My bioinformatics journal watch - year 2001 [ 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
in silico biology/computational modelling
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. Butler D. Postgenomics: Data, data, everywhere... Nature. 2001Dec 20/27; 414:840-841 [PubMed]
  2. Wu TD. Bioinformatics in the post-genomic era. Trends Biotechnol. 2001 Dec;19(12):479-80. [PubMed]
  3. Stewart JE, Mangalam H, Zhou J. Open Source Software meets gene expression. Brief Bioinform. 2001 Dec;2(4):319-28. [PubMed]
  4. Claverie JM, Abergel C, Audic S, Ogata H. Recent advances in computational genomics. Pharmacogenomics. 2001 Nov;2(4):361-72. [PubMed]
  5. Malakoff D. Bioinformatics. Petition seeks public sharing of code.  Science. 2001 Oct 5;294(5540):27. [PubMed]
  6. Wagner A, Fell DA.The small world inside large metabolic networks. Proc R Soc Lond B Biol Sci. 2001 Sep 7;268(1478):1803-10. [PubMed]
  7. Martin AC.  Can we integrate bioinformatics data on the Internet? Trends Biotechnol. 2001 Sep;19(9):327-8. [PubMed]
  8. Peri S, Ibarrola N, Blagoev B, Mann M, Pandey A. Common pitfalls in bioinformatics-based analyses: look before you leap. Trends Genet. 2001 Sep;17(9):541-5. [PubMed]
  9. Pearson WR. Training for bioinformatics and computational biology. Bioinformatics. 2001 Sep; 17:761-762 [PubMed]
  10. Magee J, Gordon JI, Whelan A. Bringing the human genome and the revolution in bioinformatics to the medical school classroom: a case report from washington university school of  medicine. Acad Med. 2001 Aug;76(8):852-5. [PubMed]
  11. Butler D. Institutes prepare for pioneering bioinformatics work.  Nature. 2001 Jul 12;412(6843):106 [PubMed]
  12. Attwood TK, Miller CJ. Which craft is best in bioinformatics?  Comput Chem. 2001 Jul;25(4):329-39. [PubMed]
  13. Butler D. Bioinformatics to be nurtured online. Nature. 2001 May 31;411(6837):513. [PubMed]
  14. Crowe S. European bioinformatics projects receive unprecedented cash boost.  Lancet. 2001 May 19;357(9268):1600. [PubMed]
  15. Butler D, Abbott A. Fresh funding offers lifeline to bioinformatics centre. Nature. 2001 May 17;411(6835):229.  [PubMed]
  16. Vingron M. Bioinformatics needs to adopt statistical thinking. Bioinformatics. 2001 May;17(5):389-90. [PubMed]
  17. O'Donovan C, Apweiler R, Bairoch A.The human proteomics initiative (HPI). Trends Biotechnol. May; 19:178-181 [PubMed]
  18. Butte AJ. Challenges in bioinformatics: infrastructure, models and analytics. Trends Biotechnol 2001. May; 19:159-160 [PubMed]
  19. Baba Y. Development of novel biomedicine based on genome science.  Eur J Pharm Sci. 2001 Apr;13(1):3-4. [PubMed]
  20. Cyranoski D. Singapore invests in bioinformatics. Nature 2001. Mar 15; 410: 293 [PubMed]
  21. Zauhar RJ. University bioinformatics programs on the rise. Nat Biotech 2001. Mar; 19:285-2869 [PubMed]
  22. Koonin EV. Computational genomics. Curr Biol 2001. Mar; 11:R155-R158. [PubMed]
  23. Strogatz SH. Exploring complex networks. Nature 2001. Mar 8; 410:268-276. [PubMed]
  24. Human Genome Project Publications:
  25. Triendl R. Japan's bioinformatics efforts misguided. Nat Biotechnol 2001 Feb; 19: 107-108 [PubMed]
  26. Brazma A.  On the Importance of Standardisation in Life Sciences.  Bioinformatics. 2001 Feb;17(2):113-114. [PubMed]
  27. Stevens R, Goble C, Baker P, Brass A. A classification of tasks in bioinformatics. Bioinformatics. 2001 Feb;17(2):180-188. [PubMed]
  28. Allen JF. Bioinformatics and discovery: induction beckons again. Bioessays. 2001 Jan;23(1):104-107. [PubMed]
  29. Baxevanis AD. Bioinformatics and the Internet.  Methods Biochem Anal. 2001;43:1-17. [PubMed]
  30. Luscombe NM, Greenbaum D, Gerstein M. What is bioinformatics? A proposed definition and overview of the field.  Methods Inf Med. 2001;40(4):346-58. [PubMed]

Applications

  1. Barbier-Brygoo H, Gaymard F, Rolland N, Joyard J. Strategies to identify transport systems in plants. Trends Plant Sci. 2001 Dec 1;6(12):577-585. [PubMed]
  2. Boismenu R, Havran WL. Intraepithelial gamma delta T cells exposed by functional genomics. Genome Biol. 2001 Nov;2(11):REVIEWS1031. [PubMed]
  3. Wang L, Wu Q, Qiu P, Mirza A, McGuirk M, Kirschmeier P, Greene JR, Wang Y, Pickett CB, Liu S. Analyses of P53 target genes in the human genome by bioinformatic and microarray approaches. J Biol Chem 2001 Nov 23;276(47):43604-10 [PubMed]
  4. Lee RC, Ambros V. An Extensive Class of Small RNAs in Caenorhabditis elegans.  Science. 2001 Oct 26;294(5543):862-4. [PubMed]
  5. Carter RJ, Dubchak I, Holbrook SR.  A computational approach to identify genes for functional RNAs in genomic sequences. Nucleic Acids Res. 2001 Oct 1;29(19):3928-38. [PubMed]
  6. Hegyi H, Gerstein M. Annotation Transfer for Genomics: Measuring Functional Divergence in Multi-Domain Proteins. Genome Res. 2001 Oct; 11:1632-1640 [PubMed]
  7. Kennedy SP, Ng WV, Salzberg SL, Hood L, DasSarma S.Understanding the Adaptation of Halobacterium Species NRC-1 to Its Extreme Environment through Computational Analysis of Its Genome Sequence. Genome Res. 2001 Oct; 11:1641-1650 [PubMed]
  8. Phan VT, Skiena SS. Dealing with errors in interactive sequencing by hybridization.  Bioinformatics. 2001 Oct;17(10):862-70. [PubMed]
  9. Kellam P. Post-genomic virology: the impact of bioinformatics, microarrays and proteomics on investigating host and pathogen interactions.  Rev Med Virol. 2001 Sep-Oct;11(5):313-29. [PubMed]
  10. Lim LP, Burge CB.  A computational analysis of sequence features involved in recognition of short introns.  Proc Natl Acad Sci U S A. 2001 Sep 25;98(20):11193-8. [PubMed][pdf]
  11. Schultze JL, Vonderheide RH. From cancer genomics to cancer immunotherapy: toward second-generation tumor antigens. Trends Immunol. 2001 Sep;22(9):516-23. [PubMed]
  12. Zagursky RJ, Russell D.  Bioinformatics: use in bacterial vaccine discovery.  Biotechniques. 2001 Sep;31(3):636-640 [PubMed]
  13. Novotny J, Rigoutsos I, Coleman D, Shenk T. In silico structural and functional analysis of the human cytomegalovirus (HHV5) genome.  J Mol Biol. 2001 Jul 27;310(5):1151-66. [PubMed]
  14. Moreno JC, Pauws E, van Kampen AH, Jedlickova M, de Vijlder JJ, Ris-Stalpers C. Cloning of Tissue-Specific Genes Using Serial Analysis of Gene Expression and a Novel Computational Substraction Approach. Genomics. 2001 Jul;75(1/3):70-76. [PubMed]
  15. Huang L, Jacob RJ, Pegg SC, Baldwin MA, Wang CC, Burlingame AA, Babbitt PC. Functional assignment of the 20S proteasome from T. Brucei using mass spectrometry and new bioinformatics approaches.  J Biol Chem. 2001 Jul 27; 276: 28327-28339 [PubMed]
  16. Wang D, Chang PS, Wang Z, Sutherland L, Richardson JA, Small E, Krieg PA, Olson EN. Activation of cardiac gene expression by myocardin, a transcriptional cofactor for serum response factor.  Cell. 2001 Jun 29;105(7):851-62. [PubMed]
  17. Davidson D, Baldock R.  Bioinformatics beyond sequence: mapping gene function in the embryo. Nat Rev Genet. 2001 Jun;2(6):409-17. [PubMed]
  18. Kel AE, Kel-Margoulis OV, Farnham PJ, Bartley SM, Wingender E, Zhang MQ.  Computer-assisted identification of cell cycle-related genes: new targets for E2F transcription factors.  J Mol Biol. 2001 May 25;309(1):99-120. [PubMed]
  19. Brancia FL, Butt A, Beynon RJ, Hubbard SJ, Gaskell SJ, Oliver SG. A combination of chemical derivatisation and improved bioinformatic tools optimises protein identification for proteomics.  Electrophoresis. 2001 Feb;22(3):552-9. [PubMed]
  20. Pires Martins R, Leach RE, Krawetz SA.  Whole-Body Gene Expression by Data Mining.  Genomics. 2001 Feb 15;72(1):34-42. [PubMed]
  21. Lexa M, Horak J, Brzobohaty B. Virtual PCR.  Bioinformatics. 2001 Feb;17(2):192-193. [PubMed]
  22. Pellegrini M.  Computational methods for protein function analysis. Curr Opin Chem Biol. 2001 Feb 1;5(1):46-50. [PubMed]
  23. Krogh A, Larsson B, von Heijne G, Sonnhammer EL. Predicting Transmembrane Protein Topology with a Hidden Markov Model: Application to Complete Genomes. J Mol Biol. 2001 Jan 19;305(3):567-580. [PubMed]
  24. Terstappen GC, Reggiani A. In silico research in drug discovery. Trends Pharmacol Sci. 2001 Jan; 22(1):23-26. [PubMed]
  25. Pavlidis P, Furey TS, Liberto M, Haussler D, Grundy WN. Promoter Region-Based Classification of Genes. Pacific Symposium on Biocomputing 2001; 6:151-164 [pdf]
  26. Danielsen M. Bioinformatics of nuclear receptors.  Methods Mol Biol. 2001;176:3-22. [PubMed]
  27. Burkle T, Hain T, Hossain H, Dudeck J, Domann E. Bioinformatics in medical practice: what is necessary for a hospital?  Medinfo. 2001;10(Pt 2):951-5. [PubMed]
  28. Dahl SG, Edvardsen O, Kristiansen K, Sylte I. Bioinformatics and receptor mechanisms of psychotropic drugs.  Biotechnol Annu Rev. 2001;7:165-77. [PubMed]
  29. Tang CM, Moxon ER. The impact of microbial genomics on antimicrobial drug development.  Annu Rev Genomics Hum Genet. 2001;2:259-69. [PubMed]
  30. Carter K, Oka AI. Bioinformatics issues for automating the annotation of genomic sequences. Genome Inform Ser Workshop Genome Inform. 2001;12:204-11. [PubMed]

Data mining

  1. Maslov S, Zhang YC. Extracting Hidden Information from Knowledge Networks. Phys Rev Lett. 2001 Dec 10;87(24):248701. [PubMed]
  2. Davuluri RV, Grosse I, Zhang MQ. Computational identification of promoters and first exons in the human genome. Nat Genet. 2001 Dec;29(4):412-7. [PubMed][web supplement]
  3. Coppel RL. Bioinformatics and the malaria genome: facilitating access and exploitation of sequence information. Mol Biochem Parasitol. 2001 Dec;118(2):139-145. [PubMed]
  4. Rehm BH. Bioinformatic tools for DNA/protein sequence analysis, functional assignment of genes and protein classification. Appl Microbiol Biotechnol. 2001 Dec;57(5-6):579-92. [PubMed]
  5. Baranova AV, Lobashev AV, Ivanov DV, Krukovskaya LL, Yankovsky NK, Kozlov AP. In silico screening for tumour-specific expressed sequences in human genome. FEBS Lett. 2001 Nov 9;508(1):143-8. [PubMed]
  6. Kanehisa M. Prediction of higher order functional networks from genomic data. Pharmacogenomics. 2001 Nov;2(4):373-85. [PubMed]
  7. Kielbasa SM, Korbel JO, Beule D, Schuchhardt J, Herzel H. Combining frequency and positional information to predict transcription factor binding sites. Bioinformatics. 2001 Nov;17(11):1019-26. [PubMed]
  8. Novichkov PS, Gelfand MS, Mironov AA. Gene recognition in eukaryotic DNA by comparison of genomic sequences. Bioinformatics. 2001 Nov;17(11):1011-8. [PubMed]
  9. Carter RJ, Dubchak I, Holbrook SR.  A computational approach to identify genes for functional RNAs in genomic sequences. Nucleic Acids Res. 2001 Oct 1;29(19):3928-38. [PubMed]
  10. Fujibuchi W, Anderson JS, Landsman D. PROSPECT improves cis-acting regulatory element prediction by integrating expression profile data with consensus pattern searches.  Nucleic Acids Res. 2001 Oct 1;29(19):3988-96. [PubMed]
  11. Pilpel Y, Sudarsanam P, Church GM.  Identifying regulatory networks by combinatorial analysis of promoter elements.  Nat Genet 2001 Oct;29(2):153-9 [PubMed]
  12. Meng F, Cargile BJ, Miller LM, Forbes AJ, Johnson JR, Kelleher NL. Informatics and multiplexing of intact protein identification in bacteria and the archaea. Nat Biotechnol. 2001 Oct;19(10):952-7. [PubMed]
  13. Levy S, Hannenhalli S, Workman C. Enrichment of regulatory signals in conserved non-coding genomic sequence. Bioinformatics. 2001 Oct;17(10):871-7. [PubMed]
  14. Bolten E, Schliep A, Schneckener S, Schomburg D, Schrader R. Clustering protein sequences-structure prediction by transitive homology.  Bioinformatics. 2001 Oct;17(10):935-41. [PubMed]
  15. Vohradsky J.  Neural model of the genetic network.   J Biol Chem. 2001 Sep 28;276(39):36168-73. [PubMed]
  16. Mjolsness E, DeCoste D. Machine learning for science: state of the art and future prospects.   Science. 2001 Sep 14;293(5537):2051-5. [PubMed]
  17. Milburn J. Beyond the genome: turning data into knowledge. Drug Discov Today. 2001 Sep 1;6(17):881-883. [PubMed]
  18. Pazos F, Valencia A. Similarity of phylogenetic trees as indicator of protein-protein interaction. Protein Eng. 2001 Sep;14(9):609-14. [PubMed]
  19. Volfovsky N, Haas BJ, Salzberg SL. A clustering method for repeat analysis in DNA sequences. Genome Biol. 2001 Aug 1; 2(8): research0027.1-0027.11 [PubMed][pdf]
  20. Murvai J. Vlahovicek K, Szepesvari C, Pongor S. Prediction of Protein Functional Domains from Sequences Using Artificial Neural Networks. Genome Res. 2001 Aug; 11: 1410-1417 [PubMed]
  21. Bertone P, Gerstein M. Integrative data mining: the new direction in bioinformatics. IEEE Eng Med Biol Mag. 2001 Jul-Aug;20(4):33-40. [PubMed]
  22. Ross BC, Czajkowski L, Hocking D, Margetts M, Webb E, Rothel L, Patterson M, Agius C, Camuglia S, Reynolds E, Littlejohn T, Gaeta B, Ng A, Kuczek ES, Mattick JS,  Gearing D, Barr IG.  Identification of vaccine candidate antigens from a genomic analysis of Porphyromonas gingivalis.  Vaccine. 2001 Jul 20;19(30):4135-42. [PubMed]
  23. Allen J. In silico veritas: Data-mining and automated discovery: the truth is in there. EMBO Rep. 2001 Jul;2(7):542-4 [PubMed]
  24. Sreekumar KR, Aravind L, Koonin EV. Computational analysis of human disease-associated genes and their protein products. Curr Opin Genet Dev 2001. Jun; 11:247-257. [PubMed]
  25. Wojcik J, Schachter V. Protein-protein interaction map inference using interacting domain profile pairs. Bioinformatics. 2001 Jun;17 Suppl 1:S296-305. [PubMed]
  26. Nielsen R. Statistical tests of selective neutrality in the age of genomics. Heredity. 2001 Jun;86(Pt 6):641-7. [PubMed]
  27. Kel AE, Kel-Margoulis OV, Farnham PJ, Bartley SM, Wingender E, Zhang MQ.  Computer-assisted identification of cell cycle-related genes: new targets for E2F transcription factors.  J Mol Biol. 2001 May 25;309(1):99-120. [PubMed]
  28. Bock JR, Gough DA. Predicting protein-protein interactions from primary structure. Bioinformatics. 2001 May;17(5):455-60. [PubMed]
  29. Hasty J, McMillen D, Isaacs F, Collins JJ. Computational studies of gene regulatory networks: in numero molecular biology. Nat Rev Genet. 2001 Apr;2(4):268-79. Review. [PubMed]
  30. Marcotte EM, Xenarios I, Eisenberg D.  Mining literature for protein-protein interactions.  Bioinformatics. 2001 Apr;17(4):359-363. [PubMed]
  31. Ding CH, Dubchak I. Multi-class protein fold recognition using support vector machines and neural networks. Bioinformatics. 2001 Apr;17(4):349-358. [PubMed]
  32. Jacq B. Protein function from the perspective of molecular interactions and genetic networks. Brief Bioinform. 2001 Mar;2(1):38-50. [PubMed]
  33. Pagni M, Jongeneel CV. Making sense of score statistics for sequence alignments. Brief Bioinform. 2001 Mar;2(1):51-67. [PubMed]
  34. Pires Martins R, Leach RE, Krawetz SA.  Whole-Body Gene Expression by Data Mining.  Genomics. 2001 Feb 15;72(1):34-42. [PubMed]
  35. Ohler U, Niemann H. Identification and analysis of eukaryotic promoters: recent computational approaches. Trends Genet. 2001 Feb;17(2):56-60. [PubMed]
  36. Wingender E, Chen X, Fricke E, Geffers R, Hehl R, Liebich I, Krull M, Matys V, Michael H, Ohnhauser R, Pruss M, Schacherer F, Thiele S, Urbach S. The TRANSFAC system on gene expression regulation. Nucleic Acids Res. 2001 Jan 1;29(1):281-3. [PubMed]
  37. Maki Y, Tominaga D, Okamoto M, Watanabe S, Eguchi Y. Development of a System for the Inference of Large Scale Genetic Networks. Pacific Symposium on Biocomputing 2001; 6:446-458 [pdf]
  38. Van Ooyen, A. Theoretical aspects of pattern analysis. In: Dijkshoorn, L., Towner, K. J., Struelens, M. (eds.) New Approaches for the Generation and Analysis of Microbial Fingerprints. Elsevier, Amsterdam. 2001 In press. [Abstract] [Full Text: PostScript] [Full Text: Word]
  39. Edwards YJ, Brocklehurst SM. Finding genes in genomic nucleotide sequences by using bioinformatics. Methods Mol Biol. 2001;175:235-47. [PubMed]
  40. Muggleton SH, Bryant CH, Srinivasan A, Whittaker A, Topp S, Rawlings C. Are grammatical representations useful for learning from biological sequence data?- a case study. J Comput Biol. 2001;8(5):493-521. [PubMed]
  41. Salama JJ, Donaldson I, Hogue CW. Automatic annotation of BIND molecular interactions from three-dimensional structures. Biopolymers. 2001 [epub ahead of print] [PubMed]

in silico biology/computational modelling

  1. Berendsen HJ. BIOINFORMATICS: Reality Simulation--Observe While It Happens. Science. 2001 Dec 14;294(5550):2304-2305. [PubMed]
  2. Tomita M. Towards computer aided design (CAD) of useful microorganisms. Bioinformatics. 2001 Dec; 17:1091-1092. [PubMed]
  3. Leung YF, Lam DSC, Pang CP. in silico biology: observation, modeling, hypothesis and verification.  Trends Genet. 2001. Nov; 17:622-623 [PubMed]
  4. Borodovsky M, Koonin E, Burge C, Fickett J, Logsdon J, Sali A, Stormo G, Zhulin I. The third georgia tech-emory international conference on bioinformatics: in silico biology; bioinformatics after human genome (november 15-18, 2001, atlanta, georgia, usa). Bioinformatics. 2001 Oct;17(10):859-61. [PubMed]
  5. Bornholdt S. Modeling genetic networks and their evolution: a complex dynamical systems perspective. Biol Chem. 2001 Sep;382(9):1289-99 [PubMed]
  6. De Groot AS, Bosma A, Chinai N, Frost J, Jesdale BM, Gonzalez MA, Martin W, Saint-Aubin C. From genome to vaccine: in silico predictions, ex vivo verification. Vaccine. 2001 Aug 14;19(31):4385-95. [PubMed]

Network/pathway reconstruction and analysis

  1. Cornish-Bowden A, Cardenas ML. Complex networks of interactions connect genes to phenotypes. Trends Biochem Sci. 2001 Aug;26(8):463-5. [PubMed]
  2. Jain E. Jain K. Integrated bioinformatics - high-throughput interpretation of pathways and biology. Trends Biotechnol. 2001. May; 19:157-158 [PubMed]
  3. Yaffe MB, Leparc GG, Lai J, Obata T, Volinia S, Cantley LC.  A motif-based profile scanning approach for genome-wide prediction of signaling pathways.  Nat Biotechnol. 2001 Apr;19(4):348-353. [PubMed]
  4. Koza JR, Mydlowec W, Lanza G, Yu J, Keane MA. Reverse Engineering of Metabolic Pathways from Observed Data Using Genetic Programming. Pacific Symposium on Biocomputing 2001; 6:434-445 [pdf]

Structure prediction

  1. Bujnicki JM. In silico analysis of the tRNA:m1A58 methyltransferase family: homology-based fold prediction and identification of new members from Eubacteria and Archaea. FEBS Lett. 2001 Oct 26;507(2):123-7. [PubMed]
  2. Lee MR. Molecular Dynamics in the Endgame of Protein Structure Prediction. J Mol Biol. 2001 Oct 19; 313:417-430 [PubMed]
  3. Simon I, Fiser A, Tusnady GE. Predicting protein conformation by statistical methods. Biochim Biophys Acta. 2001 Oct 18;1549(2):123-36. [PubMed]
  4. Baker D, Sali A. Protein structure prediction and structural genomics.  Science. 2001 Oct 5;294(5540):93-6. [PubMed]
  5. Heinemann U, Illing G, Oschkinat H. High-throughput three-dimensional protein structure determination. Curr Opin Biotechnol. 2001 Aug; 12:348-354. [PubMed]
  6. Novotny J, Rigoutsos I, Coleman D, Shenk T. In silico structural and functional analysis of the human cytomegalovirus (HHV5) genome.  J Mol Biol. 2001 Jul 27;310(5):1151-66. [PubMed]
  7. Hua S, Sun Z. A novel method of protein secondary structure prediction with high segment overlap measure: support vector machine approach.  J Mol Biol. 2001 Apr 27;308(2):397-407. [PubMed]
  8. Edwards YJ, Cottage A. Prediction of protein structure and function by using bioinformatics. Methods Mol Biol. 2001;175:341-75 [PubMed]

Languages and Algorithms

  1. Pertsemlidis A, Fondon JW 3rd. Having a BLAST with bioinformatics (and avoiding BLASTphemy). Genome Biol. 2001 Oct. 2:2002 [PubMed]
  2. Ning Z, Cox AJ, Mullikin JC. SSAHA: A Fast Search Method for Large DNA Databases. Genome Res. 2001 Oct; 11:1725-1729 [PubMed]
  3. Bejerano G, Seldin Y, Margalit H, Tishby N. Markovian domain fingerprinting: statistical segmentation of protein sequences. Bioinformatics. 2001 Oct;17(10):927-34. [PubMed]
  4. Vohradsky J. Neural model of genetic network.  J Biol Chem. 2001 Sep 28;276(39):36168-73. [PubMed]
  5. Cook DL, Farley JF, Tapscott SJ. A basis for a visual language for describing, archiving and analyzing functional models of complex biological systems. Genome Biol 2001. Mar 22; 2(4) research0012.1-10 [PubMed][pdf]
  6. Achard F, Vaysseix G, Barillot E.  XML, bioinformatics and data integration.  Bioinformatics. 2001 Feb;17(2):115-125. [PubMed]
  7. Kim JH, Ohno-Machado L, Kohane IS. Unsupervised Learning from Complex Data: The Matrix Incision Tree Algorithm. Pacific Symposium on Biocomputing 2001; 6:30-41[pdf]

Softwares

  1. Hatzigeorgiou AG, Fiziev P, Reczko M. DIANA-EST: a statistical analysis. Bioinformatics. 2001 Oct;17(10):913-9. [PubMed]
  2. Burgard AP, Moore GL, Maranas CD. Review of the TEIRESIAS-Based Tools of the IBM Bioinformatics and Pattern Discovery Group. Metab Eng. 2001 Oct;3(4):285-288. [PubMed]
  3. Wishart DS, Fortin S. The BioTools Suite. A comprehensive suite of platform-independent bioinformatics tools.  Mol Biotechnol. 2001 Sep;19(1):59-77. [PubMed]
  4. Salama JJ, Feldman HJ, Hogue CW.  VISTRAJ: exploring protein conformational space.  Bioinformatics. 2001 Sep;17(9):851-852. [PubMed]
  5. Cox DG, Canzian F. Genotype transposer: automated genotype manipulation for linkage disequilibrium analysis. Bioinformatics. 2001 Aug;17(8):738-9. [PubMed]
  6. Mrowka R. A Java applet for visualizing protein-protein interaction. Bioinformatics. 2001 Jul;17(7):669-71. [PubMed]
  7. Zhang L, Heng CK, Tan TW. Cladogramer: incorporating haplotype frequency into cladogram analysis. Bioinformatics. 2001 May;17(5):481-2. [PubMed]
  8. Trelles O. On the parallelisation of bioinformatics applications.  Brief Bioinform. 2001 May;2(2):181-94. [PubMed]
  9. Patnaik SK, Blumenfeld OO. Use of on-line tools and databases for routine sequence analyses. Anal Biochem. 2001 Feb 1; 289:1-9 [PubMed]
  10. Liu X. Brutlag DL, Liu JS. BioProspector: Discovering Conserved DNA Motifs in Upstream Regulatory Regions of Co-Expressed Genes. Pacific Symposium on Biocomputing 2001;  6:127-138 [pdf]
  11. Buerstedde JM, Prill F.  FOUNTAIN: A JAVA open-source package to assist large sequencing projects.   BMC Bioinformatics. 2001;2(1):6. [PubMed]
  12. Riva AA, Kohane IS. A web-based tool to retrieve human genome polymorphisms from public databases. Proc AMIA Symp. 2001;:558-62. [PubMed]
  13. Tolle R. Information technology tools for efficient SNP studies. Am J Pharmacogenomics. 2001;1(4):303-14. [PubMed]
Databases

Nucleic Acid Research January 1, 2001 issue, Molecular Biology Database Collection - The link to the complete issue

  1. Brizuela L, Braun P, LaBaer J. FLEXGene repository: from sequenced genomes to gene repositories for high-throughput functional biology and proteomics. Mol Biochem Parasitol. 2001 Dec;118(2):155-165. [PubMed]
  2. Varotto C, Richly E, Salamini F, Leister D. GST-PRIME: a genome-wide primer design software for the generation of gene sequence tags. Nucleic Acids Res. 2001 Nov 1;29(21):4373-4377. [PubMed]
  3. Peri S, Steen H, Pandey A. GPMAW - a software tool for analyzing proteins and peptides. Trends Biochem Sci. 2001 Nov 1; 26:687-689 [PubMed]
  4. Wheelan SJ, Church DM, Ostell JM.. Spidey: A Tool for mRNA-to-Genomic Alignments. Genome Res. 2001 Nov; 11:1952-1957 [PubMed]
  5. Schacherer F, Choi C, Gotze U, Krull M, Pistor S, Wingender E. The TRANSPATH signal transduction database: a knowledge base on signal transduction networks. Bioinformatics. 2001 Nov;17(11):1053-7. [PubMed]
  6. Prabakaran P, An J, Gromiha MM, Selvaraj S, Uedaira H, Kono H, Sarai A. Thermodynamic database for protein-nucleic acid interactions (ProNIT). Bioinformatics. 2001 Nov;17(11):1027-34. [PubMed]
  7. Scherer SW, Cheung J. Discovery of the human genome sequence in the public and private databases. Curr Biol. 2001 Oct 16;11(20):R808-R811. [PubMed]
  8. Oh JM, Brichory F, Puravs E, Kuick R, Wood C, Rouillard JM, Tra J, Kardia S, Beer D, Hanash S. A database of protein expression in lung cancer. Proteomics. 2001 Oct;1(10):1303-19. [PubMed]
  9. Xenarios I, Eisenberg D. Protein interaction databases.   Curr Opin Biotechnol. 2001 Aug;12(4):334-9. [PubMed]
  10. Sujansky W. Heterogeneous database integration in biomedicine. J Biomed Inform. 2001 Aug;34(4):285-98. [PubMed]
  11. Rodriguez-Tome P. EBI databases and services. Mol Biotechnol. 2001 Jul;18(3):199-212. [PubMed]
  12. Qian J, Stenger B, Wilson CA, Lin J, Jansen R, Teichmann SA, Park J, G Krebs W, Yu H, Alexandrov V, Echols N, Gerstein M.  PartsList: a web-based system for dynamically ranking protein folds based on disparate attributes, including whole-genome expression and interaction information. Nucleic Acids Res. 2001 Apr 15;29(8):1750-1764. [PubMed]
  13. Eyal E, Najmanovich R, Sobolev V, Edelman M.  MutaProt: a web interface for structural analysis of point mutations. Bioinformatics. 2001 Apr;17(4):381-382. [PubMed]
  14. Brookes AJ. HGBASE - a unified human SNP database. Trends Genet. 2001. Apr; 17:229 [PubMed]
  15. Riggins GJ, Strausberg RL . Genome and genetic resources from the Cancer Genome Anatomy Project. Hum Mol Genet. 2001 Apr 1;10(7):663-7. [PubMed]
  16. Winkelmann BR.  Genomics and large scale phenotypic databases.  Pharmacogenomics. 2001 Feb;2(1):3-5. [PubMed]
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Conference proceedings

Pacific Symposium of Biocomputing 2001


last updated: 4 Aug 2002
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