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Publications 2003 - CAGT

  • Su Y, Murali TM, Pavlovic V, Schaffer M, Kasif S. RankGene: identification of diagnostic genes based on expression data. Bioinformatics. 2003 Aug 12;19(12):1578-9. PMID: 12912841 [Abstract][Full Text]
  • Wu J, Kasif S, DeLisi C. Identification of functional links between genes using phylogenetic profiles. Bioinformatics. 2003 Aug 12;19(12):1524-30. PMID: 12912833 [Abstract][Full Text]
  • Zhang L, Pavlovic V, Cantor CR, Kasif S. Human-mouse gene identification by comparative evidence integration and evolutionary analysis. Genome Res. 2003 Jun;13(6A):1190-202. Epub 2003 May 12. PMID: 12743024 [Abstract][Full Text]
  • Pervouchine DD, Graber JH, Kasif S. On the normalization of RNA equilibrium free energy to the length of the sequence. Nucleic Acids Res. 2003 May 1;31(9):e49. PMID: 12711694 [Abstract][Full Text]
  • Stitziel NO, Tseng YY, Pervouchine D, Goddeau D, Kasif S, Liang J. Structural location of disease-associated single-nucleotide polymorphisms. J Mol Biol. 2003 Apr 11;327(5):1021-30. PMID: 12662927 [Abstract]
  • Letovsky S, Kasif S. Predicting protein function from protein/protein interaction data: a probabilistic approach. Bioinformatics. 2003;19 Suppl 1:i197-204. PMID: 12855458 [Abstract][Full Text]
  • Murali TM, Kasif S. Extracting conserved gene expression motifs from gene expression data. Pac Symp Biocomput. 2003;:77-88. PMID: 12603019 [Abstract][Full Text]
  • Shakhnovich BE, Harvey JM, Comeau S, Lorenz D, DeLisi C, Shakhnovich E. ELISA: structure-function inferences based on statistically significant and evolutionarily inspired observations. BMC Bioinformatics. 2003 Sep 2;4(1):34. [Abstract][Full Text]
  • Wu J, Kasif S, DeLisi C. Identification of functional links between genes using phylogenetic profiles. Bioinformatics. 2003 Aug 12;19(12):1524-30. [Abstract][Full Text (pdf)]
  • Powell CA, Spira A, Derti A, DeLisi C, Liu G, Borczuk A, Busch S, Sahasrabudhe S, Chen Y, Sugarbaker D, Bueno R, Richards WG, Brody JS. Gene expression in lung adenocarcinomas of smokers and nonsmokers. Am J Respir Cell Mol Biol. 2003 Aug;29(2):157-62. Epub 2003 Feb 21. [Abstract][Full Text]
  • Shakhnovich BE, Dokholyan NV, DeLisi C, Shakhnovich EI. Functional fingerprints of folds: evidence for correlated structure-function evolution. J Mol Biol. 2003 Feb 7;326(1):1-9. [Abstract][Full Text]
  • Bhanot G, Louzoun Y, Zhu J, DeLisi C. The importance of thermodynamic equilibrium for high throughput gene expression arrays. Biophys J. 2003 Jan;84(1):124-35. [Abstract][Full Text]
  • Peters, B., Tong, W., Sidney, J., Sette, A. & Weng, Z. (2003) Examining the Independent Binding Assumption for Binding of Peptide Epitopes to MHC-I Molecules. Bioinformatics. 19:1765-1772. [Abstract][Full Text]
  • Halees, A.S., Leyfer, D. & Weng, Z. (2003) PromoSer: A Large-scale Mammalian Promoter and Transcription Start Site Identification Service. Nucleic Acids Res. 2003 Jul 1;31(13):3554-9. [Abstract][Full Text]
  • Frith, M.C., Li, M.C. & Weng, Z. (2003) Cluster-Buster: Finding Dense Clusters of Motifs in DNA Sequences. Nucleic Acids Res. 2003 Jul 1;31(13):3666-8. [Abstract][Full Text]
  • Li, L.*, Chen, R.* & Weng, Z. (2003) *Joint First Authors RDOCK: Refinement of Rigid-body Protein Docking Predictions. Proteins. 53:693-707. [Abstract]
  • Mintseris, J. & Weng, Z. (2003) Atomic Contact Vectors in Protein-Protein Recognition. Proteins. 53:629-639. [Abstract]
  • Chen, R., Tong, W., Mintseris, J., Li, L. & Weng, Z. (2003) ZDOCK Predictions for the CAPRI Challenge. Proteins. 2003 Jul 1;52(1):68-73. [Abstract]
  • Chen, R., Li, L. & Weng, Z. (2003) ZDOCK: An Initial-stage Protein Docking Algorithm. Proteins. 2003 Jul 1;52(1):80-7. [Abstract]
  • Chen, R., Mintseris, J., Janin, J. & Weng, Z. (2003) A Protein-Protein Docking Benchmark. Proteins. 2003 Jul 1;52(1):88-91. [Abstract]
  • Chen, R. & Weng, Z. (2003) A Novel Shape Complementarity Scoring Function For Protein-Protein Docking. Proteins. 2003 May 15;51(3):397-408. [Abstract]
  • Hu, Z., Frith, M., Niu, T. & Weng, Z. (2003) SeqVISTA: A Graphical Tool for Sequence Feature Visualization and Comparison BMC Bioinformatics 4: 1. [Abstract][Full Text]
  • J.C. Prasad, S.R. Comeau, S. Vajda and C.J. Camacho. Consensus alignment for reliable framework prediction in homology modeling. BIOINFORMATICS Vol. 19 no. 13 2003, pages 1682-1691. [Abstract][Full Text]
  • Michael Silberstein, Sheldon Dennis, Lawrence Brown, Tamas Kortvelyesi Karl Clodfelter and Sandor Vajda. Identification of Substrate Binding Sites in Enzymes by Computational Solvent Mapping. J. Mol. Biol., 332, 1095-113, 2003. [Abstract]
  • Janin J, Henrick K, Moult J, Eyck L, Sternberg M, Vajda S, Vakser I, and Wodak S. CAPRI: A critical assessment of predicted interactions. Proteins, 52:2-9, 2003. [Abstract]
  • Murphy J, Gatchell D, Prasad J, and Vajda S. Combination of scoring functions improves discrimination in protein-protein docking. Proteins, 3 :840-854, 2003. [Abstract]
  • Kortvelyesi T, Silberstein M, Dennis S, and Vajda S. Improved mapping of protein binding sites. Journal of Computer-Aided Molecular Design, 17: 173-186, 2003. [Abstract]
  • Kortvelyesi T, Dennis S, Silberstein M, Brown III L, and Vajda S. Algorithms for computational solvent mapping of proteins. Proteins, 51: 340-351, 2003. [Abstract]
  • Camacho C, and Gatchell D. Successful discrimination of protein interactions. Proteins, 52:92-97, 2003. [Abstract]
  • G. Benson. Composition Alignment, Proceedings of the Workshop on Algorithms in Bioinformatics 2003, Budapest, Hungary, September 2003.
  • Daniel Segr?, Jeremy Zucker, Jeremy Katz, Xiaoxia Lin, Patrik D'haeseleer, Wayne P. Rindone, Peter Kharchenko, Dat Nguyen, Matthew A. Wright and George M. Church. From annotated genomes to metabolic flux models and kinetic parameter fitting. Omics (2003), 7(3), 301-316. [Abstract]
  • Daniel Segre', Dennis Vitkup and George Church. Analysis of optimality in natural and perturbed metabolic networks. Proc. Natl. Acad. Sci. USA (2002), 99(23), 15112-15117. [Abstract][Full Text]
  • Barak Shenhav, Daniel Segre' and Doron Lancet. Mesobiotic emergence: molecular and ensemble complexity in early evolution. Advances in Complex Systems (2003), 6 (1), 15-35. [Full Text]

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