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

General
Nature special issue: Nature insight computational biology
Applications
Data mining
in silico biology/computational modelling
Network/pathway reconstruction and analysis*
Gene prediction
Gene function prediction
Structure prediction
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. Parsons J. Bioinformatics and economics. Brief Bioinform. 2002 Dec;3(4):328-30. [PubMed]
  2. Zatz MM. Bioinformatics training in the USA. Brief Bioinform. 2002 Dec;3(4):353-60. [PubMed]
  3. Loewe L. Global computing for bioinformatics. Brief Bioinform. 2002 Dec;3(4):377-88. [PubMed]
  4. Valencia A. Bioinformatics: biology by other means. Bioinformatics. 2002 Dec;18(12):1551-2. [PubMed]
  5. Chicurel M. Bioinformatics: Bringing it all together technology feature. Nature. 2002 Oct 17;419(6908):751-7. [PubMed]
  6. Chien A, Foster I, Goddette D. Grid technologies empowering drug discovery. Drug Discov Today. 2002 Oct 15;7(20 Suppl):S176-80. [PubMed]
  7. Reifman J, Gilbert GR, Fagan L, Satava R. Military research needs in biomedical informatics. J Am Med Inform Assoc. 2002 Sep-Oct;9(5):509-19. [PubMed]
  8. Bradley D. Informatics. The genome chose its alphabet with care. Science. 2002 Sep 13;297(5588):1789-91. [PubMed]
  9. Jain E. Current trends in bioinformatics. Trends Biotechnol. 2002 Aug;20(8):317-9. [PubMed]
  10. Venkatesh T, Harlow HB. Integromics: challenges in data integration. Genome Biol. 2002 Jul 17;3(8):REPORTS4027. [PubMed]
  11. Yao T. Bioinformatics for the genomic sciences and towards systems biology. Japanese activities in the post-genome era. Prog Biophys Mol Biol. 2002 Jul;80(1-2):23. [PubMed]
  12. Stein L. Creating a bioinformatics nation. Nature. 2002 May 9;417(6885):119-20. [PubMed]
  13. Agrafiotis DK, Lobanov VS, Salemme FR. Combinatiorial informatics in the post-genomics era. Nat Rev Drug Dis. 2002 May; 1:337-346 [PubMed]
  14. Nishikawa K. Information Concept in Biology. Bioinformatics. 2002 May;18(5):649-651. [PubMed]
  15. Bayat A. Bioinformatics. BMJ. 2002 Apr 27;324(7344):1018-22. [PubMed]
  16. Fuchs R. From sequence to biology: the impact on bioinformatics. Bioinformatics. 2002 Apr; 18:505-506 [PubMed]
  17. Ouzounis C. Bioinformatics and the theoretical foundations of molecular biology. Bioinformatics. 2002 Mar;18(3):377-8. [PubMed]
  18. Ibba M. Biochemistry and bioinformatics: when worlds collide. Trends Biotechnol. 2002 Feb;20(2):53-4. [PubMed]
  19. Altman RB, Klein TE. Challenges for biomedical informatics and pharmacogenomics. Annu Rev Pharmacol Toxicol. 2002;42:113-33. [PubMed]
  20. Goodman N. Biological data becomes computer literate: new advances in bioinformatics. Curr Opin Biotechnol 2002 Feb 1; 113:68-71 [PubMed]
  21. Brzeski H. An introduction to bioinformatics. Methods Mol Biol. 2002;187:193-208. [PubMed]
  22. Myers G. Bioinformatics and genome analysis. Preface. Ernst Schering Res Found Workshop. 2002;(38):V-VIII. [PubMed]
  23. Wittliff JL, Erlander MG. Laser capture microdissection and its applications in genomics and proteomics. Methods Enzymol. 2002;356:12-25. [PubMed]
  24. Dubay CJ, Brundege JM, Hersh W, Spackman K. Delivering bioinformatics training: bridging the gaps between computer science and biomedicine. Proc AMIA Symp. 2002;:220-4. [PubMed]
Nature special issue: Nature insight computational biology. 2002 Nov 14; 420
  1. Surridge C. Computational biology. Nature. 2002 Nov 14;420(6912):205. [PubMed]
  2. Kitano H. Computational systems biology. Nature. 2002 Nov 14;420(6912):206-10. [PubMed]
  3. Searls DB. The language of genes. Nature. 2002 Nov 14;420(6912):211-7. [PubMed]
  4. Koonin EV, Wolf YI, Karev GP. The structure of the protein universe and genome evolution. Nature. 2002 Nov 14;420(6912):218-23. [PubMed]
  5. Hasty J, McMillen D, Collins JJ. Engineered gene circuits. Nature. 2002 Nov 14;420(6912):224-30. [PubMed]
  6. Rao CV, Wolf DM, Arkin AP. Control, exploitation and tolerance of intracellular noise. Nature. 2002 Nov 14;420(6912):231-7. [PubMed]
  7. Goldbeter A. Computational approaches to cellular rhythms. Nature. 2002 Nov 14;420(6912):238-45. [PubMed]
  8. Buchman TG. The community of the self. Nature. 2002 Nov 14;420(6912):246-51. [PubMed]

Applications

  1. Lockwood CR, Frayling TM. Combining genome and mouse knockout expression data to highlight binding sites for the transcription factor HNF1alpha. In Silico Biol. 2002 Dec 25 [epub ahead of print] [PubMed]
  2. Griffin JL, Muller D, Woograsingh R, Jowatt V, Hindmarsh A, Nicholson JK, Martin JE. Vitamin E deficiency and metabolic deficits in neuronal ceroid lipofuscinosis described by bioinformatics. Physiol Genomics 2002 Dec 3;11(3):195-203[PubMed]
  3. Maojo V, Iakovidis I, Martin-Sanchez F, Crespo J, Kulikowski C. Medical informatics and bioinformatics: European efforts to facilitate synergy. J Biomed Inform. 2001 Dec;34(6):423-7. [PubMed]
  4. Zhao JH, Lissarrague S, Essioux L, Sham PC. GENECOUNTING: haplotype analysis with missing genotypes. Bioinformatics. 2002 Dec;18(12):1694-1695. [PubMed]
  5. Yang AS. Structure-dependent sequence alignment for remotely related proteins. Bioinformatics. 2002 Dec;18(12):1658-65. [PubMed]
  6. Laskowski RA, Chan AW. Bioinformatics and protein design. Curr Pharm Biotechnol. 2002 Dec;3(4):317-27. [PubMed]
  7. Boutanaev AM, Kalmykova AI, Shevelyov YY, Nurminsky DI. Large clusters of co-expressed genes in the Drosophila genome. Nature 2002 Dec 12; 420:666 [PubMed][web supplement]
  8. Bergman CM, Pfeiffer BD, Rincon-Limas DE, Hoskins RA, Gnirke A, Mungall CJ, Wang AM, Kronmiller B, Pacleb J, Park S, Stapleton M, Wan K, George RA, De Jong PJ, Botas J, Rubin GM, Celniker SE. Assessing the impact of comparative genomic sequence data on the functional annotation of the Drosophila genome. Genome Biol. 2002 Dec; 12: [PubMed][pdf]
  9. Ohler U, Liao GC, Niemann H, Rubin GM. Computational analysis of core promoters in the Drosophila genome. Genome Biol. 2002 Dec; 12: [PubMed][pdf]
  10.  Marshall KE, Godden EL, Yang F, Burgers S, Buck KJ, Sikela JM. In silico discovery of gene-coding variants in murine quantitative trait loci using strain-specific genome sequence databases. Genome Biol. 2002 Dec; 12: [PubMed][pdf]
  11. Megy K, Audic S, Claverie JM. Heart-specific genes revealed by expressed sequence tag (EST) sampling. Genome Biol 2002 Dec; 12: [PubMed][pdf]
  12. Misra S, Crosby MA, Mungall CJ, Matthews BB, Campbell KS, Hradecky P, Huang Y, Kaminker JS, Millburn GH, Prochnik SE, Smith CD, Tupy JL, Whitfied EJ, Bayraktaroglu L, Berman BP, Bettencourt BR, Celniker SE, de Grey AD, Drysdale RA, Harris NL, Richter J, Russo S, Schroeder AJ, Shu SQ, Stapleton M, Yamada C, Ashburner M, Gelbart WM, Rubin GM, Lewis SE. Annotation of the Drosophila melanogaster euchromatic genome: a systematic review. Genome Biol. 2002 Dec; 12: [PubMed][pdf]
  13. Volker C, Brown JR. Bioinformatics and the discovery of novel anti-microbial targets. Curr Drug Targets Infect Disord. 2002 Dec;2(4):279-90. [PubMed]
  14. Kaessmann H, Zollner S, Nekrutenko A, Li WH. Signatures of domain shuffling in the human genome. Genome Res. 2002 Nov;12(11):1642-50. [PubMed]
  15. Lester PJ, Hubbard SJ. Comparative bioinformatic analysis of complete proteomes and protein parameters for cross-species identification in proteomics. Proteomics. 2002 Oct;2(10):1392-405. [PubMed]
  16. Carpi A, Di Maira G, Vedovato M, Rossi V, Naccari T, Floriduz M, Terzi M, Filippini F. Comparative proteome bioinformatics: Identification of a whole complement of putative protein tyrosine kinases in the model flowering plant Arabidopsis thaliana. Proteomics. 2002 Nov;2(11):1494-503. [PubMed]
  17. Katsanis N, Worley KC, Gonzalez G, Ansley SJ, Lupski JR. A computational/functional genomics approach for the enrichment of the retinal transcriptome and the identification of positional candidate retinopathy genes. Proc Natl Acad Sci U S A. 2002 Oct 29;99(22):14326-31. [PubMed][pdf]
  18. Murphy EF, Gilmour SG, Crabbe MJ. Effective experimental design: enzyme kinetics in the bioinformatics era. Drug Discov Today. 2002 Oct 15;7(20 Suppl):S187-91. [PubMed]
  19. Liebman MN. Biomedical informatics: the future for drug development. Drug Discov Today. 2002 Oct 15;7(20 Suppl):S197-203. [PubMed]
  20. Fay N, Ullmann D. Leveraging process integration in early drug discovery. Drug Discov Today. 2002 Oct 15;7(20 Suppl):S181-6. [PubMed]
  21. Huang S. Rational drug discovery: what can we learn from regulatory networks? Drug Discov Today. 2002 Oct 15;7(20 Suppl):S163-9. [PubMed]
  22. Liu Y, Engelman DM, Gerstein M. Genomic analysis of membrane protein families: abundance and conserved motifs. Genome Biol. 2002 Oct; 10: research0054. [PubMed]
  23. Kirikoshi H, Katoh M. Expression and regulation of WNT10B in human cancer: Up-regulation of WNT10B in MCF-7 cells by beta-estradiol and down-regulation of WNT10B in NT2 cells by retinoic acid. Int J Mol Med. 2002 Oct;10(4):507-11. [PubMed]
  24. Kirikoshi H, Katoh M. Expression of WNT7A in human normal tissues and cancer, and regulation of WNT7A and WNT7B in human cancer. Int J Oncol. 2002 Oct;21(4):895-900. [PubMed]
  25. Xu Q, Modrek B, Lee C. Genome-wide detection of tissue-specific alternative splicing in the human transcriptome. Nucleic Acids Res. 2002 Sep 1;30(17):3754-66. [PubMed]
  26. Wong JY, Weng Z, Moll S, Kim S, Brown CT. Identification and validation of a novel cell-recognition site (KNEED) on the 8th type III domain of fibronectin. Biomaterials. 2002 Sep;23(18):3865-70. [PubMed]
  27. Saitoh T, Katoh M. Expression and regulation of WNT5A and WNT5B in human cancer: Up-regulation of WNT5A by TNFalpha in MKN45 cells and up-regulation of WNT5B by beta-estradiol in MCF-7 cells. Int J Mol Med. 2002 Sep;10(3):345-9. [PubMed]
  28. Kirikoshi H, Katoh M. Expression of TFF1, TFF2 and TFF3 in gastric cancer. Int J Oncol. 2002 Sep;21(3):655-9. [PubMed]
  29. Escribano J, Coca-Prados M. Bioinformatics and reanalysis of subtracted expressed sequence tags from the human ciliary body: Identification of novel biological functions. Mol Vis. 2002 Aug 28; 8:315-332. [PubMed][pdf]
  30. Godlewska R, Bujnicki J, Ostrowski J, Jagusztyn-Krynicka E. The hppA gene of Helicobacter pylori encodes the class C acid phosphatase precursor. FEBS Lett. 2002 Aug 14;525(1-3):39. [PubMed]
  31. Bateman A. The SGS3 protein involved in PTGS finds a family. BMC Bioinformatics. 2002 Aug 5;3(1):21. [PubMed]
  32. Coleman SL, Buckland PR, Hoogendoorn B, Guy C, Smith K, O'Donovan MC. Experimental analysis of the annotation of promoters in the public database. Hum Mol Genet. 2002 Aug 1;11(16):1817-21. [PubMed]
  33. Li S, Liao J, Cutler G, Hoey T, Hogenesch J, Cooke M, Schultz P, Ling X. Comparative Analysis of Human Genome Assemblies Reveals Genome-Level Differences. Genomics. 2002 Aug 1; 80: 138-139. [PubMed]
  34. Ihmels J, Friedlander G, Bergmann S, Sarig O, Ziv Y, Barkai N. Revealing modular organization in the yeast transcriptional network. Nat Genet. 2002 Aug;31(4):370-7. [PubMed]
  35. Torshin I. Structural criteria of biologically active RGD-sites for analysis of protein cellular function D a bioinformatics study. Med Sci Monit. 2002 Aug;8(8):BR301-12. [PubMed]
  36. Tanabe L, Wilbur WJ. Tagging gene and protein names in biomedical text. Bioinformatics. 2002 Aug;18(8):1124-32. [PubMed]
  37. Gonnet P, Lisacek F. Probabilistic alignment of motifs with sequences. Bioinformatics. 2002 Aug;18(8):1091-101. [PubMed]
  38. Juan HF, Lin JY, Chang WH, Wu CY, Pan TL, Tseng MJ, Khoo KH, Chen ST. Biomic study of human myeloid leukemia cells differentiation to macrophages using DNA array, proteomic, and bioinformatic analytical methods. Electrophoresis. 2002 Aug;23(15):2490-2504. [PubMed]
  39. Edwards SV, Fertil B, Giron A, Deschavanne PJ. A genomic schism in birds revealed by phylogenetic analysis of DNA strings.  Syst Biol. 2002 Aug;51(4):599-613. [PubMed]
  40. De Young MP, Damania H, Scheurle D, Zylberberg C, Narayanan R. Bioinformatics-based discovery of a novel factor with apparent specificity to colon cancer. In Vivo. 2002 Jul-Aug;16(4):239-48. [PubMed]
  41. Schuffenhauer A, Zimmermann J, Stoop R, Van Der Vyver JJ, Lecchini S, Jacoby E. An Ontology for Pharmaceutical Ligands and Its Application for in Silico Screening and Library Design. J Chem Inf Comput Sci. 2002 Jul 22;42(4):947-955. [PubMed]
  42. Gerritsen ME. et al. In silico data filtering to identify new angiogenesis targets from a large in vitro gene profiling data set. Physiol. Genomics. 2002 Jul 10; 10: 13-20. [PubMed][web supplement]
  43. Fiorentino L, Stehlik C, Oliveira V, Ariza ME, Godzik A, Reed JC. A novel PAAD-containing protein that modulatesNF-kappa B induction by cytokines TNFalpha and IL1beta. J Biol Chem. 2002 Jul 1 [epub ahead of print] [PubMed]
  44. Searls DB. Bioinformatics - From Genomes to Drugs. Drug Discov Today. 2002 Jul 1;7(13):709-710. [PubMed]
  45. Osato N, Itoh M, Konno H, Kondo S, Shibata K, Carninci P, Shiraki T, Shinagawa A, Arakawa T, Kikuchi S, Sato K, Kawai J, Hayashizaki Y. A Computer-Based Method of Selecting Clones for a Full-Length cDNA Project: Simultaneous Collection of Negligibly Redundant and Variant cDNAs. Genome Res. 2002 Jul;12(7):1127-34. [PubMed]
  46. Manning BD, Tee AR, Logsdon MN, Blenis J, Cantley LC. Identification of the tuberous sclerosis complex-2 tumor suppressor gene product tuberin as a target of the phosphoinositide 3-kinase/akt pathway. Mol Cell. 2002 Jul;10(1):151-62. [PubMed]
  47. Kahn S. Bioinformatics: a holistic approach to drug discovery. Drug Discov Today. 2002 Jun 15;7(12):633-634. [PubMed]
  48. Paine K, Flower DR. Bacterial bioinformatics: pathogenesis and the genome. J Mol Microbiol Biotechnol. 2002 Jul;4(4):357-65. [PubMed]
  49. Ostermeier GC, Dix DJ, Krawetz SA. A bioinformatic strategy to rapidly characterize cDNA libraries. Bioinformatics. 2002 Jul;18(7):949-52. [PubMed]
  50. Beerenwinkel N, Schmidt B, Walter H, Kaiser R, Lengauer T, Hoffmann D, Korn K, Selbig J. Diversity and complexity of HIV-1 drug resistance: A bioinformatics approach to predicting phenotype from genotype. Proc Natl Acad Sci U S A. 2002 Jun 11;99(12):8271-8276. [PubMed][pdf]
  51. Smith HR, Heusel JW, Mehta IK, Kim S, Dorner BG, Naidenko OV, Iizuka K, Furukawa H, Beckman DL, Pingel JT, Scalzo AA, Fremont DH, Yokoyama WM. Recognition of a virus-encoded ligand by a natural killer cell activation receptor. Proc Natl Acad Sci U S A 2002 Jun 25;99(13):8826-31 [PubMed][pdf]
  52. Salse J, Piegu B, Cooke R, Delseny M. Synteny between Arabidopsis thaliana and rice at the genome level: a tool to identify conservation in the ongoing rice genome sequencing project. Nucleic Acids Res. 2002 Jun 1;30(11):2316-28. [PubMed]
  53. Reymond A, Camargo AA, Deutsch S, Stevenson BJ, Parmigiani RB, Ucla C, Bettoni F, Rossier C, Lyle R, Guipponi M, de Souza S, Iseli C, Jongeneel CV, Bucher P, Simpson AJ, Antonarakis SE. Nineteen additional unpredicted transcripts from human chromosome 21.  Genomics. 2002 Jun;79(6):824-32. [PubMed]
  54. Morgenstern B, Rinner O, Abdeddaim S, Haase D, Mayer KF, Dress AW, Mewes HW. Exon discovery by genomic sequence alignment. Bioinformatics. 2002 Jun;18(6):777-787. [PubMed]
  55. Gardiner K, Slavov D, Bechtel L, Davisson M. Annotation of human chromosome 21 for relevance to down syndrome: gene structure and expression analysis. Genomics. 2002 Jun;79(6):833-43. [PubMed]
  56. Borstnik B, Pumpernik D. Tandem repeats in protein coding regions of primate genes. Genome Res. 2002 Jun;12(6):909-15. [PubMed]
  57. Khabar KS, Dhalla M, Bakheet T, Sy C, al-Haj L. An integrated computational and laboratory approach for selective amplification of mRNAs containing the adenylate uridylate-rich element consensus sequence. Genome Res. 2002 Jun;12(6):985-95. [PubMed]
  58. Mendes P. Emerging bioinformatics for the metabolome. Brief Bioinform. 2002 Jun;3(2):134-45. [PubMed]
  59. Van Nimwegen E, Zavolan M, Rajewsky N, Siggia ED. Probabilistic clustering of sequences: Inferring new bacterial regulons by comparative genomics. Proc Natl Acad Sci U S A. 2002 May 28;99(11):7323-8. [PubMed][pdf]
  60. Augen J. Bioinformatics and information technology: reshaping the drug discovery process. Drug Discov Today. 2002 May 6;7(11):S39-S40. [PubMed]
  61. Duckworth DM, Sanseau P. In silico identification of novel therapeutic targets. Drug Discov Today. 2002 May 6;7(11):S64-S69. [PubMed]
  62. Mazhari R. "Are we there yet?!" Cardiac channelopathy and our journey toward computational medicine. Circ Res. 2002 May 3;90(8):842-3. [PubMed]
  63. Pazos F, Valencia A. In silico two-hybrid system for the selection of physically interacting protein pairs. Proteins. 2002 May 1;47(2):219-27. [PubMed]
  64. Xie H, Wasserman A, Levine Z, Novik A, Grebinskiy V, Shoshan A, Mintz L. Large-Scale Protein Annotation through Gene Ontology. Genome Res. 2002 May;12(5):785-94. [PubMed]
  65. Estrada E. Characterization of the folding degree of proteins. Bioinformatics. 2002 May;18(5):697-704. [PubMed]
  66. Toledo-Sherman LM, Chen D. High-throughput virtual screening for drug discovery in parallel. Curr Opin Drug Discov Devel. 2002 May;5(3):414-21. [PubMed]
  67. Mounsey A, Bauer P, Hope IA. Evidence Suggesting That a Fifth of Annotated Caenorhabditis elegans Genes May Be Pseudogenes.  Genome Res. 2002 May; 12: 770-775. [PubMed]
  68. Eddy SR. Computational Genomics of Noncoding RNA Genes. Cell. 2002 Apr 19; 137-140 [PubMed]
  69. Baxt WG, Shofer FS, Sites FD, Hollander JE. A neural computational aid to the diagnosis of acute myocardial infarction. Ann Emerg Med. 2002 Apr;39(4):366-73. [PubMed]
  70. Park J, Betel D, Gryfe R, Michalickova K, Di Nicola N, Gallinger S, Hogue CW, Redston M. Mutation Profiling of Mismatch Repair-deficient Colorectal Cancers Using an in Silico Genome Scan to Identify Coding Microsatellites.  Cancer Res. 2002 Mar 1;62(5):1284-1288. [PubMed]
  71. Kawaji H, Schonbach C, Matsuo Y, Kawai J, Okazaki Y, Hayashizaki Y, Matsuda H. Exploration of novel motifs derived from mouse cDNA sequences.  Genome Res. 2002 Mar;12(3):367-78. [PubMed]
  72. Semple CA, Morris SW, Porteous DJ, Evans KL. Computational comparison of human genomic sequence assemblies for a region of chromosome 4. Genome Res. 2002 Mar;12(3):424-9.[PubMed]
  73. Schachter V. Bioinformatics of large-scale protein interaction networks. Biotechniques. 2002 Mar;Suppl:16-8, 20-4, 26-7 [PubMed]
  74. Fielden MR, Matthews JB, Fertuck KC, Halgren RG, Zacharewski TR. In silico approaches to mechanistic and predictive toxicology: an introduction to bioinformatics for toxicologists. Crit Rev Toxicol. 2002 Mar;32(2):67-112. [PubMed]
  75. Bettinotti MP, Olsen A, Stroncek D. The Use of Bioinformatics to Identify the Genomic Structure of the Gene That Encodes Neutrophil Antigen NB1, CD177. Clin Immunol. 2002 Feb;102(2):138-144. [PubMed]
  76. Kanapin A, Apweiler R, Biswas M, Fleischmann W, Karavidopoulou Y, Kersey P, Kriventseva EV, Mittard V, Mulder N, Oinn T, Phan I, Servant F, Zdobnov E. Interactive InterPro-based comparisons of proteins in whole genomes. Bioinformatics. 2002 Feb;18(2):374-5. [PubMed]
  77. Brendel V, Zhu W. Computational modeling of gene structure in Arabidopsis thaliana. Plant Mol Biol. 2002 Jan;48(1-2):49-58. Review. [PubMed]
  78. Martin-Sanchez F, Maojo V, Lopez-Campos G. Integrating genomics into health information systems. Methods Inf Med. 2002;41(1):25-30. [PubMed]
  79. von Heijne G. Bioinformatics of membrane proteins. Ernst Schering Res Found Workshop. 2002;(38):17-27. [PubMed]
  80. Westerhoff HV, Getz WM, van Verseveld HW, Hofmeyr JH, Snoep JL. Bioinformatics, cellular flows, and calculation. Ernst Schering Res Found Workshop. 2002;(38):221-43. [PubMed]
  81. Kozlov K, Myasnikova E, Pisareva A, Samsonova M, Reinitz J. A method for two-dimensional registration and construction of the two-dimensional atlas of gene expression patterns in situ. In Silico Biol. 2002;2(2):125-41. [PubMed][full text]
  82. Arrigo P, Ivaldi G, Cardo PP. In silico determination of potential antisense targets for human beta-globin variants. In Silico Biol. 2002;2(2):143-50. [PubMed][full text]
  83. Cooper M, Chapman SC, Podlich DW, Hammer GL. The GP problem: quantifying gene-to-phenotype relationships.  In Silico Biol. 2002;2(2):151-64. [PubMed][full text]
  84. Lindberg DA. Medicine in the 21st century: global problems, global solutions. Methods Inf Med. 2002;41(3):235-6. [PubMed]
  85. Dahl SG, Kristiansen K, Sylte I. Bioinformatics: from genome to drug targets. Ann Med. 2002;34(4):306-12. [PubMed]
  86. Thibaut U. Bioinformatics and rational drug design: tools for discovery and better understanding of biological targets and mode of action of drugs. Scand J Gastroenterol Suppl. 2002;(236):95-9. [PubMed]
  87. Lussier YA, Sarkar IN, Cantor M. An integrative model for in-silico clinical-genomics discovery science. Proc AMIA Symp. 2002;:469-73. [PubMed]
  88. Sivakumar A. 2D Gels and bioinformatics - An eye to the future. In Silico Biol. 2002 [epub ahead of print] [PubMed]
  89. Nudelman G, Tennenbaum T, Mehr R, Unger R. PESI - An intelligent system for Prediction of Enzyme - Substrate Interactions based on experimental constraints. In Silico Biol. 2002 [epub ahead of print] [PubMed]

Data mining

  1. Hirschman L, Park JC, Tsujii J, Wong L, Wu CH. Accomplishments and challenges in literature data mining for biology. Bioinformatics. 2002 Dec;18(12):1553-61. [PubMed]
  2. Deng M, Mehta S, Sun F, Chen T. Inferring Domain-Domain Interactions From Protein-Protein Interactions. Genome Res. 2002 Oct; 12: 1540-1548. [PubMed]
  3. Thompson HG, Harris JW, Wold BJ, Quake SR, Brody JP. Identification and Confirmation of a Module of Coexpressed Genes. Genome Res. 2002 Oct; 12: 1517-1522. [PubMed]
  4. Werner-Washburne M, Wylie B, Boyack K, Fuge E, Galbraith J, Weber J, Davidson G. Comparative analysis of multiple genome-scale data sets. Genome Res. 2002 Oct;12(10):1564-73. [PubMed]
  5. Zhang Z, Harrison P, Gerstein M. Identification and analysis of over 2000 ribosomal protein pseudogenes in the human genome. Genome Res. 2002 Oct;12(10):1466-82. [PubMed]
  6. Aerts J, Wetzels Y, Cohen N, Aerssens J. Data mining of public SNP databases for the selection of intragenic SNPs. Hum Mutat. 2002 Sep;20(3):162-73. [PubMed]
  7. Zavolan M, Van Nimwegen E, Gaasterland T. Splice Variation in Mouse Full-Length cDNAs Identified by Mapping to the Mouse Genome. Genome Res. 2002 Sep;12(9):1377-85. [PubMed]
  8. De La Fuente A, Snoep JL, Westerhoff HV, Mendes P. Metabolic control in integrated biochemical systems. Eur J Biochem. 2002 Sep;269(18):4399-4408. [PubMed]
  9. Bao Z, Eddy SR. Automated de novo identification of repeat sequence families in sequenced genomes. Genome Res. 2002 Aug;12(8):1269-76. [PubMed]
  10. Chang BC, Halgamuge SK. Protein motif extraction with neuro-fuzzy optimization. Bioinformatics. 2002 Aug;18(8):1084-90. [PubMed]
  11. Walker M, Pavlovic V, Kasif S. A comparative genomic method for computational identification of prokaryotic translation initiation sites. Nucleic Acids Res. 2002 Jul 15;30(14):3181-91. [PubMed]
  12. Ball P. Data visualization: Picture this. Nature. 2002 Jul 4;418(6893):11-3. [PubMed]
  13. Kinch LN, Grishin NV. Expanding the nitrogen regulatory protein superfamily: Homology detection at below random sequence identity. Proteins 2002 Jul 1;48(1):75-84 [PubMed]
  14. Gresham D. Reversing Babel with GO. Nat Genet. 2002 Jul;31(3):230. [PubMed]
  15. Perez-Iratxeta C, Bork P, Andrade MA. Association of genes to genetically inherited diseases using data mining. Nat Genet. 2002 Jul;31(3):316-9. [PubMed][web supplement]
  16. Lin K, Kuang Y, Joseph JS, Kolatkar PR. Conserved codon composition of ribosomal protein coding genes in Escherichia coli, Mycobacterium tuberculosis and Saccharomyces cerevisiae: lessons from supervised machine learning in functional genomics. Nucleic Acids Res. 2002 Jun 1;30(11):2599-607. [PubMed]
  17. Thayer KM, Beveridge DL. Hidden Markov models from molecular dynamics simulations on DNA. Proc Natl Acad Sci U S A 2002 Jun 25;99(13):8642-7 [PubMed][pdf]
  18. Gu X, Wang Y, Gu J. Age distribution of human gene families shows significant roles of both large- and small-scale duplications in vertebrate evolution. Nat Genet. 2002 Jun;31(2):205-9. [PubMed][web supplement]
  19. Cozma D, Lukes L, Rouse J, Qiu TH, Liu ET, Hunter KW. A Bioinformatics-Based Strategy Identifies c-Myc and Cdc25A as Candidates for the Apmt Mammary Tumor Latency Modifiers.  Genome Res. 2002 Jun;12(6):969-75. [PubMed]
  20. Stevens R, Goble C, Horrocks I, Bechhofer S. Building a bioinformatics ontology using OIL. IEEE Trans Inf Technol Biomed. 2002 Jun;6(2):135-41. [PubMed]
  21. Stevens R, Goble C, Horrocks I, Bechhofer S. OILing the way to machine understandable bioinformatics resources. IEEE Trans Inf Technol Biomed. 2002 Jun;6(2):129-34. [PubMed]
  22. Blaschke C, Hirschman L, Valencia A. Information extraction in molecular biology. Brief Bioinform. 2002 Jun;3(2):154-65. [PubMed]
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in silico biology/computational modelling

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  3. Ibarra RU, Edwards JS, Palsson BO. Escherichia coli K-12 undergoes adaptive evolution to achieve in silico predicted optimal growth. Nature. 2002 Nov 14;420(6912):186-9. [PubMed]
  4. Moraru II, Schaff JC, Slepchenko BM, Loew LM. The virtual cell: an integrated modeling environment for experimental and computational cell biology. Ann N Y Acad Sci. 2002 Oct;971:595-6. [PubMed]
  5. Palsson B. In silico biology through "omics". Nat Biotechnol. 2002 Jul;20(7):649-50. [PubMed]
  6. Gershon D. Silicon dreams in the biology lab. Nature. 2002 Jul;417(6892):4-5. [PubMed]
  7. Gershon D. Cell biology gets plugged in. Nature. 2002 Jul;417(6892):6. [PubMed]
  8. Triendl R. Computerized role models. Nature. 2002 Jul;417(6892):7. [PubMed]
  9. Harris SB. Virtual rice: Japan sets up the Rice Simulator Project to create an in silico rice plant. EMBO Rep. 2002 Jun;3(6):511-513. [PubMed]
  10. Noble D. Modeling the Heart--from Genes to Cells to the Whole Organ.  Science. 2002 Mar 1;295(5560):1678-82. [PubMed]
  11. Wolkenhauer O. Mathematical modelling in the post-genome era: understanding genome expression and regulation---a system theoretic approach. Biosystems. 2002 Feb;65(1):1-18. [PubMed]
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  15. Dormann S, Deutsch A. Modeling of self-organized avascular tumor growth with a hybrid cellular automaton. In Silico Biol. 2002;2(3):393-406. [PubMed]
  16. Fen ZP. An overview on predicting the subcellular location of a protein. In Silico Biol. 2002;2(3):291-303. [PubMed]

Network/pathway reconstruction and analysis

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  3. Majewski J, Ott J. Distribution and characterization of regulatory elements in the human genome. Genome Res. 2002 Dec;12(12):1827-36. [PubMed]
  4. Grindrod P. Range-dependent random graphs and their application to modeling large small-world Proteome datasets. Phys Rev E Stat Nonlin Soft Matter Phys. 2002 Dec;66(6-2):066702. [PubMed]
  5. Cornish-Bowden A, Luz Cardenas M. Systems biology: Metabolic balance sheets. Nature. 2002 Nov 14;420(6912):129-30. [PubMed]
  6. Stelling J, Klamt S, Bettenbrock K, Schuster S, Gilles ED. Metabolic network structure determines key aspects of functionality and regulation. Nature. 2002 Nov 14;420(6912):190-3. [PubMed]
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  11. Bhan A, Galas DJ, Dewey TG. A duplication growth model of gene expression networks. Bioinformatics. 2002 Nov;18(11):1486-93. [PubMed]
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  32. Karp PD, Paley S, Romero P. The Pathway Tools software. Bioinformatics. 2002 Jul;18 Suppl 1:S225-32. [PubMed]
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  36. Brown CT, Rust AG, Clarke PJ, Pan Z, Schilstra MJ, De Buysscher T, Griffin G, Wold BJ, Cameron RA, Davidson EH, Bolouri H. New Computational Approaches for Analysis of cis-Regulatory Networks. Dev Biol. 2002 Jun 1;246(1):86-102. [PubMed]
  37. Olson EN. Deconstructing the transcriptional circuitry of development.  Dev Biol. 2002 Jun 1;246(1):1. [PubMed]
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  41. Peleg M, Yeh I, Altman RB. Modelling biological processes using workflow and Petri Net models. Bioinformatics. 2002 Jun;18(6):825-37. [PubMed]
  42. Raval A, Ghahramani Z, Wild DL. A Bayesian network model for protein fold and remote homologue recognition. Bioinformatics. 2002 Jun;18(6):788-801. [PubMed]
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  46. Bono H, Okazaki Y. Functional transcriptomes: comparative analysis of biological pathways and processes in eukaryotes to infer genetic networks among transcripts. Curr Opin Stru Biol. 2002 Jun; 12:355-361 [PubMed]
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  49. Price ND, Papin JA, Palsson B BO. Determination of Redundancy and Systems Properties of the Metabolic Network of Helicobacter pylori Using Genome-Scale Extreme Pathway Analysis. Genome Res. 2002 May;12(5):760-9. [PubMed]
  50. Guelzim N, Bottani S, Bourgine P, Kepes F. Topological and causal structure of the yeast transcriptional regulatory network. Nat Genet. 2002 May;31(1):60-3. [PubMed][web supplement]
  51. Shen-Orr SS, Milo R, Mangan S, Alon U. Network motifs in the transcriptional regulation network of Escherichia coli. Nat Genet. 2002 May;31(1):64-8. [PubMed][web supplement]
  52. Blanchette M, Tompa M. Discovery of regulatory elements by a computational method for phylogenetic footprinting. Genome Res. 2002 May;12(5):739-48. [PubMed]
  53. Loots GG, Ovcharenko I, Pachter L, Dubchak I, Rubin EM. rVista for Comparative Sequence-Based Discovery of Functional Transcription Factor Binding Sites. Genome Res. 2002 May;12(5):832-9. [PubMed]
  54. Paley SM, Karp PD. Evaluation of computational metabolic-pathway predictions for Helicobacter pylori. Bioinformatics. 2002 May;18(5):715-724. [PubMed]
  55. Snel B, Bork P, Huynen MA. The identification of functional modules from the genomic association of genes. Proc Natl Acad Sci U S A. 2002 Apr 30;99(9):5890-5. [PubMed][web supplement]
  56. Brem RB, Yvert G, Clinton R, Kruglyak L. Genetic dissection of transcriptional regulation in budding yeast. Science. 2002 Apr 26;296(5568):752-5. [PubMed]
  57. Zhu Z, Pilpel Y, Church GM. Computational Identification of Transcription Factor Binding Sites via a Transcription-factor-centric Clustering (TFCC) Algorithm. J Mol Biol. 2002 Apr 19;318(1):71-81. [PubMed]
  58. Periwal V, Szallasi Z. Trading "wet-work" for network. Nat Biotechnol. 2002 Apr;20(4):345-6. [PubMed]
  59. Schoeberl B, Eichler-Jonsson C, Gilles ED, Muller G. Computational modeling of the dynamics of the MAP kinase cascade activated by surface and internalized EGF receptors. Nat Biotechnol. 2002 Apr;20(4):370-5. [PubMed][web supplement]
  60. Zhu H, Snyder M. 'Omic' approaches for unraveling signaling networks. Curr Opin Cell Biol. 2002 Apr;14(2):173-9. [PubMed]
  61. Aguilar D, Oliva B, Aviles FX, Querol E. TranScout: prediction of gene expression regulatory proteins from their sequences. Bioinformatics. 2002 Apr; 18:597-607 [PubMed]
  62. de Jong H. Modeling and simulation of genetic regulatory systems: a literature review. J Comput Biol. 2002;9(1):67-103. [PubMed][pdf]
  63. Rojas I, Bernardi L, Ratsch E, Kania R, Wittig U, Saric J. A database system for the analysis of biochemical pathways. In Silico Biol. 2002;2(2):75-86. [PubMed][full text]
  64. Schreiber F. High quality visualization of biochemical pathways in BioPath. In Silico Biol. 2002;2(2):59-73. [PubMed][full text]
  65. Kolchanov NA, Nedosekina EA, Ananko EA, Likhoshvai VA, Podkolodny NL, Ratushny AV, Stepanenko IL, Podkolodnaya OA, Ignatieva EV, Matushkin YG. GeneNet database: description and modeling of gene networks. In Silico Biol. 2002;2(2):97-110. [PubMed][full text]
  66. Yoo C, Cooper GF. Discovery of Gene-Regulation Pathways using Local Causal Search. Proc AMIA Symp. 2002;:914-8. [PubMed]
  67. Forster M, Pick A, Raitner M, Schreiber F, Brandenburg FJ. The system architecture of the BioPath system. In Silico Biol. 2002;2(3):415-26. [PubMed]
  68. Horng JT, Huang HD, Huang SL, Yan UC, Chang YC. Mining putative regulatory elements in promoter regions of Saccharomyces cerevisiae. In Silico Biol. 2002;2(3):263-73. [PubMed]
  69. Vityaev EE, Orlov YL, Vishnevsky OV, Pozdnyakov MA, Kolchanov NA. Computer system "gene discovery" for promoter structure analysis. In Silico Biol. 2002;2(3):257-62. [PubMed] 
  70. Werner T. Finding and decrypting of promoters contributes to the elucidation of gene function. In Silico Biol. 2002;2(3):249-55. [PubMed]
  71. Hurlebaus J, Buchholz A, Alt W, Wiechert W, Takors R. MMT - A pathway modeling tool for data from rapid sampling experiments. In Silico Biol. 2002 [epub ahead of print] [PubMed]
  72. Lockwood CR, Frayling TM. Combining genome and mouse knockout expression data to highlight binding sites for the transcription factor HNF1alpha. In Silico Biol. 2002 Dec 25 [epub ahead of print] [PubMed]

Gene prediction

  1. Katoh M. Paradigm shift in gene-finding method: From bench-top approach to desk-top approach (Review). Int J Mol Med. 2002 Dec;10(6):677-82. [PubMed]
  2. Mathe C, Sagot MF, Schiex T, Rouze P. Current methods of gene prediction, their strengths and weaknesses. Nucleic Acids Res. 2002 Oct 1;30(19):4103-17. [PubMed]
  3. Meyer IM, Durbin R. Comparative ab initio prediction of gene structures using pair HMMs. Bioinformatics 2002 Oct; 18: 1309-1318. [PubMed]
  4. Shendure J, Church GM. Computational discovery of sense-antisense transcription in the human and mouse genomes. Genome Biol. 2002 Sep; 3:0044 [PubMed][pdf]
  5. Zavolan M, Van Nimwegen E, Gaasterland T. Splice Variation in Mouse Full-Length cDNAs Identified by Mapping to the Mouse Genome. Genome Res. 2002 Sep;12(9):1377-85. [PubMed]
  6. Zhang MQ. Computational prediction of eukaryotic protein-coding genes. Nat Rev Genet. 2002 Sep;3(9):698-709. [PubMed]
  7. Zheng Y, Szustakowski JD, Fortnow L, Roberts RJ, Kasif S. Computational identification of operons in microbial genomes. Genome Res. 2002 Aug;12(8):1221-30. [PubMed]
  8. Rogic S, Ouellette BF, Mackworth AK. Improving gene recognition accuracy by combining predictions from two gene-finding programs. Bioinformatics. 2002 Aug;18(8):1034-1045. [PubMed]
  9. Brent MR. Predicting full-length transcripts. Trends Biotechnol. 2002 Jul; 20:273-274. [PubMed]
  10. Zhang MQ. Predicting full-length transcripts. Trends Biotechnol. 2002 Jul; 20:274. [PubMed]
  11. Moreno-Hagelsieb G, Collado-Vides J. A powerful non-homology method for the prediction of operons in prokaryotes. Bioinformatics. 2002 Jul;18 Suppl 1:S329-36. [PubMed]
  12. Heber S, Alekseyev M, Sze SH, Tang H, Pevzner PA. Splicing graphs and EST assembly problem. Bioinformatics. 2002 Jul;18 Suppl 1:S181-8. [PubMed]
  13. Shibuya T, Rigoutsos I. Dictionary-driven prokaryotic gene finding.  Nucleic Acids Res. 2002 Jun 15;30(12):2710-25. [PubMed]
  14. Chen S, Lesnik EA, Hall TA, Sampath R, Griffey RH, Ecker DJ, Blyn LB. A bioinformatics based approach to discover small RNA genes in the Escherichia coli genome. Biosystems. 2002 Mar;65(2-3):157-77. [PubMed]

Gene function prediction

  1. Zheng Y, Roberts RJ, Kasif S. Genomic functional annotation using co-evolution profiles of gene clusters. Genome Biol. 2002 Nov; 3(11): research0060.1-0060.9. [PubMed]
  2. Kolesov G, Mewes HW, Frishman D. SNAPper: gene order predicts gene function.  Bioinformatics. 2002 Jul; 18:1017-1019. [PubMed]
  3. Wu LF, Hughes TR, Davierwala AP, Robinson MD, Stoughton R, Altschuler SJ. Large-scale prediction of Saccharomyces cerevisiae gene function using overlapping transcriptional clusters. Nat Genet. 2002 Jul;31(3):255-65. [PubMed][web supplement]
  4. Schug J, Diskin S, Mazzarelli J, Brunk BP, Stoeckert CJ Jr. Predicting gene ontology functions from ProDom and CDD protein domains. Genome Res. 2002 Apr;12(4):648-55. [PubMed]

Structure prediction

  1. Yang AS, Wang LY.  Local structure-based sequence profile database for local and global protein structure predictions. Bioinformatics. 2002 Dec;18(12):1650-7. [PubMed]
  2. Michalovich D, Overington J, Fagan R. Protein sequence analysis in silico: application of structure-based bioinformatics to genomic initiatives. Curr Opin Pharmacol. 2002 Oct; 2:574-580 [PubMed]
  3. Lahm A, Yagnik A, Tramontano A, Koch U. Hepatitis C virus proteins as targets for drug development: the role of bioinformatics and modelling. Curr Drug Targets. 2002 Aug;3(4):281-96. [PubMed]
  4. Fradera X, De La Cruz X, Silva CH, Gelpi JL, Luque FJ, Orozco M. Ligand-induced changes in the binding sites of proteins.  Bioinformatics. 2002 Jul; 18:939-948. [PubMed]
  5. Liu J, Rost B. Target space for structural genomics revisited.  Bioinformatics. 2002 Jul; 18:922-933. [PubMed]
  6. Peitsch MC. About the use of protein models.  Bioinformatics. 2002 Jul; 18:934-938. [PubMed]
  7. Rost B, Honig B, Valencia A. Bioinformatics in structural genomics. Bioinformatics. 2002 Jul; 18:897. [PubMed]
  8. Portugaly E, Kifer I, Linial M. Selecting targets for structural determination by navigating in a graph of protein families. Bioinformatics. 2002 Jul; 18:899-907. [PubMed]
  9. Abascal F, Valencia A. Clustering of proximal sequence space for the identification of protein families.  Bioinformatics. 2002 Jul; 18:908-921. [PubMed]
  10. Schonbrun J, Wedemeyer WJ, Baker D. Protein structure prediction in 2002. Curr Opin Stru Biol. 2002 Jun; 12:348-354 [PubMed]
  11. Villoutreix BO. Structural bioinformatics: methods, concepts and applications to blood coagulation proteins. Curr Protein Pept Sci. 2002 Jun;3(3):341-64. [PubMed]
  12. Kihara D, Zhang Y, Lu H, Kolinski A, Skolnick J. Ab initio protein structure prediction on a genomic scale: Application to the Mycoplasma genitalium genome. Proc Natl Acad Sci U S A. 2002 Apr 30;99(9):5993-8. [PubMed][pdf]
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  14. Koch K, Zollner F, Neumann S, Kummert F, Sagerer G. Comparing bound and unbound protein structures using energy calculation and rotamer statistics. In Silico Biol. 2002;2(3):351-68. [PubMed]

Languages and Algorithms

  1. Geer LY, Domrachev M, Lipman DJ, Bryant SH. CDART: Protein Homology by Domain Architecture. Genome Res. 2002 Oct; 12: 1619-1623. [PubMed]
  2. Wang L, Riethoven JJ, Robinson A. XEMBL: distributing EMBL data in XML format. Bioinformatics. 2002 Aug;18(8):1147-8. [PubMed]
  3. Sasson O, Linial N, Linial M. The metric space of proteins-comparative study of clustering algorithms. Bioinformatics. 2002 Jul;18 Suppl 1:S14-21. [PubMed]
  4. Delcher AL, Phillippy A, Carlton J, Salzberg SL. Fast algorithms for large-scale genome alignment and comparison. Nucleic Acids Res. 2002 Jun 1;30(11):2478-83. [PubMed]
  5. Zhu Z, Pilpel Y, Church GM. Computational Identification of Transcription Factor Binding Sites via a Transcription-factor-centric Clustering (TFCC) Algorithm. J Mol Biol. 2002 Apr 19;318(1):71-81. [PubMed]
  6. Enright AJ, Van Dongen S, Ouzounis CA. An efficient algorithm for large-scale detection of protein families. Nucleic Acids Res. 2002 Apr 1;30(7):1575-84. [PubMed]
  7. Lee C, Grasso C, Sharlow MF. Multiple sequence alignment using partial order graphs. Bioinformatics. 2002 Mar;18(3):452-64. [PubMed]
  8. Ettinger M. The complexity of comparing reaction systems. Bioinformatics. 2002 Mar;18(3):465-9. [PubMed]
  9. Almeida JS. Predictive non-linear modeling of complex data by artificial neural networks. Curr Opin Biotechnol 2002 Feb 1; 113:72-76 [PubMed]
  10. Shen SY, Yang J, Yao A, Hwang PI. Super Pairwise Alignment (SPA): An Efficient Approach to Global Alignment for Homologous Sequences. J Comput Biol. 2002;9(3):477-86. [PubMed]
  11. Hanisch D, Zimmer R, Lengauer T. ProML--the protein markup language for specification of protein sequences, structures and families. In Silico Biol. 2002;2(3):313-24. [PubMed]

Softwares

  1. Riva A, Kohane IS. SNPper: retrieval and analysis of human SNPs. Bioinformatics. 2002 Dec;18(12):1681-5. [PubMed]
  2. Perry WL 3rd. JavaScript DNA translator: DNA-aligned protein translations. Biotechniques. 2002 Dec;33(6):1318-20. [PubMed]
  3. Mungall CJ., et al. An integrated computational pipeline and database to support whole-genome sequence annotation. Genome Biol. 2002 Dec; 12: [PubMed][pdf]
  4. Lewis SE., et al. Apollo: a sequence annotation editor. Genome Biol. 2002 Dec; 12: [PubMed][pdf]
  5. Gilbert D. Pise: software for building bioinformatics webs. Brief Bioinform. 2002 Dec;3(4):405-9. [PubMed]
  6. Matthiessen MW. Affordable biocomputing for everyone: using the Internet, freeware and open-source software. Trends Biochem Sci. 2002 Nov;27(11):586-8. [PubMed]
  7. Neff MM, Turk E, Kalishman M. Web-based primer design for single nucleotide polymorphism analysis. Trends Genet. 2002 Dec; 18:613-615. [PubMed]
  8. Bohannon J. Bioinformatics. The human genome in 3D, at your fingertips. Science. 2002 Oct 25;298(5594):737. [PubMed]
  9. Palakal M, Mukhopadhyay S, Mostafa J, Raje R, N'Cho M, Mishra S. An intelligent biological information management system. Bioinformatics 2002 Oct; 18: 1283-1288. [PubMed]
  10. Lord PW, Selley JN, Attwood TK. CINEMA-MX: a modular multiple alignment editor. Bioinformatics. 2002 Oct;18(10):1402-3. [PubMed]
  11. Wilkinson MD, Block D, Crosby WL. Genquire: genome annotation browser/editor. Bioinformatics. 2002 Oct;18(10):1398-9. [PubMed]
  12. Ponomarenko JV, Orlova GV, Merkulova TI, Gorshkova EV, Fokin ON, Vasiliev GV, Frolov AS, Ponomarenko MP. rSNP_Guide: An integrated database-tools system for studying SNPs and site-directed mutations in transcription factor binding sites. Hum Mutat. 2002 Oct;20(4):239-48. [PubMed]
  13. Stein LD, Mungall C, Shu S, Caudy M, Mangone M, Day A, Nickerson E, Stajich JE, Harris TW, Arva A, Lewis S. The generic genome browser: a building block for a model organism system database. Genome Res. 2002 Oct;12(10):1599-610. [PubMed]
  14. Stajich JE, Block D, Boulez K, Brenner SE, Chervitz SA, Dagdigian C, Fuellen G, Gilbert JG, Korf I, Lapp H, Lehvaslaiho H, Matsalla C, Mungall CJ, Osborne BI, Pocock MR, Schattner P, Senger M, Stein LD, Stupka E, Wilkinson MD, Birney E. The bioperl toolkit: perl modules for the life sciences.  Genome Res. 2002 Oct;12(10):1611-8. [PubMed]
  15. Mangalam H. The Bio* toolkits--a brief overview. Brief Bioinform. 2002 Sep;3(3):296-302. [PubMed]
  16. Xuan Z, McCombie WR, Zhang MQ. GFScan: a gene family search tool at genomic DNA level. Genome Res. 2002 Jul;12(7):1142-9. [PubMed]
  17. Richards WG. Virtual screening using grid computing: the screensaver project. Nat Rev Drug Discov. 2002 Jul;1(7):551-5. [PubMed]
  18. Karp PD, Paley S, Romero P. The Pathway Tools software. Bioinformatics. 2002 Jul;18 Suppl 1:S225-32. [PubMed]
  19. Kent WJ, Sugnet CW, Furey TS, Roskin KM, Pringle TH, Zahler AM, Haussler AD. The Human Genome Browser at UCSC. Genome Res. 2002 Jun;12(6):996-1006. [PubMed]
  20. Loots GG, Ovcharenko I, Pachter L, Dubchak I, Rubin EM. rVista for Comparative Sequence-Based Discovery of Functional Transcription Factor Binding Sites. Genome Res. 2002 May;12(5):832-9. [PubMed]
  21. Wang J, Wong GK, Ni P, Han Y, Huang X, Zhang J, Ye C, Zhang Y, Hu J, Zhang K, Xu X, Cong L, Lu H, Ren X, Ren X, He J, Tao L, Passey DA, Wang J, Yang H, Yu J, Li S. A sequence assembler that masks exact repeats identified from the shotgun data. Genome Res. 2002 May;12(5):824-31.[PubMed]
  22. Yu Z, Li T, Zhao J, Luo J. PGAAS: a prokaryotic genome assembly assistant system. Bioinformatics. 2002 May;18(5):661-665. [PubMed]
  23. Zhu W, Brendel V. Gene structure identification with MyGV using cDNA evidence and protein homologs to improve ab initio predictions. Bioinformatics. 2002 May;18(5):761-762. [PubMed]
  24. Vincens P, Badel-Chagnon A, Andre C, Hazout S. D-ASSIRC: distributed program for finding sequence similarities in genomes. Bioinformatics. 2002 Mar;18(3):446-451. [PubMed]
  25. Ma B, Tromp J, Li M. PatternHunter: faster and more sensitive homology search. Bioinformatics. 2002 Mar;18(3):440-445. [PubMed]
  26. Buchan DW, Shepherd AJ, Lee D, Pearl FM, Rison SC, Thornton JM, Orengo CA. Gene 3D : Structural Assignment for Whole Genes and Genomes Using the CATH Domain Structure Database. Genome Res. 2002 Mar;12(3):503-14. [PubMed]
  27. Jones J, Field JK, Risk JM. A comparative guide to gene prediction tools for the bioinformatics amateur. Int J Oncol. 2002 Apr;20(4):697-705. [PubMed]
  28. Krieger E, Vriend G. Models@Home: distributed computing in bioinformatics using a screensaver based approach. Bioinformatics. 2002 Feb;18(2):315-318. [PubMed]
  29. Field HI, Fenyo D, Beavis RC. RADARS, a bioinformatics solution that automates proteome mass spectral analysis, optimises protein identification, and archives data in a relational database. Proteomics. 2002 Jan;2(1):36-47. [PubMed]
  30. Mulder NJ, Apweiler R. Tools and resources for identifying protein families, domains and motifs. Genome Biol 2002 Jan; 3: 2001 [PubMed]
  31. Coward E, Haas SA, Vingron M. SpliceNest: visualizing gene structure and alternative splicing based on EST clusters. Trends Genet. 2002 Jan; 18:53-55 [PubMed]
  32. Mangalam H. tacg - a grep for DNA. BMC Bioinformatics. 2002;3(1):8. [PubMed]
Databases

Nucleic Acid Research January 1, 2002 issue - The Molecular Biology Database Collection - The link to the complete issue

  1. Hill DP, Blake JA, Richardson JE, Ringwald M. Extension and Integration of the Gene Ontology (GO): Combining GO Vocabularies With External Vocabularies. Genome Res. 2002 Dec;12(12):1982-91. [PubMed]
  2. Safran M, Solomon I, Shmueli O, Lapidot M, Shen-Orr S, Adato A, Ben-Dor U, Esterman N, Rosen N, Peter I, Olender T, Chalifa-Caspi V, Lancet D. GeneCards(TM) 2002: towards a complete, object-oriented, human gene compendium. Bioinformatics. 2002 Nov;18(11):1542-1543. [PubMed]
  3. Michalickova K, Bader GD, Dumontier M, Lieu HC, Betel D, Isserlin R, Hogue CW. SeqHound: biological sequence and structure database as a platform for bioinformatics research. BMC Bioinformatics. 2002 Oct 25 [epub ahead of print][PubMed]
  4. Ponomarenko JV, Orlova GV, Merkulova TI, Gorshkova EV, Fokin ON, Vasiliev GV, Frolov AS, Ponomarenko MP. rSNP_Guide: An integrated database-tools system for studying SNPs and site-directed mutations in transcription factor binding sites. Hum Mutat. 2002 Oct;20(4):239-48. [PubMed]
  5. Stein LD, Mungall C, Shu S, Caudy M, Mangone M, Day A, Nickerson E, Stajich JE, Harris TW, Arva A, Lewis S. The generic genome browser: a building block for a model organism system database. Genome Res. 2002 Oct;12(10):1599-610. [PubMed]
  6. Thallinger GG, Trajanoski S, Stocker G, Trajanoski Z. Information management systems for pharmacogenomics. Pharmacogenomics. 2002 Sep;3(5):651-67. [PubMed]
  7. Nadkarni P, Sun K, Wiepert M. Designing and implementing special-purpose databases: lessons from the pharmacogenetic network. Pharmacogenomics. 2002 Sep;3(5):687-96. [PubMed]
  8. Zdobnov EM, Lopez R, Apweiler R, Etzold T. The EBI SRS server-new features. Bioinformatics. 2002 Aug;18(8):1149-50. [PubMed]
  9. Coussens PM, Nobis W. Bioinformatics and high throughput approach to create genomic resources for the study of bovine immunobiology. Vet Immunol Immunopathol. 2002 Jul;86(3-4):229-44. [PubMed]
  10. Siepen JA, Westhead DR. The fibril_one on-line database: Mutations, experimental conditions, and trends associated with amyloid fibril formation. Protein Sci. 2002 Jul;11(7):1862-6. [PubMed]
  11. Bober M, Wiehe K, Yung C, Onal Suzek T, Lin M, Baumgartner W Jr, Winslow R. CaGE: Cardiac gene expression knowledgebase.  Bioinformatics. 2002 Jul; 18:1013-1014. [PubMed]
  12. Rubin DL, Shafa F, Oliver DE, Hewett M, Altman RB. Representing genetic sequence data for pharmacogenomics: an evolutionary approach using ontological and relational models. Bioinformatics. 2002 Jul;18 Suppl 1:S207-15. [PubMed]
  13. Gromov P, Ostergaard M, Gromova I, Celis J. Human proteomic databases: a powerful resource for functional genomics in health and disease. Prog Biophys Mol Biol. 2002 Jul;80(1-2):3. [PubMed]
  14. Wistow G. A project for ocular bioinformatics: NEIBank. Mol Vis. 2002 Jun 15;8:161-163. [PubMed]
  15. Wistow G, Berstein SL, Touchman JW, Bouffard G, Wyatt MK, Peterson K, Behal A, Gao J, Buchoff P, Smith D. Grouping and identification of sequence tags (GRIST): Bioinformatics tools for the NEIBank database. Mol Vis. 2002 Jun 15;8:164-170. [PubMed]
  16. Wistow G, Berstein SL, Wyatt MK, Behal A, Touchman JW, Bouffard G, Smith D, Peterson K.  Expressed sequence tag analysis of adult human lens for the NEIBank Project: Over 2000 non-redundant transcripts, novel genes and splice variants. Mol Vis. 2002 Jun 15;8:171-184. [PubMed]
  17. Wistow G, Berstein SL, Ray S, Wyatt MK, Behal A, Touchman JW, Bouffard G, Smith D, Peterson K. Expressed sequence tag analysis of adult human iris for the NEIBank Project: steroid-response factors and similarities with retinal pigment epithelium. Mol Vis. 2002 Jun 15;8:185-95. [PubMed]
  18. Wistow G, Berstein SL, Wyatt MK, Ray S, Behal A, Touchman JW, Bouffard G, Smith D, Peterson K. Expressed sequence tag analysis of human retina for the NEIBank Project: Retbindin, an abundant, novel retinal cDNA and alternative splicing of other retina-preferred gene transcripts. Mol Vis. 2002 Jun 15;8:196-204. [PubMed]
  19. Wistow G, Bernstein SL, Wyatt MK, Farris RN, Behal A, Touchman JW, Bouffard G, Smith D, Peterson K. Expressed sequence tag analysis of human RPE/choroid for the NEIBank Project: Over 6000 non-redundant transcripts, novel genes and splice variants. Mol Vis. 2002 Jun 15;8:205-220. [PubMed]
  20. Berman HM, Battistuz T, Bhat TN, Bluhm WF, Bourne PE, Burkhardt K, Feng Z, Gilliland GL, Iype L, Jain S, Fagan P, Marvin J, Padilla D, Ravichandran V, Schneider B, Thanki N, Weissig H, Westbrook JD, Zardecki C. The protein data bank. Acta Crystallogr D Biol Crystallogr. 2002 Jun;58(Pt 6 Pt 1):899-907. [PubMed]
  21. Kemp GJ, Angelopoulos N, Gray PM. Architecture of a mediator for a bioinformatics database federation. IEEE Trans Inf Technol Biomed. 2002 Jun;6(2):116-22. [PubMed]
  22. Stupka E. Large-scale open bioinformatics data resources. Curr Opin Mol Ther. 2002 Jun;4(3):265-74. [PubMed]
  23. Bornberg-Bauer E, Paton NW. Conceptual data modelling for bioinformatics. Brief Bioinform. 2002 Jun;3(2):166-80. [PubMed]
  24. Dennis C. Biology databases: Information overload. Nature. 2002 May 2;417(6884):14. [PubMed]
  25. Claustres M, Horaitis O, Vanevski M, Cotton RG. Time for a unified system of mutation description and reporting: a review of locus-specific mutation databases. Genome Res. 2002 May;12(5):680-8. [PubMed]
  26. Lee Y, Sultana R, Pertea G, Cho J, Karamycheva S, Tsai J, Parvizi B, Cheung F, Antonescu V, White J, Holt I, Liang F, Quackenbush J. Cross-Referencing Eukaryotic Genomes: TIGR Orthologous Gene Alignments (TOGA). Genome Res. 2002 Mar;12(3):493-502. [PubMed]
  27. Zdobnov EM, Lopez R, Apweiler R, Etzold T. The EBI SRS server-recent developments. Bioinformatics. 2002 Feb;18(2):368-73. [PubMed]
  28. Field HI, Fenyo D, Beavis RC. RADARS, a bioinformatics solution that automates proteome mass spectral analysis, optimises protein identification, and archives data in a relational database. Proteomics. 2002 Jan;2(1):36-47. [PubMed]
  29. Baxevanis AD. The Molecular Biology Database Collection: 2002 update. Nucleic Acids Res. 2002 Jan 1;30(1):1-12. [PubMed]
  30. Freier A, Hofestadt R, Lange M, Scholz U, Stephanik A. BioDataServer: a SQL-based service for the online integration of life science data. In Silico Biol. 2002;2(2):37-57. [PubMed][full text]
  31. Rojas I, Bernardi L, Ratsch E, Kania R, Wittig U, Saric J. A database system for the analysis of biochemical pathways. In Silico Biol. 2002;2(2):75-86. [PubMed][full text]
  32. Kolchanov NA, Nedosekina EA, Ananko EA, Likhoshvai VA, Podkolodny NL, Ratushny AV, Stepanenko IL, Podkolodnaya OA, Ignatieva EV, Matushkin YG. GeneNet database: description and modeling of gene networks. In Silico Biol. 2002;2(2):97-110. [PubMed][full text]
  33. Forster M, Pick A, Raitner M, Schreiber F, Brandenburg FJ. The system architecture of the BioPath system. In Silico Biol. 2002;2(3):415-26. [PubMed]
  34. Schulze-Kremer S. Ontologies for molecular biology and bioinformatics. In Silico Biol. 2002;2(3):179-93. [PubMed]
Conference proceedings
  1. Pacific Symposium of Biocomputing 2002