Search Publications

2007 Publications

Sam L, Liu Y, Li J, Friedman C, Lussier YA.  2007.  Discovery of protein interaction networks shared by diseases. Pac Symp Biocomput. :76-87. Go to Pubmed
Joshi R, Passner JM, Rohs R, Jain R, Sosinsky A, Crickmore MA, Jacob V, Aggarwal AK, Honig B, Mann RS.  2007.  Functional specificity of a Hox protein mediated by the recognition of minor groove structure. Cell. 131(3):530-43. Go to Pubmed
Ziv E, Nemenman I, Wiggins CH.  2007.  Optimal signal processing in small stochastic biochemical networks. PLoS One. 2(10):e1077. Go to Pubmed
Kundaje A, Lianoglou S, Li X, Quigley D, Arias M, Wiggins C, Zhang L, Leslie C.  2007.  Learning regulatory programs that accurately predict differential expression with MEDUSA. Ann N Y Acad Sci. 1115:178-202. Go to Pubmed
Margolin A, Califano A.  2007.  Theory and limitations of genetic network inference from microarray data. Ann N Y Acad Sci. 1115:51-72. Go to Pubmed
David LA, Wiggins CH.  2007.  Benchmarking of dynamic Bayesian networks inferred from stochastic time-series data. Ann N Y Acad Sci. 1115:90-101. Go to Pubmed
Bussemaker HJ, Ward LD, Boorsma A.  2007.  Dissecting complex transcriptional responses using pathway-level scores based on prior information. BMC Bioinformatics. 8 Suppl 6:S6. Go to Pubmed
Bales ME, Lussier Y, Johnson SB.  2007.  Topological analysis of large-scale biomedical terminology structures. J Am Med Inform Assoc. 14(6):788-97. Go to Pubmed
Tao Y, Sam L, Li J, Friedman C, Lussier YA.  2007.  Information theory applied to the sparse gene ontology annotation network to predict novel gene function. Bioinformatics. 23(13):i529-38. Go to Pubmed
Lim WKeat, Wang K, Lefebvre C, Califano A.  2007.  Comparative analysis of microarray normalization procedures: effects on reverse engineering gene networks. Bioinformatics. 23(13):i282-8. Go to Pubmed
Rzhetsky A, Wajngurt D, Park N, Zheng T.  2007.  Probing genetic overlap among complex human phenotypes. Proc Natl Acad Sci U S A. 104(28):11694-9. Go to Pubmed
Melvin I, Ie E, Kuang R, Weston J, Stafford WNoble, Leslie C.  2007.  SVM-Fold: a tool for discriminative multi-class protein fold and superfamily recognition. BMC Bioinformatics. 8 Suppl 4:S2. Go to Pubmed
Yagoda N, von Rechenberg M, Zaganjor E, Bauer AJ, Yang WSeok, Fridman DJ, Wolpaw AJ, Smukste I, Peltier JM, J Boniface J et al.  2007.  RAS-RAF-MEK-dependent oxidative cell death involving voltage-dependent anion channels. Nature. 447(7146):864-8. Go to Pubmed
Cokol M, Rodriguez-Esteban R, Rzhetsky A.  2007.  A recipe for high impact. Genome Biol. 8(5):406. Go to Pubmed
Chen JL, Liu Y, Sam LT, Li J, Lussier Y.  2007.  Evaluation of high-throughput functional categorization of human disease genes. BMC Bioinformatics. 8 Suppl 3:S7. Go to Pubmed
Cokol M, Iossifov I, Rodriguez-Esteban R, Rzhetsky A.  2007.  How many scientific papers should be retracted? EMBO Rep. 8(5):422-3. Go to Pubmed
Sosinsky A, Honig B, Mann RS, Califano A.  2007.  Discovering transcriptional regulatory regions in Drosophila by a nonalignment method for phylogenetic footprinting. Proc Natl Acad Sci U S A. 104(15):6305-10. Go to Pubmed
Szatmari P, Paterson AD, Zwaigenbaum L, Roberts W, Brian J, Liu X-Q, Vincent JB, Skaug JL, Thompson AP, Senman L et al.  2007.  Mapping autism risk loci using genetic linkage and chromosomal rearrangements. Nat Genet. 39(3):319-28. Go to Pubmed
Bussemaker H, Foat BC, Ward LD.  2007.  Predictive modeling of genome-wide mRNA expression: from modules to molecules. Annu Rev Biophys Biomol Struct. 36:329-47. Go to Pubmed
Anastassiou D.  2007.  Computational analysis of the synergy among multiple interacting genes. Mol Syst Biol. 3:83. Go to Pubmed
Greil F, de Wit E, Bussemaker H, van Steensel B.  2007.  HP1 controls genomic targeting of four novel heterochromatin proteins in Drosophila. EMBO J. 26(3):741-51. Go to Pubmed
Lussier YA, Liu Y.  2007.  Computational approaches to phenotyping: high-throughput phenomics. Proc Am Thorac Soc. 4(1):18-25. Go to Pubmed
Varma H, Voisine C, C DeMarco T, Cattaneo E, Lo D, Hart AC, Stockwell BR.  2007.  Selective inhibitors of death in mutant huntingtin cells. Nat Chem Biol. 3(2):99-100. Go to Pubmed