institute of bioinformatics and systems biology / mips

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2009

  1. Altmaier E, Kastenmueller G, Roemisch-Margl W, Thorand B, Weinberger KM,
    Adamski J, Illig T, Doering A, Suhre K. 
    Variation in the human lipidome associated with coffee consumption as revealed
    by quantitative targeted metabolomics      
    Mol Nutr Food Res 8(3):1193-7, 2009. 
    PMID: 19810022
  2. Antonov AV, Dietmann S, Wong P, Rodchenkov I, Mewes HW. 
    PLIPS, an Automatically Collected Database of Protein Lists Reported by Proteomics Studies 
    J Proteome Res 8(3):1193-7, 2009. 
    PMID: 19216535
  3. Antonov AV, Dietmann S, Wong P, Mewes HW. 
    TICL – a web tool for network-based interpretation of compound lists inferred by high-throughput metabolomics 
    FEBS Journal 276(7):2084-2094, 2009. 
  4. Antonov AV, Dietmann S, Rodchenkov I, Mewes HW. 
    PPI spider: A tool for the interpretation of proteomics data in the context of protein-protein interaction networks. 
    Proteomics 9(10):2740-9, 2009. 
    PMID: 19405022
  5. Antonov AV, Dietmann S, Wong P, Lutter D, Mewes HW. 
    GeneSet2miRNA: finding the signature of cooperative miRNA activities in the gene lists 
    Nucleic Acids Res 37(Web Server issue):W323-8, 2009. 
    PMID: 19420064
  6. Antranikian G, Ruepp A, Gordon PM, Ballschmiter M, Zibat A, Stark M, Sensen CW, Frishman D, Liebl W, Klenk HP. 
    Rapid access to genes of biotechnologically useful enzymes by partial genome sequencing: the thermoalkaliphile Anaerobranca gottschalkii 
    J Mol Microbiol Biotechnol 16(1-2):81-90, 2009. 
    PMID: 18957864
  7. Apweiler R, Aslanidis C, Deufel T, Gerstner A, Hansen J, Hochstrasser D, Kellner R, Kubicek M, Lottspeich F, Maser E, Mewes HW, Meyer HE, Muellner S, Mutter W, Neumaier M, Nollau P, Nothwang HG, Ponten F, Radbruch A, Reinert K, Rothe G, Stockinger H, Tarnok A, Taussig MJ, Thiel A, Thiery J, Ueffing M, Valet G, Vandekerckhove J, Verhuven W, Wagener C, Wagner O, Schmitz G. 
    Approaching clinical proteomics: current state and future fields of application in fluid proteomics 
    Clin Chem Lab Med 47(6):724-44, 2009. 
    PMID: 19527139
  8. Arnold R, Brandmaier S, Kleine F, Tischler P, Heinz E, Behrens S, Niinikoski A, Mewes HW, Horn M, Rattei T. 
    Sequence-Based Prediction of Type III Secreted Proteins 
    Plos Pathog 5(4): e1000376, 2009. 
    PMID: 19390696
  9. Barnickel T, Weston J, Collobert R, Mewes HW, Stümpflen V. 
    Large scale application of neural network based semantic role labeling for automated relation extraction from biomedical texts
    PLoS One 4(7):e6393, 2009. 
    PMID: 19636432
  10. Blöchl F, Theis FJ. 
    Estimating Hidden Influences in Metabolic and Gene Regulatory Networks
    Lecture Notes in Computer Science, Independent Component Analysis and Signal Separation, 387-394, 2009.
  11. Dietmann S, Georgii E, Antonov A, Tsuda K, Mewes HW.
    The DICS repository: module-assisted analysis of disease-related gene lists 
    Bioinformatics 25(6):830-1, 2009. 
    PMID: 19176557
  12. Donaire L, Wang Y, Gonzalez-Ibeas D, Mayer KF, Aranda MA, Llave C.
    Deep-sequencing of plant viral small RNAs reveals effective and widespread targeting of viral genomes
    Virology epub, 2009. 
    PMID: 19665162
  13. Fritzmann J, Morkel M, Besser D, Budczies J, Kosel F, Brembeck FH, Stein U, Fichtner I, Schlag PM, Birchmeier W.
    A Colorectal Cancer Expression Profile that Includes Transforming Growth Factor ss Inhibitor BAMBI Predicts Metastatic Potential. 
    Gastroenterology epub, 2009. 
    PMID: 19328798
  14. Georgii E, Dietmann S, Uno T, Pagel P, Tsuda K.
    Enumeration of Condition-Dependent Dense Modules in Protein Interaction Networks 
    Bioinformatics 25(7):933-40, 2009. 
    PMID: 19213739
  15. Gruber P, Meyer-Bäse A, Foo S, Theis FJ.
    ICA, kernel methods and nonnegativity: New paradigms for dynamical component analysis of fMRI data
    Engineering Applications of Artificial Intelligence, 22(4-5):497-504, 2009. 
  16. Hackenberg M, Sturm M, Langenberger D, Falcón-Pérez JM and Aransay AM.
    miRanalyzer: a microRNA detection and analysis tool for next-generation sequencing experiments 
    Nucleic Acids Res 37(Web Server issue):W68-76, 2009.
  17. Ilyinskii PO, Schmidt T, Lukashev D, Meriin AB, Thoidis G, Frishman D, Shneider AM.
    Importance of mRNA Secondary Structural Elements for the Expression of Influenza Virus Genes
    OMICS 13(5):421-30, 2009 
    PMID: 19594376
  18. Kastenmüller G, Schenk ME, Gasteiger J, Mewes HW.
    Uncovering metabolic pathways relevant to phenotypic traits of microbial genomes 
    Genome Biol 10:R28, 2009. 
  19. Kasuga T, Mannhaupt G, Glass NL.
    Relationship between phylogenetic distribution and genomic features in Neurospora crassa 
    PLoS ONE 4(4):e5286, 2009. 
    PMID: 19461939
  20. Klamt S, Haus UU, Theis F.
    Hypergraphs and cellular networks 
    PLoS Comput Biol 5(5):e1000385, 2009. 
    PMID: 19478865
  21. Loewenstein Y, Raimondo D, Redfern O, Watson J, Frishman D, Linial M, Orengo C, Thornton J, Tramontano A .
    Protein function annotation by homology-based inference 
    Genome Biol 10:207, 2009. 
  22. Lutter D, Langmann T, Ugocsai P, Moehle C, Seibold E, Splettstoesser WD, Gruber P, Lang EW, Schmitz G .
    Analyzing time-dependent microarray data using independent component analysis derived expression modes from human macrophages infected with F. tularensis holartica 
    J Bio Informatics 42:605-611, 2009. 
  23. Mannhold R, Poda GI, Ostermann C, Tetko IV. 
    Calculation of molecular lipophilicity: State-of-the-art and comparison of log P methods on more than 96,000 compounds 
    J Pharm Sci 98(3):861-93, 2009. 
    PMID: 18683876
  24. Marr C, Huett MT. 
    Outer-totalistic cellular automata on graphs
    Physics Letters A, 373:546–549, 2009.
  25. Müller LA, Lankhorst RK, Tanksley SD, Giovannoni JJ, White R, Vrebalov J, Fei Z, van Eck J, Buels R, Mills AA, Menda N, Tecle IY, Bombarely A, Stack S, Royer SM, Chang S, Shearer LA, Kim BD, Jo S, Hur C, Choi D, Li C, Zhao J, Jiang H, Geng Y, Dai Y, Fan H, Chen J, Lu F, Shi J, Sun S, Chen J, Yang X, Lu C, Chen M, Cheng Z, Li C, Ling H, Xue Y, Wang Y, Seymour GB, Bishop GJ, Bryan G, Rogers J, Sims S, Butcher S, Buchan D, Abbott J, Beasley H, Nicholson C, Riddle C, Humphray S, McLaren K, Mathur S, Vyas S, Solanke AU, Kumar R, Gupta V, Sharma AK, Khurana P, Khurana JP, Tyagi A, Sarita , Chowdhury P, Shridhar S, Chattopadhyay D, Pandit A, Singh P, Kumar A, Dixit R, Singh A, Praveen S, Dalal V, Yadav M, Ghazi IA, Gaikwad K, Sharma TR, Mohapatra T, Singh NK, Szinay D, Jong HD, Peters S, Staverenvan Staveren M, Datema E, Fiers MW, Hamvan Ham RC, Lindhout P, Philippot M, Frasse P, Regad F, Zouine M, Bouzayen M, Asamizu E, Sato S, Fukuoka H, Tabata S, Shibata D, Botella MA, Perez-Alonso M, Fernandez-Pedrosa V, Osorio S, Mico A, Granell A, Zhang Z, He J, Huang S, Du Y, Qu D, Liu L, Liu D, Wang J, Ye Z, Yang W, Wang G, Vezzi A, Todesco S, Valle G, Falcone G, Pietrella M, Giulianovan Giuliano , Grandillovan Grandillo , Traini A, D'Agostino N, Chiusano ML, Ercolano M, Barone A, Frusciante L, Schoof H, Jöcker A, Bruggmann R, Spannagl M, Mayer KFX, Guigó R, Camara F, Rombauts S, Fawcett JA, Peer YVD, Knapp S, and DZ, Stiekema W. 
    A Snapshot of the Emerging Tomato Genome Sequence
    The Plant Genome 2(1):78-92, 2009.
  26. Mayer KF, Taudien S, Martis M, Simkova H, Suchankova P, Gundlach H, Wicker T, Petzold A, Felder M, Steuernagel B, Scholz U, Graner A, Platzer M, Dolezel J, Stein N. 
    Gene content and virtual gene order of barley chromosome 1H
    Plant Physiol 151(2):496-505, 2009. 
    PMID: 19692534
  27. Neher RA, Mitkovski M, Kirchhoff F, Neher E, Theis FJ, Zeug A. 
    Blind source separation techniques for the decomposition of multiply labeled fluorescence images 
    Biophys J 96(9):3791-800, 2009. 
    PMID: 19413985
  28. Paterson AH, Bowers JE, Bruggmann R, Dubchak I, Grimwood J, Gundlach H, Haberer G, Hellsten U, Mitros T, Poliakov A, Schmutz J, Spannagl M, Tang H, Wang X, Wicker T, Bharti AK, Chapman J, Feltus FA, Gowik U, Grigoriev IV, Lyons E, Maher CA, Martis M, Narechania A, Otillar RP, Penning BW, Salamov AA, Wang Y, Zhang L, Carpita NC, Freeling M, Gingle AR, Hash CT, Keller B, Klein P, Kresovich S, McCann MC, Ming R, Peterson DG, Mehboob-ur-Rahman, Ware D, Westhoff P, Mayer KFX, Messing J, Rokhsar DS.
    The Sorghum bicolor genome and the diversification of grasses 
    Nature 457: 551-556, 2009. 
    PMID: 19189423
  29. Sigurdardottir AG, Arnorsdottir A, Thorbjarnardottir SH, Eggertsson G, Suhre K, Kristjansson M. 
    Characteristics of mutants designed to incorporate a new ion pair into the structure of a cold adapted subtilisin-like serine proteinase 
    Biochim Biophys Acta 1794(3):512-518, 2009. 
    PMID: 19100869
  30. Schmidt T, Mewes HW, Stuempflen V. 
    A novel putative miRNA target enhancer signal 
    PLoS One 4(7):e6473, 2009. 
    PMID: 19649282
  31. Steuernagel B, Taudien S, Gundlach H, Seidel M, Ariyadasa R, Schulte D,Petzold A, Felder M, Graner A, Scholz U, Mayer KFX, Platzer M, Stein N. 
    De novo 454 sequencing of barcoded BAC pools for comprehensive gene survey and genome analysis in the complex genome of barley
    BMC Genomics 10, 547, 2009. 
    PMID: 19930547
  32. Suhre K, Geiger C. 
    Eine genomweite Assoziationsstudie mit Stoffwechselprodukten 
    BIOspektrum 03.09, 263-265, 2009. 
  33. Tetko IV, Poda GI, Ostermann C, Mannhold R. 
    Accurate In Silico log P Predictions: One Can't Embrace the Unembraceable
    QSAR & Combinatorial Science, 28(8):845-849, 2009. 
    DOI: 10.1002/qsar.200960003
  34. Tetko IV, Poda GI, Ostermann C, Mannhold R. 
    Large-Scale Evaluation of log P Predictors: Local Corrections May Compensate Insufficient Accuracy and Need of Experimentally Testing Every Other Compound
    Chemistry & Biodiversity, 6(11):1837 - 1844, 2009. 
    DOI: 10.1002/cbdv.200900075
  35. Tian F, Razansky D, Estrada GG, Semmler-Behnke M, Beyerle A, Kreyling W, Ntziachristos V, Stoeger T. 
    Surface modification and size dependence in particle translocation during early embryonic development 
    Inhal Toxicol 21(S1):92-96, 2009. 
    PMID: 19558239
  36. Tian F, Prina-Mello A, Estrada G, Beyerle A, Moeller W, Schulz H, Kreyling W, Stoeger T. 
    Macrophage cellular adaptation, localization and imaging of different size polystyrene particles
    Nano Biomedicine and Engineering 1(1): 13-26, 2009. 
    PMID: 19558239
  37. Tian F, Prina-Mello A, Estrada GG, Beyerle A, Kreyling W, Stoeger T. 
    Cell shape imaging analysis: A fast and reliable technique for the investigation of internalised carbon nanotubes in flat macrophages
    Journal of Physics  Conference Series, 151, 012033, 2009.
  38. Theis FJ, Neher R, Zeug A.
    Blind Blind Decomposition of Spectral Imaging Microscopy: A Study on Artificial and Real Test Data
    Lecture Notes in Computer Science, T. Adali et al. (Eds.): ICA 2009. 
  39. Varnek A, Gaudin C, Marcou G, Baskin I, Pandey AK, Tetko IV. 
    Inductive Transfer of Knowledge: Application of Multi-Task Learning and Feature Net Approaches to Model Tissue-Air Partition Coefficients 
    J Chem Inf Model 49(1):133-144, 2009. 
    PMID: 19125628
  40. Vollmeister E, Haag C, Zarnack K, Baumann S, König J, Mannhaupt G, Feldbrügge M. 
    Tandem KH domains of Khd4 recognize AUACCC and are essential for regulation of morphology as well as pathogenicity in Ustilago maydis
    RNA epub, 2009. 
    PMID: 19854870
  41. Waegele B, Dunger-Kaltenbach I, Fobo G, Montrone C, Mewes HW, Ruepp A. 
    CRONOS: the cross-reference navigation server 
    Bioinformatics 25(1):141-143, 2009. 
    PMID: 19010804
  42. Walter MC, Rattei T, Arnold R, Güldener U, Münsterkötter M, Nenova K,Kastenmüller G, Tischler P, Wölling A, Volz A, Pongratz N, Jost R, Mewes HW, Frishman D. 
    PEDANT covers all complete RefSeq genomes 
    Nuc Acids Res 37(Database issue):D408-11, 2009. 
    PMID: 18940859
  43. Wang X, Haberer G and Mayer KFX. 
    Discovery of cis elements between Sorghum and Rice using co-expression and evolutionary conservation 
    BMC Genomics 10:284, 2009.
  44. Webb KJ, Norton WH, Trumbach D, Meijer AH, Ninkovic J, Topp S, Heck D, Marr
    C, Wurst W, Theis FJ, Spaink HP, Bally-Cuif L. 
    Zebrafish reward mutants reveal novel transcripts mediating the behavioral effects of amphetamine.
    Genome Biol 10(7):R81, 2009 
    PMID: 19646228
  45. Wittmann DM, Bloechl F, Truembach D, Wurst W, Prakash N, Theis FJ. 
    Spatial analysis of expression patterns provides insights into gene 
    regulation at the mid-hindbrain boundary    .
    Plos Comp Biol 5(11):e1000569, 2009.
    PMID: 19936059
  46. Wittmann DM, Krumsiek J, Saez-Rodriguez J, Lauffenburger DA, Klamt S, Theis FJ. 
    Transforming Boolean models to continuous models: methodology and application to T-cell receptor signaling.
    BMC Syst Biol 3(1):98, 2009 
    PMID: 19785753
  47. Wittmann DM, Schmidl D, Bloechl F, Theis FJ.
    Reconstruction of graphs based on random walks,
    Theoretical Computer Science 410(38-40):3826-3838, 2009.
  48. Worden AZ, Lee JH, Mock T, Rouze P, Simmons MP, Aerts AL, Allen AE, Cuvelier ML, Derelle E, Everett MV, Foulon E, Grimwood J, Gundlach H, Henrissat B, Napoli C, McDonald SM, Parker MS, Rombauts S, Salamov A, Von Dassow P, Badger JH, Coutinho PM, Demir E, Dubchak I, Gentemann C, Eikrem W, Gready JE, John U, Lanier W, Lindquist EA, Lucas S, Mayer KF, Moreau H, Not F, Otillar R, Panaud O, Pangilinan J, Paulsen I, Piegu B, Poliakov A, Robbens S, Schmutz J, Toulza E, Wyss T, Zelensky A, Zhou K, Armbrust EV, Bhattacharya D, Goodenough UW, Van de Peer Y, Grigoriev IV. 
    Green evolution and dynamic adaptations revealed by genomes of the marine picoeukaryotes Micromonas 
    Science 324(5924):268-72, 2009. 
    PMID: 19359590