and regularized reconstructions of function samples from discrete means.

Osnabrück, Universität, Fachbereich Mathematik/Informatik, Diss., 2015, 90 S.

Blasi, M.

Mathematical modeling of the cooperation dynamics of Pseudomonas Aeruginosa populations.

München, Technische Universität, Zentrum Mathematik, Master-Thesis, 2015, 46 S.

Khrutska, O.

Exploring the anti-cancer drug resistance via an agent-based hybrid model.

München, Technische Universität, Zentrum Mathematik, Master-Thesis, 2015, 62 S.

Uksa, M. ; Schloter, M. ; Endesfelder, D. ; Kublik, S. ; Engel, M. ; Kautz, T. ; Köpke, U. ; Fischer, D.

Prokaryotes in subsoil - evidence for a strong spatial separation of different phyla by analysing co-occurrence networks.

Front. Microbiol. 6:1269 (2015)

Strasser, M.

From single cells to genealogies: Stochastic models of stem cell differentiation.

München, Technische Universität, Fakultät Wissenschaftszentrum Weihenstephan, Diss., 2015, 150 S.

Wang, L. ; Belagiannis, V. ; Marr, C. ; Theis, F.J. ; Yang, G.Z. ; Navab, N.

Anatomic-landmark detection using graphical context modelling.

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Loos, C. ; Marr, C. ; Theis, F.J. ; Hasenauer, J.

Approximate bayesian computation for stochastic single-cell time-lapse data using multivariate test statistics.

Lecture Notes Comp. Sci. 9308, 52-63 (2015)

Scherb, H. ; Voigt, K. ; Kusmierz, R.

Ionizing radiation and the human gender proportion at birth - a concise review of the literature and complementary analyses of historical and recent data.

Early Hum. Dev. 91, 841-850 (2015)

Flynn, R.M. ; Mallén, G. ; Engel, M. ; Ahmed, A. ; Rossi, P.

Characterizing aquifer heterogeneity using bacterial and bacteriophage tracers.

J. Environ. Qual. 44, 1448-1458 (2015)

Zwirglmaier, K. ; Keiz, K. ; Engel, M. ; Geist, J. ; Raeder, U.

Seasonal and spatial patterns of microbial diversity along a trophic gradient in the interconnected lakes of the Osterseen Lake District, Bavaria.

Front. Microbiol. 6:1168 (2015)

Marr, C. ; Hasenauer, J. ; Theis, F.J.

Models and methods for systems biology and systems medicine: The Institute of Computational Biology at the Helmholtz Zentrum München.

Systembiologie.de 9, 40-43 (2015)

Feigelman, J. ; Popovic, N. ; Marr, C.

A case study on the use of scale separation-based analytical propagators for parameter inference in models of stochastic gene regulation.

J. Coupled Syst. Multiscale Dyn. 3, 164-173 (2015)

Stückler, F.

Network-based analysis of genetic and nutritional effects on human metabolism.

Berlin: epubli GmbH, 2015, 156 S. (Zugl. München, Technische Universität, Fakultät Wissenschaftszentrum Weihenstephan, Diss., 2015)

Illner, K.

Probabilistic blind source separation for data with network structures.

München, Technische Universität, Fakultät für Mathematik, Diss., 2015, 176 S.

Preusse, M. ; Marr, C. ; Saunders, S. ; Maticzka, D. ; Lickert, H. ; Backofen, R. ; Theis, F.J.

SimiRa: A tool to identify coregulation between microRNAs and RNA-binding proteins.

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Tsang, J.C.H. ; Yu, Y. ; Burke, S. ; Buettner, F. ; Wang, C. ; Kolodziejczyk, A.A. ; Teichmann, S.A. ; Lu, L. ; Liu, P.

Single-cell transcriptomic reconstruction reveals cell cycle and multi-lineage differentiation defects in Bcl11a-deficient hematopoietic stem cells.

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Filipczyk, A. ; Marr, C. ; Hastreiter, S. ; Feigelman, J. ; Schwarzfischer, M. ; Hoppe, P.S. ; Loeffler, D. ; Kokkaliaris, K.D. ; Endele, M. ; Schauberger, B. ; Hilsenbeck, O. ; Skylaki, S. ; Hasenauer, J. ; Anastassiadis, K. ; Theis, F.J. ; Schroeder, T.

Network plasticity of pluripotency transcription factors in embryonic stem cells.

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Strasser, M. ; Feigelman, J. ; Theis, F.J. ; Marr, C.

Inference of spatiotemporal effects on cellular state transitions from time-lapse microscopy.

BMC Syst. Biol. 9:61 (2015)

Kohler, D. ; Müller, J. ; Wever, U.

Cellular non-deterministic automata and partial differential equations.

Physica D 311-312, 1-16 (2015)

Iske, A. ; Demaret, L.

Optimally sparse image approximation by adaptive linear splines over anisotropic triangulations.

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Dirmeier, S.

Network regression with applications to systems medicine.

München, Ludwig-Maximilians-Universität & Technische Universität, Bioinformatik, Master-Thesis, 2015, 97 S.

Strobl, A.N. ; Vickers, A.J. ; van Calster, B. ; Steyerberg, E. ; Leach, R.J. ; Thompson, I.M. ; Ankerst, D.P.

Improving patient prostate cancer risk assessment: Moving from static, cross mark globally-applied to dynamic, practice-specific risk calculators.

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Storath, M. ; Demaret, L. ; Massopust, P.

Signal analysis based on complex wavelet signs.

Appl. Comput. Harmon. Anal. 42, 199-223 (2015)

Ilmonen, P. ; Nordhausen, K. ; Oja, H. ; Theis, F.J.

An affine equivariant robust second-order BSS method.

Lecture Notes Comp. Sci. 9237, 328-335 (2015)

Garzorz, N.V. ; Krause, L. ; Lauffer, F. ; Atenhan, A. ; Thomas, J. ; Theis, F.J. ; Biedermann, T. ; Schmidt-Weber, C.B. ; Eyerich, S. ; Eyerich, K.

Molecular diagnostics of psoriasis and eczema-a novel approach to establish personalised therapy.

J. Invest. Dermatol. 135, S1 (2015)

Massopust, P.

On local fractal functions in Banach spaces.

AIP Conf. Proc. 1648:640002 (2015)

Müller, J. ; Kuttler, C.

Methods and models in mathematical biology : Deterministic and stochastic approaches.

Lecture Notes Math. Model. Life Sci., 711 S. (2015)

Chronakova, A. ; Schloter-Hai, B. ; Radl, V. ; Endesfelder, D. ; Quince, C. ; Elhottova, D. ; Simek, M. ; Schloter, M.

Response of archaeal and bacterial soil communities to changes associated with outdoor cattle overwintering.

PLoS ONE 10:e0135627 (2015)

Meyer, S.U. ; Sass, S. ; Müller, N.S. ; Krebs, S. ; Bauersachs, S. ; Kaiser, S. ; Blum, H. ; Thirion, C. ; Krause, S. ; Theis, F.J. ; Pfaffl, M.W.

Integrative analysis of MicroRNA and mRNA data reveals an orchestrated function of MicroRNAs in skeletal myocyte differentiation in response to TNF-α or IGF1.

PLoS ONE 10:e0135284 (2015)

Krause, L. ; Haubold, B. ; Börsch-Haubold, A.G.

Social exclusion changes histone modifications H3K4me3 and H3K27ac in liver tissue of wild house mice.

PLoS ONE 10:e0133988 (2015)

Krumsiek, J. ; Mittelstraß, K. ; Do, K.T. ; Stückler, F. ; Ried, J.S. ; Adamski, J. ; Peters, A. ; Illig, T. ; Kronenberg, F. ; Friedrich, N. ; Nauck, M. ; Pietzner, M. ; Mook-Kanamori, D.O. ; Suhre, K. ; Gieger, C. ; Grallert, H. ; Theis, F.J. ; Kastenmüller, G.

Gender-specific pathway differences in the human serum metabolome.

Metabolomics 11, 1815-1833 (2015)

Müller, S. ; Raulefs, S. ; Bruns, P. ; Afonso-Grunz, F. ; Plötner, A. ; Thermann, R. ; Jager, C. ; Schlitter, A.M. ; Kong, B. ; Regel, I. ; Roth, W.K. ; Rotter, B. ; Hoffmeier, K. ; Kahl, G.F. ; Koch, I. ; Theis, F.J. ; Kleeff, J. ; Winter, P. ; Michalski, C.W.

Erratum to: Next-generation sequencing reveals novel differentially regulated mRNAs, lncRNAs, miRNAs, sdRNAs and a piRNA in pancreatic cancer.

Mol. Cancer 14:144 (2015)

Emerenini, B.O. ; Hense, B.A. ; Kuttler, C. ; Eberl, H.J.

A mathematical model of quorum sensing induced biofilm detachment.

PLoS ONE 10:e0132385 (2015)

Scialdone, A. ; Natarajan, K.N. ; Saraiva, L.R. ; Proserpio, V. ; Teichmann, S.A. ; Stegle, O. ; Marioni, J.C. ; Buettner, F.

Computational assignment of cell-cycle stage from single-cell transcriptome data.

Methods 85, 54-61 (2015)

Yousri, N.A. ; Mook-Kanamori, D.O. ; El-Din Selim, M.M. ; Takiddin, A.H. ; Al-Homsi, H. ; Al-Mahmoud, K.A.S. ; Karoly, E.D. ; Krumsiek, J. ; Do, K.T. ; Neumaier, U. ; Mook-Kanamori, M.J. ; Rowe, J. ; Chidiac, O.M. ; McKeon, C. ; Al Muftah, W.A. ; Kader, S.A. ; Kastenmüller, G. ; Suhre, K.

Erratum to: A systems view of type 2 diabetes-associated metabolic perturbations in saliva, blood and urine at different timescales of glycaemic control.

Diabetologia 58, 2199 (2015)

Raue, A. ; Steiert, B. ; Schelker, M. ; Kreutz, C. ; Maiwald, T. ; Hass, H. ; Vanlier, J. ; Tönsing, C. ; Adlung, L. ; Engesser, R. ; Mader, W. ; Heinemann, T. ; Hasenauer, J. ; Schilling, M. ; Höfer, T. ; Klipp, E. ; Theis, F.J. ; Klingmüller, U. ; Schöberl, B. ; Timmer, J.

Data2Dynamics: A modeling environment tailored to parameter estimation in dynamical systems.

Bioinformatics 31, 3558-3560 (2015)

Gabrys, H. ; Buettner, F. ; Schubert, K. ; Mescher, H. ; Debus, J. ; Sterzing, F. ; Bangert, M.

TH-AB-304-12: Validation of a morphological xerostomia prediction model.

Med. Phys. 42:3703 (2015)

Grech, V. ; Scherb, H.

Hurricane Katrina: Influence on the male-to-female birth ratio.

Med. Princ. Pract. 24, 477-485 (2015)

Hasenauer, J. ; Jagiella, N. ; Hross, S. ; Theis, F.J.

Data-driven modelling of biological multi-scale processes.

J. Coupled Syst. Multiscale Dyn. 3, 101-121 (2015)

Scherb, H.

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Int. J. Risk Saf. Med. 27, 107-110 (2015)

Masserdotti, G. ; Gillotin, S. ; Sutor, B. ; Drechsel, D. ; Irmler, M. ; Jørgensen, H.F. ; Sass, S. ; Theis, F.J. ; Beckers, J. ; Berninger, B. ; Guillemot, F. ; Götz, M.

Transcriptional mechanisms of proneural factors and REST in regulating neuronal reprogramming of astrocytes.

Cell Stem Cell 17, 74-88 (2015)

Efendiyev, M.A. ; Otani, M. ; Eberl, H.J.

A coupled PDE/ODE model of mitochondrial swelling: Large-time behavior of the homogeneous Dirichlet problem.

J. Coupled Syst. Multiscale Dyn., DOI: 10.1166/jcsmd.2015.1070 (2015)

Münch, K.M. ; Müller, J. ; Wienecke, S. ; Bergmann, S. ; Heyber, S. ; Biedendieck, R. ; Münch, R. ; Jahn, D.

Polar fixation of plasmids during recombinant protein production in Bacillus megaterium results in population heterogeneity.

Appl. Environ. Microbiol. 81, 5976-5986 (2015)

Bartel, J. ; Krumsiek, J. ; Schramm, K. ; Adamski, J. ; Gieger, C. ; Herder, C. ; Carstensen, M. ; Peters, A. ; Rathmann, W. ; Roden, M. ; Strauch, K. ; Suhre, K. ; Kastenmüller, G. ; Prokisch, H. ; Theis, F.J.

The human blood metabolome-transcriptome interface.

PLoS Genet. 11:e1005274 (2015)

Sonner, S. ; Efendiyev, M.A. ; Eberl, H.J.

On the well-posedness of mathematical models for multicomponent biofilms.

Math. Meth. Appl. Sci. 38, 3753–3775 (2015)

Yousri, N.A. ; Mook-Kanamori, D.O. ; Selim, M.M.E.D. ; Takiddin, A.H. ; Al-Homsi, H. ; Al-Mahmoud, K.A.S. ; Karoly, E.D. ; Krumsiek, J. ; Do, K.T. ; Neumaier, U. ; Mook-Kanamori, M.J. ; Rowe, J. ; Chidiac, O.M. ; McKeon, C. ; Al Muftah, W.A. ; Kader, S.A. ; Kastenmüller, G. ; Suhre, K.

A systems view of type 2 diabetes-associated metabolic perturbations in saliva, blood and urine at different timescales of glycaemic control.

Diabetologia 58, 1855-1867 (2015)

Ocone, A. ; Haghverdi, L. ; Müller, N.S. ; Theis, F.J.

Reconstructing gene regulatory dynamics from high-dimensional single-cell snapshot data.

Bioinformatics 31, i89-i96 (2015)

Linnemann, J. ; Miura, H. ; Meixner, L.K. ; Irmler, M. ; Kloos, U. ; Hirschi, B. ; Bartsch, H.S. ; Sass, S. ; Beckers, J. ; Theis, F.J. ; Gabka, C. ; Sotlar, K. ; Scheel, C.

Quantification of regenerative potential in primary human mammary epithelial cells.

Development 142, 3239-3251 (2015)

Kohler, D. ; Marzouk, Y.M. ; Müller, J. ; Wever, U.

A new network approach to Bayesian inference in partial differential equations.

Int. J. Numer. Methods Eng. 104, 313-329 (2015)

Gumpinger, A.C.

Time series analysis of gene expression data using transfer entropy.

München, Technische Universität, Fakultät für Mathematik, Master-Thesis, 2015, 70 S.

Graessel, A. ; Hauck, S.M. ; von Toerne, C. ; Kloppmann, E. ; Goldberg, T. ; Koppensteiner, H. ; Schindler, M. ; Knapp, B. ; Krause, L. ; Dietz, K. ; Schmidt-Weber, C.B. ; Suttner, K.

A combined omics approach to generate the surface atlas of human naive CD4⁺ T cells during early TCR activation.

Mol. Cell. Proteomics 14, 2085-2102 (2015)

Matos, M.R. ; Knapp, B. ; Kaderali, L.

lpNet: A linear programming approach to reconstruct signal transduction networks.

Bioinformatics 31, 3231-3233 (2015)

Sadic, D. ; Schmidt, K. ; Groh, S. ; Kondofersky, I. ; Ellwart, J.W. ; Fuchs, C. ; Theis, F.J. ; Schotta, G.

Atrx promotes heterochromatin formation at retrotransposons.

EMBO Rep. 16, 836-850 (2015)

Lechtenberg, L.

Model selection in deterministic models of mRNA transfection.

München, Ludwig-Maximilians-Universität, Fakultät für Physik, Master-Thesis, 2015, 90 S.

Wilson, N.K. ; Kent, D.G. ; Buettner, F. ; Shehata, M. ; Macaulay, I.C. ; Calero-Nieto, F.J. ; Sánchez Castillo, M. ; Oedekoven, C.A. ; Diamanti, E. ; Schulte, R. ; Ponting, C.P. ; Voet, T. ; Caldas, C. ; Stingl, J. ; Green, A.R. ; Theis, F.J. ; Göttgens, B.

Combined single-cell functional and gene expression analysis resolves heterogeneity within stem cell populations.

Cell Stem Cell 16, 712-724 (2015)

Heinig, M. ; Colomé-Tatché, M. ; Taudt, A. ; Rintisch, C. ; Schäfer, S. ; Pravenec, M. ; Hubner, N. ; Vingron, M. ; Johannes, F.

histoneHMM: Differential analysis of histone modifications with broad genomic footprints.

BMC Bioinformatics 16:60 (2015)

Sass, S.

Integration of multiple omics levels for the analysis of adipocyte differentiation.

München, Technische Universität, Fakultät Wissenschaftszentrum Weihenstephan, Diss., 2015, 166 S.

Haghverdi, L. ; Buettner, F. ; Theis, F.J.

Diffusion maps for high-dimensional single-cell analysis of differentiation data.

Bioinformatics 31, 2989-2998 (2015)

Lupperger, V.

Bioimage informatic analysis of the spatial impact on cell state transitions.

München, Ludwig-Maximilians-Universität & Technische Universität, Bioinformatik, Master-Thesis, 2015, 57 S.

Waldraff, S.

Analysis of multivariate expression profiles of astrocytes of postnatal and adult mice.

München, Ludwig-Maximilians-Universität & Technische Universität, Bioinformatik, Master-Thesis, 2015, 72 S.

Barbosa, J.S. ; Sanchez-Gonzalez, R. ; di Giaimo, R. ; Baumgart, E.V. ; Theis, F.J. ; Götz, M. ; Ninkovic, J.

Live imaging of adult neural stem cell behavior in the intact and injured zebrafish brain.

Science 348, 789-793 (2015)

Cui, H. ; Hense, B.A. ; Müller, J. ; Schröder, P.

Short term uptake and transport process for metformin in roots of Phragmites australis and Typha latifolia.

Chemosphere 134, 307-312 (2015)

Kaufmann, S. ; Fuchs, C. ; Gonik, M. ; Khrameeva, E.E. ; Mironov, A.A. ; Frishman, D.

Inter-chromosomal contact networks provide insights into mammalian chromatin organization.

PLoS ONE 10:e0126125 (2015)

Müller, J. ; Jiang, H.

Graphical limit sets for general cellular automata.

Theor. Comput. Sci. 580, 14-27 (2015)

Loos, C.

Analysis of single-cell data using ODE constrained mixture modeling and approximate Bayesian computation.

München, Technische Universität, Fakultät für Mathematik, Master-Thesis, 2015, 88 S.

Höffler, J.

Gene signatures of epithelial-mesenchymal transition in embryonic stem cells.

München, Ludwig-Maximilians-Universität & Technische Universität, Bioinformatik, Bachelor-Thesis, 2015, 43 S.

Frikel, J. ; Quinto, E.T.

Artifacts in incomplete data tomography with applications to photoacoustic tomography and sonar.

SIAM J. Appl. Math. 75, 703-725 (2015)

Christensen, O. ; Forster, B. ; Massopust, P.

Directional time-frequency analysis via continuous frames.

Bull. Austral. Math. Soc. 92, 268-281 (2015)

Kondofersky, I. ; Fuchs, C. ; Theis, F.J.

Identifying latent dynamic components in biological systems.

IET Syst. Biol. 9, 193-203 (2015)

Müller, S. ; Raulefs, S. ; Bruns, P. ; Afonso-Grunz, F. ; Plötner, A. ; Thermann, R. ; Jager, C. ; Schlitter, A.M. ; Kong, B. ; Regel, I. ; Roth, W.K. ; Rotter, B. ; Hoffmeier, K. ; Kahl, G.F. ; Koch, I. ; Theis, F.J. ; Kleeff, J. ; Winter, P. ; Michalski, C.W.

Next-generation sequencing reveals novel differentially regulated mRNAs, lncRNAs, miRNAs, sdRNAs and a piRNA in pancreatic cancer.

Mol. Cancer 14:94 (2015)

Bonifacio, E. ; Ziegler, A.-G. ; Klingensmith, G. ; Schober, E. ; Bingley, P.J. ; Rottenkolber, M. ; Theil, A. ; Eugster, A. ; Puff, R. ; Peplow, C. ; Buettner, F. ; Lange, K. ; Hasford, J. ; Achenbach, P.

Effects of high-dose oral insulin on immune responses in children at high risk for type 1 diabetes: The Pre-POINT randomized clinical trial.

JAMA 313, 1541-1549 (2015)

Helmbrecht, M.S. ; Soellner, H. ; Castiblanco-Urbina, M.A. ; Winzeck, S. ; Sundermeier, J. ; Theis, F.J. ; Fouad, K. ; Huber, A.B.

A critical period for postnatal adaptive plasticity in a model of motor axon miswiring.

PLoS ONE 10:e0123643 (2015)

Weinmann, A. ; Storath, M.

Iterative Potts and Blake-Zisserman minimization for the recovery of functions with discontinuities from indirect measurements.

Proc. R. Soc. London A 471:20140638 (2015)

Theis, F.J. ; Ugelvig, L.V. ; Marr, C. ; Cremer, S.

Opposing effects of allogrooming on disease transmission in ant societies.

Philos. Trans. R. Soc. B - Biol. Sci. 370, DOI: 10.1098/rstb.2014.0108 (2015)

Popovic, N. ; Marr, C. ; Swain, P.S.

A geometric analysis of fast-slow models for stochastic gene expression.

J. Math. Biol. 72, 87-122 (2015)

Wieczorek, M. ; Frikel, J. ; Vogel, J. ; Eggl, E. ; Kopp, F. ; Noel, P.B. ; Pfeiffer, F. ; Demaret, L. ; Lasser, T.

X-ray computed tomography using curvelet sparse regularization.

Med. Phys. 42, 1555-1565 (2015)

Weinmann, A. ; Storath, M. ; Demaret, L.

The L¹-Potts functional for robust jump-sparse reconstruction.

SIAM J. Numer. Anal. 53, 644-673 (2015)

Demaret, L. ; Iske, A.

Optimal N-term approximation by linear splines over anisotropic Delaunay triangulations.

Math. Comput. 84, 1241-1264 (2015)

Uecker, H. ; Müller, J.P.H. ; Hense, B.A.

Erratum to: Individual-based model for quorum sensing with background flow.

Bull. Math. Biol. 77, 580 (2015)

Hug, S.

From low-dimensional model selection to high-dimensional inference: tailoring Bayesian methods to biological dynamical systems.

München, Technische Universität, Fakultät für Mathematik, Diss., 2015, 212 S.

Wahl, S. ; Vogt, S. ; Stückler, F. ; Krumsiek, J. ; Bartel, J. ; Kacprowski, T. ; Schramm, K. ; Carstensen, M. ; Rathmann, W. ; Roden, M. ; Jourdan, C. ; Kangas, A.J. ; Soininen, P. ; Ala-Korpela, M. ; Nöthlings, U. ; Boeing, H. ; Theis, F.J. ; Meisinger, C. ; Waldenberger, M. ; Suhre, K. ; Homuth, G. ; Gieger, C. ; Kastenmüller, G. ; Illig, T. ; Linseisen, J. ; Peters, A. ; Prokisch, H. ; Herder, C. ; Thorand, B. ; Grallert, H.

Multi-omic signature of body weight change: Results from a population-based cohort study.

BMC Med. 13:48 (2015)

Hug, S. ; Schwarzfischer, M. ; Hasenauer, J. ; Marr, C. ; Theis, F.J.

An adaptive scheduling scheme for calculating Bayes factors with thermodynamic integration using Simpson’s rule.

Stat. Comp. 26, 663-677 (2015)

Calzolari, F. ; Michel, J. ; Baumgart, E.V. ; Theis, F.J. ; Götz, M. ; Ninkovic, J.

Fast clonal expansion and limited neural stem cell self-renewal in the adult subependymal zone.

Nat. Neurosci. 18, 490-492 (2015)

Barnsley, M.F. ; Massopust, P.

Bilinear fractal interpolation and box dimension.

J. Approx. Theory 192, 362-378 (2015)

Griese, M. ; Kirmeier, H.G. ; Liebisch, G. ; Rauch, D. ; Stückler, F. ; Schmitz, G. ; Zarbock, R.

Surfactant lipidomics in healthy children and childhood interstitial lung disease.

PLoS ONE 10:e0117985 (2015)

Hense, B.A. ; Schuster, M.

Core principles of bacterial autoinducer systems.

Microbiol. Mol. Biol. Rev. 79, 153-169 (2015)

Moignard, V. ; Woodhouse, S. ; Haghverdi, L. ; Lilly, A.J. ; Tanaka, Y. ; Wilkinson, A.C. ; Buettner, F. ; Macaulay, I.C. ; Jawaid, W. ; Diamanti, E. ; Nishikawa, S.I. ; Piterman, N. ; Kouskoff, V. ; Theis, F.J. ; Fisher, J. ; Gottgens, B.

Decoding the regulatory network of early blood development from single-cell gene expression measurements.

Nat. Biotechnol. 33, 269-276 (2015)

Illner, K. ; Miettinen, J. ; Fuchs, C. ; Taskinen, S. ; Nordhausen, K. ; Oja, H. ; Theis, F.J.

Model selection using limiting distributions of second-order blind source separation algorithms.

Signal Process. 113, 95-103 (2015)

Kong, B. ; Bruns, P. ; Raulefs, S. ; Rieder, S. ; Paul, L. ; da Costa, O.P. ; Buch, T. ; Theis, F.J. ; Michalski, C.W. ; Kleeff, J.

Metabolism gene signatures and surgical site infections in abdominal surgery.

Int. J. Surg. 14, 67-74 (2015)

Pérez-Velázquez, J. ; Quinones, B. ; Hense, B.A. ; Kuttler, C.

A mathematical model to investigate quorum sensing regulation and its heterogeneity in Pseudomonas syringae on leaves.

Ecol. Complex. 21, 128-141 (2015)

Buettner, F. ; Natarajan, K.N. ; Casale, F.P. ; Proserpio, V. ; Scialdone, A. ; Theis, F.J. ; Teichmann, S.A. ; Marioni, J.C. ; Stegle, O.

Computational analysis of cell-to-cell heterogeneity in single-cell RNA-sequencing data reveals hidden subpopulations of cells.

Nat. Biotechnol. 33, 155-160 (2015)

Schmidt, J. ; Panzilius, E. ; Bartsch, H.S. ; Irmler, M. ; Beckers, J. ; Kari, V. ; Linnemann, J. ; Dragoi, D. ; Hirschi, B. ; Kloos, U. ; Sass, S. ; Theis, F.J. ; Kahlert, S. ; Johnsen, S.A. ; Sotlar, K. ; Scheel, C.

Stem-cell-like properties and epithelial plasticity arise as stable traits after transient Twist1 activation.

Cell Rep. 10, 131-139 (2015)

Obermaier, J. ; Stavropoulou, F.

Generalized polynomial chaos expansions with weights.

J. Comput. Anal. Appl. 18, 30-45 (2015)

Altschuh, J. ; Lenoir, D. ; Rehfeldt, F. ; Brüggemann, R.

Applicability domain of nonlinear property-property relationships - example: Estimation of vapour pressure.

Match-Commun. Math. Comput. Chem. 73, 303-326 (2015)

Do, K.T. ; Kastenmüller, G. ; Mook-Kanamori, D.O. ; Yousri, N.A. ; Theis, F.J. ; Suhre, K. ; Krumsiek, J.

Network-based approach for analyzing intra- and interfluid metabolite associations in human blood, urine, and saliva.

J. Proteome Res. 14, 1183-1194 (2015)

Eisenhofer, S. ; Efendiyev, M.A. ; Otani, M. ; Schulz, S. ; Zischka, H.

On the ODE-PDE coupling model of the mitochondrial swelling process.

Discrete Contin. Dyn. Syst.-Ser. B 20, 1031-1057 (2015)

Lukowiak, M.C. ; Wettmarshausen, S. ; Hidde, G. ; Landsberger, P. ; Boenke, V. ; Rodenacker, K. ; Braun, U. ; Friedrich, J.F. ; Gorbushina, A.A. ; Haag, R.

Polyglycerol coated polypropylene surfaces for protein and bacteria resistance.

Polym. Chem. 6, 1350-1359 (2015)

Gevertz, J.L. ; Aminzare, Z. ; Norton, K.-A. ; Pérez-Velázquez, J. ; Volkening, A. ; Rejniak, K.A.

Emergence of anti-cancer drug resistance: Exploring the importance of the microenvironmental niche via a spatial model.

IMA Vol. Math. Appl. 158, 1-34 (2015)

Hense, B.A. ; Kuttler, C. ; Müller, J.

Functionality of autoinducer systems in complex environments.

In: Hagen, S.J.* [Eds.]: The Physical Basis of Bacterial Quorum Communication. New York: Springer, 2015. 83-103

Gölgeli Matur, M. ; Müller, J. ; Kuttler, C. ; Hense, B.A.

An approximative approach for single cell spatial modeling of quorum sensing.

J. Comput. Biol. 22, 227-235 (2015)

Peter, L. ; Mateus, D. ; Chatelain, P. ; Schworm, N. ; Stangl, S. ; Multhoff, G. ; Navab, N.

Leveraging random forests for interactive exploration of large histological images.

Lecture Notes Comp. Sci. 8673, 1-8 (2015)

Storath, M. ; Weinmann, A. ; Frikel, J. ; Unser, M.

Joint image reconstruction and segmentation using the Potts model.

Inverse Probl. 31:025003 (2015)

Bergmann, R. ; Weinmann, A.

Inpainting of cycling data using first and second order differences.

Lecture Notes Comp. Sci. 8932, 155-168 (2015)

Sass, S. ; Buettner, F. ; Müller, N.S. ; Theis, F.J.

RAMONA: A web application for gene set analysis on multilevel omics data.

Bioinformatics 31, 128-130 (2015)

Dong, Y. ; Görner, T. ; Kunis, S.

An algorithm for total variation regularized photoacoustic imaging.

Adv. Comput. Math. 41, 423-438 (2015)

Cortijo, S. ; Wardenaar, R. ; Colomé-Tatché, M. ; Gilly, A. ; Etcheverry, M. ; Labadie, K. ; Caillieux, E. ; Hospital, F. ; Aury, J.M. ; Wincker, P. ; Roudier, F. ; Jansen, R.C. ; Colot, V. ; Johannes, F.

Mapping the epigenetic basis of complex traits.

Science 343, 1145-1148 (2014)

Cortijo, S. ; Wardenaar, R. ; Colomé-Tatché, M. ; Johannes, F. ; Colot, V.

Genome-wide analysis of DNA methylation in Arabidopsis using MeDIP-chip.

Methods Mol. Biol. 1112, 125-149 (2014)

Scherb, H. ; Kusmierz, R. ; Voigt, K.

To the editor.

Acta Med. (Hradec Králové) 57, 168-169 (2014)

Kazeroonian, A. ; Theis, F.J. ; Hasenauer, J.

Modeling of stochastic biological processes with non-polynomial propensities using non-central conditional moment equation.

IFAC PapersOnline 19, 1729-1735 (2014)

Beuttenmüller, D.

Approximation with respect to disc polynomials.

München, Technische Universität, Fakultät für Mathematik, Diss., 2014, 105 S.

Reversat, A. ; Buggenthin, F. ; Merrin, J. ; Leithner, A. ; de Vries, I. ; Theis, F.J. ; Marr, C. ; Sixt, M.

Morphodynamic analysis of T lymphocyte migration in confined microenvironments.

Mol. Biol. Cell 25:P537 (2014)

Gutierrez, B. ; Mateus, D. ; Shiban, E. ; Meyer, B.U. ; Lehmberg, J. ; Navab, N.A.

A sparse approach to build shape models with routine clinical data.

In: Proceedings (IEEE International Symposium on Biomedical Imaging, ISBI, 29. April - 02.May 2014, Beijing, China). Piscataway, NJ: IEEE, 2014. 258-261

Rieke, N. ; Hennersperger, C. ; Mateus, D. ; Navab, N.A.

Ultrasound interactive segmentation with tensor-graph methods.

In: Proceedings (IEEE International Symposium on Biomedical Imaging, ISBI, 29. April - 02.May 2014, Beijing, China). Piscataway, NJ: IEEE, 2014. 690-693

Calvo-Vidal, N. ; Patel, J. ; Krumsiek, J. ; Dupont, T. ; Goldstein, R.S. ; Yang, S.N. ; Melnick, A. ; Chiosis, G. ; Cerchietti, L.

Hsp90 at the hub of metabolic homeostasis in malignant B cells.

Blood 124 (2014)

Kopp, M.

Extension of multi-level ontology analysis including adaption to continuous input values.

München, Ludwig-Maximilians-Universität & Technische Universität, Bioinformatik, Master-Thesis, 2014, 65 S.

Winkler, S.

From deterministic Boolean networks to stochastik continous models.

München, Technische Universität, Fakultät für Mathematik, Master-Thesis, 2014, 181 S.

Quaranta, M. ; Knapp, B. ; Garzoz, N. ; Mattii, M. ; Pullabhatla, V. ; Pennino, D. ; Andres, C. ; Traidl-Hoffmann, C. ; Cavani, A. ; Theis, F.J. ; Ring, J. ; Schmidt-Weber, C.B. ; Eyerich, S. ; Eyerich, K.

Intraindividual genome expression analysis reveals opposing immune reaction in psoriasis and eczema.

Br. J. Dermatol. 171, E135 (2014)

Bergmann, R. ; Laus, F. ; Steidl, G. ; Weinmann, A.

Second order differences of cyclic data and applications in variational denoising.

SIAM J. Imaging Sci. 7, 2916-2953 (2014)

Morath, V. ; Truong, D.J.J. ; Albrecht, F. ; Polte, I. ; Ciccone, R.A. ; Funke, L.F. ; Reichart, L. ; Wolf, C.G. ; Brunner, A.D. ; Fischer, K. ; Schneider, P.C. ; Brüggenthies, J.B. ; Fröhlich, F. ; Wiedemann, G. ; Reski, R. ; Skerra, A.

Design and characterization of a modular membrane protein anchor to functionalize the moss Physcomitrella patens with extracellular catalytic and/or binding activities.

ACS Synth. Biol. 3, 990-994 (2014)

Rintisch, C. ; Heinig, M. ; Bauerfeind, A. ; Schäfer, S. ; Mieth, C. ; Patone, G. ; Hummel, O. ; Chen, W. ; Cook, S. ; Cuppen, E. ; Colomé-Tatché, M. ; Johannes, F. ; Jansen, R.C. ; Neil, H. ; Werner, M. ; Pravenec, M. ; Vingron, M. ; Hubner, N.

Natural variation of histone modification and its impact on gene expression in the rat genome.

Genome Res. 24, 942-953 (2014)

Bongini, M. ; Fornasier, M. ; Fröhlich, F. ; Haghverdi, L.

Sparse control of force field dynamics.

In: (7th International Conference on Network Games, Control and Optimization, NetGCoop 2014, 29 - 31 October 2014). 2014. 195-200

Fröhlich, F. ; Theis, F.J. ; Hasenauer, J.

Uncertainty analysis for non-identifiable dynamical systems: Profile likelihoods, bootstrapping and more.

Lecture Notes Comp. Sci. 8859, 61-72 (2014)

Fröhlich, F. ; Hross, S. ; Theis, F.J. ; Hasenauer, J.

Radial basis function approximations of Bayesian parameter posterior densities for uncertainty analysis.

Lecture Notes Comp. Sci. 8859, 73-85 (2014)

Nielsen, T.H. ; Diaz, Z. ; Christodoulopoulos, R. ; Charbonneau, F. ; Qureshi, S. ; Rousseau, C. ; Benlimame, N. ; Camlioglu, E. ; Constantin, A.M. ; Oros, K.K. ; Krumsiek, J. ; Crump, M. ; Morin, R.D. ; Cerchietti, L. ; Johnson, N.A. ; Petrogiannis-Haliotis, T. ; Miller, W.H. ; Assouline, S.E. ; Mann, K.K.

Methods for sample acquisition and processing of serial blood and tumor biopsies for multicenter diffuse large B-cell lymphoma clinical trials.

Cancer Epidemiol. Biomarkers Prev. 23, 2688-2693 (2014)

Winkler, C. ; Krumsiek, J. ; Buettner, F. ; Angermüller, C. ; Giannopoulou, E.Z. ; Theis, F.J. ; Ziegler, A.-G. ; Bonifacio, E.

Erratum to: Feature ranking of type 1 diabetes susceptibility genes improves prediction of type 1 diabetes.

Diabetologia 58, 206 (2014)

Waldera-Lupa, D.M. ; Kalfalah, F. ; Florea, A.M. ; Sass, S. ; Kruse, F.E. ; Rieder, V. ; Tigges, J. ; Fritsche, E. ; Krutmann, J. ; Busch, H. ; Boerries, M. ; Meyer, H.E. ; Boege, F. ; Theis, F.J. ; Reifenberger, G. ; Stühler, K.

Proteome-wide analysis reveals an age-associated cellular phenotype of in situ aged human fibroblasts.

Aging 6, 856-878 (2014)

Löhning, M. ; Reble, M. ; Hasenauer, J. ; Yu, S. ; Allgöwer, F.

Model predictive control using reduced order models: Guaranteed stability for constrained linear systems.

J. Process Contr. 24, 1647-1659 (2014)

Peng, T. ; Wang, L. ; Bayer, C. ; Conjeti, S. ; Baust, M. ; Navab, N.A.

Shading correction for whole slide image using low rank and sparse decomposition.

Lecture Notes Comp. Sci. 8673, 33-40 (2014)

Hennersperger, C. ; Mateus, D. ; Baust, M. ; Navab, N.A.

A quadratic energy minimization framework for signal loss estimation from arbitrarily sampled ultrasound data.

Lecture Notes Comp. Sci. 8674, 373-380 (2014)

Ceruto, T. ; Lapeira, O. ; Tonch, A. ; Plant, C. ; Espín, R.A. ; Rosete, A.

Mining medical data to obtain fuzzy predicates.

Lecture Notes Comp. Sci. 8649, 103-117 (2014)

Khakhutskyy, V. ; Schwarzfischer, M. ; Hubig, N. ; Plant, C. ; Marr, C. ; Rieger, M.A. ; Schröder, T. ; Theis, F.J.

Centroid clustering of cellular lineage trees.

Lecture Notes Comp. Sci. 8649, 15-29 (2014)

Goebl, S. ; Meyer-Baese, A.C. ; Lobbes, M.B.I. ; Plant, C.

Segmentation and kinetic analysis of breast lesions in DCE-MR imaging using ICA.

Lecture Notes Comp. Sci. 8649, 45-59 (2014)

Bernhardt, M.

Mathematical modelling of combined radiation and chemotherapy.

München, Technische Universität, Fakultät für Mathematik, Master-Thesis, 2014, 137 S.

Schwarzfischer, M.

Quantification and analysis of single-cell protein dynamics in stem cells using time-lapse microscopy.

München, Technische Universität, Fakultät Wissenschaftszentrum Weihenstephan, Diss., 2014

Weinmann, A. ; Demaret, L. ; Storath, M.

Total variation regularization for manifold-valued data.

SIAM J. Imaging Sci. 7, 2226-2257 (2014)

Storath, M. ; Weinmann, A.

Fast partitioning of vector-valued images.

SIAM J. Imaging Sci. 7, 1826-1852 (2014)

Filbir, F. ; Kunis, S. ; Seyfried, R.

Effective discretization of direct reconstruction schemes for photoacoustic imaging in spherical geometries.

SIAM J. Numer. Anal. 52, 2722-2742 (2014)

Storath, M. ; Weinmann, A. ; Unser, M.

Unsupervised texture segmentation using monogenic curvelets and the Potts model.

In: Proceedings of the ICIP 2014 (IEEE International Conference on Image Processing (ICIP 2014), 27 - 30 October 2014, Paris, France). IEEE, 2014. 4348-4352

Görner, T. ; Kunis, S.

Effective discretization of the two-dimensional wave equation.

Proc. Appl. Math. Mech. 14, 947-948 (2014)

Kämmerer, L. ; Kunis, S. ; Melzer, I. ; Potts, D. ; Volkmer, T.

Computational methods for the Fourier analysis of sparse high-dimensional functions.

Lecture Notes Comp. Sci. Eng. 102, 347-363 (2014)

Roylance, R. ; Endesfelder, D. ; Jamal-Hanjani, M. ; Burrell, R.A. ; Gorman, P.A. ; Sander, J. ; Murphy, N.C. ; Birkbak, N.J. ; Hanby, A.M. ; Speirs, V. ; Johnston, S.D. ; Kschischo, M. ; Swanton, C.

Expression of regulators of mitotic fidelity are associated with intercellular heterogeneity and chromosomal instability in primary breast cancer.

Breast Cancer Res. Treat. 148, 221-229 (2014)

Illner, K. ; Fuchs, C. ; Theis, F.J.

Bayesian blind source separation applied to the lymphocyte pathway.

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Illner, K. ; Fuchs, C. ; Theis, F.J.

Single-cell analysis: Biology at high resolution.

Sep. Sci. Appl. 34, 24-26 (2014)

Illner, K. ; Fuchs, C. ; Theis, F.J.

Einzelzellanalysen: Biologie in Hochauflösung.

GIT Fachz. Lab. 9, 28-30 (2014)

Illner, K. ; Fuchs, C. ; Theis, F.J.

Bayesian blind source separation for data with network structure.

J. Comput. Biol. 21, 855-865 (2014)

Schmidt, A.M. ; Fagerer, S.R. ; Jefimovs, K. ; Buettner, F. ; Marro, C. ; Siringil, E.C. ; Boehlen, K.L. ; Pabst, M. ; Ibáñez, A.J.

Molecular phenotypic profiling of a Saccharomyces cerevisiae strain at the single-cell level.

Analyst 139, 5709-5717 (2014)

Scherb, H. ; Voigt, K. ; Kusmierz, R.

Nuclear energy: Danger only in case of accidents?

In: Gomez, M.* ; Sonnenschein, M.* ; Vogel, U.* ; Winter, A.* ; Rapp, B.* ; Giesen, N.* [Eds.]: Proceedings of the 28th International Conference on Informatics for Environmental Protection (EnviroInfo 2014 - ICT for Energy Efficiency, 10 - 12 September 2014, Oldenburg, Germany). Oldenburg: BIS-Verlag, 2014. 119-126

Voigt, K. ; Scherb, H. ; Bartoszczuk, P.

The impact on human health and the environment of different types of German and Polish power plants: A first scoring approach in Germany.

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Scherb, H. ; Kusmierz, R. ; Voigt, K.

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Int. J. Risk Saf. Med. 26, 173-174 (2014)

Röck, K. ; Tigges, J. ; Sass, S. ; Schütze, A. ; Florea, A.M. ; Fender, A.C. ; Theis, F.J. ; Krutmann, J. ; Boege, F. ; Fritsche, E. ; Reifenberger, G. ; Fischer, J.W.

miR-23a-3p causes cellular senescence by targeting hyaluronan synthase2: Possible implication for skin aging.

J. Invest. Dermatol. 135, 369-377 (2014)

Bartel, S. ; Schulz, N. ; Alessandrini, F. ; Theis, F.J. ; Eickelberg, O. ; Kicic, A. ; Freishtat, R.J. ; Krauss-Etschmann, S.

MicroRNA-based identification of epithelial SEC14L3 loss in experimental and human paediatric asthma.

Allergy 69, 40-41 (2014)

Aichler, M. ; Motschmann, M. ; Jütting, U. ; Luber, B. ; Becker, K. ; Ott, K. ; Lordick, F. ; Langer, R. ; Feith, M. ; Siewert, J.R. ; Walch, A.K.

Epidermal Growth Factor Receptor (EGFR) is an independent adverse prognostic factor in esophageal adenocarcinoma patients treated with cisplatin-based neoadjuvant chemotherapy.

Oncotarget 5, 6620-6632 (2014)

Endesfelder, D. ; Burrell, R.A. ; Kanu, N. ; McGranahan, N. ; Howell, M. ; Parker, P.J. ; Downward, J. ; Swanton, C. ; Kschischo, M.

Chromosomal instability selects gene copy number variants encoding core regulators of proliferation in ER⁺ breast cancer.

Cancer Res. 74, 4853-4863 (2014)

Hentzschel, F. ; Hammerschmidt-Kamper, C. ; Börner, K. ; Heiss, K. ; Knapp, B. ; Sattler, J.M. ; Kaderali, L. ; Castoldi, M. ; Bindman, J.G. ; Malato, Y. ; Willenbring, H. ; Mueller, A.K. ; Grimm, D.

AAV8-mediated in vivo overexpression of miR-155 enhances the protective capacity of genetically-attenuated malarial parasites.

Mol. Ther. 22, 2130-2141 (2014)

Winkler, C. ; Krumsiek, J. ; Buettner, F. ; Angermüller, C. ; Giannopoulou, E.Z. ; Theis, F.J. ; Ziegler, A.-G. ; Bonifacio, E.

Feature ranking of type 1 diabetes susceptibility genes improves prediction of type 1 diabetes.

Diabetologia 57, 2521-2529 (2014)

Roselius, L. ; Langemann, D. ; Müller, J. ; Hense, B.A. ; Filges, S. ; Jahn, D. ; Münch, R.

Modeling and analysis of a gene-regulatory feed-forward loop with basal expression of the second regulator.

J. Theor. Biol. 363, 290-299 (2014)

Feuchtinger, A. ; Stiehler, T. ; Jütting, U. ; Marjanovic, G. ; Luber, B. ; Langer, R. ; Walch, A.K.

Image analysis of immunohistochemistry is superior to visual scoring as shown for patient outcome of esophageal adenocarcinoma.

Histochem. Cell Biol. 143, 1-9 (2014)

Matthes, M. ; Preusse, M. ; Zhang, J. ; Schechter, J. ; Mayer, D. ; Lentes, B. ; Theis, F.J. ; Prakash, N. ; Wurst, W. ; Trümbach, D.

Mouse IDGenes: A reference database for genetic interactions in the developing mouse brain.

Database 2014:bau083 (2014)

Angerer, P.

Subpopulation identification and analysis in multivariate data

München, Ludwig-Maximilians-Universität & Technische Universität, Bioinformatik, Master-Thesis, 2014, 49 S.

Thalheimer, F.B. ; Wingert, S. ; de Giacomo, P. ; Haetscher, N. ; Brill, B. ; Theis, F.J. ; Hennighausen, L. ; Schroeder, T. ; Rieger, M.

Cytokine-regulated GADD45G induces differentiation and lineage selection in hematopoietic stem cells.

Exp. Hematol. 42, S57 (2014)

Moignard, V. ; Woodhouse, S. ; Haghverdi, L. ; Lilly, J. ; Tanaka, Y. ; Wilkinson, A. ; Buettner, F. ; Nishikawa, S. ; Piterman, N. ; Kouskoff, V. ; Theis, F.J. ; Fisher, J. ; Göttgens, B.

Decoding the transcriptional program for blood development from whole tissue single-cell gene expression measurements.

Exp. Hematol. 42, S52 (2014)

Meyer-Bäse, A. ; Plant, C. ; Górriz Sáez, J.M.

Advanced computer vision approaches in biomedical image analysis.

Comput. Math. Methods Med. 2014:347265 (2014)

Vinnikov, I.A. ; Hajdukiewicz, K. ; Reymann, J. ; Beneke, J. ; Czajkowski, R. ; Roth, L.C. ; Novak, M. ; Roller, A. ; Dörner, N. ; Starkuviene, V. ; Theis, F.J. ; Erfle, H. ; Schütz, G. ; Grinevich, V. ; Konopka, W.

Hypothalamic miR-103 protects from hyperphagic obesity in mice.

J. Neurosci. 34, 10659-10674 (2014)

Ebert, M.A. ; Gulliford, S.L. ; Buettner, F. ; Foo, K. ; Haworth, A. ; Kennedy, A. ; Joseph, D.J. ; Denham, J.W.

Two non-parametric methods for derivation of constraints from radiotherapy dose-histogram data.

Phys. Med. Biol. 59, N101-N111 (2014)

Ehler, M. ; Filbir, F.

ξ-coverings of Hölder-Zygmund type spaces on data-defined manifolds.

Abstract Appl. Anal. 2014:402918 (2014)

Buddrus-Schiemann, K. ; Rieger, M. ; Mühlbauer, M. ; Barbarossa, M.V. ; Kuttler, C. ; Hense, B.A. ; Rothballer, M. ; Uhl, J. ; Fonseca, J.R. ; Schmitt-Kopplin, P. ; Schmid, M. ; Hartmann, A.

Analysis of N-acylhomoserine lactone dynamics in continuous cultures of Pseudomonas putida IsoF by use of ELISA and UHPLC/qTOF-MS-derived measurements and mathematical models.

Anal. Bioanal. Chem. 406, 6373-6383 (2014)

Chui, C.K. ; Filbir, F. ; Mhaskar, H.N.

Representation of functions on big data: Graphs and trees.

Appl. Comput. Harmon. Anal. 38, 489-509 (2014)

Garzorz-Stark, N. ; Knapp, B. ; Quaranta, M. ; Mattii, M. ; Theis, F.J. ; Ring, J. ; Schmidt-Weber, C.B. ; Eyerich, S. ; Eyerich, K.

Eczema ≠ eczema: The transcriptional heterogeneity of eczema.

Br. J. Dermatol. 170, E19 (2014)

Quaranta, M. ; Eyerich, S. ; Knapp, B. ; Nasorri, F. ; Scarponi, C. ; Mattii, M. ; Garzorz-Stark, N. ; Harlfinger, A.T. ; Jaeger, T. ; Grosber, M. ; Pennino, D. ; Mempel, M. ; Schnopp, C. ; Theis, F.J. ; Albanesi, C. ; Cavani, A. ; Schmidt-Weber, C.B. ; Ring, J. ; Eyerich, K.

Allergic contact dermatitis in psoriasis patients: Typical, delayed, and non-interacting.

PLoS ONE 9:e101814 (2014)

Voigt, K. ; Brüggemann, R. ; Scherb, H. ; Cok, I. ; Schramm, K.-W.

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Storath, M. ; Weinmann, A. ; Demaret, L.

Jump-sparse and sparse recovery using potts functionals.

IEEE Trans. Signal Process. 62, 3654-3666 (2014)

Feigelman, J. ; Theis, F.J. ; Marr, C.

MCA: Multiresolution Correlation Analysis, a graphical tool for subpopulation identification in single-cell gene expression data.

BMC Bioinformatics 15:240 (2014)

Quaranta, M. ; Knapp, B. ; Garzorz-Stark, N. ; Mattii, M. ; Pullabhatla, V. ; Pennino, D. ; Andres, C. ; Traidl-Hoffmann, C. ; Cavani, A. ; Theis, F.J. ; Ring, J. ; Schmidt-Weber, C.B. ; Eyerich, S. ; Eyerich, K.

Intraindividual genome expression analysis reveals a specific molecular signature of psoriasis and eczema.

Sci. Transl. Med. 6:244ra90 (2014)

Grote, J. ; Krysciak, D. ; Schorn, A. ; Dahlke, R.I. ; Soonvald, L. ; Müller, J. ; Hense, B.A. ; Schwarzfischer, M. ; Sauter, M. ; Schmeisser, C. ; Streit, W.R.

Evidence of autoinducer-dependent and autoinducer-independent heterogeneous gene expression in Sinorhizobium fredii NGR234.

Appl. Environ. Microbiol. 80, 5572-5582 (2014)

Kroiss, M.

Using deep neural networks to predict the lineage choice of hematopoietic stem cells from time-lapse microscopy images.

München, Ludwig-Maximilians-Universität & Technische Universität, Bioinformatik, Master-Thesis, 2014, 72 S.

Pauly, O. ; Diotte, B. ; Fallavollita, P. ; Weidert, S. ; Euler, E. ; Navab, N.

Machine learning-based augmented reality for improved surgical scene understanding.

Comput. Med. Imaging Graph. 41, 55-60 (2014)

Garzorz, N.V. ; Quaranta, M. ; Knapp, B. ; Mattii, M. ; Andres, C. ; Theis, F.J. ; Ring, J. ; Schmidt-Weber, C.B. ; Eyerich, S. ; Eyerich, K.

Intra-individual genome expression analysis reveals a specific molecular signature of psoriasis and eczema.

J. Invest. Dermatol. 134, S1 (2014)

Hasenauer, J. ; Hasenauer, C. ; Hucho, T. ; Theis, F.J.

ODE constrained mixture modelling: A method for unraveling subpopulation structures and dynamics.

PLoS Comput. Biol. 10:e1003686 (2014)

Müller, J. ; Hense, B.A. ; Marozava, S. ; Kuttler, C. ; Meckenstock, R.U.

Model selection for microbial nutrient uptake using a cost-benefit approach.

Math. Biosci. 255, 52-70 (2014)

Fehringer, A. ; Lasser, T. ; Zanette, I. ; Noel, P.B. ; Pfeiffer, F.

A versatile tomographic forward- and back-projection approach on multi-GPUs.

Proc. SPIE 9034:90344F (2014)

Vogel, J. ; Duliu, A. ; Oyamada, Y. ; Gardiazabal, J. ; Lasser, T. ; Ziai, M. ; Hein, R. ; Navab, N.A.

Towards robust identification and tracking of nevi in sparse photographic time series.

Proc. SPIE 9035:90353D (2014)

Thalheimer, F.B. ; Wingert, S. ; de Giacomo, P. ; Haetscher, N. ; Rehage, M. ; Brill, B. ; Theis, F.J. ; Hennighausen, L. ; Schroeder, T. ; Rieger, M.A.

Cytokine-regulated GADD45G induces differentiation and lineage selection in hematopoietic stem cells.

Stem Cell Rep. 3, 34-43 (2014)

Fuchs, C.

Mische und herrsche.

Laborpraxis 38, 20-22 (2014)

Jauernig, M.

Simulation framework of fluorescence microscopy movies to evaluate single cell quantification tools

München, Ludwig-Maximilians-Universität & Technische Universität, Bioinformatik, Bachelor-Thesis, 2014, 51 S.

Ried, J.S. ; Shin, S.Y. ; Krumsiek, J. ; Illig, T. ; Theis, F.J. ; Spector, T.D. ; Adamski, J. ; Wichmann, H.-E. ; Strauch, K. ; Soranzo, N. ; Suhre, K. ; Gieger, C.

Novel genetic associations with serum level metabolites identified by phenotype set enrichment analyses.

Hum. Mol. Genet. 23, 5847-5857 (2014)

Uecker, H. ; Müller, J. ; Hense, B.A.

Individual-based model for quorum sensing with background flow.

Bull. Math. Biol. 76, 1727-1746 (2014)

Walker, A. ; Pfitzner, B. ; Neschen, S. ; Kahle-Stephan, M. ; Harir, M. ; Lucio, M. ; Moritz, F. ; Tziotis, D. ; Witting, M. ; Rothballer, M. ; Engel, M. ; Schmid, M. ; Endesfelder, D. ; Klingenspor, M. ; Rattei, T. ; zu Castell, W. ; Hrabě de Angelis, M. ; Hartmann, A. ; Schmitt-Kopplin, P.

Distinct signatures of host-microbial meta-metabolome and gut microbiome in two C57BL/6 strains under high-fat diet.

ISME J. 8, 2380-2396 (2014)

Kohler, D.

State-discrete probabilistic methods for partial differential equations.

München, Technische Universität, Fakultät für Mathematik, Diss., 2014, 144 S.

Meyer, S.U. ; Stoecker, K. ; Sass, S. ; Theis, F.J. ; Pfaffl, M.W.

Posttranscriptional regulatory networks: From expression profiling to integrative analysis of mRNA and microRNA data.

Methods Mol. Biol. 1160, 165-188 (2014)

Shin, S.Y. ; Fauman, E.B. ; Petersen, A.-K. ; Krumsiek, J. ; Santos, R. ; Huang, J. ; Arnold, M. ; Erte, I. ; Forgetta, V. ; Yang, T.P. ; Walter, K. ; Menni, C. ; Chen, L. ; Vasquez, L. ; Valdes, A.M. ; Hyde, C.L. ; Wang, V. ; Ziemek, D. ; Roberts, P. ; Xi, L. ; Grundberg, E. ; Waldenberger, M. ; Richards, J.B. ; Mohney, R.P. ; Milburn, M.V. ; John, S.L. ; Trimmer, J. ; Theis, F.J. ; Overington, J.P. ; Suhre, K. ; Brosnan, M.J. ; Gieger, C. ; Kastenmüller, G. ; Spector, T.D. ; Soranzo, N.

An atlas of genetic influences on human blood metabolites.

Nat. Genet. 46, 543-550 (2014)

Quaranta, M. ; Knapp, B. ; Theis, F.J. ; Ring, J. ; Schmidt-Weber, C.B. ; Eyerich, S. ; Eyerich, K.

Intra-individual genome expression analysis reveals a specific molecular signature of psoriasis and eczema.

Exp. Dermatol. 23, E20 (2014)

Seyfried, R.

Summability methods for the inversion of the spherical mean operator.

Aachen: Shaker, 2014 (Zugl. Osnabrück, Universität Osnabrück, Fakultät für Mathematik und Informatik, Diss., 2014)

Neumann, S. ; Hasenauer, J. ; Pollak, N. ; Scheurich, P.

Dominant negative effects of TNF-Related Apoptosis-Inducing Ligand (TRAIL) receptor 4 on TRAIL receptor 1 signaling by formation of heteromeric complexes.

J. Biol. Chem. 289, 16576-16587 (2014)

Brüggemann, R. ; Scherb, H. ; Schramm, K.-W. ; Cok, I. ; Voigt, K.

Ecotoxicol. Environ. Saf. 105, 29-35 (2014)

Krause, J.

Deterministic posterior approximations for a copula-based MCMC sampler.

München, Ludwig-Maximilians-Universität, Fakultät für Mathematik, Informatik und Statistik, Master-Thesis, 2014, 62 S.

Wallner, L.C.

Pseudomonas Syringae growth in the phyllosphere: Revisiting mathematical modelling approaches.

München, Technische Universität, Fakultät für Mathematik, Bachelor-Thesis, 2014, 23 S.

Pasquini, L. ; Tonch, A. ; Plant, C. ; Zherdin, A. ; Ortner, M. ; Kurz, A. ; Förstl, H. ; Zimmer, C. ; Grimmer, T. ; Wohlschäger, A. ; Riedl, V. ; Sorg, C.

Intrinsic brain activity of cognitively normal older persons resembles more that of patients both with and at-risk for Alzheimer's disease than that of healthy younger persons.

Brain Connect. 4, 323-336 (2014)

Lyubenova, L. ; Yazici, A. ; Tutus, Y. ; Fuchs, C. ; Michalke, B. ; Schröder, P. ; Cakmak, I.

Survey of barley genotypic variation in re-translocation of foliar applied Zn, Fe and Se.

International Conference on Agronomic, Molecular Genetics and Human Nutrition Approaches for Improving the Nutritional Quality and Safety of Food Crops, 68-69 (2014)

Eskova, A. ; Knapp, B. ; Matelska, D. ; Reusing, S. ; Arjonen, A. ; Lisauskas, T. ; Pepperkok, R. ; Russell, R.K. ; Eils, R. ; Ivaska, J. ; Kaderali, L. ; Erfle, H. ; Starkuviene, V.

RNAi screen identifies KIF15 as a novel regulator of integrin endocytic trafficking.

J. Cell Sci. 127, 2433-2447 (2014)

Hilsenbeck, O.

Maximally interesting extremal regions (MINER) and a probabilistic model for cell tracking.

München, Ludwig-Maximilians-Universität & Technische Universität, Bioinformatik, Master-Thesis, 2014, 85 S.

Buettner, F. ; Moignard, V. ; Göttgens, B. ; Theis, F.J.

Probabilistic PCA of censored data: Accounting for uncertainties in the visualisation of high-throughput single-cell qPCR data.

Bioinformatics 30, 1867-1875 (2014)

Baumann, S. ; Rockstroh, M. ; Bartel, J. ; Krumsiek, J. ; Otto, W. ; Jungnickel, H. ; Potratz, S. ; Luch, A. ; Wilscher, E. ; Theis, F.J. ; von Bergen, M. ; Tomm, J.M.

Subtoxic concentrations of benzo[a]pyrene induce metabolic changes and oxidative stress in non-activated and affect the mTOR pathway in activated Jurkat T cells.

J. Integr. OMICS, DOI: 10.5584/jiomics.v4i1.157 (2014)

Hartmann, A. ; Rothballer, M. ; Hense, B.A. ; Schröder, P.

Bacterial quorum sensing compounds are important modulators of microbe-plant interactions.

Front. Plant Sci. 5:131 (2014)

Akcan, T.

Development of biomarkers by integration of data and prior knowledge

München, Ludwig-Maximilians-Universität & Technische Universität, Bioinformatik, Bachelor-Thesis, 2014, 46 S.

Floegel, A. ; Wientzek, A. ; Bachlechner, U. ; Jacobs, S. ; Drogan, D. ; Prehn, C. ; Adamski, J. ; Krumsiek, J. ; Schulze, M.B. ; Pischon, T. ; Boeing, H.

Linking diet, physical activity, cardiorespiratory fitness and obesity to serum metabolite networks: Findings from a population-based study.

Int. J. Obes. 38, 1388-1396 (2014)

Shen, H. ; Xu, W. ; Peng, S. ; Scherb, H. ; She, J. ; Voigt, K. ; Alamdar, A. ; Schramm, K.-W.

Pooling samples for "top-down" molecular exposomics research: The methodology.

Environ. Health 13:8 (2014)

Endesfelder, D. ; zu Castell, W. ; Ardissone, A. ; Davis-Richardson, A.G. ; Achenbach, P. ; Hagen, M. ; Pflueger, M. ; Gano, K.A. ; Fagen, J.R. ; Drew, J.C. ; Brown, C.T. ; Kolaczkowski, B. ; Atkinson, M.J. ; Schatz, D. ; Bonifacio, E. ; Triplett, E.W. ; Ziegler, A.-G.

Compromised gut microbiota networks in children with anti-islet cell autoimmunity.

Diabetes 63, 2006-2014 (2014)

Alfonso, J.C.L. ; Jagiella, N. ; Nuñez, L. ; Herrero, M.A. ; Drasdo, D.

Estimating dose painting effects in radiotherapy: A mathematical model.

PLoS ONE 9:e89380 (2014)

Wenzel, T.

Entropy coding of adaptive sparse data representations by context mining.

Hamburg, Universität, Fachbereich Mathematik, Master-Thesis, 2014, 148 S.

Kohler, D. ; Müller, J. ; Wever, U.

Cellular probabilistic automata - a novel method for uncertainty propagation.

SIAM ASA J. Uncertain. Quantif. 2, 29-54 (2014)

Grigoriev, I. ; zu Castell, W. ; Tsvetkov, P. ; Antonov, A.V.

AERS spider: An online interactive tool to mine statistical associations in Adverse Event Reporting System.

Pharmacoepidemiol. Drug Saf. 23, 795-801 (2014)

Carvalho, A.N. ; Sonner, S.

Pullback exponential attractors for evolution processes in Banach spaces: Properties and applications.

Commun. Pure Appl. Anal. 13, 1141-1165 (2014)

Yang, D. ; Lutter, D. ; Burtscher, I. ; Uetzmann, L. ; Theis, F.J. ; Lickert, H.

miR-335 promotes mesendodermal lineage segregation and shapes a transcription factor gradient in the endoderm.

Development 141, 514-525 (2014)

Bajikar, S.S. ; Fuchs, C. ; Roller, A. ; Theis, F.J. ; Janes, K.A.

Parameterizing cell-to-cell regulatory heterogeneities via stochastic transcriptional profiles.

Proc. Natl. Acad. Sci. U.S.A. 111, E626-E635 (2014)

Frikel, J. ; Quinto, E.T.

How to characterize and decrease artifacts in limited angle tomography using microlocal analysis.

Inverse Probl.:55769 (2014)

Brüggemann, R. ; Carlsen, L. ; Voigt, K. ; Wieland, R.

PyHasse software for partial order analysis: Scientific background and description of selected modules.

In: Brüggemann, R.* ; Carlsen, L.* ; Wittmann, J.* [Eds.]: Multi-Indicator Systems and Modelling in Partial Order. New York [u.a.]: Springer, 2014. 389-423

Voigt, K. ; Brüggemann, R. ; Scherb, H. ; Cok, I. ; Mazmanci, B. ; Mazmanci, M.A. ; Turgut, C. ; Schramm, K.-W.

PyHasse software features applied on the evaluation of chemicals in human breast milk samples in Turkey.

In: Brüggemann, R.* ; Carlsen, L.* ; Wittmann, J.* [Eds.]: Multi-Indicator Systems and Modelling in Partial Order. New York [u.a.]: Springer, 2014. 343-357

Efendiyev, M.A. ; Zhigun, A. ; Senba, T.

On a weak attractor of a class of PDEs with degenerate diffusion and chemotaxis.

J. Math. Soc. Jpn. 66, 1133-1153 (2014)

Jordaan, K. ; Toókos, F.

Orthogonality and asymptotics of pseudo-Jacobi polynomials for non-classical parameters.

J. Approx. Theory 178, 1-12 (2014)

Isensee, J. ; Diskar, M. ; Waldherr, S. ; Buschow, R. ; Hasenauer, J. ; Prinz, A. ; Allgöwer, F. ; Herberg, F.W. ; Hucho, T.

Pain modulators regulate the dynamics of PKA-RII phosphorylation in subgroups of sensory neurons.

J. Cell Sci. 127, 216-229 (2014)

Hiepe, P. ; Herrmann, K.H. ; Güllmar, D. ; Ros, C. ; Siebert, T. ; Blickhan, R. ; Hahn, K. ; Reichenbach, J.R.

Fast low-angle shot diffusion tensor imaging with stimulated echo encoding in the muscle of rabbit shank.

NMR Biomed. 27, 146-157 (2014)

Hasenauer, J. ; Wolf, V. ; Kazeroonian, A. ; Theis, F.J.

Method of conditional moments (MCM) for the chemical master equation: A unified framework for the method of moments and hybrid stochastic-deterministic models.

J. Math. Biol. 69, 687-735 (2014)

Eberl, H.J. ; Efendiyev, M.A. ; Wrzosek, D. ; Zhigun, A.

Analysis of a degenerate biofilm model with a nutrient taxis term.

Discrete Contin. Dyn. Syst.-Ser. A 34, 99-119 (2014)

Onyango, N.O. ; Müller, J.

Determination of optimal vaccination strategies using an orbital stability threshold from periodically driven systems.

J. Math. Biol. 68, 763-784 (2014)

Albrecht, E. ; Waldenberger, M. ; Krumsiek, J. ; Evans, A.M. ; Jeratsch, U. ; Breier, M. ; Adamski, J. ; Koenig, W. ; Zeilinger, S. ; Fuchs, C. ; Klopp, N. ; Theis, F.J. ; Wichmann, H.-E. ; Suhre, K. ; Illig, T. ; Strauch, K. ; Peters, A. ; Gieger, C. ; Kastenmüller, G. ; Döring, A. ; Meisinger, C.

Metabolite profiling reveals new insights into the regulation of serum urate in humans.

Metabolomics 10, 141-151 (2014)

Beatson, R.K. ; zu Castell, W. ; Xu, Y.

A Pólya criterion for (strict) positive-definiteness on the sphere.

IMA J. Numer. Anal. 34, 550-568 (2014)

Wardenaar, R. ; Liu, H. ; Colot, V. ; Colomé-Tatché, M. ; Johannes, F.

Evaluation of MeDIP-chip in the context of whole-genome bisulfite sequencing (WGBS-seq) in Arabidopsis.

Methods Mol. Biol. 1067, 203-224 (2013)

Wieczorek, M. ; Frikel, J. ; Vogel, J. ; Pfeiffer, F. ; Demaret, L. ; Lasser, T.

Curvelet sparse regularization for differential phase-contrast X-ray imaging.

In: Proceedings (Fully Three-Dimensional Image Reconstruction in Radiology and Nuclear Medicine, 16 - 21 June 2013, Granlibakken Resort, Lake Tahoe, California). 2013. 489-492

Landsberger, P. ; Boenke, V. ; Gorbushina, A.A. ; Rodenacker, K. ; Pierce, B.F. ; Kratz, K. ; Lendlein, A.

Bacterial attachment on poly[acrylonitrile-co-(2-methyl-2-propene-1- sulfonic acid)] surfaces.

Mat. Res. Soc. Symp. Proc. 1569, 85-90 (2013)

Fuchs, C.

Estimation of cell-to-cell regulatory heterogeneities from cell populations.

Hum. Hered. 76, 100-101 (2013)

Knapp, B. ; Kaderali, L.

Reconstruction of cellular signal transduction networks using perturbation assays and linear programming.

PLoS ONE 8:e69220 (2013)

Kong, B. ; Wu, W. ; Cheng, T. ; Schlitter, A.M. ; Bruns, P. ; Jaeger, C. ; Regel, I. ; Raulefs, S. ; Behler, N. ; Irmler, M. ; Beckers, J. ; Erkan, M. ; Theis, F.J. ; Esposito, I. ; Kleeff, J. ; Michalski, C.W.

Identification and characterization of an Aldh1a3-positive subtype of pancreatic ductal adenocarcinoma mediated by oncogenic Krasg12d/Erk-Mtor axis.

Pancreas 42, 1360-1361 (2013)

Kong, B. ; Behler, N. ; Bruns, P. ; Schlitter, A.M. ; Valkovska, N. ; Fritzsche, S. ; Raulefs, S. ; Regel, I. ; Erkan, M. ; Theis, F.J. ; Esposito, I. ; Kleeff, J. ; Michalski, C.W.

Pancreatic progenitor expansion, mesenchymal cell proliferation and inflammation are required during early carcinogenesis.

Pancreas 42, 1360 (2013)

Kuruoglu, E.E. ; Theis, F.J.

Dependent component analysis.

EURASIP J. Adv. Signal Process. 2013:185 (2013)

Demaret, L.

Geometric anisotropy in image approximation.

München, Technische Universität, Fakultät für Mathematik, Habil.-Schr., 2013

Obermüller, T.

Reduction of limited-angle artifacts in computed tomography.

München, Technische Universität, Fakultät für Mathematik, Bachelor-Thesis, 2013, 34 S.

Fiedler, A.K.

Cell type structured populations models for the analysis of CFSE-data with continuous and discrete age structure.

München, Technische Universität, Fakultät für Mathematik, Master-Thesis, 2013, 54 S.

Efendiyev, M.A. ; Zhigun, A.

On a global uniform pull-back attractor of a class of PDEs with degenerate diffusion and chemotaxis.

Adv. Math. Sci. Appl. 23, 437-460 (2013)

Vehlow, C. ; Hasenauer, J. ; Krämer, A. ; Raue, A. ; Hug, S. ; Timmer, J. ; Radde, N. ; Theis, F.J. ; Weiskopf, D.

iVUN: Interactive Visualization of Uncertain biochemical reaction Networks.

BMC Bioinformatics 14:S2 (2013)

Angermüller, C.

Machine learning for predicting type 1 diabetes with high-throughput data.

München, Ludwig-Maximilians-Universität & Technische Universität, Bioinformatik, Master-Thesis, 2013, 68 S.

Do, K.T.

Metabolic analysis of multiple bodyfluids in the Qatar metabolomics study of diabetes.

München, Ludwig-Maximilians-Universität & Technische Universität, Bioinformatik, Master-Thesis, 2013, 110 S.

Drexler, B.

Model-driven analysis of metabolic changes in adipocates during differentiation.

München, Ludwig-Maximilians-Universität & Technische Universität, Bioinformatik, Master-Thesis, 2013, 108 S.

Neumaier, U.

A systems biological approach on phenomic and metabolic relationships in the Qatar metabolomics study of diabetes.

München, Ludwig-Maximilians-Universität & Technische Universität, Bioinformatik, Master-Thesis, 2013, 92 S.

Zierer, J.

Identification of uni- and multivariante biomarkers in metabolomics data from lymphoma patients.

München, Ludwig-Maximilians-Universität & Technische Universität, Bioinformatik, Master-Thesis, 2013, 147 S.

Fischer, S.

Quantification of marker expression for endoderm and mesoderm segregation.

München, Ludwig-Maximilians-Universität & Technische Universität, Bioinformatik, Bachelor-Thesis, 2013, 57 S.

Hamm, C.

Mechanisms of transcriptional regulation of microRNA genes.

München, Ludwig-Maximilians-Universität & Technische Universität, Bioinformatik, Bachelor-Thesis, 2013, 39 S.

Leidig, L.

Development of a programm for automatic quantification of mammospheres in limiting dilution assays.

München, Ludwig-Maximilians-Universität & Technische Universität, Bioinformatik, Bachelor-Thesis, 2013, 40 S.

Punga, S.

Supervised lipid raft cluster identification in hematopoietic stem cells.

München, Ludwig-Maximilians-Universität & Technische Universität, Bioinformatik, Bachelor-Thesis, 2013, 31 S.

Rauscher, B.

Analysis of the mouse 200 dataset by integrating transcriptomics and metabolomics data for multilevel ontology analysis.

München, Ludwig-Maximilians-Universität & Technische Universität, Bioinformatik, Bachelor-Thesis, 2013, 48 S.

Seitz, A.

Development and application of a single cell quantification tool for microscopy images.

München, Ludwig-Maximilians-Universität & Technische Universität, Bioinformatik, Bachelor-Thesis, 2013, 60 S.

Frank, F.

Assessment of the integration based method to calculate profile likelihoods for mathematical models in biology.

München, Technische Universität, Fakultät für Mathematik, Master-Thesis, 2013, 72 S.

Fröhlich, F.

Approximation and analysis of probability densities using radial basis functions.

München, Technische Universität, Fakultät für Mathematik, Master-Thesis, 2013, 93 S.

Kretschmar, T.

Structural analysis of the neural networks in mouse retina and Caenorhabditis elegans.

München, Technische Universität, Fakultät für Mathematik, Master-Thesis, 2013, 84 S.

Kumberger, P.

A reaction-diffusion-advection model for bacterial quorum sensing.

München, Technische Universität, Fakultät für Mathematik, Master-Thesis, 2013, 72 S.

Mund, A.

Altersstrukturierte Modellierung und Analyse der evolutionären Stabilität von bakteriellem Quorum Sensing.

München, Technische Universität, Fakultät für Mathematik, Master-Thesis, 2013, 50 S.

Thon, M.

Die Sätze von Faber und Privalov.

München, Technische Universität, Fakultät für Mathematik, Master-Thesis, 2013, 71 S.

Webersinke, R.

Mathematical modelling of tumour radiotherapy.

München, Technische Universität, Fakultät für Mathematik, Master-Thesis, 2013, 126 S.

Jochner, S. ; Höfler, J. ; Beck, I. ; Göttlein, A. ; Ankerst, D.P. ; Traidl-Hoffmann, C. ; Menzel, A.

Nutrient status: A missing factor in phenological and pollen research?

J. Exp. Bot. 64, 2081-2092 (2013)

Stavropoulou, F.

Generalized Wiener expansions for individual based control: Theory and applications.

München, Technische Universität, Fakultät für Mathematik, Diss., 2013, 121 S.

Demaret, L. ; Friedrich, F. ; Liebscher, V. ; Winkler, G.

Complexity L⁰-penalized M-estimation: Consistency in more dimensions.

Axioms 2, 311-344 (2013)

Bartel, S. ; Schulz, N. ; Theis, F.J. ; Alessandrini, F. ; Takenaka, S. ; Eickelberg, O. ; Krauss-Etschmann, S.

SEC14L3 is de-regulated in murine experimental asthma via miRNA-mediated down-regulation of CREB.

Allergy 68, 233-233 (2013)

Ehler, M. ; Kunis, S.

Phase retrieval using time and Fourier magnitude measurements.

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Heider, S. ; Kunis, S. ; Potts, D. ; Veit, M.

A sparse Prony FFT.

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Horger, T. ; Oelker, A. ; Kuttler, C. ; Pérez-Velázquez, J.

Mathematical modeling of tumor-induced angiogenesis using porous medium diffusion.

Int. J. Biomath. Biostat. 2, 145-165 (2013)

Gölgeli Matur, M.

Mathematical modeling of quorum sensing: Two different approaches.

München, Technische Universität, Fakultät für Mathematik, Diss., 2013, 109 S.

Barbarossa, M.V.

On a class of neutral equations with state-dependent delay in population dynamics.

München, Technische Universität, Fakultät für Mathematik, Diss., 2013, 194 S.

Storath, M.

Amplitude and sign decompositions by complex wavelets - Theory and applications to image analysis.

München, Technische Universität, Fakultät für Mathematik, Diss., 2013, 131 S.

Frikel, J. ; Quinto, E.T.

Characterization and reduction of artifacts in limited angle tomography.

Inverse Probl. 29:125007 (2013)

McLachlan, M. ; Schramm, K.-W. ; Lenoir, D. ; Voigt, K. ; Hollert, H.

Obituary Otto Hutzinger.

Env. Sci. Europe 25:28 (2013)

Kazeroonian, A. ; Hasenauer, J. ; Theis, F.J.

Parameter estimation for stochastic biochemical processes: A comparison of moment equation and fintie state projection.

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Sass, S. ; Buettner, F. ; Müller, N.S. ; Theis, F.J.

A modular framework for gene set analysis integrating multilevel omics data.

Nucleic Acids Res. 41, 9622-9633 (2013)

Castaneda, V. ; Mateus, D. ; Navab, N.

Stereo time-of-flight with constructive interference.

IEEE Trans. Pattern Anal. Mach. Intell. 36, 1402-1413 (2013)

Efendiyev, M.A. ; Zhigun, A.

On a global uniform pullback attractor of a class of PDEs with degenerate diffusion and chemotaxis in one dimension.

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Matthies, P. ; Sharma, K. ; Okur, A. ; Gardiazabal, J. ; Vogel, J. ; Lasser, T. ; Navab, N.

First use of mini gamma cameras for intra-operative robotic SPECT reconstruction.

Lecture Notes Comp. Sci. 8149, 163-170 (2013)

Chatelain, P. ; Pauly, O. ; Peter, L. ; Ahmadi, S.A. ; Plate, A. ; Bötzel, K. ; Navab, N.

Learning from multiple experts with random forests: Application to the segmentation of the midbrain in 3D ultrasound.

Lecture Notes Comp. Sci. 8150, 230-237 (2013)

Rupprecht, C. ; Pauly, O. ; Theobalt, C. ; Illic, S.

3D semantic parameterization for human shape modeling: Application to 3D animation.

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Heinrich, S. ; Geissen, E.M. ; Kamenz, J. ; Trautmann, S. ; Widmer, C. ; Drewe, P. ; Knop, M. ; Radde, N. ; Hasenauer, J. ; Hauf, S.

Determinants of robustness in spindle assembly checkpoint signalling.

Nat. Cell Biol. 15, 1328-1239 (2013)

Prigarin, S.M. ; Sandau, K. ; Kazmierczak, M. ; Hahn, K.

Estimation of fractal dimension: A survey with numerical experiments and software description.

Int. J. Biomath. Biostat. 2, 167-180 (2013)

Voigt, K. ; Brüggemann, R. ; Scherb, H. ; Cok, I. ; Mazmanci, B. ; Mazmanci, M.A. ; Turgut, C. ; Schramm, K.-W.

Organochlorine pesticides in the environment and humans: Necessity for comparative data evaluation.

In: Wittmann, J.* ; Müller, M.* [Eds.]: Simulation in den Umwelt- und Geowissenschaften (Simulation in den Umwelt- und Geowissenschaften, Workshop Leipzig 2013). Aachen: Shaker, 2013. 9-22 (ASIM-Mitteilung ; 146)

Voigt, K. ; Scherb, H.

Environment and health: A challenge for computer science.

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Scherb, H. ; Voigt, K. ; Kusmierz, R.

The human sex odds at birth in France: A preliminary geo-spatial-temporal approach in the vicinity of French nuclear facilities (NF).

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Buggenthin, F. ; Marr, C. ; Schwarzfischer, M. ; Hoppe, P.S. ; Hilsenbeck, O. ; Schroeder, T. ; Theis, F.J.

An automatic method for robust and fast cell detection in bright field images from high-throughput microscopy.

BMC Bioinformatics 14:297 (2013)

Raue, A. ; Schilling, M. ; Bachmann, J. ; Matteson, A. ; Schelker, M. ; Kaschek, D. ; Hug, S. ; Kreutz, C. ; Harms, B.D. ; Theis, F.J. ; Klingmüller, U. ; Timmer, J.

Lessons learned from quantitative dynamical modeling in systems biology.

PLoS ONE 8:e74335 (2013)

Efendiyev, M.A.

Attractors for degenerate parabolic type equations.

Providence, Rhode Island: American Mathematical Society, 2013. (Mathematical Surveys and Monographs ; 192)

Bartel, S. ; Schulz, N. ; Theis, F.J. ; Alessandrini, F. ; Takenaka, S. ; Eickelberg, O. ; Krauss-Etschmann, S.

miRNA-based identification of SEC14L3 deregulation in murine experimental asthma.

Eur. Respir. J. 42 (2013)

Hock, S. ; Hasenauer, J. ; Theis, F.J.

Modeling of 2D diffusion processes based on microscopy data: Parameter estimation and practical identifiability analysis.

BMC Bioinformatics 14:S7 (2013)

Degenfeld-Schonburg, S. ; Lasser, R.

Multipliers on L^p-spaces for hypergroups.

Rocky Mt. J. Math. 43, 1115-1139 (2013)

Müller, J. ; Hense, B.A. ; Fuchs, T.M. ; Utz, M. ; Pötzsche, C.

Bet-hedging in stochastically switching environments.

J. Theor. Biol. 336, 144-157 (2013)

Scherb, H. ; Kusmierz, R. ; Voigt, K.

Increased sex ratio in Russia and Cuba after Chernobyl: A radiological hypothesis.

Environ. Health 12:63 (2013)

Gallenberger, M.V.

Kernel-based methods for parameter estimation in multidimensional systems.

Herzogenrath: Shaker, 2013, 110 S. (Zugl. München, Technische Universität, Diss., 2013) (Berichte aus der Mathematik)

Rinck, A. ; Preusse, M. ; Laggerbauer, B. ; Lickert, H. ; Engelhardt, S. ; Theis, F.J.

The human transcriptome is enriched for miRNA-binding sites located in cooperativity-permitting distance.

RNA Biol. 10, 1125-1135 (2013)

Zhigun, A.

Biofilm models with various nonlinear effects: Long-time behavior of solutions.

München, Technische Universität, Fakultät für Mathematik, Diss., 2013, 99 S.

Eisenhofer, S.

A coupled system of ordinary and partial differential equations modeling the swelling of mitochondria.

München, Technische Universität, Fakultät für Mathematik, Diss., 2013, 145 S.

Frikel, J.

Reconstructions in limited angle X-ray tomography: Characterization of classical reconstructions and adapted curvelet sparse regularization.

München, Technische Universität, Fakultät für Mathematik, Diss., 2013, 122 S.

Vogel, J. ; Lasser, T. ; Gardiazabal, J. ; Navab, N.

Trajectory optimization for intra-operative nuclear tomographic imaging.

Med. Image Anal. 17, 723-731 (2013)

Hock, S. ; Ng, Y.K. ; Hasenauer, J. ; Wittmann, D.M. ; Lutter, D. ; Trümbach, D. ; Wurst, W. ; Prakash, N. ; Theis, F.J.

Sharpening of expression domains induced by transcription and microRNA regulation within a spatio-temporal model of mid-hindbrain boundary formation.

BMC Syst. Biol. 7:48 (2013)

Peter, L. ; Pauly, O. ; Jansen, S.B.G. ; Smethurst, P.A. ; Ouwehand, W.H. ; Navab, N.

Automatic event detection within thrombus formation based on integer programming.

Lecture Notes Comp. Sci. 7766, Springer, 215-224 (2013)

Wahl, S. ; Holzapfel, C. ; Yu, Z. ; Breier, M. ; Kondofersky, I. ; Fuchs, C. ; Singmann, P. ; Prehn, C. ; Adamski, J. ; Grallert, H. ; Illig, T. ; Wang-Sattler, R. ; Reinehr, T.

Metabolomics reveals determinants of weight loss during lifestyle intervention in obese children.

Catal. Lett. 9, 1157-1167 (2013)

Gardiazabal, J. ; Reichl, T. ; Okur, A. ; Lasser, T. ; Navab, N.

First flexible robotic intra-operative nuclear imaging for image-guided surgery.

Lecture Notes Comp. Sci. 7915, Springer, 81-90 (2013)

Hug, S. ; Raue, A. ; Hasenauer, J. ; Bachmann, J. ; Klingmüller, U. ; Timmer, J. ; Theis, F.J.

High-dimensional Bayesian parameter estimation: Case study for a model of JAK2/STAT5 signaling.

Math. Biosci. 246, 293-304 (2013)

Kirişli, H.A. ; Schaap, M. ; Metz, C.T. ; Dharampal, A.S. ; Meijboom, W.B. ; Papadopoulou, S.L. ; Dedic, A. ; Nieman, K. ; de Graaf, M.A. ; Meijs, M.F.L. ; Cramer, M.J. ; Broersen, A. ; Cetin, S. ; Eslami, A. ; Flórez-Valencia, L. ; Lor, K.L. ; Matuszewski, B. ; Melki, I. ; Mohr, B. ; Öksüz, I. ; Shahzad, R. ; Wang, C. ; Kitslaar, P.H. ; Unal, G. ; Katouzian, A. ; Orkisz, M. ; Chen, C.M. ; Precioso, F. ; Najman, L. ; Masood, S. ; Ünay, D. ; van Vliet, L. ; Moreno, R. ; Goldenberg, R. ; Vucini, E. ; Krestin, G.P. ; Niessen, W.J. ; van Walsum, T.

Standardized evaluation framework for evaluating coronary artery stenosis detection, stenosis quantification and lumen segmentation algorithms in computed tomography angiography.

Med. Image Anal. 17, 859-876 (2013)

Nagy, B. ; Toókos, F.

Bernstein inequality in L^α norms.

Acta Sci. Math. 79, 129-174 (2013)

Forster, B. ; Garunkstis, R. ; Massopust, P. ; Steuding, J.

Complex B-splines and Hurwitz zeta functions.

LMS J. Comput. Math. 16, 61-77 (2013)

Carvalho, A.N. ; Sonner, S.

Pullback exponential attractors for evolution processes in Banach spaces: Theoretical results.

Commun. Pure Appl. Anal. 12, 3047-3071 (2013)

Voigt, K. ; Scherb, H. ; Brüggemann, R. ; Schramm, K.-W.

Discrete mathematical data analysis approach: A valuable assessment method for sustainable chemistry.

Sci. Total Environ. 454-455, 149-153 (2013)

Dräxl, S. ; Müller, J. ; Li, W.B. ; Michalke, B. ; Scherb, H. ; Hense, B.A. ; Tschiersch, J. ; Kanter, U. ; Schäffner, A.

Caesium accumulation in yeast and plants is selectively repressed by loss of the SNARE Sec22p/SEC22.

Nat. Commun. 4:2092 (2013)

Schneider, K. ; Fuchs, C. ; Dobay, A. ; Rottach, A. ; Qin, W.H. ; Wolf, P. ; Alvarez-Castro, J.M. ; Nalaskowski, M.M. ; Kremmer, E. ; Schmid, V. ; Leonhardt, H. ; Schermelleh, L.

Dissection of cell cycle-dependent dynamics of Dnmt1 by FRAP and diffusion-coupled modeling.

Nucleic Acids Res. 41, 4860-4876 (2013)

Ispiryan, R. ; Grigoriev, I. ; zu Castell, W. ; Schäffner, A.

A segmentation procedure using colour features applied to images of Arabidopsis thaliana.

Funct. Plant Biol. 40, 1065-1075 (2013)

Hahn, K.R. ; Myers, N. ; Prigarin, S.M. ; Rodenacker, K. ; Kurz, A. ; Förstl, H. ; Zimmer, C. ; Wohlschläger, A.M. ; Sorg, C.

Selectively and progressively disrupted structural connectivity of functional brain networks in Alzheimer's disease - revealed by a novel framework to analyze edge distributions of networks detecting disruptions with strong statistical evidence.

Neuroimage 81, 96-109 (2013)

Voigt, K. ; Brüggemann, R. ; Scherb, H. ; Cok, I. ; Mazmanci, B. ; Mazmanci, M.A. ; Turgut, C. ; Schramm, K.-W.

Evaluation of organochlorine pesticides in breast milk samples in Turkey applying features of the partial order technique.

Int. J. Environ. Health Res. 23, 226-246 (2013)

Schulz, S. ; Schmitt, S. ; Wimmer, R. ; Aichler, M. ; Eisenhofer, S. ; Lichtmannegger, J. ; Eberhagen, C. ; Artmann, R. ; Toókos, F. ; Walch, A.K. ; Krappmann, D. ; Brenner-Jan, C. ; Rust, C. ; Zischka, H.

Progressive stages of mitochondrial destruction caused by cell toxic bile salts.

Biochim. Biophys. Acta-Biomembr. 1828, 2121-2133 (2013)

Eslami, A. ; Karamalis, A. ; Katouzian, A. ; Navab, N.

Segmentation by retrieval with guided random walks: Application to left ventricle segmentation in MRI.

Med. Image Anal. 17, 236-253 (2013)

zu Castell, W.

Complex systems: Chances and risks for experimental data analysis.

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Czaja, W. ; Ehler, M.

Schroedinger eigenmaps for the analysis of biomedical data.

IEEE Trans. Pattern Anal. Mach. Intell. 35, 1274-1280 (2013)

Brüggemann, R. ; Restrepo, G. ; Voigt, K. ; Annoni, P.

Weighting intervals and ranking, exemplified by leaching potential of pesticides.

Match-Commun. Math. Comput. Chem. 69, 413-432 (2013)

Lasser, R. ; Obermaier, J. ; Wagner, J.

On the spectrum of tridiagonal operators and the support of orthogonalization measures.

Arch. Math. 100, 289-299 (2013)

Müller, A. ; Faubert, P. ; Hagen, M. ; zu Castell, W. ; Polle, A. ; Schnitzler, J.-P. ; Rosenkranz, M.

Volatile profiles of fungi - chemotyping of species and ecological functions.

Fungal Genet. Biol. 54, 25-33 (2013)

Dancer, E.N. ; Du, Y. ; Efendiyev, M.A.

Quasilinear elliptic equations on half- and quarter-spaces.

Adv. Nonlinear Stud. 13, 115-136 (2013)

Efendiyev, M.A.

Evolution equations arising in the modelling of life sciences.

Basel: Birkhäuser, 2013. 219 S. (International Series of Numerical Mathematics ; 163)

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Apoe, Mbl2 and Psp plasma protein levels correlate with diabetic phenotype in NZO mice - an optimized rapid workflow for SRM-based quantification.

J. Proteome Res. 12, 1331-1343 (2013)

Lasser, R.

Almost-convergent sequences with respect to polynomial hypergroups.

Acta Math. Hung. 138, 127-139 (2013)

Allgöwer, F. ; Hasenauer, J. ; Waldherr, S.

Model falsification, semidefinite programming.

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Spatially dependent regularization parameter selection in total generalized variation models for image restoration.

Int. J. Comput. Math. 90, 109-123 (2013)

Colomé-Tatché, M. ; Cortijo, S. ; Wardenaar, R. ; Morgado, L. ; Lahouze, B. ; Sarazin, A. ; Etcheverry, M. ; Martin, A. ; Feng, S. ; Duvernois-Berthet, E. ; Labadie, K. ; Wincker, P. ; Jacobsen, S.E. ; Jansen, R.C. ; Colot, V. ; Johannes, F.

Features of the Arabidopsis recombination landscape resulting from the combined loss of sequence variation and DNA methylation.

Proc. Natl. Acad. Sci. U.S.A. 109, 16240-16245 (2012)

Seifert, M. ; Cortijo, S. ; Colomé-Tatché, M. ; Johannes, F. ; Roudier, F. ; Colot, V.

MeDIP-HMM: Genome-wide identification of distinct DNA methylation states from high-density tiling arrays.

Bioinformatics 28, 2930-2939 (2012)

Buettner, F. ; Alexander, E. ; Mcnair, H. ; Gulliford, S. ; Partridge, M. ; Dearnaley, D.

SU‐E‐T‐255: A Novel Rectal Obturator for Prostate Radiotherapy Improves the Spatial Distribution of Dose and Reduces the Predicted Risk for Rectal Bleeding and Subjective Sphincter Control.

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TU‐C‐BRA‐02: The Relevance of the Spatial Distribution of Dose for Complications after Head and Neck and Prostate Radiotherapy.

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Sparse representation of video data by adaptive tetrahedralizations.

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Towards a complete framework for deformable surface recovery using RGBD cameras.

Vortrag: IROS'12 Workshop on Color-Depth Fusion in Robotics, 7 - 12 October 2012, Vila Moura, Portugal (2012)

Mateus, D. ; Wachinger, C. ; Atasoy, S. ; Schwarz, L. ; Navab, N.

Learning manifolds: Design analysis for medical applications.

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Held, S.

Monogenic wavelet frames for image analysis.

München, Technische Universität, Fakultät für Mathematik, Diss., 2012, 196 S.

Katouzian, A. ; Karamalis, A. ; Sheet, D. ; Konofagou, E. ; Baseri, B. ; Carlier, S.G. ; Eslami, A. ; König, A. ; Navab, N. ; Laine, A.F.

Iterative self-organizing atherosclerotic tissue labeling in intravascular ultrasound images and comparison with virtual histology.

IEEE Trans. Bio. Med. Eng. 59, 3039-3049 (2012)

Katouzian, A. ; Karamalis, A. ; Lisauskas, J. ; Eslami, A. ; Navab, N.

IVUS-histology image registration.

Lecture Notes Comp. Sci. 7359, 141-149 (2012)

Glocker, B. ; Pauly, O. ; Konokoglu, E. ; Criminisi, A.

Joint classification-regression forests for spatially structured multi-object segmentation.

Lecture Notes Comp. Sci. 7475, 870-881 (2012)

Abdurahman, S. ; Jerebko, A. ; Mertelmeier, T. ; Lasser, T. ; Navab, N.

Out-of-plane artifact reduction in tomosynthesis based on regression modeling and outlier detection.

Lecture Notes Comp. Sci. 7361, 729-736 (2012)

Ehler, M. ; Hirn, M.

Sparse endmember extraction and demixing.

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Supervised classification for customized intraoperative augmented reality visualization.

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Chen, Y. ; Hrabe, T. ; Pfeffer, S. ; Pauly, O. ; Mateus, D. ; Navab, N. ; Förster, F.

Detection and identification of macromolecular complexes in cryo-electron tomograms using support vector machines.

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Pauly, O. ; Ahmadi, S.A. ; Plate, A. ; Boetzel, K. ; Navab, N.

Detection of substantia nigra echogenicities in 3D transcranial ultrasound for early diagnosis of Parkinson disease.

Lecture Notes Comp. Sci. 15, 443-450 (2012)

Hofmann, M.

On representation and uniqueness of invariant means on hypergroups.

München, Technische Universität, Fakultät für Mathematik, Diss., 2012, 62 S.

Lasser, R. ; Obermaier, J.

Strongly invariant means on commutative hypergroups.

Colloq. Math. 129, 119-131 (2012)

Wiese, T.

Radon transform and Hilbert space sampling theory.

München, Technische Universität, Fakultät für Mathematik, Diplom-Arbeit, 2012

Schmelcher, S.

A fast curvelet transform for sparse reconstruction in limited angle tomography.

München, Technische Universität, Fakultät für Mathematik, Master-Thesis, 2012, 74 S.

Nagler, J.

Efficient low-resolution approximation of ultrasound images.

München, Technische Universität, Fakultät für Mathematik, Master-Thesis, 2012, 67 S.

Hilger, A.

Estimation of fusion protein copy numbers from noisy fluorescence intensity data of mouse embryonic stem cells.

München, Ludwig-Maximilians-Universität, Fakultät für Mathematik, Informatik und Statistik, Master-Thesis, 2012, 94 S.

Serva, A. ; Knapp, B. ; Tsai, Y.T. ; Claas, C. ; Lisauskas, T. ; Matula, P. ; Harder, N. ; Kaderali, L. ; Rohr, K.B. ; Erfle, H. ; Eils, R. ; Braga, V. ; Starkuviene, V.

miR-17-5p regulates endocytic trafficking through targeting TBC1D2/Armus.

PLoS ONE 7:e52555 (2012)

Knapp, B. ; Kaderali, L.

Single-cell analysis of high-content, high-throughput cellular assays.

In: Genomics II: Bacteria, Viruses and Metabolic Pathways. iConcept Press Ltd, 2012.

Theis, F.J. ; Cichocki, A.* ; Yeredor, A.* ; Zibulevsky, M.*[Eds.]

Latent variable analysis and signal separation : 10th International Conference, LVA/ICA 2012, Tel Aviv, Israel, March 12-15, 2012, Proceedings.

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Endesfelder, D.

Analysis of causes and consequences of chromosomal instability in cancer.

Universität Duisburg-Essen, Medizinische Fakultät, Diss., 2012, 100 S.

Rickert, D.

Parameter estimation in an NF-κB model.

München, Ludwig-Maximilians-Universität & Technische Universität, Bioinformatik, Master-Thesis, 2012, 70 S.

Streppel, B.

Data mining approaches for analyzing single cell stem cell data.

München, Ludwig-Maximilians-Universität & Technische Universität, Bioinformatik, Master-Thesis, 2012, 72 S.

Sachs, M.

Statistical analysis of asymmetric cell fate choice on cellular genealogies.

München, Technische Universität, Fakultät für Mathematik, Master-Thesis, 2012, 70 S.

Schindele, A.

Krümmungsprofil in Schwarz-Weiß-Bildern.

München, Technische Universität, Fakultät für Mathematik, Master-Thesis, 2012, 48 S.

Schröder, K.

Reconstruction of band-pass signals from zero sets.

München, Technische Universität, Fakultät für Mathematik, Master-Thesis, 2012

Jeratsch, U.

Evaluation of differences in metabolic reaction systems on the basis of correlations.

München, Ludwig-Maximilians-Universität, Fakultät für Statistik, Diplom-Arbeit, 2012, 80 S.

Köhler, J.

Approximate Bayesian parameter estimation in stochastic models of biochemical reactions.

München, Ludwig-Maximilians-Universität, Fakultät für Statistik, Master-Thesis, 2012, 108 S.

Ehler, M. ; Filbir, F.D. ; Mhaskar, H.N.

Learning biomedical data locally using diffusion geometry techniques.

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Peng, C. ; Li, N. ; Ng, Y.K. ; Zhang, J. ; Meier, F. ; Theis, F.J. ; Merkenschlager, M. ; Chen, W. ; Wurst, W. ; Prakash, N.

A unilateral negative feedback loop between miR-200 microRNAs and Sox2/E2F3 controls neural progenitor cell-cycle exit and differentiation.

J. Neurosci. 32, 13292-13308 (2012)

Andres, C. ; Hasenauer, J. ; Schittler, D. ; Allgöwer, F.

Threshold-free population analysis identifies larger DRG neurons to respond stronger to NGF stimulation.

PLoS ONE 7:e34257 (2012)

Hasenauer, J. ; Heinrich, J. ; Doszczak, M. ; Scheurich, P. ; Weiskopf, D. ; Allgöwer, F.

A visual analytics approach for models of heterogeneous cell populations.

EURASIP J. Bioinf. Syst. Biol. 2012:4 (2012)

Hasenauer, J. ; Löhning, M. ; Khammash, M. ; Allgöwer, F.

Dynamical optimization using reduced order models: A method to guarantee performance.

J. Process Contr. 22, 1490-1501 (2012)

Metzger, P. ; Hasenauer, J. ; Allgöwer, F.

Modeling and analysis of division-, age-, and label-structured cell populations.

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Schittler, D. ; Hasenauer, J. ; Allgöwer, F.

A model for proliferating cell populations that accounts for cell types.

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Vehlow, C. ; Hasenauer, J. ; Krämer, A. ; Radde, N. ; Allgöwer, F. ; Weiskopf, D.

Uncertainty-aware visual analysis of biochemical reaction networks.

In: IEEE Symposium on Biological Data Visualization (BioVis). Seattle, USA: IEEE, 2012. 91-98

Waldherr, S. ; Hasenauer, J. ; Allgöwer, F.

Set based uncertainty analysis and parameter estimation for biological networks with the bioSDP Toolbox.

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Johannes, F. ; Colomé-Tatché, M.

Concerning epigenetics and inbreeding.

Nat. Rev. Genet. 12, 376 (2011)

Roux, F. ; Colomé-Tatché, M. ; Edelist, C. ; Wardenaar, R. ; Guerche, P. ; Hospital, F. ; Colot, V. ; Jansen, R.C. ; Johannes, F.

Genome-wide epigenetic perturbation jump-starts patterns of heritable variation found in nature.

Genetics 188, 1015-1017 (2011)

Johannes, F. ; Colomé-Tatché, M.

Quantitative epigenetics through epigenomic perturbation of isogenic lines.

Genetics 188, 215-227 (2011)

Colomé-Tatché, M. ; Klempt, C. ; Santos, L. ; Vekua, T.

Adiabatic spin cooling using high-spin Fermi gases.

New J. Phys. 13:113021 (2011)

Colomé-Tatché, M. ; Petrov, D.S.

Parametric excitation of a 1D gas in integrable and nonintegrable cases.

Phys. Rev. Lett. 106:125302 (2011)

Storath, M.

Short Communication: Separation of Edges in X-Ray Images by Microlocal Analysis.

Vortrag: Jahrestagung der Gesellschaft für Angewandte Mathematik und Mechanik, 18-21 April 2011, Graz. (2011)

Scherb, H. ; Voigt, K.

Ionizing radiation and the human sex odds at birth.

Vortrag: The Chernobyl Catastrophe: Taking Stock of 25 Years of Ecological and Health Damages, 5-8 April 2011, Berlin, Charité. (2011)

zu Castell, W.

Contributions to the theory of positive definite functions and their role in applications.

München, Technische Universität, Habil.-Schr., 2011, 196 S.

Massopust, P.

The multiscale structure of fractal functions and wavelets.

München, Technische Universität, Habil.-Schr., 2011, 90 S.

Röhser, M.

A practical approach to wedgelet-based image compression.

Aachen, Rheinisch-Westfälische Technische Hochschule, Fakultät für Mathematik, Informatik, Naturwissenschaften, Diplom-Arbeit, 2011

Knapp, B. ; Rebhan, I. ; Kumar, A. ; Matula, P. ; Kiani, N.A. ; Binder, M. ; Erfle, H. ; Rohr, K.B. ; Eils, R. ; Bartenschlager, R. ; Kaderali, L.

Normalizing for individual cell population context in the analysis of high-content cellular screens.

BMC Bioinformatics 12:485 (2011)

Knapp, B. ; Kaderali, L.

Linear model for network inference using RNA interference data.

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Demaret, L. ; Iske, A.

Anisotropic triangulation methods in adaptive image approximation.

Springer Proc. Math. 3, 47-68 (2011)

Lang, E.W. ; Schachtner, R. ; Lutter, D. ; Herold, D. ; Kodewitz, A. ; Blöchl, F. ; Theis, F.J. ; Keck, I.R. ; Górriz Sáez, J.M. ; Gomez, P. ; Gómez Vilda, P. ; Tomé, A.M.

Exploratory matrix factorization techniques for large scale biomedical data sets.

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Bruns, P.

Reverse engineering of a continous regulatory network for the differentiation of glutamatergic neurons from high-throughput data.

München, Ludwig-Maximilians-Universität & Technische Universität, Bioinformatik, Master-Thesis, 2011, 70 S.

Kroiss, M.

A toolbox for systematic model reduction.

München, Ludwig-Maximilians-Universität & Technische Universität, Bioinformatik, Bachelor-Thesis, 2011, 30 S.

Buggenthin, F.

Computational prediction of hematopoietic cell fates using single cell time lapse imaging.

München, Technische Universität & Ludwig-Maximilians-Universität, Fakultät für Informatik, Diplom-Arbeit, 2011, 99 S.

Schauberger, B.

Models of murine embryonic stem cell dynamics on multiple scales.

München, Technische Universität & Ludwig-Maximilians-Universität, Fakultät für Informatik, Diplom-Arbeit, 2011, 99 S.

Landerer, C.

A qualitative model to study the role of pitchfork and the primary cilium in the hedgehog signaling pathway.

München, Ludwig-Maximilians-Universität & Technische Universität, Bioinformatik, Bachelor-Thesis, 2011, 50 S.

Hilsenbeck, O.

Automated cell lineage construction from time-lapse microscopy data.

München, Ludwig-Maximilians-Universität & Technische Universität, Bioinformatik, Bachelor-Thesis, 2011, 48 S.

Böhm, S.

Mathematical models of avascular tumor growth and treatments.

München, Technische Universität, Fakultät für Mathematik, Bachelor-Thesis, 2011, 32 S.

Waelkens, P.

Automatic segementation of the carotid artery in freehand ultrasound.

München, Technische Universität, Fakultät für Mathematik, Master-Thesis, 2011, 31 S.

Preusse, M.

Beyond enrichment: Measuring microRNA-pathway association in signaling networks.

München, Technische Universität, Fakultät für Chemie, Master-Thesis, 2011, 80 S.

Hasenauer, J. ; Waldherr, S. ; Doszczak, M. ; Radde, N. ; Scheurich, P. ; Allgöwer, F.

Identification of models of heterogeneous cell populations from population snapshot data.

BMC Bioinformatics 12:125 (2011)

Hasenauer, J. ; Doszczak, M. ; Scheurich, P. ; Weiskopf, D. ; Allgöwer, F.

Visualization methods and support vector machines as tools for determining markers in models of heterogeneous populations: Proapoptotic signaling as a case study.

In: Koeppl, H.* ; Acimovic, J.* ; Kesselin, J.* ; Mäki-Marttunen, T.* [Eds.]: Proceedings of 8th International Workshop on Computational Systems Biology. 2011. 61-64

Hasenauer, J. ; Waldherr, S. ; Doszczak, M. ; Radde, N. ; Scheurich, P. ; Allgöwer, F.

Analysis of heterogeneous cell populations: A density-based modeling and identification framework.

J. Process Contr. 21, 1417-1425 (2011)

Löhning, M. ; Hasenauer, J. ; Allgöwer, F.

Trajectory-based model reduction of nonlinear biochemical networks employing the observability normal form.

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Löhning, M. ; Hasenauer, J. ; Allgöwer, F.

Steady state stability preserving nonlinear model reduction using sequential convex optimization.

In: Proceedings of the IEEE Conference on Decision and Control. 2011. 7158-7163

Schittler, D. ; Hasenauer, J. ; Allgöwer, F.

A generalized population model for cell proliferation: Integrating division numbers and label dynamics.

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Waldherr, S. ; Hasenauer, J. ; Doszczak, M. ; Scheurich, P. ; Allgöwer, F.

Global uncertainty analysis for a model of TNF-induced NF-κB signalling.

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Weber, P. ; Hasenauer, J. ; Allgöwer, F. ; Radde, N.

Parameter estimation and identifiability of biological networks using relative data.

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Johannes, F. ; Wardenaar, R. ; Colomé-Tatché, M. ; Mousson, F. ; de Graaf, P. ; Mokry, M. ; Guryev, V. ; Timmers, H.T. ; Cuppen, E. ; Jansen, R.C.

Comparing genome-wide chromatin profiles using ChIP-chip or ChIP-seq.

Bioinformatics 26, 1000-1006 (2010)

Rodríguez, K. ; Argüelles, A. ; Colomé-Tatché, M. ; Vekua, T. ; Santos, L.

Mott-insulator phases of spin-3/2 fermions in the presence of quadratic zeeman coupling.

Phys. Rev. Lett. 105:050402 (2010)

Colomé-Tatché, M. ; Matveenko, S.I. ; Shlyapnikov, G.V.

Finite-size effects for the gap in the excitation spectrum of the one-dimensional Hubbard model.

Phys. Rev. A 81:013611 (2010)

Berschneider, G.J.

Conditionally positive definite kernels: An abstract approach.

Aachen: Shaker, 2010, 94 S. (Zugl. München, Technische Universität, Fakultät für Mathematik, Diss., 2010)

Naim, G.

Untersuchung von erweiterten Wedgelets-Zerlegungen.

Bonn, Rheinische Friedrich-Wilhelms-Universität, Mathematisch-Naturwissenschaftliche Fakultät, Diplom-Arbeit, 2010

Hinnenthal, M.

Erweiterung der kontextuellen Kompressionsmethoden mit Hilfe von Delaunay- Triangulierungen.

München, Technische Universität, Fakultät für Mathematik, Diplom-Arbeit, 2010, 103 S.

Börner, K. ; Hermle, J. ; Sommer, C. ; Brown, N.P. ; Knapp, B. ; Glass, B. ; Kunkel, J. ; Torralba, G. ; Reymann, J. ; Beil, N. ; Beneke, J. ; Pepperkok, R. ; Schneider, R. ; Ludwig, T. ; Hausmann, M. ; Hamprecht, F. ; Erfle, H. ; Kaderali, L. ; Kräusslich, H.G. ; Lehmann, M.J.

From experimental setup to bioinformatics: An RNAi screening platform to identify host factors involved in HIV-1 replication.

Biotechnol. J. 5, 39-49 (2010)

Heinig, M. ; Petretto, E. ; Wallace, C. ; Bottolo, L. ; Rotival, M. ; Lu, H. ; Li, Y. ; Sarwar, R. ; Langley, S.R. ; Bauerfeind, A. ; Hummel, O. ; Lee, Y.A. ; Paskas, S. ; Rintisch, C. ; Saar, K. ; Cooper, J. ; Buchan, R. ; Gray, E.E. ; Cyster, J.G. ; Erdmann, J. ; Hengstenberg, C. ; Maouche, S. ; Ouwehand, W.H. ; Rice, C.M. ; Samani, N.J. ; Schunkert, H. ; Goodall, A.H. ; Schulz, H. ; Roider, H.G. ; Vingron, M. ; Blankenberg, S. ; Münzel, T. ; Zeller, T. ; Szymczak, S. ; Ziegler, A. ; Tiret, L. ; Smyth, D.J. ; Pravenec, M. ; Aitman, T.J. ; Cambien, F. ; Clayton, D.G. ; Todd, J.A. ; Hubner, N. ; Cook, S.A.

A trans-acting locus regulates an anti-viral expression network and type 1 diabetes risk.

Nature 467, 460-464 (2010)

Manke, T. ; Heinig, M. ; Vingron, M.

Quantifying the effect of sequence variation on regulatory interactions.

Hum. Mutat. 31, 477-483 (2010)

Azadov, K.

Anfrageoptimierung, Visualisierung und automatisierte Auswertung von annotierten Stammzell-Differenzierungsbäumen.

München, Technische Universität & Ludwig-Maximilians-Universität, Fakultät für Informatik, Diplom-Arbeit, 2010, 60 S.

Röh, S.

Regulation of neuronal stem cell differentiation.

München, Ludwig-Maximilians-Universität & Technische Universität, Bioinformatik, Master-Thesis, 2010

Strasser, M.

Stochastic modeling in gene switches.

München, Ludwig-Maximilians-Universität & Technische Universität, Bioinformatik, Master-Thesis, 2010, 81 S.

Drexler, B.

Fatty acid pool reconstruction from metabolomics measurements of phosphatidylcholines.

München, Ludwig-Maximilians-Universität & Technische Universität, Bioinformatik, Bachelor-Thesis, 2010, 49 S.

Angermann, M.

Breast cancer classification with support vector machines.

München, Technische Universität, Fakultät für Mathematik, Diplom-Arbeit, 2010, 85 S.

Hock, S.

Spatial modeling of differentiation of mid- and hindbrain.

München, Technische Universität, Fakultät für Mathematik, Diplom-Arbeit, 2010, 108 S.

Stückler, F.

Computational modeling of human mitochondrial beta-oxidation.

München, Technische Universität, Fakultät für Chemie, Master-Thesis, 2010, 80 S.

Hasenauer, J. ; Breindl, C. ; Waldherr, S. ; Allgöwer, F.

Approximative classification of regions in parameter spaces of nonlinear ODEs yielding different qualitative behavior.

In: Proceedings (Proc. IEEE Conf. on Dec. and Contr. (CDC)). 2010. 4114-4119

Hasenauer, J. ; Rumschinski, P. ; Waldherr, S. ; Borchers, S. ; Allgöwer, F. ; Findeisen, R.

Guaranteed steady state bounds for uncertain (bio-)chemical processes using infeasibility certificates.

J. Process Contr. 20, 1076-1083 (2010)

Hasenauer, J. ; Waldherr, S. ; Wagner, K. ; Allgöwer, F.

Parameter identification, experimental design and model falsification for biological network models using semidefinite programming.

IET Syst. Biol. 4, 119-130 (2010)

Hasenauer, J. ; Waldherr, S. ; Radde, N. ; Doszczak, M. ; Scheurich, P. ; Allgöwer, F.

A maximum likelihood estimator for parameter distributions in heterogeneous cell populations.

Procedia Comp. Sci. 1, 1649-1657 (2010)

Hasenauer, J. ; Waldherr, S. ; Doszczak, M. ; Scheurich, P. ; Allgöwer, F.

Density-based modeling and identification of biochemical networks in cell populations.

In: Kothare, M.* ; Tade, M.* ; Moses, O.* ; Wouwer, A.* ; Smets, I.* [Eds.]: Proceedings (Proc. of the 9th Int. Symp. on Dynamics and Control of Process Syst.). 2010. 320-325 ( ; 9)

Krämer, A. ; Hasenauer, J. ; Allgöwer, F. ; Radde, N.

Computation of the posterior entropy in a Bayesian framework for parameter estimation in biological networks.

In: Proceedings (Proc. of the IEEE Int. Conf. on Control Applications, CCA, September 8-10, 2010). 2010. 493-498

Schittler, D. ; Hasenauer, J. ; Allgöwer, F. ; Waldherr, S.

Cell differentiation modeled via a coupled two-switch regulatory network.

Chaos 20:045121 (2010)

Rieber, N. ; Knapp, B. ; Eils, R. ; Kaderali, L.

RNAither, an automated pipeline for the statistical analysis of high-throughput RNAi screens.

Bioinformatics 25, 678-679 (2009)

Georgiev, P.G. ; Theis, F.J.

Optimization techniques for data representations with biomedical applications.

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Friedel, C.C. ; Krumsiek, J. ; Zimmer, R.

Bootstrapping the interactome: Unsupervised identification of protein complexes in yeast.

J. Comput. Biol. 16, 971-987 (2009)

Krumsiek, J.

Computational modeling of regulatory networks in hematopoietic differentiation.

München, Technische Universität & Ludwig-Maximilians-Universität, Fakultät für Informatik, Diplom-Arbeit, 2009, 82 S.

Schreiber, K.

Metabolic network reconstruction

München, Ludwig-Maximilians-Universität & Technische Universität, Bioinformatik, Master-Thesis, 2009, 63 S.

Schwarzfischer, M.

Single-cell analysis of multipotente hematopoietic progenitor cells.

München, Technische Universität & Ludwig-Maximilians-Universität, Fakultät für Informatik, Diplom-Arbeit, 2009, 70 S.

Rickert, D.

Empirical reduction of signaling networks.

München, Ludwig-Maximilians-Universität & Technische Universität, Bioinformatik, Bachelor-Thesis, 2009, 67 S.

Hangauer, A.

Construction of coiflets associated with multiwavelets.

München, Technische Universität, Fakultät für Mathematik, Diplom-Arbeit, 2009, 62 S.

Schmalkalt, S.

Directional filtering in images demonstrated in the case of nerve fibres.

München, Technische Universität, Fakultät für Mathematik, Diplom-Arbeit, 2009

Waldherr, S. ; Hasenauer, J. ; Allgöwer, F.

Estimation of biochemical network parameter distributions in cell populations.

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Friedel, C.C. ; Krumsiek, J. ; Zimmer, R.

Bootstrapping the interactome: Unsupervised identification of protein complexes in yeast.

Lecture Notes Comp. Sci. 4955, 3-16 (2009)

Colomé-Tatché, M.

Two-component repulsive Fermi gases with population imbalance in elongated harmonic traps.

Phys. Rev. A 78:033612 (2008)

Begemann, M. ; Sargin, D. ; Rossner, M.J. ; Bartels, C. ; Theis, F.J. ; Wichert, S.P. ; Stender, N. ; Fischer, B. ; Sperling, S. ; Stawicki, S. ; Wiedl, A. ; Falkai, P. ; Nave, K.A. ; Ehrenreich, H.

Episode-specific differential gene expression of peripheral blood mononuclear cells in rapid cycling supports novel treatment approaches.

Mol. Med. 14, 546-552 (2008)

Adamcio, B. ; Sargin, D. ; Stradomska, A. ; Medrihan, L. ; Gertler, C. ; Theis, F.J. ; Zhang, M. ; Müller, M. ; Hassouna, I. ; Hannke, K. ; Sperling, S. ; Radyushkin, K. ; El-Kordi, A. ; Schulze, L. ; Ronnenberg, A. ; Wolf, F. ; Brose, N. ; Rhee, J.S. ; Zhang, W. ; Ehrenreich, H.

Erythropoietin enhances hippocampal long-term potentiation and memory.

BMC Biol. 6:37 (2008)

Lutter, D. ; Ugocsai, P. ; Grandl, M. ; Orso, E. ; Theis, F.J. ; Lang, E.W. ; Schmitz, G.

Analyzing M-CSF dependent monocyte/macrophage differentiation: expression modes and meta-modes derived from an independent component analysis.

BMC Bioinformatics 9:100 (2008)

Zieker, D. ; Königsrainer, I. ; Traub, F. ; Nieselt, K. ; Knapp, B. ; Schillinger, C. ; Stirnkorb, C. ; Fend, F. ; Northoff, H. ; Kupka, S. ; Brücher, B.L. ; Königsrainer, A.

PGK1 a potential marker for peritoneal dissemination in gastric cancer.

Cell. Physiol. Biochem. 21, 429-436 (2008)

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A robust model for spatiotemporal dependencies.

Neurocomp. 71, 2209-2216 (2008)

Treu, G. ; Fuchs, F. ; Dargatz, C.

Implicit authorization for social location disclosure.

J. Software 3, 26 (2008)

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ProCope - protein complex prediction and evaluation.

Bioinformatics 24, 2115-2116 (2008)

Aberer, A.

Species-specific microRNA regulatory networks.

München, Technische Universität & Ludwig-Maximilians-Universität, Fakultät für Informatik, Bachelor-Thesis, 2008, 47 S.

Gutch, H.W. ; Theis, F.J.

Independent subspace analysis is unique, given irreducibility.

Lecture Notes Comp. Sci. 4666, 49-56 (2007)

Kawanabe, M. ; Theis, F.J.

Joint low-rank approximation for extracting non-Gaussian subspaces.

Signal Process. 87, 1890-1903 (2007)

Theis, F.J. ; Kawanabe, M.

Colored subspace analysis.

Lecture Notes Comp. Sci. 4666, 121-128 (2007)

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Robust sparse component analysis based on a generalized Hough transform.

EURASIP J. Adv. Signal Process. 2007:052105 (2007)

Marr, C. ; Müller-Linow, M. ; Hütt, M.-T.

Regularizing capacity of metabolic networks.

Phys. Rev. E 75:041917 (2007)

Treu, G. ; Fuchs, F. ; Dargatz, C.

Implicit authorization for accessing location data in a social context.

In: Proceedings (Proceedings of the 2nd International Conference on Availability, Reliability and Security, ARES 2007, 10-13 April 2007, Vienna). 2007. 263-270

Drechsler, F.

Wavelet-sets and reflection groups.

München, Technische Universität, Fakultät für Mathematik, Diplom-Arbeit, 2007, 52 S.

Marr, C. ; Hütt, M.-T.

Phys. Lett. A 349, 302-305 (2006)

Dargatz, C.

A diffusion approximation for an epidemic model.

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Dargatz, C. ; Georgescu, V. ; Held, L.

Stochastic modelling of the spatial spread of influenza in Germany.

Austrian J. Stat. 35, 5-20 (2006)

Marr, C. ; Hütt, M.-T.