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Publications 2005 - CAGT

  • Lee S, Kohane I, Kasif S. Genes involved in complex adaptive processes tend to have highly conserved upstream regions in mammalian genomes. BMC Genomics. 2005 Nov 27;6:168. PMID: 16309559 [Abstract][Full Text]
  • Zheng Y, Anton BP, Roberts RJ, Kasif S. Phylogenetic detection of conserved gene clusters in microbial genomes. BMC Bioinformatics. 2005 Oct 3;6:243. PMID: 16202130 [Abstract][Full Text]
  • Szustakowski JD, Kasif S, Weng Z. Less is more: towards an optimal universal description of protein folds. Bioinformatics. 2005 Sep 1;21 Suppl 2:ii66-ii71. PMID: 16204127 [Abstract][Full Text]
  • Rachlin J, Ding C, Cantor C, Kasif S. Computational tradeoffs in multiplex PCR assay design for SNP genotyping. BMC Genomics. 2005 Jul 25;6:102.PMID: 16042802 [Abstract][Full Text]
  • Wu CJ, Kasif S. GEMS: a web server for biclustering analysis of expression data. Nucleic Acids Res. 2005 Jul 1;33(Web Server issue):W596-9. PMID: 15980544 [Abstract][Full Text]
  • Rachlin J, Ding C, Cantor C, Kasif S. MuPlex: multi-objective multiplex PCR assay design. Nucleic Acids Res. 2005 Jul 1;33(Web Server issue):W544-7. PMID: 15980531 [Abstract][Full Text]
  • Zheng Y, Roberts RJ, Kasif S, Guan C. Characterization of two new aminopeptidases in Escherichia coli. J Bacteriol. 2005 Jun;187(11):3671-7. PMID: 15901689 [Abstract][Full Text]
  • Suyog Rao, Alfredo Rodriguez and G. Benson. Evaluating distance functions for clustering tandem repeats [Full Text]

  • Wu, J., J.C. Mellor, C. DeLisi. (2005). Deciphering protein network organization using phylogenetic profile groups. Genome Inform Ser Workshop Genome Inform 16(1):142-9. [Abstract][Full Text]
  • Hu Z, Mellor J, Wu J, Yamada T, Holloway D, Delisi C. VisANT: data-integrating visual framework for biological networks and modules. Nucleic Acids Res. 2005 Jul 1;33. [Abstract][Full Text]
  • Shakhnovich BE, Deeds E, Delisi C, Shakhnovich E. Protein structure and evolutionary history determine sequence space topology. Genome Res. 2005 Mar;15(3):385-92. [Abstract][Full Text]
  • Anderson, R.J., Weng, Z, Campbell, R.K. & Jiang, X. (2005) Main-chain conformational tendencies of amino acids. Proteins, in press. [Abstract]
  • Mintseris, J. & Weng, Z. (2005). Structure, function, and evolution of transient and obligate protein-protein interactions. PNAS 102(31), 10930-10935. [Abstract][Full Text]
  • Mintseris, J., Wiehe, K., Pierce, B., Anderson, R., Chen, R., Janin, J. & Weng, Z. (2005) Protein-Protein Docking Benchmark 2.0: an update. Proteins 60(2), 214-216. [Abstract]
  • Wiehe, K., Pierce, B., Mintseris, J., Tong, W., Anderson, R., Chen, R. & Weng, Z. (2005) ZDOCK and RDOCK performance in CAPRI rounds 3, 4, and 5. Proteins 60(2), 207-213. [Abstract]
  • Pierce, B., Tong, W. & Weng, Z. (2005) M-ZDOCK: A Grid-based Approach for Cn Symmetric Multimer Docking. Bioinformatics 21(8), 1472-1476. [Abstract][Full Text]
  • Haverty, P. M., Weng, Z. & Hansen, U. (Accepted) Transcriptional Regulatory Networks Activated by PI3K and ERK Transduced Growth Signals in Human Glioblastoma Cells. J. Comput. Sci. & Tech. [Abstract]
  • Yanai, I.*, Yu, Y.*, Zhu, X., Cantor, C. & Weng, Z. (2005) (*Joint First Authors) An Avidin-like Domain that Does Not Bind Biotin Is Adopted for Oligomerization by the Extracellular Mosaic Protein Fibropellin. Protein Science, Vol 14, 417-423. [Abstract][Full Text]
  • Zhu, J. & Weng, Z. (2005) FAST: A Novel Protein Structure Alignment Algorithm. Proteins: Structure Function, and Bioinformatics, Vol 58, 618-627. [Abstract]
  • Tompa M, Li N, Bailey TL, Church GM, De Moor B, Eskin E, Favorov AV, Frith MC, Fu Y, Kent WJ, Makeev VJ, Mironov AA, Noble WS, Pavesi G, Pesole G, Regnier M, Simonis N, Sinha S, Thijs G, van Helden J, Vandenbogaert M, Weng Z, Workman C, Ye C, Zhu Z. (2005) Assessing computational tools for the discovery of transcription factor binding sites. Nature Biotechnology, Vol 23, 137-144. [Abstract]
  • Shu-Hsien Sheu, Taner Kaya, David J. Waxman, and Sandor Vajda. Exploring the Binding Site Structure of PPAR? Ligand-Binding Domain by Computational Solvent Mapping. Biochemistry, 2005, 44, 1193-1209. [Abstract]
  • Shu-Hsien Sheu, David R. Lancia Jr, Karl Clodefelter, Melissa R. Landon and Sandor Vajda. PRECISE: a Database of Predicted and Consensus Interaction Sites in Enzymes. Nucleic Acids Research, 2005 Jan 1; Vol 33 Database Issue:D206-11. [Abstract][Full Text]
  • Daniel Segrè, Alexander DeLuna, George M. Church and Roy Kishony. Modular epistasis in yeast metabolism. Nature Genetics (2005), 37(1), 77-83. [Abstract]
  • Daniel Segrè. Ventimila geni sotto i mari dei tropici (Review, in Italian). Darwin (2005) May-June, 56-61.
  • Daniel Segrè. Life as a cellular automaton (Review of the The Principles of Life by Tibor Gánti). Journal of Biogeography (in press)

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