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Publications 2004 - CAGT

  • Noga Alon, Richard Beigel and Simon Kasif and Steven Rudich and Benny Sudakov, Learning a Hidden Matching, SIAM Journal of Computing, 2004. [Abstract]
  • Zheng Y, Roberts RJ, Kasif S. Identification of genes with fast-evolving regions in microbial genomes. Nucleic Acids Res. 2004 Dec 2;32(21):6347-57. Print 2004. PMID: 15576679 [Abstract][Full Text]
  • Zhang L, Kasif S, Cantor CR, Broude NE. GC/AT-content spikes as genomic punctuation marks. Proc Natl Acad Sci U S A. 2004 Nov 30;101(48):16855-60. Epub 2004 Nov 17. PMID: 15548610 [Full Text]
  • Tullai JW, Schaffer ME, Mullenbrock S, Kasif S, Cooper GM. Identification of transcription factor binding sites upstream of human genes regulated by the phosphatidylinositol 3-kinase and MEK/ERK signaling pathways. J Biol Chem. 2004 May 7;279(19):20167-77. Epub 2004 Feb 9. PMID: 14769801 [Abstract][Full Text]
  • Zheng Y, Roberts RJ, Kasif S. Segmentally variable genes: a new perspective on adaptation. PLoS Biol. 2004 Apr;2(4):E81. Epub 2004 Apr 13. PMID: 15094797 [Abstract][Full Text]
  • Karaoz U, Murali TM, Letovsky S, Zheng Y, Ding C, Cantor CR, Kasif S. Whole-genome annotation by using evidence integration in functional-linkage networks. Proc Natl Acad Sci U S A. 2004 Mar 2;101(9):2888-93. Epub 2004 Feb 23. PMID: 4981259 [Abstract][Full Text]
  • Wu CJ, Fu Y, Murali TM, Kasif S. Gene expression module discovery using Gibbs sampling. Genome Inform. 2004;15(1):239-48. PMID: 15712126 [Full Text]
  • Stitziel NO, Binkowski TA, Tseng YY, Kasif S, Liang J. topoSNP: a topographic database of non-synonymous single nucleotide polymorphisms with and without known disease association. Nucleic Acids Res. 2004 Jan 1;32(Database issue):D520-2. PMID: 14681472 [Abstract][Full Text]
  • Shakhnovich BE, Reddy TE, Galinsky K, Mellor J, Delisi C. Comparisons of predicted genetic modules: identification of co-expressed genes through module gene flow. Genome Inform Ser Workshop Genome Inform. 2004;15(1):221-8. [Abstract][Full Text]
  • Shakhnovich BE, Harvey JM, Delisi C. ELISA: a unified, multidimensional view of the protein domain universe. Genome Inform Ser Workshop Genome Inform. 2004;15(1):213-20. [Abstract][Full Text]
  • Mellor JC, Wu J, Delisi C. Constructing networks with correlation maximization methods. Genome Inform Ser Workshop Genome Inform. 2004;15(1):149-59. [Abstract][Full Text]
  • DeLisi C. Systems biology, the second time around. Environ Health Perspect. 2004 Nov;112(16):A926-7. [Full Text]
  • Hu Z, Mellor J, Wu J, DeLisi C. VisANT: an online visualization and analysis tool for biological interaction data. BMC Bioinformatics. 2004 Feb 19;5(1):17. [Abstract][Full Text]
  • The ENCODE Project Consortium (2004) The ENCODE (ENCyclopedia Of DNA Elements) Project Science, Vol 306, 636-640.
  • Haverty, PM., Hsiao, L., Gullans, SR., Hansen, U. & Weng, Z. (2004) Limited Agreement among Three Global Gene Expression Methods Highlights the Requirement for Non-Global Validation. Bioinformatics. Vol 20, 3431-3441. [Abstract][Full Text]
  • Hu, Z. Fu, Y. Halees, A. S. Kielbasa, S. M. & Weng, Z. (2004) SeqVISTA: a New Module of Integrated Computational Tools for Studying Transcriptional Regulation. Nucleic Acids Res., Vol 32, Web Server Issue, W235-W241. [Abstract][Full Text]
  • Mintseris, J. & Weng, Z. (2004) Optimizing Protein Representations with Information Theory. Genome Informatics, 15(1):160-169. [Full Text]
  • Halees, A. S. & Weng, Z. (2004) PromoSer: Improvements on Algorithm, Visualization and Accessibility. Nucleic Acids Res., Vol 32, Web Server Issue, W191-W194. [Abstract][Full Text]
  • Fu, Y., Frith, M.C., Haverty, P.M. & Weng, Z. (2004) MotifViz: an Analysis and Visualization Tool for Motif Discovery. Nucleic Acids Res., Vol. 32, Web Server Issue, W420-W423. [Abstract][Full Text]
  • Haverty, P.M., Frith, M.C. & Weng, Z. (2004) CARRIE Web Service: Automated Transcriptional Regulatory Network Inference and Interactive Analysis. Nucleic Acids Res., Vol. 32, Web Server Issue, W213-W216. [Abstract][Full Text]
  • Leyfer, D., Bond, A., Tworog, E., Perron, D., Maska, S., Brito, A., Kamens, J., Weng, Z. & Voss, J. (2004) Cis-Element Clustering Correlates with Dose-Dependent Pro- and Anti- Signaling Effects of IL18. Genes and Immunity, June 10, 1-9. [Abstract]
  • Haverty, P.M. & Weng, Z. (2004) CisML, an XML-based Format for Sequence Motif Detection Software .Bioinformatics, 20(11), 1815-1817. [Abstract][Full Text]
  • Frith, M. C., Fu, Y., Yu, L., Chen, J. F., Hansen, U. & Weng, Z. (2004) Detection of Functional DNA Motifs via Statistical Overrepresentation. Nucleic Acids Res. 2004 Feb 26; 32(4):1372-1381. [Abstract][Full Text]
  • Frith, M. C.*, Halees, A. S.*, Hansen, U. & Weng, Z. (2004) *Joint First Authors Site2genome: Locating Short DNA Sequences in Whole Genomes. Bioinformatics. 20(9):1468-1469. [Abstract][Full Text]
  • Haverty, P. M., Hansen, U. & Weng, Z. (2004) Computational Inference of Transcriptional Regulatory Networks from Expression Profiling and Transcription Factor Binding Site Identification . Nucleic Acids Res. 2004 Jan 1;32(1):179-188. [Abstract][Full Text]
  • Frith, M. C., Hansen, U., Spouge, J. L. & Weng, Z. (2004) Finding Functional Sequence Elements by Multiple Local Alignment. Nucleic Acids Res. 2004 Jan 1;32(1):189-200. [Abstract][Full Text]
  • Rajamani D, Thiel S, Vajda S, Camacho CJ. Anchor residues in protein-protein interactions. Proc. Natl. Acad. Sci. USA. 2004 Aug 3;101(31):11287-92. [Abstract][Full Text]
  • Stephen R. Comeau, David W. Gatchell, Sandor Vajda and Carlos J. Camacho. ClusPro: a fully automated algorithm for protein-protein docking. Nucleic Acids Research Vol. 32, Web Server issue. [Abstract][Full Text]
  • J.C. Prasad, Camacho C. J., Vajda, S. Consensus alignment server for reliable comparative modeling with distant templates. Nucleic Acids Research Vol. 32, Web Server issue. [Abstract][Full Text]
  • Camacho C, and Vajda S. Protein protein docking: is the glass half-full or half-empty? TRENDS in Biotechnology. 2004 Mar;22(3):110-6. [Abstract]
  • Stephen R. Comeau, David W. Gatchell, Sandor Vajda and Carlos J. Camacho. ClusPro: an automated docking and discrimination method for the prediction of protein complexes. BIOINFORMATICS Vol. 20 no. 1 2004, pages 45-50. [Abstract][Full Text]
  • P. E. Warburton, J. Giordano, F. Cheung, Y. Gelfand and G. Benson. Inverted Repeat Structure of the Human Genome: The X-Chromosome Contains a Preponderance of Large, Highly Homologous Inverted Repeats That Contain Testes Genes , Genome Research, 14:1861-1869, 2004. [Abstract][Full Text]
  • D. Ahlbrandt, G. Benson, W. Casey. Minimal Entropy Probability Paths Between Genome Families, Journal of Mathematical Biology, 48(5):563-90. [Abstract]
  • Daniel Segr?. The regulatory software of cellular metabolism (Commentary of Ihmels et al. Nat. Biotech. 2003). Trends in Biotechnology (2004), 22 (6), 261-265. [Abstract]
  • Daniel Segre' and Doron Lancet. Theoretical and computational approaches to the study of the origins of life. In Origins: Genesis, Evolution and Diversity of Life (2004), COLE series, Vol.6, Kluwer, J. Seckbach (ed.)

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