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. Arkhipov A, Shan Y, Das R, Endres NF, Eastwood MP, Wemmer DE, Kuriyan J, Shaw DE, (2013) Architecture and membrane interactions of the EGF receptor, Cell.
2. Chan JM, Rabadan R., (2013) Quantifying pathogen surveillance using temporal genomic data, MBio.
3. Contreras JL, Floratos A, Holden AL, (2013) The International Serious Adverse Events Consortium's data sharing model, Nat Biotechnol.
4. Dey F, Cliff Zhang Q, Petrey D, Honig B, (2013) Toward a "structural BLAST": Using structural relationships to infer function, Protein Sci.
5. Endres NF, Das R, Smith AW, Arkhipov A, Kovacs E, Huang Y, Pelton JG, Shan Y, Shaw DE, Wemmer DE, Groves JT, Kuriyan J, (2013) Conformational coupling across the plasma membrane in activation of the EGF receptor, Cell.
6. Eydgahi H, Chen WW, Muhlich JL, Vitkup D, Tsitsiklis JN, Sorger PK, (2013) Properties of cell death models calibrated and compared using Bayesian approaches, Mol Syst Biol.
7. Li Q, Seo JH, Stranger B, McKenna A, Pe'er I, Laframboise T, Brown M, Tyekucheva S, Freedman ML, (2013) Integrative eQTL-based analyses reveal the biology of breast bancer risk loci., Cell.
8. Maute RL, Schneider C, Sumazin P, Holmes A, Califano A, Basso K, Dalla-Favera R, (2013) tRNA-derived microRNA modulates proliferation and the DNA damage response and is down-regulated in B cell lymphoma, Proc Natl Acad Sci U S A.
9. Nygaard R, Zou Y, Dror RO, Mildorf TJ, Arlow DH, Manglik A, Pan AC, Liu CW, Fung JJ, Bokoch MP, Thian FS, Kobilka TS, Shaw DE, Mueller L, Prosser RS, Kobilka BK, (2013) The dynamic process of β(2)-adrenergic receptor activation, Cell.
10. Ostrov N, Wingler LM, Cornish VW, (2013) Gene assembly and combinatorial libraries in S. cerevisiae via reiterative recombination, Methods Mol Biol.
11. Rodriguez-Barrueco R. Marshall N, Silva JM, (2013) Pooled shRNA screenings: experimental approach, Methods Mol Biol.
12. Rossi D, Rasi S, Spina V, Bruscaggin A, Monti S, Ciardullo C, Deambrogi C, Khiabanian H, Serra R, Bertoni F, Forconi F, Laurenti L, Marasca R, Dal-Bo M, Rossi FM, Bulian P, Nomdedeu J, Del Poeta G, Gattei V, Pasqualucci L, Rabadan R, Foà R, Dalla-Favera R, Gaidano G, (2013) Integrated mutational and cytogenetic analysis identifies new prognostic subgroups in chronic lymphocytic leukemia, Blood.
13. Schmidt AG, Xu H, Khan AR, O'Donnell T, Khurana S, King LR, Manischewitz J, Golding H, Suphaphiphat P, Carfi A, Settembre EC, Dormitzer PR, Kepler TB, Zhang R, Moody MA, Haynes BF, Liao HX, Shaw DE, Harrison SC, (2013) Preconfiguration of the antigen-binding site during affinity maturation of a broadly neutralizing influenza virus antibody, Proc Natl Acad Sci U S A.
14. Shibata M, Shen MM, (2013) The roots of cancer: stem cells and the basis for tumor heterogeneity, Bioessays.
15. Singh AP, Zafer S, Pe'er I, (2013) Metaseq: privacy preserving meta-analysis of sequencing-based association studies, Pac Symp Biocomput.
16. Tzoneva G, Perez-Garcia A, Carpenter Z, Khiabanian H, Tosello V, Allegretta M, Paietta E, Racevskis J, Rowe JM, Tallman MS, Paganin M, Basso G, Hof J, Kirschner-Schwabe R, Palomero T, Rabadan R, Ferrando A, (2013) Activating mutations in the NT5C2 nucleotidase gene drive chemotherapy resistance in relapsed ALL, Nat Med.
17. Wang ZA, Mitrofanova A, Bergren SK, Abate-Shen C, Cardiff RD, Califano A, Shen MM, (2013) Lineage analysis of basal epithelial cells reveals their unexpected plasticity and supports a cell-of-origin model for prostate cancer heterogeneity, Nat Cell Biol.
18. Weirauch MT, Cote A, Norel R, Annala M, Zhao Y, Riley TR, Saez-Rodriguez J, Cokelaer T, Vedenko A, Talukder S; DREAM5 Consortium, Agius P, Arvey A, Bucher P, Callan CG Jr, Chang CW, Chen CY, Chen YS, Chu YW, Grau J, Grosse I, Jagannathan V, Keilwagen J, Kiełbasa SM, Kinney JB, Klein H, Kursa MB, Lähdesmäki H, Laurila K, Lei C, Leslie C, Linhart C, Murugan A, Myšičková A, Noble WS, Nykter M, Orenstein Y, Posch S, Ruan J, Rudnicki WR, Schmid CD, Shamir R, Sung WK, Vingron M, Zhang Z, Bussemaker HJ, Morris QD, Bulyk ML, Stolovitzky G, Hughes TR, (2013) Evaluation of methods for modeling transcription factor sequence specificity, Nat Biotechnol.
19. Yu J, Putcha P, Califano A, Silva JM, (2013) Pooled shRNA screenings: computational analysis, Methods Mol Biol.
20. Zhang C, Srinivasan Y, Arlow DH, Fung JJ, Palmer D, Zheng Y, Green HF, Pandey A, Dror RO, Shaw DE, Weis WI, Coughlin SR, Kobilka BK, (2013) High-resolution crystal structure of human protease-activated receptor 1, Nature. 2012 Dec 20;492(7429):387-92.
21. Zhang QC, Petrey D, Garzón JI, Deng L, Honig B, (2013) PrePPI: a structure-informed database of protein-protein interactions, Nucleic Acids Res.
22. Cheng WY, Yang TH, Anastassiou D, (2013) Biomolecular events in cancer revealed by attractor metagenes, PLoS Comput Biol.
23. Jin F, Irshad S, Yu W, Belakavadi M, Chekmareva M, Ittmann MM, Abate-Shen C, Fondell JD, (2013) ERK and AKT signaling pathways promote MED1 overexpression in prostate cancer cells in association with elevated proliferation and tumorigenicity, Mol Cancer Res.
24. Letso RR, Bauer AJ, Lunn MR, Yang WS, Stockwell BR, (2013) Small molecule screen reveals regulation of survival motor neuron protein abundance by Ras proteins, ACS Chem Biol.
25. Matos MJ, Vilar S, Gonzalez-Franco RM, Uriarte E, Santana L, Friedman C, Tatonetti NP, Viña D, Fontenla JA, (2013) Novel (coumarin-3-yl)carbamates as selective MAO-B inhibitors: Synthesis, in vitro and in vivo assays, theoretical evaluation of ADME properties and docking study, Eur J Med Chem.
26. Pan AC, Borhani DW, Dror RO, Shaw DE, (2013) Molecular determinants of drug-receptor binding kinetics, Drug Discov Today.
27. Piana S, Lindorff-Larsen K, Shaw DE, (2013) Atomic-level description of ubiquitin folding, Proc Natl Acad Sci U S A.
28. Sonabend AM, Yun J, Lei L, Leung R, Soderquist C, Crisman C, Gill BJ, Carminucci A, Sisti J, Castelli M, Sims PA, Bruce JN, Canoll P, (2013) Murine cell line model of proneural glioma for evaluation of anti-tumor therapies, J Neurooncol.
29. Trifonov V, Pasqualucci L, Favera RD, Rabadan R, (2013) MutComFocal: an integrative approach to identifying recurrent and focal genomic alterations in tumor samples, BMC Syst Biol.
30. Vilar S, Uriarte E, Santana L, Tatonetti NP, Friedman C, (2013) Detection of drug-drug interactions by modeling interaction profile fingerprints, PLoS One.
31. White RW, Tatonetti NP, Shah NH, Altman RB, Horvitz E, (2013) Web-scale pharmacovigilance: listening to signals from the crowd, J Am Med Inform Assoc.
32. Wu Y, Honig B, Ben-Shaul A, (2013) Theory and simulations of adhesion receptor dimerization on membrane surfaces, Biophys J.
33. Yu L, Wynn J, Cheung YH, Shen Y, Mychaliska GB, Crombleholme TM, Azarow KS, Lim FY, Chung DH, Potoka D, Warner BW, Bucher B, Stolar C, Aspelund G, Arkovitz MS, Chung WK, (2013) Variants in GATA4 are a rare cause of familial and sporadic congenital diaphragmatic hernia, Hum Genet.
34. Eom T, Zhang C, Wang H, Lay K, Fak J, Noebels JL, Darnell RB, (2013) NOVA-dependent regulation of cryptic NMD exons controls synaptic protein levels after seizure, Elife.
35. Finck R, Simonds EF, Jager A, Krishnaswamy S, Sachs K, Fantl W, Pe'er D, Nolan GP, Bendall SC, (2013) Normalization of mass cytometry data with bead standards, Cytometry A.
36. Jia AY, Castillo-Martin M, Domingo-Domenech J, Bonal DM, Sánchez-Carbayo M, Silva JM, Cordon-Cardo C, (2013) A common microRNA signature consisting of miR-133a, miR-139-3p, and miR-142-3p clusters bladder carcinoma in situ with normal umbrella cells, Am J Pathol.
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37. Andreopoulos, B., Anastassiou, D., (2012) Integrated Analysis Reveals hsa-miR-142 as a Representative of a Lymphocyte-Specific Gene Expression and Methylation Signature, Cancer Inform
38. Bansal, M., Califano, A., (2012) Genome-wide dissection of posttranscriptional and posttranslational interactions, Methods Mol Biol
39. Borhani, D. W., Shaw, D. E., (2012) The future of molecular dynamics simulations in drug discovery, J Comput Aided Mol Des
40. Brasch, J., Harrison, O. J., Honig, B., Shapiro, L., (2012) Thinking outside the cell: how cadherins drive adhesion, Trends Cell Biol
41. Califano, A., Kellis, M., Stolovitzky, G., (2012) Preface: RECOMB Systems Biology, Regulatory Genomics, and DREAM 2011 special issue, J Comput Biol
42. Chen, Y., Sheng, R., Kallberg, M., Silkov, A., Tun, M. P., Bhardwaj, N., Kurilova, S., Hall, R. A., Honig, B., Lu, H., Cho, W., (2012) Genome-wide functional annotation of dual-specificity protein- and lipid-binding modules that regulate protein interactions, Mol Cell
43. Cheng, W. Y., Kandel, J. J., Yamashiro, D. J., Canoll, P., Anastassiou, D., (2012) A multi-cancer mesenchymal transition gene expression signature is associated with prolonged time to recurrence in glioblastoma, Plos One
44. Dapito, D. H., Mencin, A., Gwak, G. Y., Pradere, J. P., Jang, M. K., Mederacke, I., Caviglia, J. M., Khiabanian, H., Adeyemi, A., Bataller, R., Lefkowitch, J. H., Bower, M., Friedman, R., Sartor, R. B., Rabadan, R., Schwabe, R. F., (2012) Promotion of hepatocellular carcinoma by the intestinal microbiota and TLR4, Cancer Cell
45. Della Gatta, G., Palomero, T., Perez-Garcia, A., Ambesi-Impiombato, A., Bansal, M., Carpenter, Z. W., De Keersmaecker, K., Sole, X., Xu, L., Paietta, E., Racevskis, J., Wiernik, P. H., Rowe, J. M., Meijerink, J. P., Califano, A., Ferrando, A. A., (2012) Reverse engineering of TLX oncogenic transcriptional networks identifies RUNX1 as tumor suppressor in T-ALL, Nat Med
46. Dror, R. O., Dirks, R. M., Grossman, J. P., Xu, H., Shaw, D. E., (2012) Biomolecular simulation: a computational microscope for molecular biology, Annu Rev Biophys
47. Eletsky, A., Petrey, D., Zhang, Q. C., Lee, H. W., Acton, T. B., Xiao, R., Everett, J. K., Prestegard, J. H., Honig, B., Montelione, G. T., Szyperski, T., (2012) Solution NMR structures reveal unique homodimer formation by a winged helix-turn-helix motif and provide first structures for protein domain family PF10771, J Struct Funct Genomics
48. Freddolino, P. L., Goodarzi, H., Tavazoie, S., (2012) Fitness Landscape Transformation through a Single Amino Acid Change in the Rho Terminator, PLoS Genet
49. Freddolino, P. L., Tavazoie, S., (2012) Beyond Homeostasis: A Predictive-Dynamic Framework for Understanding Cellular Behavior, Annu Rev Cell Dev Biol
50. Goodarzi, H., Najafabadi, H. S., Oikonomou, P., Greco, T. M., Fish, L., Salavati, R., Cristea, I. M., Tavazoie, S., (2012) Systematic discovery of structural elements governing stability of mammalian messenger RNAs, Nature
51. Greenbaum, B. D., Li, O. T., Poon, L. L., Levine, A. J., Rabadan, R., (2012) Viral reassortment as an information exchange between viral segments, Proc Natl Acad Sci U S A
52. Guha, S., Rosenfeld, J. A., Malhotra, A. K., Lee, A. T., Gregersen, P. K., Kane, J. M., Pe'er, I., Darvasi, A., Lencz, T., (2012) Implications for health and disease in the genetic signature of the Ashkenazi Jewish population, Genome Biol
53. Henn, B. M., Hon, L., Macpherson, J. M., Eriksson, N., Saxonov, S., Pe'er, I., Mountain, J. L., (2012) Cryptic distant relatives are common in both isolated and cosmopolitan genetic samples, Plos One
54. Iliadis, A., Anastassiou, D., Wang, X., (2012) A unified framework for haplotype inference in nuclear families, Ann Hum Genet
55. Jensen, M. O., Jogini, V., Borhani, D. W., Leffler, A. E., Dror, R. O., Shaw, D. E., (2012) Mechanism of voltage gating in potassium channels, Science
56. Jin, X., Walker, M. A., Felsovalyi, K., Vendome, J., Bahna, F., Mannepalli, S., Cosmanescu, F., Ahlsen, G., Honig, B., Shapiro, L., (2012) Crystal structures of Drosophila N-cadherin ectodomain regions reveal a widely used class of Ca(2)+-free interdomain linkers, Proc Natl Acad Sci U S A
57. Kenny, E. E., Pe'er, I., Karban, A., Ozelius, L., Mitchell, A. A., Ng, S. M., Erazo, M., Ostrer, H., Abraham, C., Abreu, M. T., Atzmon, G., Barzilai, N., Brant, S. R., Bressman, S., Burns, E. R., Chowers, Y., Clark, L. N., Darvasi, A., Doheny, D., Duerr, R. H., Eliakim, R., Giladi, N., Gregersen, P. K., Hakonarson, H., Jones, M. R., Marder, K., McGovern, D. P., Mulle, J., Orr-Urtreger, A., Proctor, D. D., Pulver, A., Rotter, J. I., Silverberg, M. S., Ullman, T., Warren, S. T., Waterman, M., Zhang, W., Bergman, A., Mayer, L., Katz, S., Desnick, R. J., Cho, J. H., Peter, I., (2012) A genome-wide scan of Ashkenazi Jewish Crohn's disease suggests novel susceptibility loci, PLoS Genet
58. Kreimer, A., Litvin, O., Hao, K., Molony, C., Pe'er, D., Pe'er, I., (2012) Inference of modules associated to eQTLs, Nucleic Acids Res
59. Kruse, A. C., Hu, J., Pan, A. C., Arlow, D. H., Rosenbaum, D. M., Rosemond, E., Green, H. F., Liu, T., Chae, P. S., Dror, R. O., Shaw, D. E., Weis, W. I., Wess, J., Kobilka, B. K., (2012) Structure and dynamics of the M3 muscarinic acetylcholine receptor, Nature
60. Lefebvre, C., Rieckhof, G., Califano, A., (2012) Reverse-engineering human regulatory networks, Wiley Interdiscip Rev Syst Biol Med
61. Lindorff-Larsen, K., Maragakis, P., Piana, S., Eastwood, M. P., Dror, R. O., Shaw, D. E., (2012) Systematic validation of protein force fields against experimental data, Plos One
62. Lindorff-Larsen, K., Trbovic, N., Maragakis, P., Piana, S., Shaw, D. E., (2012) Structure and dynamics of an unfolded protein examined by molecular dynamics simulation, J Am Chem Soc
63. Martinez, M. R., Corradin, A., Klein, U., Alvareza, M. J., Toffolo, G. M., di Camillo, B., Califano, A., Stolovitzky, G. A., (2012) Quantitative modeling of the terminal differentiation of B cells and mechanisms of lymphomagenesis, Proc Natl Acad Sci U S A
64. McIsaac, R. S., Petti, A. A., Bussemaker, H. J., Botstein, D., (2012) Perturbation-based analysis and modeling of combinatorial regulation in the yeast sulfur assimilation pathway, Mol Biol Cell
65. Meyer, P., Hoeng, J., Rice, J. J., Norel, R., Sprengel, J., Stolle, K., Bonk, T., Corthesy, S., Royyuru, A., Peitsch, M. C., Stolovitzky, G., (2012) Industrial methodology for process verification in research (IMPROVER): toward systems biology verification, Bioinformatics
66. Nicoletti, P., Cartsos, V. M., Palaska, P. K., Shen, Y., Floratos, A., Zavras, A. I., (2012) Genomewide pharmacogenetics of bisphosphonate-induced osteonecrosis of the jaw: the role of RBMS3, Oncologist
67. Ntziachristos, P., Tsirigos, A., Van Vlierberghe, P., Nedjic, J., Trimarchi, T., Flaherty, M. S., Ferres-Marco, D., da Ros, V., Tang, Z., Siegle, J., Asp, P., Hadler, M., Rigo, I., De Keersmaecker, K., Patel, J., Huynh, T., Utro, F., Poglio, S., Samon, J. B., Paietta, E., Racevskis, J., Rowe, J. M., Rabadan, R., Levine, R. L., Brown, S., Pflumio, F., Dominguez, M., Ferrando, A., Aifantis, I., (2012) Genetic inactivation of the polycomb repressive complex 2 in T cell acute lymphoblastic leukemia, Nat Med
68. Petti, A. A., McIsaac, R. S., Ho-Shing, O., Bussemaker, H. J., Botstein, D., (2012) Combinatorial Control of Diverse Metabolic and Physiological Functions by Transcriptional Regulators of the Yeast Sulfur Assimilation Pathway, Mol Biol Cell
69. Raval, A., Piana, S., Eastwood, M. P., Dror, R. O., Shaw, D. E., (2012) Refinement of protein structure homology models via long, all-atom molecular dynamics simulations, Proteins
70. Rossi, D., Rasi, S., Fabbri, G., Spina, V., Fangazio, M., Forconi, F., Marasca, R., Laurenti, L., Bruscaggin, A., Cerri, M., Monti, S., Cresta, S., Fama, R., De Paoli, L., Bulian, P., Gattei, V., Guarini, A., Deaglio, S., Capello, D., Rabadan, R., Pasqualucci, L., Dalla-Favera, R., Foa, R., Gaidano, G., (2012) Mutations of NOTCH1 are an independent predictor of survival in chronic lymphocytic leukemia, Blood
71. Shan, Y., Eastwood, M. P., Zhang, X., Kim, E. T., Arkhipov, A., Dror, R. O., Jumper, J., Kuriyan, J., Shaw, D. E., (2012) Oncogenic Mutations Counteract Intrinsic Disorder in the EGFR Kinase and Promote Receptor Dimerization, Cell
72. Tan, A. Y., Riley, T. R., Coady, T., Bussemaker, H. J., Manley, J. L., (2012) TLS/FUS (translocated in liposarcoma/fused in sarcoma) regulates target gene transcription via single-stranded DNA response elements, Proc Natl Acad Sci U S A
73. Velez, C., Palamara, P. F., Guevara-Aguirre, J., Hao, L., Karafet, T., Guevara-Aguirre, M., Pearlman, A., Oddoux, C., Hammer, M., Burns, E., Pe'er, I., Atzmon, G., Ostrer, H., (2012) The impact of Converso Jews on the genomes of modern Latin Americans, Human Genetics
74. Vilar, S., Harpaz, R., Uriarte, E., Santana, L., Rabadan, R., Friedman, C., (2012) Drug-drug interaction through molecular structure similarity analysis, J Am Med Inform Assoc
75. Zhang QC, Petrey D, Garzón JI, Deng L, Honig B., (2012) PrePPI: a structure-informed database of protein-protein interactions.,
76. Bisikirska BC, Adam SJ, Alvarez MJ, Rajbhandari P, Cox R, Lefebvre C, Wang K, Rieckhof GE, Felsher DW, Califano A., (2012) STK38 is a critical upstream regulator of MYC's oncogenic activity in human B-cell lymphoma.,
77. Gilman SR, Chang J, Xu B, Bawa TS, Gogos JA, Karayiorgou M, Vitkup D., (2012) Diverse types of genetic variation converge on functional gene networks involved in schizophrenia.,
78. Pencheva N, Tran H, Buss C, Huh D, Drobnjak M, Busam K, Tavazoie SF., (2012) Convergent Multi-miRNA Targeting of ApoE Drives LRP1/LRP8-Dependent Melanoma Metastasis and Angiogenesis.,
79. Iliadis A, Anastassiou D, Wang X., (2012) Fast and accurate haplotype frequency estimation for large haplotype vectors from pooled DNA data.,
80. Palamara PF, Lencz T, Darvasi A, Pe'er I., (2012) Length distributions of identity by descent reveal fine-scale demographic history.,
81. Singer S, Zhao R, Barsotti AM, Ouwehand A, Fazollahi M, Coutavas E, Breuhahn K, Neumann O, Longerich T, Pusterla T, Powers MA, Giles KM, Leedman PJ, Hess J, Grunwald D, Bussemaker HJ, Singer RH, Schirmacher P, Prives C., (2012) Nuclear Pore Component Nup98 Is a Potential Tumor Suppressor and Regulates Posttranscriptional Expression of Select p53 Target Genes.,
82. Zhuang Z, Gusev A, Cho J, Pe'er I., (2012) Detecting identity by descent and homozygosity mapping in whole-exome sequencing data.,
83. Zhang QC, Petrey D, Deng L, Qiang L, Shi Y, Thu CA, Bisikirska B, Lefebvre C, Accili D, Hunter T, Maniatis T, Califano A, Honig B., (2012) Structure-based prediction of protein-protein interactions on a genome-wide scale., Nature.
84. Urban TJ, Shen Y, Stolz A, Chalasani N, Fontana RJ, Rochon J, Ge D, Shianna KV, Daly AK, Lucena MI, Nelson MR, Molokhia M, Aithal GP, Floratos A, Pe'er I, Serrano J, Bonkovsky H, Davern TJ, Lee WM, Navarro VJ, Talwalkar JA, Goldstein DB, Watkins PB; Drug-Induced Liver Injury Network; DILIGEN; EUDRAGENE; Spanish DILI Registry; International Serious Adverse Events Consortium., (2012) Limited contribution of common genetic variants to risk for liver injury due to a variety of drugs.,
85. Plata G, Fuhrer T, Hsiao TL, Sauer U, Vitkup D., (2012) Global probabilistic annotation of metabolic networks enables enzyme discovery.,
86. Yang Y, Wu J, Demir A, Castillo-Martin M, Melamed RD, Zhang G, Fukunaga-Kanabis M, Perez-Lorenzo R, Zheng B, Silvers DN, Brunner G, Wang S, Rabadan R, Cordon-Cardo C, Celebi JT., (2012) GAB2 induces tumor angiogenesis in NRAS-driven melanoma.,
87. Harrison OJ, Vendome J, Brasch J, Jin X, Hong S, Katsamba PS, Ahlsen G, Troyanovsky RB, Troyanovsky SM, Honig B, Shapiro L., (2012) Nectin ectodomain structures reveal a canonical adhesive interface.,
88. Rossi D, Trifonov V, Fangazio M, Bruscaggin A, Rasi S, Spina V, Monti S, Vaisitti T, Arruga F, Famà R, Ciardullo C, Greco M, Cresta S, Piranda D, Holmes A, Fabbri G, Messina M, Rinaldi A, Wang J, Agostinelli C, Piccaluga PP, Lucioni M, Tabbò F, Serra R, Franceschetti S, Deambrogi C, Daniele G, Gattei V, Marasca R, Facchetti F, Arcaini L, Inghirami G, Bertoni F, Pileri SA, Deaglio S, Foà R, Dalla-Favera R, Pasqualucci L, Rabadan R, Gaidano G., (2012) The coding genome of splenic marginal zone lymphoma: activation of NOTCH2 and other pathways regulating marginal zone development.,
89. Campbell CL, Palamara PF, Dubrovsky M, Botigué LR, Fellous M, Atzmon G, Oddoux C, Pearlman A, Hao L, Henn BM, Burns E, Bustamante CD, Comas D, Friedman E, Pe'er I, Ostrer H., (2012) North African Jewish and non-Jewish populations form distinctive, orthogonal clusters.,
90. Anthony SJ, St Leger JA, Pugliares K, Ip HS, Chan JM, Carpenter ZW, Navarrete-Macias I, Sanchez-Leon M, Saliki JT, Pedersen J, Karesh W, Daszak P, Rabadan R, Rowles T, Lipkin WI., (2012) Emergence of fatal avian influenza in New England harbor seals.,
91. Singh D, Chan JM, Zoppoli P, Niola F, Sullivan R, Castano A, Liu EM, Reichel J, Porrati P, Pellegatta S, Qiu K, Gao Z, Ceccarelli M, Riccardi R, Brat DJ, Guha A, Aldape K, Golfinos JG, Zagzag D, Mikkelsen T, Finocchiaro G, Lasorella A, Rabadan R, Iavarone A., (2012) Transforming fusions of FGFR and TACC genes in human glioblastoma.,
92. Wang J, Kobayashi T, Floc'h N, Kinkade CW, Aytes A, Dankort D, Lefebvre C, Mitrofanova A, Cardiff RD, McMahon M, Califano A, Shen MM, Abate-Shen C., (2012) B-Raf activation cooperates with PTEN loss to drive c-Myc expression in advanced prostate cancer.,
93. Califano A, Butte AJ, Friend S, Ideker T, Schadt E., (2012) Leveraging models of cell regulation and GWAS data in integrative network-based association studies.,
94. Halberg N, Alarcon C, Tavazoie SF., (2012) microRNA regulation of cancer-endothelial interactions: vesicular microRNAs on the move...,
95. Silverstein SC, Rabadan R., (2012) How many neutrophils are enough (redux, redux)?,
96. Freddolino PL, Tavazoie S., (2012) The dawn of virtual cell biology.,
97. Floc'h N, Kinkade CW, Kobayashi T, Aytes A, Lefebvre C, Mitrofanova A, Cardiff RD, Califano A, Shen MM, Abate-Shen C., (2012) Dual targeting of the Akt/mTOR signaling pathway inhibits castration-resistant prostate cancer in a genetically engineered mouse model.,
98. Girgis HS, Harris K, Tavazoie S., (2012) Large mutational target size for rapid emergence of bacterial persistence.,
99. Prabhu S, Pe'er I., (2012) Ultrafast genome-wide scan for SNP-SNP interactions in common complex disease.,
100. Romanini DW, Peralta-Yahya P, Mondol V, Cornish VW, (2012) A heritable recombination system for synthetic Darwinian evolution in yeast, ACS Synth Biol. 2012 Dec 21;1(12):602-609.
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101. 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
102. Pe'er, D., N. Hacohen , (2011) Principles and strategies for developing network models in cancer, Cell
103. 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
104. 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
105. 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
106. 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
107. 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
108. Dewal, N, Hu, Y, Freedman, M. L, Laframboise, T, Pe'er, I., (2011) Calling amplified haplotypes in next generation tumor sequence data, Genome Res
109. Freddolino, P. L, Amini, S, Tavazoie, S., (2011) Newly identified genetic variations in common MG1655 stock cultures, J Bacteriol
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213. 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
214. 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
215. 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
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220. Sethumadhavan, S., Kaiser, G.E., (2009) COMPASS: A Community-Drive Parallelization Advisor for Sequential Software., 2nd International Workshop on Multicore Software Engineering
221. 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
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232. 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
233. 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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236. 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
237. Chu, M., Murphy, C., Kaiser, G. , (2008) Distributed In Vivo Testing of Software Applications, 1st IEEE International Conference on Software Testing, Verification, and Validation
238. 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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262. 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
263. 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
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295. 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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