My bioinformatics journal watch - year 2000 [ 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
Network/ pathway reconstruction and analysis*
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. Hagen JB. The origins of bioinformatics.  Nat Rev Genet. 2000 Dec;1(3):231-6. [PubMed]
  2. Saviotti PP, deLooze MA, Michelland S, Catherine D. The changing marketplace of bioinformatics. Nat Biotechnol. 2000 Dec;18(12):1247-1249. [PubMed]
  3. Ramsay M. Synergism: bioinformatics and biological experimentation. Mol Med Today. 2000 Dec 1;6(12):458. [PubMed]
  4. Dunham I. The gene guessing game.Yeast. 2000 Sep 30;17(3):218-224. [PubMed]
  5. Claverie JM. From Bioinformatics to Computational Biology.  Genome Res. 2000 Sep;10(9):1277-1279. [PubMed]
  6. Milosavljevic A.The Economic Value of Bioinformation. Bioinformatics. 2000 Jul;16(7):571-572. [PubMed]
  7. Paton NW, Khan SA, Hayes A, Moussouni F, Brass A, Eilbeck K, Goble CA, Hubbard SJ, Oliver SG. Conceptual modelling of genomic information. Bioinformatics. 2000 Jun;16(6):548-557. [PubMed]
  8. Aravind L. Guilt by Association: Contextual Information in Genome Analysis. Genome Res. 2000 Aug;10(8):1074-1077. [PubMed]
  9. Huynen M, Snel B, Lathe W 3rd, Bork P. Predicting Protein Function by Genomic Context: Quantitative Evaluation and Qualitative Inferences. Genome Res. 2000 Aug;10(8):1204-1210. [PubMed]
  10. Tsoka S, Ouzounis CA. Recent developments and future directions in computational genomics. FEBS Lett. 2000 Aug 25;480(1):42-48. [PubMed]
  11. Strivens M. Not who you know, but what you know. Trends Biotechnol. 2000 Jun;18(6):227-8. [PubMed]
  12. Aparicio SA. How to count ... human genes. Nat Genet. 2000 Jun;25(2):129-30. [PubMed]
  13. Smaglik P. Researchers take a gamble on the human genome. Nature. 2000 May 18;405(6784):264. [PubMed][pdf]
  14. Ouzounis C. Two or three myths about bioinformatics. Bioinformatics. 2000 Mar;16(3):187-9. [PubMed]
  15. Bork P. Powers and pitfalls in sequence analysis: the 70% hurdle. Genome Res. 2000 Apr;10(4):398-400. Review. [PubMed]
  16. Lim HA, Venkatesh TV. Bioinformatics in the pre- and post-genomic eras. Trends Biotechnol. 2000 Apr;18(4):133-5. [PubMed]
  17. Heger A, Holm L. Towards a covering set of protein family profiles. Prog Biophys Mol Biol. 2000 Jan 1;73(5):321-337. [PubMed]
  18. Antonio BA, Sakata K, Sasaki T. Rice at the forefront of plant genome informatics. Genome Inform Ser Workshop Genome Inform. 2000;11:3-11. [PubMed]

Applications

  1. Fagan R, Swindells M.  Bioinformatics, target discovery and the pharmaceutical/biotechnology industry.  Curr Opin Mol Ther. 2000 Dec;2(6):655-61. [PubMed]
  2. Schwikowski B, Uetz P, Fields S. A network of protein-protein interactions in yeast. Nat Biotechnol. 2000 Dec;18(12):1257-1261. [PubMed][Web]
  3. Gilbert DR, Schroeder M, van Helden J. Interactive visualization and exploration of relationships between biological objects. Trends Biotechnol. 2000 Dec 1;18(12):487-494. [PubMed]
  4. Newman JR, Wolf E, Kim PS. A computationally directed screen identifying interacting coiled coils from Saccharomyces cerevisiae. Proc Natl Acad Sci U S A. 2000 Nov 21;97(24):13203-13208. [PubMed][pdf]
  5. Manson McGuire A, Church GM. Predicting regulons and their cis-regulatory motifs by comparative genomics. Nucleic Acids Res. 2000 Nov 15;28(22):4523-30. [PubMed]
  6. Huminiecki L, Bicknell R. In Silico Cloning of Novel Endothelial-Specific Genes. Genome Res. 2000 Nov;10(11):1796-1806. [PubMed]
  7. de Souza SJ, Camargo AA, Briones MR, Costa FF, Nagai MA, Verjovski-Almeida S, Zago MA, Andrade LE, Carrer H, El-Dorry HF, Espreafico EM, Habr-Gama A, Giannella-Neto D, Goldman GH, Gruber A, Hackel C, Kimura ET, Maciel RM, Marie SK, Martins EA, Nobrega MP, Paco-Larson ML, Pardini MI, Pereira GG, Pesquero JB, Rodrigues V, Rogatto  SR, da Silva ID, Sogayar MC, de Fatima Sonati M, Tajara EH, Valentini SR, Acencio M, Alberto FL, Amaral ME,  Aneas I, Bengtson MH, Carraro DM, Carvalho AF, Carvalho LH, Cerutti JM, Correa ML, Costa MC, Curcio C, Gushiken T, Ho PL, Kimura E, Leite LC, Maia G, Majumder P, Marins M, Matsukuma A, Melo AS, Mestriner CA, Miracca EC, Miranda DC, Nascimento AL, Nobrega FG, Ojopi EP, Pandolfi JR, Pessoa LG, Rahal P, Rainho CA, da  Ro's N, de Sa RG, Sales MM, da Silva NP, Silva TC, da Silva W Jr, Simao DF, Sousa JF, Stecconi D, Tsukumo F, Valente V, Zalcberg H, Brentani RR, Reis LF, Dias-Neto E, Simpson AJ. Identification of human chromosome 22 transcribed sequences with ORF expressed sequence tags. Proc Natl Acad Sci U S A. 2000 Nov 7;97(23):12690-12693. [PubMed][pdf]
  8. Glassbrook N, Beecher C, Ryals J. Metabolic profiling on the right path. Nat Biotechnol. 2000 Nov;18(11):1142-1143. [PubMed]
  9. Chakravarti DN, Fiske MJ, Fletcher LD, Zagursky RJ. Application of genomics and proteomics for identification of bacterial gene products as potential vaccine candidates. Vaccine. 2000 Nov 8;19(6):601-12. [PubMed]
  10. Bortoluzzi S, d'Alessi F, Danieli GA. A computational reconstruction of the adult human heart transcriptional profile. J Mol Cell Cardiol. 2000 Nov;32(11):1931-8. [PubMed]
  11. Sana TR, Debets R, Timans JC, Bazan JF, Kastelein RA. Computational Identification, Cloning, and Characterization of IL-1R9, a Novel Interleukin-1 Receptor-like Gene Encoded over an Unusually Large Interval of Human Chromosome Xq22.2-q22.3. Genomics. 2000 Oct 15;69(2):252-262. [PubMed]
  12. Zhang QH, Ye M, Wu XY, Ren SX, Zhao M, Zhao CJ, Fu G, Shen Y, Fan HY, Lu G, Zhong M, Xu XR, Han ZG,Zhang JW, Tao J, Huang QH, Zhou J, Hu GX, Gu J, Chen SJ, Chen Z. Cloning and Functional Analysis of cDNAs with Open Reading Frames for 300 Previously Undefined Genes Expressed in CD34+ Hematopoietic Stem/Progenitor Cells. Genome Res. 2000 Oct;10(10):1546-1560 [PubMed]
  13. Tsoka S, Ouzounis CA. Prediction of protein interactions: metabolic enzymes are frequently involved in gene fusion. Nat Genet. 2000 Oct;26(2):141-142. [PubMed]
  14. Cohen BA, Mitra RD, Hughes JD, Church GM. A computational analysis of whole-genome expression data reveals chromosomal domains of gene expression. Nat Genet. 2000 Oct;26(2):183-186. [PubMed]
  15. Nadimpalli R, Yalpani N, Johal GS, Simmons CR. Prohibitins, Stomatins, and Plant Disease Response Genes Compose a Protein Superfamily That Controls Cell Proliferation, Ion Channel Regulation, and Death.  J Biol Chem. 2000 Sep 15;275(38):29579-29586. [PubMed]
  16. Hu R, Han Z, Song H, Peng Y, Huang Q, Ren S, Gu Y, Huang C, Li Y, Jiang C, Fu G, Zhang Q, Gu B, Dai M, Mao Y, Gao G, Rong R, Ye M, Zhou J, Xu S, Gu J, Shi J, Jin W, Zhang C, Wu T, Huang  G. Gene expression profiling in the human hypothalamus-pituitary-adrenal axis and full-length cDNA cloning. Proc Natl Acad Sci U S A. 2000 Aug 15;97(17):9543-8.[PubMed][pdf]
  17. Semple CA, Morris SW, Porteous DJ, Evans KL.  In silico identification of transcripts and SNPs from a region of 4p linked with bipolar affective disorder. Bioinformatics. 2000 Aug;16(8):735-8. [PubMed]
  18. Batzoglou S, Pachter L, Mesirov JP, Berger B, Lander ES. Human and mouse gene structure: comparative analysis and application to exon prediction. Genome Res. 2000 Jul;10(7):950-8. [PubMed]
  19. Liang F, Holt I, Pertea G, Karamycheva S, Salzberg SL, Quackenbush J.Gene index analysis of the human genome estimates approximately 120, 000 genes. Nat Genet. 2000 Jun;25(2):239-40. [PubMed]
  20. Roest Crollius H, Jaillon O, Bernot A, Dasilva C, Bouneau L, Fischer C, Fizames C, Wincker P, Brottier P, Quetier F, Saurin W, Weissenbach J. Estimate of human gene number provided by genome-wide analysis using Tetraodon nigroviridis DNA sequence. Nat Genet. 2000 Jun;25(2):235-8. [PubMed]
  21. Ewing B, Green P. Analysis of expressed sequence tags indicates 35,000 human genes. Nat Genet. 2000 Jun;25(2):232-4. [PubMed]
  22. Schultz J, Doerks T, Ponting CP, Copley RR, Bork P. More than 1,000 putative new human signalling proteins revealed by EST data mining. Nat Genet. 2000 Jun;25(2):201-4. [PubMed]
  23. Pagel M. Phylogenetic--evolutionary approaches to bioinformatics. Brief Bioinform. 2000 May;1(2):117-30. [PubMed]
  24. Bortoluzzi S, d'Alessi F, Romualdi C, Danieli GA.The human adult skeletal muscle transcriptional profile reconstructed by a novel computational approach. Genome Res. 2000 Mar;10(3):344-9. [PubMed]
  25. Pertea M, Salzberg SL, Gardner MJ. Finding genes in Plasmodium falciparum. Nature. 2000 Mar 2;404(6773):34; discussion 34-5. [PubMed]
  26. Hughes JD, Estep PW, Tavazoie S, Church GM. Computational identification of cis-regulatory elements associated with groups of functionally related genes in Saccharomyces cerevisiae. J Mol Biol. 2000 Mar 10;296(5):1205-14. [PubMed]
  27. Botka C, Wittig T, Graul R, Nielsen C, Higaki K, Amidon G, Sadee W. Human Proton/Oligopeptide Transporter (POT) Genes: Identification of Putative Human Genes Using Bioinformatics. AAPS PharmSci. 2000;2(2):E16. [PubMed]

Data mining

  1. Jordan P, Matos P, Veríssimo F. Gene Cloning at the Computer Screen: Possibilities and Problems. Biochemical and Biophysical Research Communications. 2000 Dec, 279: 741-743 [Abstract]
  2. Moler EJ, Chow ML, Mian IS. Analysis of molecular profile data using generative and discriminative methods. Physiol Genomics. 2000 Dec 18;4(2):109-126. [PubMed]
  3. Schwikowski B, Uetz P, Fields S. A network of protein-protein interactions in yeast. Nat Biotechnol. 2000 Dec;18(12):1257-1261. [PubMed][Web]
  4. Gilbert DR, Schroeder M, van Helden J. Interactive visualization and exploration of relationships between biological objects. Trends Biotechnol. 2000 Dec 1;18(12):487-494. [PubMed]
  5. Wiehe T, Guigo R, Miller W. Genome sequence comparisons: hurdles in the fast lane to functional genomics. Brief Bioinform. 2000 Nov;1(4):381-8. [PubMed]
  6. Gerlt JA, Babbitt. Can sequence determine function? Review. Genome Biology 2000; 1;5:1-10 [pdf]
  7. Black DL. Protein diversity from alternative splicing: A challenge for bioinformatics and post-genome biology. Cell. 2000 Oct 27; 103: 367-370. [PubMed]
  8. Stefanini FM, Camussi A.The reduction of large molecular profiles to informative components using a Genetic Algorithm. Bioinformatics. 2000 Oct;16(10):923-931. [PubMed]
  9. Niiler E. Bioinformaticians develop new data mining tools. Nat Med. 2000 Oct;6(10):1071. [PubMed]
  10. Ison JC. Exploring protein domain structure. Brief Bioinform. 2000 Sep;1(3):305-12. [PubMed]
  11. Manduchi E, Grant GR, McKenzie SE, Overton GC, Surrey S, Stoeckert Jr CJ Jr. Generation of patterns from gene expression data by assigning confidence to differentially expressed genes. Bioinformatics. 2000 Aug;16(8):685-98. [PubMed]
  12. Eisenberg D, Marcotte EM, Xenarios I, Yeates TO. Protein function in the post-genomic era.  Nature. 2000 Jun 15;405(6788):823-6. Review. [PubMed]
  13. Liang F, Holt I, Pertea G, Karamycheva S, Salzberg SL, Quackenbush J. Gene index analysis of the human genome estimates approximately 120, 000 genes. Nat Genet. 2000 Jun;25(2):239-40. [PubMed]
  14. Roest Crollius H, Jaillon O, Bernot A, Dasilva C, Bouneau L, Fischer C, Fizames C, Wincker P, Brottier P, Quetier F, Saurin W, Weissenbach J. Estimate of human gene number provided by genome-wide analysis using Tetraodon nigroviridis DNA sequence. Nat Genet. 2000 Jun;25(2):235-8. [PubMed]
  15. Ewing B, Green P. Analysis of expressed sequence tags indicates 35,000 human genes. Nat Genet. 2000 Jun;25(2):232-4. [PubMed]
  16. Schultz J, Doerks T, Ponting CP, Copley RR, Bork P. More than 1,000 putative new human signalling proteins revealed by EST data mining. Nat Genet. 2000 Jun;25(2):201-4. [PubMed]
  17. Bourne PE. Bioinformatics meets data mining: time to dance? Trends Biotechnol. 2000 Jun;18(6):228-30. [PubMed]
  18. Pertea M, Salzberg SL, Gardner MJ. Finding genes in Plasmodium falciparum. Nature. 2000 Mar 2;404(6773):34; discussion 34-5. [PubMed]

Network/ pathway reconstruction and analysis

  1. D'haeseleer P, Liang S, Somogyi R.  Genetic network inference: from co-expression clustering to reverse engineering. Bioinformatics. 2000 Aug;16(8):707-26. [PubMed]
  2. Akutsu T, Miyano S, Kuhara S. Inferring qualitative relations in genetic networks and metabolic pathways. Bioinformatics. 2000 Aug;16(8):727-34. [PubMed]
  3. Hughes JD, Estep PW, Tavazoie S, Church GM.Computational identification of cis-regulatory elements associated with groups of functionally related genes in Saccharomyces cerevisiae. J Mol Biol. 2000 Mar 10;296(5):1205-14. [PubMed]
  4. Cornish-Bowden A, Cardenas ML. From genome to cellular phenotype--a role for metabolic flux analysis? Nat Biotechnol. 2000 Mar;18(3):267-8. [PubMed]
  5. Schuster S, Fell DA, Dandekar T. A general definition of metabolic pathways useful for systematic organization and analysis of complex metabolic networks. Nat Biotechnol. 2000 Mar;18(3):326-32. [PubMed]
  6. Akutsu T, Miyano S, Kuhara S. Algorithms for identifying Boolean networks and related biological networks based on matrix multiplication and fingerprint function. J Comput Biol. 2000;7(3-4):331-43. [PubMed]
  7. Akutsu T, Miyano S, Kuhara S. Algorithms for inferring qualitative models of biological networks. Pac Symp Biocomput. 2000;:293-304. [PubMed][pdf]
  8. Stephenson TA. An Introduction to Bayesian Network Theory and Usage. 2000 [pdf]

Structure prediction

  1. Lengauer T, Zimmer R. Protein structure prediction methods for drug design. Brief Bioinform. 2000 Sep;1(3):275-88. [PubMed]

Languages and Algorithms

  1. Stefanini FM, Camussi A.The reduction of large molecular profiles to informative components using a Genetic Algorithm. Bioinformatics. 2000 Oct;16(10):923-931. [PubMed]
  2. Barillot E, Achard F. XML: a lingua franca for science? Trends Biotechnol. 2000 Aug;18(8):331-3. [PubMed]
  3. Giegerich R. A systematic approach to dynamic programming in bioinformatics. Bioinformatics. 2000 Aug;16(8):665-77. [PubMed]
  4. Woolf PJ, Wang Y.A fuzzy logic approach to analyzing gene expression data. Physiol Genomics. 2000 Jun 29;3(1):9-15. [PubMed]
  5. Stormo GD. Gene-finding approaches for eukaryotes. Genome Res. 2000 Apr;10(4):394-7. Review. [PubMed]
  6. Hughes JD, Estep PW, Tavazoie S, Church GM. Computational identification of cis-regulatory elements associated with groups of functionally related genes in Saccharomyces cerevisiae. J Mol Biol. 2000 Mar 10;296(5):1205-14. [PubMed]
  7. Stevens R, Miller C. Wrapping and interoperating bioinformatics resources using CORBA. Brief Bioinform. 2000 Feb;1(1):9-21. [PubMed]

Softwares

  1. Cheung KH, Kumar A, Snyder M, Miller P. An integrated web interface for large-scale characterization of sequence data. Funct Integr Genomics. 2000 1:70-75 [link to journal]
  2. Wojcik J, Schachter V. Proteomic databases and software on the web.  Brief Bioinform. 2000 Sep;1(3):250-9. [PubMed]
  3. Jareborg N, Durbin R. Alfresco-A Workbench for Comparative Genomic Sequence Analysis. Genome Res. 2000 Aug;10(8):1148-1157. [PubMed]
  4. Baillie DL, Rose AM.WABA Success: A Tool for Sequence Comparison between Large Genomes. Genome Res. 2000 Aug;10(8):1071-1073. [PubMed]
  5. Bingham J, Sudarsanam S.Visualizing large hierarchical clusters in hyperbolic space. Bioinformatics. 2000 Jul;16(7):660-661. [PubMed]
  6. Curwen VA, Williams GW, Bard JB. GHOST: a gene homology online search tool. Trends Genet. 2000 Jul;16(7):321-3. No abstract available. [PubMed]
  7. Wang Y, Geer LY, Chappey C, Kans JA, Bryant SH.Cn3D: sequence and structure views for Entrez. Trends Biochem Sci. 2000 Jun;25(6):300-2. No abstract available. [PubMed]
  8. Rice P, Longden I, Bleasby A.EMBOSS: the European Molecular Biology Open Software Suite. Trends Genet. 2000 Jun;16(6):276-7. [PubMed]
  9. Hughes JD, Estep PW, Tavazoie S, Church GM.Computational identification of cis-regulatory elements associated with groups of functionally related genes in Saccharomyces cerevisiae. J Mol Biol. 2000 Mar 10;296(5):1205-14. [PubMed]
  10. Searls DB.  Bioinformatics tools for whole genomes. Annu Rev Genomics Hum Genet. 2000;1:251-79. [PubMed]
Databases
  1. Southan C.  Website Review: InterPro (The Integrated Resource of Protein Domains and Functional Sites). http://www.ebi.ac.uk/interpro/. Yeast. 2000 Dec;17(4):327-334. [PubMed]
  2. Kawamoto S, Yoshii J, Mizuno K, Ito K, Miyamoto Y, Ohnishi T, Matoba R, Hori N, Matsumoto Y, Okumura T, Nakao Y, Yoshii H, Arimoto J, Ohashi H, Nakanishi H, Ohno I, Hashimoto J, Shimizu K, Maeda K, Kuriyama H, Nishida K, Shimizu-Matsumoto A, Adachi W, Ito R, Kawasaki S, Chae KS, Murakawa K, Yokoyama M, Fukushima A, Hishiki T, Nakaya A, Sese J, Monma N, Nikaido H, Morishita S, Matsubara K, Okubo K. BodyMap: A Collection of 3' ESTs for Analysis of Human Gene Expression Information. Genome Res. 2000 Nov;10(11):1817-1827. [PubMed]
  3. Stevens R, Goble CA, Bechhofer S. Ontology-based knowledge representation for bioinformatics. Brief Bioinform. 2000 Nov;1(4):398-414. [PubMed]
  4. Wojcik J, Schachter V. Proteomic databases and software on the web.  Brief Bioinform. 2000 Sep;1(3):250-9. [PubMed]
  5. Ison JC, O'Leary SB, Bleasby AJ, Moss D. Information resources for the bioinformatician. Brief Bioinform. 2000 Sep;1(3):229-35. [PubMed]
  6. Dicks J. Plant genome databases: from references to inference tools. Brief Bioinform. 2000 May;1(2):138-50. [PubMed]
  7. Law AS, Archibald AL. Farm animal genome databases. Brief Bioinform. 2000 May;1(2):151-60. [PubMed]
  8. Ashburner M, Ball CA, Blake JA, Botstein D, Butler H, Cherry JM, Davis AP, Dolinski K, Dwight SS, Eppig JT, Harris MA, Hill DP, Issel-Tarver L, Kasarskis A, Lewis S,  Matese JC, Richardson JE, Ringwald M, Rubin GM, Sherlock G. Gene ontology: tool for the unification of biology. The Gene Ontology Consortium. Nat Genet. 2000 May;25(1):25-9. [PubMed]
  9. Aach J, Rindone W, Church GM. Systematic management and analysis of yeast gene expression data. Genome Res. 2000 Apr;10(4):431-45. [PubMed]
  10. Combet C, Blanchet C, Geourjon C, Deleage G. NPS@: network protein sequence analysis. Trends Biochem Sci. 2000 Mar;25(3):147-50. Review. [PubMed]
  11. McGarvey PB, Huang H, Barker WC, Orcutt BC, Garavelli JS, Srinivasarao GY, Yeh LS, Xiao C, Wu CH. PIR: a new resource for bioinformatics. Bioinformatics. 2000 Mar;16(3):290-1. [PubMed]
  12. Attwood TK. The role of pattern databases in sequence analysis. Brief Bioinform. 2000 Feb;1(1):45-59. [PubMed]
Conference proceedings

Pacific Symposium of Biocomputing 2000
The International Conference on Computational Molecular Biology 2000


last updated: 19 Aug 2002
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