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From CAGT

Publications 2008 - CAGT

  • Pierce B., Weng Z. A combination of rescoring and refinement significantly improves protein docking performance,, Proteins 2008, 72(1):270-279 [Abstract][PDF]
  • Johnson DS, Li W, Gordon DB, Bhattacharjee A, Curry B, Ghosh J, Brizuela L, Carroll JS, Brown M, Flicek P, Koch CM, Dunham I, Bieda M, Xu X, Farnham PJ, Kapranov P, Nix DA, Gingeras TR, Zhang X, Holster H, Jiang N11, Green R, Song JS, McCuine SA, Anton E, Nguyen L, Trinklein ND, Ye Z, Ching K, Hawkins D, Ren B, Scacheri PC, Rozowsky J, Karpikov A, Euskirchen G, Weissman S, Gerstein M, Snyder M, Yang A, Moqtaderi Z, Hirsch H, Shulha HP, Fu Y, Weng Z, Struhl K, Myers RM, Lieb JS, and Liu XS. Systematic evaluation of variability in ChIP-chip experiments using predefined DNA targets,, Genome Research 2008, 18, 393-403. [Abstract][PDF]
  • Zhang X., Guo C., Chen Y., Shulha H. P., Schnetz M. P., LaFramboise T., Bartels C. F., Markowitz S., Weng Z., Scacheri P. C., Wang Z. Epitope tagging of endogenous proteins for genome-wide ChIP-chip studies,, Nat Methods 2008, 5(2):163-5 [Abstract][PDF]
  • Hwang H., Pierce B., Mintseris J., Janin J., Weng Z. Protein-protein docking benchmark version 3.0,, Proteins 2008, 73(3):705-709 [Abstract][PDF]
  • Weng Z., Guigo R. In silico meets in vivo,, Genome Biol. 2008, Feb 25;9(2):302 [Abstract][PDF]
  • Ghildiyal M., Seitz H., Horwich M.D., Li C., Du T., Lee S., Xu J., Kittler E.L., Zapp M.L., Weng Z., Zamore P.D. Endogenous siRNAs Derived from Transposons and mRNAs in Drosophila Somatic Cells,, Science 2008, May 23;320(5879):1077-81 [Abstract][PDF]
  • Yutao Fu, Manisha Sinha, Craig L. Peterson, and Zhiping Weng. The Insulator binding protein CTCF positions 20 nucleosomes around its binding sites across the human genome,, PLoS Genetics 2008, 4(7) [Abstract][PDF]
  • G. Benson and D.Y.F. Mak. Proceedings of the 15th String Processing and Information Retrieval Symposium,, SPIRE 2008, Melbourne, Australia, [PDF]
  • G. Benson and D.Y.F. Mak. Exact Distribution of a Spaced Seed Statistic for applications in DNA Repeat Detection,, Proceedings of the 2008 International Workshop on Applied Probability, IWAP 2008, Compiè gne, France, July [PDF]
  • Evan S. Snitkin and Daniel Segrè. Optimality criteria for the prediction of metabolic fluxes in yeast mutants,, Genome Informatics 2008, 20: 123-134 [PDF]
  • William J. Riehl and Daniel Segrè. Optimal metabolic regulation using a constraint-based model,, Genome Informatics 2008, 20: 159-170 [PDF]
  • Hsuan-Chao Chiu and Daniel Segrè. Comparative determination of biomass composition in differentially active metabolic states,, Genome Informatics 2008, 20: 171-182 [PDF]
  • Evan S. Snitkin, Aimee M. Dudley, Daniel M. Janse, Kaisheen Wong, George M. Church, and Daniel Segrè. Model-driven analysis of experimentally determined growth phenotypes for 465 yeast gene deletion mutants under 16 different conditions,, Genome Biology 2008, 9:R140 [Full Text][PDF]
  • Linghu B, Snitkin ES, Holloway DT, Gustafson AM, Xia Y, DeLisi C. High-precision high-coverage functional inference from integrated data sources,, BMC Bioinformatics 2008, 9: 119 [PDF]
  • Kim PM, Sboner A, Xia Y, Gerstein M. The role of disorder in interaction networks: a structural analysis,, Molecular Systems Biology 2008, 4: 179 [PDF]
  • Franzosa E, Xia Y. Structural perspectives on protein evolution,, Annual Reports in Computational Chemistry 2008, 4: 3-21 [Abstract]
  • Wang Y, Xia Y. Condition specific subnetwork identification using an optimization model,, Lecture Notes in Operations Research 2008, 9: 333-340 [PDF]
  • Yam AY, Xia Y, Lin HTJ, Burlingame A, Gerstein M, Frydman J. Defining the TRiC/CCT interactome links chaperonin function to stabilization of newly made proteins with complex topologies,, Nature Structural & Molecular Biology 2008, 15: 1255-1262 [PDF]

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