institute of bioinformatics and systems biology / mips

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. 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
3. 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
4. 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
   
5. 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
6. 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
7. 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
8. Smialowski P, Frishman D, Kramer S.
   Pitfalls of supervised feature selection 
   Bioinformatics 26(3):440-3, 2010
   PMID: 19880370
9. Smialowski P, Frishman D.
   Protein Crystallizability 
   Methods in Molecular Biology, ed.: Oliviero Varugo and Frank Eisenhaber, Humana Press, Vienna, 609:385-400.
   PMID: 20221931
   
10. 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
11. The International Brachypodium Initiative.
    Genome sequencing and analysis of the model grass Brachypodium distachyon
    Nature 463, 763-768, 2010.
    PMID: 20148030
    

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 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.
37. 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.
    
38. 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
39. Villa AE, Tetko IV.
    Cross-frequency coupling in mesiotemporal EEG recordings of epileptic patients
    J Physiol Paris epub, 2009.
    PMID: 19944158
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

2008

1. Altmaier E, Ramsay SL, Graber A, Mewes HW, Weinberger KM, Suhre K.
   Bioinformatics analysis of targeted metabolomics - uncovering old and new tales of diabetic mice under medication
   Endocrinology 149(7):3478-89, 2008.
   PMID: 18372322
2. Antonov AV, Mewes HW.
   Complex phylogenetic profiling reveals fundamental genotype-phenotype associations
   Comput Biol Chem 32(6):412-6, 2008.
   PMID: 18753010
3. Antonov A, Schmidt T, Wang Y, Mewes HW.
   ProfCom: a web tool for profiling the complex functionality of gene groups identified from high-throughput data
   Nuc Acids Res 36(Web Server issue):W347-51, 2008.
   PMID: 18460543
4. Antonov A, Dietmann S, Mewes HW.
   Consecutive KEGG pathway models for the interpretation of high-throughput genomics data
   Lecture Notes in Informatics Edts. Beyer A;Schroeder M, GCB, 2008.
   
5. Antonov A, Dietmann S, Mewes HW.
   KEGG spider: interpretation of genomics data in the context of the global gene metabolic network
   Genome Biology 9(12):R179, 2008.
   
6. Brockmann D and Theis F.
   Money circulation, trackable items, and the emergence of universal human mobility patterns.
   IEEE Pervasive Computing 7(4):28–35, 2008.
   
7. Elstner M, Andreoli C, Ahting U, Tetko I, Klopstock T, Meitinger T, Prokisch H.
   MitoP2: An Integrative Tool for the Analysis of the Mitochondrial Proteome.
   Mol Biotechnol 40(3):306-15, 2008.
   PMID: 18780189
8. Feldbrügge M, Zarnack K, Vollmeister E, Baumann S, Koepke J, König J, Münsterkötter M, Mannhaupt G.
   The posttranscriptional machinery of Ustilago maydis
   Fungal Genet Biol 45 Suppl 1:S40-6, 2008.
   PMID: 18468465
9. Fitzgerald LA, Boucher PT, Yanai-Balser G, Suhre K, Graves MV, Van Etten JL.
   Putative gene promoter sequences in the chlorella viruses
   Virology 380:388-393, 2008.
   PMID: 18768195
   
10. Gieger, C, Geistlinger, L, Altmaier, E, Hrabé de Angelis, M, Kronenberg, F, Meitinger, T, Mewes, HW, Wichmann, HE, Weinberger, KM, Adamski, J, Illig, T, Suhre K
    Genetics Meets Metabolomics: A Genome-Wide Association Study of Metabolite Profiles in Human Serum
    PLoS Genetics 4(11):e1000282, 2008.
    
11. Greiner S, Wang X, Rauwolf U, Silber MV, Mayer K, Meurer J, Haberer G, Herrmann RG.
    The complete nucleotide sequences of the five genetically distinct plastid genomes of Oenothera, subsection Oenothera: I. sequence evaluation and plastome evolution
    Nucleic Acids Res 36(7):2366-78, 2008.
    PMID: 18299283
12. Greiner S, Wang X, Rauwolf U, Silber MV, Mayer K, Meurer J, Haberer G, Herrmann RG.
    The complete nucleotide sequences of the five genetically distinct plastid genomes of Oenothera, subsection Oenothera: II. A microevolutionary view using bioinformatics and formal genetic data
    Mol Biol Evol 25(9):2019-30, 2008.
    PMID: 18614526
13. Grimm M, Stephan R, Iversen C, Manzardo GG, Rattei T, Riedel K,Ruepp A, Frishman D, Lehner A.
    Cellulose as an Extracellular Matrix Component Present in Enterobacter sakazakii Biofilms
    Journal of Food Protection 71(1):13-8, 2008.
    PMID: 18236657
14. Irmler M, Hartl D, Schmidt T, Schuchardt J, Lach C, Meyer HE, Hrabé de Angelis M, Klose J, Beckers J
    An approach to handling and interpretation of ambiguous data in transcriptome and proteome comparisons
    Proteomics 8(6):1165-9, 2008.
    PMID: 18283664
15. Ishihama Y, Schmidt T, Rappsilber J, Mann M, Hartl FU, Kerner MJ, Frishman D.
    Protein abundance profiling of the Escherichia coli cytosol
    BMC Genomics 9:102, 2008.
    PMID: 18304323
16. Karthikeyan M, Krishnan S, Pandey AK, Bender A, Tropsha A.
    Distributed Chemical Computing Using ChemStar: An Open Source Java Remote Method Invocation Architecture Applied to Large Scale Molecular Data from PubChem.
    J Chem Inf Model 48(4):691-703, 2008.
    PMID: 18402434
17. Kastenmüller G, Gasteiger J, Mewes HW.
    An environmental perspective on large-scale genome clustering based on metabolic capabilities.
    Bioinformatics 24(16):i56-62, 2008.
    PMID: 18689840
18. Kuhn KA, Knoll A, Mewes HW, Schwaiger M, Bode A, Broy M, Daniel H, Feussner H, Gradinger R, Hauner H, Höfler H, Holzmann B, Horsch A, Kemper A, Krcmar H, Kochs EF, Lange R, Leidl R, Mansmann U, Mayr EW, Meitinger T, Molls M, Navab N, Nüsslin F, Peschel C, Reiser M, Ring J, Rummeny EJ, Schlichter J, Schmid R, Wichmann E, Ziegler S.
    Informatics and Medicine - From Molecules to Populations.
    Methods Inf Med 47, 2008.
    
19. Loy A, Arnold R, Tischler P, Rattei T, Wagner M, Horn M.
    probeCheck - a central resource for evaluating oligonucleotide probe coverage and specificity.
    Environ Microbiol 10(10):2894-8, 2008.
    PMID: 18647333
20. Marr C, Geertz M, Hütt MT, Muskhelishvili G.
    Dissecting the logical types of network control in gene expression profiles.
    BMC Syst Biol. 2:18, 2008.
    PMID: 18284674
21. Mewes, HW, Dietmann S, Frishman D, Gregory R, Mannhaupt G, Mayer K, Muensterkötter M, Ruepp A, Spannagl M, Stuempflen V, Rattei T.
    MIPS: Analysis and annotation of genome information in 2007.
    Nuc Acids Res. 36(Database issue):D196-201, 2008.
    PMID: 18158298
22. Moes D, Himmelbach A, Korte A, Haberer G, Grill E
    Nuclear localization of the mutant protein phosphatase abi1 is required for insensitivity towards ABA responses in Arabidopsis.
    Plant J. 54(5):806-19, 2008.
    PMID: 18298671
23. Pagel P, Oesterheld M, Tovstukhina O, Strack N, Stümpflen V, Frishman D.
    DIMA 2.0 predicted and known domain interactions.
    Nucleic Acids Res 36(Database issue):D651-5, 2008.
    PMID: 17999995
24. Pfeiffer F, Schuster SC, Broicher A, Falb M, Palm P, Rodewald K, Ruepp A, Soppa J, Tittor J, Oesterhelt D.
    Evolution in the laboratory: the genome of Halobacterium salinarum strain R1 as compared to strain NRC-1
    Genomics 91(4):335-46, 2008.
    PMID: 18313895
25. Rattei T, Tischler P, Arnold R; Hamberger F, Krebs J, Krumsiek J, Wachinger, B, Stuempflen V, Mewes HW.
    SIMAP: structuring the network of protein similarities
    Nuc Acids Res 36(Database issue):D289-92, 2008.
    PMID: 18037617
26. Rensing SA, Lang D, Zimmer AD, Terry A, Salamov A, Shapiro H, Nishiyama T, Perroud PF, Lindquist EA, Kamisugi Y, Tanahashi T, Sakakibara K, Fujita T, Oishi K, Shin-I T, Kuroki Y, Toyoda A, Suzuki Y, Hashimoto SI, Yamaguchi K, Sugano S, Kohara Y, Fujiyama A, Anterola A, Aoki S, Ashton N, Barbazuk WB, Barker E, Bennetzen JL, Blankenship R, Cho SH, Dutcher SK, Estelle M, Fawcett JA, Gundlach H, Hanada K, Heyl A, Hicks KA, Hughes J, Lohr M, Mayer K, Melkozernov A, Murata T, Nelson DR, Pils B, Prigge M, Reiss B, Renner T, Rombauts S, Rushton PJ, Sanderfoot A, Schween G, Shiu SH, Stueber K, Theodoulou FL, Tu H, Van de Peer Y, Verrier PJ, Waters E, Wood A, Yang L, Cove D, Cuming AC, Hasebe M, Lucas S, Mishler BD, Reski R, Grigoriev IV, Quatrano RS, Boore JL.
    The Physcomitrella Genome Reveals Evolutionary Insights into the Conquest of Land by Plants.
    Science 319(5859):64-9, 2008.
    PMID: 18079367
    
27. Ruepp A, Brauner B, Dunger-Kaltenbach I, Frishman G, Montrone C, Stransky M, Wägele B, Schmidt T, Noubibou Doudieu O, Stümpflen V, Mewes HW.
    CORUM: the Comprehensive Resource of Mammalian Protein Complexes
    Nuc Acids Res 36(Database issue):D646-50, 2008.
    PMID: 17965090
    
28. Seong KY, Zhao X, Xu JR, Guldener U, Kistler HC.
    Conidial germination in the filamentous fungus Fusarium graminearum.
    Fungal Genet Biol 45(4):389-99, 2008.
    PMID: 17950638
    
29. Schachtner R, Lutter D, Knollmüller P, Tomé AM, Theis FJ, Schmitz G, Stetter M, Vilda PG, Lang EW.
    Knowledge - based Gene Expression Classification via Matrix Factorization.
    Bioinformatics 24(15):1688-97, 2008.
    PMID: 18535085
    
30. Schmidt, T and Frishman, D.
    Assignment of isochores for all completely sequenced vertebrate genomes using a consensus
    Genome Biol 9(6):R104, 2008.
    PMID: 18590563
31. Suhre K, Schmitt-Kopplin P.
    MassTRIX: Mass TRanslator Into Pathways
    Nuc Acids Res 36(Web Server issue): W481-4, 2008.
    PMID: 18442993
32. Surmeli D, Ratmann O, Mewes HW, Tetko IV.
    FunCat functional inference with belief propagation and feature integration
    Comput Biol Chem 32(5):375-7, 2008.
    PMID: 18684672
33. Tetko IV.
    Internet in Drug Design and Discovery
    The Open Applied Informatics Journal 2(1), 2008.
    
    
34. Tetko IV.
    Associative neural network
    Methods Mol Biol 458:185-202, 2008.
    PMID: 19065811
35. Tetko IV, Jaroszewicz I, Platts JA, Kuduk-Jaworska J.
    Calculation of lipophilicity for Pt(II) complexes: Experimental comparison of several methods
    J Inorg Biochem 102(7):1424-1437, 2008.
    PMID: 18289687
    
36. Tetko IV, Rodchenkov IV, Walter MC, Rattei T, Mewes HW.
    Beyond the "Best" Match: Machine Learning Annotation of Protein Sequences by Integration of Different Sources of Information
    Bioinformatics 24(5):621-8, 2008.
    PMID: 18174184
    
37. Tetko IV, Sushko I, Pandey AK, Zhu H, Tropsha A, Papa E, Öberg T, Todeschini R, Fourches D, Varnek A.
    Critical Assessment of QSAR Models of Environmental Toxicity against Tetrahymena pyriformis: Focusing on Applicability Domain and Overfitting by Variable Selection
    J Chem Inf Model 48(9):1733-1746, 2008.
    PMID: 18729318
    
38. Theis F, Gruber P, Keck I, and Lang E.
    A robust model for spatiotemporal dependencies
    Neurocomputing 71(10-12):2209–2216, 2008.
    
39. The Rice Annotation Project.
    The Rice Annotation Project Database (RAP-DB): 2008 update
    Nucleic Acids Res 36: D1028-D1033, 2008.
    PMID: 18089549
    
40. Tian F, Prina-Mello A, Estrada GG, Beyerle A, Moeller W, Schulz H, Kreyling W, Stoeger T.
    A novel assay for the quantification of internalized nanoparticles in macrophages.
    Nanotoxicology 2(4):232-242, 2008.
    DOI: 10.1080/17435390802504229
    
41. Varnek A, Fourches D, Horvath D, Klimchuk O, Gaudin C, Vayer P, Solov'ev V, Hoonakker F, Tetko IV, Marcou G.
    ISIDA - Platform for Virtual Screening Based on Fragment and Pharmacophoric Descriptors
    Current Computer - Aided Drug Design 4(3), 4191-198, 2008.
    
42. Waegele B, Schmidt T, Mewes HW, Ruepp A.
    OREST: the online resource for EST analysis
    Nucleic Acids Res 36(Web Server issue):W140-4, 2008.
    PMID: 18463135
    
43. Wang-Sattler R, Yu Y, Mittelstrass K, Lattka E, Altmaier E, Gieger C, Ladwig KH, Dahmen N, Weinberger KM, Hao P, Lui L, Li Y, Wichmann HE, Adamski J, Suhre K, Illig, T.
    Metabolic profiling reveals distinct variations linked to nicotine consumption in humans - first results from the KORA Study
    PLoS One 3(12):e3863, 2008.
    
44. Wong P, Frishman D.
    Designability and disease
    Methods Mol Biol 484:491-504, 2008.
    PMID: 18592197
    
45. Wong P, Althammer S, Hildebrand A, Kirschner A, Pagel P, Geissler B, Smialowski P, Bloechl F, Oesterheld M, Schmidt T, Strack N, Theis F, Ruepp A, Frishman D.
    An evolutionary and structural characterization of mammalian protein complex organization
    BMC Genomics 9(1):629, 2008.
    PMID: 19108706
    
46. Zhu H, Tropsha A, Fourches D, Varnek A, Papa E, Gramatica P, Öberg T, Dao P, Cherkasov A, Tetko IV.
    Combinatorial QSAR Modeling of Chemical Toxicants Tested against Tetrahymena pyriformis
    J Chem Inf Model 48(4):766-84, 2008.
    PMID: 18311912
    

2007

1. Antonov,A. and Mewes,H.W.
   Revealing Comprehensive Genotype-Phenotype Associations through Logic Relationships.
   GCB 2007 185-197.
   
2. Artamonova II, Frishman G, Frishman D.
   Applying negative rule mining to improve genome annotation
   BMC Bioinformatics 8(1):261, 2007.
   PMID: 17659089
3. Artamonova II, Gelfand MS.
   Comparative genomics and evolution of alternative splicing: the pessimists' science.
   Chem Rev 107(8):3407-30, 2007.
   PMID: 17645315
4. Ballvora A, Jöcker A, Viehöver P, Ishihara H, Paal J, Meksem K, Bruggmann R, Schoof H, Weisshaar B, Gebhardt C.
   Comparative sequence analysis of Solanum and Arabidopsis in a hot spot for pathogen resistance on potato chromosome V reveals a patchwork of conserved and rapidly evolving genome segments
   BMC Genomics 2;8(1):112, 2007.
   PMID: 17474978
5. Brugger K, Chen L, Stark M, Zibat A, Redder P, Ruepp A, Awayez M, She Q, Garrett RA, Klenk HP.
   The genome of Hyperthermus butylicus: a sulfur-reducing, peptide fermenting, neutrophilic Crenarchaeote growing up to 108 degrees C.
   Archaea 2(2):127-35, 2007
   PMID: 17350933
6. Cuomo CA, Güldener U, Xu JR, Trail F, Turgeon BG, Di Pietro A, Walton JD, Ma L, Baker SE, Rep M, Adam G, Antoniw J, Baldwin T, Calvo S, Chang Y, DeCaprio D, Gale LR, Gnerre S, Goswami RS, Hammond-Kosack K, Harris LJ, Hilburn K, Kennell JC, Kroken S, Magnuson JK, Mannhaupt G, Mauceli E, Mewes HW, Mitterbauer R, Muehlbauer G, Münsterkötter M, Nelson D, O'Donnell K, Ouellet T, Qi W, Quesneville H, Roncero MIG, Seong K, Tetko IV, Urban M, Waalwijk C, Ward T, Yao J, Birren BW, and Kistler C.
   The Fusarium graminearum Genome Reveals a Link Between Localized Polymorphism and Pathogen Specialization
   Science 317(5843):1400-1402.
   PMID: 17823352
7. Datson NA, Morsink MC, Atanasova S, Armstrong VW, Zischler H, Schlumbohm C, Dutilh BE, Huynen MA, Waegele B, Ruepp A, de Kloet ER, Fuchs E.
   Development of the first marmoset-specific DNA microarray (EUMAMA): a new genetic tool for large-scale expression profiling in a non-human primate
   BMC Genomics 8(1):190, 2007.
   PMID: 17592630
8. Eggert M, Seeck U, Semmler M, Maass U, Dietmann S, Schulz M, Dotzlaw H, Neeck G.
   An evaluation of anti-TNF-alpha-therapy in patients with ankylosing spondylitis: imbalanced activation of NF kappa B subunits in lymphocytes and modulation of serum cortisol concentration
   Rheumatol Int 27(9):841-6.
   PMID: 17242904
9. Emmersen J, Rudd S, Mewes HW, Tetko IV.
   Separation of sequences from host-pathogen interface using triplet nucleotide frequencies.
   Fungal Genet Biol 44(4):231-41, 2007.
   PMID: 17218127
10. Eyueboglu B, Pfister K, Haberer G, Chevalier D, Fuchs A, Mayer KF, Schneitz K.
    Molecular characterisation of the STRUBBELIG-RECEPTOR FAMILY of genes encoding putative leucine-rich repeat receptor-like kinases in Arabidopsis thaliana.
    BMC Plant Biol 7:16, 2007.
    PMID: 17397538
11. Farre-Castany MA, Schwaller B, Gregory P, Barski J, Mariethoz C, Eriksson JL, Tetko IV, Wolfer D, Celio MR, Schmutz I, Albrecht U, Villa AE.
    Differences in locomotor behavior revealed in mice deficient for the calcium-binding proteins parvalbumin, calbindin D-28k or both.
    Behav Brain Res 178(2):250-61, 2007.
    PMID: 17275105
12. Frishman D.
    Protein Annotation at Genomic Scale: The Current Status
    Chem Rev 107(8):3448-66, 2007.
    PMID: 17658902
13. Giraldez T, Afonso-Oramas D, Cruz-Muros I, Garcia-Marin V, Pagel P, González-Hernández T, Alvarez de la Rosa D.
    Cloning and functional expression of a new epithelial sodium channel & subunit isoform differentially expressed in neurons of the human and monkey telencephalon
    J Neurochem 102(4): 1304-15, 2007.
    PMID: 17472699
14. Hallen HE, Huebner M, Shiu SH, Guldener U, Trail F.
    Gene expression shifts during perithecium development in Gibberella zeae (anamorph Fusarium graminearum), with particular emphasis on ion transport proteins.
    Fungal Genet Biol 44(11):1146-56, 2007.
    PMID: 17555994
15. Hlubek F, Brabletz T, Budczies J, Pfeiffer S, Jung A, Kirchner T.
    Heterogeneous expression of Wnt/beta-catenin target genes within colorectal cancer.
    Int J Cancer 121(9):1941-8, 2007.
    PMID: 17631641
16. Kawanabe M and Theis F.
    Joint low-rank approximation for extracting non-gaussian subspaces.
    Signal Processing 2007.
    
17. Kerrien S, Orchard S, Montecchi-Palazzi L, Aranda B, Quinn AF, Vinod N, Bader GD, Xenarios I, Wojcik J, Sherman D, Tyers M, Salama JJ, Moore S, Ceol A, Chatr-Aryamontri A, Oesterheld M, Stumpflen V, Salwinski L, Nerothin J, Cerami E, Cusick ME, Vidal M, Gilson M, Armstrong J, Woollard P, Hogue C, Eisenberg D, Cesareni G, Apweiler R, Hermjakob H.
    Broadening the Horizon - Level 2.5 of the HUPO-PSI Format for Molecular Interactions.
    BMC Biol. 5(1):44, 2007.
    PMID: 17925023
18. Klee K, Ernst R, Spannagl M, Mayer KFX.
    Apollo2Go: a web service adapter for the Apollo genome viewer to enable distributed genome annotation.
    BMC Bioinformatics 8(1):320, 2007.
    PMID:17760972
19. Kovalishyn VV, Kholodovych V, Tetko IV, Welsh WJ.
    Volume learning algorithm significantly improved PLS model for predicting the estrogenic activity of xenoestrogens.
    J Mol Graph Model 26(2):591-4, 2007.
    PMID: 17433745
20. Krumsiek J, Arnold R, Rattei T.
    Gepard: A rapid and sensitive tool for creating dotplots on genome scale.
    Bioinformatics 23(8):1026-8, 2007.
    PMID: 17309896
21. Mannhaupt G, Feldmann H.
    Genomic Evolution of the Proteasome System Among Hemiascomycetous Yeasts.
    J Mol Evol. 65(5):529-40, 2007.
    PMID: 17909694
22. Muensterkoetter M, Steinberg G.
    The fungus Ustilago maydis and humans share disease-related proteins that are not found in Saccharomyces cerevisiae.
    BMC Genomics 8(1):473, 2007.
    PMID: 18096044
23. Oesterheld M, Mewes HW, Stuempflen V.
    Analysis of integrated biomolecular networks using a generic network analysis suite.
    J Int Bio. 4(3), 2007.
    
24. Orchard S, Salwinski L, Kerrien S, Montecchi-Palazzi L, Oesterheld M, Stümpflen V, Ceol A, Chatr-aryamontri A, Armstrong J, Woollard P, Salama JJ, Moore S, Wojcik J, Bader GD, Vidal M, Cusick ME, Gerstein M, Gavin AC, Superti-Furga G, Greenblatt J, Bader J, Uetz P, Tyers M, Legrain P, Fields S, Mulder N, Gilson M, Niepmann M, Burgoon L, De Las Rivas J, Prieto C, Perreau VM, Hogue C, Mewes HW, Apweiler R, Xenarios I, Eisenberg D, Cesareni G, Hermjakob H.
    The minimum information required for reporting a molecular interaction experiment (MIMIx).
    Nature Biotech 25, 894 - 898, 2007.
    PMID: 17687370
25. Pagel P, Strack N, Oesterheld M, Stümpflen V, Frishman D.
    Computational prediction of domain interactions.
    Methods Mol Biol 396:3-16, 2007.
    PMID: 18025682
26. The Rice annotation Project
    Curated Genome Annotation of Oryza sativa ssp. japonica and Comparative Genome Analysis with Arabidopsis thaliana
    Genome Res Feb;17(2):175-83, 2007.
    PMID: 17210932
27. Riley L, Schmidt T, Wagner C, Volz A, Artamonova I, Heumann K, Mewes HW, Frishman, D.
    PEDANT genome database: ten years online.
    Nucleic Acids Res 35(Database Issue): D354-D357, 2007.
    PMID: 17148486
    
28. Schmidt T, Hombach M, Frishman D.
    Comparative analysis of isochores in mammalian genomes.
    GCB 2007 6-7, 2007.
    
29. Spannagl M, Noubibou O, Haase D, Yang L, Gundlach H, Klee K, Haberer G, Schoof H, Mayer KFX.
    MIPSPlantsDB – Plant database resource for integrative and comparative plant genome research.
    Nucleic Acids Res 35(Database Issue): D834-D840, 2007.
    PMID: 17202173
30. Spannagl M, Haberer G, Ernst R, Schoof H, Mayer KF.
    MIPS Plant Genome Information Resources.
    Methods Mol Biol 406:137-60, 2007.
    PMID: 18287691
31. Stuempflen V, Mewes HW.
    Neue Informaitonstechnologien zur Nutzung biologischer Daten
    BIOspektrum 3: 281-283, 2007.
    
32. Stümpflen V, Barnickel T, Nenova K.
    Large Scale Knowledge Representation of Distributed Biomedical Information Scaling Topic Maps
    Lecture Notes in Artificial Intelligence 4999: 116-127, TMRA, 2007.
    
33. Suhre K.
    Inference of gene function based on gene fusion events: the rosetta-stone method.
    Methods Mol Biol 396:31-42, 2007.
    PMID: 18025684
34. Theis F, Georgiev P, and Cichocki A.
    Robust sparse component analysis based on a generalized hough transform.
    EURASIP Journal on Applied Signal Processing 2007.
    
35. Varnek A, Kireeva N, Tetko IV, Baskin II, Solov'ev VP.
    Exhaustive QSPR Studies of a Large Diverse Set of Ionic Liquids: How Accurately Can We Predict Melting Points?
    J Chem Inf Model 47(3):1111-22, 2007.
    PMID: 17381081

2006

1. Antonov AV, Mewes HW.
   BIOREL: The benchmark resource to estimate the relevance of the gene networks.
   FEBS Lett 580(3):844-848, 2006.
   PMID: 16414044
   
2. Antonov AV, Tetko IV, Mewes HW.
   A systematic approach to infer biological relevance and biases of gene network structures.
   Nucleic Acids Res 34(1):e6, 2006.
   PMID: 16407322
   
3. Antonov AV, Mewes HW.
   Complex functionality of gene groups identified from high-throughput data.
   J Mol Biol 363(1):289-296, 2006.
   PMID: 16959266
4. Balakin KV, Savchuk NP, Tetko IV.
   In Silico Approaches to Prediction of Aqueous and DMSO Solubility of Drug-like Compounds: Trends, Problems and Solutions
   Curr Med Chem 13(2), 223-241, 2006.
   PMID: 16472214
   
5. Bhonde MR, Hanski ML, Budczies J, Cao M, Gillissen B, Moorthy D, Simonetta F, Scherubl H, Truss M, Hagemeier C, Mewes HW, Daniel PT, Zeitz M, Hanski C.
   DNA damage-induced expression of p53 suppresses mitotic checkpoint kinase hMps1: the lack of this suppression in p53mut cells contributes to apoptosis.
   J Biol Chem 281(13):8675-8685, 2006.
   PMID: 16446370
   
6. Bruggmann R, Bharti AK, Gundlach H, Lai J, Young S, Pontaroli AC, Wei F, Haberer G, Fuks G, Du C, Raymond C, Estep MC, Liu R, Bennetzen JL, Chan AP, Rabinowicz PD, Quackenbush J, Barbazuk WB, Wing RA, Birren B, Nusbaum C, Rounsley S, Mayer KFX, Messing J.
   Uneven chromosome contraction and expansion in the maize genome
   Genome Res 16(10):1241-51, 2006.
   PMID: 16902087
   
7. Cannon SB, Sterck L, Rombauts S, Sato S, Cheung F, Gouzy J, Wang X, Mudge J, Vasdewani J, Scheix T, Spannagl M, Monaghan E, Nicholson C, Humphray SJ, Schoof H, Mayer KF, Rogers J, Quetier F, Oldroyd GE, Debelle F, Cook DR, Retzel EF, Roe BA, Town CD, Tabata S, Van de Peer Y, Young ND.
   Legume genome evolution viewed through the Medicago truncatula and Lotus japonicus genomes.
   Proc Natl Acad Sci U S A 103(40):14959-64, 2006.
   PMID: 17003129
   
8. Dietmann S, Aguilar D, Mader M, Oesterheld M, Ruepp A, Stuempflen V, Mewes HW.
   Resources and Tools for Investigating Biomolecular Networks in Mammals
   Curr Pharm Des 12(29):3723-3724, 2006.
   
9. Domoney C, Duc G, Ellis TH, Ferrandiz C, Firnhaber C, Gallardo K, Hofer J, Kopka J, Kuster H, Madueno F, Munier-Jolain NG, Mayer K, Thompson R, Udvardi M, Salon C.
   Genetic and genomic analysis of legume flowers and seeds
   Curr Opin Plant Biol 9(2):133-41, 2006.
   PMID: 16480914
   
10. Ernst R, Mayer KFX.
    Bioinformatics integration of heterogeneous data: the PlaNet approach as a model for plant and legume genomics
    Grain Legumes 46, 2nd quarter, 2006.
    
11. Güldener U, Münsterkötter M, Mannhaupt G, Haase D, Oesterheld M, Stumpflen V, Mewes, HW, Adam, G.
    FGDB: A comprehensive fungal genome resource on the plant pathogen Fusarium graminearum
    Nucl Acids Res 34(Database issue):D456-8, 2006.
    PMID: 16381910
    
12. Güldener U, Münsterkötter M, Oesterheld M, Pagel P, Ruepp A, Mewes HW, Stumpflen V.
    MPact: the MIPS protein interaction resource on yeast.
    Nucl Acids Res 34(Database issue):D436-41, 2006.
    PMID: 16381906
    
13. Güldener U, Seong KY, Boddu J, Cho S, Trail F, Xu JR, Adam G, Mewes HW, Muehlbauer GJ, Kistler HC.
    Development of a Fusarium graminearum Affymetrix GeneChip for profiling fungal gene expression in vitro and in planta.
    Fungal Genet Biol 43(5):316-25, 2006.
    PMID: 16531083
    
14. Haberer G, Mader MT, Kosarev P, Spannagl M, Yang L, Mayer KF.
    Large-scale Cis-element Detection by Analysis of Correlated Expression and Sequence Conservation between Arabidopsis and Brassica oleracea.
    Plant Physiol 142(4):1589-602, 2006.
    PMID: 17028152
    
15. Lehner A, Riedel K, Rattei T, Ruepp A, Frishman D, Breeuwer P, Diep B, Eberl L, Stephan R.
    Molecular characterization of the alpha glucosidase activity in Enterobacter sakazakii reveals the presence of a putative gene cluster for palatinose metabolism
    Sys App Micro 29(8):609-25, 2006.
    PMID: 16563686
    
16. Lehner A, Grimm M, Rattei T, Ruepp A,Frishman D, Manzardo G, Stephan R.
    Cloning and characterization of Enterobacter sakazakii pigment genes and in situ spectroscopic analysis of the pigment
    Fems Micro Let 265(2):244-8, 2006.
    PMID: 17069626
    
17. Kämper J, Kahmann R, Bölker M, Ma L, Brefort T, Saville BJ, Banuett F, Kronstad JW, Gold SE, Müller O, Perlin MH, Wösten HAB, de Vries R, Ruiz-Herrera J, Reynaga-Peña CG, Snetselaar K, McCann M, Pérez-Martín J, Feldbrügge M, Basse CW, Steinberg G, Ibeas JI, Holloman W, Guzman P, Farman M, Stajich JE, Sentandreu R, González-Prieto JM, Kennell JC, Molina L, Schirawski J, Mendoza-Mendoza A, Greilinger D, Münch K, Rössel N, Scherer M, Vranes M, Ladendorf O, Vincon V, Fuchs U, Sandrock B, Meng S, Ho ECH, Cahill MJ, Boyce KJ, Klose J, Klosterman SJ, Deelstra HJ, Ortiz-Castellanos L, Li W, Sanchez-Alonso P, Schreier PH, Häuser-Hahn I, Vaupel M, Koopmann E, Friedrich G, Voss H, Schlüter T, Margolis J, Platt D, Swimmer C, Gnirke A, Chen F, Vysotskaia V, Mannhaupt G, Güldener U, Münsterkötter M, Haase D, Oesterheld M, Mewes HW, Mauceli EW, DeCaprio D, Wade CM, Butler J, Young S, Jaffe DB, Calvo S, Nusbaum C, Galagan J and Birren BW.
    Insights from the genome of the biotrophic fungal plant pathogen Ustilago maydis
    Nature 444(7115):97-101, 2006.
    PMID: 17080091
    
18. Mewes HW, Frishman D, Mayer K, Münsterkötter M, Noubibou O, Pagel P, Rattei T, Oesterheld M, Ruepp A, Stumpflen V.
    MIPS: analysis and annotation of proteins from whole genomes in 2005
    Nucl Acids Res 34(suppl_1):D169-D172, 2006.
    PMID: 16381839
    
19. Michel K, Abderhalden O, Bruggmann R, Dudler R.
    Transcriptional changes in powdery mildew infected wheat and Arabidopsis leaves undergoing syringolin-triggered hypersensitive cell death at infection sites.
    Plant Mol Biol 62(4-5):561-78, 2006.
    PMID: 16941219
    
20. Pagel P, Oesterheld M, Stuempflen V, Frishman D.
    The DIMA web resource -- exploring the protein domain network
    Bioinformatics 22(8):997-8, 2006.
    PMID: 16481337
    
21. Prokisch H, Andreoli C, Ahting U, Heiss K, Ruepp A, Scharfe C, Meitinger, T.
    MitoP2: the mitochondrial proteome database--now including mouse data
    Nucl Acids Res 34(Database issue):D705-11, 2006.
    PMID: 16381964
    
22. Rattei T, Arnold R, Tischler P, Lindner D, Stumpflen V, Mewes HW.
    SIMAP: the similarity matrix of proteins
    Nucl Acids Res 34(Database issue):D252-6, 2006.
    PMID: 16381858
    
23. Ruepp A, Doudieu ON, Oever J, Brauner B, Dunger-Kaltenbach I, Fobo G, Frishman G, Montrone C, Skornia C, Wanka S, Rattei T, Pagel P, Riley L, Frishman D, Surmeli D, Tetko I, Oesterheld M, Stümpflen V and Mewes HW.
    The Mouse Functional Genome Database (MfunGD): functional annotation of proteins in the light of their cellular context
    Nucl Acids Res 34(Database issue):D568-71, 2006.
    PMID: 16381934
    
24. Ruepp A, Mewes HW.
    Prediction and Classification of Protein Functions.
    Drug Discov. Today: Tech 3, 145-151, 2006.
    
    
25. Smialowski P, Schmidt T, Cox J, Kirschner A, Frishman D.
    Will my protein crystallize? A sequence-based predictor.
    Proteins 62(2). 343-55, 2006.
    PMID: 16315316
    
26. Schmidt T, Frishman D.
    PROMPT: a protein mapping and comparison too.
    BMC Bioinformatics 7,331, 2006.
    PMID: 16817977
    
27. Strous M, Pelletier E, Mangenot S, Rattei T, Lehner A, Taylor MW, Horn M, Daims H, Bartol-Mavel D, Wincker P, Barbe V, Fonknechten N, Vallenet D, Segurens B, Schenowitz-Truong C, Medigue C, Collingro A, Snel B, Dutilh BE, Op den Camp HJM, van der Drift C, Cirpus I, van de Pas-Schoonen KT, Harhangi HR, van Niftrik L, Schmid M, Keltjens J, van de Vossenberg J, Kartal B, Meier H, Frishman D, Huynen MA, Mewes HW, Weissenbach J, Jetten MSM, Wagner M, Le Paslier D.
    Deciphering the evolution and metabolism of an anammox bacterium from a community genome
    Nature 440(7085): 790-794, 2006.
    PMID: 16598256
    
28. Stümpflen, V, Gregory R, Nenova, K.
    From Biological Data to Biological Knowledge
    Lecture Notes in Artificial Intelligence 4438: 62-66, TMRA, 2006.
    
29. Tetko IV, Solovev VP, Antonov AV, Yao X, Doucet JP, Fan B, Hoonakker F, Fourches D, Jost P, Lachiche N, Varnek A.
    Benchmarking of linear and non-linear approaches for quantitative structure-property relationship studies of metal complexation with ionophores
    J Chem Inf Model 46(2):808-19, 2006.
    PMID: 16563012
    
30. Tetko IV, Haberer G, Rudd S, Meyers B, Mewes HW, Mayer KFX.
    Spatiotemporal Expression Control Correlates with Intragenic Scaffold Matrix Attachment Regions (S/MARs) in Arabidopsis thaliana
    PloS Comput Biol 2(3):e21, 2006.
    PMID: 16604187
    
31. Tetko IV, Bruneau P, Mewes HW, Rohrer DC, Poda GI.
    Can We Estimate the Accuracy of ADMET-Tox Predictions?
    Drug Discovery Today 11(15-16):700-7, 2006.
    PMID: 16846797 Preprint
    
32. Wang Y, Hindemitt T, Mayer KFX.
    Significant sequence similarities in promoters and precursors of Arabidopsis thaliana non-conserved microRNAs
    Bioinformatics 22(21):2585-9, 2006.
    PMID: 16901935
    
33. Wong P, Frishman D.
    Fold Designability, Distribution and Disease
    PloS Comp Biol 2(5):e40, 2006.
    PMID: 16680196

2005

1. Antonov AV, Tetko IV, Kosykh D, Surmeli D, Mewes HW.
   Exploiting scale-free information from expression data for cancer classification
   Comput Biol Chem 29(4):288-93, 2005.
   PMID: 16039906
   
2. Arnold R, Rattei T, Tischler P, Truong M, Stuempflen V, Mewes, HW.
   SIMAP-The similarity matrix of proteins
   Bioinformatics 21: ii42-ii46, 2005.
   PMID: 16204123
   
3. Artamanova II, Frishman G, Gelfand MS, Frishman D.
   Mining sequence annotation databanks for association patterns
   Bioinformatics 21(Suppl_3):iii49-iii57, 2005.
   PMID: 16306393
   
4. Borodovsky M, Rzhetsky A, Frishman D.
   The Fifth Georgia Tech--Oak Ridge National Laboratory International Conference in Bioinformatics: in silico Biology, Computational Genomics and Evolutionary Biology
   Bioinformatics 21(Suppl_3): iii1, 2005.
   PMID: 16306386
   
5. Bruggmann R, Abderhalden O, Reymond P, Dudler R.
   Analysis of epidermis- and mesophyll-specific transcript accumulation in powdery mildew-inoculated wheat leaves.
   Plant Mol Biol 58(2):247-67, 2005.
   PMID: 16027977
   
6. Ernst R.
   PlaNet: A powerful portal for accessing plant genome data and analysis tools via web services
   GARNish, 2005.
   
7. Facius A, Englbrecht C, Birzele F, Groscurth A, Benjamin S, Wanka S, Mewes HW.
   PRIME: a graphical interface for integrating genomic/proteomic databases.
   Proteomics 5(1):76-80, 2005.
   PMID: 15744835
   
8. Friedel CC, Jahn KH, Sommer S, Rudd S, Mewes HW, Tetko IV.
   Support vector machines for separation of mixed plant-pathogen EST collections based on codon usage.
   Bioinformatics 21(8):1383-8, 2005.
   PMID: 15585526
   
9. Germain H, Rudd S, Zotti C, Caron S, O'brien M, Chantha SC, Lagace M, Major F, Matton DP.
   A 6374 Unigene Set Corresponding to Low Abundance Transcripts Expressed Following Fertilization in Solanum chacoense Bitt, and Characterization of 30 Receptor-like Kinases
   Plant Mol Biol 59, 515-532, 2005.
   PMID: 16235114
   
10. Guldener U, Munsterkotter M, Kastenmuller G, Strack N, van Helden J, Lemer C, Richelles J, Wodak SJ, Garcia-Martinez J, Perez-Ortin JE, Michael H, Kaps A, Talla E, Dujon B, Andre B, Souciet JL, De Montigny J, Bon E, Gaillardin C, Mewes HW.
    CYGD: the Comprehensive Yeast Genome Database.
    Nucleic Acids Res 33(Database issue):D364-8, 2005.
    PMID: 15608217
    
11. Haberer G, Young S, Bharti AK, Gundlach H, Raymond C, Fuks G, Butler E, Wing RA, Rounsley S, Birren B, Nusbaum C, Mayer KFX, Messing J.
    Structure and Architecture of the Maize Genome
    Plant Physiology 139: 1612-1624, 2005.
    PMID: 16339807
    
12. Hindemitt T, Mayer KFX
    CREDO: a web-based tool for computational detection of conserved sequence motifs in noncoding sequences
    Bioinformatics 21(23):4304-6, 2005.
    PMID: 16204349
    
13. Kasuga T, Townsend JP, Tian C, Gilbert LB, Mannhaupt G, Taylor JW, Glass NL.
    Long-oligomer microarray profiling in Neurospora crassa reveals the transcriptional program underlying biochemical and physiological events of conidial germination.
    Nucleic Acids Res. 33(20):6469-6485, 2005.
    PMID: 16287898
    
14. Kerner MJ, Naylor DJ, Ishihama Y, Maier T, Chang HC, Stines AP, Georgopoulos C, Frishman D, Hayer-Hartl M, Mann M, Hartl FU.
    Proteome-wide analysis of chaperonin-dependent protein folding in Escherichia coli.
    Cell 122(2):209-20, 2005.
    PMID: 16051146
    
15. Kindermann B, Doring F, Budczies J, Daniel H.
    Zinc-sensitive genes as potential new target genes of the metal transcription factor-1 (MTF-1)
    Biochem Cell Biol 83(2):221-9, 2005.
    PMID: 15864330
    
16. Pagel P, Kovac S, Oesterheld M, Brauner B, Dunger-Kaltenbach I, Frishman G, Montrone C, Mark P, Stumpflen V, Mewes HW, Ruepp A, Frishman D.
    The MIPS mammalian protein-protein interaction database.
    Bioinformatics. 21(6):832-4, 2005
    PMID: 15531608
    
17. Neverov AD, Artamonova II, Nurtdinov RN, Frishman D, Gelfand M, Mironov A.
    Alternative splicing and protein function.
    BMC Bioinformatics. 6(1):266, 2005.
    PMID: 16274476
    
18. Riley ML, Schmidt T, Wagner C, Mewes HW, Frishman D.
    The PEDANT genome database in 2005
    Nucleic Acids Res. 33(Web Server issue):D308-D310, 2005.
    PMID: 15608204
    
19. Rudd S, Schoof H, Mayer K.
    PlantMarkers--a database of predicted molecular markers from plants
    Nucleic Acids Res 33(Database issue):D628-32., 2005
    PMID: 15608276
    
20. Rudd S, Tetko IV.
    Eclair--a web service for unravelling species origin of sequences sampled from mixed host interfaces.
    Nucleic Acids Res 33(Web Server issue):W724-7, 2005.
    PMID: 15980572
    
21. Schoof H, Spannagl M, Yang L, Ernst R, Gundlach H, Haase D, Haberer G, Mayer, KFX.
    Munich Information Center for Protein Sequences Plant Genome Resources. A Framework for Integrative and Comparative Analyses
    Plant Physiol 138(3):1301-1309, 2005.
    PMID: 16010004
    
22. Tetko IV
    Computing Chemistry on the Web
    Drug Discovery Today 10(22):1497-500, 2005.
    PMID: 16257371
    
23. Tetko IV, Abagyan R, Oprea TI.
    Surrogate data - a secure way to share corporate data
    J Comput Aided Mol Des 19(9-10):749-64, 2005.
    PMID: 16267691
    
24. Tetko IV, Gasteiger J, Todeschini R, Mauri A, Livingstone D, Ertl P, Palyulin VA, Radchenko EV, Zefirov NS, Makarenko AS, Tanchuk VY, Prokopenko VV.
    Virtual computational chemistry laboratory--design and description
    J Comput Aided Mol Des 19(6):453-63, 2005.
    PMID: 16231203
    
25. Tetko IV, Brauner B, Dunger-Kaltenbach I, Frishman G, Montrone C, Fobo G, Ruepp A, Antonov AV, Surmeli D, Mewes HW.
    MIPS bacterial genomes functional annotation benchmark dataset.
    Bioinformatics 21(10):2520-1, 2005.
    PMID: 15769832
    
26. Tetko IV, Facius A, Ruepp A, Mewes HW.
    Super paramagnetic clustering of protein sequences.
    BMC Bioinformatics 6(1):82, 2005.
    PMID: 15804359
    
27. Wang Y, Tetko IV, Hall MA, Frank E, Facius A, Mayer KF, Mewes HW.
    Gene selection from microarray data for cancer classification - a machine learning approach
    Computational Biol and Chem 29(1):37-46, 2005.
    PMID: 15680584
    
28. Wilkinson, M., Schoof, H., Ernst, R., Haase, D.
    BioMOBY Successfully Integrates Distributed Heterogeneous Bioinformatics Web Services. The PlaNet Exemplar Case
    Plant Physiol 138(1):5-17, 2005.
    PMID: 15888673
    
29. Wong P, Fritz A, Frishman D.
    Designability, Aggregation Propensity and Duplication of Disease-related Proteins
    Protein Eng Des Sel 18(10):503-508, 2005.
    PMID: 16155116
    

2004

1. Andreoli C, Prokisch H, Hortnagel K, Mueller JC, Munsterkotter M, Scharfe C and Meitinger T.
   MitoP2, an integrated database on mitochondrial proteins in yeast and man.
   Nucleic Acids Res 32 Database issue:D459-62, 2004.
   PMID: 14681457
   
2. Antonov AV, Tetko IV, Mader MT, Budczies J and Mewes HW.
   Optimization models for cancer classification: extracting gene interaction information from microarray expression data.
   Bioinformatics 20(5):644-52. Jan 22, 2004.
   PMID: 15033871
   
3. Antonov AV, Tetko IV, Prokopenko VV, Kosykh D, Mewes HW.
   Web portal for classification of expression data using maximal margin linear programming.
   Bioinformatics 2004 Jun 24
   PMID: 15217811
   
4. Borkovich KA, Alex LA, Yarden O, Freitag M, Turner GE, Read ND, Seiler S, Bell-Pedersen D, Paietta J, Plesofsky N, Plamann M, Goodrich-Tanrikulu M, Schulte U, Mannhaupt G, Nargang FE, Radford A, Selitrennikoff C, Galagan JE, Dunlap JC, Loros JJ, Catcheside D, Inoue H, Aramayo R, Polymenis M, Selker EU, Sachs MS, Marzluf GA, Paulsen I, Davis R, Ebbole DJ, Zelter A, Kalkman ER, O'Rourke R, Bowring F, Yeadon J, Ishii C, Suzuki K, Sakai W and Pratt R.
   Lessons from the genome sequence of Neurospora crassa: tracing the path from genomic blueprint to multicellular organism.
   Microbiol Mol Biol Rev 68(1):1-108, 2004.
   PMID: 15007097
   
5. Crass T, Antes I, Basekow R, Bork P, Buning C, Christensen M, Claussen H, Ebeling C, Ernst P, Gailus-Durner V, Glatting KH, Gohla R, Gossling F, Grote K, Heidtke K, Herrmann A, O'Keeffe S, Kiesslich O, Kolibal S, Korbel JO, Lengauer T, Liebich I, van der Linden M, Luz H, Meissner K, von Mering C, Mevissen HT, Mewes HW, Michael H, Mokrejs M, Muller T, Pospisil H, Rarey M, Reich JG, Schneider R, Schomburg D, Schulze-Kremer S, Schwarzer K, Sommer I, Springstubbe S, Suhai S, Thoppae G, Vingron M, Warfsmann J, Werner T, Wetzler D, Wingender E and Zimmer R.
   The Helmholtz Network for Bioinformatics: an integrative web portal for bioinformatics resources.
   Bioinformatics 20(2):268-70, 2004.
   PMID: 14734319
   
6. Englbrecht CC, Schoof H and Bohm S.
   Conservation, diversification and expansion of C2H2 zinc finger proteins in the Arabidopsis thaliana genome.
   BMC Genomics 5(1):39, 2004.
   PMID: 15236668
   
7. Greenwood AD, Englbrecht CC, Macphee RD.
   Characterization of an endogenous retrovirus class in elephants and their relatives.
   BMC Evol Biol Oct 11;4(1):38, 2004.
   PMID: 15476555
   
8. Haberer G, Hindemitt T, Meyers BC and Mayer KF.
   Transcriptional Similarities, Dissimilarities, and Conservation of cis-Elements in Duplicated Genes of Arabidopsis.
   Plant Physiol Oct, 136(2):3009-22, 2004.
   PMID: 15489284
   
9. Horn M, Collingro A, Schmitz-Esser S, Beier CL, Purkhold U, Fartmann B, Brandt P, Nyakatura GJ, Droege M, Frishman D, Rattei T, Mewes HW and Wagner M.
   Illuminating the evolutionary history of chlamydiae.
   Science 304(5671):728-30. Apr 08, 2004.
   PMID: 15073324
   
10. Imanishi T, Itoh T, Suzuki Y, O'Donovan C, Fukuchi S, Koyanagi KO, Barrero RA, Tamura T, Yamaguchi-Kabata Y, Tanino M, Yura K, Miyazaki S, Ikeo K, Homma K, Kasprzyk A, Nishikawa T, Hirakawa M, Thierry-Mieg J, Thierry-Mieg D, Ashurst J, Jia L, Nakao M, Thomas MA, Mulder N, Karavidopoulou Y, Jin L, Kim S, Yasuda T, Lenhard B, Eveno E, Suzuki Y, Yamasaki C, Takeda J, Gough C, Hilton P, Fujii Y, Sakai H, Tanaka S, Amid C, Bellgard M, Bonaldo Mde F, Bono H, Bromberg SK, Brookes AJ, Bruford E, Carninci P, Chelala C, Couillault C, de Souza SJ, Debily MA, Devignes MD, Dubchak I, Endo T, Estreicher A, Eyras E, Fukami-Kobayashi K, Gopinath GR, Graudens E, Hahn Y, Han M, Han ZG, Hanada K, Hanaoka H, Harada E, Hashimoto K, Hinz U, Hirai M, Hishiki T, Hopkinson I, Imbeaud S, Inoko H, Kanapin A, Kaneko Y, Kasukawa T, Kelso J, Kersey P, Kikuno R, Kimura K, Korn B, Kuryshev V, Makalowska I, Makino T, Mano S, Mariage-Samson R, Mashima J, Matsuda H, Mewes HW, Minoshima S, Nagai K, Nagasaki H, Nagata N, Nigam R, Ogasawara O, Ohara O, Ohtsubo M, Okada N, Okido T, Oota S, Ota M, Ota T, Otsuki T, Piatier-Tonneau D, Poustka A, Ren SX, Saitou N, Sakai K, Sakamoto S, Sakate R, Schupp I, Servant F, Sherry S, Shiba R, Shimizu N, Shimoyama M, Simpson AJ, Soares B, Steward C, Suwa M, Suzuki M, Takahashi A, Tamiya G, Tanaka H, Taylor T, Terwilliger JD, Unneberg P, Veeramachaneni V, Watanabe S, Wilming L, Yasuda N, Yoo HS, Stodolsky M, Makalowski W, Go M, Nakai K, Takagi T, Kanehisa M, Sakaki Y, Quackenbush J, Okazaki Y, Hayashizaki Y, Hide W, Chakraborty R, Nishikawa K, Sugawara H, Tateno Y, Chen Z, Oishi M, Tonellato P, Apweiler R, Okubo K, Wagner L, Wiemann S, Strausberg RL, Isogai T, Auffray C, Nomura N, Gojobori T and Sugano S.
    Integrative annotation of 21,037 human genes validated by full-length cDNA clones.
    PLoS Biol 2(6):856-75. Apr 20, 2004.
    PMID: 15103394
    
11. Lai J, Dey N, Kim CS, Bharti AK, Rudd S, Mayer KF, Larkins BA, Becraft P and Messing J.
    Characterization of the maize endosperm transcriptome and its comparison to the rice genome.
    Genome Res 14(10A):1932-7, 2004.
    PMID: 15466291
    
12. Laux H, Tomer R, Mader MT, Smida J, Budczies J, Kappler R, Hahn H, Blochinger M, Schnitzbauer U, Eckardt-Schupp F, Hofler H, Becker KF.
    Tumor-associated E-cadherin mutations do not induce Wnt target gene expression, but affect E-cadherin repressors.
    Genome Res 14(10A):1932-7, 2004.
    PMID: 15311212
    
13. Messing J, Bharti AK, Karlowski WM, Gundlach H, Kim HR, Yu Y, Wei F, Fuks G, Soderlund CA, Mayer KF and Wing RA.
    Sequence composition and genome organization of maize.
    Proc Natl Acad Sci U S A 101(40):14349-54. Sep 23, 2004.
    PMID: 15388850
    
14. Mewes HW, Amid C, Arnold R, Frishman D, Guldener U, Mannhaupt G, Munsterkotter M, Pagel P, Strack N, Stumpflen V, Warfsmann J and Ruepp A.
    MIPS: analysis and annotation of proteins from whole genomes.
    Nucleic Acids Res 32 Database issue:D41-4, 2004.
    PMID: 14681354
    
15. Mayer K, Rudd S, Schoof H.
    Arabidopsis and its use in cereal genomics. Cereal Genomics
    Cereal Genomics Kluwer Academic Publishers, Dordrecht, Netherlands, 2004.
    
16. Pagel P, Mewes HW and Frishman D.
    Conservation of protein-protein interactions - lessons from ascomycota.
    Trends Genet 20(2):72-6, 2004.
    PMID: 14746987
    
17. Pagel P, Wong P, Frishman D.
    A Domain Interaction Map Based on Phylogenetic Profiling.
    J Mol Biol 344(5):1331-1346, 2004.
    PMID: 15561146
    
18. Rabus R, Ruepp A, Frickey T, Rattei T, Fartmann B, Stark M, Bauer M, Zibat A, Lombardot T, Becker I, Amann J, Gellner K, Teeling H, Leuschner WD, Glockner FO, Lupas AN, Amann R and Klenk HP.
    The genome of Desulfotalea psychrophila, a sulfate-reducing bacterium from permanently cold Arctic sediments.
    Environ Microbiol 6(9):887-902, 2004.
    PMID: 15305914
    
19. Rudd S, Frisch M, Grote K, Meyers BC, Mayer K and Werner T.
    Genome-wide in silico mapping of scaffold/matrix attachment regions in Arabidopsis suggests correlation of intragenic scaffold/matrix attachment regions with gene expression.
    Plant Physiol 135:715-22, 2004.
    PMID: 15208419
20. Ruepp A, Zollner A, Maier D, Albermann K, Hani J, Mokrejs M, Tetko I, Guldener U, Mannhaupt G, Munsterkotter M and Mewes HW.
    The FunCat, a functional annotation scheme for systematic classification of proteins from whole genomes.
    Nucleic Acids Res 32(18):5539-45, 2004.
    PMID: 15486203
    
21. Schoof H, Ernst R, Nazarov V, Pfeifer L, Mewes HW and Mayer KF.
    MIPS Arabidopsis thaliana Database (MAtDB): an integrated biological knowledge resource for plant genomics.
    Nucleic Acids Res 32 Database issue:D373-6, 2004.
    PMID: 14681437
    
22. Schoof H, Ernst R and Mayer KF.
    The PlaNet consortium: A network of European plant databases connecting plant genome data in an integrated biological knowledge resource.
    Comparative and Functional Genomics 5, 184-189 (2004).
    
23. Schrick K, Nguyen D, Karlowski WM and Mayer KF.
    START lipid/sterol-binding domains are amplified in plants and are predominantly associated with homeodomain transcription factors.
    Genome Biol 5(6):R41. May 27, 2004.
    PMID: 15186492
    
24. Serfling E, Berberich-Siebelt F, Avots A, Chuvpilo S, Klein-Hessling S, Jha MK, Kondo E, Pagel P, Schulze-Luehrmann J, Palmetshofer A.
    NFAT and NF-kappaB factors-the distant relatives.
    Int J Biochem Cell Biol 2004 Jul;36(7):1166-70.
    PMID: 15109564
    
25. Shiu SH, Karlowski WM, Pan R, Tzeng YH, Mayer KF and Li WH.
    Comparative analysis of the receptor-like kinase family in Arabidopsis and rice.
    Plant Cell 16(5):1220-34. Apr 22, 2004.
    PMID: 15105442
    

2003

1. Aichinger C, Hansson K, Eichhorn H, Lessing F, Mannhaupt G, Mewes W and Kahmann R.
   Identification of plant-regulated genes in Ustilago maydis by enhancer-trapping mutagenesis.
   Mol Genet Genomics 270(4):303-14. Oct 02, 2003.
   PMID: 14523645
   
2. Bon E, Casaregola S, Blandin G, Llorente B, Neuveglise C, Munsterkotter M, Guldener U, Mewes HW, Van Helden J, Dujon B and Gaillardin C.
   Molecular evolution of eukaryotic genomes: hemiascomycetous yeast spliceosomal introns.
   Nucleic Acids Res 31(4):1121-35, 2003.
   PMID: 12582231
   
3. Brenner ED, Stevenson DW, McCombie RW, Katari MS, Rudd SA, Mayer KF, Palenchar PM, Runko SJ, Twigg RW, Dai G, Martienssen RA, Benfey PN and Coruzzi GM.
   Expressed sequence tag analysis in Cycas, the most primitive living seed plant.
   Genome Biol 4(12):R78. Nov 18, 2003.
   PMID: 14659015
   
4. Frishman D, Mokrejs M, Kosykh D, Kastenmuller G, Kolesov G, Zubrzycki I, Gruber C, Geier B, Kaps A, Albermann K, Volz A, Wagner C, Fellenberg M, Heumann K and Mewes HW.
   The PEDANT genome database.
   Nucleic Acids Res 31(1):207-11, 2003.
   PMID: 12519983
   
5. Schoof H
   Towards interoperability in genome databases> the MAtDB (MIPS Arabidopsis thaliana database) experience.
   Comp Funct Genom 4:255-258, 2003.
   
6. Galagan JE, Calvo SE, Borkovich KA, Selker EU, Read ND, Jaffe D, FitzHugh W, Ma LJ, Smirnov S, Purcell S, Rehman B, Elkins T, Engels R, Wang S, Nielsen CB, Butler J, Endrizzi M, Qui D, Ianakiev P, Bell-Pedersen D, Nelson MA, Werner-Washburne M, Selitrennikoff CP, Kinsey JA, Braun EL, Zelter A, Schulte U, Kothe GO, Jedd G, Mewes W, Staben C, Marcotte E, Greenberg D, Roy A, Foley K, Naylor J, Stange-Thomann N, Barrett R, Gnerre S, Kamal M, Kamvysselis M, Mauceli E, Bielke C, Rudd S, Frishman D, Krystofova S, Rasmussen C, Metzenberg RL, Perkins DD, Kroken S, Cogoni C, Macino G, Catcheside D, Li W, Pratt RJ, Osmani SA, DeSouza CP, Glass L, Orbach MJ, Berglund JA, Voelker R, Yarden O, Plamann M, Seiler S, Dunlap J, Radford A, Aramayo R, Natvig DO, Alex LA, Mannhaupt G, Ebbole DJ, Freitag M, Paulsen I, Sachs MS, Lander ES, Nusbaum C and Birren B.
   The genome sequence of the filamentous fungus Neurospora crassa.
   Nature 422(6934):859-68, 2003.
   PMID: 12712197
   
7. Karlowski WM, Schoof H, Janakiraman V, Stuempflen V and Mayer KF.
   MOsDB: an integrated information resource for rice genomics.
   Nucleic Acids Res 31(1):190-2, 2003.
   PMID: 12519979
   
8. Kota R, Rudd S, Facius A, Kolesov G, Thiel T, Zhang H, Stein N, Mayer K and Graner A.
   Snipping polymorphisms from large EST collections in barley (Hordeum vulgare L.).
   Mol Genet Genomics 270(1):24-33. Aug 23, 2003.
   PMID: 12938038
   
9. Mannhaupt G, Montrone C, Haase D, Mewes HW, Aign V, Hoheisel JD, Fartmann B, Nyakatura G, Kempken F, Maier J and Schulte U.
   What's in the genome of a filamentous fungus? Analysis of the Neurospora genome sequence.
   Nucleic Acids Res 31(7):1944-54, 2003.
   PMID: 12655011
   
10. Rudd S
    Expressed sequence tags: alternative or complement to whole genome sequences?
    Trends Plant Sci 8(7):321-9, 2003.
    PMID: 12878016
    
11. Rudd S, Mewes HW and Mayer KF.
    Sputnik: a database platform for comparative plant genomics.
    Nucleic Acids Res 31(1):128-32, 2003.
    PMID: 12519965
    
12. Mewes HW
    Sequence and Genome Bioinformatics.
    In Gasteiger J (ed.), Handbook of Chemoinformatics. Wiley-VCH, Weinheim, Vol. 4.
    
13. Schoof H and Karlowski WM.
    Comparison of rice and Arabidopsis annotation.
    Curr Opin Plant Biol 6(2):106-12, 2003.
    PMID: 12667865
    
14. Schmidt F, Schmid M, Jungblut PR, Mattow J, Facius A, Pleissner KP
    Iterative data analysis is the key for exhaustive analysis of peptide mass fingerprints from proteins separated by two-dimensional electrophoresis.
    J Am Soc Mass Spectrom 14(9):943-56, 2003.
    PMID: 12954163
    
15. Tornow S and Mewes HW.
    Functional modules by relating protein interaction networks and gene expression.
    Nucleic Acids Res 31(21):6283-9, 2003.
    PMID: 14576317
    
16. Wong P, Kolesov G, Frishman D and Houry WA.
    Phylogenetic web profiler.
    Bioinformatics 19(6):782-3, 2003.
    PMID: 12691995
    

2002

1. Kolesov, G., H. W. Mewes, and D. Frishman.
   SNAPper: gene order predicts gene function.
   Bioinformatics 18: 1017-1019, 2002.
   PMID: 12117803
   
2. Kolesov, G., H.-W. Mewes, and D. Frishman.
   SNAPping up Functionally Related Genes Based on Context Information.
   In Mewes, H.-W., H. Seidel and B. Weiss Eds.
   Ernst Schering Research Foundation Workshop Volume 38: Bioinformatics and Genome Analysis.
   Springer-Verlag, Berlin, 2002.
3. Morgenstern, B., O. Rinner, B. Abdeddaim, D. Haase, K. F. X. Mayer, A. Dress, and H.-W. Mewes.
   Exon Discovery by Genomic Sequence Alignment.
   Bioinformatics 18: 777-787, 2002.
   PMID: 12075013
   
4. Beckers, J., J. Hoheisel, W. Mewes, M. Vingron, and M. Hrabé de Angelis.
   Molecular Phenotyping of Mouse Mutant Resources by RNA Expression Profiling.
   Current Genomics 3: 121-129, 2002.
5. Briza, P., E. Bogengruber, A. Thur, M. Rutzler, M. Munsterkotter, I. W. Dawes, and M. Breitenbach.
   Systematic analysis of sporulation phenotypes in 624 non-lethal homozygous deletion strains of Saccharomyces cerevisiae.
   Yeast 19: 403-422, 2002.
   PMID: 11921089
   
6. Frishman, D., Kaps A., H. W. Mewes.
   Online genomics facilities in the new millennium.
   Pharmacogenomics. 3: 265-271, 2002.
   PMID: 11972447
   
7. Kosarev, P., K. F. Mayer, and C. S. Hardtke.
   Evaluation and classification of RING-finger domains encoded by the Arabidopsis genome.
   Genome Biol 3: RESEARCH0016, 2002.
   PMID: 11983057
8. Mayer, K. and H. W. Mewes.
   How can we deliver the large plant genomes? Strategies and perspectives.
   Curr.Opin.Plant Biol 5: 173-177, 2002.
   PMID: 11856615
   
9. Mewes, H. W., D. Frishman, U. Guldener, G. Mannhaupt, K. Mayer, M. Mokrejs, B. Morgenstern, M. Munsterkotter, S. Rudd, and B. Weil.
   MIPS: a database for genomes and protein sequences.
   Nucleic Acids Res 30: 31-34, 2002.
   PMID: 11752246
   
10. Frishman, D.
    Knowledge-based selection of targets for structural genomics.
    Protein Engineering 15:169-183, 2002. PMID: 11932488
    
11. Schoof, H., P. Zaccaria, H. Gundlach, K. Lemcke, S. Rudd, G. Kolesov, R. Arnold, H. W. Mewes, and K. F. Mayer.
    MIPS Arabidopsis thaliana Database (MAtDB): an integrated biological knowledge resource based on the first complete plant genome.
    Nucleic Acids Res 30: 91-93, 2002.
    PMID: 11752263
    
12. Schulte, U., I. Becker, H. W. Mewes, and G. Mannhaupt.
    Large scale analysis of sequences from Neurospora crassa.
    J.Biotechnol. 94: 3-13, 2002.
    PMID: 11792448
    
13. Wu, C. H., H. Huang, L. Arminski, J. Castro-Alvear, Y. Chen, Z. Z. Hu, R. S. Ledley, K. C. Lewis, H. W. Mewes, B. C. Orcutt, B. E. Suzek, A. Tsugita, C. R. Vinayaka, L. S. Yeh, J. Zhang, and W. C. Barker.
    The Protein Information Resource: an integrated public resource of functional annotation of proteins.
    Nucleic Acids Res 30: 35-37, 2002.
    PMID: 11752247
    

2001

1. Barker, W. C., J. S. Garavelli, Z. Hou, H. Huang, R. S. Ledley, P. B. McGarvey, H. W. Mewes, B. C. Orcutt, F. Pfeiffer, A. Tsugita, C. R. Vinayaka, C. Xiao, L. S. Yeh, and C. Wu.
   Protein Information Resource: a community resource for expert annotation of protein data.
   Nucleic Acids Research 29: 29-32, 2001.
2. Bevan, M., K. Mayer, O. White, J. A. Eisen, D. Preuss, T. Bureau, S. L. Salzberg, and H. W. Mewes.
   Sequence and Analysis of the Arabidopsis Genome.
   Curr.Opin.Plant Biol. 4: 105-110, 2001.
3. Frishman, D., K. Albermann, J. Hani, K. Heumann, A. Metanomski, A. Zolllner, and H. W. Mewes.
   Functional and structural genomics using PEDANT.
   Bioinformatics 17: 144-157, 2001.
4. Geier, B., G. Kastenmüller, M. Fellenberg, H. W. Mewes, and B. Morgenstern.
   The HIB database of annotated UniGene clusters.
   Bioinformatics 17: 571-572, 2001.
5. Heidenreich, B., K. Mayer, H. Sandermann, and D. Ernst.
   Mercury induced genes in Arabidopsis thaliana: identification of induced genes upon long term mercuric ion exposure.
   Plant, Cell and Environment 24: 1227-1234, 2001.
6. Kolesov, G., H. W. Mewes, and D. Frishman.
   Snapping up functionally related genes based on context information: a colinearity-free approach.
   J.Mol.Biol. 311: 639-656, 2001.
7. Mayer, K., G. Murphy, R. Tarchini, R. Wambutt, G. Volckaert, T. Pohl, A. Duesterhoeft, W. Stiekema, K. D. Entian, N. Terryn, K. Lemcke, D. Haase, C. R. Hall, A. M. van Dodeweerd, S. V. Tingey, H. W. Mewes, M. W. Bevan, and I. Bancroft.
   Conservation of microstructure between a sequenced region of the genome of rice and multiple segments of the genome of Arabidopsis thaliana.
   Genome Res. 11: 1167-1174, 2001.
8. Wiemann, S., B. Weil, R. Wellenreuther, H. Gassenhuber, S. Glassl, W. Ansorge, M. Bocher, H. Blöcker, S. Bauersachs, H. Blum, J. Lauber, A. Düsterhöft, A. Beyer, K. Kohrer, N. Strack, H. W. Mewes, B. Ottenwalder, Obermaier B., J. Tampe, D. Heubner, Wambutt R., B. Korn, M. Klein, and A. Poustka.
   Toward a Catalog of Human Genes and Proteins: Sequencing and Analysis of 500 Novel Complete Protein Coding Human cDNAs.
   Genome Res. 11: 422-435, 2001.

2000

1. Barker, W. C., J. S. Garavelli, H. Huang, P. B. McGarvey, B. C. Orcutt, G. Y. Srinivasarao, C. Xiao, L. S. Yeh, R. S. Ledley, J. F. Janda, F. Pfeiffer, H. W. Mewes, A. Tsugita, and C. Wu.
   The Protein Information Resource (PIR).
   Nucleic Acids Res. 28: 41-44, 2000.
2. Fellenberg, M., Albermann, K, Zollner, A., Mewes, H. W., and Hani, J. .
   Integrative Analysis of Protein Interaction Data. 8, 152-161. 2000.
   Menlo Park, California, AAAI Press. Conf. on Intelligent Systems for Molecular Biology (ISMB). Altmann, R., Bailey, T. L., Bourne, P., Gribskov, M., Lengauer, T., Shindyalov, I. N., Ten Eyck, L. F., and Weissig, H.
3. Mewes, H. W., D. Frishman, C. Gruber, B. Geier, D. Haase, A. Kaps, K. Lemcke, G. Mannhaupt, F. Pfeiffer, C. ller, S. Stocker, and B. Weil.
   MIPS: a database for genomes and protein sequences.
   Nucleic Acids Res. 28: 37-40, 2000.
4. Ruepp, A., Graml, W., Santos-Martinez, M. L., Koretke, K. K., Mewes, H. W., Frishman, D., Stocker, S., Lupas, A. N., and Baumeister, W.
   The genome of Thermoplasma acidophilum, a scavenger in an extremely acidic environment.
   Nature 407, 508-513. 9-28-2000.
5. Salanoubat, M., K. Lemcke, M. Rieger, W. Ansorge, M. Unseld, B. Fartmann, G. Valle, H. Blocker, M. Perez-Alonso, B. Obermaier, M. Delseny, M. Boutry, L. A. Grivell, R. Mache, P. Puigdomenech, S. de, V, N. Choisne, F. Artiguenave, C. Robert, P. Brottier, P. Wincker, L. Cattolico, J. Weissenbach, W. Saurin, F. Quetier, M. Schafer, S. Muller-Auer, C. Gabel, M. Fuchs, V. Benes, E. Wurmbach, H. Drzonek, H. Erfle, N. Jordan, S. Bangert, R. Wiedelmann, H. Kranz, H. Voss, R. Holland, P. Brandt, G. Nyakatura, A. Vezzi, M. D'Angelo, A. Pallavicini, S. Toppo, B. Simionati, A. Conrad, K. Hornischer, G. Kauer, T. H. Lohnert, G. Nordsiek, J. Reichelt, M. Scharfe, O. Schon, M. Bargues, J. Terol, J. Climent, P. Navarro, C. Collado, A. Perez-Perez, B. Ottenwalder, D. Duchemin, R. Cooke, M. Laudie, C. Berger-Llauro, B. Purnelle, D. Masuy, M. de Haan, A. C. Maarse, J. P. Alcaraz, A. Cottet, E. Casacuberta, A. Monfort, A. Argiriou, M. flores, R. Liguori, D. Vitale, G. Mannhaupt, D. Haase, H. Schoof, S. Rudd, P. Zaccaria, H. W. Mewes, and K. F. Mayer.
   Sequence and analysis of chromosome 3 of the plant Arabidopsis thaliana. European Union Chromosome 3 Arabidopsis Sequencing Consortium, The Institute for Genomic Research & Kazusa DNA Research Institute.
   Nature 408: 820-822, 2000.
6. Scharfe, C., P. Zaccaria, K. Hoertnagel, M. Jaksch, T. Klopstock, M. Dembowski, R. Lill, H. Prokisch, K. D. Gerbitz, W. Neupert, H. W. Mewes, and T. Meitinger.
   MITOP, the mitochondrial proteome database: 2000 update.
   Nucleic Acids Res. 28: 155-158, 2000.
7. Strimmer, K. and V. Moulton.
   Likelihood analysis of phylogenetic networks using directed graphical models.
   Mol Biol Evol. 17: 875-881, 2000.
8. Tabata, S., T. Kaneko, Y. Nakamura, H. Kotani, T. Kato, E. Asamizu, N. Miyajima, S. Sasamoto, T. Kimura, T. Hosouchi, K. Kawashima, M. Kohara, M. Matsumoto, A. Matsuno, A. Muraki, S. Nakayama, N. Nakazaki, K. Naruo, S. Okumura, S. Shinpo, C. Takeuchi, T. Wada, A. Watanabe, M. Yamada, M. Yasuda, S. Sato, B. M. de la, E. Huang, L. Spiegel, L. Gnoj, A. O'Shaughnessy, R. Preston, K. Habermann, J. Murray, D. Johnson, T. Rohlfing, J. Nelson, T. Stoneking, K. Pepin, J. Spieth, M. Sekhon, J. Armstrong, M. Becker, E. Belter, H. Cordum, M. Cordes, L. Courtney, W. Courtney, M. Dante, H. Du, J. Edwards, J. Fryman, B. Haakensen, E. Lamar, P. Latreille, S. Leonard, R. Meyer, E. Mulvaney, P. Ozersky, A. Riley, C. Strowmatt, C. Wagner-McPherson, A. Wollam, M. Yoakum, M. Bell, N. Dedhia, L. Parnell, R. Shah, M. Rodriguez, L. H. See, D. Vil, J. Baker, K. Kirchoff, K. Toth, L. King, A. Bahret, B. Miller, M. Marra, R. Martienssen, W. R. McCombie, R. K. Wilson, G. Murphy, I. Bancroft, G. Volckaert, R. Wambutt, and A. Dusterhoft.
   Sequence and analysis of chromosome 5 of the plant Arabidopsis thaliana. The Kazusa DNA Research Institute, The Cold Spring Harbor and Washington University in St Louis Sequencing Consortium & The European Union Arabidopsis Genome Sequencing Consortium.
   Nature 408: 823-826, 2000.
9. The Arabidopsis Genome Initiative.
   Analysis of the genome sequence of the flowering plant Arabidopsis thaliana.
   Nature 408: 796-815, 2000.
10. Wambutt, R. and et al.
    Progress in Arabidopsis genome sequencing and functional genomics.
    J Biotechnol. 78: 281-292, 2000.

1999

1. Barker, W. C., J. S. Garavelli, P. B. McGarvey, C. R. Marzec, B. C. Orcutt, G. Y. Srinivasarao, L. S. L. Yeh, R. S. Ledley, H. W. Mewes, F. Pfeiffer, A. Tsugita, and C. Wu.
   The PIR-International Protein Sequence Database.
   Nucleic Acids Research 27: 39-43, 1999.
2. Bevan, M., I. Bancroft, H. W. Mewes, R. Martienssen, and R. McCombie.
   Clearing a path through the jungle: progress in Arabidopsis genomics.
   Bioessays 21: 110-120, 1999.
3. Entian, K. D., T. Schuster, J. H. Hegemann, D. Becher, H. Feldmann, U. Güldener, R. Götz, M. Hansen, C. P. Hollenberg, G. Jansen, W. Kramer, S. Klein, P. Kötter, J. Kricker, H. Launhardt, G. Mannhaupt, A. Maierl, P. Meyer, H. W. Mewes, T. Munder, R. K. Niedenthal, R. M. Ramazani, A. Röhmer, A. Römer, M. Rose, B. Schäfer, M.-L. Siegler, J. Vetter, N. Wilhelm, K. Wolf, F. K. Zimmermann, A. Zolllner, and A. Hinnen.
   Functional analysis of 150 deletion mutants in Saccharomyces cerevisiae by a systematic approach.
   Mol.Gen.Genet. 1999.
4. Frishman, D. and H. W. Mewes.
   Genome-based structural biology.
   Progress in Biophysics & Molecular Biology 72: 1-17, 1999.
5. Frishman, D., A. Mironov, and M. Gelfand.
   Starts of bacterial genes: estimating the reliability of computer predictions [In Process Citation].
   Gene 234: 257-265, 1999.
6. Giegerich, R., Haase, D., and Rehmsmeier, M.
   Prediction and Visualization of Structural Switches in RNA. 126-137. 1999.
   World Scientific. Pacific Symposium on BIOCOMPUTING '99.
   Altmann, R. B., Dunker, A. K., Hunter, L., Klein, T. E., and Lauderdale, K.
7. Houry, W., D. Frishman, C. Eckerskorn, Lottspeich F., and F. U. Hartl.
   Identification of in vivo substrates of the chaperonin GroEL.
   Nature 402: 147-154, 1999.
8. Kal, A. J., A. J. van Zonneveld, V. Benes, M. van den Berg, M. G. Koerkamp, K. Albermann, N. Strack, J. M. Ruijter, A. Richter, B. Dujon, W. Ansorge, and H. F. Tabak.
   Dynamics of gene expression revealed by comparison of serial analysis of gene expression transcript profiles from yeast grown on two different carbon sources.
   Mol Biol Cell 10: 1859-1872, 1999.
9. Mayer, K., C. Schuller, R. Wambutt, G. Murphy, G. Volckaert, T. Pohl, A. Dusterhoft, W. Stiekema, K. D. Entian, N. Terryn, B. Harris, W. Ansorge, P. Brandt, L. Grivell, M. Rieger, M. Weichselgartner, S. de, V, B. Obermaier, R. Mache, M. Muller, M. Kreis, M. Delseny, P. Puigdomenech, M. Watson, W. R. McCombie, T. Schmidtheini, B. Reichert, D. Portatelle, M. Perez-Alonso, M. Boutry, I. Bancroft, P. Vos, Hoheisel J.D., W. Zimmermann, H. Wedler, P. Ridley, S. A. Langham, B. McCullagh, L. Bilham, J. Robben, J. Van der Schueren, B. Grymonprez, Y.-J. Chuang, Vandenbussche F., M. Braeken, I. Weltjens, M. Voet, I. Bastiaens, R. Aert, E. Defoor, T. Weitzenegger, G. Bothe, U. Ramsperger, H. Hilbert, M. Braun, E. Holzer, A. Brandt, S. Peters, M. van Staveren, W. Dirkse, P. Mooijman, R. Klein-Lankhorst, M. Rose, J. Hauf, P. Kötter, S. Berneiser, S. Hempel, M. Feldpausch, S. Lamberth, H. Van den Daele, A. De Keyser, C. Buysshaert, J. Gielen, R. Villarroel, R. De Clerck, M. Van Montagu, J. Rogers, A. Cronin, M. Quail, S. Bray-Allen, L. Clark, J. Doggett, S. Hall, M. Kay, N. Lennard, K. McLay, R. Mayes, A. Pettett, M. A. Rajandream, M. Lyne, V. Benes, S. Rechmann, D. Borkova, H. Blöcker, M. Scharfe, M. Grimm, T. H. Löhnert, S. Dose, M. de Haan, A. Maarse, M. Schäfer, S. Müller-Auer, C. Gabel, M. Fuchs, B. Fartmann, K. Granderath, D. Dauner, A. Herzl, S. Neumann, A. Argiriou, D. Vitale, R. Liguori, E. Piravandi, O. Massenet, F. Quigley, G. Clabauld, A. Mündlein, R. Felber, S. Schnabl, R. Hiller, W. Schmidt, A. Lechamy, S. Aubourg, F. Chefdor, R. Cooke, C. Berger, A. Montfort, E. Casacuberta, T. Gibbons, N. Weber, M. Vandenbol, M. Bargues, J. Terol, A. Torres, A. Perez-Perez, B. Pumelle, E. Bent, S. Johnson, D. Tacon, T. Jesse, L. Heijnen, S. Schwarz, P. Scholler, S. Heber, P. Francs, C. Bielke, D. Frishman, D. Haase, K. Lemcke, H. W. Mewes, S. Stocker, P. Zaccaria, M. Bevan, and The Cold Spring Harbour Sequencing Consortium.
   Sequence and analysis of chromosome 4 of the plant Arabidopsis thaliana.
   Nature 402: 769-777, 1999.
10. Mewes, H. W., K. Heumann, A. Kaps, K. Mayer, F. Pfeiffer, S. Stocker, and D. Frishman.
    MIPS: a database for genomes and protein sequences.
    Nucleic Acid Research 27: 44-48, 1999.
11. Mewes, H. W.
    Carving the Infrastructure - Bioinformatics for Genomics.
    European BioPharmaceutical Review March: 58-60, 1999.
12. Mewes, H. W., A. Maierl, and D. Frishman.
    Protein sequences and genome databases.
    In Kellner, M., F. Lottspeich, and Meyer H.E., eds.
    Microcharacterization of proteins. 1999, 301-318.
13. Scharfe, C., P. Zaccaria, K. Hoertnagel, M. Jaksch, T. Klopstock, R. Lill, H. Prokisch, K.-D. Gerbitz, H. W. Mewes, and T. Meitinger.
    MITOP: database for mitochondria-related proteins, genes and diseases.
    Nucleic Acids Research 27: 153-155, 1999.
14. Srinivasarao, G. Y., L. S. L. Yeh, C. R. Marzec, B. C. Orcutt, W. C. Barker, and F. Pfeiffer.
    Database of protein sequence alignments: PIR-ALN.
    Nucleic Acids Res 27: 284-285, 1999.
15. Strack, N. and Mewes, H. W.
    SESAM: Seed Extraction Sequence Analysis Method. Giegerich, R. and Wingender, E. Proceedings of the German Conference on Bioinformatics GCB '99(Computer Science and Biology), 59-65. 1999.
    Braunschweig, Bielefeld. German Conference on Bioinformatics. 6-4-0099.

1998

1. Barker, W. C., J. S. Garavelli, D. H. Haft, L. T. Hunt, C. R. Marzec, B. C. Orcutt, G. Y. Srinivasarao, L. S. L. Yeh, R. S. Ledley, H. W. Mewes, F. Pfeiffer, and A. Tsugita.
   The PIR-International Protein Sequence Database.
   Nucleic Acids Research 26: 27-32, 1998.
2. Bevan, M., I. Bancroft, E. Bent, K. Love, H. Goodman, C. Dean, R. Bergkamp, W. Dirkse, M. Vanstaveren, W. Stiekema, L. Drost, P. Ridley, S. A. Hudson, K. Patel, G. Murphy, P. Piffanelli, H. Wedler, E. Wedler, R. Wambutt, T. Weitzenegger, T. M. Pohl, N. Terryn, J. Gielen, R. Villarroel, R. Declerck, R. De Clerck, M. Van Montagu, A. Lecharny, S. Auborg, I. Gy, M. Kreis, N. Lao, T. Kavanagh, S. Hempel, P. Kotter, K. D. Entian, M. Rieger, M. Schaeffer, B. Funk, M. Mueller-Auer, M. Silvey, R. James, A. Montfort, A. Pons, P. Puigdomenech, A. Douka, E. Voukelatou, D. Milioni, P. Hatzopoulos, E. Piravandi, B. Obermaier, H. Hilbert, A. Düsterhöft, T. Moores, J. D. G. Jones, T. Eneva, K. Palme, V. Benes, S. Rechman, W. Ansorge, R. Cooke, C. Berger, M. Delseny, M. Voet, G. Volckaert, H. W. Mewes, S. Klostermann, C. Schueller, and N. Chalwatzis.
   Analysis of 1.9 MB of contiguous sequence from chromosome 4 of A. thaliana.
   Nature 391: 485-488, 1998.
3. Frishman, D., A. Mironov, H. W. Mewes, and M. Gelfand.
   Combining diverse evidence for gene recognition in completely sequenced bacterial genomes.
   Nucleic Acids Research 26: 2941-2947, 1998.
4. Frishman, D., K. Heumann, A. Lesk, and H. W. Mewes.
   Comprehensive, comprehensible, distributed and intelligent databases: current status.
   Bioinformatics 14: 551-561, 1998.
5. Hani, J. and H. Feldmann.
   tRNA genes and retroelements in the yeast genome.
   Nucleic Acids Res 26: 689-96, 1998.
6. Hartung, K., D. Frishman, A. Hinnen, and S. Woelfl.
   Single-read sequence tags of a limited number of genomic DNA fragments provide an inexpensive tool for comparative genome analysis.
   Yeast 14: 1327-1332, 1998.
7. Koesel, S., E. M. Grasbon-Frodl, U. Mautsch, R. Egensperger, U. von Eitzen, D. Frishman, S. Hofmann, K.-D. Gerbitz, P. Mehraein, and Graeber M.B.
   Sequence analysis of mitochondrial complex I genes in pathologically proved Parkinson disease.
   Neurogenetics 1: 197-204, 1998.
8. Mewes, H. W., D. Frishman, A. Zollner, and K. Heumann.
   The Bioinformatics of the Yeast Genome.
   In Brown, A. J. P. and M. F. Tuite, eds.
   Yeast Gene Analysis. Academic Press. 1998, 33-52.
9. Mewes, H. W., J. Hani, F. Pfeiffer, and D. Frishman.
   MIPS: a database for protein sequences and complete genomes.
   Nucleic Acids Research 26: 33-7, 1998.
10. Muckenthaler, M., N. Gunkel, D. Frishman, A. Cyrklaff, P. Tomancak, and M. W. Hentze.
    Iron regulatory protein-1 (IRP-1) is highly conserved in the invertebrate species Drosophila Melanogaster and Caenorhabditis elegans.
    European Journal of Biochemistry 254: 230-237, 1998.

1997

1. Boehm, S., D. Frishman, and H. W. Mewes.
   Variations of the C2Hc zinc finger motif in the yeast genome.
   Nucleic Acids Research 25: 2464-2469, 1997.
2. Bussey, H., R. K. Storms, A. Ahmed, K. Albermann, E. Allen, W. Ansorge, R. Araujo, A. Aparicio, B. Barrell, K. Badcock, V. Benes, D. Botstein, S. Bowman, M. Bruckner, J. Carpenter, J. M. Cherry, E. Chung, C. Churcher, F. Coster, K. Davis, R. W. Davis, F. S. Dietrich, H. Delius, T. Dipaolo, E. Dubois, A. Düsterhöft, Z. Du, M. Duncan, A. Favello, M. Floeth, N. Fortin, J. D. Friesen, M. Fritz, L. Fulton, S. Gattung, A. Goffeau, T. Greco, J. Hall, K. Hallsworth, J. Hawkins, U. Hebling, K. Heumann, H. Hilbert, L. Hillier, S. Hunicke-Smith, R. Hyman, M. Jier, D. Johnson, L. Johnston, S. Kalman, J. Kirsten, K. Kleine, C. Komp, T. Kucaba, O. Kurdi, Y. Langston, D. Lashkari, P. Latreille, F. Le, H. Lew, A. Lin, D. Lin, E. J. Louis, R. Marathe, E. Mardis, S. Menezes, F. Messenguy, H. W. Mewes, N. Miller, S. Mirtipati, D. Moestl, S. Mueller-Auer, A. Namath, U. Nentwich, J. Nelson, M. Nhan, P. Oefner, A. Pauley, D. Pearson, D. Peluso, F. X. Petel, T. M. Pohl, B. Purnelle, M. A. Rajandream, S. Rechmann, M. Rieger, L. Rifken, L. Riles, D. Roberts, M. Schaefer, M. Scharfe, B. Scherens, S. Schramm, M. Schroeder, A. M. Sdicu, L. Stellyes, A. Taich, E. Trevaskis, L. A. Urrestarazu, S. Ushinsky, M. Vaudin, F. Vierendeels, S. Vissers, H. Voss, S. V. Walsh, R. Wambutt, Y. Wang, R. Waterston, E. Wedler, H. Wedler, L. Wilcox, R. Wilson, E. Winnett, P. Wohldman, W. W. Zhong, A. Zollner, D. H. Vo, and J. Hani.
   The nucleotide sequence of Saccharomyces cerevisiae chromosome XVI.
   Nature 387: 103-105, 1997.
3. Dujon, B., K. Albermann, M. Aldea, D. Alexandraki, W. Ansorge, J. Arino, V. Benes, C. Bohn, M. Bolotin-Fukuhara, R. Bordonne, J. Boyer, A. Camasses, A. Casamayor, C. Casas, G. Cheret, C. Cziepluch, B. Daignanfornier, D. V. Dang, M. Dehaan, H. Delius, P. Durand, C. Fairhead, H. Feldmann, L. Gaillon, F. Galisson, F. J. Gamo, C. Gancedo, A. Goffeau, S. E. Goulding, L. A. Grivell, B. Habbig, N. J. Hand, J. H. U. Hani, U. Hebling, Y. Hernando, E. Herrero, K. Heumann, R. Hiesel, F. Hilger, B. Hofmann, C. P. Hollenberg, B. Hughes, J. C. Jauniaux, A. Kalogeropoulos, C. Katsoulou, E. Kordes, M. J. Lafuente, O. Landt, E. J. Louis, A. C. Maarse, A. Madania, G. Mannhaupt, C. Marck, R. P. Martin, H. W. Mewes, G. Michaux, V. Paces, A. G. Parle-McDermott, B. M. Pearson, A. Perrin, B. Pettersson, O. Poch, T. M. Pohl, R. Poirey, D. Portetelle, A. Pujol, B. Purnelle, M. R. Rad, S. Rechmann, C. Schwager, M. Schweizer, F. Sor, F. Sterky, I. A. Tarassov, C. Teodoru, H. Tettelin, A. Thierry, E. Tobiasch, M. Tzermia, M. Uhlen, M. Unseld, M. Valens, M. Vendenbol, I. Vetter, C. Vleck, M. Voet, G. Volckaert, H. Voss, R. Wambutt, H. Wedler, S. Wiemann, B. Winsor, K. H. Wolfe, A. Zollner, E. Zumstein, and K. Kleine.
   The nucleotide sequence of Saccharomyces Cerevisiae Chromosome XV.
   Nature 387: 98-102, 1997.
4. Frishman, D. and H. W. Mewes.
   Protein structural classes in five complete genomes.
   Nature Struct.Biol. 4: 626-628, 1997.
5. Frishman, D. and H. W. Mewes.
   PEDANTic genome analysis.
   Trends Genet. 13: 415-416, 1997.
6. Heumann, K., M. Bähr, A. Maierl, A. Gleissner, W. Peng, M. Gerstner, P. Maierl, K. Albermann, J. Hani, A. Zollner, G. Fobo, F. Pfeiffer, D. Frishman, P. Jordan, and H. W. Mewes.
   The Yeast Genome CD-ROM.
   Nature 1997.
7. Jacq, C., J. Altmoerbe, B. Andre, W. Arnold, A. Bahr, J. P. G. Ballesta, M. Bargues, L. Baron, A. Becker, N. Biteau, H. Bloecker, C. Blugeon, J. Boskovic, P. Brandt, M. Bruckner, M. J. Buitrago, F. Coster, T. Delaveau, F. Delrey, B. Dujon, L. G. Eide, J. M. Garciacantalejo, A. Goffeau, A. Gomezperis, C. Granotier, H. Bloecker, P. Brandt, F. Foury, J. L. Jauniaux, B. Purnelle, F. Coster, A. Goffeau, L. Paulin, A.-M. Saren, P. Laamanen, E. Louis, J. Perea, C. Blugeon, T. Delaveu, J. E. Perez-Ortin, D. Salom, A. Gomez-Peris, M. Perez-Alonso, N. Paricio, M. Bargues, T. M. Pohl, H. Prydz, I. G. Eide, S. W. Rasmussen, M. Rieger, S. Mueller-Auer, M. Brueckner, M. Schaefer, G. Wagner, E. R. Schmidt, A. Bahr, C. Kraemer, P. Hankeln, S. Moeller-Rieker, H. P. Saluz, S. Woelfl, V. Hanemann, L. A. Urrestarazu, B. Andre, S. Vissers, G. Volckaert, P. Verhasselt, M. Voet, R. Wambutt, H. Wedler, E. Wedler, M. Scharfe, J. D. Hoheisel, P. Scholler, S. Schwarz, H. W. Mewes, J. Hani, K. Heumann, K. Kleine, P. Zaccaria, A. C. B. B. Zollner, C. M. Churcher, R. Connor, D. Harris, D. F. Harris, L. Murphy, K. Oliver, M. A. Rajandream, L. Shore, S. V. S. D. F. S. Walsh, J. Mulligan, E. Allen, R. Araujo, E. Aviles, A. Berno, J. Carpenter, E. Chen, J. M. Cherry, E. Chung, M. Duncan, S. Hunicke-Smith, R. Hyman, C. Komp, D. Kashkari, H. Lew, D. Lin, D. Mosedale, K. Nakahara, A. Namath, P. Oefner, C. Oh, F. X. Petel, D. Roberts, S. Schramm, M. Schroeder, T. Shogren, N. Shroff, A. Winant, M. Yelton, D. Botstein, R. W. S. J. M. Davis, S. Andrew, R. Brinman, J. Cooper, H. Ding, Z. Du, A. Favello, L. Fulton, S. Gattung, T. Greco, J. Kirsten, T. Kucaba, K. Hallsworth, J. Hawkins, L. Hillier, M. Jier, D. Johnson, L. Johnston, Y. Langston, P. Latrille, T. Le, E. Mardis, S. Menezes, N. Miller, M. Nhan, A. Pauley, D. Peluso, L. Rifken, L. Riles, A. Taich, E. Trevaskis, D. Vignati, L. Wilcox, P. Wohldman, M. Vaudin, R. Wilson, and R. Waterston.
   The nucleotide sequence of Saccharomyces Cerevisiae chromosome IV.
   Nature 387: 75-78, 1997.
8. Johnston, M., L. Hillier, L. Riles, K. Albermann, B. Andre, W. Ansorge, V. Benes, M. Bruckner, H. Delius, E. Dubois, A. Dusterhoft, K. D. Entian, M. Floeth, A. Goffeau, U. Hebling, K. Heumann, D. Heussneitzel, H. Hilbert, F. Hilger, K. Kleine, P. Kotter, E. J. Louis, F. Messenguy, H. W. Mewes, T. Miosga, D. Möstl, S. Müller-Auer, U. Nentwich, B. Obermaier, E. Piravandi, T. M. Pohl, D. Portelle, B. Purnelle, S. Rechmann, M. Rieger, M. Rinke, M. Rose, M. Scharfe, B. Scherens, P. Scholler, C. Schwager, S. Schwarz, A. P. Underwood, L. A. Urrestarazu, M. Vandenbol, P. Verhasselt, F. Vierendeels, M. Voet, G. Volckaert, H. Voss, R. Wambutt, E. Wedler, F. K. Zimmermann, A. Zollner, J. Hani, and Hoheisel J.D.
   The nucleotide sequence of Saccharomyces cerevisiae chromosome XII.
   Nature 387: 87-90, 1997.
9. Kammerer, S., N. Arnold, W. Gutensohn, H. W. Mewes, W. H. Kunau, G. Hofler, A. A. Roscher, and A. Braun.
   Genomic organization and molecular characterization of a gene encoding HSPXF, a human peroxisomal farnesylated protein.
   Genomics 45: 200-210, 1997.
10. Kaps, A., K. Heumann, D. Frishman, M. Bähr, and H. W. Mewes.
    Visualization and Analysis of the Complete Yeast Genome. In Hofestädt, R. and Lengauer T., eds.
    Bioinformatics. Berlin-Heidelberg, Springer Verlag. 1997, 178-188.
11. Mewes, H. W., K. Albermann, M. Bahr, D. Frishman, A. Gleissner, J. Hani, K. Heumann, K. Kleine, A. Maierl, S. G. Oliver, F. Pfeiffer, and A. Zollner.
    Chart of duplications.
    Nature 387: 33-34, 1997.
12. Mewes, H. W., F. Pfeiffer, and K. Heumann.
    Sequenzdatenbanken: Vom Gen zum Genom.
    Biospektrum 3: 26-31, 1997.
13. Mewes, H. W., K. Albermann, M. Bahr, D. Frishman, A. Gleissner, J. Hani, K. Heumann, K. Kleine, A. Maierl, S. G. Oliver, F. Pfeiffer, and A. Zollner.
    Chromosome maps.
    Nature 387: 9-32, 1997.
14. Mewes, H. W., D. Frishman, and K. Heumann.
    Das Hefegenom - von der Sequenz zur Funktion.
    Spektrum der Wissenschaften 8: 22-29, 1997.
15. Mewes, H. W., K. Albermann, M. Bahr, D. Frishman, A. Gleissner, J. Hani, K. Heumann, K. Kleine, A. Maierl, S. G. Oliver, F. Pfeiffer, and A. Zollner.
    Overview of the yeast genome.
    Nature 387: 7-8, 1997.
16. Mewes, H. W., K. Albermann, K. Heumann, S. Liebl, and F. Pfeiffer.
    MIPS - a database for protein sequences, homology data and yeast genome information.
    Nucleic Acids Research 25: 28-30, 1997.
17. Mewes, H. W., K. Albermann, M. Bahr, D. Frishman, A. Gleissner, J. Hani, K. Heumann, K. Kleine, A. Maierl, S. G. Oliver, F. Pfeiffer, and A. Zollner.
    Gazetteer.
    Nature 387: 35-65, 1997.
18. Philippsen, P., K. Kleine, R. Pohlmann, A. Dusterhoft, K. Hamberg, J. H. Hegemann, B. Obermaier, L. A. Urrestarazu, R. Aert, K. Albermann, R. Altmann, B. Andre, V. Baladron, J. P. G. Ballesta, A. M. Becam, J. Beinhauer, J. Boskovic, M. J. Buitrago, F. Bussereau, F. Coster, M. Crouzet, M. Dangelo, F. Dalpero, A. Deantoni, F. Delrey, F. Doignon, H. Domdey, E. Dubois, T. Fiedler, U. Fleig, M. Floeth, C. Fritz, C. Gaillardin, J. M. Garcia-Cantalejo, N. Glansdorff, A. Goffeau, U. Gueldener, J. H. Hegemann, C. Herbert, K. Heumann, D. Heuss-Neitzel, H. Hilbert, K. Hinni, I. Iraqui Houssaini, M. Jacquet, A. Jiminez, J. L. Jonniaux, L. Karpfinger, G. Lanfranchi, A. Lepingle, H. Levesque, R. Lyck, M. Maftahi, L. Mallet, K. C. T. Maurer, F. Messenguy, D. Möstl, H. W. Mewes, F. Nasr, J. M. Nicaud, R. K. Niedenthal, B. Obermaier, D. Pandolfo, A. Pierard, E. Piravandi, R. J. Planta, T. Pohl, B. Purnelle, C. Rebischung, M. Remacha, J. L. Revuelta, M. Rinke, J. E. Saiz, F. Sartorello, B. Scherens, M. Sen-Gupta, A. Soler-Mira, J. H. M. Urbanus, L. A. Urrestarazu, G. Valle, L. Van Dyck, P. Verhasselt, F. Vierendeels, S. Vissers, M. Voet, G. Volckaert, A. Wach, R. Wambutt, H. Wedler, A. Zollner, and J. Hani.
    The nucleotide sequence of Saccharomyces cerevisiae chromosome XIV and its evolutionary implications.
    Nature 387: 93-98, 1997.
19. Tettelin, H., M. L. A. Carbone, K. Albermann, M. Albers, J. Arroyo, U. Backes, T. Barreiros, I. Bertani, A. J. Bjourson, M. Bruckner, C. V. Bruschi, G. Carignani, L. Castagnoli, E. Cerdan, M. L. Clemente, A. Coblenz, M. Coglievina, E. Coissac, E. Defoor, S. Delbino, H. Delius, D. Delneri, P. Dewergifosse, B. Dujon, P. Durand, A. Goffeau, P. Guerreiro, J. Hani, M. Hansen, U. Hebling, K. Hernandez, K. H. F. Heumann, B. Hofmann, K. J. Indge, C. M. James, R. Klima, P. Kötter, B. Kramer, W. Kramer, G. Lauquin, H. Leuther, E. J. Louis, E. Maillier, A. Marconi, E. Martegani, M. J. Mazon, C. Mazzoni, A. D. K. McReynolds, P. Melchioretto, H. W. Mewes, O. Minenkova, S. Müller-Auer, A. Nawrocki, P. Netter, R. Neu, C. Nombela, S. G. Oliver, L. Panzeri, S. Paoluzi, P. Plevani, D. Portetelle, F. Portillo, S. Potier, B. Purnelle, M. Rieger, L. Riles, T. Rinaldi, C. Rodrigues-Pousada, E. Rodriguez-Belmonte, A. M. Rodriguez-Torres, M. Rose, M. Ruzzi, M. Saliola, M. Sanchez-Perez, B. Schäfer, M. Schäfer, M. Scharfe, T. Schmidheini, A. Schreer, J. Skala, J. L. S. H. Y. Souciet, E. Talla, A. Thierry, M. Vandenbol, Q. J. M. van der Aart, L. Van Dyck, M. Vanoni, P. Verhasselt, M. Voet, G. Volckaert, R. Wambutt, M. D. Watson, N. Weber, E. Wedler, H. Wedler, P. Wipfli, K. Wolf, L. F. Wright, P. Zaccaria, M. Zimmermann, A. Zollner, and K. Kleine.
    The nucleotide sequence of Saccharomyces cerevisiae chromosome VII.
    Nature 387: 81-84, 1997.
20. Wegener, A., W. Gimbel, T. Werner, J. Hani, D. Ernst, and H. Sandermann.
    Cloning of ozone-inducible protein from Pinus sylvestris with high sequence similarity to vertebrate 3-hydroxy-3-methylglutaryl-CoA-synthetase.
    Biochimica et Biophysica Acta 1350: 247-252, 1997.
21. Wegener, A., W. Gimbel, T. Werner, J. Hani, D. Ernst, and H. Sandermann.
    Sequence analysis and ozone-induced accumulation of polyubiquitin mRNA in Pinus sylvestris.
    Can.J.Forest Res. 27: 945-948, 1997.

1996

1. Galibert, F., D. Alexandraki, A. Baur, E. Boles, N. Chalwatzis, J. C. Chuat, F. Coster, C. Cziepluch, M. Dehaan, H. Domdey, P. Durand, K. D. Entian, M. Gatius, A. Goffeau, L. A. Grivell, A. Hennemann, C. J. Herbert, K. Heumann, F. Hilger, C. P. Hollenberg, M. E. Huang, C. Jacq, J. C. Jauniaux, C. Katsoulou, L. Kirchrath, K. Kleine, E. Kordes, P. Kötter, S. Liebl, E. J. Louis, V. Manus, H. W. Mewes, T. Miosga, B. Obermaier, J. Perea, T. Pohl, D. Portetelle, A. Pujol, B. Purnelle, R. M. Ramezani, SW. Rasmussen, M. Rose, R. Rossau, I. Schaaff-Gerstenschläger, P. H. M. Smits, T. Scarcez, N. Soriano, D. Tovan, M. Tzermia, A. Van Broekhoven, M. Vandenbol, H. Wedler, D. von Wettstein, R. Wambutt, M. Zagulski, A. Zollner, and L. Karpfinger-Hartl.
   Complete nucleotide sequence of Saccharomyces CerevisiaeChromosome X.
   EMBO Journal 15: 2031-2049, 1996.
2. George, D. G., W. C. Barker, H. W. Mewes, F. Pfeiffer, and A. Tsugita.
   The PIR-International protein sequence database.
   Nucleic Acids Research 24: 17-20, 1996.
3. Goffeau, A., B. G. Barrell, H. Bussey, R. W. Davis, B. Dujon, H. Feldmann, F. Galibert, J. D. Hoheisel, C. Jacq, M. Johnston, E. J. Louis, H. W. Mewes, Y. Murakami, P. Philippsen, H. Tettelin, and S. G. Oliver.
   Life with 6000 genes.
   Science 274: 546 ff., 1996.
4. Heumann, K. and Mewes, H. W.
   The Hashed Position Tree (HPT): A Suffix Tree Variant for Large Data Sets Stored on Slow Mass Storage Devices.
   Ziviani, N., Baeza-Yates, A., Guimaraes, G. . Proceedings of the Third South American Workshop on String Processing.
5. Heumann, K., Harris, C., and Mewes, H. W.
   A top-down approach to whole genome visualization.
   Gaasterland T., Karp P., Karplus K., Ouzounis C., Sander C., and Valencia A. 98-108. 1996.
   Menlo Park, California, AAAI Press. 1996.
6. Heumann, K. and Mewes, H. W.
   A theoretical model of genome redundancy. Hofestädt, R., Lengauer, T., Löffler, M., and Schomburg, D.
   Proceedings of the German Conference on Bioinformatics '96, 221-223. 1996. Leipzig, Univ. of Leipzig. Computer Science and Biology.
7. Kaps, A., K. Heumann, A. Maierl, and H. W. Mewes.
   Genomanalyse und WWW: Vom Klon zum Klick.
   it + ti 9-15, 1996.
8. Mewes, H. W., M. Baehr, A. Zollner, and K. Heumann.
   The complete sequence of S. cerevisiaeas a dynamic data resource.
   Microbial & Comparative Genomics 1: 204, 1996.

1995

1. Ackermann, H. W., A. Elzanowski, G. Fobo, and G. Stewart.
   Relationships of tailed phages: a survey of protein sequence identity.
   Arch.Virol. 140: 1871-1884, 1995.
2. Heumann, K., C. Harris, A. Kaps, S. Liebl, A. Maierl, F. Pfeiffer, and H. W. Mewes.
   An Integrated Services Approach to Biological Sequence Databases. In Schomburg, ed.
   Bioinformatics: From Nucleic Acids ant Proteins to Cell Metabolism. Braunschweig, GBF. 1995.
3. Mewes, H. W. and K. Heumann.
   Genome Analysis: Pattern Search in Biological Macromolecules.
   In Galil Z., U. E., ed. Combinatorial Pattern Matching. Berlin-Heidelberg, Springer Verlag. 1995, 261-285.
4. Thummler, F., P. Algarra, and G. M. Fobo.
   Sequence similarities of phytochrome to protein kinases: implication for the structure, function and evolution of the phytochrome gene family.
   FEBS Lett. 357: 149-155, 1995.
5. Vassarotti, A., B. Dujon, H. Feldmann, H. W. Mewes, and A. Goffeau.
   Structure and Organisation of the European Yeast Genome Sequencing Network.
   J.Biotechnol. 41: 131-137, 1995.

1994

1. Dujon, B., D. Alexandraki, B. Andre, W. Ansorge, V. Baladron, J. P. G. Ballesta, A. Banrevi, P. A. Bolle, M. Bolotin-Fukuhara, P. Bossier, G. Bou, J. Boyer, M. J. Bultrago, G. Cheret, L. Colleaux, B. Dalgnan-Fornier, R. F. del, C. Dion, H. Domdey, A. Duesterhoeft, S. Duesterhus, K. D. Entian, H. Erfle, P. F. Esteban, H. Feldmann, L. Fernandes, G. M. Fobo, C. Fritz, H. Fukuhara, C. Gabel, L. Gaillon, J. M. Carcia-Cantalejo, J. J. Garcia-Ramirez, M. E. Gent, M. Ghazvini, A. Goffeau, A. Gonzalez, D. Grothues, P. Guerreiro, J. Hegemann, N. Hewitt, F. Hilger, C. P. Hollenberg, O. Horaitis, K. J. Indge, A. Jacquier, C. M. James, JC. Jauniaux, A. Jimenez, H. Keuchel, L. Kirchrath, K. Kleine, P. Koetter, P. Legrain, S. Liebl, EJ. Louis, e. S. A. Maia, C. Marck, A. L. Monnier, D. Moestl, S. Mueller, B. Obermaier, SG. Oliver, C. Pallier, S. Pascolo, F. Pfeiffer, P. Philippsen, RJ. Planta, FM. Pohl, T. M. Pohl, R. Poehlmann, D. Portetelle, B. Purnelle, V. Puzos, M. R. Rad, S. W. Rasmussen, M. Remacha, J. L. Revuelta, G. F. Richard, M. Rieger, C. Rodrigues-Pousada, M. Rose, T. Rupp, M. A. Santos, C. Schwager, C. Sensen, J. Skala, H. Soares, F. Sor, J. Stegemann, H. Tettelin, A. Thierry, M. Tzermia, L. A. Urrestarazu, D. L. van, V.-R. J. C. van, M. Valens, M. Vandenbol, C. Vilela, S. Vissers, W. D. von, H. Voss, S. Wiemann, G. Xu, J. Zimmermann, M. Haasemann, I. Becker, and H. W. Mewes.
   The complete sequence of chromosome XI of Saccharomyces Cerevisiae.
   Nature 396: 371-379, 1994.
2. Feldmann, H., M. Aigle, G. Aljinovic, B. Andre, MC. Baclet, C. Barthe, A. Baur, AM. Becam, N. Biteau, E. Boles, T. Brandt, M. Brendel, M. Bruckner, F. Bussereau, C. Christiansen, R. Contreras, M. Crouzet, C. Cziepluch, N. Demolis, T. Delaveau, F. Doignon, H. Domdey, S. Dusterhus, E. Dubois, B. Dujon, M. Elbakkoury, KD. Entian, M. Feuermann, W. Fiers, GM. Fobo, C. Fritz, H. Gassenhuber, N. Glansdorff, A. Goffeau, LA. Grivell, M. Dehaan, Hein., C., CJ. Herbert, CP. Hollenberg, K. Holmstrom, C. Jacq, M. Jacquet, J. C. Jauniaux, JL. Jonniaux, T. Kallesoe, P. Kiesau, L. Kirchrath, P. Kotter, S. Koroll, S. Liebl, M. Logghe, A. J. E. Lohan, E. J. Louis, Z. Y. Li, M. J. Maat, L. Mallet, G. Mannhaupt, F. Messenguy, T. Miosga, F. Molemans, S. Muller, F. Nasr, B. Obermaier, J. Perea, A. Pierard, E. Piravandi, FM. Pohl, TM. Pohl, S. Potier, M. Proft, B. Purnelle, MR. Rad, M. Rieger, M. Rose, I. Schaaff-Gerstenschlager, B. Scherens, C. Schwarzlose, J. Skala, P. P. Slonimski, P. H. M. Smits, J. L. Souciet, H. Y. Steensma, R. Stucka, A. Urrestarazu, Q. Vanderaart, L. Vandyck, A. Vassarotti, I. Vetter, F. Vierendeels, S. Vissers, G. Wagner, P. Dewergifosse, K. H. Wolfe, M. Zagulski, F. K. Zimmermann, H. W. Mewes, and K. Kleine.
   Complete DNA-Sequence of Yeast Chromosome II.
   EMBO Journal 13: 5795-5809, 1994.
3. George, D. G., W. C. Barker, H. W. Mewes, F. Pfeiffer, and A. Tsugita.
   The PIR-International Protein Sequence Database.
   Nucleic Acids Research 22: 3569-3573, 1994.
4. Heumann, K., DG. George, and H. W. Mewes.
   A New Concept of Sequence Data Distribution on Wide Area Networks.
   CABIOS 10: 519-526, 1994.
5. Mewes, H. W. and D. G. George.
   Protein Sequences and Sequence Databases. In Kellner R., Lottspeich F., and Meyer H.W., eds. Microcharacterization of Proteins. Weinheim, Verlag Chemie. 1994, 209-222.
6. Mewes, H. W., R. Doelz, and D. G. George.
   Sequence Databases: an indespensible source for biotechnological research.
   J.Biotechnol. 35: 239-256, 1994.

1993

1. Barker, W. C., D. G. George, H. W. Mewes, F. Pfeiffer, and A. Tsugita.
   The PIR-International Protein Sequence Database.
   Nucleic Acids Research 21: 3089-3092, 1993.
2. George, D. G., B. C. Orcutt, H. W. Mewes, and A. Tsugita.
   An Object-Oriented Sequence Database Definition Language (SDDL).
   Protein Seq.Data Anal. 5: 357-399, 1993.

1992

1. Barker, W. C., D. G. George, H. W. Mewes, and A. Tsugita.
   The PIR-International Protein Sequence Database.
   Nucleic Acids Research 20: 2023-2026, 1992.
2. Mewes, H. W. and J. Sgouros.
   Erste Sequenzierung eines kompletten Chromosoms.
   Spektrum der Wissenschaften 18-23, 1992.
3. Oliver, S. G., d. A. Q. J. M. van, M. L. Agostoni-Carbone, M. Aigle, L. Alberghina, D. Alexandraki, G. Antoine, R. Anwar, J. P. G. Ballesta, P. Benit, G. Berben, E. Bergantino, N. Biteau, PA. Bolle, M. Bolotin-Fukuhara, A. Brown, A. J. P. Brown, J. M. Buhler, C. Carcano, G. Carignani, H. Cederberg, R. Chanet, R. Contreras, M. Crouzet, B. Daignan-Fornier, E. Defoor, M. Delgado, J. Demolder, C. Doira, E. Dubois, B. Dujon, A. Dusterhoft, D. Erdmann, M. Esteban, F. Fabre, C. Fairhead, G. Faye, H. Feldmann, W. Fiers, MC. Francingues-Gaillard, L. Franco, L. Frontali, H. Fukuhara, LJ. Fuller, P. Galland, M. E. Gent, D. Gigot, V. Gilliquet, N. Glansdorff, A. Goffeau, M. Grenson, P. Grisanti, L. A. Grivell, H. M. de, M. Haasemann, D. Hatat, J. Hoenicka, J. Hegemann, C. J. Herbert, F. Hilger, S. Hohmann, C. P. Hollenberg, K. Huse, F. Iborra, K. J. Indge, K. Isono, C. Jacq, M. Jacquet, C. M. James, J. C. Jauniaux, Y. Jia, A. Jimenez, A. Kelly, U. Kleinhans, P. Kreisl, G. Lanfranchi, C. Lewis, d. L. C. G. van, G. Lucchini, K. Lutzenkirchen, M. J. Maat, G. Mannhaupt, E. Martegani, A. Mathieu, C. T. C. Maurer, D. McConnell, R. A. McKee, F. Messenguy, H. W. Mewes, F. Molemans, M. A. Montague, F. M. Muzi, L. Navas, C. S. Newlon, D. Noone, C. Pallier, L. Panzeri, B. M. Pearson, J. Perea, P. Philippsen, A. Pierard, R. J. Planta, P. Plevani, B. Poetsch, F. Pohl, B. Purnelle, R. M. Ramezani, S. W. Rasmussen, A. Raynal, M. Remacha, P. Richterich, A. B. Roberts, F. Rodriguez, E. Sanz, I. Schaaff-Gerstenschlager, B. Scherens, B. Schweitzer, Y. Shu, J. Skala, P. P. Slonimski, F. Sor, C. Soustelle, R. Spiegelberg, L. I. Stateva, H. Y. Steensma, S. Steiner, A. Thierry, G. Thireos, M. Tzermia, L. A. Urrestarazu, G. Valle, I. Vetter, V.-R. J. C. van, M. Voet, G. Volckaert, P. Vreken, H. Wang, J. R. Warmington, D. von Wettstein, B. L. Wicksteed, C. Wilson, H. Wurst, G. Xu, F. K. Zimmermann, and J. G. Sgouros.
   The complete DNA sequence of yeast chromosome III.
   Nature 357: 38-46, 1992.
4. Simpson, R. J., A. Tsugita, J. E. Celis, J. I. Garrels, and H. W. Mewes.
   Workshop on two-dimensional gel protein databases.
   Electrophoresis 13: 1055-1061, 1992.

1991

1. Mewes, H. W.
   MIPS - European node for protein sequence data.
   CODATA Bulletin 23: 62-63, 1991.
2. Mewes, H. W.
   Databanks on biological macromolecules.
   In Collins, J. and A. J. Driesel, eds.
   Genome analysis: from sequence to function. Huethig Buch Verlag. 1991, 109-112.

1989

1. Mewes, H. W., A. Elzanowski, and D. G. George.
   Protein Sequence Database Management, Data Structure, and Data Access.
   Biochem.Soc.Trans. 17: 843-845, 1989.
2. Mewes, H. W., D. G. George, W. C. Barker, and A. Tsugita.
   International Cooperation Among Protein Sequence Databanks. In Wittmann-Liebold, B., ed. Methods in Protein Sequence Analysis.
   Berlin Heidelberg New York, Springer. 1989, 357-360.

1988

1. Mewes, H. W. and A. Tsugita.
   Additional protein sequence databanks. In Lesk A.M., ed. Computational moleclar biology. Sources and methods for sequence data analysis.
   Oxford, Oxford University Press. 1988, 38-40.
2. Mewes, H. W. and Pfeiffer, F.
   A Detailed Assessment on the Bioinformatics Network Required for the Collection and Processing of the Yeast Genome Sequence Data.
   A.Goffeau. 1988. Brussels.

1987

1. George, D. G., H. W. Mewes, and H. Kihara.
   A Standardized Format for Sequence Data Exchange.
   Protein Seq.Data Anal. 1: 27-39, 1987.