Publications
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.
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1. Mugler, A., B. Grinshpun, R. Franks, C. H. Wiggins, (2011) Statistical method for revealing form-function relations in biological networks, Proceedings of the National Academy of Sciences of the United States of America
2. Pe'er, D., N. Hacohen , (2011) Principles and strategies for developing network models in cancer, Cell
3. Pasqualucci, L., D. Dominguez-Sola, A. Chiarenza, G. Fabbri, A. Grunn, V. Trifonov, L. H. Kasper, S. Lerach, H. Tang, J. Ma, D. Rossi, A. Chadburn, V. V. Murty, C. G. Mullighan, G. Gaidano, R. Rabadan, P. K. Brindle, R. Dalla-Favera, (2011) Inactivating mutations of acetyltransferase genes in B-cell lymphoma, Nature
4. Harpaz, R., H. Perez, H. S. Chase, R. Rabadan, G. Hripcsak, C. Friedman, (2011) Biclustering of adverse drug events in the FDA's spontaneous reporting system, Clinical pharmacology and therapeutics
5. Slattery, M, Riley, T, Liu, P, Abe, N, Gomez-Alcala, P, Dror, I, Zhou, T, Rohs, R, Honig, B, Bussemaker, H. J, Mann, R. S., (2011) Cofactor Binding Evokes Latent Differences in DNA Binding Specificity between Hox Proteins, Cell
6. Gusev, A, Shah, M. J, Kenny, E. E, Ramachandran, A, Lowe, J. K, Salit, J, Lee, C. C, Levandowsky, E. C, Weaver, T. N, Doan, Q. C, Peckham, H. E, McLaughlin, S. F, Lyons, M. R, Sheth, V. N, Stoffel, M, De La Vega, F. M, Friedman, J. M, Breslow, J. L, Pe'er, I., (2011) Low-pass Genomewide Sequencing and Variant Inference Using Identity-by-descent in an Isolated Human Population, Genetics
7. Birsoy, K, Berry, R, Wang, T, Ceyhan, O, Tavazoie, S, Friedman, J. M, Rodeheffer, M. S., (2011) Analysis of gene networks in white adipose tissue development reveals a role for ETS2 in adipogenesis, Development
8. Dewal, N, Hu, Y, Freedman, M. L, Laframboise, T, Pe'er, I., (2011) Calling amplified haplotypes in next generation tumor sequence data, Genome Res
9. Freddolino, P. L, Amini, S, Tavazoie, S., (2011) Newly identified genetic variations in common MG1655 stock cultures, J Bacteriol
10. Floratos, A, Honig, B, Pe'er, D, Califano, A., (2011) Using systems and structure biology tools to dissect cellular phenotypes, J Am Med Inform Assoc
11. Luan, B, Martyna, G, Stolovitzky, G., (2011) Characterizing and Controlling the Motion of ssDNA in a Solid-State Nanopore, Biophys J
12. Luan, B, Stolovitzky, G, Martyna, G., (2011) Slowing and controlling the translocation of DNA in a solid-state nanopore, Nanoscale
13. Amini, S, Hottes, A. K, Smith, L. E, Tavazoie, S., (2011) Fitness landscape of antibiotic tolerance in Pseudomonas aeruginosa biofilms, PLoS Pathog
14. Sumazin, P, Yang, X, Chiu, H. S, Chung, W. J, Iyer, A, Llobet-Navas, D, Rajbhandari, P, Bansal, M, Guarnieri, P, Silva, J, Califano, A., (2011) An extensive microRNA-mediated network of RNA-RNA interactions regulates established oncogenic pathways in glioblastoma, Cell
15. Kuziemko, A, Honig, B, Petrey, D., (2011) Using structure to explore the sequence alignment space of remote homologs, PLoS Comput Biol
16. Shen, Y, Gu, Y, Pe'er, I., (2011) A hidden Markov model for copy number variant prediction from whole genome resequencing data, BMC Bioinformatics
17. Basso, K, Mussolin, L, Lettieri, A, Brahmachary, M, Lim, W. K, Califano, A, Basso, G, Biondi, A, Cazzaniga, G, Rosolen, A., (2011) T-cell lymphoblastic lymphoma shows differences and similarities with T-cell acute lymphoblastic leukemia by genomic and gene expression analyses, Genes Chromosomes Cancer
18. Inigo, S, Alvarez, M. J, Strasser, B, Califano, A, Cerdan, P. D., (2011) PFT1, the MED25 subunit of the plant Mediator complex, promotes flowering through CONSTANS dependent and independent mechanisms in Arabidopsis, Plant J
19. Gusev, A, Palamara, P. F, Aponte, G, Zhuang, Z, Darvasi, A, Gregersen, P, Pe'er, I., (2011) The Architecture of Long-Range Haplotypes Shared within and across Populations, Mol Biol Evol
20. Califano, A., (2011) Striking a balance between feasible and realistic biological models, Sci Transl Med
21. Vilar, S, Harpaz, R, Chase, H. S, Costanzi, S, Rabadan, R, Friedman, C., (2011) Facilitating adverse drug event detection in pharmacovigilance databases using molecular structure similarity: application to rhabdomyolysis, J Am Med Inform Assoc
22. Meyer, P, Alexopoulos, L. G, Bonk, T, Califano, A, Cho, C. R, de la Fuente, A, de Graaf, D, Hartemink, A. J, Hoeng, J, Ivanov, N. V, Koeppl, H, Linding, R, Marbach, D, Norel, R, Peitsch, M. C, Rice, J. J, Royyuru, A, Schacherer, F, Sprengel, J, Stolle, K, Vitkup, D, Stolovitzky, G., (2011) Verification of systems biology research in the age of collaborative competition, Nat Biotechnol
23. Prill, R. J, Saez-Rodriguez, J, Alexopoulos, L. G, Sorger, P. K, Stolovitzky, G., (2011) Crowdsourcing network inference: the DREAM predictive signaling network challenge, Sci Signal
24. Wolpaw, A. J, Shimada, K, Skouta, R, Welsch, M. E, Akavia, U. D, Pe'er, D, Shaik, F, Bulinski, J. C, Stockwell, B. R., (2011) Modulatory profiling identifies mechanisms of small molecule-induced cell death, Proc Natl Acad Sci U S A
25. Kruithof-de Julio, M, Alvarez, M. J, Galli, A, Chu, J, Price, S. M, Califano, A, Shen, M. M., (2011) Regulation of extra-embryonic endoderm stem cell differentiation by Nodal and Cripto signaling, Development
26. Amini, S, Tavazoie, S., (2011) Antibiotics and the post-genome revolution, Curr Opin Microbiol
27. Hottes, A. K, Tavazoie, S., (2011) Microarray-based genetic footprinting strategy to identify strain improvement genes after competitive selection of transposon libraries, Methods Mol Biol
28. Pasqualucci, L, Trifonov, V, Fabbri, G, Ma, J, Rossi, D, Chiarenza, A, Wells, V. A, Grunn, A, Messina, M, Elliot, O, Chan, J, Bhagat, G, Chadburn, A, Gaidano, G, Mullighan, C. G, Rabadan, R, Dalla-Favera, R., (2011) Analysis of the coding genome of diffuse large B-cell lymphoma, Nature Genetics
29. Wu, Y, Vendome, J, Shapiro, L, Ben-Shaul, A, Honig, B., (2011) Transforming binding affinities from three dimensions to two with application to cadherin clustering, Nature
30. Holmes, A. B, Hawson, A, Liu, F, Friedman, C, Khiabanian, H, Rabadan, R., (2011) Discovering disease associations by integrating electronic clinical data and medical literature, Plos One
31. Oskarsson, T, Acharyya, S, Zhang, X. H, Vanharanta, S, Tavazoie, S. F, Morris, P. G, Downey, R. J, Manova-Todorova, K, Brogi, E, Massague, J., (2011) Breast cancer cells produce tenascin C as a metastatic niche component to colonize the lungs, Nat Med
32. Fischer, M, Zhang, Q. C, Dey, F, Chen, B. Y, Honig, B, Petrey, D., (2011) MarkUs: a server to navigate sequence-structure-function space, Nucleic Acids Res
33. Fabbri, G, Rasi, S, Rossi, D, Trifonov, V, Khiabanian, H, Ma, J, Grunn, A, Fangazio, M, Capello, D, Monti, S, Cresta, S, Gargiulo, E, Forconi, F, Guarini, A, Arcaini, L, Paulli, M, Laurenti, L, Larocca, L. M, Marasca, R, Gattei, V, Oscier, D, Bertoni, F, Mullighan, C. G, Foa, R, Pasqualucci, L, Rabadan, R, Dalla-Favera, R, Gaidano, G., (2011) Analysis of the chronic lymphocytic leukemia coding genome: role of NOTCH1 mutational activation, J Exp Med
34. Gilman, S. R, Iossifov, I, Levy, D, Ronemus, M, Wigler, M, Vitkup, D., (2011) Rare de novo variants associated with autism implicate a large functional network of genes involved in formation and function of synapses, Neuron
35. Zhu, J, Yu, Y, Ulbrich, M. H, Li, M. H, Isacoff, E. Y, Honig, B, Yang, J., (2011) Structural model of the TRPP2/PKD1 C-terminal coiled-coil complex produced by a combined computational and experimental approach, Proc Natl Acad Sci U S A
36. Shen, Y, Song, R, Pe'er, I., (2011) Coverage tradeoffs and power estimation in the design of whole-genome sequencing experiments for detecting association, Bioinformatics
37. Gusev, A, Kenny, E. E, Lowe, J. K, Salit, J, Saxena, R, Kathiresan, S, Altshuler, D. M, Friedman, J. M, Breslow, J. L, Pe'er, I., (2011) DASH: a method for identical-by-descent haplotype mapping uncovers association with recent variation, Am J Hum Genet
38. Zhang, Q. C, Deng, L, Fisher, M, Guan, J, Honig, B, Petrey, D., (2011) PredUs: a web server for predicting protein interfaces using structural neighbors, Nucleic Acids Res
39. Harrer, S, Waggoner, P. S, Luan, B, Afzali-Ardakani, A, Goldfarb, D. L, Peng, H, Martyna, G, Rossnagel, S. M, Stolovitzky, G. A., (2011) Electrochemical protection of thin film electrodes in solid state nanopores, Nanotechnology
40. Rudin, C, Waltz, D, Anderson, R, Boulanger, A, Salleb-Aouissi, A, Chow, M, Dutta, H, Gross, P, Huang, B, Ierome, S., (2011) Machine Learning for the New York City Power Grid, IEEE Trans Pattern Anal Mach Intell
41. Vendome, J, Posy, S, Jin, X, Bahna, F, Ahlsen, G, Shapiro, L, Honig, B., (2011) Molecular design principles underlying beta-strand swapping in the adhesive dimerization of cadherins, Nat Struct Mol Biol
42. Kim, H, Watkinson, J, Anastassiou, D., (2011) Biomarker discovery using statistically significant gene sets, J Comput Biol
43. Pe'er, D, Hacohen, N., (2011) Principles and strategies for developing network models in cancer, Cell
44. Pasqualucci, L, Dominguez-Sola, D, Chiarenza, A, Fabbri, G, Grunn, A, Trifonov, V, Kasper, L. H, Lerach, S, Tang, H, Ma, J, Rossi, D, Chadburn, A, Murty, V. V, Mullighan, C. G, Gaidano, G, Rabadan, R, Brindle, P. K, Dalla-Favera, R., (2011) Inactivating mutations of acetyltransferase genes in B-cell lymphoma, Nature
45. Harrison, O. J, Jin, X, Hong, S, Bahna, F, Ahlsen, G, Brasch, J, Wu, Y, Vendome, J, Felsovalyi, K, Hampton, C. M, Troyanovsky, R. B, Ben-Shaul, A, Frank, J, Troyanovsky, S. M, Shapiro, L, Honig, B., (2011) The extracellular architecture of adherens junctions revealed by crystal structures of type I cadherins, Structure
46. Png, K. J, Yoshida, M, Zhang, X. H, Shu, W, Lee, H, Rimner, A, Chan, T. A, Comen, E, Andrade, V. P, Kim, S. W, King, T. A, Hudis, C. A, Norton, L, Hicks, J, Massague, J, Tavazoie, S. F., (2011) MicroRNA-335 inhibits tumor reinitiation and is silenced through genetic and epigenetic mechanisms in human breast cancer, Genes Dev
47. Brasch, J, Harrison, O. J, Ahlsen, G, Carnally, S. M, Henderson, R. M, Honig, B, Shapiro, L., (2011) Structure and binding mechanism of vascular endothelial cadherin: a divergent classical cadherin, J Mol Biol
48. Shechtman, C. F, Henneberry, A. L, Seimon, T. A, Tinkelenberg, A. H, Wilcox, L. J, Lee, E, Fazlollahi, M, Munkacsi, A. B, Bussemaker, H. J, Tabas, I, Sturley, S. L., (2011) Loss of subcellular lipid transport due to ARV1 deficiency disrupts organelle homeostasis and activates the unfolded protein response, J Biol Chem
49. Shen, Y, Nicoletti, P, Floratos, A, Pirmohamed, M, Molokhia, M, Geppetti, P, Benemei, S, Giomi, B, Schena, D, Vultaggio, A, Stern, R, Daly, M. J, John, S, Nelson, M. R, Pe'er, I., (2011) Genome-wide association study of serious blistering skin rash caused by drugs, Pharmacogenomics J
50. Harpaz, R, Perez, H, Chase, H. S, Rabadan, R, Hripcsak, G, Friedman, C., (2011) Biclustering of adverse drug events in the FDA's spontaneous reporting system, Clin Pharmacol Ther
51. Behnke-Parks, W. M, Vendome, J, Honig, B, Maliga, Z, Moores, C, Rosenfeld, S. S., (2011) Loop L5 acts as a conformational latch in the mitotic kinesin Eg5, J Biol Chem
52. Kenny, E. E, Kim, M, Gusev, A, Lowe, J. K, Salit, J, Smith, J. G, Kovvali, S, Kang, H. M, Newton-Cheh, C, Daly, M. J, Stoffel, M, Altshuler, D. M, Friedman, J. M, Eskin, E, Breslow, J. L, Pe'er, I., (2011) Increased power of mixed models facilitates association mapping of 10 loci for metabolic traits in an isolated population, Human Molecular Genetics
53. Roberts, R. J, Chang, Y. C, Hu, Z, Rachlin, J. N, Anton, B. P, Pokrzywa, R. M, Choi, H. P, Faller, L. L, Guleria, J, Housman, G, Klitgord, N, Mazumdar, V, McGettrick, M. G, Osmani, L, Swaminathan, R, Tao, K. R, Letovsky, S, Vitkup, D, Segre, D, Salzberg, S. L, Delisi, C, Steffen, M, Kasif, S., (2011) COMBREX: a project to accelerate the functional annotation of prokaryotic genomes, Nucleic Acids Res
54. Cheung, Y. H, Watkinson, J, Anastassiou, D., (2011) Conditional meta-analysis stratifying on detailed HLA genotypes identifies a novel type 1 diabetes locus around TCF19 in the MHC, Human Genetics
55. Cadeiras, M, von Bayern, M, Sinha, A, Shahzad, K, Latif, F, Lim, W. K, Grenett, H, Tabak, E, Klingler, T, Califano, A, Deng, M. C., (2011) Drawing networks of rejection - a systems biological approach to the identification of candidate genes in heart transplantation, J Cell Mol Med
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56. Bu, D. X., Rai, V., Shen, X., Rosario, R., Lu, Y., D'Agati, V., Yan, S. F., Friedman, R. A., Nuglozeh, E., Schmidt, A. M., (2010) Activation of the ROCK1 branch of the transforming growth factor-beta pathway contributes to RAGE-dependent acceleration of atherosclerosis in diabetic ApoE-null mice, Circ Res
57. Zhou, X., Sumazin, P., Rajbhandari, P., Califano, A., (2010) A systems biology approach to transcription factor binding site prediction, PLoS One
58. Chastanet, A. Vitkup, D. Yuan, G. C. Norman, T. M. Liu, J. S. Losick, R. M., (2010) Broadly heterogeneous activation of the master regulator for sporulation in Bacillus subtilis, Proc Natl Acad Sci U S A
59. Chen, J. Sam, L. Huang, Y. Lee, Y. Li, J. Liu, Y. Xing, H. R. Lussier, Y. A., (2010) Protein interaction network underpins concordant prognosis among heterogeneous breast cancer signatures, J Biomed Inform
60. Ciatto, C. Bahna, F. Zampieri, N. VanSteenhouse, H. C. Katsamba, P. S. Ahlsen, G. Harrison, O. J. Brasch, J. Jin, X. Posy, S. Vendome, J. Ranscht, B. Jessell, T. M. Honig, B. Shapiro, L., (2010) T-cadherin structures reveal a novel adhesive binding mechanism, Nat Struct Mol Biol
61. Harrison, O. J. Bahna, F. Katsamba, P. S. Jin, X. Brasch, J. Vendome, J. Ahlsen, G. Carroll, K. J. Price, S. R. Honig, B. Shapiro, L., (2010) Two-step adhesive binding by classical cadherins, Nat Struct Mol Biol
62. Hsiao, T. L. Revelles, O. Chen, L. Sauer, U. Vitkup, D., (2010) Automatic policing of biochemical annotations using genomic correlations, Nat Chem Biol
63. Kitayner, M. Rozenberg, H. Rohs, R. Suad, O. Rabinovich, D. Honig, B. Shakked, Z., (2010) Diversity in DNA recognition by p53 revealed by crystal structures with Hoogsteen base pairs, Nat Struct Mol Biol
64. Klein, U. Lia, M. Crespo, M. Siegel, R. Shen, Q. Mo, T. Ambesi-Impiombato, A. Califano, A. Migliazza, A. Bhagat, G. Dalla-Favera, R., (2010) The DLEU2/miR-15a/16-1 cluster controls B cell proliferation and its deletion leads to chronic lymphocytic leukemia, Cancer Cell
65. Lee, Y. Yang, X. Huang, Y. Fan, H. Zhang, Q. Wu, Y. Li, J. Hasina, R. Cheng, C. Lingen, M. W. Gerstein, M. B. Weichselbaum, R. R. Xing, H. R. Lussier, Y. A., (2010) Network modeling identifies molecular functions targeted by miR-204 to suppress head and neck tumor metastasis, PLoS Comput Biol
66. Lu, X. J. Olson, W. K. Bussemaker, H. J., (2010) The RNA backbone plays a crucial role in mediating the intrinsic stability of the GpU dinucleotide platform and the GpUpA/GpA miniduplex, Nucleic Acids Res
67. Rohs, R. Jin, X. West, S. M. Joshi, R. Honig, B. Mann, R. S., (2010) Origins of Specificity in Protein-DNA Recognition, Annu Rev Biochem
68. Sanchez-Garcia, F. Akavia, U. D. Mozes, E. Pe'er, D., (2010) JISTIC: Identification of Significant Targets in Cancer, BMC Bioinformatics
69. Swapneel Sheth, Nipun Arora, Christian Murphy, Gail Kaiser, (2010) weHelp: A Reference Architecture for Social Recommender Systems, 3rd International Workshop on Social Software Engineering
70. van Batenburg, M. F. Li, H. Polman, J. A. Lachize, S. Datson, N. A. Bussemaker, H. J. Meijer, O. C., (2010) Paired hormone response elements predict caveolin-1 as a glucocorticoid target gene, PLoS One
71. Yang, X. Huang, Y. Crowson, M. Li, J. Maitland, M. L. Lussier, Y. A., (2010) Kinase inhibition-related adverse events predicted from in vitro kinome and clinical trial data, J Biomed Inform
72. Akavia, U. D., O. Litvin, J. Kim, F. Sanchez-Garcia, D. Kotliar, H. C. Causton, P. Pochanard, E. Mozes, L. A. Garraway and D. Pe'er, (2010) An integrated approach to uncover drivers of cancer., Cell
73. Basso, K., M. Saito, P. Sumazin, A. A. Margolin, K. Wang, W. K. Lim, Y. Kitagawa, C. Schneider, M. J. Alvarez, A. Califano R. Dalla-Favera, (2010) Integrated biochemical and computational approach identifies BCL6 direct target genes controlling multiple pathways in normal germinal center B cells, Blood
74. Carro, M. S., W. K. Lim, M. J. Alvarez, R. J. Bollo, X. Zhao, E. Y. Snyder, E. P. Sulman, S. L. Anne, F. Doetsch, H. Colman, A. Lasorella, K. Aldape, A. Califano, A. Iavarone, (2010) The transcriptional network for mesenchymal transformation of brain tumours, Nature
75. Koehnke, J., P. S. Katsamba, G. Ahlsen, F. Bahna, J. Vendome, B. Honig, L. Shapiro, X. Jin, (2010) Splice form dependence of beta-neurexin/neuroligin binding interactions, Neuron
76. Lee, H., Z. Li, A. Silkov, M. Fischer, D. Petrey, B. Honig, D. Murray, (2010) High-throughput computational structure-based characterization of protein families: START domains and implications for structural genomics, J Struct Funct Genomics
77. Lefebvre, C., P. Rajbhandari, M. J. Alvarez, P. Bandaru, W. K. Lim, M. Sato, K. Wang, P. Sumazin, M. Kustagi, B. C. Bisikirska, K. Basso, P. Beltrao, N. Krogan, J. Gautier, R. Dalla-Favera, A. Califano, (2010) A human B-cell interactome identifies MYB and FOXM1 as master regulators of proliferation in germinal centers, Molecular Systems Biology
78. Li, X., C. Panea, C. H. Wiggins, V. Reinke, C. Leslie, (2010) Learning "graph-mer" motifs that predict gene expression trajectories in development, PLoS computational biology
79. Norel, R., D. Petrey, B. Honig, (2010) PUDGE: a flexible, interactive server for protein structure prediction, Nucleic Acids Res
80. West, S. M., R. Rohs, R. S. Mann, B. Honig, (2010) Electrostatic interactions between arginines and the minor groove in the nucleosome, J Biomol Struct Dyn
81. Zhang, Q. C., D. Petrey, R. Norel, B. H. Honig , (2010) Protein interface conservation across structure space, Proc Natl Acad Sci U S A
82. Chen, B. Y., B. Honig, (2010) VASP: a volumetric analysis of surface properties yields insights into protein-ligand binding specificity, PLoS Comput Biol
83. Cheng, L., J. Zhu, W. H. Hui, X. Zhang, B. Honig, Q. Fang, Z. H. Zhou, (2010) Backbone model of an aquareovirus virion by cryo-electron microscopy and bioinformatics, J Mol Biol
84. Mugler, A., A. M. Walczak, C. H. Wiggins , (2010) Information-optimal transcriptional response to oscillatory driving, Physical review letters
85. Love, J., F. Mancia, L. Shapiro, M. Punta, B. Rost, M. Girvin, D. N. Wang, M. Zhou, J. F. Hunt, T. Szyperski, E. Gouaux, R. MacKinnon, A. McDermott, B. Honig, M. Inouye, G. Montelione, W. A. Hendrickson, (2010) The New York Consortium on Membrane Protein Structure (NYCOMPS): a high-throughput platform for structural genomics of integral membrane proteins, J Struct Funct Genomics
86. Singarapu, K. K., J. L. Mills, R. Xiao, T. Acton, M. Punta, M. Fischer, B. Honig, B. Rost, G. T. Montelione, T. Szyperski , (2010) Solution NMR structures of proteins VPA0419 from Vibrio parahaemolyticus and yiiS from Shigella flexneri provide structural coverage for protein domain family PFAM 04175, Proteins
87. Trifonov, V., L. Pascualucci, R. Dalla-Favera, R. Rabadan , (2010) Fractal-like Distributions over the Rational Numbers in High-throughput Biological and Clinical Data, Nature Precedings
88. Van Vlierberghe, P., T. Palomero, H. Khiabanian, J. Van der Meulen, M. Castillo, N. Van Roy, B. De Moerloose, J. Philippe, S. Gonzalez-Garcia, M. L. Toribio, T. Taghon, L. Zuurbier, B. Cauwelier, C. J. Harrison, C. Schwab, M. Pisecker, S. Strehl, A. W. Langerak, J. Gecz, E. Sonneveld, R. Pieters, E. Paietta, J. M. Rowe, P. H. Wiernik, Y. Benoit, J. Soulier, B. Poppe, X. Yao, C. Cordon-Cardo, J. Meijerink, R. Rabadan, F. Speleman, A. Ferrando , (2010) PHF6 mutations in T-cell acute lymphoblastic leukemia, Nature genetics
89. Wu, Y., X. Jin, O. Harrison, L. Shapiro, B. H. Honig, A. Ben-Shaul , (2010) Cooperativity between trans and cis interactions in cadherin-mediated junction formation, Proc Natl Acad Sci U.S.A
90. Zhu, J., L. Cheng, Q. Fang, Z. H. Zhou, B. Honig , (2010) Building and refining protein models within cryo-electron microscopy density maps based on homology modeling and multiscale structure refinement, J Mol Biol
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91. 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. 30(5):744-52.
92. 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, Mol Syst Biol. 5:310.
93. 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 459(7247):717-21.
94. Gusev A, Lowe JK, Stoffel M, Daly MJ, Altshuler D, Breslow JL, Friedman JM, Pe'er I., (2009) Whole population, genome-wide mapping of hidden relatedness, Genome Res. 19(2):318-26.
95. 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, (2009) Linking molecular affinity and cellular specificity in cadherin-mediated adhesion, Proc Natl Acad Sci U S A. 106(28):11594-9. PMID: 19553217
96. 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. 27(6):549-55. PMID: 19465925
97. 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. 5(1):e1000358. PMID: 19180192
98. Lim, W. K., Lyashenko, E., Califano, A., (2009) Master regulators used as breast cancer metastasis classifier, Pac Symp Biocomput. 2009:504-15. PMID: 19209726
99. 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. 106(16):6441-6. PMID: 19223586
100. 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 323(5918):1218-22. PMID: 19164706
101. Liu, Y. Sam, L. Li, J. Lussier, Y. A., (2009) Robust methods for accurate diagnosis using pan-microbiological oligonucleotide microarrays, BMC Bioinformatics 10(Suppl 2):S11. PMID: 19208186
102. 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. 5(2):e1000365. PMID: 19197348
103. Lussier, Y.A., Lee, Y., Radivojac, P., Ofran, Y., Butte, A., Kann, M. , (2009) Molecular Bioinformatics for Disease - Session Introduction, Pacific Symposium on Biocomputing
104. Melvin, I., Weston, J., Leslie, C., Noble, W. S., (2009) RANKPROP: a web server for protein remote homology detection, Bioinformatics 25(1):121-2. PMID: 18990723
105. 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. 23(5):1325-37. PMID: 19124556
106. 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
107. 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
108. Nimrod, G., Szilagyi, 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. PMID: 19233205
109. Prabhu, S., Pe'er, I., (2009) Overlapping pools for high-throughput targeted resequencing, Genome Res. 19(7):1254-61. PMID: 19447964
110. Raj, A., Wiggins, C. H., (2009) An information-theoretic derivation of min-cut based clustering., IEEE Transactions on Information Theory
111. 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. 16(2):201-12. PMID: 19193145
112. 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. 10 Suppl 2:S8. PMID: 19208196
113. Sethumadhavan, S., Kaiser, G.E., (2009) COMPASS: A Community-Drive Parallelization Advisor for Sequential Software., 2nd International Workshop on Multicore Software Engineering
114. Walczak, A. M., Mugler, A., Wiggins, C. H, (2009) A stochastic spectral analysis of transcriptional regulatory cascades, Proc Natl Acad Sci U S A. 106(16):6529-34. PMID: 19351901
115. Waltz, D., Buchanan, B. G., (2009) Computer science. Automating science, Science. 324(5923):43-4. PMID: 19342574
116. 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. 2009:264-75. PMID: 19209707
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118. 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., Dev Cell. 17(2):210-21. PMID: 19686682
119. 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. PMID: 19362815
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122. Alvarez, M. J., Sumazin, P., Rajbhandari, P., Califano, A., (2009) Correlating measurements across samples improves accuracy of large-scale expression profile experiments, Genome Biol
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123. 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
124. 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. PMID: 18079152
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127. 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
128. Chu, M., Murphy, C., Kaiser, G. , (2008) Distributed In Vivo Testing of Software Applications, 1st IEEE International Conference on Software Testing, Verification, and Validation
129. 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. PMID: 18348202
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147. Amer-Yahia, S., M. Benedikt, Lakshmanan, L., J. Stoyanovich , (2008) Efficient Network-Aware Search in Collaborative Tagging Sites., Proceedings of the VLDB Conference
148. 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. 3(9):e3112.
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152. 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
153. 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
154. Murphy, C., K. Shen, G. Kaiser, (2008) Using JML Runtime Assertion Checking to Perform Metamorphic Testing in Applications without Test Oracles., 2nd IEEE International Conference on Software Testing, Verification and Validation
155. Murphy, C., Shen, K., Kaiser, G.E. , (2008) Automatic System Testing of Programs without Test Oracles, International Symposium on Testing and Analysis
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160. 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
161. 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., Environ Health Perspect. 116(11):1500-8. PMID: 19057703
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186. Tao, Y., Patel, C., Friedman, C., Lussier, Y.A., (2007) PIE: A Phenotype Interface Engine for Automated Representation in PATO and “Semantic Webâ€-Based Exchange of Clinical Data and Narratives, AMIA Annual Symposium Proceedings, 2007
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