My bioinformatics journal watch - year 2003 Jan-Jun [ 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
Softwares
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. Brown SM. Bioinformatics becomes respectable. Biotechniques. 2003 Jun;34(6):1124-7. [PubMed]
  2. Winslow RL, Boguski MS. Genome informatics: current status and future prospects. Circ Res. 2003 May 16;92(9):953-61. [PubMed]
  3. Altman RB. The expanding scope of bioinformatics: sequence analysis and beyond. Heredity. 2003 May;90(5):345. [PubMed]
  4. Jamison DC. Open Bioinformatics. Bioinformatics 2003 Apr 12; 19: 679-680. [PubMed]
  5. Kanehisa M, Bork P. Bioinformatics in the post-sequence era. Nat Genet. 2003 Mar;33 Suppl:305-10. [PubMed]
  6. Jain E. Practical bioinformatics. Pharmacogenomics. 2003 Mar;4(2):119-21. [PubMed]
  7. Louis JC. Asia bioinformatics: a new import-export industry. Drug Discov Today. 2003 Feb 15;8(4):147-9. [PubMed]
  8. Miller CJ, Attwood TK. Opinion: Bioinformatics goes back to the future. Nat Rev Mol Cell Biol. 2003 Feb;4(2):157-62. [PubMed]
  9. Elkin PL. Primer on medical genomics part V: bioinformatics. Mayo Clin Proc. 2003 Jan;78(1):57-64. [PubMed]
  10. Parker DS, Gorlick MM, Lee CJ. Evolving from Bioinformatics in-the-Small to Bioinformatics in-the-Large. OMICS. 2003 Spring;7(1):37-48. [PubMed]
  11. Wiemer J, Schubert F, Granzow M, Ragg T, Fieres J, Mattes J, Eils R. Informatics United. Methods Inf Med. 2003;42(2):126-33. [PubMed]
    Maojo V, Martin-Sanchez F, Billhardt H, Iakovidis I, Kulikowski C. Establishing an agenda for biomedical informatics. Methods Inf Med. 2003;42(2):121-5. [PubMed]
  12. Harrison R. Protecting innovation in bioinformatics and in-silico biology. BioDrugs. 2003;17(4):227-31. [PubMed]
  13. Giometti CS. Proteomics and bioinformatics. Adv Protein Chem. 2003;65:353-69. [PubMed]

Applications

  1. Petrovsky N, Schonbach C, Brusic V. Bioinformatic strategies for better understanding of immune function. In Silico Biol. 2003 Jun 12 [Epub ahead of print] [PubMed]
  2. Wolff H, Brack-Werner R, Neumann M, Werner T, Schneider R. Integrated functional and bioinformatics approach for the identification and experimental verification of RNA signals: application to HIV-1 INS. Nucleic Acids Res. 2003 Jun 1;31(11):2839-51. [PubMed]
  3. Kasukawa T, Furuno M, Nikaido I, Bono H, Hume DA, Bult C, Hill DP, Baldarelli R, Gough J, Kanapin A, Matsuda H, Schriml LM, Hayashizaki Y, Okazaki Y, Quackenbush J. Development and Evaluation of an Automated Annotation Pipeline and cDNA Annotation System. Genome Res. 2003 Jun; 13: 1542-1551. [PubMed][pdf][web supplement]
  4. Gilbert D. Protein family alignment annotation. Brief Bioinform. 2003 Jun;4(2):192-6. [PubMed]
  5. Lio P. Dimensionality and dependence problems in statistical genomics. Brief Bioinform. 2003 Jun;4(2):168-77. [PubMed]
  6. Saraf MC, Moore GL, Maranas CD. Using multiple sequence correlation analysis to characterize functionally important protein regions. Protein Eng. 2003 Jun;16(6):397-406. [PubMed]
  7. Lohmuller T, Wenzler D, Hagemann S, Kiess W, Peters C, Dandekar T, Reinheckel T. Toward computer-based cleavage site prediction of cysteine endopeptidases. Biol Chem. 2003 Jun;384(6):899-909. [PubMed]
  8. Zagursky RJ, Olmsted SB, Russell DP, Wooters JL. Bioinformatics: how it is being used to identify bacterial vaccine candidates. Expert Rev Vaccines. 2003 Jun;2(3):417-36. [PubMed]
  9. Noskov VN, Leem SH, Solomon G, Mullokandov M, Chae JY, Yoon YH, Shin YS, Kouprina N, Larionov V. A novel strategy for analysis of gene homologues and segmental genome duplications. J Mol Evol. 2003 Jun;56(6):702-10. [PubMed]
  10. Cai YD, Chou KC. Nearest neighbour algorithm for predicting protein subcellular location by combining functional domain composition and pseudo-amino acid composition. Biochem Biophys Res Commun. 2003 May 30;305(2):407-11. [PubMed]
  11. Ng SK, Zhang Z, Tan SH. Integrative approach for computationally inferring protein domain interactions. Bioinformatics. 2003 May 22;19(8):923-9. [PubMed]
  12. Wen XY, Hegele RA, Wang J, Wang DY, Cheung J, Wilson M, Yahyapour M, Bai Y, Zhuang L, Skaug J, Young TK, Connelly PW, Koop BF, Tsui LC, Stewart AK. Identification of a novel lipase gene mutated in lpd mice with hypertriglyceridemia and associated with dyslipidemia in humans. Hum Mol Genet. 2003 May 15;12(10):1131-1143. [PubMed]
  13. Eils R, Athale C. Computational imaging in cell biology. J Cell Biol. 2003 May 12;161(3):477-81. [PubMed]
  14. Sanishvili R, Yakunin AF, Laskowski RA, Skarina T, Evdokimova E, Doherty-Kirby A, Lajoie GA, Thornton JM, Arrowsmith CH, Savchenko A, Joachimiak A, Edwards AM. Integrating structure, bioinformatics and enzymology to discover function: BioH, a new carboxylesterase from E. coli. J Biol Chem. 2003 May 5 [epub ahead of print] [PubMed]
  15. Smith DJ. Applications of bioinformatics and computational biology to influenza surveillance and vaccine strain selection. Vaccine. 2003 May 1;21(16):1758-61. [PubMed]
  16. Gatto JG. The changing face of bioinformatics. Drug Discov Today. 2003 May 1;8(9):375-6. [PubMed]
  17. Zhang Z, Gerstein M.  Identification and characterization of over 100 mitochondrial ribosomal protein pseudogenes in the human genome. Genomics. 2003 May; 81: 468-480. [PubMed]
  18. Elkon R, Linhart C, Sharan R, Shamir R, Shiloh Y. Genome-wide in silico identification of transcriptional regulators controlling the cell cycle in human cells. Genome Res. 2003 May;13(5):773-80. [PubMed]
  19. Brusic V, Petrovsky N. Bioinformatics for characterisation of allergens, allergenicity and allergic crossreactivity. Trends Immunol. 2003 May;24(5):225-8. [PubMed]
  20. Iliopoulos I, Tsoka S, Andrade MA, Enright AJ, Carroll M, Poullet P, Promponas V, Liakopoulos T, Palaios G, Pasquier C, Hamodrakas S, Tamames J, Yagnik AT, Tramontano A, Devos D, Blaschke C, Valencia A, Brett D, Martin D, Leroy C, Rigoutsos I, Sander C, Ouzounis CA. Evaluation of annotation strategies using an entire genome sequence. Bioinformatics 2003 Apr 12; 19: 717-726. [PubMed]
  21. Das S, Chaudhuri K. Identification of a unique IAHP (IcmF associated homologous proteins) cluster in Vibrio cholerae and other proteobacteria through in silico analysis. In Silico Biol. 2003 Apr 3 [Epub ahead of print] [PubMed]
  22. Jensen LJ, Skovgaard M, Sicheritz-Ponten T, Jorgensen MK, Lundegaard C, Pedersen CC, Petersen N, Ussery D. Analysis of two large functionally uncharacter-ized regions in the Methanopyrus kandleri AV19 genome. BMC Genomics. 2003 Apr 2 [epub ahead of print] [PubMed][pdf]
  23. Taylor MD, Mainprize TG, Rutka JT. Bioinformatics in neurosurgery. Neurosurgery. 2003 Apr;52(4):723-31. [PubMed]
  24. Liu R, McEachin RC, States DJ. Computationally Identifying Novel NF-kappa B-Regulated Immune Genes in the Human Genome. Genome Res. 2003 Apr;13(4):654-61. [PubMed]
  25. Gaulton A, Attwood TK. Bioinformatics approaches for the classification of G-protein-coupled receptors. Curr Opin Pharmacol. 2003 Apr;3(2):114-20. [PubMed]
  26. Nandi T, Kannan K, Ramachandran S. The low complexity proteins from enteric pathogenic bacteria: Taxonomic parallels embedded in diversity. In Silico Biol. 2003 Mar 23 [Epub ahead of print] [PubMed]
  27. Lyubetsky VA, V'yugin VV. Methods of horizontal gene transfer determination using phylogenetic data. In Silico Biol. 2003 Mar 16 [epub ahead of print] [PubMed]
  28. Stern MD, Anisimov SV, Boheler KR. Can transcriptome size be estimated from SAGE catalogs? Bioinformatics 2003 Mar; 19: 443-448. [PubMed]
  29. Papoian GA, Wolynes PG. The physics and bioinformatics of binding and folding-an energy landscape perspective. Biopolymers. 2003 Mar;68(3):333-49. [PubMed]
  30. Fiscella M, Perry JW, Teng B, Bloom M, Zhang C, Leung K, Pukac L, Florence K, Concepcion A, Liu B, Meng Y, Chen C, Cochrane Elgin E, Kanakaraj P, Kaufmann TE, Porter J, Cibotti R, Mei Y, Zhou J, Chen G, Roschke V, Komatsoulis G, Mansfield B, Ruben S, Sanyal I, Migone TS. TIP, a T-cell factor identified using high-throughput screening increases survival in a graft-versus-host disease model. Nat Biotechnol. 2003 Mar;21(3):302-7. [PubMed]
  31. Bian H, Reidhaar-Olson JF, Hammer J. The use of bioinformatics for identifying class II-restricted T-cell epitopes. Methods. 2003 Mar;29(3):299-309. [PubMed]
  32. Subramanian S, Mishra RK, Singh L.  Genome-wide analysis of microsatellite repeats in humans: their abundance and density in specific genomic regions. Genome Biol. 2003 Feb;4(2):R13. [PubMed][pdf]
  33. Zhu Y, King BL, Parvizi B, Brunk BP, Stoeckert CJ Jr, Quackenbush J, Richardson J, Bult CJ. Integrating computationally assembled mouse transcript sequences with the Mouse Genome Informatics (MGI) database. Genome Biol. 2003 Feb;4(2):R16. [PubMed][pdf]
  34. Mootha VK, Lepage P, Miller K, Bunkenborg J, Reich M, Hjerrild M, Delmonte T, Villeneuve A, Sladek R, Xu F, Mitchell GA, Morin C, Mann M, Hudson TJ, Robinson B, Rioux JD, Lander ES. Identification of a gene causing human cytochrome c oxidase deficiency by integrative genomics. Proc Natl Acad Sci U S A. 2003 Jan 21;100(2):605-610. [PubMed]
  35. Bissantz C, Bernard P, Hibert M, Rognan D. Protein-based virtual screening of chemical databases. II. Are homology models of G-Protein Coupled Receptors suitable targets? Proteins. 2003 Jan 1;50(1):5-25. [PubMed]
  36. Jenkins JL, Kao RY, Shapiro R. Virtual screening to enrich hit lists from high-throughput screening: a case study on small-molecule inhibitors of angiogenin. Proteins. 2003 Jan 1;50(1):81-93. [PubMed]
  37. Mrowka R, Liebermeister W, Holste D. Does mapping reveal correlation between gene expression and protein-protein interaction? Nat Genet. 2003 Jan;33(1):15-6. [PubMed]
  38. Ge H, Liu Z, Church GM, Vidal M. Reply to "Does mapping reveal correlation between gene expression and protein-protein interaction?". Nat Genet. 2003 Jan;33(1):16-7. [PubMed]
  39. Zhang YM, Marrakchi H, White SW, Rock CO. The application of computational methods to explore the diversity and structure of bacterial fatty acid synthase. J Lipid Res. 2003 Jan;44(1):1-10. [PubMed]
  40. Swenson KI, Winkler KE, Means AR. A New Identity for MLK3 as an NIMA-related, Cell Cycle-regulated Kinase That Is Localized near Centrosomes and Influences Microtubule Organization. Mol Biol Cell. 2003 Jan;14(1):156-72. [PubMed]
  41. Collins JE, Goward ME, Cole CG, Smink LJ, Huckle EJ, Knowles S, Bye JM, Beare DM, Dunham I. Reevaluating human gene annotation: a second-generation analysis of chromosome 22. Genome Res. 2003 Jan;13(1):27-36. [PubMed]
  42. Xuan Z, Wang J, Zhang MQ. Computational comparison of two mouse draft genomes and the human golden path. Genome Biol. 2003 Jan;4(1):R1. [PubMed][pdf]
  43. Cash HD, Hoyle JW, Sutton AJ. Development under extreme conditions: forensic bioinformatics in the wake of the World Trade Center disaster. Pac Symp Biocomput. 2003;:638-53. [PubMed]
  44. Grant AM, Moshyk AM, Kushniruk A, Moehr JR. Reflections on an Arranged Marriage between Bioinformatics and Health Informatics. Methods Inf Med. 2003;42(2):116-20. [PubMed]
  45. Siregar P, Julen N, Sinteff JP. Computational integrative physiology: at the convergence of the life and computational sciences. Methods Inf Med. 2003;42(2):177-84. [PubMed]
  46. Moreau Y, Antal P, Fannes G, De Moor B. Probabilistic graphical models for computational biomedicine. Methods Inf Med. 2003;42(2):161-8. [PubMed]
  47. Sarachan BD, Simmons MK, Subramanian P, Temkin JM. Combining Medical Informatics and Bioinformatics toward Tools for Personalized Medicine. Methods Inf Med. 2003;42(2):111-5. [PubMed]
  48. Grant AM, Moshyk AM, Kushniruk A, Moehr JR. Reflections on an Arranged Marriage between Bioinformatics and Health Informatics. Methods Inf Med. 2003;42(2):116-20. [PubMed]
  49. Wiemer J, Schubert F, Granzow M, Ragg T, Fieres J, Mattes J, Eils R. Informatics United. Methods Inf Med. 2003;42(2):126-33. [PubMed]
    Maojo V, Martin-Sanchez F, Billhardt H, Iakovidis I, Kulikowski C. Establishing an agenda for biomedical informatics. Methods Inf Med. 2003;42(2):121-5. [PubMed]
  50. Rigden DJ, Galperin MY, Jedrzejas MJ. Analysis of structure and function of putative surface-exposed proteins encoded in the Streptococcus pneumoniae genome: a bioinformatics-based approach to vaccine and drug design. Crit Rev Biochem Mol Biol. 2003;38(2):143-68. [PubMed]

Data mining

  1. Daniel Navarro J, Niranjan V, Peri S, Kiran Jonnalagadda C, Pandey A. From biological databases to platforms for biomedical discovery. Trends Biotechnol. 2003 Jun;21(6):263-8. [PubMed]
  2. Sun CH, McCaffery JM, Reiner DS, Gillin FD. Mining the giardia lamblia genome for new cyst wall proteins. J Biol Chem. 2003 Apr 9 [epub ahead of print] [PubMed]
  3. Wu Y, Wang X, Liu X, Wang Y. Data-Mining Approaches Reveal Hidden Families of Proteases in the Genome of Malaria Parasite. Genome Res. 2003 Apr;13(4):601-616. [PubMed]
  4. Lio P. Statistical bioinformatic methods in microbial genome analysis. Bioessays. 2003 Mar;25(3):266-73. [PubMed]
  5. Liu G, Program NC, Zhao S, Bailey JA, Sahinalp SC, Alkan C, Tuzun E, Green ED, Eichler EE. Analysis of Primate Genomic Variation Reveals a Repeat-Driven Expansion of the Human Genome. Genome Res. 2003 Mar;13(3):358-368. [PubMed]
  6. Pandey A, Peri S, Thacker C, Whipple CA, Collins JJ, Mann M. Computational and experimental analysis reveals a novel Src family kinase in the C. elegans genome. Bioinformatics. 2003 Jan 22;19(2):169-172. [PubMed]
  7. Becquet C, et al. Strong-association-rule mining for large-scale gene-expression data analysis: a case study on human SAGE data. Genome Biol. 2002 Dec; 12: [PubMed][pdf]
  8. Lord PW, Stevens RD, Brass A, Goble CA. Semantic similarity measures as tools for exploring the gene ontology. Pac Symp Biocomput. 2003;:601-12. [PubMed]
  9. Lambrix P, Edberg A. Evaluation of ontology merging tools in bioinformatics. Pac Symp Biocomput. 2003;:589-600. [PubMed]
  10. Breton V, Medina R, Montagnat J. DataGrid, Prototype of a Biomedical Grid. Methods Inf Med. 2003;42(2):143-7. [PubMed]

Literature mining

  1. Nenadic G, Spasic I, Ananiadou S.  Terminology-driven mining of biomedical literature. Bioinformatics. 2003 May 22;19(8):938-43. [PubMed]
  2. Majoros WH, Subramanian GM, Yandell MD. Identification of key concepts in biomedical literature using a modified Markov heuristic. Bioinformatics. 2003 Feb;19(3):402-7. [PubMed]
  3. Raychaudhuri S, Altman RB. A literature-based method for assessing the functional coherence of a gene group. Bioinformatics. 2003 Feb;19(3):396-401. [PubMed]

Database mining

  1. Daniel Navarro J, Niranjan V, Peri S, Kiran Jonnalagadda C, Pandey A. From biological databases to platforms for biomedical discovery. Trends Biotechnol. 2003 Jun;21(6):263-8. [PubMed]
  2. Faria-Campos AC, Cerqueira GC, Anacleto C, Carvalho CM, Ortega JM. Mining microorganism EST databases in the quest for new proteins. Genet Mol Res. 2003 Mar 31;2(1):169-77. [PubMed]
  3. Brown S, Chang JL, Sadee W, Babbitt PC. A semiautomated approach to gene discovery through expressed sequence tag data mining: discovery of new human transporter genes. AAPS PharmSci. 2003;5(1):E1. [PubMed]

in silico biology/computational modelling

  1. Schmeichel KL, Bissell MJ. Modeling tissue-specific signaling and organ function in three dimensions. J Cell Sci. 2003 Jun 15; 116, 2377-2388. [PubMed]
  2. Ginkel M, Kremling A, Nutsch T, Rehner R, Gilles ED. Modular modeling of cellular systems with ProMoT/Diva. Bioinformatics. 2003 Jun 12;19(9):1169-76. [PubMed]
  3. Selinger DW, Wright MA, Church GM. On the complete determination of biological systems. Trends Biotechnol. 2003 Jun;21(6):251-4.  [PubMed]
  4. Alland D, Whittam TS, Murray MB, Cave MD, Hazbon MH, Dix K, Kokoris M, Duesterhoeft A, Eisen JA, Fraser CM, Fleischmann RD. Modeling bacterial evolution with comparative-genome-based marker systems: application to Mycobacterium tuberculosis evolution and pathogenesis. J Bacteriol. 2003 Jun;185(11):3392-9. [PubMed]
  5. Thum KE, Shasha DE, Lejay LV, Coruzzi GM. Light- and carbon-signaling pathways. Modeling circuits of interactions. Plant Physiol. 2003 Jun;132(2):440-52. [PubMed]
  6. Shimizu TS, Aksenov SV, Bray D. A Spatially Extended Stochastic Model of the Bacterial Chemotaxis Signalling Pathway. J Mol Biol. 2003 May 30; 329:291-309  [PubMed]
  7. Fuellen G, Spitzer M, Cullen P, Lorkowski S.  BLASTing proteomes, yielding phylogenies. In Silico Biol. 2003 May 24 [Epub ahead of print] [PubMed]
  8. Mellman I, Misteli T. Computational cell biology. J Cell Biol. 2003 May 12;161(3):463-4. [PubMed]
  9. Vilar JM, Guet CC, Leibler S. Modeling network dynamics: the lac operon, a case study. J Cell Biol. 2003 May 12;161(3):471-6. [PubMed]
  10. Huang GS, Hong MY, Liu YC. Incorporation of DNA chip technology to the simulation and validation of flux analysis in yeast diauxic growth. Life Sci. 2003 Apr 18;72(22):2525-31. [PubMed]
  11. Kajita A, Yamamura M, Kohara Y. Computer simulation of the cellular arrangement using physical model in early cleavage of the nematode Caenorhabditis elegans. Bioinformatics 2003 Apr 12; 19: 704-716. [PubMed]
  12. Price ND, Papin JA, Schilling CH, Palsson BO.  Genome-scale microbial in silico models: the constraints-based approach. Trends Biotechnol 2003 Apr; 21: 162-169. [PubMed]
  13. Tchuraev RN, Galimzyanov AV. Parametric stability evaluation in computer experiments on the mathematical model of Drosophila control gene subnetwork. In Silico Biol. 2003 Mar 30 [epub ahead of print] [PubMed]
  14. Van De Waterbeemd H, Gifford E. ADMET in silico modelling: towards prediction paradise? Nat Rev Drug Discov. 2003 Mar;2(3):192-204. [PubMed]
  15. Teuscher C, Mange D, Stauffer A, Tempesti G. Bio-inspired computing tissues: towards machines that evolve, grow, and learn. Biosystems. 2003 Feb;68(2-3):235-44. [PubMed]
  16. Holcombe M, Holcombe L, Gheorghe M, Talbot N. A hybrid machine model of rice blast fungus, Magnaporthe grisea. Biosystems. 2003 Feb;68(2-3):223-8. [PubMed]
  17. Siva K, Elber R. Ion permeation through the gramicidin channel: atomically detailed modeling by the Stochastic Difference Equation. Proteins. 2003 Jan 1;50(1):63-80. [PubMed]
  18. Steven Wiley H, Shvartsman SY, Lauffenburger DA. Computational modeling of the EGF-receptor system: a paradigm for systems biology. Trends Cell Biol. 2003 Jan;13(1):43-50. [PubMed]
  19. Antoniotti M, Policriti A, Ugel N, Mishra B. Model building and model checking for biochemical processes. Cell Biochem Biophys. 2003;38(3):271-86. [PubMed]

Network/pathway reconstruction and analysis

  1. Isaacs FJ, Hasty J, Cantor CR, Collins JJ. Prediction and measurement of an autoregulatory genetic module. Proc Natl Acad Sci U S A. 2003 Jun 24;100(13):7714-9. [PubMed][pdf]
  2. Matsuno H, Tanaka Y, Aoshima H, Doi A, Matsui M, Miyano S. Biopathways representation and simulation on hybrid functional Petri net. In Silico Biol. 2003 Jun 23 [Epub ahead of print] [PubMed]
  3. Chen M, Hofestaedt R. Quantitative Petri net model of gene regulated metabolic networks in the cell. In Silico Biol. 2003 Jun 7 [Epub ahead of print] [PubMed]
  4. Zevedei-Oancea I, Schuster S. Topological analysis of metabolic networks based on Petri net theory. In Silico Biol. 2003 Jun 7 [Epub ahead of print] [PubMed]
  5. Shimizu TS, Aksenov SV, Bray D. A Spatially Extended Stochastic Model of the Bacterial Chemotaxis Signalling Pathway. J Mol Biol. 2003 May 30; 329:291-309  [PubMed]
  6. Atkinson MR, Savageau MA, Myers JT, Ninfa AJ. Development of Genetic Circuitry Exhibiting Toggle Switch or Oscillatory Behavior in Escherichia coli. Cell. 2003 May 30;113(5):597-607. [PubMed][web supplement]
  7. Gagneur J, Jackson DB, Casari G. Hierarchical analysis of dependency in metabolic networks. Bioinformatics. 2003 May 22;19(8):1027-34. [PubMed]
  8. Krishnamurthy L, Nadeau J, Ozsoyoglu G, Ozsoyoglu M, Schaeffer G, Tasan M, Xu W. Pathways database system: an integrated system for biological pathways. Bioinformatics. 2003 May 22;19(8):930-7. [PubMed]
  9. Steuer R, Kurths J, Fiehn O, Weckwerth W. Observing and interpreting correlations in metabolomic networks. Bioinformatics. 2003 May 22;19(8):1019-26. [PubMed]
  10. Vilar JM, Guet CC, Leibler S. Modeling network dynamics: the lac operon, a case study. J Cell Biol. 2003 May 12;161(3):471-6. [PubMed]
  11. Bu D, Zhao Y, Cai L, Xue H, Zhu X, Lu H, Zhang J, Sun S, Ling L, Zhang N, Li G, Chen R. Topological structure analysis of the protein-protein interaction network in budding yeast. Nucleic Acids Res. 2003 May 1;31(9):2443-50. [PubMed][web supplement]
  12. Lee JM, Sonnhammer EL. Genomic gene clustering analysis of pathways in eukaryotes. Genome Res. 2003 May;13(5):875-82. [PubMed]
  13. Papin JA, Price ND, Wiback SJ, Fell DA, Palsson BO. Metabolic pathways in the post-genome era. Trends Biochem Sci. 2003 May;28(5):250-8. [PubMed]
  14. Pawson T, Nash P. Assembly of cell regulatory systems through protein interaction domains. Science. 2003 Apr 18;300(5618):445-52. [PubMed][web supplement]
  15. Buchler NE, Gerland U, Hwa T. On schemes of combinatorial transcription logic. Proc Natl Acad Sci U S A. 2003 Apr 17 [epub ahead of print] [PubMed][web supplement]
  16. Trost E, Hackl H, Maurer M, Trajanoski Z. Java editor for biological pathways. Bioinformatics 2003 Apr 12; 19: 786-787. [PubMed]
  17. Tyson JJ, Chen KC, Novak B. Sniffers, buzzers, toggles and blinkers: dynamics of regulatory and signaling pathways in the cell. Curr Opin Cell Biol. 2003 Apr; 15: 221-231. [PubMed]
  18. Alm E, Arkin AP. Biological networks. Curr Opin Struct Biol. 2003 Apr;13(2):193-202. [PubMed]
  19. Tchuraev RN, Galimzyanov AV. Parametric stability evaluation in computer experiments on the mathematical model of Drosophila control gene subnetwork. In Silico Biol. 2003 Mar 30 [epub ahead of print] [PubMed]
  20. Kikuchi S, Tominaga D, Arita M, Takahashi K, Tomita M. Dynamic modeling of genetic networks using genetic algorithm and S-system. Bioinformatics. 2003 Mar 22;19(5):643-650. [PubMed]
  21. Freier A, Hofestaedt R, Lange M. iUDB: An object-oriented system for modelling, integration and analysis of gene controlled metabolic networks. In Silico Biol. 2003 Mar 17 [epub ahead of print] [PubMed]
  22. Bundschuh R, Hayot F, Jayaprakash C. Fluctuations and slow variables in genetic networks. Biophys J. 2003 Mar;84(3):1606-15. [PubMed]
  23. Holme P, Huss M, Jeong H. Subnetwork hierarchies of biochemical pathways. Bioinformatics 2003 Mar; 19: 532-538. [PubMed]
  24. Hucka M, Finney A, Sauro HM, Bolouri H, Doyle JC, Kitano H, Arkin AP, Bornstein BJ, Bray D, Cornish-Bowden A, Cuellar AA, Dronov S, Gilles ED, Ginkel M, Gor V, Goryanin II, Hedley WJ, Hodgman TC, Hofmeyr JH, Hunter PJ, Juty NS, Kasberger JL, Kremling A, Kummer U, Le Novere N, Loew LM, Lucio D, Mendes P, Minch E, Mjolsness ED, Nakayama Y, Nelson MR, Nielsen PF, Sakurada T, Schaff JC, Shapiro BE, Shimizu TS, Spence HD, Stelling J, Takahashi K, Tomita M, Wagner J, Wang J. The systems biology markup language (SBML): a medium for representation and exchange of biochemical network models. Bioinformatics 2003 Mar; 19: 524-531. [PubMed]
  25. Peregrin-Alvarez JM, Tsoka S, Ouzounis CA. The phylogenetic extent of metabolic enzymes and pathways. Genome Res. 2003 Mar;13(3):422-7. [PubMed]
  26. Ebenhoh O, Heinrich R. Stoichiometric design of metabolic networks: multifunctionality, clusters, optimization, weak and strong robustness. Bull Math Biol. 2003 Mar;65(2):323-57. [PubMed]
  27. Davidson EH, McClay DR, Hood L. Regulatory gene networks and the properties of the developmental process. Proc Natl Acad Sci U S A. 2003 Feb 18;100(4):1475-80. [PubMed][pdf]
  28. Madan Babu M, Teichmann SA. Evolution of transcription factors and the gene regulatory network in Escherichia coli. Nucleic Acids Res. 2003 Feb 15;31(4):1234-44. [PubMed]
  29. Zupan B, Demsar J, Bratko I, Juvan P, Halter JA, Kuspa A, Shaulsky G. GenePath: a system for automated construction of genetic networks from mutant data. Bioinformatics. 2003 Feb 12;19(3):383-389. [PubMed]
  30. Rives AW, Galitski T. Modular organization of cellular networks. Proc Natl Acad Sci U S A. 2003 Feb 4;100(3):1128-33. [PubMed]
  31. Price ND, Reed JL, Papin JA, Famili I, Palsson BO. Analysis of Metabolic Capabilities Using Singular Value Decomposition of Extreme Pathway Matrices. Biophys J. 2003 Feb; 84:794-804. [PubMed]
  32. Yu JW, Lemmon MA. Genome-wide analysis of signaling domain function. Curr Opin Chem Biol. 2003 Feb; 7:103-109. [PubMed]
  33. Forster J, Famili I, Fu P, Palsson B BO, Nielsen J. Genome-Scale Reconstruction of the Saccharomyces cerevisiae Metabolic Network. Genome Res. 2003 Feb;13(2):244-53. [PubMed][web supplement]
  34. Klamt S, Stelling J. Two approaches for metabolic pathway analysis? Trends Biotechnol. 2003 Feb;21(2):64-9. [PubMed]
  35. De Jong H, Geiselmann J, Hernandez C, Page M. Genetic Network Analyzer: qualitative simulation of genetic regulatory networks. Bioinformatics. 2003 Feb;19(3):336-44. [PubMed]
  36. Sivakumaran S, Hariharaputran S, Mishra J, Bhalla US. The Database of Quantitative Cellular Signaling: management and analysis of chemical kinetic models of signaling networks. Bioinformatics. 2003 Feb;19(3):408-15 [PubMed]
  37. Kaufman M, Thomas R. Emergence of complex behaviour from simple circuit structures. C R Biol. 2003 Feb;326(2):205-14. [PubMed]
  38. Creighton C, Hanash S. Mining gene expression databases for association rules. Bioinformatics. 2003 Jan;19(1):79-86. [PubMed]
  39. Ma H, Zeng AP. Reconstruction of metabolic networks from genome data and analysis of their global structure for various organisms. Bioinformatics. 2003 Jan;19(2):270-7. [PubMed][web supplement]
  40. Klamt S, Stelling J, Ginkel M, Gilles ED. FluxAnalyzer: exploring structure, pathways, and flux distributions in metabolic networks on interactive flux maps. Bioinformatics. 2003 Jan;19(2):261-9. [PubMed]
  41. Soinov LA, Krestyaninova MA, Brazma A. Towards reconstruction of gene networks from expression data by supervised learning. Genome Biol. 2003 Jan;4(1):R6. [PubMed][pdf]
  42. Smith VA, Jarvis ED, Hartemink AJ. Influence of Network Topology and Data Collection on Network Inference. Pacific Symposium on Biocomputing 2003; 8:164-175. [PubMed][pdf]

Promter/regulatory sequence analysis

  1. Kel-Margoulis OV, Tchekmenev D, Kel AE, Goessling E, Hornischer K, Lewicki-Potapov B, Wingender E. Composition-sensitive analysis of the human genome for regulatory signals. In Silico Biol. 2003 Jun 27 [Epub ahead of print] [PubMed]
  2. Ettwiller LM, Rung J, Birney E. Discovering Novel cis-Regulatory Motifs Using Functional Networks. Genome Res. 2003 May;13(5):883-95. [PubMed]
  3. Danilova LV, Lyubetsky VA, Gelfand MS. An algorithm for identification of regulatory signals in unaligned DNA sequences, its testing and parallel implementation. In Silico Biol. 2003 Apr 14 [epub ahead of print] [PubMed]
  4. Zheng J, Wu J, Sun Z. An approach to identify over-represented cis-elements in related sequences. Nucleic Acids Res. 2003 Apr 1;31(7):1995-2005. [PubMed]
  5. Blekas K, Fotiadis DI, Likas A. Greedy mixture learning for multiple motif discovery in biological sequences. Bioinformatics. 2003 Mar 22;19(5):607-17. [PubMed]
  6. Aerts S, Thijs G, Coessens B, Staes M, Moreau Y, Moor BD. Toucan: deciphering the cis-regulatory logic of coregulated genes. Nucleic Acids Res. 2003 Mar 15;31(6):1753-64. [PubMed]
  7. Levitsky VG, Katokhin AV. Recognition of eukaryotic promoters using a genetic algorithm based on iterative discriminant analysis. In Silico Biol. 2003 Feb 27 [epub ahead of print] [PubMed]
  8. Stavrovskaya ED, Mironov AA. Two genetic algorithms for identification of regulatory signals. In Silico Biol. 2003 Feb 11 [epub ahead of print] [PubMed]
  9. Trinklein ND, Aldred SJ, Saldanha AJ, Myers RM. Identification and functional analysis of human transcriptional promoters. Genome Res. 2003 Feb;13(2):308-12. [PubMed]
  10. Poluliakh N, Takagi T, Nakai K. MELINA: motif extraction from promoter regions of potentially co-regulated genes. Bioinformatics. 2003 Feb;19(3):423-4. [PubMed]
  11. Zhang LH, Liu de P, Liang CC. Finding regulatory sequences. Int J Biochem Cell Biol. 2003 Jan;35(1):95-103. [PubMed]
  12. Werner T. Promoters can contribute to the elucidation of protein function. Trends Biotechnol. 2003 Jan;21(1):9-13. [PubMed]
  13. Elnitski L, Hardison RC, Li J, Yang S, Kolbe D, Eswara P, O'Connor MJ, Schwartz S, Miller W, Chiaromonte F. Distinguishing regulatory DNA from neutral sites. Genome Res. 2003 Jan;13(1):64-72. [PubMed]
  14. Levitsky VG, Katokhin AV. Recognition of eukaryotic promoters using a genetic algorithm based on iterative discriminant analysis. In Silico Biol. 2003 Feb 27 [epub ahead of print] [PubMed]
  15. Stavrovskaya ED, Mironov AA. Two genetic algorithms for identification of regulatory signals. In Silico Biol. 2003 Feb 11 [epub ahead of print] [PubMed]

Protein-protein interaction analysis

  1. Pawson T, Nash P. Assembly of cell regulatory systems through protein interaction domains. Science. 2003 Apr 18;300(5618):445-52. [PubMed][web supplement]
  2. Huynen MA, Snel B, Mering C, Bork P.  Function prediction and protein networks. Curr Opin Cell Biol. 2003 Apr; 15: 191-198. [PubMed]
  3. Goldberg DS, Roth FP. Assessing experimentally derived interactions in a small world. Proc Natl Acad Sci U S A. 2003 Apr 15;100(8):4372-6. [PubMed][pdf]
  4. Yu JW, Lemmon MA. Genome-wide analysis of signaling domain function. Curr Opin Chem Biol. 2003 Feb; 7:103-109. [PubMed]
  5. Bader GD, Hogue CW. An automated method for finding molecular complexes in large protein interaction networks. BMC Bioinformatics 2003 Jan 13;4(1):2 [PubMed]
  6. Nordman N, Valjakka J, Perakyla M. Analysis of the binding energies of testosterone, 5alpha-dihydrotestosterone, androstenedione and dehydroepiandrosterone sulfate with an antitestosterone antibody. Proteins. 2003 Jan 1;50(1):135-43. [PubMed]
  7. Wang T, Wade RC. Implicit solvent models for flexible protein-protein docking by molecular dynamics simulation. Proteins. 2003 Jan 1;50(1):158-69. [PubMed]
  8. Alexov E. Role of the protein side-chain fluctuations on the strength of pair-wise electrostatic interactions: comparing experimental with computed pK(a)s. Proteins. 2003 Jan 1;50(1):94-103. [PubMed]
  9. Franzot G, Carugo O. Computational approaches to protein-protein interaction. J Struct Funct Genomics. 2003;4(4):245-55. [PubMed]

Gene prediction

  1. Volfovsky N, Haas BJ, Salzberg SL. Computational discovery of internal micro-exons. Genome Res. 2003 Jun;13(6):1216-21. [PubMed][pdf][web supplement]
  2. Freudenberg J. Genome-wide prediction of disease-relevant genes and variants. Curr Opin Drug Discov Devel. 2003 May;6(3):304-9. [PubMed]
  3. Snyder M, Gerstein M. GENOMICS: Defining Genes in the Genomics Era. Science. 2003 Apr 11;300(5617):258-60. [PubMed]
  4. Li L, Brunk BP, Kissinger JC, Pape D, Tang K, Cole RH, Martin J, Wylie T, Dante M, Fogarty SJ, Howe DK, Liberator P, Diaz C, Anderson J, White M, Jerome ME, Johnson EA, Radke JA, Stoeckert CJ Jr, Waterston RH, Clifton SW, Roos DS, Sibley LD. Gene Discovery in the Apicomplexa as Revealed by EST Sequencing and Assembly of a Comparative Gene Database. Genome Res. 2003 Mar;13(3):443-54. [PubMed]
  5. Alexandersson M, Cawley S, Pachter L. SLAM: Cross-Species Gene Finding and Alignment with a Generalized Pair Hidden Markov Model. Genome Res. 2003 Mar;13(3):496-502. [PubMed]
  6. Lunde CF, Morrow DJ, Roy LM, Walbot V. Progress in maize gene discovery: a project update. Funct Integr Genomics. 2003 Mar;3(1-2):25-32. [PubMed]
  7. Pedersen JS, Hein J. Gene finding with a hidden Markov model of genome structure and evolution. Bioinformatics. 2003 Jan 22;19(2):219. [PubMed]
  8. Parra G, Agarwal P, Abril JF, Wiehe T, Fickett JW, Guigo R. Comparative gene prediction in human and mouse. Genome Res. 2003 Jan;13(1):108-17. [PubMed]
  9. Flicek P, Keibler E, Hu P, Korf I, Brent MR. Leveraging the mouse genome for gene prediction in human: from whole-genome shotgun reads to a global synteny map. Genome Res. 2003 Jan;13(1):46-54. [PubMed]
  10. Brown S, Chang JL, Sadee W, Babbitt PC. A semiautomated approach to gene discovery through expressed sequence tag data mining: discovery of new human transporter genes. AAPS PharmSci. 2003;5(1):E1. [PubMed]

Gene function prediction

  1. Vazquez A, Flammini A, Maritan A, Vespignani A. Global protein function prediction from protein-protein interaction networks. Nat Biotechnol. 2003 Jun;21(6):697-700. [PubMed]
  2. Nagashima T, Silva DG, Petrovsky N, Socha LA, Suzuki H, Saito R, Kasukawa T, Kurochkin IV, Konagaya A, Schonbach C. Inferring Higher Functional Information for RIKEN Mouse Full-Length cDNA Clones With FACTS. Genome Res. 2003 Jun;13(6B):1520-33. [PubMed][pdf][web supplement]
  3. King OD, Foulger RE, Dwight SS, White JV, Roth FP. Predicting gene function from patterns of annotation. Genome Res. 2003 May;13(5):896-904. [PubMed]
  4. Huynen MA, Snel B, Mering C, Bork P.  Function prediction and protein networks. Curr Opin Cell Biol. 2003 Apr; 15: 191-198. [PubMed]
  5. McCarter JP, Mitreva MD, Martin J, Dante M, Wylie T, Rao U, Pape D, Bowers Y, Theising B, Murphy CV, Kloek AP, Chiapelli BJ, Clifton SW, Bird DM, Waterston RH. Analysis and functional classification of transcripts from the nematode Meloidogyne incognita. Genome Biol. 2003 Apr;4(4):R26. [PubMed][pdf][web supplement]
  6. Jensen LJ, Gupta R, Staerfeldt HH, Brunak S. Prediction of human protein function according to Gene Ontology categories. Bioinformatics. 2003 Mar 22;19(5):635-642. [PubMed]
  7. Keck HP, Wetter T. Functional classification of proteins using a nearest neighbour algorithm. In Silico Biol. 2003 Feb 17 [Epub ahead of print] [PubMed]
  8. Raychaudhuri S, Altman RB. A literature-based method for assessing the functional coherence of a gene group. Bioinformatics. 2003 Feb;19(3):396-401. [PubMed]
  9. Wu CH, Huang H, Yeh LS, Barker WC. Protein family classification and functional annotation. Comput Biol Chem. 2003 Feb;27(1):37-47. [PubMed]
  10. Werner T. Promoters can contribute to the elucidation of protein function. Trends Biotechnol. 2003 Jan;21(1):9-13. [PubMed]
  11. Liang MP, Brutlag DL, Altman RB. Automated construction of structural motifs for predicting functional sites on protein structures. Pac Symp Biocomput. 2003;:204-15. [PubMed]

Structure prediction

  1. McLaughlin WA, Berman HM. Statistical models for discerning protein structures containing the DNA-binding helix-turn-helix motif. J Mol Biol. 2003 Jun 27;330(1):43-55. [PubMed]
  2. Carugo O. Prediction of polypeptide fragments exposed to the solvent. In Silico Biol. 2003 Jun 24 [Epub ahead of print] [PubMed]
  3. Ginalski K, Elofsson A, Fischer D, Rychlewski L. 3D-Jury: a simple approach to improve protein structure predictions. Bioinformatics. 2003 May 22;19(8):1015-8. [PubMed]
  4. Contreras-Moreira B, Fitzjohn PW, Bates PA. In silico Protein Recombination: Enhancing Template and Sequence Alignment Selection for Comparative Protein Modelling. J Mol Biol 2003 May 2; 328: 593-608. [PubMed]
  5. Vankayalapati H, Bearss DJ, Saldanha JW, Munoz RM, Rojanala S, Von Hoff DD, Mahadevan D. Targeting aurora2 kinase in oncogenesis: a structural bioinformatics approach to target validation and rational drug design. Mol Cancer Ther. 2003 Mar;2(3):283-94. [PubMed]
  6. Klepeis JL, Pieja MJ, Floudas CA. Hybrid Global Optimization Algorithms for Protein Structure Prediction: Alternating Hybrids. Biophys. J. 2003 Feb; 84: 869-882. [PubMed]
  7. Giorgetti A, Carloni P. Molecular modeling of ion channels: structural predictions. Curr Opin Chem Biol. 2003 Feb;7(1):150-6. [PubMed]
  8. Edwards YJ, Cottage A. Bioinformatics methods to predict protein structure and function. A practical approach. Mol Biotechnol. 2003 Feb;23(2):139-66. [PubMed]
  9. Liu Z, Jiang L, Gao Y, Liang S, Chen H, Han Y, Lai L. Beyond the rotamer library: genetic algorithm combined with the disturbing mutation process for upbuilding protein side-chains. Proteins. 2003 Jan 1;50(1):49-62. [PubMed]
  10. von Ohsen N, Sommer I, Zimmer R. Profile-profile alignment: a powerful tool for protein structure prediction. Pac Symp Biocomput. 2003;:252-63. [PubMed]
  11. Liang MP, Brutlag DL, Altman RB. Automated construction of structural motifs for predicting functional sites on protein structures. Pac Symp Biocomput. 2003;:204-15. [PubMed]
  12. Fauman EB, Hopkins AL, Groom CR. Structural bioinformatics in drug discovery. Methods Biochem Anal. 2003;44:477-97. [PubMed]
  13. Altman RB, Dugan JM. Defining bioinformatics and structural bioinformatics. Methods Biochem Anal. 2003;44:3-14. [PubMed]
  14. Bourne PE. CASP and CAFASP experiments and their findings. Methods Biochem Anal. 2003;44:501-7. [PubMed]

Comparative Genomics (theoretical)

  1. Janaki C, Joshi RR.  Accelerating comparative genomics using parallel computing. In Silico Biol. 2003 Jun 24 [Epub ahead of print] [PubMed]
  2. Hampson S, McLysaght A, Gaut B, Baldi P. LineUp: Statistical Detection of Chromosomal Homology With Application to Plant Comparative Genomics. Genome Res. 2003 May;13(5):999-1010. [PubMed]
  3. Martin MJ, Herrero J, Mateos A, Dopazo J. Comparing bacterial genomes through conservation profiles. Genome Res. 2003 May;13(5):991-8. [PubMed]
  4. Cooper GM, Brudno M, Program NC, Green ED, Batzoglou S, Sidow A. Quantitative Estimates of Sequence Divergence for Comparative Analyses of Mammalian Genomes. Genome Res. 2003 May;13(5):813-820. [PubMed]
  5. Hughes AL, Friedman R. Parallel evolution by gene duplication in the genomes of two unicellular fungi. Genome Res. 2003 May;13(5):794-9. [PubMed]
  6. Newman T, Trask BJ. Complex Evolution of 7E Olfactory Receptor Genes in Segmental Duplications. Genome Res. 2003 May;13(5):781-93. [PubMed]
  7. Wong P, Kolesov G, Frishman D, Houry WA. Phylogenetic Web Profiler. Bioinformatics 2003 Apr 12; 19: 782-783. [PubMed]
  8. Pennacchio LA, Rubin EM. Comparative genomic tools and databases: providing insights into the human genome. J Clin Invest. 2003 Apr;111(8):1099-106. [PubMed]
  9. Alexandersson M, Cawley S, Pachter L. SLAM: Cross-Species Gene Finding and Alignment with a Generalized Pair Hidden Markov Model. Genome Res. 2003 Mar;13(3):496-502. [PubMed]
  10. Luc N, Risler JL, Bergeron A, Raffinot M. Gene teams: a new formalization of gene clusters for comparative genomics. Comput Biol Chem. 2003 Feb;27(1):59-67. [PubMed]
  11. Schwartz S, Kent WJ, Smit A, Zhang Z, Baertsch R, Hardison RC, Haussler D, Miller W. Human-Mouse Alignments with BLASTZ. Genome Res. 2003 Jan;13(1):103-7. [PubMed]
  12. Couronne O, Poliakov A, Bray N, Ishkhanov T, Ryaboy D, Rubin E, Pachter L, Dubchak I. Strategies and tools for whole-genome alignments. Genome Res. 2003 Jan;13(1):73-80. [PubMed]
  13. Flicek P, Keibler E, Hu P, Korf I, Brent MR. Leveraging the mouse genome for gene prediction in human: from whole-genome shotgun reads to a global synteny map. Genome Res. 2003 Jan;13(1):46-54. [PubMed]
  14. Pevzner P, Tesler G. Genome rearrangements in Mammalian evolution: lessons from human and mouse genomes. Genome Res. 2003 Jan;13(1):37-45. [PubMed]
  15. Frazer KA, Elnitski L, Church DM, Dubchak I, Hardison RC. Cross-species sequence comparisons: a review of methods and available resources. Genome Res. 2003 Jan;13(1):1-12. [PubMed]

Languages and Algorithms

  1. Bruhn RE, Burton PJ. Designing XML schemas for bioinformatics. Biotechniques. 2003 Jun;34(6):1200-2, 1204, 1206 passim. [PubMed]
  2. Danilova LV, Lyubetsky VA, Gelfand MS. An algorithm for identification of regulatory signals in unaligned DNA sequences, its testing and parallel implementation. In Silico Biol. 2003 Apr 14 [epub ahead of print] [PubMed]
  3. Hucka M, Finney A, Sauro HM, Bolouri H, Doyle JC, Kitano H, Arkin AP, Bornstein BJ, Bray D, Cornish-Bowden A, Cuellar AA, Dronov S, Gilles ED, Ginkel M, Gor V, Goryanin II, Hedley WJ, Hodgman TC, Hofmeyr JH, Hunter PJ, Juty NS, Kasberger JL, Kremling A, Kummer U, Le Novere N, Loew LM, Lucio D, Mendes P, Minch E, Mjolsness ED, Nakayama Y, Nelson MR, Nielsen PF, Sakurada T, Schaff JC, Shapiro BE, Shimizu TS, Spence HD, Stelling J, Takahashi K, Tomita M, Wagner J, Wang J. The systems biology markup language (SBML): a medium for representation and exchange of biochemical network models. Bioinformatics 2003 Mar; 19: 524-531. [PubMed]
  4. Stavrovskaya ED, Mironov AA. Two genetic algorithms for identification of regulatory signals. In Silico Biol. 2003 Feb 11 [epub ahead of print] [PubMed]
  5. Chuang TJ, Lin WC, Lee HC, Wang CW, Hsiao KL, Wang ZH, Shieh D, Lin SC, Ch'ang LY. A complexity reduction algorithm for analysis and annotation of large genomic sequences. Genome Res. 2003 Feb;13(2):313-22. [PubMed]
  6. Smith L, Yeganova L, Wilbur WJ. Hidden Markov models and optimized sequence alignments. Comput Biol Chem. 2003 Feb;27(1):77-84. [PubMed]
  7. Pevzner P, Tesler G. Genome rearrangements in Mammalian evolution: lessons from human and mouse genomes. Genome Res. 2003 Jan;13(1):37-45. [PubMed]

Softwares

  1. Wiezer A, Merkl R. secureBLAST. In Silico Biol. 2003 Jun 21 [Epub ahead of print] [PubMed]
  2. Xie T, Hood L. ACGT-a comparative genomics tool. Bioinformatics. 2003 May 22;19(8):1039-40. [PubMed]
  3. Castillo-Davis CI, Hartl DL. GeneMerge-post-genomic analysis, data mining, and hypothesis testing. Bioinformatics. 2003 May 1;19(7):891-2. [PubMed]
  4. Hoebeke M, Nicolas P, Bessieres P. MuGeN: simultaneous exploration of multiple genomes and computer analysis results. Bioinformatics. 2003 May 1;19(7):859-64. [PubMed]
  5. Bard J. Ontologies: Formalising biological knowledge for bioinformatics. Bioessays. 2003 May;25(5):501-6. [PubMed]
  6. Svensson BA, Kreeft AJ, Van Ommen GJ, Den Dunnen JT, Boer JM. GeneHopper: a web-based search engine to link gene-expression platforms through GenBank accession numbers. Genome Biol 2003 May;4(5):R35 [PubMed][pdf]
  7. Hampson S, McLysaght A, Gaut B, Baldi P. LineUp: Statistical Detection of Chromosomal Homology With Application to Plant Comparative Genomics. Genome Res. 2003 May;13(5):999-1010. [PubMed]
  8. Meyer F, Goesmann A, McHardy AC, Bartels D, Bekel T, Clausen J, Kalinowski J, Linke B, Rupp O, Giegerich R, Puhler A. GenDB--an open source genome annotation system for prokaryote genomes. Nucleic Acids Res. 2003 Apr 15;31(8):2187-95. [PubMed]
  9. Wong P, Kolesov G, Frishman D, Houry WA. Phylogenetic Web Profiler. Bioinformatics 2003 Apr 12; 19: 782-783. [PubMed]
  10. Berriz GF, White JV, King OD, Roth FP. GoFish finds genes with combinations of Gene Ontology attributes. Bioinformatics 2003 Apr 12; 19: 788-789. [PubMed]
  11. Trost E, Hackl H, Maurer M, Trajanoski Z. Java editor for biological pathways. Bioinformatics 2003 Apr 12; 19: 786-787. [PubMed]
  12. Brudno M, Do CB, Cooper GM, Kim MF, Davydov E, Program NC, Green ED, Sidow A, Batzoglou S. LAGAN and Multi-LAGAN: Efficient Tools for Large-Scale Multiple Alignment of Genomic DNA. Genome Res. 2003 Apr;13(4):721-731. [PubMed]
  13. Devulder G, Perriere G, Baty F, Flandrois JP. BIBI, a Bioinformatics Bacterial Identification Tool. J Clin Microbiol. 2003 Apr;41(4):1785-7. [PubMed]
  14. Pennacchio LA, Rubin EM. Comparative genomic tools and databases: providing insights into the human genome. J Clin Invest. 2003 Apr;111(8):1099-106. [PubMed]
  15. Zhang CT, Zhang R, Ou HY. The Z curve database: a graphic representation of genome sequences. Bioinformatics. 2003 Mar 22;19(5):593-9. [PubMed]
  16. Kossenkov A, Manion FJ, Korotkov E, Moloshok TD, Ochs MF. ASAP: automated sequence annotation pipeline for web-based updating of sequence information with a local dynamic database. Bioinformatics. 2003 Mar 22;19(5):675-676. [PubMed]
  17. Freier A, Hofestaedt R, Lange M. iUDB: An object-oriented system for modelling, integration and analysis of gene controlled metabolic networks. In Silico Biol. 2003 Mar 17 [epub ahead of print] [PubMed]
  18. Martin W, Sbai H, De Groot AS. Bioinformatics tools for identifying class I-restricted epitopes. Methods. 2003 Mar;29(3):289-98. [PubMed]
  19. McDonald CJ, Schadow G, Barnes M, Dexter P, Overhage JM, Mamlin B, McCoy JM. Open Source software in medical informatics-why, how and what. Int J Med Inf. 2003 Mar;69(2-3):175-84. [PubMed]
  20. Takai D, Jones PA. The CpG Island Searcher: A New WWW Resource. In Silico Biol. 2003 Feb 4 [Epub ahead of print] [PubMed]
  21. Bray N, Dubchak I, Pachter L. AVID: A Global Alignment Program. Genome Res. 2003 Jan;13(1):97-102. [PubMed]
  22. Jaffe DB, Butler J, Gnerre S, Mauceli E, Lindblad-Toh K, Mesirov JP, Zody MC, Lander ES. Whole-genome sequence assembly for Mammalian genomes: arachne 2. Genome Res. 2003 Jan;13(1):91-6. [PubMed]
  23. Mullikin JC, Ning Z. The phusion assembler. Genome Res. 2003 Jan;13(1):81-90. [PubMed]
  24. Couronne O, Poliakov A, Bray N, Ishkhanov T, Ryaboy D, Rubin E, Pachter L, Dubchak I. Strategies and tools for whole-genome alignments. Genome Res. 2003 Jan;13(1):73-80. [PubMed]
  25. Frazer KA, Elnitski L, Church DM, Dubchak I, Hardison RC. Cross-species sequence comparisons: a review of methods and available resources. Genome Res. 2003 Jan;13(1):1-12. [PubMed]
  26. Lambrix P, Edberg A. Evaluation of ontology merging tools in bioinformatics. Pac Symp Biocomput. 2003;:589-600. [PubMed]

Databases

Nucleic Acid Research January 1, 2003 issue - The Molecular Biology Database Collection - The link to the complete issue
  1. Davuluri RV, Sun H, Saranyan PK, Matthews N, Molina C, Kurtz M, Erich G. AGRIS: Arabidopsis Gene Regulatory Information Server, an information resource of Arabidopsis cis-regulatory elements and transcription factors. BMC Bioinformatics. 2003 Jun 23 [Epub ahead of print] [PubMed][pdf]
  2. Koike A, Kobayashi Y, Takagi T. Kinase Pathway Database: An Integrated Protein-Kinase and NLP-Based Protein-Interaction Resource. Genome Res. 2003 Jun;13(6):1231-43. [PubMed][pdf]
  3. Krishnamurthy L, Nadeau J, Ozsoyoglu G, Ozsoyoglu M, Schaeffer G, Tasan M, Xu W. Pathways database system: an integrated system for biological pathways. Bioinformatics. 2003 May 22;19(8):930-7. [PubMed]
  4. Stein LD. Integrating biological databases. Nat Rev Genet. 2003 May;4(5):337-45. [PubMed]
  5. Golden JB. Prioritizing the human genome: knowledge management for drug discovery. Curr Opin Drug Discov Devel. 2003 May;6(3):310-6. [PubMed]
  6. Giardine B, Elnitski L, Riemer C, Makalowska I, Schwartz S, Miller W, Hardison RC. GALA, a Database for Genomic Sequence Alignments and Annotations. Genome Res. 2003 Apr;13(4):732-41. [PubMed]
  7. Camon E, Magrane M, Barrell D, Binns D, Fleischmann W, Kersey P, Mulder N, Oinn T, Maslen J, Cox A, Apweiler R. The Gene Ontology Annotation (GOA) Project: Implementation of GO in SWISS-PROT, TrEMBL, and InterPro.  Genome Res 2003 Apr;13(4):662-72 [PubMed]
  8. Reich DE, Gabriel SB, Altshuler D. Quality and completeness of SNP databases. Nat Genet. 2003 Apr;33(4):457-8. [PubMed][web supplement]   
  9. Pennacchio LA, Rubin EM. Comparative genomic tools and databases: providing insights into the human genome. J Clin Invest. 2003 Apr;111(8):1099-106. [PubMed]
  10. Sivakumaran S, Hariharaputran S, Mishra J, Bhalla US. The Database of Quantitative Cellular Signaling: management and analysis of chemical kinetic models of signaling networks. Bioinformatics. 2003 Feb;19(3):408-15 [PubMed]
  11. Bader GD, Betel D, Hogue CW. BIND: the Biomolecular Interaction Network Database. Nucleic Acids Res. 2003 Jan 1;31(1):248-50. [PubMed]
  12. Ng SK, Zhang Z, Tan SH, Lin K. InterDom: a database of putative interacting protein domains for validating predicted protein interactions and complexes. Nucleic Acids Res. 2003 Jan 1;31(1):251-4 [PubMed]
  13. Ji ZL, Chen X, Zhen CJ, Yao LX, Han LY, Yeo WK, Chung PC, Puy HS, Tay YT, Muhammad A, Chen YZ. KDBI: Kinetic Data of Bio-molecular Interactions database. Nucleic Acids Res. 2003 Jan 1;31(1):255-7. [PubMed]
  14. von Mering C, Huynen M, Jaeggi D, Schmidt S, Bork P, Snel B. STRING: a database of predicted functional associations between proteins. Nucleic Acids Res. 2003 Jan 1;31(1):258-61. [PubMed]
  15. Mulder NJ, Apweiler R, Attwood TK, Bairoch A, Barrell D, Bateman A, Binns D, Biswas M, Bradley P, Bork P, Bucher P, Copley RR, Courcelle E, Das U, Durbin R, Falquet L, Fleischmann W, Griffiths-Jones S, Haft D, Harte N, Hulo N, Kahn D, Kanapin A, Krestyaninova M, Lopez R, Letunic I, Lonsdale D, Silventoinen V, Orchard SE, Pagni M, Peyruc D, Ponting CP, Selengut JD, Servant F, Sigrist CJ, Vaughan R, Zdobnov EM. The InterPro Database, 2003 brings increased coverage and new features. Nucleic Acids Res. 2003 Jan 1;31(1):315-8. [PubMed]
  16. Matys V, Fricke E, Geffers R, Gossling E, Haubrock M, Hehl R, Hornischer K, Karas D, Kel AE, Kel-Margoulis OV, Kloos DU, Land S, Lewicki-Potapov B, Michael H, Munch R, Reuter I, Rotert S, Saxel H, Scheer M, Thiele S, Wingender E. TRANSFAC: transcriptional regulation, from patterns to profiles. Nucleic Acids Res. 2003 Jan 1;31(1):374-8. [PubMed]
  17. Krull M, Voss N, Choi C, Pistor S, Potapov A, Wingender E. TRANSPATH((R)): an integrated database on signal transduction and a tool for array analysis. Nucleic Acids Res. 2003 Jan 1;31(1):97-100. [PubMed]
  18. Yeh I, Karp PD, Noy NF, Altman RB. Knowledge acquisition, consistency checking and concurrency control for Gene Ontology (GO). Bioinformatics. 2003 Jan;19(2):241-8. [PubMed]
  19. Waters M, Boorman G, Bushel P, Cunningham M, Irwin R, Merrick A, Olden K, Paules R, Selkirk J, Stasiewicz S, Weis B, Van Houten B, Walker N, Tennant R. Systems toxicology and the Chemical Effects in Biological Systems (CEBS) knowledge base. EHP Toxicogenomics. 2003 Jan;111(1T):15-28. [PubMed]
  20. Bernstein PA. Applying generic schema management to bioinformatics. OMICS. 2003 Spring;7(1):99-100. [PubMed]
  21. Patel JM. The role of declarative querying in bioinformatics. OMICS. 2003 Spring;7(1):89-91. [PubMed]
  22. Eckart JD, Sobral BW. A Life Scientist's Gateway to Distributed Data Management and Computing: The PathPort/ToolBus Framework. OMICS. 2003 Spring;7(1):79-88. [PubMed]
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Conference proceedings

  1. Pacific Symposium of Biocomputing 2003
last updated: 24 Aug 2003
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