Search Publications

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
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
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
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
Margolin A, Wang K, Lim WKeat, Kustagi M, Nemenman I, Califano A.  2006.  Reverse engineering cellular networks. Nat Protoc. 1(2):662-71. 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
Palomero T, Lim WKeat, Odom DT, Sulis MLuisa, Real PJ, Margolin A, Barnes KC, O'Neil J, Neuberg D, Weng AP et al.  2006.  NOTCH1 directly regulates c-MYC and activates a feed-forward-loop transcriptional network promoting leukemic cell growth. Proc Natl Acad Sci U S A. 103(48):18261-6. Go to Pubmed
Liu Y, Li J, Sam L, Goh C-S, Gerstein M, Lussier YA.  2006.  An integrative genomic approach to uncover molecular mechanisms of prokaryotic traits. PLoS Comput Biol. 2(11):e159. Go to Pubmed
Lussier Y, Borlawsky T, Rappaport D, Liu Y, Friedman C.  2006.  PhenoGO: assigning phenotypic context to gene ontology annotations with natural language processing. Pac Symp Biocomput. :64-75. Go to Pubmed
Rodriguez-Esteban R, Iossifov I, Rzhetsky A.  2006.  Imitating manual curation of text-mined facts in biomedicine. PLoS Comput Biol. 2(9):e118. Go to Pubmed
Döbereiner H-G, Dubin-Thaler BJ, Hofman JM, Xenias HS, Sims TN, Giannone G, Dustin ML, Wiggins C, Sheetz MP.  2006.  Lateral membrane waves constitute a universal dynamic pattern of motile cells. Phys Rev Lett. 97(3):038102. Go to Pubmed
Moorman C, Sun LV, Wang J, de Wit E, Talhout W, Ward LD, Greil F, Lu X-J, White KP, Bussemaker H et al.  2006.  Hotspots of transcription factor colocalization in the genome of Drosophila melanogaster. Proc Natl Acad Sci U S A. 103(32):12027-32. Go to Pubmed
Varadan V, Miller DM, Anastassiou D.  2006.  Computational inference of the molecular logic for synaptic connectivity in C. elegans. Bioinformatics. 22(14):e497-506. Go to Pubmed
Ofran Y, Yachdav G, Mozes E, Soong T-tsen, Nair R, Rost B.  2006.  Create and assess protein networks through molecular characteristics of individual proteins. Bioinformatics. 22(14):e402-7. Go to Pubmed
Foat BC, Morozov AV, Bussemaker H.  2006.  Statistical mechanical modeling of genome-wide transcription factor occupancy data by MatrixREDUCE. Bioinformatics. 22(14):e141-9. Go to Pubmed
Friedman C, Borlawsky T, Shagina L, H Xing R, Lussier Y.  2006.  Bio-Ontology and text: bridging the modeling gap. Bioinformatics. 22(19):2421-9. Go to Pubmed
Halasz G, van Batenburg MF, Perusse J, Hua S, Lu X-J, White KP, Bussemaker H.  2006.  Detecting transcriptionally active regions using genomic tiling arrays. Genome Biol. 7(7):R59. Go to Pubmed
Bussemaker H.  2006.  Modeling gene expression control using Omes Law. Mol Syst Biol. 2:2006.0013. Go to Pubmed
Margolin A, Nemenman I, Basso K, Wiggins C, Stolovitzky G, Dalla-Favera R, Califano A.  2006.  ARACNE: an algorithm for the reconstruction of gene regulatory networks in a mammalian cellular context. BMC Bioinformatics. 7 Suppl 1:S7. Go to Pubmed
Kundaje A, Middendorf M, Shah M, Wiggins C, Freund Y, Leslie C.  2006.  A classification-based framework for predicting and analyzing gene regulatory response. BMC Bioinformatics. 7 Suppl 1:S5. Go to Pubmed
Anastassiou D, Liu H, Varadan V.  2006.  Variable window binding for mutually exclusive alternative splicing. Genome Biol. 7(1):R2. Go to Pubmed
Koster DA, Wiggins C, Dekker NH.  2006.  Multiple events on single molecules: unbiased estimation in single-molecule biophysics. Proc Natl Acad Sci U S A. 103(6):1750-5. Go to Pubmed
Boorsma A, Foat BC, Vis D, Klis F, Bussemaker H.  2005.  T-profiler: scoring the activity of predefined groups of genes using gene expression data. Nucleic Acids Res. 33(Web Server issue):W592-5. Go to Pubmed
Cavelier G, Anastassiou D.  2005.  Phenotype analysis using network motifs derived from changes in regulatory network dynamics. Proteins. 60(3):525-46. Go to Pubmed
Chen CPeter, Posy S, Ben-Shaul A, Shapiro L, Honig B.  2005.  Specificity of cell-cell adhesion by classical cadherins: Critical role for low-affinity dimerization through beta-strand swapping. Proc Natl Acad Sci U S A. 102(24):8531-6. Go to Pubmed
Weston J, Leslie C, Ie E, Zhou D, Elisseeff A, Noble WStafford.  2005.  Semi-supervised protein classification using cluster kernels. Bioinformatics. 21(15):3241-7. Go to Pubmed
Punta M, Rost B.  2005.  PROFcon: novel prediction of long-range contacts. Bioinformatics. 21(13):2960-8. Go to Pubmed
Alarcón M, Yonan AL, Gilliam TC, Cantor R, Geschwind DH.  2005.  Quantitative genome scan and Ordered-Subsets Analysis of autism endophenotypes support language QTLs. Mol Psychiatry. 10(8):747-57. Go to Pubmed
Fan H, Mark AE, Zhu J, Honig B.  2005.  Comparative study of generalized Born models: protein dynamics. Proc Natl Acad Sci U S A. 102(19):6760-4. Go to Pubmed
Nair R, Rost B.  2005.  Mimicking cellular sorting improves prediction of subcellular localization. J Mol Biol. 348(1):85-100. Go to Pubmed
Basso K, Margolin A, Stolovitzky G, Klein U, Dalla-Favera R, Califano A.  2005.  Reverse engineering of regulatory networks in human B cells. Nat Genet. 37(4):382-90. Go to Pubmed
Cantor MN, Sarkar INeil, Bodenreider O, Lussier Y.  2005.  Genestrace: phenomic knowledge discovery via structured terminology. Pac Symp Biocomput. :103-14. Go to Pubmed
Siggers TW, Silkov A, Honig B.  2005.  Structural alignment of protein--DNA interfaces: insights into the determinants of binding specificity. J Mol Biol. 345(5):1027-45. Go to Pubmed
Tao Y, Friedman C, Lussier Y.  2005.  Visualizing information across multidimensional post-genomic structured and textual databases. Bioinformatics. 21(8):1659-67. Go to Pubmed
Stolc V, Gauhar Z, Mason C, Halasz G, van Batenburg MF, Rifkin SA, Hua S, Herreman T, Tongprasit W, Barbano PEmilio et al.  2004.  A gene expression map for the euchromatic genome of Drosophila melanogaster. Science. 306(5696):655-60. Go to Pubmed
Middendorf M, Kundaje A, Wiggins C, Freund Y, Leslie C.  2004.  Predicting genetic regulatory response using classification. Bioinformatics. 20 Suppl 1:i232-40. Go to Pubmed
Nair R, Rost B.  2004.  LOCnet and LOCtarget: sub-cellular localization for structural genomics targets. Nucleic Acids Res. 32(Web Server issue):W517-21. Go to Pubmed
Rost B, Yachdav G, Liu J.  2004.  The PredictProtein server. Nucleic Acids Res. 32(Web Server issue):W321-6. Go to Pubmed
Gao F, Foat BC, Bussemaker H.  2004.  Defining transcriptional networks through integrative modeling of mRNA expression and transcription factor binding data. BMC Bioinformatics. 5:31. Go to Pubmed
Liu J, Rost B.  2004.  CHOP proteins into structural domain-like fragments. Proteins. 55(3):678-88. Go to Pubmed
Weston J, Elisseeff A, Zhou D, Leslie C, Noble WStafford.  2004.  Protein ranking: from local to global structure in the protein similarity network. Proc Natl Acad Sci U S A. 101(17):6559-63. Go to Pubmed
Lussier Y, Li J.  2004.  Terminological mapping for high throughput comparative biology of phenotypes. Pac Symp Biocomput. :202-13. Go to Pubmed
Zhang XH-F, Heller KA, Hefter I, Leslie C, Chasin LA.  2003.  Sequence information for the splicing of human pre-mRNA identified by support vector machine classification. Genome Res. 13(12):2637-50. Go to Pubmed
Tang CL, Xie L, Y Y Koh I, Posy S, Alexov E, Honig B.  2003.  On the role of structural information in remote homology detection and sequence alignment: new methods using hybrid sequence profiles. J Mol Biol. 334(5):1043-62. Go to Pubmed
Petrey D, Xiang Z, Tang CL, Xie L, Gimpelev M, Mitros T, Soto CS, Goldsmith-Fischman S, Kernytsky A, Schlessinger A et al.  2003.  Using multiple structure alignments, fast model building, and energetic analysis in fold recognition and homology modeling. Proteins. 53 Suppl 6:430-5. Go to Pubmed
Klein U, Tu Y, Stolovitzky G, Keller JL, Haddad J, Miljkovic V, Cattoretti G, Califano A, Dalla-Favera R.  2003.  Gene expression dynamics during germinal center transit in B cells. Ann N Y Acad Sci. 987:166-72. Go to Pubmed
Liu AH, Zhang X, Stolovitzky G, Califano A, Firestein SJ.  2003.  Motif-based construction of a functional map for mammalian olfactory receptors. Genomics. 81(5):443-56. Go to Pubmed
Bussemaker H, Li H, Siggia ED.  2001.  Regulatory element detection using correlation with expression. Nat Genet. 27(2):167-71. Go to Pubmed
Anastassiou D.  2000.  Frequency-domain analysis of biomolecular sequences. Bioinformatics. 16(12):1073-81. Go to Pubmed
Califano A, Stolovitzky G, Tu Y.  2000.  Analysis of gene expression microarrays for phenotype classification. Proc Int Conf Intell Syst Mol Biol. 8:75-85. Go to Pubmed
Bussemaker H, Li H, Siggia ED.  2000.  Building a dictionary for genomes: identification of presumptive regulatory sites by statistical analysis. Proc Natl Acad Sci U S A. 97(18):10096-100. Go to Pubmed
Grillo HC, Wilcox BR.  1989.  Choosing cardiothoracic surgical residents. Ann Thorac Surg. 47(3):333. Go to Pubmed

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