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Publications 2007 - CAGT

  • Reddy TE, Shakhnovich BE, Roberts DS, Russek SJ, DeLisi, C. Positional clustering improves computational binding site detection and identifies novel cis-regulatory sites in mammalian GABAA receptor subunit genes. Nucleic Acids Res. 2007 February;35(3):e20. [Abstract][Full Text]

  • Reddy TE, DeLisi C, Shakhnovich, BE. Binding Site Graphs: A New Graph Theoretical Framework for Prediction of Transcription Factor Binding Sites. PLoS Computational Biology, Vol. preprint, No. 2007 (1 April 2007), e90.eor. [Abstract][Full Text][Map of Transcription Factor Binding Motifs in S. cerevisiae]

  • Tullai JW, Schaffer ME, Mullenbrock S, Sholder G, Kasif S, Cooper GM. Immediate-early and delayed primary response genes are distinct in function and genomic architecture, J Biol Chem. 2007 Jun 15; [Abstract][Full Text]
  • Liu M, Liberzon A, Kong SW, Lai WR, Park PJ, Kohane IS, Kasif S. Network-based analysis of affected biological processes in type 2 diabetes models. PLoS Genet. 2007 Jun 15;3(6):e96. PMID: 17571924 [Abstract][Full Text]
  • Nariai N, Kolaczyk ED, Kasif S. Probabilistic protein function prediction from heterogeneous genome-wide data. PLoS ONE. 2007 Mar 28;2:e337. PMID: 17396164 [Abstract][Full Text]
  • Zhang L, Kasif S, Cantor AC. Quantifying DNA-protein binding specificities by using oligonucleotide mass tags and mass spectroscopy. Proc Natl Acad Sci U S A. 2007 Feb 27;104(9):3061-6. Epub 2007 Feb 20. PMID: 17360609 [Abstract][Full Text]
  • Tullai JW, Chen J, Schaffer ME, Kamenetsky E, Kasif S, Cooper GM. Glycogen synthase kinase-3 represses cyclic AMP response element-binding protein (CREB)-targeted immediate early genes in quiescent cells. J Biol Chem. 2007 Mar 30;282(13):9482-91. Epub 2007 Feb 3. Erratum in: J Biol Chem. 2007 May 11;282(19):14684. PMID: 17277356 [Abstract][Full Text]
  • Denise Y.F. Mak, Gary Benson (2007) All hits all the time: parameter free calculation of seed sensitivity, APBC 2007 conference in Hon Kong
  • B. Kennedy, I. Lim, Gary Benson, J. Vincent, M. Ferenc, B. Heinrich, L. Jarzylo, H.-Y. Man, and J. Deshler. 3'-UTR SIRF: A Database for Identifying Clusters of Short Interspersed Repeats in 3' Untranslated Regions,, BMC Bioinformatics 2007, 8:274 doi:10.1186/1471-2105-8-274 [Abstract][Full Text]
  • J. Giordano, Y. Ge, Y. Gelfand, G. Benson, and P. Warburton. Evolutionary History of Mammalian Transposons Determined by Genome-wide Defragmentation, PLOS Computational Biology, (doi:) [Abstract][Full Text]
  • J. Laidlaw, Y. Gelfand, K.-W. Ng, H. Garner, R. Ranganathan, G. Benson, and J. Fondon, III. Elevated Basal Slippage Mutation Rates among the Canidae, Journal of Heredity, (doi:10.1093/jhered/esm017), PLoS Comput Biol. 2007 July; 3(7): e137. doi: 10.1371/journal.pcbi.0030137 [Abstract][Full Text]
  • W.Tembe, N. Zavaljevski, E. Bode, C. Chase, J. Geyer, L. Wasieloski, G. Benson and J. Reifman. Oligonucleotide Fingerprint Identification for Microarray-Based Pathogen Diagnostic Assays, Bioinformatics 2007 23(1):5-13; doi:10.1093/bioinformatics/btl549. [Abstract][Full Text]
  • Alon N, Asodi V, Cantor C, Kasif S, Rachlin J. Multi-node graphs: a framework for multiplexed biological assays. J Comput Biol. 2006 Dec;13(10):1659-72. PMID: 17238837 [Abstract][Full Text]
  • Faith JJ, Hayete B, Thaden JT, Mogno I, Wierzbowski J, Cottarel G, Kasif S, Collins JJ, Gardner TS. Large-Scale Mapping and Validation of Escherichia coli, Transcriptional Regulation from a Compendium of Expression Profiles., PLoS Biol. 2007 Jan 9;5(1):e8 PMID: 17214507 [Abstract][Full Text]
  • Zhang J, Kasif S, Cantor CR. Proc Natl Acad Sci U S A, 2007, to appear.
  • Wiehe K, Pierce B, Tong W, Hwang H, Mintseris J, Weng Z (2007) The Performance of ZDOCK and ZRANK in Rounds 6-11 of CAPRI Proteins 69(4), 719-725. [Abstract]
  • Peckham HE, Thurman RE, Fu Y, Stamatoyannopoulos JA, Noble WS, Struhl K, Weng Z(2007) Nucleosome Positioning Signals in Genomic DNA. Genome Research, 17, 1170-1177. [Abstract]
  • Mintseris J, Pierce B, Wiehe K, Anderson R, Chen R, and Weng Z (2007) Integrating Statistical Pair Potentials into Protein Complex Prediction. Proteins, 69(3), 511-520. [Abstract]
  • Xi H., Shulha H.P., Lin J.M., Vales T.R., Fu Y., Bodine D.M., McKay R.D.J, Chenoweth J.G., Tesar P.J., Furey T.S., Ren B., Weng Z.+, Crawford G.E.+ (2007) Identification and characterization of cell type-specific and ubiquitous chromatin regulatory structures in the human genome. PLoS Genetics, 8, 8-20. [Abstract][Full Text]
  • The ENCODE Consortium (2007) Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project. Nature 447, 799-816. Weng Z. was as a co-chair for the ENCODE Transcriptional Regulation analysis group and a co-corresponding author of this Nature article. [Abstract]
  • Trinklein ND*, Karaoz U*, Wu J*, Halees A*, Aldred SF, Collin PJ, Zheng D, Zhang ZD, Gerstein M, Snyder M, Myers RM+, Weng Z+ (2007) Integrated analysis of experimental datasets reveals many novel promoters in 1% of the human genome. *Authors contributed equally, +Co-corresponding authors,Genome Research 17, 720-731.
  • Christoph M. Koch, Robert M. Andrews, Paul Flicek, Shane C. Dillon, Ulas Karaoz, Gayle K. Clelland, Sarah Wilcox, David M. Beare, Joanna C. Fowler, Phillippe Couttet, Keith D. James, Gregory C. Lefebvre, Alexander W. Bruce, Oliver M. Dovey, Peter D. Ellis, Pawandeep Dhami, Cordelia F. Langford, Zhiping Weng, Ewan Birney, Nigel P. Carter, David Vetrie, and Ian Dunham (2007) The landscape of histone modifications across 1% of the human genome in five human cell lines. Genome Research 17, 691-707. [Abstract][Full Text]
  • Zhang ZD, Paccanaro A, Fu Y, Weissman S, Weng Z, Chang J, Snyder M, Gerstein MB (2007) Statistical analysis of the genomic distribution and correlation of regulatory elements in the ENCODE regions. Genome Research 17, 787-97. [Abstract][Full Text]
  • Heintzman ND, Stuart RK, Hon G, Fu Y, Ching CW, Hawkins RD, Barrera LO, Van Calcar S, Qu C, Ching KA, Wang W, Weng Z, Green RD, Crawford GE, Ren B (2007) Distinct and predictive chromatin signatures of transcriptional promoters and enhancers in the human genome. Nature Genetics, 39(3):311-8. [Abstract]
  • Xi H, Yu Y, Foley J, Halees A, Weng Z (2007) Analysis of Overrepresented Motifs in Human Core Promoters Reveals Dual Regulatory Roles of YY1. Genome Research 17, 798-806. [Abstract][Full Text]
  • Lin J, Collins PJ, Trinklein ND, Fu Y, Xi H, Myers RM, Weng Z (2007) Transcription Factor Binding and Modified Histones in Human Bidirectional Promoters. Genome Research 17, 818-827. [Abstract][Full Text]
  • Pierce B, Weng Z (2007) ZRANK: Reranking Protein Docking Predictions with an Optimized Energy Function. Proteins 67(4): 1078-1086. [Abstract]
  • Pierce B, Phillips AT, Weng Z (2007) Structure Prediction of Protein Complexes. In Xu Y, Xu D & Liang J. (Eds.), Computational Methods for Protein Structure Prediction and Modeling Volume 2: Structure Prediction. (pp. 109-134). New York: Springer. [Full Text]
  • Matthew A. Wright, Peter Kharchenko, George M. Church and Daniel Segrè, Chromosomal periodicity of evolutionarily conserved gene pairs, Proc. Natl. Acad. Sci. USA (2007), 104 (25), 10559-10564. [Abstract][Full Text]
  • McClellan AJ, Xia Y, Deutschbauer AM, Davis RW, Gerstein M, Frydman J. Diverse cellular functions of the Hsp90 molecular chaperone uncovered using systems approaches. Cell 131: 121-135 (2007). [PDF] [Highlighted in Nature Structural & Molecular Biology, Faculty of 1000]

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