Home      Labs      Publications      People      Tools   

From CAGT

Publications 2002 - CAGT

  • Kasif S, Weng Z, Derti A, Beigel R, DeLisi C. A computational framework for optimal masking in the synthesis of oligonucleotide microarrays. Nucleic Acids Res. 2002 Oct 15;30(20):e106. PMID: 12384608 [Abstract][Full Text]
  • Zheng Y, Roberts RJ, Kasif S. Genomic functional annotation using co-evolution profiles of gene clusters. Genome Biol. 2002 Oct 10;3(11):RESEARCH0060. Epub 2002 Oct 10. PMID: 12429059 [Abstract][Full Text]
  • Zheng Y, Szustakowski JD, Fortnow L, Roberts RJ, Kasif S. Computational identification of operons in microbial genomes. Genome Res. 2002 Aug;12(8):1221-30. PMID: 12176930 [Abstract][Full Text]
  • Walker M, Pavlovic V, Kasif S A comparative genomic method for computational identification of prokaryotic translation initiation sites. Nucleic Acids Res. 2002 Jul 15;30(14):3181-91. PMID: 12136100 [Abstract][Full Text]
  • Pavlovic V, Garg A, Kasif S. A Bayesian framework for combining gene predictions. Bioinformatics. 2002 Jan;18(1):19-27. PMID: 11836207 [Abstract][Full Text]
  • Yanai I, DeLisi C. The society of genes: networks of functional links between genes from comparative genomics. Genome Biol. 2002 Oct 25;3(11):research0064. Epub 2002 Oct 25. [Abstract][Full Text]
  • Kasif S, Weng Z, Derti A, Beigel R, DeLisi C. A computational framework for optimal masking in the synthesis of oligonucleotide microarrays. Nucleic Acids Res. 2002 Oct 15;30(20):e106. [Abstract][Full Text]
  • Harrison R, DeLisi C. Condition specific transcription factor binding site characterization in Saccharomyces cerevisiae. Bioinformatics. 2002 Oct;18(10):1289-96. [Abstract][Full Text]
  • Yanai I, Mellor JC, DeLisi C. Identifying functional links between genes using conserved chromosomal proximity. Trends Genet. 2002 Apr;18(4):176-9. [Abstract][Full Text]
  • Mellor JC, Yanai I, Clodfelter KH, Mintseris J, DeLisi C. Predictome: a database of putative functional links between proteins. Nucleic Acids Res. 2002 Jan 1;30(1):306-9. [Abstract][Full Text]
  • Weng Z, DeLisi C. Protein therapeutics: promises and challenges for the 21st century. Trends Biotechnol. 2002 Jan;20(1):29-35. Review. [Abstract][Full Text]
  • Harrison R, DeLisi C. A hypothesis driven approach to condition specific transcription factor binding site characterization in S.C. SAC 2002:151-158. [Abstract]
  • Yanai I, Mellor JC, DeLisi C. Beyond Sequence Similarity: Functional Analysis in the Age of the Genome. Evolution of Genomic Technologies, Functional Genomics Series, vol 1, eds. McCormack S, Galas D. 2002.
  • Kasif, S., Weng, Z. Derti, A., Beigel, R. & DeLisi, C. (2002) A Computational Framework for Optimal Masking in the Synthesis of Oligonucleotide Microarrays. Nucleic Acid Research 30(20): e106. [Abstract][Full Text]
  • Wong, J. Y., Weng, Z., Moll, S., Kim, S. & Brown, C. (2002) Identification and validation of a novel cell-recognition site (KNEED) on the 8th type III domain of fibronectin. Biomaterials 23: 3865-3870. [Abstract]
  • Brown, C.T., Weng, Z., Zhang, H. & Wong, J.Y. (2002) Mutational Analysis Verifies that "KNEED" Sequence of Fibronectin Participates in Cell-substrate Interactions. Polym. Prep. 43(2): 754. [Abstract]
  • Frith, M.C., Hansen, U. & Weng, Z. (2002) A Gibbs Sampling Algorithm to Detect Clustered Cis-elements. Proceedings of the Third International Conference on Bioinformatics of Genome Regulation and Structure (1) 59-61.
  • Anderson, R. & Weng, Z. Bioinformatics. Encyclopedia of Sciences, 2002.
  • J.D. Szustakowski and Z. Weng. (2002) K2: Protein structure comparison and their statistical significance. Evolutionary Computation in Bioinformatics. Edited by G. Fogel and D. Corne, Morgan Kaufman.
  • Betley JN, Frith MC, Graber JH, Choo S, Deshler JO. (2002) A ubiquitous and conserved signal for RNA localization in chordates. Curr Biol. 12(20):1756-61. [Abstract][Full Text]
  • Yu Zheng, Joseph D. Szustakowski, Lance Fortnow, Rich Roberts, Simon Kasif. (2002) Computational identification of operons in microbial genomes. Genome Research 12(8):1221-30. [Abstract][Full Text]
  • Martin C. Frith, John L. Spouge, Ulla Hansen, Zhiping Weng. (2002) Statistical significance of clusters of motifs represented by position specific scoring matrices in nucleotide sequences. Nucleic Acids Research 30(14):3214-24. [Abstract][Full Text]
  • Chen, R. & Weng, Z. (2002) Docking Unbound Proteins Using Shape Complementarity, Desolvation, and Electrostatics. Proteins: Structure, Function, and Genetics. 47:281-294. [Abstract]
  • Barbara L. Resendes, Nahid G. Robertson, Joseph D. Szustakowski, Robert J. Resendes, Zhiping Weng, and Cynthia C. Morton (2002) Gene Discovery in the Auditory System: Characterization of Additional Cochlear-Expressed Sequences. Journal of the Association for Research in Otolaryngology 3(1):45-53. [Abstract]
  • Haverty, PM., Weng, Z., Hsiao, L., Best, N., Auerbach, K., Jensen, RV., Gullans, SR. 2002) HugeIndex: A Database of High Density Oligonucleotide Array Data from Normal Human Tissues Nucleic Acids Research. 30(1): 214-217. [Abstract][Full Text]
  • Camacho C, and Vajda S. Protein-protein association kinetics and protein docking. Curr Opin Struct Biol. 12(1):36-40, 2002. [Abstract]
  • Dennis S, Kortvelyesi T, and Vajda S. Computational mapping identifies the binding sites of organic solvents on proteins. Proc. Natl. Acad. Sci. USA. 99(7): 4290-4295, 2002. [Abstract][Full Text]
  • Dennis S, and Vajda S. Semiglobal simplex optimization and its application to determining the preferred solvation sites of proteins. J. Comp. Chem. 23(3): 319-334, 2002. [Abstract]
  • Peter P. Valko, and Sandor Vajda. Inversion of Noise-free Laplace Transforms: Towards a Standardized Set of Test Problems. Inverse Problems in Engineering Volume 10, Number 5, Year 2002, pp. 467 - 483. [Abstract]
  • G. Benson. A new distance measure for comparing sequence profiles based on path lengths along an entropy surface, Proceedings of the European Conference on Computational Biology 2002, Bioinformatics, 18: Supplement 2, S44-S52, 2002. [Abstract][Full Text]
  • D. Marras, L. Bruggeman, N. Tanji, M. Mansukhani, A. Cara, M. Ross, G. Benson, V. D'Agati, M. Klotman, and P. Klotman. Evolution of HIV-1 quasispecies in kidney epithelium in HIV-associated nephropathy, Nature Medicine, 8:522-526, 2002. [Abstract][Full Text]
  • J. Walewski, J. Gutierrez, W. Branch-Elliman, D. Stump, T. Keller, A. Rodriguez, G. Benson, and A. Branch. Mutation Master: Profiles of Substitutions in Hepatitis C Virus RNA of the Core, Alternate Reading Frame and NS2 Coding Regions, RNA, 8:557-571, 2002. [Abstract][Full Text]

Protein Engineering