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

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

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

  1. Eddy SR. How do RNA folding algorithms work? Nat Biotechnol. 2004 Nov;22(11):1457-8. [PubMed]
  2. Eddy SR. What is a hidden Markov model? Nat Biotechnol. 2004 Oct;22(10):1315-6. [PubMed]
  3. Pevzner PA. Educating biologists in the 21st century: bioinformatics scientists vs. bioinformatics technicians. Bioinformatics. 2004 Sep 22;20(14):2159-61. [PubMed]
  4. Eddy SR. What is Bayesian statistics? Nat Biotechnol. 2004 Sep;22(9):1177-8. [PubMed]
  5. Wiley HS, Michaels GS. Should software hold data hostage? Nat Biotechnol. 2004 Aug;22(8):1037-8. [PubMed]
  6. Palfreyman N. The construction of meaning in computational integrative biology. OMICS. 2004 Summer;8(2):95-105. [PubMed]
  7. Eddy SR. What is dynamic programming? Nat Biotechnol. 2004 Jul;22(7):909-10. [PubMed]

Applications

  1. Van de Peer Y. COMPUTATIONAL APPROACHES TO UNVEILING ANCIENT GENOME DUPLICATIONS. Nat Rev Genet. 2004 Oct; 10 [PubMed]
  2. Scott MS, Thomas DY, Hallett MT. Predicting Subcellular Localization via Protein Motif Co-Occurrence. Genome Res. 2004 Oct;14(10):1957-66. [PubMed]
  3. Caenepeel S, Charydczak G, Sudarsanam S, Hunter T, Manning G. The mouse kinome: Discovery and comparative genomics of all mouse protein kinases. Proc Natl Acad Sci U S A. 2004 Aug 10;101(32):11707-12.[PubMed]
  4. Costa Ld Lda F, Barbosa MS, Manoel ET, Streicher J, Muller GB. Mathematical characterization of three-dimensional gene expression patterns. Bioinformatics 2004 Jul 22; 20: 1653-1662. [PubMed]
  5. Knaup P, Ammenwerth E, Brandner R, Brigl B, Fischer G, Garde S, Lang E, Pilgram R, Ruderich F, Singer R, Wolff AC, Haux R, Kulikowski C. Towards clinical bioinformatics: advancing genomic medicine with informatics methods and tools. Methods Inf Med. 2004;43(3):302-7. [PubMed]
  6. Maojo V, Martin-Sanchez F. Bioinformatics: towards new directions for public health. Methods Inf Med. 2004;43(3):208-14. [PubMed]
  7. Cai L, Huang H, Blackshaw S, Liu JS, Cepko C, Wong WH. Clustering analysis of SAGE data using a Poisson approach. Genome Biol. 2004;5(7):R51. [PubMed]

Data mining

Literature mining

  1. Schuemie MJ, Weeber M, Schijvenaars BJ, van Mulligen EM, van der Eijk CC, Jelier R, Mons B, Kors JA. Distribution of information in biomedical abstracts and full-text publications. Bioinformatics. 2004 Nov 1;20(16):2597-604. [PubMed]
  2. Perez AJ, Perez-Iratxeta C, Bork P, Thode G, Andrade MA. Gene annotation from scientific literature using mappings between keyword systems. Bioinformatics. 2004 Sep 1; [PubMed]
  3. Hakenberg J, Schmeier S, Kowald A, Klipp E, Leser U. Finding kinetic parameters using text mining. OMICS. 2004 Summer;8(2):131-52. [PubMed]

Database mining

Data integration

  1. Lanckriet GR, De Bie T, Cristianini N, Jordan MI, Noble WS. A statistical framework for genomic data fusion. Bioinformatics. 2004 Nov 1;20(16):2626-35. [PubMed]
  2. De La Fuente A, Bing N, Hoeschele I, Mendes P. Discovery of meaningful associations in genomic data using partial correlation coefficients. Bioinformatics. 2004 Jul 29 [Epub ahead of print] [PubMed]
  3. Cui Y, Zhou M, Wong WH. Integrated analysis of microarray data and gene function information. OMICS. 2004 Summer;8(2):106-17. [PubMed]
  4. Toyoda T, Wada A. Omic space: coordinate-based integration and analysis of genomic phenomic interactions. Bioinformatics 2004 Jul 22; 20: 1759-1765. [PubMed]
  5. Balasubramanian R, LaFramboise T, Scholtens D, Gentleman R. A graph theoretic approach to testing associations between disparate sources of functional genomics data. Bioinformatics. 2004 Jul 15;. [Epub ahead of print] [PubMed]

in silico biology/computational modelling

  1. Stelling J. Mathematical models in microbial systems biology. Curr Opin Microbiol. 2004 Oct;7(5):513-8. [PubMed]
  2. Nicholson JK, Holmes E, Lindon JC, Wilson ID. The challenges of modeling mammalian biocomplexity. Nat Biotechnol. 2004 Oct;22(10):1268-74. [PubMed]
  3. Ishii N, Robert M, Nakayama Y, Kanai A, Tomita M. Toward large-scale modeling of the microbial cell for computer simulation. J Biotechnol. 2004 Sep 30;113(1-3):281-94. [PubMed]
  4. Reed JL, Palsson BO. Genome-scale in silico models of E. coli have multiple equivalent phenotypic states: assessment of correlated reaction subsets that comprise network states. Genome Res. 2004 Sep;14(9):1797-805. [PubMed]
  5. Kremling A, Fischer S, Gadkar K, Doyle FJ, Sauter T, Bullinger E, Allgower F, Gilles ED. A benchmark for methods in reverse engineering and model discrimination: problem formulation and solutions. Genome Res. 2004 Sep;14(9):1773-85. [PubMed]
  6. Salwinski L, Eisenberg D. In silico simulation of biological network dynamics. Nat Biotechnol. 2004 Aug;22(8):1017-9. [PubMed]
  7. Brito RM, Dubitzky W, Rodrigues JR. Protein folding and unfolding simulations: a new challenge for data mining. OMICS. 2004 Summer;8(2):153-66. [PubMed]
  8. Yugi K, Tomita M. A general computational model of mitochondrial metabolism in a whole organelle scale Bioinformatics 2004 Jul 22; 20: 1795-1796.  [PubMed]

Network/pathway reconstruction and analysis

  1. Aburatani S, Goto K, Saito S, Fumoto M, Imaizumi A, Sugaya N, Murakami H, Sato M, Toh H, Horimoto K. ASIAN: a website for network inference. Bioinformatics. 2004 Nov 1;20(16):2853-6. [PubMed]
  2. Ludemann A, Weicht D, Selbig J, Kopka J. PaVESy: Pathway Visualization and Editing System. Bioinformatics. 2004 Nov 1;20(16):2841-4. [PubMed]
  3. Berg J, Lassig M. Local graph alignment and motif search in biological networks. Proc Natl Acad Sci U S A. 2004 Oct 12;101(41):14689-94. [PubMed]
  4. Simonis N, Wodak SJ, Cohen GN, van Helden J. Combining pattern discovery and discriminant analysis to predict gene co-regulation. Bioinformatics. 2004 Oct 12;20(15):2370-9. [PubMed]
  5. Sosa N, Kremling A, Ratsch E, Rojas I. Web-based visualisation of the transcriptional control network of Escherichia coli. In Silico Biol. 2004 Sep 25;4(3):0042. [Epub ahead of print][PubMed]
  6. Mao L, Resat H. Probabilistic representation of gene regulatory networks. Bioinformatics. 2004 Sep 22;20(14):2258-69. [PubMed]
  7. Luscombe NM, Babu MM, Yu H, Snyder M, Teichmann SA, Gerstein M. Genomic analysis of regulatory network dynamics reveals large topological changes. Nature. 2004 Sep 16;431(7006):308-12. [PubMed]
  8. Baral C, Chancellor K, Tran N, Tran NL, Joy A, Berens M. A knowledge based approach for representing and reasoning about signaling networks. Bioinformatics. 2004 Aug 4;20 Suppl 1:I15-I22. [PubMed]
  9. Papin JA, Stelling J, Price ND, Klamt S, Schuster S, Palsson BO. Comparison of network-based pathway analysis methods. Trends Biotechnol. 2004 Aug;22(8):400-5. [PubMed]
  10. Yu J, Smith VA, Wang PP, Hartemink AJ, Jarvis ED. Advances to Bayesian network inference for generating causal networks from observational biological data. Bioinformatics. 2004 Jul 29;. [Epub ahead of print] [PubMed]
  11. Ashkenasy G, Jagasia R, Yadav M, Ghadiri MR. Design of a directed molecular network. Proc Natl Acad Sci U S A. 2004 Jul 27;101(30):10872-7. [PubMed]
  12. Kashtan N, Itzkovitz S, Milo R, Alon U. Efficient sampling algorithm for estimating subgraph concentrations and detecting network motifs. Bioinformatics 2004 Jul 22; 20: 1746-1758. [PubMed]
  13. Voit EO, Almeida J. Decoupling dynamical systems for pathway identification from metabolic profiles. Bioinformatics 2004 Jul 22; 20: 1670-1681. [PubMed]
  14. Wei GH, Liu DP, Liang CC. Charting gene regulatory networks: strategies, challenges and perspectives. Biochem J. 2004 Jul 1;381(Pt 1):1-12. [PubMed]
  15. Wuchty S. Evolution and topology in the yeast protein interaction network. Genome Res. 2004 Jul;14(7):1310-4. [PubMed]
  16. Kutalik Z, Cho KH, Wolkenhauer O. Optimal sampling time selection for parameter estimation in dynamic pathway modeling. Biosystems. 2004 Jul;75(1-3):43-55. [PubMed]

Promter/regulatory sequence analysis

  1. Grad YH, Roth FP, Halfon MS, Church GM. Prediction of similarly acting cis-regulatory modules by subsequence profiling and comparative genomics in Drosophila melanogaster and D.pseudoobscura. Bioinformatics. 2004 Nov 1;20(16):2738-50. [PubMed]
  2. Keles S, van der Laan MJ, Vulpe C. Regulatory motif finding by logic regression. Bioinformatics. 2004 Nov 1;20(16):2799-811. [PubMed]
  3. Tadesse MG, Vannucci M, Lio P. Identification of DNA regulatory motifs using Bayesian variable selection. Bioinformatics. 2004 Nov 1;20(16):2553-61. [PubMed]
  4. Bajic VB, Tan SL, Suzuki Y, Sugano S. Promoter prediction analysis on the whole human genome. Nat Biotechnol. 2004 Nov;22(11):1467-73. [PubMed]
  5. Sinha S, Schroeder MD, Unnerstall U, Gaul U, Siggia ED. Cross-species comparison significantly improves genome-wide prediction of cis-regulatory modules in Drosophila. BMC Bioinformatics. 2004 Sep 09;5(1):129.[PubMed]
  6. Elkon R, Zeller KI, Linhart C, Dang CV, Shamir R, Shiloh Y. In silico identification of transcriptional regulators associated with c-Myc. Nucleic Acids Res. 2004;32(17):4955-61. [PubMed]
  7. Nardone J, Lee DU, Ansel KM, Rao A. Bioinformatics for the 'bench biologist': how to find regulatory regions in genomic DNA. Nat Immunol. 2004 Aug;5(8):768-74. [PubMed]
  8. Kato M, Hata N, Banerjee N, Futcher B, Zhang MQ. Identifying combinatorial regulation of transcription factors and binding motifs. Genome Biol. 2004;5(8):R56. [PubMed]
  9. Kellis M, Patterson N, Birren B, Berger B, Lander ES. Methods in comparative genomics: genome correspondence, gene identification and regulatory motif discovery. J Comput Biol. 2004;11(2-3):319-55. [PubMed]
  10. Kechris KJ, Van Zwet E, Bickel PJ, Eisen MB. Detecting DNA regulatory motifs by incorporating positional trends in information content. Genome Biol. 2004;5(7):R50. [PubMed]
  11. Korbel JO, Jensen LJ, Von Mering C, Bork P. Analysis of genomic context: prediction of functional associations from conserved bidirectionally transcribed gene pairs. Nat Biotechnol. 2004 Jul;22(7):911-7. [PubMed]

Protein-protein interaction analysis

  1. Poyatos JF, Hurst LD. How biologically relevant are interaction-based modules in protein networks? Genome Biol. 2004;5(11):R93. [PubMed]
  2. Lemos B, Meiklejohn CD, Hartl DL. Regulatory evolution across the protein interaction network. Nat Genet. 2004 Oct;36(10):1059-60. [PubMed]
  3. Albert I, Albert R. Conserved network motifs allow protein-protein interaction prediction. Bioinformatics. 2004 Jul 9;. [Epub ahead of print][PubMed]

Gene prediction

  1. Issac B, Raghava GP. EGPred: prediction of eukaryotic genes using ab initio methods after combining with sequence similarity approaches. Genome Res. 2004 Sep;14(9):1756-66. [PubMed]
  2. Kellis M, Patterson N, Birren B, Berger B, Lander ES. Methods in comparative genomics: genome correspondence, gene identification and regulatory motif discovery. J Comput Biol. 2004;11(2-3):319-55. [PubMed]
  3. Zhang Z, Gerstein M. Large-scale analysis of pseudogenes in the human genome. Curr Opin Genet Dev. 2004 Aug;14(4):328-35. [PubMed]
  4. Wang L, Trawick JD, Yamamoto R, Zamudio C. Genome-wide operon prediction in Staphylococcus aureus. Nucleic Acids Res. 2004;32(12):3689-702. [PubMed]

Gene function prediction

  1. Pazos F, Sternberg MJ. Automated prediction of protein function and detection of functional sites from structure. Proc Natl Acad Sci U S A. 2004 Oct 12;101(41):14754-9. [PubMed]
  2. Jansen R, Gerstein M. Analyzing protein function on a genomic scale: the importance of gold-standard positives and negatives for network prediction. Curr Opin Microbiol. 2004 Oct;7(5):535-45. [PubMed]
  3. Perez AJ, Perez-Iratxeta C, Bork P, Thode G, Andrade MA. Gene annotation from scientific literature using mappings between keyword systems. Bioinformatics. 2004 Sep 1; [PubMed]
  4. Huynen MA, Snel B, Van Noort V. Comparative genomics for reliable protein-function prediction from genomic data. Trends Genet. 2004 Aug;20(8):340-4. [PubMed]

Structure prediction

  1. Simossis VA, Heringa J. Integrating protein secondary structure prediction and multiple sequence alignment. Curr Protein Pept Sci. 2004 Aug;5(4):249-66. [PubMed]

Comparative Genomics (theoretical)

  1. Kellis M, Patterson N, Birren B, Berger B, Lander ES. Methods in comparative genomics: genome correspondence, gene identification and regulatory motif discovery. J Comput Biol. 2004;11(2-3):319-55. [PubMed]

Languages and Algorithms

  1. Shapiro BE, Hucka M, Finney A, Doyle J. MathSBML: a package for manipulating SBML-based biological models. Bioinformatics. 2004 Nov 1;20(16):2829-31. [PubMed]
  2. Xirasagar S, Gustafson S, Merrick BA, Tomer KB, Stasiewicz S, Chan DD, Yost KJ 3rd, Yates JR 3rd, Sumner S, Xiao N, Waters MD. CEBS object model for systems biology data, SysBio-OM. Bioinformatics. 2004 Sep 1; [PubMed]
  3. Eddy SR. Where did the BLOSUM62 alignment score matrix come from? Nat Biotechnol. 2004 Aug;22(8):1035-6. [PubMed]
  4. Roux-Rouquie M, Caritey N, Gaubert L, Rosenthal-Sabroux C. Using the Unified Modelling Language (UML) to guide the systemic description of biological processes and systems. Biosystems. 2004 Jul;75(1-3):3-14. [PubMed]

Software

  1. Ludemann A, Weicht D, Selbig J, Kopka J. PaVESy: Pathway Visualization and Editing System. Bioinformatics. 2004 Nov 1;20(16):2841-4. [PubMed]
  2. Gilbert D. Bioinformatics software resources. Brief Bioinform. 2004 Sep;5(3):300-4. [PubMed]
  3. Swertz MA, (Bert) De Brock EO, Van Hijum SA, De Jong A, Buist G, Baerends RJ, Kok J, Kuipers OP, Jansen RC. Molecular Genetics Information System (MOLGENIS): alternatives in developing local experimental genomics databases. Bioinformatics. 2004 Sep 1; [PubMed]
  4. Nucleic Acids Research Web Server Issue. 2004 Jul 1

Databases

  1. Chen N, Lawson D, Bradnam K, Harris TW, Stein LD.  WormBase as an Integrated Platform for the C. elegans ORFeome. Genome Res. 2004 Oct;14(10b):2155-2161. [PubMed]

Conference proceedings

ISMB/ECCB 2004 conference proceedings

last updated:  6 Dec 2004
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