Publications

Author ID

Effraim PR, Wang J, Englander MT, Avins J, Leyh TS, Gonzalez RL, Cornish VW. 2009. Natural amino acids do not require their native tRNAs for efficient selection by the ribosome.. Nat Chem Biol. 5(12):947-53.▶ Go to Pubmed

Mugler A, Walczak AM, Wiggins CH. 2009. Spectral solutions to stochastic models of gene expression with bursts and regulation.. Phys Rev E Stat Nonlin Soft Matter Phys. 80(4 Pt 1):041921.▶ Go to Pubmed

Iossifov I, Rodriguez-Esteban R, Mayzus I, Millen KJ, Rzhetsky A. 2009. Looking at cerebellar malformations through text-mined interactomes of mice and humans.. PLoS Comput Biol. 5(11):e1000559.▶ Go to Pubmed

Chen B-J, Causton HC, Mancenido D, Goddard NL, Perlstein EO, Pe'er D. 2009. Harnessing gene expression to identify the genetic basis of drug resistance.. Mol Syst Biol. 5:310.▶ Go to Pubmed

Rohs R, West SM, Sosinsky A, Liu P, Mann RS, Honig B. 2009. The role of DNA shape in protein-DNA recognition.. Nature. 461(7268):1248-53.▶ Go to Pubmed

Bonnen PE, Lowe JK, Altshuler DM, Breslow JL, Stoffel M, Friedman JM, Pe'er I. 2010. European admixture on the Micronesian island of Kosrae: lessons from complete genetic information.. Eur J Hum Genet. 18(3):309-16.▶ Go to Pubmed

Khiabanian H, Trifonov V, Rabadan R. 2009. Reassortment patterns in Swine influenza viruses.. PLoS One. 4(10):e7366.▶ Go to Pubmed

Petrey D, Fischer M, Honig B. 2009. Structural relationships among proteins with different global topologies and their implications for function annotation strategies.. Proc Natl Acad Sci U S A. 106(41):17377-82.▶ Go to Pubmed

Wang K, Saito M, Bisikirska B, Alvarez M, Lim WKeat, Rajbhandari P, Shen Q, Nemenman I, Basso K, Margolin A, Klein U, Dalla-Favera R, Califano A. 2009. Genome-wide identification of post-translational modulators of transcription factor activity in human B cells.. Nat Biotechnol. 27(9):829-39.▶ Go to Pubmed

Khiabanian H, Farrell GM, St George K, Rabadan R. 2009. Differences in patient age distribution between influenza A subtypes.. PLoS One. 4(8):e6832.▶ Go to Pubmed

Zhao X, Arca DD', Lim WKeat, Brahmachary M, Carro MStella, Ludwig T, Cardo CCordon, Guillemot F, Aldape K, Califano A, Iavarone A, Lasorella A. 2009. The N-Myc-DLL3 cascade is suppressed by the ubiquitin ligase Huwe1 to inhibit proliferation and promote neurogenesis in the developing brain.. Dev Cell. 17(2):210-21.▶ Go to Pubmed

Katsamba PS, Carroll K, Ahlsen G, Bahna F, Vendome J, Posy S, Rajebhosale M, Price SR, Jessell T, Ben-Shaul A, Shapiro L, Honig B. 2009. Linking molecular affinity and cellular specificity in cadherin-mediated adhesion.. Proc Natl Acad Sci U S A. 106(28):11594-9.▶ Go to Pubmed

Saito M, Novak U, Piovan E, Basso K, Sumazin P, Schneider C, Crespo M, Shen Q, Bhagat G, Califano A, Chadburn A, Pasqualucci L, Dalla-Favera R. 2009. BCL6 suppression of BCL2 via Miz1 and its disruption in diffuse large B cell lymphoma.. Proc Natl Acad Sci U S A. 106(27):11294-9.▶ Go to Pubmed

Daly AK, Donaldson PT, Bhatnagar P, Shen Y, Pe'er I, Floratos A, Daly MJ, Goldstein DB, John S, Nelson MR, Graham J, B Park K, Dillon JF, Bernal W, Cordell HJ, Pirmohamed M, Aithal GP, Day CP. 2009. HLA-B*5701 genotype is a major determinant of drug-induced liver injury due to flucloxacillin.. Nat Genet. 41(7):816-9.▶ Go to Pubmed

Trifonov V, Khiabanian H, Rabadan R. 2009. Geographic dependence, surveillance, and origins of the 2009 influenza A (H1N1) virus.. N Engl J Med. 361(2):115-9.▶ Go to Pubmed

Khan AA, Betel D, Miller ML, Sander C, Leslie C, Marks DS. 2009. Transfection of small RNAs globally perturbs gene regulation by endogenous microRNAs.. Nat Biotechnol. 27(6):549-55.▶ Go to Pubmed

Prabhu S, Pe'er I. 2009. Overlapping pools for high-throughput targeted resequencing.. Genome Res. 19(7):1254-61.▶ Go to Pubmed

Basso K, Sumazin P, Morozov P, Schneider C, Maute RL, Kitagawa Y, Mandelbaum J, Haddad J, Chen C-Z, Califano A, Dalla-Favera R. 2009. Identification of the human mature B cell miRNome.. Immunity. 30(5):744-52.▶ Go to Pubmed

Trifonov V, Khiabanian H, Greenbaum B, Rabadan R. 2009. The origin of the recent swine influenza A(H1N1) virus infecting humans.. Euro Surveill. 14(17)▶ Go to Pubmed

Compagno M, Lim WKeat, Grunn A, Nandula SV, Brahmachary M, Shen Q, Bertoni F, Ponzoni M, Scandurra M, Califano A, Bhagat G, Chadburn A, Dalla-Favera R, Pasqualucci L. 2009. Mutations of multiple genes cause deregulation of NF-kappaB in diffuse large B-cell lymphoma.. Nature. 459(7247):717-21.▶ Go to Pubmed

Rohs R, West SM, Liu P, Honig B. 2009. Nuance in the double-helix and its role in protein-DNA recognition.. Curr Opin Struct Biol. 19(2):171-7.▶ Go to Pubmed

Walczak AM, Mugler A, Wiggins C. 2009. A stochastic spectral analysis of transcriptional regulatory cascades.. Proc Natl Acad Sci U S A. 106(16):6529-34.▶ Go to Pubmed

Waltz D, Buchanan BG. 2009. Computer science. Automating science.. Science. 324(5923):43-4.▶ Go to Pubmed

Petrey D, Honig B. 2009. Is protein classification necessary? Toward alternative approaches to function annotation. Curr Opin Struct Biol. 19(3):363-8.▶ Go to Pubmed

Nimrod G, Szilágyi A, Leslie C, Ben-Tal N. 2009. Identification of DNA-binding proteins using structural, electrostatic and evolutionary features.. J Mol Biol. 387(4):1040-53.▶ Go to Pubmed

Litvin O, Causton HC, Chen B-J, Pe'er D. 2009. Modularity and interactions in the genetics of gene expression.. Proc Natl Acad Sci U S A. 106(16):6441-6.▶ Go to Pubmed

Lim WKeat, Lyashenko E, Califano A. 2009. Master regulators used as breast cancer metastasis classifier.. Pac Symp Biocomput. :504-15.▶ Go to Pubmed

Wang K, Alvarez M, Bisikirska B, Linding R, Basso K, Dalla-Favera R, Califano A. 2009. Dissecting the interface between signaling and transcriptional regulation in human B cells.. Pac Symp Biocomput. :264-75.▶ Go to Pubmed

Sam LT, Mendonça EA, Li J, Blake J, Friedman C, Lussier Y. 2009. PhenoGO: an integrated resource for the multiscale mining of clinical and biological data.. BMC Bioinformatics. 10 Suppl 2:S8.▶ Go to Pubmed

Liu Y, Sam L, Li J, Lussier Y. 2009. Robust methods for accurate diagnosis using pan-microbiological oligonucleotide microarrays.. BMC Bioinformatics. 10 Suppl 2:S11.▶ Go to Pubmed

Lowe JK, Maller JB, Pe'er I, Neale BM, Salit J, Kenny EE, Shea JL, Burkhardt R, J Smith G, Ji W, Noel M, Foo JNee, Blundell ML, Skilling V, Garcia L, Sullivan ML, Lee HE, Labek A, Ferdowsian H, Auerbach SB, Lifton RP, Newton-Cheh C, Breslow J, Stoffel M, Daly MJ, Altshuler D, Friedman JM. 2009. Genome-wide association studies in an isolated founder population from the Pacific Island of Kosrae.. PLoS Genet. 5(2):e1000365.▶ Go to Pubmed

Sachs K, Itani S, Carlisle J, Nolan GP, Pe'er D, Lauffenburger DA. 2009. Learning signaling network structures with sparsely distributed data.. J Comput Biol. 16(2):201-12.▶ Go to Pubmed

Lee S-I, Dudley AM, Drubin D, Silver PA, Krogan N, Pe'er D, Koller D. 2009. Learning a prior on regulatory potential from eQTL data.. PLoS Genet. 5(1):e1000358.▶ Go to Pubmed

Liu J, Ghanim M, Xue L, Brown CD, Iossifov I, Angeletti C, Hua S, Nègre N, Ludwig M, Stricker T, Al-Ahmadie HA, Tretiakova M, Camp RL, Perera-Alberto M, Rimm DL, Xu T, Rzhetsky A, White KP. 2009. Analysis of Drosophila segmentation network identifies a JNK pathway factor overexpressed in kidney cancer.. Science. 323(5918):1218-22.▶ Go to Pubmed

Meyer NJ, Huang Y, Singleton PA, Sammani S, Moitra J, Evenoski C, Husain AN, Mitra S, Moreno-Vinasco L, Jacobson JR, Lussier Y, Garcia JGN. 2009. GADD45a is a novel candidate gene in inflammatory lung injury via influences on Akt signaling.. FASEB J. 23(5):1325-37.▶ Go to Pubmed

Margolin AA, Palomero T, Sumazin P, Califano A, Ferrando AA, Stolovitzky G. 2009. ChIP-on-chip significance analysis reveals large-scale binding and regulation by human transcription factor oncogenes.. Proc Natl Acad Sci U S A. 106(1):244-9.▶ Go to Pubmed

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, Lussier YA, Natarajan V, Garcia JGN. 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. 2009. RANKPROP: a web server for protein remote homology detection.. Bioinformatics. 25(1):121-2.▶ Go to Pubmed

Gusev A, Lowe JK, Stoffel M, Daly MJ, Altshuler D, Breslow J, Friedman JM, Pe'er I. 2009. Whole population, genome-wide mapping of hidden relatedness.. Genome Res. 19(2):318-26.▶ 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, Chiang ET, Lang GD, Husain AN, Dudek SM, Jacobson JR, Ye SQ, Lussier Y, Garcia JGN. 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, Tabak E, Marboe CC, Califano A, Deng MC. 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, Kennedy D, Jagadish HV, Schmidt J, Athey B, Califano A, Musen M, Altman R, Kikinis R, Kohane I, Delp S, D Parker S, Toga AW. 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, Zinzani PLuigi, Pileri SA. 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, Gergel J, Hatchwell E, T Gilliam C, Gershon ES, Nowak NJ, Dobyns WB, Cook EH. 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, Ratain MJ, Lussier Y, Garcia JGN. 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, Christian SL. 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, Smith R, Lessnick SL, Sahasrabudhe S, Stockwell BR. 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, Feuk L, Qian C, Bryson SE, Jones MB, Marshall CR, Scherer SW, Vieland VJ, Bartlett C, Mangin LVonne, Goedken R, Segre A, Pericak-Vance MA, Cuccaro ML, Gilbert JR, Wright HH, Abramson RK, Betancur C, Bourgeron T, Gillberg C, Leboyer M, Buxbaum JD, Davis KL, Hollander E, Silverman JM, Hallmayer J, Lotspeich L, Sutcliffe JS, Haines JL, Folstein SE, Piven J, Wassink TH, Sheffield V, Geschwind DH, Bucan M, W Brown T, Cantor R, Constantino JN, T Gilliam C, Herbert M, Lajonchere C, Ledbetter DH, Lese-Martin C, Miller J, Nelson S, Samango-Sprouse CA, Spence S, State M, Tanzi RE, Coon H, Dawson G, Devlin B, Estes A, Flodman P, Klei L, McMahon WM, Minshew N, Munson J, Korvatska E, Rodier PM, Schellenberg GD, Smith M, M Spence A, Stodgell C, Tepper PGuo, Wijsman EM, Yu C-E, Rogé B, Mantoulan C, Wittemeyer K, Poustka A, Felder B, Klauck SM, Schuster C, Poustka F, Bölte S, Feineis-Matthews S, Herbrecht E, Schmötzer G, Tsiantis J, Papanikolaou K, Maestrini E, Bacchelli E, Blasi F, Carone S, Toma C, Van Engeland H, de Jonge M, Kemner C, Koop F, Koop F 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, Aster JC, Sigaux F, Soulier J, A Look T, Young RA, Califano A, Ferrando A. 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, van Steensel B. 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

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