The activities of the Center build upon the substantial research record of the Center's Faculty members. The following is a select list of publications related to planned deliverables.
| 2009 | ||
| Basso, K. Sumazin, P. Morozov, P. Schneider, C. Maute, R. L. Kitagawa, Y. Mandelbaum, J. Haddad, J., Jr. Chen, C. Z. Califano, A. Dalla-Favera, R., (2009) "Identification of the human mature B cell miRNome," Immunity | ||
| Chen, B.J., Causton, H.C., Goddard, N.L., Perlstein, E.O., Pe’er, D., (2009) "Harnessing gene expression to identify the genetic basis of drug resistance," Molecular Systems Biology, under review | ||
| Compagno, M. Lim, W. K. Grunn, A. Nandula, S. V. 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 | ||
| Gusev, A. Lowe, J. K. Stoffel, M. Daly, M. J. Altshuler, D. Breslow, J. L. Friedman, J. M. Pe'er, I., (2009) "Whole population, genome-wide mapping of hidden relatedness," Genome Res | ||
| Khan, A. A., Betel, D., Miller, M. L., Sander, C., Leslie, C. S., Marks, D. S., (2009) "Transfection of small RNAs globally perturbs gene regulation by endogenous microRNAs," Nat Biotechnol, in press | ||
| Lee, S. I., Dudley, A. M., Drubin, D., Silver, P. A., Krogan, N. J., Pe'er, D., Koller, D., (2009) "Learning a prior on regulatory potential from eQTL data," PLoS Genet | ||
| Lim, W., Lyashenko, E., Califano, A., (2009) "Master Regulators Used As Breast Cancer Metastasis Classifier," Pacific Symposium on Biocomputing | ||
| Lim, W. K., Lyashenko, E., Califano, A., (2009) "Master regulators used as breast cancer metastasis classifier," Pac Symp Biocomput | ||
| Litvin, O., Causton, H. C., Chen, B. J., Pe'er, D., (2009) "Modularity and interactions in the genetics of gene expression," Proc Natl Acad Sci U S A | ||
| Liu, J., Ghanim, M., Xue, L., Brown, C. D., Iossifov, I., Angeletti, C., Hua, S., Negre, N., Ludwig, M., Stricker, T., Al-Ahmadie, H. A., Tretiakova, M., Camp, R. L., Perera-Alberto, M., Rimm, D. L., Xu, T., Rzhetsky, A., White, K. P., (2009) "Analysis of Drosophila segmentation network identifies a JNK pathway factor overexpressed in kidney cancer," Science | ||
| Liu, Y. Sam, L. Li, J. Lussier, Y. A., (2009) "Robust methods for accurate diagnosis using pan-microbiological oligonucleotide microarrays," BMC Bioinformatics | ||
| Lowe, J. K. Maller, J. B. Pe'er, I. Neale, B. M. Salit, J. Kenny, E. E. Shea, J. L. Burkhardt, R. Smith, J. G. Ji, W. Noel, M. Foo, J. N. Blundell, M. L. Skilling, V. Garcia, L. Sullivan, M. L. Lee, H. E. Labek, A. Ferdowsian, H. Auerbach, S. B. Lifton, R. P. Newton-Cheh, C. Breslow, J. L. Stoffel, M. Daly, M. J. Altshuler, D. M. Friedman, J. M., (2009) "Genome-wide association studies in an isolated founder population from the Pacific Island of Kosrae," PLoS Genet | ||
| Lussier, Y.A., Lee, Y., Radivojac, P., Ofran, Y., Butte, A., Kann, M. , (2009) "Molecular Bioinformatics for Disease - Session Introduction," Pacific Symposium on Biocomputing | ||
| Melvin, I., Weston, J., Leslie, C., Noble, W. S., (2009) "RANKPROP: a web server for protein remote homology detection," Bioinformatics | ||
| Meyer, N. J. Huang, Y. Singleton, P. A. Sammani, S. Moitra, J. Evenoski, C. L. Husain, A. N. Mitra, S. Moreno-Vinasco, L. Jacobson, J. R. Lussier, Y. A. Garcia, J. G., (2009) "GADD45a is a novel candidate gene in inflammatory lung injury via influences on Akt signaling," Faseb J | ||
| Murphy, C., G. Kaiser, I. Vo, M. Chu , (2009) "Quality Assurance of Software Applications Using the In Vivo Testing Approach.," 2nd IEEE International Conference on Software Testing, Verification and Validation | ||
| Murphy, C., G. Kaiser, K. Loveland, S. Hasan, (2009) "Retina: Helping Students and Instructors Based on Observed Programming Activities.," 40th ACM Technical Symposium on Computer Science Education | ||
| Murphy, C., K. Shen, G. Kaiser, (2009) "Using JML Runtime Assertion Checking to Perform Metamorphic Testing in Applications without Test Oracles.," 2nd IEEE International Conference on Software Testing, Verification and Validation | ||
| Murphy, C., Shen, K., Kaiser, G.E. , (2009) "Automatic System Testing of Programs without Test Oracles.," International Symposium on Testing and Analysis | ||
| Nimrod, G., Szilagyi, A., Leslie, C., Ben-Tal, N., (2009) "Identification of DNA-binding proteins using structural, electrostatic and evolutionary features," J Mol Biol | ||
| Prabhu, S., Pe'er, I., (2009) "Overlapping pools for high-throughput targeted resequencing," Genome Res | ||
| Raj, A., Wiggins, C. H., (2009) "An information-theoretic derivation of min-cut based clustering.," IEEE Transactions on Information Theory | ||
| Sachs, K., Itani, S., Carlisle, J., Nolan, G. P., Pe'er, D., Lauffenburger, D. A., (2009) "Learning signaling network structures with sparsely distributed data," J Comput Biol | ||
| Sam, L. T. Mendonca, E. A. Li, J. Blake, J. Friedman, C. Lussier, Y. A., (2009) "PhenoGO: an integrated resource for the multiscale mining of clinical and biological data," BMC Bioinformatics | ||
| Sethumadhavan, S., Kaiser, G.E., (2009) "COMPASS: A Community-Drive Parallelization Advisor for Sequential Software.," 2nd International Workshop on Multicore Software Engineering | ||
| Walczak, A. M., Mugler, A., Wiggins, C. H, (2009) "A stochastic spectral analysis of transcriptional regulatory cascades," Proc Natl Acad Sci U S A | ||
| Waltz, D., Buchanan, B. G., (2009) "Computer science. Automating science," Science | ||
| Wang, K. Alvarez, M. J. Bisikirska, B. C. 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 | ||
| Wang K, Saito M, Bisikirska BC, Alvarez MJ, Lim WK, Rajbhandari P, Shen Q, Nemenman I, Basso K, Margolin AA, Klein U, Dalla-Favera R, Califano A., (2009) "Genome-wide identification of post-translational modulators of transcription factor activity in human B cells.," | ||
| Zhao X, D' Arca D, Lim WK, Brahmachary M, Carro MS, Ludwig T, Cardo CC, 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.," | ||
| Katsamba P, Carroll K, Ahlsen G, Bahna F, Vendome J, Posy S, Rajebhosale M, Price S, Jessell TM, Ben-Shaul A, Shapiro L, Honig BH. , (2009) "Linking molecular affinity and cellular specificity in cadherin-mediated adhesion.," | ||
| Rohs R, West SM, Liu P, Honig B., (2009) "Nuance in the double-helix and its role in protein-DNA recognition.," | ||
| Petrey D, Honig B., (2009) "Is protein classification necessary? Toward alternative approaches to function annotation.," | ||
| 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.," | ||
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| 2008 | ||
| Murphy, C., Kim, E., Kaiser, G., Cannon, A., (2008) "Backstop: Debugging Tools for Novice Java Programmers," 39th ACM SIGCSE Technical Symposium on Computer Science Education, March 2008 | ||
| Jabado, O. J., Liu, Y., Conlan, S., Quan, P. L., Hegyi, H., Lussier, Y., Briese, T., Palacios, G., Lipkin, W. I. , (2008) "Comprehensive viral oligonucleotide probe design using conserved protein regions.," Nucleic Acids Res 36(1): e3. | ||
| Koehnke, J., Jin, X., Budreck, E.C., 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. | ||
| Koehnke, J., Jin, X., Trbovic, N., Katsamba, P. S., Brasch, J., Ahlsen, G., Scheiffele, P., Honig, B., Palmer, A.G., 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. | ||
| Murphy, C., Phung, D., Kaiser, G. , (2008) "A Distance Learning Approach to Teaching eXtreme Programming," 13th ACM Annual Conference on Innovation and Technology in Computer Science Education, June | ||
| Chu, M., Murphy, C., Kaiser, G. , (2008) "Distributed In Vivo Testing of Software Applications," 1st IEEE International Conference on Software Testing, Verification, and Validation | ||
| Pe'er, I., R. Yelensky, et al., (2008) "Estimation of the multiple testing burden for genomewide association studies of nearly all common variants," Genet Epidemiol 32(4): 381-5 | ||
| Iossifov, I., Zheng, T., Baron, M., Gilliam, T.C., Rzhetsky, A., (2008) "Genetic-linkage mapping of complex hereditary disorders to a whole-genome molecular-interaction network," Genome Res. | ||
| Moreno-Vinasco, L., Gomberg-Maitland, M., Maitland, M.L., Desai, A.A., Singleton, P.A., Sammani, S., Sam, L., Liu, Y., Husain, A.N., Lang, R.M., Ratain, M.J., Lussier, Y.A., and Garcia, J., (2008) "Genomic Assessment of a Multi-Kinase Inhibitor, Sorafenib, in a Rodent Model of Pulmonary Hypertension," Physiological Genomics: 1-64 | ||
| de Wit, E., Braunschweig, U., Greil, F., Bussemaker, H.J., van Steensel, B. , (2008) "Global chromatin domain organization of the Drosophila genome," PLoS Genet 4(3): e1000045 | ||
| Hung, C., Madduri, R., Keshav, K., Oster, S., Langella, S., Martin, S., Mock, S., (2008) "Integrating caGrid and TeraGrid, TeraGrid Conference Proceedings," TeraGrid Conference Proceedings, 2008 | ||
| Lussier, Y. A., Lee,Y., Radivojac, P., Ofran, Y., Punta, M., Butte, A., Kann, M., (2008) "Molecular Bioinformatics for Disease: Protein Interactions and and Phenomics," Pacific Symposium on Biocomputing 13: 228-230 | ||
| Stoyanovich, J., Pe’er, I., (2008) "MutaGeneSys: estimating individual disease susceptibility based on genome-wide SNP array data," Bioinformatics 24(3) | ||
| 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 | ||
| Christian, S. L., C. W. Brune, et al., (2008) "Novel submicroscopic chromosomal abnormalities detected in autism spectrum disorder," Biol Psychiatry 63(12): 1111-7 | ||
| Yao, L., Rzhetsky, A., (2008) "Quantitative systems-level determinants of human genes targeted by successful drugs," Genome Res 18(2): 206-13 | ||
| Kumar, R. A., S. KaraMohamed, et al., (2008) "Recurrent 16p11.2 microdeletions in autism," Hum Mol Genet 17(4): 628-38 | ||
| Ross, K. A., Stoyanovich, J., (2008) "Schema Polynomials and Applications," International Conference on Extending Database Technology | ||
| 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): 952-66 | ||
| Rodriguez-Esteban, R., Rzhetsky, A., (2008) "Six senses in the literature. The bleak sensory landscape of biomedical texts," EMBO Rep 9(3): 212-5 | ||
| Mani, K. M., Lefebvre, C., Wang, K., Lim, W.K., 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 | ||
| Piccaluga PP, Califano A, Klein U, Agostinelli C, Bellosillo B, Gimeno E, Serrano S, Solè F, Zang Y, Falini B, Zinzani PL, Pileri SA., (2008) "Gene expression analysis provides a potential rationale for revising the histological grading of follicular lymphomas," Haematologica, May 19 | ||
| 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, Parker DS, Toga AW., (2008) "iTools: A Framework for Classification, Categorization and Integration of Computational Biology Resources," PLoS One, 3(5): p. e2265 | ||
| Cadeiras M, Bayern M, Burke E, Dedrick R, Gangadin A, Latif F, Shazad K, Sinha A, Tabak EG, Marboe CC, Califano A, and Deng MC, (2008) "Gene expression profiles of patients with antibody-mediated rejection after cardiac transplantation," J Heart Lung Transplant. Aug;27(8):932-4. | ||
| Amer-Yahia, S., M. Benedikt, Lakshmanan, L., J. Stoyanovich , (2008) "Efficient Network-Aware Search in Collaborative Tagging Sites.," Proceedings of the VLDB Conference | ||
| Boorsma, A., Lu, X.-J., Zakrzewska, A., Snyder, B., Klis, F.M., Bussemaker, H.J., (2008) "Inferring condition-specific modulation of transcription factor activity through regulon-based analysis of genomewide expression.," PLoS ONE | ||
| Feldman, I. Rzhetsky, A. Vitkup, D., (2008) "Network properties of genes harboring inherited disease mutations," Proc Natl Acad Sci U S A | ||
| Hong, S.B. Huang, Y. Moreno-Vinasco, L. Sammani, S. Moitra, J. Barnard, J. W. Ma, S. F. Mirzapoiazova, T. Evenoski, C. Reeves, R. R. Chiang, E. T. Lang, G. D. Husain, A. N. Dudek, S. M. Jacobson, J. R. Ye, S. Q. Lussier, Y. A. Garcia, J. G., (2008) "Essential role of pre-B-cell colony enhancing factor in ventilator-induced lung injury," Am J Respir Crit Care Med | ||
| Iossifov, I., Zheng, T., Baron, M., Gilliam, T. C., Rzhetsky, A., (2008) "Genetic-linkage mapping of complex hereditary disorders to a whole-genome molecular-interaction network," Genome Res | ||
| Jabado, O.J., Liu, Y., Conlan, S., Quan, P.L., Hegyi, H., Lussier, Y., Briese, T., Palacios, G., Lipkin, W.I. , (2008) "Comprehensive viral oligonucleotide probe design using conserved protein regions.," Nucleic Acids Res. | ||
| Katsamba, P. S., Carroll, K., Ahlsen, G., Bahna, F., Vendome, J., Posy, S., Rajebhosale, M., Price, S., Jessell, T. M., Ben-Shaul, A., Shapiro, L., B. Honig, (2008) "Linking molecular affinity and cellular specificity in cadherin-mediated adhesion," PNAS, in press | ||
| Koehnke, J., Jin, X., Budreck, E. C., 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 | ||
| Koehnke, J., Jin, X., Trbovic, N., Katsamba, P. S., Brasch, J., Ahlsen, G., Scheiffele, P., Honig, B., Palmer, A. G., 3rd Shapiro, L., (2008) "Crystal structures of beta-neurexin 1 and beta-neurexin 2 ectodomains and dynamics of splice insertion sequence 4," Structure | ||
| 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 | ||
| Mani, K. M., Lefebvre, C., Wang, K., Lim, W. K., 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 | ||
| Melvin, I., Weston, J., Leslie, C. S., Noble, W. S., (2008) "Combining classifiers for improved classification of proteins from sequence or structure," BMC Bioinformatics | ||
| Murphy, C., S. Sheth, G. Kaiser and L. Wilcox , (2008) "genSpace: Exploring Social Networking Metaphors for Knowledge Sharing and Scientific Collaborative Work.," 1st International Workshop on Social Software Engineering and Applications | ||
| Murphy, C., G. Kaiser, L. Hu and L. Wu, (2008) "Properties of Machine Learning Applications for Use in Metamorphic Testing.," 20th International Conference on Software Engineering and Knowledge Engineering | ||
| Murphy, C., Phung, D., Kaiser, G.E., (2008) "A Distance Learning Approach to Teaching eXtreme Programming.," 13th ACM Annual Conference on Innovation and Technology in Computer Science Education | ||
| 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 | ||
| Rodriguez-Esteban, R., Rzhetsky, A., (2008) "Six senses in the literature. The bleak sensory landscape of biomedical texts," EMBO Rep | ||
| Rzhetsky, A., Seringhaus, M., Gerstein, M., (2008) "Seeking a new biology through text mining," Cell | ||
| Sarin, S., Prabhu, S., O'Meara, M. M., Pe'er, I., Hobert, O., (2008) "Caenorhabditis elegans mutant allele identification by whole-genome sequencing," Nat Methods | ||
| Shatkay, H., Pan, F., Rzhetsky, A., Wilbur, W. J., (2008) "Multi-dimensional classification of biomedical text: toward automated, practical provision of high-utility text to diverse users," Bioinformatics | ||
| 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 | ||
| Stoyanovich, J., Yahia, S. A., Marlow, C., Yu, C., (2008) "Leveraging Tagging to Model User Interests in del.icio.us.," Proceeding of the AAAI Spring Symposium on Social Information Processing | ||
| Wang, T., Moreno-Vinasco, L., Huang, Y., Lang, G.D., Linares, J.D., Goonewardena, S.N., Grabavoy, A., Samet, J.M., Geyh, A.S., Breysse, P.N., Lussier, Y.A., Natarajan, V., Garcia, J.G.N., (2008) "Murine Lung Responses to Ambient Baltimore Particulate Matter: Genomic Analysis and Contribution to Airway Hyperresponsiveness.," Environmental Health Prospectives | ||
| Ward, L.D., Bussemaker, H.J., (2008) "Predicting functional transcription factor binding through alignment-free, affinity-based analysis of orthologous promoter sequences," Bioinformatics | ||
| Yao, L., Rzhetsky, A., (2008) "Quantitative systems-level determinants of human genes targeted by successful drugs," Genome Res | ||
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| 2007 | ||
| Anastassiou D, Liu H, Varadan V, (2007) "Variable Window Binding for Mutually Exclusive Alternative Splicing," Genome Biology, Vol. 7, Issue 1, pp. R2.1-R2.12. | ||
| Fan H, Mark A E, Zhu J, Honig B, (2007) "Comparative Study of Generalized Born Models: Protein Dynamics," PNAS 102:6760-6764 | ||
| Siggers T, Silkov A, Honig B, (2007) "Structural Alignment of Protein- DNA Interfaces: Insights into the Determinants of Binding Specificity," J. Mol. Biol.: 1027-1045 | ||
| Anastassiou, D, (2007) "Computational Analysis of the Synergy Among Multiple Interacting Genes," (Review Article), Molecular Systems Biology, Vol. 3, No. 83, February 2007 | ||
| Autism Genome Project Consortium, (2007) "Mapping autism risk loci using genetic linkage and chromosomal rearrangements," Nat. Genet. 39: 319-328 | ||
| Bussemaker, H.J., Foat, B.C., Ward, L.D., (2007) "Predictive Modeling of Genome-Wide mRNA Expression: From Modules to Molecules," Annual Reviews in Biophysics and Biomolecular Structure. 36: 329-347. PMID: 17311525 | ||
| Chen, J. L., L. Sam, et al, (2007) "High-throughput functional classification of human disease genes," BMC Bioinformatics 8(Suppl 3) (S7 ): doi:10.1186/1471-2105-8-S3-S7 | ||
| Cokol, M., Iossifov, I., Rodriguez-Esteban, R., Rzhetsky, A, (2007) "How many scientific papers should be retracted?," EMBO Rep 8, 422-423. PMID: 17471252 | ||
| Greil, F., de Wit, E., Bussemaker, H.J., van Steensel, B, (2007) "HP1 controls genomic targeting of four novel heterochromatin proteins in Drosophila," EMBO J. 26:741-51. PMID: 17255947 | ||
| Lussier, Y. A. and Y. Liu, (2007) "Computational approaches to phenotyping: high-throughput phenomics," Proc Am Thorac Soc 4(1): 18-25 | ||
| Pantazatosa, S. P., J. Li, et al. , (2007) "Cross-Scale Mapping of Gene Expression to Neuroimaging Datasets via Semantic Decomposition," MEDINFO | ||
| Phung D., Valetto G., Kaiser G.E., Liu T., Kender J.R., (2007) "Adaptive Synchronization of Semantically Compressed Instructional Videos for Collaborative Distance Learning," International Journal of Distance Education Technologies, Idea Group Publishing, 5(2):56-73, 2007 | ||
| Ross, K. A., A. Janevski, J. Stoyanovich, (2007) "A Faceted Query Engine Applied to Archaeology," Internet Archeology 21, April 2007 | ||
| Sam, L., Y. Liu, et al., (2007) "Discovery of Protein Interaction Networks Shared by Diseases," Pacific Symposium on Biocomputing(12): 76-87 | ||
| J. Sebat, B. Lakshumi, D. Malhotra, C. Lese-Martin, J. Troge, T. Walsh, B. Yamrom, S. Yoon, A. Krasnitz, J. Kendall, A. Leotta, D. Pai, R. Zhang, J.Hicks, S.J. Spence, A. Lee, K. Puura, T. Lehtimaki, D. Ledbetter, P.K. Gregersen, J. Bregman, J.S. Sutcliffe, V. Jobanputra, D. Warburton, M-K. King, D. Skuse, D.H. Geschwind, T. C. Gilliam, K. Ye, and M. Wigler, (2007) "Strong association of de novo copy number mutations with autism," Science, 316: 445-449 | ||
| Sosinsky, A., Honig, B., Mann, R.S., Califano, A., (2007) "Discovering transcriptional regulatory regions in Drosophila by a non-alignment method for phylogenetic footprinting," Proc Natl Acad Sci USA. 104:6305-10. PMID: 17395715 | ||
| Murphy, C., Kaiser, G., Arias, M. , (2007) "An Approach to Software Testing of Machine Learning Applications.," 19th International Conference on Software Engineering and Knowledge Engineering, July 2007 | ||
| Lim, W., Califano, A., (2007) "Assembling a compendium of druggable apoptosis regulators," in Proc. Of the 4th Annual RECOMB Satellite on Regulatory Genomics, Boston MA. | ||
| Lussier, Y., Bodenreider, O., (2007) "Clinical Ontologies for Discovery Applications," Knowledge Discovery in the Life Sciences. Springer Verlag 2007(XXII): 450 p. | ||
| Zhang, L., Leslie, C., Lee, H.C., Kundaje, A., Ie, E., Xin, X., Freund, Y. , (2007) "CP motifs, Hap1 and Heme Signaling," International Proceedings of the 15th International Conference on Cytochrome P450: Biochemistry, Biophysics, Functional Genomics: 45-51. | ||
| Chen, J. L., Liu, Y., Sam, L.T., Li, J., Lussier, Y.A., (2007) "High-throughput functional classification of human disease genes," BMC Bioinformatics 8 (Suppl 3) (S7 ) | ||
| Cokol, M., I. Iossifov, et al., (2007) "How many scientific papers should be retracted?," EMBO Rep 8(5): 422-3 | ||
| Boorsma, A., Lu, X.J., Zakrzewska, A., Snyder, B., Klis, F.M., Bussemaker, H.J., (2007) "Inferring transcription factor co-modulation networks through regulon-based expression analysis," Proceedings of RECOMB Sattellite Meeting on Systems Biology, San Diego, CA, November 2007 | ||
| Tao, Y., Sam, L., Li, J., Friedman, C., Lussier, Y.A., (2007) "Information Theory Applied to the Sparse Geneontology Annotation Network to Predict Novel Gene Function," Bioinformatics 23: i529–i538 | ||
| 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," Annals of the New York Academy of Sciences 2007, 1115:178-202 | ||
| Melvin, I., Ie, E., Weston, J., Noble, W. S., Leslie, C., (2007) "Multi-class protein classification using adaptive codes," Journal of Machine Learning Research 8: 1557-1581 | ||
| Murphy, C., Kaiser, G., Arias, M., (2007) "Parameterizing Random Test Data According to Equivalence Classes," 2nd ACM International Workshop on Random Testing, November 2007 | ||
| Sam, L. T., Mendonça, E.A., Friedman, C., Lussier, Y.A., (2007) "PhenoGO: A Resource for the Multiscale Integration of Clinical and Biological Data," BMC Bioinformatics | ||
| Tao, Y., Patel, C., Friedman, C., Lussier, Y.A., (2007) "PIE: A Phenotype Interface Engine for Automated Representation in PATO and “Semantic Web”-Based Exchange of Clinical Data and Narratives," AMIA Annual Symposium Proceedings, 2007 | ||
| Rzhetsky, A., D. Wajngurt, et al., (2007) "Probing genetic overlap among complex human phenotypes," Proc Natl Acad Sci U S A 104(28): 11694-9 | ||
| Griffith, R., Virmani, R., Kaiser, G., (2007) "RAS Models: A Building Block for Self-Healing Benchmarks," 8th International Workshop on Performability Modeling of Computer and Communication Systems, September | ||
| Cokol, M., Rodriguez-Esteban, R., Rzhetsky, A., (2007) "A recipe for high impact," Genome Biology 8(5): 406 | ||
| Griffith, R., Virmani, R., Kaiser, G., (2007) "The Role of Reliability, Availability and Serviceability (RAS) Models in the Design and Evaluation of Self-Healing Systems," 3rd International Conference on Self-Organization and Autonomous Systems in Computing and Communications, September | ||
| Stoyanovich, J., Bedathur, S., Berberich, K., Weikum, G., (2007) "Semantically Enriched Graph-Based Authority Propagation," Proceedings of the Tenth International Workshop on the Web and Databases | ||
| Melvin, I., Ie, E., Kuang, R., Weston, J., Noble, W. S., Leslie, C., (2007) "SVM-Fold: a tool for discriminative multi-class protein fold and superfamily recognition," BMC Bioinformatics 8 (Supp 4)(S2) | ||
| Margolin, A. A. and A. Califano, (2007) "Ann N Y Acad Sci 1115: 51-72," Theory and limitations of genetic network inference from microarray data | ||
| Bales, M. E., Lussier, Y.A., Johnson, S.B., (2007) "Topological Analysis of Large-scale Biomedical Terminology Structures," Journal of the American Medical Informatics Association 14: 788-797 | ||
| Joshi, R. Passner, J. M. Rohs, R. Jain, R. Sosinsky, A. Crickmore, M. A. Jacob, V. Aggarwal, A. K. Honig, B. Mann, R. S., (2007) "Functional specificity of a Hox protein mediated by the recognition of minor groove structure," Cell | ||
| Lefebvre, C., Lim, W.K., Basso, K., Dalla Favera, R., Califano, A., (2007) "A context-specific network of protein-DNA and protein-protein interactions reveals new regulatory motifs in human B cells.," Lecture Notes in Bioinformatics | ||
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| 2006 | ||
| Lussier YA, Rappaport D, Borlawsky T, Friedman C, (2006) "PhenoGO: assigning phenotypic context to gene ontology annotations with natural language processing," Pacific Symposium on Biocomputing, pp. 64-75 | ||
| Bussemaker, H, (2006) "Modeling gene expression control using Omes Law," Molecular Systems Biology (published online), 2006. doi:10.1038(msb4100055) | ||
| Dobereiner H-G, Dubin-Thaler BJ, Hofman J, Xenias HS, Sims, TN, Giannone G, Dustin ML, Wiggins CH, Sheetz, MP., (2006) "Lateral Membrane Waves Constitute a Universal Dynamic Pattern of Motile Cells," | ||
| Foat BC, M.A., Bussemaker HJ, (2006) "Statistical mechanical modeling of genome-wide transcription factor occupancy data by MatrixREDUCE," Proceedings of ISMB | ||
| Halasz G, Van Batenburg MF., Perusse J, Hua S, White KP, Bussemaker HJ, (2006) "Detecting Transcriptionally Active Regions Using Genomic Tiling Arrays," | ||
| Friedman, C., T. Borlawsky, et al, (2006) "Bio-Ontology and text: bridging the modeling gap," Bioinformatics 22(19): 2421-9 | ||
| Goh, C. S., T. A. Gianoulis, et al, (2006) "Integration of curated databases to identify genotype-phenotype associations," BMC Genomics 7: 257 | ||
| Griffith R., Kaiser G, (2006) "A Runtime Adaptation Framework for Native C and Byt code Applications," Proceedings of 3rd IEEE International Conference on Autonomic Computing, 2006 | ||
| Griffith R., Hellerstein J.L., Kaiser G., Diao Y, (2006) "Dynamic Adaptation of Temporal Event Correlation for QoS Management in Distributed Systems," Proceedings of 14th IEEE International Workshop on Quality of Service, 2006 | ||
| Griffith R., Valetto G., Kaiser G, (2006) "Effecting Runtime Reconfiguration in Managed Execution Environments," In Parishar M., Hariri S. (eds.), Autonomic Computing: Concepts, Infrastructure, and Applications, ch. 18, CRC, 2006 | ||
| Gross P., Kaiser G, (2006) "Automated Component Interconnection for Scaling Scale-Resistant Services," Proceedings of 21st IEEE/ACM International Conference on Automated Software Engineering, 2006 | ||
| Gupta S., Becker H., Kaiser G., Stolfo S, (2006) "Verifying Genre-based Clustering Approach to Content Extraction," Proceedings of 15th World Wide Web Conference, 2006 | ||
| Halasz, G., van Batenburg, M.F., Perusse, J., Hua, S., White, K.P., Bussemaker, H.J., (2006) "Detecting Transcriptionally Active Regions Using Genomic Tiling Arrays," Genome Biology 7:R59.1-10. PMID: 16859498 | ||
| Koster, D.A., C.H. Wiggins, and N.H. Dekker, (2006) "Multiple events on single molecules: unbiased estimation in single-molecule biophysics," Proc Natl Acad Sci U S A, 2006. 103(6): p. 1750-5 | ||
| Kundaje A, M Middendorf, M Shah, C Wiggins, Y Freund and C Leslie., (2006) "A classification-based framework for predicting and analyzing gene regulatory response," BMC Bioinformatics (Special issue on "New Problems and Methods in Computational Biology"), 2006. 7(Supp 1)(S5) | ||
| Liu, Y., J. Li, et a., (2006) "An integrative genomic approach to uncover molecular mechanisms of prokaryotic traits," PLoS Comput Biol 2(11): e159 | ||
| Margolin AA, Nemenman I, Basso K, Wiggins C, Stolovitzky G, Dalla Favera R and Califano A, (2006) "ARACNE: An Algorithm for the Reconstruction of Gene Regulatory Networks in a Mammalian Cellular Context," BMC Bioinformatics, 2006. 7(Supplement 1)(S7) | ||
| Margolin AA, Wang K, Lim WK, Kustagi M, Nemenman I, Califano A, (2006) "Reverse Engineering Cellular Networks," Nature Protocols, in press, 2006 | ||
| Moorman, C., Sun, L.V., Wang, J., de Wit, E. Talhout, W., Ward, L.D., Greil, F., White, K.P.*, Bussemaker, H.J.*, van Steensel, B., (2006) "Hotspots of transcription factor colocalization in the genome of Drosophila melanogaster," Proc. Natl. Acad. Sci. U S A., 103:12027-32. PMID: 16880385, [Joint last authorship; highlighted in Nature; listed as "must read paper" on Faculty of 1000] | ||
| Ofran, Y., Yachdav, G., Mozes, E., Soong, T., Rost, B., (2006) "Create and assess protein networks through molecular characteristics of individual proteins," Bioinformatics (ISMB Proceedings), 22: e402-e407. PMID: 16873500 | ||
| Palomero T., Lim, W.K., Odom, D.T., Sulis, M.L., Real, P.J., Margolin, A., Barnes, K.C., O'Neil, J., Neuberg, D., Weng, A.P., Aster, J.C., Sigaux, F. Soulier, J., Look, A.T., Young, R.A., Califano, A., Ferrando, A.A. , (2006) "NOTCH1 directly regulates c-MYC and activates a feed-forward-loop transcriptional network promoting leukemic cell growth," Proc. Natl. Acad. Sci USA; 103:18261-18266. PMID: 17114293 | ||
| parekh J., Kaiser G., Gross P., Valetto G., (2006) "Retrofitting Autonomic Capabilities onto Legacy Systems," Journal of Cluster Computing, Kluwer, 9(2):141-159, 2006 | ||
| Rodrigues-Esteban, R., Iossifov, I., Rzhetsky, A., (2006) "Imitating manual curation of text-mined facts in biomedicine," | ||
| Ross, K.A., (2006) "Alpha Radiation is a Major Germ-Line Mutagen over Evolutionary Timescales," Evolutionary Ecology Research, 8(6), 2006, 1013-1028 | ||
| Rzhetsky, A., Zheng, T., Weinreb, C. , (2006) "Self-correcting maps of molecular pathways," PLoS ONE 1, e61. PMID: 1718369 | ||
| Rzhetsky, A., Iossifov, I., Loh, J. M., White, K. P. , (2006) "Microparadigms: chains of collective reasoning in publications about molecular interactions," Proc Natl Acad Sci U S A 103, 4940-4945. PMID: 16543380 | ||
| Varadan V., Miller D. III, and Anastassiou D., (2006) "Computational Inference of the Molecular Logic for Synaptic Connectivity in C. elegans," Bioinformatics, Vol. 22, Issue 14 – ISMB 2006, pp. e497-e506, July 2006 | ||
| Wang, K., I. Nemenman, N. Banerjee, A. A. Margolin and A. Califano, (2006) "Genome-wide Discovery of Modulators of Transcriptional Interactions in Human B Lymphocytes," Proceedings of RECOMB, 2006 | ||
| Wang, K., I. Nemenman, N. Banerjee, A. A. Margolin and A. Califano, (2006) "MINDY: An Algorithm for the Genome-wide Discovery of Modulators of Transcriptional Interactions," Journal of Computational Biology, submitted, 2006 | ||
| Weston J, Leslie C., E Ie, D Zhou, A Elisseeff, WS Noble, (2006) "Semi-Supervised Protein Classification using Cluster Kernels," Book Chapter for "Semi-Supervised Learning (Editors: O. Chapelle, B. Scholkopf and A. Zien), in press, 2006 | ||
| Weston J, K.R., Leslie C, Noble WS, (2006) "Ranking by Semi-Supervised Network Propagation," BMCBioinformatics (Special issue on "New Problems and Methods in Computational Biology"). 2006. 7(Supp 1)(S10) | ||
| Wilbur, W. J., Rzhetsky, A., Shatkay, H. , (2006) "New directions in biomedical text annotation: definitions, guidelines and corpus construction," BMC Bioinformatics 7, 356. PMID: 16867190 | ||
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| 2005 | ||
| Boorsma A, Foat BC, Vis D, Klis F, Bussemaker HJ, (2005) "T-profiler: scoring the activity of predefined groups of genes using gene expression data," Nucleic Acids Res. 2005 Jul 1;33(Web Server issue):W592-5 | ||
| Cantor MN, Sarkar IN, Bodenreider O, Lussier YA, (2005) "Genestrace: Phenomic Knowledge Discovery Via Structured Terminology," Pac Symp Biocomput.;103-14 | ||
| Cavelier G, Anastassiou D, (2005) "Phenotype Analysis Using Network Motifs Derived from Changes in Regulatory Network Dynamics," Proteins, Vol. 60, Issue 3, pp. 525-546 | ||
| Chen CP, 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 ß-strand Swapping," PNAS. 102:8531-8536 | ||
| Ie E, Weston J, Noble WS and Leslie C, (2005) "Adaptive codes for multi-class protein classification," Proceedings of the International Conference on Machine Learning , August 7-11, 2005, Bonn, Germany | ||
| Lussier YA, (2005) "Ontologies and Natural Language Processing," Russ Altman, Shankar Subramaniam. Volume 4: Bioinformatics. Encyclopedia of Genetics, Genomics, Proteomics and Bioinformatics, John Wiley & Sons (in press) | ||
| Middendorf M, Kundaje A, Freund Y, Wiggins C, Leslie C, (2005) "Motif discovery through predictive modeling of gene regulation," Proceedings of the Ninth Annual International Conference on Research in Computational Molecular Biology (RECOMB 2005) | ||
| Nair R, Rost B, (2005) "Mimicking cellular sorting improves prediction of subcellular localization," J Mol Biol 348, 85-100 | ||
| Punta M, Rost B, (2005) "PROFcon: novel prediction of long-range contacts," Bioinformatics, 21, 2960-2968 | ||
| Tao Y, Friedman C, Lussier YA, (2005) "Visualizing information across multidimensional post-genomic structured and textual databases," Bioinformatics ;21(8):1659-67. Epub 2004 Dec 14 | ||
| Wang X, Anastassiou D, Guo D, (2005) "Statistical Inference of Transcriptional Regulatory Networks," Genomic Signal Processing and Statistics, E. Dougherty et al. (Ed.), Hindawi Pub., New York | ||
| Alarcon, M., A.L. Yonan, T.C. Gilliam, R.M. Cantor, and D.H. Geschwind, (2005) "Quantitative genome scan and Ordered-Subsets Analysis of autism endophenotypes support language QTLs," Mol Psychiatry, 2005. 10(8): p. 747-57 | ||
| Basso, K., A.A. Margolin, G. Stolovitzky, U. Klein, R. Dalla-Favera, and A. Califano, (2005) "Reverse engineering of regulatory networks in human B cells," Nat Genet, 2005. 37(4): p. 382-90 | ||
| Kuang, R., J. Weston, W.S. Noble, and C. Leslie, (2005) "Motif-based protein ranking by network propagation," Bioinformatics, 2005. 21(19): p. 3711-8 | ||
| Noble, W.S., R. Kuang, C. Leslie, and J. Weston, (2005) "Identifying remote protein homologs by network propagation," Febs J, 2005. 272(20): p. 5119-28 | ||
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| 2004 | ||
| Gao F, Foat BC, Bussemaker HJ, (2004) "Defining transcriptional networks through integrative modeling of mRNA expression and transcription factor binding data," BMC Bioinformatics. 2004 Mar 18;5:31 | ||
| Liu J, Rost B, (2004) "CHOP proteins into structural domain-like fragments," Proteins 55, 678-688 | ||
| Lussier YA, Li J, (2004) "Terminological Mapping For High Throughput Comparative Biology of Phenotypes," Pac Symp Biocomput;:202-13 | ||
| Middendorf M, Kundaje A, Wiggins C, Freund Y, Leslie C, (2004) "Predicting genetic regulatory response using classification," Proceedings of the Twelfth International Conference on Intelligent Systems in Molecular Biology (ISMB 2004) | ||
| Nair R, Rost B, (2004) "LOCnet and LOCtarget: Sub-cellular localization for structural genomics targets," Nucl Acids Res 32 (Web server issue) , W517-W521 | ||
| Rost B, Yachdav G, Liu J, (2004) "The PredictProtein server," Nucl Acids Res , 32 (Web server issue) , W321-W326 | ||
| Stolc V, Gauhar Z, Mason C, Halasz G, van Batenburg MF, Rifkin SA, Hua S, Herreman T, Tongprasit W, Barbano PE, Bussemaker HJ, White KP, (2004) "A gene expression map for the euchromatic genome of Drosophila melanogaster," Science. 2004 Oct 22;306(5696):655-60 | ||
| Sussillo D, Kundaje A, and Anastassiou D, (2004) "Spectrogram Analysis of Genomes," EURASIP Journal on Applied Signal Processing, special issue on Genomic Signal Processing, Vol. 2004, No. 1, pp. 29-42 | ||
| Weston J, Eliseeff A, Zhou D, Leslie C, Noble WS, (2004) "Protein ranking: from local to global structure in the protein similarity network," Proceedings of the National Academy of Science . 101(17):6559-6563 | ||
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| 2003 | ||
| Klein U, Tu Y, Stolovitzky GA, Keller JL, Haddad J Jr, Miljkovic V, Cattoretti G, Califano A, Dalla-Favera R, (2003) "Gene expression dynamics during B cell germinal center reaction," Proc Natl Acad Sci U S A;100(5):2639-44. Epub 2003 Feb 25 | ||
| Liu AH, Zhang X, Stolovitzky GA , Califano A, Firestein SJ, (2003) "Motif-based construction of a functional map for mammalian olfactory receptors," Genomics;81(5):443-56 | ||
| Petrey D, Xiang Z, Tang CL, Xie L, Gimpelev M, Mitros T, Soto CS, Goldsmith-Fischman S, Kernytsky A, Schlessinger A, Koh IYY, Alexov E, Honig B, (2003) "Using Multiple Structure Alignments, Fast Model Building , and Energetic Analysis in Fold Recognition and Homology Modeling," Proteins: Struc., Func. and Genet. 53:430-435 | ||
| Tang CL, Xie L, Koh IYY, 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. 334:1043-1062 | ||
| Zhang X, Heller K, Hefter I, Leslie C, Chasin L, (2003) "Sequence Information for the Splicing of Human pre-mRNA Identified by Support Vector Machine Classification," Genome Research 13:2637-2650 | ||
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| 2001 | ||
| Bussemaker HJ, Li H, Siggia ED, (2001) "Regulatory element detection using correlation with expression," Nat Genet. 2001 Feb;27(2):167-71 | ||
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| 2000 | ||
| Anastassiou D, (2000) "Frequency-Domain Analysis of Biomolecular Sequences," Bioinformatics, vol. 16, no. 12, December 2000, pp. 1073-1081 | ||
| Bussemaker HJ, 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. 2000 Aug 29;97(18):10096-100 | ||
| 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 | ||
