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Publications 2009 - CAGT

  • Haidar, JN., Pierce, B., Yu, Y., Tong, W., Li, M., and Weng, Z. Structure-Based Design of a T-Cell Receptor Leads to Nearly 100-Fold Improvement in Binding Affinity for pepMHC, Proteins 2009, 74(4):948-960 [Abstract][PDF]
  • Hwang H., Pierce B. and Weng Z. Protein-Protein Docking, In Ruth Nussinov, Computational Protein-Protein Interactions 2009, CRC Press. In Press.
  • S. Fishman, S. Factor, C. Balestrieri, X. Fan, A. DiBisceglie, S. Desai, G. Benson, and A. Branch. Mutations in the Hepatitis C Virus Core Gene Are Associated with Advanced Liver Disease and Hepatocellular Carcinoma, Clinical Cancer Research 2009, 15:3205-3213 doi: 10.1158/1078-0432.CCR-08-2418 [Abstract]
  • D.Y.F. Mak and G. Benson. All Hits All The Time: Parameter Free Calculation of Spaced Seed Sensitivity, Bioinformatics 2009, 25(3):302-308 doi: 10.1093/bioinformatics/btn643 [Abstract]
  • D.Y.F. Mak and G. Benson. Consensus RNA Secondary Structure Prediction by Ranking k-Length Stems, Proceedings of the 2009 International Conference on Bioinformatics and Computational Biology (BIOCOMP'09) 2009, Las Vegas, Nevada [PDF]
  • Varun Mazumdar, Evan Snitkin, Salomon Amar and Daniel Segrè. Metabolic network model of a human oral pathogen, Journal of Bacteriology 2009, Jan; 191(1), 74-90 [Abstract][PDF][Cover]
  • Franzosa E, Linghu B, Xia Y. Computational reconstruction of protein-protein interaction networks: algorithms and issues, Methods in Molecular Biology 2009, 541: 89-100 [PDF]
  • Xia Y, Franzosa EA, Gerstein MB. Integrated assessment of genomic correlates of protein evolutionary rate, PLoS Computational Biology 2009, 5: e1000413 [PDF]
  • Franzosa EA, Xia Y. Structural determinants of protein evolution are context-sensitive at the residue level, Molecular Biology and Evolution 2009, 26: 2387-2395 [PDF]
  • Linghu B, Snitkin ES, Hu Z, Xia Y, DeLisi C. Genome-wide prioritization of disease genes and identification of disease-disease associations from an integrated human functional linkage network, Genome Biology 2009, 10: R91 [PDF]
  • Voevodski K, Teng SH, Xia Y. Finding local communities in protein networks, BMC Bioinformatics 2009, 10: 297 [PDF]
  • Wang Y, Zhang XS, Xia Y. Predicting eukaryotic transcriptional cooperativity by Bayesian network integration of genome-wide data, Nucleic Acids Research 2009, 37: 5943-5958 [PDF]
  • Wang Y, Wang RS, Joshi T, Xu D, Zhang XS, Chen L, Xia Y. A linear programming framework for inferring gene regulatory networks by integrating heterogeneous data, Handbook of Research on Computational Methodologies in Gene Regulatory Networks 2009, 450-475 [PDF]
  • Pan C, Gao Q, Xie J, Xia Y, Epstein IR. Precipitation patterns with polygonal boundaries between electrolytes, Physical Chemistry Chemical Physics 2009, 11: 11033-11039 [PDF]
  • Voevodski K, Teng SH, Xia Y. Spectral affinity in protein networks, BMC Systems Biology 2009. In Press.

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