institute of bioinformatics and systems biology / mips

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2010

  1. Alphonse S, Durand E, Douzi B, Waegele B, Darbon H, Filloux A, Voulhoux R, Bernard C. 
    Structure of the Pseudomonas aeruginosa XcpT pseudopilin, a major component of the type II secretion system
    J Struct Biol 169(1):75-80, 2010. 
    PMID: 19747550
  2. Altmaier E, Kastenmüller G, Römisch-Margl W, Thorand B, Weinberger KM, Illig T, Adamski J, Döring A, Suhre K. 
    Questionnaire-based self-reported nutrition habits associate with serum metabolism as revealed by quantitative targeted metabolomics
    Eur J Epidemiol epub, 2010. 
    PMID: 21116839
  3. Antonov A. 
    Mining protein lists from proteomics studies: applications for drug discovery
    Exp Opin Drug Dis 5(4):323-331, 2010. 
    DOI: 10.1517/17460441003716796
  4. Antonov A, Schmidt EE, Dietmann S, Krestyaninova M, Hermjakob H
    R spider: a network-based analysis of gene lists by combining signaling and metabolic pathways from Reactome and KEGG databases
    Nuc Acids Res (Web Server Issue), 38 Suppl:W78-83, 2010. 
    PMID: 20519200
  5. Arnold R, Jehl A, Rattei T.
    Targeting effectors: the molecular recognition of Type III secreted proteins.
    Microbes Infect. 2010 May;12(5):346-58. Epub 2010 Feb 21.
    PMID: 20178857
  6. Bao C, Tian F, Estrada G. 
    Improved visualisation of internalised carbon nanotubes by maximising cell spreading on nanostructured substrates
    Nano Biomedicine and Engineering,  2(4): 201-210, 2010.
    DOI: 10.5101/nbe.v2i4.p201-210
  7. Bastow R, Beynon J, Estelle M, Friesner J, Grotewold E, Lavagi I, Lindsey K, Meyers B, Provart N, Benfey P, Birney E, Braun P, Brendel V, Buell R, Caccamo M, Carrington J, Cherry M, Ecker J, Eppig J, Forster M, Gutiérrez R, Hilson P, Huala E, Katari M, Kersey P, Kudla J, Ma H, Matsui M, Matthews K, May S, Mayer K, Millar A, Millar H, Mjolsness E, Mockler T, Nikolau B, Nordborg M, Rawlings C, Schofield P, Schoof H, Schroeder JI, Sen TZ, Stanzione D, Town C, Toyoda T, Vision T, Walsh S, Wang X, Ware D, Weckwerth W, Yang W.
    An international bioinformatics infrastructure to underpin the Arabidopsis community.
    Plant Cell. 2010 Aug;22(8):2530-6. Epub 2010 Aug 31.
    PMID: 20807877
  8. Bhaskar S, Tian F, Stoeger T, Kreyling W, de la Fuente JM, Grazú V, Borm P, Estrada G, Ntziachristos V, Razansky D. 
    Multifunctional Nanocarriers for diagnostics, drug delivery and targeted treatment across blood-brain barrier: perspectives on tracking and neuroimaging
    Part Fibre Toxicol 7:3, 2010. 
    PMID: 20199661
  9. Blöchl F, Hartsperger ML, Stümpflen V, Theis FJ. 
    Uncovering the structure of heterogeneous biological data: fuzzy graph partitioning in the k-partite setting
    Lecture Notes in Informatics Edts. Schomburg D, Grote A, GCB, 2010.
  10. Büttner F, Ellwanger D, Mewes HW, Stümpflen V. 
    Large scale analysis reveals novel insights in the characteristics of miRNA targeting
    Lecture Notes in Informatics Edts. Schomburg D, Grote A, GCB, 2010.
  11. Das M, Reichman JR, Haberer G, Welzl G, Aceituno FF, Mader MT, Watrud LS,
    Pfleeger TG, Gutierrez RA, Schaeffner AR, Olszyk DM.
    A composite transcriptional signature differentiates responses towards closely
    related herbicides in Arabidopsis thaliana and Brassica napus
    Plant Mol Biol 72(4-5):545-56, 2010. 
    PMID: 20043233
  12. Dietmann S, Lee W, Wong P, Rodchenkov I, Antonov AV.
    CCancer: a bird’s eye view on gene lists reported in cancer-related studies
    Nuc Acids Res (Web Server Issue), epub, 2010. 
    PMID: 20529879
  13. Fuchs H, Durner VG, Adler T, Aguilar-Pimentel JA, Becker L, Calzada-Wack J, Da Silva-Buttkus P, Neff F, Götz A, Hans W, Hölter SM, Horsch M, Kastenmüller G, Kemter E, Lengger C, Maier H, Matloka M, Möller G, Naton B, Prehn C, Puk O, Rácz I, Rathkolb B, Römisch-Margl W, Rozman J, Wang-Sattler R, Schrewe A, Stöger C, Tost M, Adamski J, Aigner B, Beckers J, Behrendt H, Busch DH, Esposito I, Graw J, Illig T, Ivandic B, Klingenspor M, Klopstock T, Kremmer E, Mempe M, Neschen S, Ollert M, Schulz H, Suhre K, Wolf E, Wurst W, Zimmer A, Hrabě de Angelis M.
    Mouse Phenotyping
    Methods  epub, 2010. 
    PMID: 20708688
  14. Greeff M, Schmid-Hempel P,
    Influence of co-evolution with a parasite, Nosema whitei, and population
    size on recombination rates and fitness in the red flour beetle, Tribolium
    castaneum
    Genetica epub, 2010. 
    PMID: 20383780
  15. Grisel N, Zoller S, Kunzli-Gontarczyk M, Lampart T, Munsterkotter M, Brunner
    I, Bovet L, Metraux JP, Sperisen C.
    Transcriptome responses to aluminum stress in roots of aspen (Populus tremula)
    BMC Plant Biol 10(1):185, 2010. 
    PMID: 20727216
  16. Haack TB, Danhauser K, Haberberger B, Hoser J, Strecker V, Boehm D, Uziel G,
    Lamantea E, Invernizzi F, Poulton J, Rolinski B, Iuso A, Biskup S, Schmidt T,
    Mewes HW, Wittig I, Meitinger T, Zeviani M, Prokisch H.
    Exome sequencing identifies ACAD9 mutations as a cause of complex I deficiency
    Nat Genet in press, 2010. 
    PMID: 21057504
  17. Hartsperger ML, Blöchl F, Stümpflen V, Theis FJ
    Structuring heterogeneous biological information using fuzzy clustering of k-partite graphs  
    BMC Bioinformatics 11:522, 2010. 
    DOI: 10.1186/1471-2105-11-522
  18. Hartsperger ML,  Strache R, Stümpflen V
    HiNO: An Approach for Inferring Hierarchical Organization from Regulatory Networks  
    PLOS One 5(11): e13698, 2010.
    DOI: 10.1371/journal.pone.0013698.
  19. Illig T, Gieger C, Zhai G, Romisch-Margl W, Wang-Sattler R, Prehn C,
    Altmaier E, Kastenmueller G, Kato BS, Mewes HW, Meitinger T, de Angelis MH,
    Kronenberg F, Soranzo N, Wichmann HE, Spector TD, Adamski J, Suhre K. 
    A genome-wide perspective of genetic variation in human metabolism  
    Nat Genet 42(2):137-41, 2010. 
    PMID: 20037589
  20. Konopka W, Kiryk A, Novak M, Herwerth M, Parkitna JR, Wawrzyniak M, Kowarsch A, Michaluk P, Dzwonek J, Arnsperger T, Wilczynski G, Merkenschlager M, Theis FJ, Köhr G, Kaczmarek L, Schütz G.. 
    MicroRNA Loss Enhances Learning and Memory in Mice
    J Neurosci 30(44):14835-14842, 2010. 
    PMID: 21048142
  21. Kowarsch A, Marr C, Schmidl D, Ruepp A, Theis FJ. 
    Tissue-specific target analysis of disease-associated micrornas in human signaling pathways
     Plos ONE 5(6): e11154, 2010. 
    PMID: 20614023
  22. Kowarsch A, Fuchs A, Frishman D, Pagel P. 
    Correlated mutations: a hallmark of phenotypic amino Acid substitutions
    PLoS Comput Biol 6(9), 2010. 
    PMID: 20862353
  23. Kowarsch A, Blochl F, Bohl S, Saile M, Gretz N, Klingmuller U, Theis FJ. 
    Knowledge-based matrix factorization temporally resolves the cellular responses to IL-6 stimulation
    BMC Bioinf 11:585, 2010. 
    PMID: 21118515
  24. Kreuzpointner L, Simon P, Theis FJ. 
    The a(d) coefficient as a descriptive measure of the within-group agreement of ratings
    Br J Math Stat Psychol 63(Pt 2):341-60, 2010. 
    PMID: 20298645
  25. Krumsiek J, Poelsterl S, Wittmann DM, Theis FJ. 
    Odefy - From discrete to continuous models
    BMC Bioinf. 11:233, 2010.
    PMID: 20459647
  26. Lang S, Gruber K, Mihajlovic S, Arnold R, Gruber CJ, Steinlechner S, Jehl MA, Rattei T, Fröhlich KU, Zechner EL.
    Molecular recognition determinants for type IV secretion of diverse families of conjugative relaxases.
    Mol Microbiol. 2010 Dec;78(6):1539-55. doi: 10.1111/j.1365-2958.2010.07423.x. Epub 2010 Oct 15.
    PMID: 21143323
  27. Liebovitch LS, Shehadeh LA, Jirsa VK, Hütt MT, Marr C. 
    Determining the Properties of Gene Regulatory Networks from Expression Data
    Handbook of Research on Computational Methodologies in Gene Regulatory Networks Medical Information Science Reference (IBI Global), 2010.
  28. Lucio M, Fekete A, Weigert C, Wägele B, Zhao X, Chen J, Fritsche A, Häring HU, Schleicher ED, Xu G, Schmitt-Kopplin P, Lehmann R. 
    Insulin sensitivity is reflected by characteristic metabolic fingerprints--a Fourier transform mass spectrometric non-targeted metabolomics approach.
    PLoS One 5(11): e13953. 2010. 
    doi:10.1371/journal.pone.0013953,
  29. Lutter D, Marr C, Krumsiek J, Lang EW, Theis FJ. 
    Intronic microRNAs support their host genes by mediating synergistic and antagonistic regulatory effects
    BMC Genomics 11:224, 2010. 
    PMID: 20370903
  30. Marr C, Theis FJ, Liebovitch LS, and Hütt MT. 
    Patterns of Subnet Usage Reveal Distinct Scales of Regulation in the Transcriptional Regulatory Network of Escherichia coli
    Plos Comp Biol 6: e1000836, 2010. 
    PMID: 20617198
  31. Mewes HW, Wachinger B, Stümpflen V. 
    Perspectives of a Systems Biology of the Synapse: How to Transform an Indefinite Data Space into a Model
    Pharmacopsychiatry 43(S1): S2-S8, 2010. 
    PMID: 20480444
  32. Meyer-Baese A, Theis F, Emmett MR. 
    Robust Stability Analysis and Design Under Consideration of Multiple Feedback Loops of the Tryptophan Regulatory Network of Escherichia coli
    Adv Exp Med Biol 680:189-97, 2010. 
    PMID: 20865501
  33. Raia V, Schilling M, Böhm M, Hahn B, Kowarsch A, Raue A, Sticht C, Bohl S, Saile M, Möller P, Gretz N, Timmer J, Theis F, Lehmann WD, Lichter P, Klingmüller U. 
    Dynamic Mathematical Modeling of IL13-induced Signaling in Hodgkin and Primary Mediastinal B-cell Lymphoma Allows Prediction of Therapeutic Targets  
    Cancer Res epub, 2010. 
    PMID: 21127196
  34. Rattei T, Tischler P, Götz S, Jehl MA, Hoser J, Arnold R, Conesa A, Mewes HW. 
    SIMAP, a comprehensive database of pre-calculated protein sequence 
    similarities, domains, annotations and clusters      
    Nucleic Acids Res 38(Database issue), 2010. 
    PMID: 19906725
  35. Ruepp A, Waegele B, Lechner M, Brauner B, Dunger-Kaltenbach I, Fobo G, Frishman G, Montrone C, Mewes HW. 
    CORUM: the comprehensive resource of mammalian protein complexes - 2009 
    Nucleic Acids Res 38(Database issue), 2010. 
    PMID: 19884131
  36. Ruepp A, Kowarsch A, Schmidl D, Bruggenthin F, Brauner B, Dunger I, Fobo G, Frishman G, Montrone C, Theis FJ. 
    PhenomiR: a knowledgebase for microRNA expression in diseases and biological processe
    Genome Biology 11: R6, 2010. 
    PMID: 20089154
  37. Rupp M, Schneider G. 
    Graph kernels for molecular similarity
    Molecular Informatics 29(4), 266--273, 2010. 
    DOI:10.1002/minf.200900080
  38. Rupp M, Körner R, Tetko IV. 
    Estimation of Acid Dissociation Constants Using Graph Kernels
    Molecular Informatics 29(10):731–740, 2010. 
    DOI:10.1002/minf.201000072
  39. Schallau A, Arzenton F, Johnston AJ, Haehnel U, Koszegi D, Blattner F, Altschmied L, Haberer G, Barcaccia G, Baeumlein H. 
    Identification and genetic analysis of the APOSPORY locus in Hypericum perforatum L.
    Plant J. epub, 2010 
    PMID: 20202173
  40. Schinko T, Berger H, Lee W, Gallmetzer A, Pirker K, Pachlinger R, Buchner I, Reichenauer T, Güldener U, Strauss J. 
    Transcriptome analysis of nitrate assimilation in Aspergillus nidulans reveals connections to nitric oxide metabolism.
    Mol Microbiol. 78(3):720-38, 2010 
    PMID: 20969648
  41. Schirawski J, Mannhaupt G, Münch K, Brefort T, Schipper K, Doehlemann G, Di Stasio M, Rössel N, Mendoza-Mendoza A, Pester D, Müller O, Winterberg B,
    Meyer E, Ghareeb H, Wollenberg T, Münsterkötter M, Wong P, Walter M, Stukenbrock E, Güldener U, Kahmann R 
    Pathogenicity Determinants in Smut Fungi Revealed by Genome Comparison
    Science 330(6010):1546-1548, 2010.
    DOI: 10.1126/science.1195330
  42. Smialowski P, Frishman D, Kramer S. 
    Pitfalls of supervised feature selection  
    Bioinformatics 26(3):440-3, 2010
    PMID: 19880370
  43. Smialowski P, Frishman D. 
    Protein Crystallizability  
    Methods in Molecular Biology, ed.: Oliviero Varugo and Frank Eisenhaber, Humana Press, Vienna, 609:385-400.
    PMID: 20221931
  44. Smialowski P, Pagel P, Wong P, Brauner B, Dunger I, Fobo G, Frishman G, Montrone C, Rattei T, Frishman D, Ruepp A. 
    The Negatome database a reference set of non-interacting protein pairs  
    Nucleic Acids Res 38(Database issue), 2010. 
    PMID: 19920129
  45. Steri R, Rupp M, Proschak E, Schroeter T, Zettl H, Hansen K, Schwarz O, Müller-Kuhrt L, Müller KR, Schneider G, Schubert-Zsilavecz M. 
    Truxillic acid derivatives act as peroxisome proliferator-activated receptor gamma activators
    Bioorg Med Chem Lett 20(9):2920-3, 2010. 
    PMID: 20347594
  46. Sturm M, Hackenberg M, Langenberger D, Frishman D.
    TargetSpy: a supervised machine learning approach for microRNA target prediction
    BMC Bioinformatics  11:292, 2010. 
    PMID: 20509939
  47. Suhre K, Meisinger C, Döring A, Altmaier E, Belcredi P, Gieger C, Chang D, Milburn MV, Gall WE, Weinberger KM, Mewes HW, Hrabé de Angelis M, Wichmann HE, Kronenberg F, Adamski J, Illig T
    Metabolic Footprint of Diabetes: A Multiplatform Metabolomics Study in an Epidemiological Setting
    PLoS ONE 5(11): e13953, 2010. 
    PMID: 21085649
  48. Sushko I, Novotarskyi S, Körner R, Pandey AK, Kovalishyn VV, Prokopenko VV, Tetko IV. 
    Applicability domain for in silico models to achieve accuracy of experimental measurements
    Journal of Chemometrics 24:3, 202-208, 2010.
    DOI:10.1002/cem.1296.
  49. Sushko I, Novotarskyi S, Körner R, Pandey AK, Cherkasov A, Li J, Gramatica P, Hansen K, Schroeter T, Müller KR, Xi L, Liu H, Yao X, Öberg T, Hormozdiari F, Dao P, Sahinalp C, Todeschini R, Polishchuk P, Artemenko A, Kuz'min V, Martin TM, Young DM, Fourches D, Muratov E, Tropsha A, Baskin I, Horvath D, Marcou G, Muller C, Varnek A, Prokopenko VV, Tetko IV.
    Applicability domains for classification problems: benchmarking of distance to models for ames mutagenicity set
    J Chem Inf Model 50(12):2094-111, 2010.
    PMID: 21033656
  50. The International Brachypodium Initiative. 
    Genome sequencing and analysis of the model grass Brachypodium distachyon
    Nature 463, 763-768, 2010. 
    PMID: 20148030
  51. Theis FJ, Bohl S, Klingmueller U. 
    Theoretical Analysis of Time-to-Peak Responses in Biological Reaction Networks
    Bull Math Biol 463, 763-768, 2010. 
    PMID: 20499193
  52. Thiemann C, Theis F, Grady D, Brune R, Brockmann D. 
    The structure of borders in a small world.
    PLoS One 5(11):e15422, 2010. 
    PMID: 21124970
  53. Weikard R, Altmaier E, Suhre K, Weinberger KM, Hammon HM, Albrecht E,
    Setoguchi K, Takasuga A, Kuehn C. 
    Metabolomic profiles indicate distinct physiological pathways affected by two
    loci with major divergent effect on Bos taurus growth and lipid deposition
     Physiol Genomics epub, 2010. 
    PMID: 20647382
  54. Villa AE, Tetko IV. 
    Cross-frequency coupling in mesiotemporal EEG recordings of epileptic patients
    J Physiol Paris 104(3-4):197-202, 2010. 
    PMID: 19944158
  55. Wittmann DM, Marr C, Theis FJ. 
    Biologically meaningful update rules increase the critical connectivity of
    generalized Kauffman networks
    J Theor Biol 266(3):436-48, 2010. 
    PMID: 20654629
  56. Yu Z, Haberer G, Matthes M, Rattei T, Mayer KF, Gierl A, Torres-Ruiz RA. 
    Impact of natural genetic variation on the transcriptome of autotetraploid
    Arabidopsis thaliana
    Proc Natl Acad Sci U S A. epub, 2010. 
    PMID: 20876110