Search Publications

2008 Publications

Shen Y, Sarin S, Liu Y, Hobert O, Pe'er I.  2008.  Comparing platforms for C. elegans mutant identification using high-throughput whole-genome sequencing. PLoS One. 3(12):e4012. Go to Pubmed
Wang T, Moreno-Vinasco L, Huang Y, Lang GD, Linares JD, Goonewardena SN, Grabavoy A, Samet JM, Geyh AS, Breysse PN et al.  2008.  Murine lung responses to ambient particulate matter: genomic analysis and influence on airway hyperresponsiveness. Environ Health Perspect. 116(11):1500-8. Go to Pubmed
Kundaje A, Xin X, Lan C, Lianoglou S, Zhou M, Zhang L, Leslie C.  2008.  A predictive model of the oxygen and heme regulatory network in yeast. PLoS Comput Biol. 4(11):e1000224. Go to Pubmed
Melvin I, Weston J, Leslie C, Noble WStafford.  2008.  Combining classifiers for improved classification of proteins from sequence or structure. BMC Bioinformatics. 9:389. Go to Pubmed
Boorsma A, Lu X-J, Zakrzewska A, Klis F, Bussemaker H.  2008.  Inferring condition-specific modulation of transcription factor activity in yeast through regulon-based analysis of genomewide expression. PLoS One. 3(9):e3112. Go to Pubmed
Shatkay H, Pan F, Rzhetsky A, W Wilbur J.  2008.  Multi-dimensional classification of biomedical text: toward automated, practical provision of high-utility text to diverse users. Bioinformatics. 24(18):2086-93. Go to Pubmed
Miloushev VZ, Bahna F, Ciatto C, Ahlsen G, Honig B, Shapiro L, Palmer AG.  2008.  Dynamic properties of a type II cadherin adhesive domain: implications for the mechanism of strand-swapping of classical cadherins. Structure. 16(8):1195-205. Go to Pubmed
Sarin S, Prabhu S, M O'Meara M, Pe'er I, Hobert O.  2008.  Caenorhabditis elegans mutant allele identification by whole-genome sequencing. Nat Methods. 5(10):865-7. Go to Pubmed
Hong S-B, Huang Y, Moreno-Vinasco L, Sammani S, Moitra J, Barnard JW, Ma S-F, Mirzapoiazova T, Evenoski C, Reeves RR et al.  2008.  Essential role of pre-B-cell colony enhancing factor in ventilator-induced lung injury. Am J Respir Crit Care Med. 178(6):605-17. Go to Pubmed
Cadeiras M, Bayern M, Burke E, Dedrick R, Gangadin A, Latif F, Latif F, Shahzad K, Shazad K, Sinha A et al.  2008.  Gene expression profiles of patients with antibody-mediated rejection after cardiac transplantation. J Heart Lung Transplant. 27(8):932-4. Go to Pubmed
Hofman JM, Wiggins CH.  2008.  Bayesian approach to network modularity. Phys Rev Lett. 100(25):258701. Go to Pubmed
Rzhetsky A, Seringhaus M, Gerstein M.  2008.  Seeking a new biology through text mining. Cell. 134(1):9-13. Go to Pubmed
Ward LD, Bussemaker H.  2008.  Predicting functional transcription factor binding through alignment-free and affinity-based analysis of orthologous promoter sequences. Bioinformatics. 24(13):i165-71. Go to Pubmed
Dinov ID, Rubin D, Lorensen W, Dugan J, Ma J, Murphy S, Kirschner B, Bug W, Sherman M, Floratos A et al.  2008.  iTools: a framework for classification, categorization and integration of computational biology resources. PLoS One. 3(5):e2265. Go to Pubmed
Piccaluga PPaolo, Califano A, Klein U, Agostinelli C, Bellosillo B, Gimeno E, Serrano S, Solè F, Zang Y, Falini B et al.  2008.  Gene expression analysis provides a potential rationale for revising the histological grading of follicular lymphomas. Haematologica. 93(7):1033-8. Go to Pubmed
Iossifov I, Zheng T, Baron M, T Gilliam C, Rzhetsky A.  2008.  Genetic-linkage mapping of complex hereditary disorders to a whole-genome molecular-interaction network. Genome Res. 18(7):1150-62. Go to Pubmed
Posy S, Shapiro L, Honig B.  2008.  Sequence and structural determinants of strand swapping in cadherin domains: do all cadherins bind through the same adhesive interface? J Mol Biol. 378(4):954-68. Go to Pubmed
Christian SL, Brune C, Sudi J, Kumar RA, Liu S, Karamohamed S, Badner JA, Matsui S, Conroy J, McQuaid D et al.  2008.  Novel submicroscopic chromosomal abnormalities detected in autism spectrum disorder. Biol Psychiatry. 63(12):1111-7. Go to Pubmed
de Wit E, Braunschweig U, Greil F, Bussemaker H, van Steensel B.  2008.  Global chromatin domain organization of the Drosophila genome. PLoS Genet. 4(3):e1000045. Go to Pubmed
Pe'er I, Yelensky R, Altshuler D, Daly MJ.  2008.  Estimation of the multiple testing burden for genomewide association studies of nearly all common variants. Genet Epidemiol. 32(4):381-5. Go to Pubmed
Koehnke J, Jin X, Trbovic N, Katsamba PS, Brasch J, Ahlsen G, Scheiffele P, Honig B, Palmer AG, Shapiro L.  2008.  Crystal structures of beta-neurexin 1 and beta-neurexin 2 ectodomains and dynamics of splice insertion sequence 4. Structure. 16(3):410-21. Go to Pubmed
Feldman I, Rzhetsky A, Vitkup D.  2008.  Network properties of genes harboring inherited disease mutations. Proc Natl Acad Sci U S A. 105(11):4323-8. Go to Pubmed
Rodriguez-Esteban R, Rzhetsky A.  2008.  Six senses in the literature. The bleak sensory landscape of biomedical texts. EMBO Rep. 9(3):212-5. Go to Pubmed
Moreno-Vinasco L, Gomberg-Maitland M, Maitland ML, Desai AA, Singleton PA, Sammani S, Sam L, Liu Y, Husain AN, Lang RM et al.  2008.  Genomic assessment of a multikinase inhibitor, sorafenib, in a rodent model of pulmonary hypertension. Physiol Genomics. 33(2):278-91. Go to Pubmed
Mani KM, Lefebvre C, Wang K, Lim WKeat, Basso K, Dalla-Favera R, Califano A.  2008.  A systems biology approach to prediction of oncogenes and molecular perturbation targets in B-cell lymphomas. Mol Syst Biol. 4:169. Go to Pubmed
Koehnke J, Jin X, Budreck EC, Posy S, Scheiffele P, Honig B, Shapiro L.  2008.  Crystal structure of the extracellular cholinesterase-like domain from neuroligin-2. Proc Natl Acad Sci U S A. 105(6):1873-8. Go to Pubmed
Kumar RA, Karamohamed S, Sudi J, Conrad DF, Brune C, Badner JA, T Gilliam C, Nowak NJ, Cook EH, Dobyns WB et al.  2008.  Recurrent 16p11.2 microdeletions in autism. Hum Mol Genet. 17(4):628-38. Go to Pubmed
Yao L, Rzhetsky A.  2008.  Quantitative systems-level determinants of human genes targeted by successful drugs. Genome Res. 18(2):206-13. Go to Pubmed
Jabado OJ, Liu Y, Conlan S, P Quan L, Hegyi H, Lussier Y, Briese T, Palacios G, Lipkin WI.  2008.  Comprehensive viral oligonucleotide probe design using conserved protein regions. Nucleic Acids Res. 36(1):e3. Go to Pubmed
Stoyanovich J, Pe'er I.  2008.  MutaGeneSys: estimating individual disease susceptibility based on genome-wide SNP array data. Bioinformatics. 24(3):440-2. Go to Pubmed
Foat BC, Tepper RG, Bussemaker HJ.  2008.  TransfactomeDB: a resource for exploring the nucleotide sequence specificity and condition-specific regulatory activity of trans-acting factors. Nucleic Acids Res. 36(Database issue):D125-31. Go to Pubmed