My bioinformatics journal watch - year 2003 Jul-Dec [ this week | 2004 Jul-Dec | 2004 Jan-Jun | 2003 Jul-Dec | 2003 Jan-Jun | 2002 | 2001 | 2000 | 1999 | 1998 | 1997 | 1996 & before ]

General
Applications
Data mining
   Literature mining
   Database mining
in silico biology/computational modelling
Network/pathway reconstruction and analysis*
   Promter/regulatory sequence analysis*
Protein-protein interaction analysis
Gene prediction
Gene function prediction
Structure prediction
Comparative Genomics (theoretical)
Languages and Algorithms
Software
Databases
Conference proceedings

*Network/pathway studies using microarray technology are put under the microarray section of My functional genomics journal watch; the articles in this page are primarily theoretical. 
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General

  1. Kemmeren P, Holstege FC. Integrating functional genomics data. Biochem Soc Trans. 2003 Dec;31(Pt 6):1484-7. [PubMed]
  2. Lopez R, Duggan K, Harte N, Kibria A. Public services from the European Bioinformatics Institute. Brief Bioinform. 2003 Dec;4(4):332-40. [PubMed]
  3. Bishop M. Omics research and bioinformatics--joined-up thinking or anarchy? Brief Bioinform. 2003 Dec;4(4):313. [PubMed]
  4. Ouzounis CA, Valencia A. Early bioinformatics: the birth of a discipline—a personal view. Bioinformatics 2003 Nov 22; 19: 2176-2190.  [PubMed]
  5. Buckingham S. Bioinformatics: programmed for success. Nature. 2003 Sep 11;425(6954):209-15. [PubMed]
  6. Vision T. An international showcase of bioinformatics research. Genome Biol. 2003;4(9):337. [PubMed]
  7. Storey JD, Tibshirani R. Statistical significance for genomewide studies. Proc Natl Acad Sci U S A. 2003 Aug 5;100(16):9440-5. [PubMed][pdf]
  8. Maojo V, Kulikowski CA. Bioinformatics and Medical Informatics: Collaboration on the Road to Genomic Medicine? J Am Med Inform Assoc. 2003 Aug 4 [Epub ahead of print] [PubMed]
  9. Stevens RD, Robinson AJ, Goble CA. myGrid: personalised bioinformatics on the information grid. Bioinformatics. 2003 Jul;19 Suppl 1:I302-I304. [PubMed]
  10. Rowe A, Kalaitzopoulos D, Osmond M, Ghanem M, Guo Y. The discovery net system for high throughput bioinformatics. Bioinformatics. 2003 Jul;19 Suppl 1:I225-I231. [PubMed]
  11. Oinn TM. Talisman-rapid application development for the grid. Bioinformatics. 2003 Jul;19 Suppl 1:I212-I214. [PubMed]
  12. Ray HN, Mootha VK, Boxwala AA. Building an application framework for integrative genomics. Proc AMIA Symp. 2003;:981. [PubMed]

Applications

  1. Torralba AS. Susceptibility of non-linear systems as an approach to metabolic responses. Bioinformatics. 2003 Dec 12;19(18):2428-35. [PubMed]
  2. Mills R, Rozanov M, Lomsadze A, Tatusova T, Borodovsky M. Improving gene annotation of complete viral genomes. Nucl. Acids. Res. 2003 Dec 1; 31: 7041-7055. [PubMed]
  3. Krishnan VG, Westhead DR. A comparative study of machine-learning methods to predict the effects of single nucleotide polymorphisms on protein function. Bioinformatics 2003 Nov 22; 19: 2199-2209. [PubMed]
  4. Thareau V, Dehais P, Serizet C, Hilson P, Rouze P, Aubourg S. Automatic design of gene-specific sequence tags for genome-wide functional studies. Bioinformatics 2003 Nov 22; 19: 2191-2198. [PubMed]
  5. Chou KC, Cai YD. A new hybrid approach to predict subcellular localization of proteins by incorporating gene ontology. Biochem Biophys Res Commun. 2003 Nov 21;311(3):743-7. [PubMed]
  6. Dozmorov I, Saban MR, Knowlton N, Centola M, Saban R. Connective molecular pathways of experimental bladder inflammation. Physiol Genomics. 2003 Nov 11;15(3):209-22. [PubMed]
  7. Bortoluzzi S, Romualdi C, Bisognin A, Danieli GA. Disease genes and intracellular protein networks. Physiol Genomics. 2003 Nov 11;15(3):223-7. [PubMed]
  8. Siew N, Fischer D. Analysis of singleton ORFans in fully sequenced microbial genomes. Proteins. 2003 Nov 1;53(2):241-51. [PubMed]
  9. Clark HF, Gurney AL, Abaya E, Baker K, Baldwin D, Brush J, Chen J, Chow B, Chui C, Crowley C, Currell B, Deuel B, Dowd P, Eaton D, Foster J, Grimaldi C, Gu Q, Hass PE, Heldens S, Huang A, Kim HS, Klimowski L, Jin Y, Johnson S, Lee J, Lewis L, Liao D, Mark M, Robbie E, Sanchez C, Schoenfeld J, Seshagiri S, Simmons L, Singh J, Smith V, Stinson J, Vagts A, Vandlen R, Watanabe C, Wieand D, Woods K, Xie MH, Yansura D, Yi S, Yu G, Yuan J, Zhang M, Zhang Z, Goddard A, Wood WI, Godowski P. The Secreted Protein Discovery Initiative (SPDI), a Large-Scale Effort to Identify Novel Human Secreted and Transmembrane Proteins: A Bioinformatics Assessment. Genome Res. 2003 Oct;13(10):2265-70.  [PubMed]
  10. Lengauer T. Analyzing resistance phenomena in HIV with bioinformatics methods. Bioinformatics. 2003 Oct;19 Suppl 2:II92. [PubMed]
  11. Thomson R, Hodgman TC, Yang ZR, Doyle AK. Characterizing proteolytic cleavage site activity using bio-basis function neural networks. Bioinformatics. 2003 Sep 22;19(14):1741-7. [PubMed]
  12. Schulz A, Schoneberg T. The structural evolution of a P2Y-like G-protein-coupled receptor. J Biol Chem. 2003 Sep 12; [PubMed]
  13. Park KJ, Kanehisa M. Prediction of protein subcellular locations by support vector machines using compositions of amino acids and amino acid pairs. Bioinformatics. 2003 Sep 1;19(13):1656-63. [PubMed]
  14. Li S, Cutler G, Liu JJ, Hoey T, Chen L, Schultz PG, Liao J, Ling XB. A comparative analysis of HGSC and Celera human genome assemblies and gene sets. Bioinformatics. 2003 Sep 1;19(13):1597-1605. [PubMed]
  15. Mi H, Vandergriff J, Campbell M, Narechania A, Majoros W, Lewis S, Thomas PD, Ashburner M. Assessment of Genome-Wide Protein Function Classification for Drosophila melanogaster. Genome Res. 2003 Sep;13(9):2118-28. [PubMed][pdf]
  16. McCormack TJ. Comparison of K+-channel genes within the genomes of Anopheles gambiae and Drosophila melanogaster. Genome Biol. 2003;4(9):R58. [PubMed]
  17. Kesmir C, Van Noort V, De Boer RJ, Hogeweg P. Bioinformatic analysis of functional differences between the immunoproteasome and the constitutive proteasome. Immunogenetics. 2003 Aug 30 [Epub ahead of print] [PubMed]
  18. Anantharaman V, Aravind L. Application of comparative genomics in the identification and analysis of novel families of membrane-associated receptors in bacteria. BMC Genomics. 2003 Aug 12 [Epub ahead of print] [PubMed][pdf]
  19. Baker ML, Jiang W, Bowman BR, Hong Zhou Z, Quiocho FA, Rixon FJ, Chiu W. Architecture of the herpes simplex virus major capsid protein derived from structural bioinformatics. J Mol Biol. 2003 Aug 8;331(2):447-56. [PubMed]
  20. Banatao DR, Altman RB, Klein TE. Microenvironment analysis and identification of magnesium binding sites in RNA. Nucleic Acids Res. 2003 Aug 1;31(15):4450-60. [PubMed]
  21. Whittaker PA. What is the relevance of bioinformatics to pharmacology? Trends Pharmacol Sci. 2003 Aug;24(8):434-9. [PubMed]
  22. Gustafsson C. et al.,  Putting engineering back into protein engineering: bioinformatic approaches to catalyst design.  Curr Opin Biotechnol. 2003 Aug; [PubMed]
  23. Dowsey AW, Dunn MJ, Yang GZ. The role of bioinformatics in two-dimensional gel electrophoresis. Proteomics. 2003 Aug;3(8):1567-96. [PubMed]
  24. Franco OL, Rigden DJ. Fold recognition analysis of glycosyltransferases families: further members of structural superfamilies. Glycobiology. 2003 Jul 24 [Epub ahead of print] [PubMed]
  25. McCutcheon JP, Eddy SR. Computational identification of non-coding RNAs in Saccharomyces cerevisiae by comparative genomics. Nucl. Acids. Res. 2003 Jul 15; 31: 4119-4128. [PubMed][pdf][web supplement]
  26. Lord PW, Stevens RD, Brass A, Goble CA. Investigating semantic similarity measures across the Gene Ontology: the relationship between sequence and annotation. Bioinformatics. 2003 Jul 1;19(10):1275-83. [PubMed]
  27. Chiang DY, Moses AM, Kellis M, Lander ES, Eisen MB. Phylogenetically and spatially conserved word pairs associated with gene-expression changes in yeasts. Genome Biol. 2003 Jul;4(7):R43. [PubMed][pdf]
  28. Enault F, Suhre K, Abergel C, Poirot O, Claverie JM. Annotation of bacterial genomes using improved phylogenomic profiles. Bioinformatics. 2003 Jul;19 Suppl 1:I105-I107. [PubMed]
  29. Kalinina OV, Makeev VJ, Sutormin RA, Gelfand MS, Rakhmaninova AB. The channel in transporters is formed by residues that are rare in transmembrane helices. In Silico Biol. 2003;3(1-2):194-204. [PubMed]
  30. Robinson-Rechavi M, Laudet V. Bioinformatics of nuclear receptors. Methods Enzymol. 2003;364:95-118. [PubMed]

Data mining

  1. Rocco D, Critchlow T. Automatic discovery and classification of bioinformatics Web sources. Bioinformatics. 2003 Oct 12;19(15):1927-33. [PubMed]
  2. LaBaer J. Mining the literature and large datasets. Nat Biotechnol. 2003 Sep;21(9):976-7. [PubMed]
  3. Su Y, Murali TM, Pavlovic V, Schaffer M, Kasif S. RankGene: identification of diagnostic genes based on expression data. Bioinformatics. 2003 Aug 12;19(12):1578-9. [PubMed][web supplement]
  4. Searls DB. Data integration-connecting the dots. Nat Biotechnol. 2003 Aug;21(8):844-5. [PubMed]
  5. Torto TA, Li S, Styer A, Huitema E, Testa A, Gow NA, Van West P, Kamoun S. EST Mining and Functional Expression Assays Identify Extracellular Effector Proteins From the Plant Pathogen Phytophthora. Genome Res. 2003 Jul;13(7):1675-85. [PubMed][pdf][web supplement]
  6. Yamanishi Y, Vert JP, Nakaya A, Kanehisa M. Extraction of correlated gene clusters from multiple genomic data by generalized kernel canonical correlation analysis. Bioinformatics. 2003 Jul;19 Suppl 1:I323-I330. [PubMed]

Literature mining

  1. Becker KG, Hosack DA, Dennis G Jr, Lempicki RA, Bright T, Cheadle C, Engel JH. PubMatrix: a tool for multiplex literature mining. BMC Bioinformatics. 2003 Dec 10 [Epub ahead of print] [PubMed]
  2. Yu H, Hatzivassiloglou V, Rzhetsky A, Wilbur WJ. Automatically identifying gene/protein terms in MEDLINE abstracts. J Biomed Inform. 2002 Oct-Dec;35(5-6):322-30. [PubMed]
  3. Novichkova S, Egorov S, Daraselia N. MedScan, a natural language processing engine for MEDLINE abstracts. Bioinformatics. 2003 Sep 1;19(13):1699-706. [PubMed]  
  4. LaBaer J. Mining the literature and large datasets. Nat Biotechnol. 2003 Sep;21(9):976-7. [PubMed]
  5. Raychaudhuri S, Chang JT, Imam F, Altman RB. The computational analysis of scientific literature to define and recognize gene expression clusters. Nucleic Acids Res. 2003 Aug 1;31(15):4553-60. [PubMed]
  6. Shatkay H, Feldman R. Mining the biomedical literature in the genomic era: an overview. J Comput Biol. 2003;10(6):821-55. [PubMed]

Database mining

  1. Ratan RR. Mining genome databases for therapeutic gold: SIM2 is a novel target for treatment of solid tumors. Trends Pharmacol Sci. 2003 Oct;24(10):508-10. [PubMed]
  2. LaBaer J. Mining the literature and large datasets. Nat Biotechnol. 2003 Sep;21(9):976-7. [PubMed]

in silico biology/computational modelling

  1. Ciliberto A, Novak B, Tyson JJ. Mathematical model of the morphogenesis checkpoint in budding yeast. J Cell Biol. 2003 Dec 22;163(6):1243-54. [PubMed]
  2. Werner E. In silico multicellular systems biology and minimal genomes. Drug Discov Today. 2003 Dec 15;8(24):1121-7. [PubMed]
  3. Forger DB, Peskin CS. A detailed predictive model of the mammalian circadian clock. Proc Natl Acad Sci U S A. 2003 Dec 9;100(25):14806-11. [PubMed][PDF] [Supporting Information]
  4. Slepchenko BM, Schaff JC, Macara I, Loew LM. Quantitative cell biology with the Virtual Cell. Trends Cell Biol. 2003 Nov;13(11):570-6. [PubMed]
  5. Kim PM, Tidor B. Limitations of quantitative gene regulation models: a case study. Genome Res. 2003 Nov;13(11):2391-5. [PubMed]
  6. Kauffman KJ, Prakash P, Edwards JS. Advances in flux balance analysis. Curr Opin Biotechnol. 2003 Oct;14(5):491-6. [PubMed]
  7. Lee DY, Yun H, Park S, Lee SY. MetaFluxNet: the management of metabolic reaction information and quantitative metabolic flux analysis. Bioinformatics. 2003 Nov 1;19(16):2144-2146. [PubMed]
  8. Lukashin AV, Lukashev ME, Fuchs R. Topology of gene expression networks as revealed by data mining and modeling. Bioinformatics. 2003 Oct 12;19(15):1909-16. [PubMed]
  9. Mathematical Modeling Predicts How Proteins Affect Cellular Communication. PLoS Biol. 2003 Oct;1(1):E32. [PubMed]
  10. Takahashi K, Ishikawa N, Sadamoto Y, Sasamoto H, Ohta S, Shiozawa A, Miyoshi F, Naito Y, Nakayama Y, Tomita M. E-Cell 2: Multi-platform E-Cell simulation system. Bioinformatics. 2003 Sep 1;19(13):1727-1729. [PubMed]
  11. Hayashi Y, Sakaguchi K, Kobayashi M, Kobayashi M, Kikuchi Y, Ichiishi E. Molecular evaluation using in silico protein interaction profiles. Bioinformatics. 2003 Aug 12;19(12):1514-1523. [PubMed]
  12. Frank M, Gutbrod P, Hassayoun C, Von Der Lieth CW. Dynamic molecules: molecular dynamics for everyone. An internet-based access to molecular dynamic simulations: basic concepts. J Mol Model (Online). 2003 Aug 8 [Epub ahead of print] [PubMed]
  13. Gutteridge A, Bartlett GJ, Thornton JM. Using a neural network and spatial clustering to predict the location of active sites in enzymes. J Mol Biol. 2003 Jul 18;330(4):719-34. [PubMed]
  14. Sauro HM, Hucka M, Finney A, Wellock C, Bolouri H, Doyle J, Kitano H. Next generation simulation tools: the Systems Biology Workbench and BioSPICE integration. OMICS. 2003 Winter;7(4):355-72. [PubMed]
  15. Zak DE, Pearson RK, Vadigepalli R, Gonye GE, Schwaber JS, Doyle FJ 3rd. Continuous-time identification of gene expression models. OMICS. 2003 Winter;7(4):373-86. [PubMed]
  16. Sauro HM, Hucka M, Finney A, Wellock C, Bolouri H, Doyle J, Kitano H. Next generation simulation tools: the Systems Biology Workbench and BioSPICE integration. OMICS. 2003 Winter;7(4):355-72. [PubMed]
  17. Mishra B, Daruwala RS, Zhou Y, Ugel N, Policriti A, Antoniotti M, Paxia S, Rejali M, Rudra A, Cherepinsky V, Silver N, Casey W, Piazza C, Simeoni M, Barbano P, Spivak M, Feng J, Gill O, Venkatesh M, Cheng F, Sun B, Ioniata I, Anantharaman T, Hubbard EJ, Pnueli A, Harel D, Chandru V, Hariharan R, Wigler M, Park F, Lin SC, Lazebnik Y, Winkler F, Cantor CR, Carbone A, Gromov M. A sense of life: computational and experimental investigations with models of biochemical and evolutionary processes. OMICS. 2003 Fall;7(3):253-68. [PubMed]

Network/pathway reconstruction and analysis

  1. Von Mering C, Zdobnov EM, Tsoka S, Ciccarelli FD, Pereira-Leal JB, Ouzounis CA, Bork P. Genome evolution reveals biochemical networks and functional modules. Proc Natl Acad Sci U S A. 2003 Dec 23;100(26):15428-33. [PubMed][PDF] [Supporting Information]
  2. Strong M, Graeber TG, Beeby M, Pellegrini M, Thompson MJ, Yeates TO, Eisenberg D. Visualization and interpretation of protein networks in Mycobacterium tuberculosis based on hierarchical clustering of genome-wide functional linkage maps. Nucleic Acids Res. 2003 Dec 15;31(24):7099-7109. [PubMed] [Supplementary Material]
  3. Chin CS, Samanta MP. Global snapshot of a protein interaction network-a percolation based approach. Bioinformatics. 2003 Dec 12;19(18):2413-9. [PubMed]
  4. Rojdestvenski I. Metabolic pathways in three dimensions. Bioinformatics. 2003 Dec 12;19(18):2436-41. [PubMed]
  5. Kauffman S, Peterson C, Samuelsson B, Troein C. Random Boolean network models and the yeast transcriptional network. Proc Natl Acad Sci U S A. 2003 Dec 9;100(25):14796-9. [PubMed] [PDF] [Supporting Information]
  6. Li H, Wang W. Dissecting the transcription networks of a cell using computational genomics. Curr Opin Genet Dev. 2003 Dec;13(6):611-6.  [PubMed]
  7. Schlitt T, Palin K, Rung J, Dietmann S, Lappe M, Ukkonen E, Brazma A. From Gene Networks to Gene Function. Genome Res. 2003 Dec; 13: 2568-2576.  [PubMed][Supplemental Research Data]
  8. Stark J, Brewer D, Barenco M, Tomescu D, Callard R, Hubank M. Reconstructing gene networks: what are the limits? Biochem Soc Trans. 2003 Dec;31(Pt 6):1519-25. [PubMed]  
  9. Soinov LA. Supervised classification for gene network reconstruction. Biochem Soc Trans. 2003 Dec;31(Pt 6):1497-502. [PubMed]
  10. Cho KH, Wolkenhauer O. Analysis and modelling of signal transduction pathways in systems biology. Biochem Soc Trans. 2003 Dec;31(Pt 6):1503-9. [PubMed]
  11. Famili I, Forster J, Nielsen J, Palsson BO. Saccharomyces cerevisiae phenotypes can be predicted by using constraint-based analysis of a genome-scale reconstructed metabolic network. Proc Natl Acad Sci U S A. 2003 Nov 11;100(23):13134-9. [PubMed][pdf][web supplement]
  12. Bortoluzzi S, Romualdi C, Bisognin A, Danieli GA. Disease genes and intracellular protein networks. Physiol Genomics. 2003 Nov 11;15(3):223-7. [PubMed]
  13. Nikitin A, Egorov S, Daraselia N, Mazo I. Pathway studio—the analysis and navigation of molecular networks. Bioinformatics. 2003 Nov 1;19(16):2155-7.  [PubMed]
  14. Tornow S, Mewes HW. Functional modules by relating protein interaction networks and gene expression. Nucleic Acids Res. 2003 Nov 1;31(21):6283-9. [PubMed]
  15. Qin H, Lu HH, Wu WB, Li WH. Evolution of the yeast protein interaction network. Proc Natl Acad Sci U S A. 2003 Oct 28;100(22):12820-4. [PubMed][pdf][web supplement]
  16. Spirin V, Mirny LA. Protein complexes and functional modules in molecular networks. Proc Natl Acad Sci U S A. 2003 Oct 14;100(21):12123-8. [PubMed][pdf][web supplement]
  17. Han K, Ju BH. A fast layout algorithm for protein interaction networks. Bioinformatics. 2003 Oct 12;19(15):1882-8. [PubMed]
  18. Qian J, Lin J, Luscombe NM, Yu H, Gerstein M. Prediction of regulatory networks: genome-wide identification of transcription factor targets from gene expression data. Bioinformatics. 2003 Oct 12;19(15):1917-26. [PubMed]
  19. Bader JS. Greedily building protein networks with confidence. Bioinformatics. 2003 Oct 12;19(15):1869-74. [PubMed]
  20. Lukashin AV, Lukashev ME, Fuchs R. Topology of gene expression networks as revealed by data mining and modeling. Bioinformatics. 2003 Oct 12;19(15):1909-16. [PubMed]
  21. Gomez SM, Noble WS, Rzhetsky A. Learning to predict protein-protein interactions from protein sequences. Bioinformatics. 2003 Oct 12;19(15):1875-1881. [PubMed]
  22. Manke T, Bringas R, Vingron M. Correlating Protein–DNA and Protein–Protein Interaction Networks. J Mol Biol. 2003 Oct 10;333(1):75-85.  [PubMed]
  23. Quackenbush J. Genomics. Microarrays--guilt by association. Science. 2003 Oct 10;302(5643):240-1. [PubMed]
  24. Stuart JM, Segal E, Koller D, Kim SK. A gene-coexpression network for global discovery of conserved genetic modules. Science. 2003 Oct 10;302(5643):249-55. [PubMed][web supplement]
  25. Boyer F, Viari A. Ab initio reconstruction of metabolic pathways. Bioinformatics. 2003 Oct;19 Suppl 2:II26-II34. [PubMed]
  26. Friedman N. Probabilistic models for identifying regulation networks. Bioinformatics. 2003 Oct;19 Suppl 2:II57. [PubMed]
  27. Remy E, Mosse B, Chaouiya C, Thieffry D. A description of dynamical graphs associated to elementary regulatory circuits. Bioinformatics. 2003 Oct;19 Suppl 2:II172-II178. [PubMed]
  28. Perrin BE, Ralaivola L, Mazurie A, Bottani S, Mallet J, D'Alche-Buc F. Gene networks inference using dynamic Bayesian networks. Bioinformatics. 2003 Oct;19 Suppl 2:II138-II148. [PubMed]
  29. Tamada Y, Kim S, Bannai H, Imoto S, Tashiro K, Kuhara S, Miyano S. Estimating gene networks from gene expression data by combining Bayesian network model with promoter element detection. Bioinformatics. 2003 Oct;19 Suppl 2:II227-II236. [PubMed]
  30. Wuchty S, Oltvai ZN, Barabasi AL. Evolutionary conservation of motif constituents in the yeast protein interaction network. Nat Genet. 2003 Oct;35(2):176-9. [PubMed]
  31. Shmulevich I, Lahdesmaki H, Dougherty ER, Astola J, Zhang W. The role of certain Post classes in Boolean network models of genetic networks. Proc Natl Acad Sci U S A. 2003 Sep 16;100(19):10734-9. [PubMed][pdf]
  32. Famili I, Palsson BO. Systemic metabolic reactions are obtained by singular value decomposition of genome-scale stoichiometric matrices. J Theor Biol. 2003 Sep 7;224(1):87-96. [PubMed]
  33. Roy S, Khanna S, Wallace WA, Lappalainen J, Rink C, Cardounel AJ, Zweier JL, Sen CK. Characterization of perceived hyperoxia in isolated primary cardiac fibroblasts and in the reoxygenated heart. J Biol Chem. 2003 Sep 2 [Epub ahead of print] [PubMed]
  34. McShan DC, Rao S, Shah I. PathMiner: predicting metabolic pathways by heuristic search. Bioinformatics. 2003 Sep 1;19(13):1692-8. [PubMed]  
  35. Ahn SK. A bioinformatics-based approach for the prediction and identification of novel proteins potentially involved in phosphorylation signalling pathways. Int J Mol Med. 2003 Sep;12(3):391-7. [PubMed]
  36. Deville Y, Gilbert D, van Helden J, Wodak SJ. An overview of data models for the analysis of biochemical pathways. Brief Bioinform. 2003 Sep;4(3):246-59. [PubMed]
  37. Wu J, Kasif S, DeLisi C. Identification of functional links between genes using phylogenetic profiles. Bioinformatics. 2003 Aug 12;19(12):1524-30. [PubMed]
  38. Voss K, Heiner M, Koch I. Steady state analysis of metabolic pathways using Petri nets. In Silico Biol. 2003 Aug 7;3(3):0031. [PubMed]
  39. Bolouri H, Davidson EH. Transcriptional regulatory cascades in development: Initial rates, not steady state, determine network kinetics. Proc Natl Acad Sci U S A. 2003 Aug 5;100(16):9371-6. [PubMed][pdf][web supplement]
  40. Yu H, Luscombe NM, Qian J, Gerstein M. Genomic analysis of gene expression relationships in transcriptional regulatory networks. Trends Genet. 2003 Aug;19(8):422-7. [PubMed]
  41. Bergman A, Siegal ML. Evolutionary capacitance as a general feature of complex gene networks. Nature. 2003 Jul 31;424(6948):549-52. [PubMed][web supplement]
  42. Ma HW, Zeng AP. The connectivity structure, giant strong component and centrality of metabolic networks. Bioinformatics. 2003 Jul 22;19(11):1423-30. [PubMed]
  43. Kurata H et al., CADLIVE for constructing a large-scale biochemical network based on a simulation-directed notation and its application to yeast cell cycle. Nucl. Acids. Res. 2003 Jul 15; 31: 4071-4084. [PubMed][pdf]
  44. Gardner TS, di Bernardo D, Lorenz D, Collins JJ. Inferring genetic networks and identifying compound mode of action via expression profiling. Science. 2003 Jul 4;301(5629):102-5. [PubMed]
  45. Conant GC, Wagner A. Convergent evolution of gene circuits. Nat Genet. 2003 Jul;34(3):264-6. [PubMed][web supplement]
  46. Stark J, Callard R, Hubank M. From the top down: towards a predictive biology of signalling networks. Trends Biotechnol. 2003 Jul;21(7):290-3.  [PubMed]
  47. Segal E, Yelensky R, Koller D. Genome-wide discovery of transcriptional modules from DNA sequence and gene expression. Bioinformatics. 2003 Jul;19 Suppl 1:I273-I282. [PubMed]
  48. Segal E, Wang H, Koller D. Discovering molecular pathways from protein interaction and gene expression data. Bioinformatics. 2003 Jul;19 Suppl 1:I264-I272. [PubMed]
  49. Gat-Viks I, Shamir R. Chain functions and scoring functions in genetic networks. Bioinformatics. 2003 Jul;19 Suppl 1:I108-I117. [PubMed]
  50. Vadigepalli R, Chakravarthula P, Zak DE, Schwaber JS, Gonye GE. PAINT: A Promoter Analysis and Interaction Network Generation Tool for Gene Regulatory Network Identification. OMICS. 2003 Fall;7(3):235-52. [PubMed]

Promter/regulatory sequence analysis

  1. Wang T, Stormo GD. Combining phylogenetic data with co-regulated genes to identify regulatory motifs. Bioinformatics. 2003 Dec 12;19(18):2369-80. [PubMed] 
  2. Cooper GM, Sidow A. Genomic regulatory regions: insights from comparative sequence analysis. Curr Opin Genet Dev. 2003 Dec;13(6):604-10.  [PubMed]
  3. Djordjevic M, Sengupta AM, Shraiman BI. A biophysical approach to transcription factor binding site discovery. Genome Res. 2003 Nov;13(11):2381-90. [PubMed]
  4. Qian J, Lin J, Luscombe NM, Yu H, Gerstein M. Prediction of regulatory networks: genome-wide identification of transcription factor targets from gene expression data. Bioinformatics. 2003 Oct 12;19(15):1917-26. [PubMed]
  5. Narasimhan C, LoCascio P, Uberbacher E. Background rareness-based iterative multiple sequence alignment algorithm for regulatory element detection. Bioinformatics. 2003 Oct 12;19(15):1952-63. [PubMed]
  6. Gordon L, Chervonenkis AY, Gammerman AJ, Shahmuradov IA, Solovyev VV. Sequence alignment kernel for recognition of promoter regions. Bioinformatics. 2003 Oct 12;19(15):1964-71. [PubMed]
  7. King OD, Roth FP. A non-parametric model for transcription factor binding sites. Nucleic Acids Res. 2003 Oct 1;31(19):E116. [PubMed]
  8. Aerts S, Van Loo P, Thijs G, Moreau Y, De Moor B. Computational detection of cis -regulatory modules. Bioinformatics. 2003 Oct;19 Suppl 2:II5-II14. [PubMed]
  9. Bailey TL, Noble WS. Searching for statistically significant regulatory modules. Bioinformatics. 2003 Oct;19 Suppl 2:II16-II25. [PubMed]
  10. Dieterich C, Herwig R, Vingron M. Exploring potential target genes of signaling pathways by predicting conserved transcription factor binding sites. Bioinformatics. 2003 Oct;19 Suppl 2:II50-II56. [PubMed]
  11. Price A, Ramabhadran S, Pevzner PA. Finding subtle motifs by branching from sample strings. Bioinformatics. 2003 Oct;19 Suppl 2:II149-II155. [PubMed]
  12. Qiu P. Recent advances in computational promoter analysis in understanding the transcriptional regulatory network. Biochem Biophys Res Commun. 2003 Sep 26;309(3):495-501. [PubMed]
  13. Mignone F, Grillo G, Liuni S, Pesole G. Computational identification of protein coding potential of conserved sequence tags through cross-species evolutionary analysis. Nucleic Acids Res. 2003 Aug 1;31(15):4639-45. [PubMed]
  14. Sharan R, Ovcharenko I, Ben-Hur A, Karp RM. CREME: a framework for identifying cis-regulatory modules in human-mouse conserved segments. Bioinformatics. 2003 Jul;19 Suppl 1:I283-I291. [PubMed]
  15. Johansson O, Alkema W, Wasserman WW, Lagergren J. Identification of functional clusters of transcription factor binding motifs in genome sequences: the MSCAN algorithm. Bioinformatics. 2003 Jul;19 Suppl 1:I169-I176. [PubMed]
  16. Rombauts S, Florquin K, Lescot M, Marchal K, Rouze P, Van De Peer Y. Computational Approaches to Identify Promoters and cis-Regulatory Elements in Plant Genomes. Plant Physiol. 2003 Jul;132(3):1162-76. [PubMed]
  17. Vadigepalli R, Chakravarthula P, Zak DE, Schwaber JS, Gonye GE. PAINT: A Promoter Analysis and Interaction Network Generation Tool for Gene Regulatory Network Identification. OMICS. 2003 Fall;7(3):235-52. [PubMed]
  18. Hofestadt R. Petri nets and the simulation of metabolic networks. In Silico Biol. 2003;3(3):321-2. [PubMed]

Protein-protein interaction analysis

  1. Gertz J, Elfond G, Shustrova A, Weisinger M, Pellegrini M, Cokus S, Rothschild B. Inferring protein interactions from phylogenetic distance matrices. Bioinformatics. 2003 Nov 1;19(16):2039-2045.  [PubMed]
  2. Temkin JM, Gilder MR. Extraction of protein interaction information from unstructured text using a context-free grammar. Bioinformatics. 2003 Nov 1;19(16):2046-53.  [PubMed]
  3. Jansen R, Yu H, Greenbaum D, Kluger Y, Krogan NJ, Chung S, Emili A, Snyder M, Greenblatt JF, Gerstein M. A bayesian networks approach for predicting protein-protein interactions from genomic data. Science. 2003 Oct 17;302(5644):449-53. [PubMed][web supplement]
  4. Gomez SM, Noble WS, Rzhetsky A. Learning to predict protein-protein interactions from protein sequences. Bioinformatics. 2003 Oct 12;19(15):1875-1881. [PubMed]
  5. Krause R, Von Mering C, Bork P. A comprehensive set of protein complexes in yeast: mining large scale protein-protein interaction screens. Bioinformatics. 2003 Oct 12;19(15):1901-8. [PubMed]
  6. Han K, Ju BH. A fast layout algorithm for protein interaction networks. Bioinformatics. 2003 Oct 12;19(15):1882-8. [PubMed]
  7. Manke T, Bringas R, Vingron M. Correlating Protein–DNA and Protein–Protein Interaction Networks. J Mol Biol. 2003 Oct 10;333(1):75-85.  [PubMed]
  8. Hayashida M, Ueda N, Akutsu T. Inferring strengths of protein-protein interactions from experimental data using linear programming. Bioinformatics. 2003 Oct;19 Suppl 2:II58-II65. [PubMed]
  9. Zhu J, Zhu Q, Shi Y, Liu H. How well can we predict native contacts in proteins based on decoy structures and their energies? Proteins. 2003 Sep 1;52(4):598-608. [PubMed]
  10. Hayashi Y, Sakaguchi K, Kobayashi M, Kobayashi M, Kikuchi Y, Ichiishi E. Molecular evaluation using in silico protein interaction profiles. Bioinformatics. 2003 Aug 12;19(12):1514-1523. [PubMed]
  11. Segal E, Wang H, Koller D. Discovering molecular pathways from protein interaction and gene expression data. Bioinformatics. 2003 Jul;19 Suppl 1:I264-I272. [PubMed]
  12. Letovsky S, Kasif S. Predicting protein function from protein/protein interaction data: a probabilistic approach. Bioinformatics. 2003 Jul;19 Suppl 1:I197-I204. [PubMed]
  13. Ju BH, Han K. Complexity management in visualizing protein interaction networks. Bioinformatics. 2003 Jul;19 Suppl 1:I177-I179. [PubMed]

Gene prediction

  1. Moore JE, Lake JA. Gene structure prediction in syntenic DNA segments. Nucleic Acids Res. 2003 Dec 15;31(24):7271-9. [PubMed]
  2. Wang Y, Liu J, Zhao T, Ji Q. Recognizing translation initiation sites of eukaryotic genes based on the cooperatively scanning model. Bioinformatics. 2003 Oct 12;19(15):1972-7. [PubMed]
  3. Saeys Y, Degroeve S, Aeyels D, Van De Peer Y, Rouze P. Fast feature selection using a simple estimation of distribution algorithm: a case study on splice site prediction. Bioinformatics. 2003 Oct;19 Suppl 2:II179-II188. [PubMed]
  4. Cawley SL, Pachter L. HMM sampling and applications to gene finding and alternative splicing. Bioinformatics. 2003 Oct;19 Suppl 2:II36-II41. [PubMed]
  5. Stanke M, Waack S. Gene prediction with a hidden Markov model and a new intron submodel. Bioinformatics. 2003 Oct;19 Suppl 2:II215-II225. [PubMed]
  6. Wang J, Kraemer E. GFPE: gene-finding program evaluation. Bioinformatics. 2003 Sep 1;19(13):1712-3. [PubMed] 
  7. Pennisi E. BIOINFORMATICS: Gene Counters Struggle to Get the Right Answer. Science. 2003 Aug 22;301(5636):1040-1.  [PubMed]
  8. Taher L, Rinner O, Garg S, Sczyrba A, Brudno M, Batzoglou S, Morgenstern B. AGenDA: homology-based gene prediction. Bioinformatics. 2003 Aug 12;19(12):1575-1577. [PubMed]
  9. Kotlar D, Lavner Y. Gene prediction by spectral rotation measure: a new method for identifying protein-coding regions. Genome Res. 2003 Aug;13(8):1930-7. [PubMed][pdf]
  10. Bajic VB, Seah SH. Dragon gene start finder: an advanced system for finding approximate locations of the start of gene transcriptional units. Genome Res. 2003 Aug;13(8):1923-9. [PubMed][pdf]
  11. Nelander S, Mostad P, Lindahl P. Prediction of cell type-specific gene modules: identification and initial characterization of a core set of smooth muscle-specific genes. Genome Res. 2003 Aug;13(8):1838-54. [PubMed][pdf][web supplement 1][web supplement 2]
  12. Shah SP, McVicker GP, Mackworth AK, Rogic S, Ouellette BF. GeneComber: combining outputs of gene prediction programs for improved results. Bioinformatics. 2003 Jul 1;19(10):1296-7. [PubMed]
  13. Bockhorst J, Craven M, Page D, Shavlik J, Glasner J. A Bayesian network approach to operon prediction. Bioinformatics. 2003 Jul 1;19(10):1227-1235. [PubMed]
  14. Lai EC, Tomancak P, Williams RW, Rubin GM. Computational identification of Drosophila microRNA genes. Genome Biol. 2003 Jul;4(7):R42.  [PubMed][pdf]
  15. Wang Y, Ou H, Guo F. Recognition of translation initiation sites of eukaryotic genes based on an em algorithm. J Comput Biol. 2003;10(5):699-708. [PubMed]
  16. Tech M, Merkl R. YACOP: Enhanced gene prediction obtained by a combination of existing methods. In Silico Biol. 2003;3(4):441-51. [PubMed]

Gene function prediction

  1. Berriz GF, King OD, Bryant B, Sander C, Roth FP. Characterizing gene sets with FuncAssociate. Bioinformatics. 2003 Dec 12;19(18):2502-2504. [PubMed]
  2. Khan S, Situ G, Decker K, Schmidt CJ. GoFigure: Automated Gene Ontology(TM) annotation. Bioinformatics. 2003 Dec 12;19(18):2484-5. [PubMed]
  3. Schlitt T, Palin K, Rung J, Dietmann S, Lappe M, Ukkonen E, Brazma A. From Gene Networks to Gene Function. Genome Res. 2003 Dec; 13: 2568-2576.  [PubMed][Supplemental Research Data]
  4. Krishnan VG, Westhead DR. A comparative study of machine-learning methods to predict the effects of single nucleotide polymorphisms on protein function. Bioinformatics 2003 Nov 22; 19: 2199-2209. [PubMed]
  5. Scheel H, Tomiuk S, Hofmann K. Elucidation of ataxin-3 and ataxin-7 function by integrative bioinformatics. Hum Mol Genet. 2003 Nov 1; [PubMed]
  6. Tornow S, Mewes HW. Functional modules by relating protein interaction networks and gene expression. Nucleic Acids Res. 2003 Nov 1;31(21):6283-9. [PubMed]
  7. Dezsoo Z, Oltvai ZN, Barabasi AL. Bioinformatics Analysis of Experimentally Determined Protein Complexes in the Yeast Saccharomyces cerevisiae. Genome Res. 2003 Nov;13(11):2450-4. [PubMed]
  8. Samanta MP, Liang S. Predicting protein functions from redundancies in large-scale protein interaction networks. Proc Natl Acad Sci U S A. 2003 Oct 28;100(22):12579-83. [PubMed][pdf]
  9. Clare A, King RD. Predicting gene function in Saccharomyces cerevisiae. Bioinformatics. 2003 Oct;19 Suppl 2:II42-II49. [PubMed]
  10. Shakhnovich BE, Harvey JM, Comeau S Jr, Lorenz D, Delisi C, Shakhnovich EI. ELISA: Structure-Function Inferences Based on Statistically Significant and Evolutionarily Inspired Observations. BMC Bioinformatics. 2003 Sep 2;4(1):34. [PubMed]
  11. Mi H, Vandergriff J, Campbell M, Narechania A, Majoros W, Lewis S, Thomas PD, Ashburner M. Assessment of Genome-Wide Protein Function Classification for Drosophila melanogaster. Genome Res. 2003 Sep;13(9):2118-28. [PubMed]
  12. Strong M, Mallick P, Pellegrini M, Thompson MJ, Eisenberg D. Inference of protein function and protein linkages in Mycobacterium tuberculosis based on prokaryotic genome organization: a combined computational approach. Genome Biol. 2003;4(9):R59. [PubMed]
  13. Scheel H, Tomiuk S, Hofmann K. Elucidation of ataxin-3 and ataxin-7 function by integrative bioinformatics. Hum Mol Genet. 2003 Aug 27 [Epub ahead of print] [PubMed]
  14. Chiang JH, Yu HC. MeKE: discovering the functions of gene products from biomedical literature via sentence alignment. Bioinformatics. 2003 Jul 22;19(11):1417-22. [PubMed]
  15. Troyanskaya OG, Dolinski K, Owen AB, Altman RB, Botstein D. A Bayesian framework for combining heterogeneous data sources for gene function prediction (in Saccharomyces cerevisiae). Proc Natl Acad Sci U S A. 2003 Jul 8;100(14):8348-53. [PubMed][pdf]
  16. Letovsky S, Kasif S. Predicting protein function from protein/protein interaction data: a probabilistic approach. Bioinformatics. 2003 Jul;19 Suppl 1:I197-I204. [PubMed]
  17. Yost C, Hauser L, Larimer F, Thompson D, Beliaev A, Zhou J, Xu Y, Xu D. A computational study of Shewanella oneidensis MR-1: structural prediction and functional inference of hypothetical proteins. OMICS. 2003 Summer;7(2):177-91. [PubMed]
  18. Kim SH, Shin DH, Choi IG, Schulze-Gahmen U, Chen S, Kim R. Structure-based functional inference in structural genomics. J Struct Funct Genomics. 2003;4(2-3):129-35. [PubMed]

Structure prediction

  1. Shah M, Passovets S, Kim D, Ellrott K, Wang L, Vokler I, LoCascio P, Xu D, Xu Y. A computational pipeline for protein structure prediction and analysis at genome scale. Bioinformatics. 2003 Oct 12;19(15):1985-96. [PubMed]
  2. Klepeis JL, Floudas CA. ASTRO-FOLD: A Combinatorial and Global Optimization Framework for Ab Initio Prediction of Three-Dimensional Structures of Proteins from the Amino Acid Sequence. Biophys J. 2003 Oct;85(4):2119-46. [PubMed]
  3. Harrison A, Pearl F, Sillitoe I, Slidel T, Mott R, Thornton J, Orengo C. Recognizing the fold of a protein structure. Bioinformatics. 2003 Sep 22;19(14):1748-59. [PubMed]
  4. Kong Y, Ma J. A Structural-informatics Approach for Mining beta-Sheets: Locating Sheets in Intermediate-resolution Density Maps. J Mol Biol. 2003 Sep 12;332(2):399-413. [PubMed]
  5. Sattar R, Ali SA, Abbasi A. Bioinformatics of granzymes: sequence comparison and structural studies on granzyme family by homology modeling. Biochem Biophys Res Commun. 2003 Sep 5;308(4):726-35. [PubMed]
  6. Ward JJ, McGuffin LJ, Buxton BF, Jones DT. Secondary structure prediction with support vector machines. Bioinformatics. 2003 Sep 1;19(13):1650-5. [PubMed]
  7. Cootes AP, Muggleton SH, Sternberg MJ. The automatic discovery of structural principles describing protein fold space. J Mol Biol. 2003 Jul 18;330(4):839-50. [PubMed]
  8. Yang AS, Wang LY. Local structure prediction with local structure-based sequence profiles. Bioinformatics. 2003 Jul 1;19(10):1267-74. [PubMed]
  9. Yost C, Hauser L, Larimer F, Thompson D, Beliaev A, Zhou J, Xu Y, Xu D. A computational study of Shewanella oneidensis MR-1: structural prediction and functional inference of hypothetical proteins. OMICS. 2003 Summer;7(2):177-91. [PubMed]

Comparative Genomics (theoretical)

  1. Pennisi E. Evolution. Genome comparisons hold clues to human evolution. Science. 2003 Dec 12;302(5652):1876-7. [PubMed]
  2. Clark AG, Glanowski S, Nielsen R, Thomas PD, Kejariwal A, Todd MA, Tanenbaum DM, Civello D, Lu F, Murphy B, Ferriera S, Wang G, Zheng X, White TJ, Sninsky JJ, Adams MD, Cargill M. Inferring nonneutral evolution from human-chimp-mouse orthologous gene trios. Science. 2003 Dec 12;302(5652):1960-3. [PubMed]
  3. Dubchak I, Frazer K. Multi-species sequence comparison: the next frontier in genome annotation. Genome Biol. 2003;4(12):122.[PubMed]
  4. Durand D, Sankoff D. Tests for gene clustering. J Comput Biol. 2003;10(3-4):453-82. [PubMed]

Languages and Algorithms

  1. Gotea V, Veeramachaneni V, Makalowski W. Mastering seeds for genomic size nucleotide BLAST searches. Nucleic Acids Res. 2003 Dec 1;31(23):6935-41. [PubMed]
  2. Hamelryck T, Manderick B. PDB file parser and structure class implemented in Python. Bioinformatics. 2003 Nov 22;19(17):2308-10. [PubMed]
  3. Li L, Stoeckert CJ Jr, Roos DS. OrthoMCL: Identification of Ortholog Groups for Eukaryotic Genomes. Genome Res. 2003 Sep;13(9):2178-89. [PubMed]
  4. Thomas PD, Campbell MJ, Kejariwal A, Mi H, Karlak B, Daverman R, Diemer K, Muruganujan A, Narechania A. PANTHER: A Library of Protein Families and Subfamilies Indexed by Function. Genome Res. 2003 Sep;13(9):2129-41. [PubMed][pdf]

Software

  1. Goesmann A, Linke B, Rupp O, Krause L, Bartels D, Dondrup M, McHardy AC, Wilke A, Puhler A, Meyer F. Building a BRIDGE for the integration of heterogeneous data from functional genomics into a platform for systems biology. J Biotechnol. 2003 Dec 19;106(2-3):157-67. [PubMed]
  2. Brugger K, Redder P, Skovgaard M. MUTAGEN: Multi-User Tool for Annotating GENomes. Bioinformatics. 2003 Dec 12;19(18):2480-1. [PubMed]
  3. Duran AL, Yang J, Wang L, Sumner LW. Metabolomics spectral formatting, alignment and conversion tools (MSFACTs). Bioinformatics 2003 Nov 22; 19: 2283-2293. [PubMed]
  4. Carter K, Bellgard M. MASV-Multiple (BLAST) Annotation System Viewer. Bioinformatics. 2003 Nov 22;19(17):2313-5. [PubMed]
  5. Lee DY, Yun H, Park S, Lee SY. MetaFluxNet: the management of metabolic reaction information and quantitative metabolic flux analysis. Bioinformatics. 2003 Nov 1;19(16):2144-2146. [PubMed]
  6. Nikitin A, Egorov S, Daraselia N, Mazo I. Pathway studio—the analysis and navigation of molecular networks. Bioinformatics. 2003 Nov 1;19(16):2155-7.  [PubMed]
  7. Vernikos GS, Gkogkas CG, Promponas VJ, Hamodrakas SJ. GeneViTo: Visualizing gene-product functional and structural features in genomic datasets. BMC Bioinformatics. 2003 Oct 31;4(1):53. [PubMed]
  8. Carver T, Bleasby A. The design of Jemboss: a graphical user interface to EMBOSS. Bioinformatics. 2003 Sep 22;19(14):1837-43. [PubMed]
  9. Del Val C, Glatting KH, Suhai S. cDNA2Genome: a tool for mapping and annotating cDNAs. BMC Bioinformatics. 2003 Sep 10 [Epub ahead of print][PubMed]
  10. Herron-Olson L, Freeman J, Zhang Q, Retzel EF, Kapur V. MGView: an alignment and visualization tool to enhance gap closure of microbial genomes. Nucleic Acids Res. 2003 Sep 1;31(17):E106. [PubMed]
  11. Takahashi K, Ishikawa N, Sadamoto Y, Sasamoto H, Ohta S, Shiozawa A, Miyoshi F, Naito Y, Nakayama Y, Tomita M. E-Cell 2: Multi-platform E-Cell simulation system. Bioinformatics. 2003 Sep 1;19(13):1727-1729. [PubMed]
  12. McShan DC, Rao S, Shah I. PathMiner: predicting metabolic pathways by heuristic search. Bioinformatics. 2003 Sep 1;19(13):1692-8. [PubMed]  
  13. Novichkova S, Egorov S, Daraselia N. MedScan, a natural language processing engine for MEDLINE abstracts. Bioinformatics. 2003 Sep 1;19(13):1699-706. [PubMed]  
  14. Yang J, Wang J, Yao ZJ, Jin Q, Shen Y, Chen R. GenomeComp: a visualization tool for microbial genome comparison. J Microbiol Methods. 2003 Sep;54(3):423-6. [PubMed]
  15. Huang X, Wang J, Aluru S, Yang SP, Hillier L. PCAP: A Whole-Genome Assembly Program. Genome Res. 2003 Sep;13(9):2164-70. [PubMed][pdf]
  16. Huntley D, Hummerich H, Smedley D, Kittivoravitkul S, McCarthy M, Little P, Sergot M. GANESH: Software for Customized Annotation of Genome Regions. Genome Res. 2003 Sep;13(9):2195-202. [PubMed][pdf]
  17. Quackenbush J. Open-source software accelerates bioinformatics. Genome Biol. 2003;4(9):336. [PubMed]
  18. Charlebois RL, Clarke GD, Beiko RG, St Jean A. Characterization of species-specific genes using a flexible, web-based querying system. FEMS Microbiol Lett. 2003 Aug 29;225(2):213-20. [PubMed]
  19. Ronquist F, Huelsenbeck JP. MrBayes 3: Bayesian phylogenetic inference under mixed models. Bioinformatics. 2003 Aug 12;19(12):1572-1574. [PubMed]
  20. Lambrix P, Habbouche M, Perez M. Evaluation of ontology development tools for bioinformatics. Bioinformatics. 2003 Aug 12;19(12):1564-71. [PubMed]
  21. Paquola AC, Nishyiama MY Jr, Reis EM, Da Silva AM, Verjovski-Almeida S. ESTWeb: bioinformatics services for EST sequencing projects. Bioinformatics. 2003 Aug 12;19(12):1587-8. [PubMed] 
  22. Hoon S, Ratnapu KK, Chia JM, Kumarasamy B, Juguang X, Clamp M, Stabenau A, Potter S, Clarke L, Stupka E. Biopipe: a flexible framework for protocol-based bioinformatics analysis. Genome Res. 2003 Aug;13(8):1904-15. [PubMed][pdf][web supplement]
  23. Gibson R, Smith DR. Genome visualization made fast and simple. Bioinformatics. 2003 Jul 22;19(11):1449-50. [PubMed]
  24. Hoon S, Ratnapu KK, Chia JM, Kumarasamy B, Juguang X, Clamp M, Stabenau A, Potter S, Clarke L, Stupka E. Biopipe: A Flexible Framework for Protocol-Based Bioinformatics Analysis. Genome Res. 2003 Jul 17 [Epub ahead of print] [PubMed]
  25. Nucleic Acid Research July 1; 2003 Web Server Issue
  26. Shah SP, McVicker GP, Mackworth AK, Rogic S, Ouellette BF. GeneComber: combining outputs of gene prediction programs for improved results. Bioinformatics. 2003 Jul 1;19(10):1296-7. [PubMed]
  27. Sauro HM, Hucka M, Finney A, Wellock C, Bolouri H, Doyle J, Kitano H. Next generation simulation tools: the Systems Biology Workbench and BioSPICE integration. OMICS. 2003 Winter;7(4):355-72. [PubMed]
  28. Altermann E, Klaenhammer TR. GAMOLA: a new local solution for sequence annotation and analyzing draft and finished prokaryotic genomes. OMICS. 2003 Summer;7(2):161-9. [PubMed]
  29. Lindvall JM, Blomberg KE, Smith CI. In silico tools for signal transduction research. Brief Bioinform. 2003 Dec;4(4):315-24. [PubMed]

Databases

  1. Nadeau TP, Sullivan KA, Teorey TJ, Feldman EL. Applying database technology to clinical and basic research bioinformatics projects. J Integr Neurosci. 2003 Dec;2(2):201-17. [PubMed]
  2. Iacovoni JS. GeneHuggers: database mining and application connectivity tools for subsequence analyses of the human genome. Bioinformatics. 2003 Nov 22;19(17):2316-8. [PubMed]
  3. Matthiessen MW. BioWareDB: the biomedical software and database search engine. Bioinformatics. 2003 Nov 22;19(17):2319-20. [PubMed]
  4. Cornell M, Paton NW, Hedeler C, Kirby P, Delneri D, Hayes A, Oliver SG. GIMS: an integrated data storage and analysis environment for genomic and functional data. Yeast. 2003 Nov;20(15):1291-306. [PubMed]
  5. Peri S, Navarro JD, Amanchy R, Kristiansen TZ, Jonnalagadda CK, Surendranath V, Niranjan V, Muthusamy B, Gandhi TK, Gronborg M, Ibarrola N, Deshpande N, Shanker K, Shivashankar HN, Rashmi BP, Ramya MA, Zhao Z, Chandrika KN, Padma N, Harsha HC, Yatish AJ, Kavitha MP, Menezes M, Choudhury DR, Suresh S, Ghosh N, Saravana R, Chandran S, Krishna S, Joy M, Anand SK, Madavan V, Joseph A, Wong GW, Schiemann WP, Constantinescu SN, Huang L, Khosravi-Far R, Steen H, Tewari M, Ghaffari S, Blobe GC, Dang CV, Garcia JG, Pevsner J, Jensen ON, Roepstorff P, Deshpande KS, Chinnaiyan AM, Hamosh A, Chakravarti A, Pandey A. Development of human protein reference database as an initial platform for approaching systems biology in humans. Genome Res. 2003 Oct;13(10):2363-71. [PubMed]
  6. Mooney SD, Altman RB. MutDB: annotating human variation with functionally relevant data. Bioinformatics. 2003 Sep 22;19(14):1858-60. [PubMed]
  7. Leinonen R, Nardone F, Oyewole O, Redaschi N, Stoehr P. The EMBL sequence version archive. Bioinformatics. 2003 Sep 22;19(14):1861-2. [PubMed]
  8. Tatusov RL, Fedorova ND, Jackson JJ, Jacobs AR, Kiryutin B, Koonin EV, Krylov DM, Mazumder R, Mekhedov SL, Nikolskaya AN, Rao BS, Smirnov S, Sverdlov AV, Vasudevan S, Wolf YI, Yin JJ, Natale DA. The COG database: an updated version includes eukaryotes. BMC Bioinformatics. 2003 Sep 11 [Epub ahead of print] [PubMed]
  9. Janssen P, Enright AJ, Audit B, Cases I, Goldovsky L, Harte N, Kunin V, Ouzounis CA. COmplete GENome Tracking (COGENT): a flexible data environment for computational genomics. Bioinformatics. 2003 Jul 22;19(11):1451-2. [PubMed]
  10. Lord PW, Stevens RD, Brass A, Goble CA. Investigating semantic similarity measures across the Gene Ontology: the relationship between sequence and annotation. Bioinformatics. 2003 Jul 1;19(10):1275-83. [PubMed]
  11. Bruskiewich RM, Cosico AB, Eusebio W, Portugal AM, Ramos LM, Reyes MT, Sallan MA, Ulat VJ, Wang X, McNally KL, Sackville Hamilton R, McLaren CG. Linking genotype to phenotype: the International Rice Information System (IRIS). Bioinformatics. 2003 Jul;19 Suppl 1:I63-I65. [PubMed]

Conference proceedings

  1. ISMB 2003 issue; Bioinformatics 2003 Jul 3.
last updated: 13 Apr 2004
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