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.
List of Publications in 2013
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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.
List of Publications in 2012
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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.
List of Publications in 2011
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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
110. 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
111. Luan, B,
Martyna, G,
Stolovitzky, G., (2011)
Characterizing and Controlling the Motion of ssDNA in a Solid-State Nanopore, Biophys J
112. Luan, B,
Stolovitzky, G,
Martyna, G., (2011)
Slowing and controlling the translocation of DNA in a solid-state nanopore, Nanoscale
113. Amini, S,
Hottes, A. K,
Smith, L. E,
Tavazoie, S., (2011)
Fitness landscape of antibiotic tolerance in Pseudomonas aeruginosa biofilms, PLoS Pathog
114. 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
115. Kuziemko, A,
Honig, B,
Petrey, D., (2011)
Using structure to explore the sequence alignment space of remote homologs, PLoS Comput Biol
116. Shen, Y,
Gu, Y,
Pe'er, I., (2011)
A hidden Markov model for copy number variant prediction from whole genome resequencing data, BMC Bioinformatics
117. 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
118. 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
119. 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
120. Califano, A., (2011)
Striking a balance between feasible and realistic biological models, Sci Transl Med
121. 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
122. 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
123. 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
124. 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
125. 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
126. Amini, S,
Tavazoie, S., (2011)
Antibiotics and the post-genome revolution, Curr Opin Microbiol
127. 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
128. 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
129. 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
130. 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
131. 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
132. 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
133. 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
134. 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
135. 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
136. 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
137. 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
138. 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
139. 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
140. 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
141. 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
142. Kim, H,
Watkinson, J,
Anastassiou, D., (2011)
Biomarker discovery using statistically significant gene sets, J Comput Biol
143. Pe'er, D,
Hacohen, N., (2011)
Principles and strategies for developing network models in cancer, Cell
144. 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
145. 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
146. 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
147. 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
148. 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
149. 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
150. 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
151. 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
152. 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
153. 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
154. 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
155. 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
156. Wingler LM, Cornish VW, (2011)
Reiterative Recombination for the in vivo assembly of libraries of multigene pathways.,
157. Hoskins AA, Friedman LJ, Gallagher SS, Crawford DJ, Anderson EG, Wombacher R, Ramirez N, Cornish VW, Gelles J, Moore MJ., (2011)
Ordered and dynamic assembly of single spliceosomes.,
158. Herman AG, Hayano M, Poyurovsky MV, Shimada K, Skouta R, Prives C, Stockwell BR., (2011)
Discovery of Mdm2-MdmX E3 ligase inhibitors using a cell-based ubiquitination assay.,
159. Wolpaw AJ, Shimada K, Skouta R, Welsch ME, Akavia UD, Pe'er D, Shaik F, Bulinski JC, Stockwell BR., (2011)
Modulatory profiling identifies mechanisms of small molecule-induced cell death.,
List of Publications in 2010
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160. 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
161. Zhou, X., Sumazin, P., Rajbhandari, P., Califano, A., (2010)
A systems biology approach to transcription factor binding site prediction, PLoS One
162. 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
163. 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
164. 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
165. 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
166. Hsiao, T. L.
Revelles, O.
Chen, L.
Sauer, U.
Vitkup, D., (2010)
Automatic policing of biochemical annotations using genomic correlations, Nat Chem Biol
167. 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
168. 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
169. 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
170. 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
171. 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
172. Sanchez-Garcia, F.
Akavia, U. D.
Mozes, E.
Pe'er, D., (2010)
JISTIC: Identification of Significant Targets in Cancer, BMC Bioinformatics
173. Swapneel Sheth, Nipun Arora, Christian Murphy, Gail Kaiser, (2010)
weHelp: A Reference Architecture for Social Recommender Systems, 3rd International Workshop on Social Software Engineering
174. 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
175. 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
176. 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
177. 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
178. 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
179. 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
180. Lee, H.,
Z. Li,
A. Silkov,
M. Fischer,
D. Petrey,
B. Honig,
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High-throughput computational structure-based characterization of protein families: START domains and implications for structural genomics, J Struct Funct Genomics
181. 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
182. 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
183. Norel, R.,
D. Petrey,
B. Honig, (2010)
PUDGE: a flexible, interactive server for protein structure prediction, Nucleic Acids Res
184. 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
185. Zhang, Q. C.,
D. Petrey,
R. Norel,
B. H. Honig , (2010)
Protein interface conservation across structure space, Proc Natl Acad Sci U S A
186. Chen, B. Y.,
B. Honig, (2010)
VASP: a volumetric analysis of surface properties yields insights into protein-ligand binding specificity, PLoS Comput Biol
187. 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
188. Mugler, A.,
A. M. Walczak,
C. H. Wiggins , (2010)
Information-optimal transcriptional response to oscillatory driving, Physical review letters
189. 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
190. Singarapu, K. K.,
J. L. Mills,
R. Xiao,
T. Acton,
M. Punta,
M. Fischer,
B. Honig,
B. Rost,
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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
191. 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
192. 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
193. 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
194. 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
195. Floratos A,
Smith K,
Ji Z,
Watkinson J,
Califano A., (2010)
geWorkbench: an open source platform for integrative genomics., Bioinformatics
196. Wombacher R, Heidbreder M, van de Linde S, Sheetz MP, Heilemann M, Cornish VW, Sauer M., (2010)
Live-cell super-resolution imaging with trimethoprim conjugates.,
197. Hoffstrom BG, Kaplan A, Letso R, Schmid RS, Turmel GJ, Lo DC, Stockwell BR., (2010)
Inhibitors of protein disulfide isomerase suppress apoptosis induced by misfolded proteins.,
List of Publications in 2009
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198. 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.
199. 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.
200. 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.
201. 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.
202. 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
203. 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
204. 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
205. Lim, W. K.,
Lyashenko, E.,
Califano, A., (2009)
Master regulators used as breast cancer metastasis classifier, Pac Symp Biocomput. 2009:504-15. PMID: 19209726
206. 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
207. 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
208. 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
209. 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
210. Lussier, Y.A.,
Lee, Y.,
Radivojac, P.,
Ofran, Y.,
Butte, A.,
Kann, M. , (2009)
Molecular Bioinformatics for Disease - Session Introduction, Pacific Symposium on Biocomputing
211. 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
212. 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
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
216. Prabhu, S.,
Pe'er, I., (2009)
Overlapping pools for high-throughput targeted resequencing, Genome Res. 19(7):1254-61. PMID: 19447964
217. Raj, A.,
Wiggins, C. H., (2009)
An information-theoretic derivation of min-cut based clustering., IEEE Transactions on Information Theory
218. 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
219. 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
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
222. Waltz, D.,
Buchanan, B. G., (2009)
Computer science. Automating science, Science. 324(5923):43-4. PMID: 19342574
223. 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
224. 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., Nat Biotechnol. 27(9):829-39. PMID: 19741643
225. 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
226. 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
227. Petrey D, Honig B., (2009)
Is protein classification necessary? Toward alternative approaches to function annotation., Curr Opin Struct Biol. 19(3):363-8. PMID: 19269161
228. Saito M, Novak U, Piovan E, Basso K, Sumazin P, Schneider C, Crespo M, Shen Q, Bhagat G, Califano A, Chadburn A, Pasqualucci L, Dalla-Favera R., (2009)
BCL6 suppression of BCL2 via Miz1 and its disruption in diffuse large B cell lymphoma., Proc Natl Acad Sci U S A. 106(27):11294-9. PMID: 19549844
229. Alvarez, M. J., Sumazin, P., Rajbhandari, P., Califano, A., (2009)
Correlating measurements across samples improves accuracy of large-scale expression profile experiments, Genome Biol
230. Daly AK,
Donaldson PT,
Bhatnagar P,
Shen Y,
Pe'er I,
Floratos A,
Daly MJ,
Goldstein DB,
John S,
Nelson MR,
Graham J,
Park BK,
Dillon JF,
Bernal W,
Cordell HJ,
Pirmohamed M,
Aithal GP,
Day CP, (2009)
HLA-B*5701 genotype is a major determinant of drug-induced liver injury due to flucloxacillin., Nature Genetics
231. Effraim PR, Wang J, Englander MT, Avins J, Leyh TS, Gonzalez RL Jr, Cornish VW., (2009)
Natural amino acids do not require their native tRNAs for efficient selection by the ribosome.,
List of Publications in 2008
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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
234. 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. PMID: 18250328
235. 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. PMID: 18334216
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
239. 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. 2008 Jul;18(7):1150-62. PMID: 18417725
240. 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, Physiol Genomics. 33(2):278-91. PMID: 18303084.
241. 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
242. 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
243. 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
244. Stoyanovich, J., Pe’er, I., (2008)
MutaGeneSys: estimating individual disease susceptibility based on genome-wide SNP array data, Bioinformatics. 24(3):440-2. PMID: 18048395
245. 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
246. Christian, S. L., C. W. Brune, et al., (2008)
Novel submicroscopic chromosomal abnormalities detected in autism spectrum disorder, Biol Psychiatry 63(12): 1111-7
247. Yao, L., Rzhetsky, A., (2008)
Quantitative systems-level determinants of human genes targeted by successful drugs, Genome Res 18(2): 206-13. PMID: 18083776
248. Kumar RA, KaraMohamed S, Sudi J, Conrad DF, Brune C, Badner JA, Gilliam TC, Nowak NJ, Cook EH Jr, Dobyns WB, Christian SL., (2008)
Recurrent 16p11.2 microdeletions in autism, Hum Mol Genet 17(4): 628-38. PMID: 18156158
249. Ross, K. A., Stoyanovich, J., (2008)
Schema Polynomials and Applications, International Conference on Extending Database Technology
250. 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. PMID: 18395225
251. Rodriguez-Esteban, R., Rzhetsky, A., (2008)
Six senses in the literature. The bleak sensory landscape of biomedical texts, EMBO Rep 9(3): 212-5. PMID: 18311168
252. 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. PMID: 18277385
253. 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. 93(7):1033-8. PMID: 18492688
254. 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
255. 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.
256. Amer-Yahia, S.,
M. Benedikt,
Lakshmanan,
L., J. Stoyanovich , (2008)
Efficient Network-Aware Search in Collaborative Tagging Sites., Proceedings of the VLDB Conference
257. 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.
258. 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. 178(6):605-17. PMID: 18658108
259. Kundaje, A.
Xin, X.
Lan, C.
Lianoglou, S.
Zhou, M.
Zhang, L.
Leslie, C., (2008)
A predictive model of the oxygen and heme regulatory network in yeast, PLoS Comput Biol. 4(11):e1000224. PMID: 19008939
260. Melvin, I.,
Weston, J.,
Leslie, C. S.,
Noble, W. S., (2008)
Combining classifiers for improved classification of proteins from sequence or structure, BMC Bioinformatics 9:389. PMID: 18808707
261. 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
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
264. Murphy, C.,
Shen, K.,
Kaiser, G.E. , (2008)
Automatic System Testing of Programs without Test Oracles, International Symposium on Testing and Analysis
265. Rzhetsky, A.,
Seringhaus, M.,
Gerstein, M., (2008)
Seeking a new biology through text mining, Cell. 134(1):9-13. PMID: 18614002
266. 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. 5(10):865-7. PMID: 18677319
267. 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. 24(18):2086-93. PMID: 18718948
268. Shen, Y.,
Sarin, S.,
Liu, Y.,
Hobert, O.,
Pe'er, I., (2008)
Comparing platforms for C. elegans mutant identification using high-throughput whole-genome sequencing, PLoS One. 3(12):e4012. PMID: 19107202
269. 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
270. 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
271. Ward, L.D.,
Bussemaker, H.J., (2008)
Predicting functional transcription factor binding through alignment-free, affinity-based analysis of orthologous promoter sequences, Bioinformatics 24(13):i165-71. PMID: 18586710
List of Publications in 2007
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272. 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.
273. Fan H, Mark A E, Zhu J, Honig B, (2007)
Comparative Study of Generalized Born Models: Protein Dynamics, PNAS 102:6760-6764
274. Anastassiou, D, (2007)
Computational Analysis of the Synergy Among Multiple Interacting Genes, (Review Article), Molecular Systems Biology, Vol. 3, No. 83, February 2007
275. Autism Genome Project Consortium et al., (2007)
Mapping autism risk loci using genetic linkage and chromosomal rearrangements, Nat. Genet. 39(3): 319-328
276. 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
277. 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 ): doi:10.1186/1471-2105-8-S3-S7 PMID: 17493290
278. Cokol, M., Iossifov, I., Rodriguez-Esteban, R., Rzhetsky, A, (2007)
How many scientific papers should be retracted?, EMBO Rep 8(5), 422-423. PMID: 17471252
279. 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
280. Lussier, Y. A. and Y. Liu, (2007)
Computational approaches to phenotyping: high-throughput phenomics, Proc Am Thorac Soc 4(1): 18-25 PMID: 17202287
281. Pantazatosa, S. P., J. Li, et al. , (2007)
Cross-Scale Mapping of Gene Expression to Neuroimaging Datasets via Semantic Decomposition, MEDINFO
282. 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
283. Ross, K. A., A. Janevski, J. Stoyanovich, (2007)
A Faceted Query Engine Applied to Archaeology, Internet Archeology 21, April 2007
284. Sam, L., Y. Liu, et al., (2007)
Discovery of Protein Interaction Networks Shared by Diseases, Pacific Symposium on Biocomputing(12): 76-87
285. Sebat, J., 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(5823):445-9. PMID: 17363630
286. 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
287. 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
288. 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.
289. Lussier, Y., Bodenreider, O., (2007)
Clinical Ontologies for Discovery Applications, Knowledge Discovery in the Life Sciences. Springer Verlag 2007(XXII): 450 p.
290. 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.
291. 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. PMID: 17646340
292. 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. PMID: 17934055
293. 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
294. Murphy, C., Kaiser, G., Arias, M., (2007)
Parameterizing Random Test Data According to Equivalence Classes, 2nd ACM International Workshop on Random Testing, November 2007
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
296. 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. PMID: 17609372
297. 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
298. Cokol, M., Rodriguez-Esteban, R., Rzhetsky, A., (2007)
A recipe for high impact, Genome Biology 8(5): 406
299. 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
300. 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
301. 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 Suppl 4:S2. PMID: 17570145
302. Margolin, A. A. and A. Califano, (2007)
Theory and limitations of genetic network inference from microarray data, Ann N Y Acad Sci 1115: 51-72. PMID: 17925348
303. 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(6): 788-797
304. 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. 2007 131(3):530-43. PMID: 17981120
305. 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
306. Yagoda N, von Rechenberg M, Zaganjor E, Bauer AJ, Yang WS, Fridman DJ, Wolpaw AJ, Smukste I, Peltier JM, Boniface JJ, Smith R, Lessnick SL, Sahasrabudhe S, Stockwell BR., (2007)
RAS-RAF-MEK-dependent oxidative cell death involving voltage-dependent anion channels.,
307. Varma H, Voisine C, DeMarco CT, Cattaneo E, Lo DC, Hart AC, Stockwell BR., (2007)
Selective inhibitors of death in mutant huntingtin cells., Selective inhibitors of death in mutant huntingtin cells.
List of Publications in 2006
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308. 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. PMID: 17094228
309. Bussemaker, H, (2006)
Modeling gene expression control using Omes Law, Molecular Systems Biology 2:2006.0013
310. 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, Phys Rev Lett. 97(3):038102.
311. Foat BC, Morozov AV, Bussemaker HJ., (2006)
Statistical mechanical modeling of genome-wide transcription factor occupancy data by MatrixREDUCE, Bioinformatics 22(14):e141-9.
312. Friedman C, Borlawsky T, Shagina L, Xing HR, Lussier YA., (2006)
Bio-Ontology and text: bridging the modeling gap, Bioinformatics 22(19): 2421-9
313. Goh CS, Gianoulis TA, Liu Y, Li J, Paccanaro A, Lussier YA, Gerstein M., (2006)
Integration of curated databases to identify genotype-phenotype associations, BMC Genomics 7: 257
314. 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
315. 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
316. 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
317. 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
318. 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
319. 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
320. 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, 103(6): p. 1750-5. PMID: 16439482
321. Kundaje A, Middendorf M, Shah M, Wiggins CH, Freund Y, Leslie C., (2006)
A classification-based framework for predicting and analyzing gene regulatory response, BMC Bioinformatics (Special issue on "New Problems and Methods in Computational Biology") 7(Supp 1)(S5). PMID: 16723008
322. Liu Y, Li J, Sam L, Goh CS, Gerstein M, Lussier YA., (2006)
An integrative genomic approach to uncover molecular mechanisms of prokaryotic traits, PLoS Comput Biol 2(11): e159. PMID: 17112314
323. 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). PMID: 16723010
324. Margolin AA, Wang K, Lim WK, Kustagi M, Nemenman I, Califano A, (2006)
Reverse Engineering Cellular Networks, Nat Protoc.1(2):662-71. PMID: 17406294
325. 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(32):12027-32. PMID: 16880385.
[Joint last authorship; highlighted in Nature; listed as "must read paper" on Faculty of 1000]
326. 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
327. 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
328. 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
329. Rodrigues-Esteban, R., Iossifov, I., Rzhetsky, A., (2006)
Imitating manual curation of text-mined facts in biomedicine, PLoS Comput Biol. 2(9):e118. PMID: 16965176
330. Ross, K.A., (2006)
Alpha Radiation is a Major Germ-Line Mutagen over Evolutionary Timescales, Evolutionary Ecology Research, 8(6), 2006, 1013-1028
331. Rzhetsky, A., Zheng, T., Weinreb, C. , (2006)
Self-correcting maps of molecular pathways, PLoS ONE 1, e61. PMID: 17183692
332. 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
333. 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. PMID: 16873513
334. 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
335. 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
336. 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). PMID: 16723003
337. 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
List of Publications in 2005
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338. 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
339. Cantor MN, Sarkar IN, Bodenreider O, Lussier YA, (2005)
Genestrace: Phenomic Knowledge Discovery Via Structured Terminology, Pac Symp Biocomput.;103-14
340. 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
341. 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
342. 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
343. 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)
344. 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)
S. Miyano et al. (Eds.): RECOMB 2005, LNBI 3500, pp. 538–552, 2005.
Springer-Verlag Berlin Heidelberg 2005
345. Nair R, Rost B, (2005)
Mimicking cellular sorting improves prediction of subcellular localization, J Mol Biol 348, 85-100
346. Punta M, Rost B, (2005)
PROFcon: novel prediction of long-range contacts, Bioinformatics. 21(13):2960-8. PMID: 15890748
347. Siggers T, Silkov A, Honig B, (2005)
Structural Alignment of Protein- DNA Interfaces: Insights into the Determinants of Binding Specificity, J Mol Biol. 345(5):1027-45.
348. 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
349. 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
350. 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
351. 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
352. 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. PMID: 16076885
353. 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. PMID: 16218946
354. Weston J, Leslie C., E Ie, D Zhou, A Elisseeff, WS Noble, (2005)
Semi-Supervised Protein Classification using Cluster Kernels, Book Chapter for "Semi-Supervised Learning (Editors: O. Chapelle, B. Scholkopf and A. Zien), in press, 2006.
Bioinformatics. 2005 Aug 1;21(15):3241-7. Epub 2005 May 19.
List of Publications in 2004
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355. 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
356. Liu J, Rost B, (2004)
CHOP proteins into structural domain-like fragments, Proteins 55, 678-688
357. Lussier YA, Li J, (2004)
Terminological Mapping For High Throughput Comparative Biology of Phenotypes, Pac Symp Biocomput;:202-13
358. 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)
359. Nair R, Rost B, (2004)
LOCnet and LOCtarget: Sub-cellular localization for structural genomics targets, Nucl Acids Res 32 (Web server issue) , W517-W521
360. Rost B, Yachdav G, Liu J, (2004)
The PredictProtein server, Nucl Acids Res , 32 (Web server issue) , W321-W326
361. 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
362. 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
363. 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. PMID: 15087500
List of Publications in 2003
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364. 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. PMID: 12727636
365. 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
366. 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
367. 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
368. 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
List of Publications in 2001
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369. Bussemaker HJ, Li H, Siggia ED, (2001)
Regulatory element detection using correlation with expression, Nat Genet. 2001 Feb;27(2):167-71
List of Publications in 2000
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370. Anastassiou D, (2000)
Frequency-Domain Analysis of Biomolecular Sequences, Bioinformatics, vol. 16, no. 12, December 2000, pp. 1073-1081
371. 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
372. 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