Search Publications

2012 Publications

Romanini DW, Peralta-Yahya P, Mondol V, Cornish VW.  2012.  A Heritable Recombination System for Synthetic Darwinian Evolution in Yeast. ACS Synth Biol. 1(12):602-609. Go to Pubmed
Yang X, Li H, Regan K, Li J, Huang Y, Lussier YA.  2012.  Towards mechanism classifiers: expression-anchored Gene Ontology signature predicts clinical outcome in lung adenocarcinoma patients. AMIA Annu Symp Proc. 2012:1040-9. Go to Pubmed
Zhang C, Srinivasan Y, Arlow DH, Fung JJosé, Palmer D, Zheng Y, Green HF, Pandey A, Dror RO, Shaw DE et al.  2012.  High-resolution crystal structure of human protease-activated receptor 1. Nature. 492(7429):387-92. Go to Pubmed
Bisikirska B, Adam SJ, Alvarez M, Rajbhandari P, Cox R, Lefebvre C, Wang K, Rieckhof G, Felsher DW, Califano A.  2012.  STK38 is a critical upstream regulator of MYC's oncogenic activity in human B-cell lymphoma. Oncogene. Go to Pubmed
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. Nat Neurosci. 15(12):1723-8. Go to Pubmed
Iliadis A, Anastassiou D, Wang X.  2012.  Fast and accurate haplotype frequency estimation for large haplotype vectors from pooled DNA data. BMC Genet. 13:94. Go to Pubmed
Palamara PFrancesco, Lencz T, Darvasi A, Pe'er I.  2012.  Length distributions of identity by descent reveal fine-scale demographic history. Am J Hum Genet. 91(5):809-22. Go to Pubmed
Singer S, Zhao R, Barsotti AM, Ouwehand A, Fazlollahi M, Coutavas E, Breuhahn K, Neumann O, Longerich T, Pusterla T et al.  2012.  Nuclear pore component Nup98 is a potential tumor suppressor and regulates posttranscriptional expression of select p53 target genes. Mol Cell. 48(5):799-810. Go to Pubmed
Zhuang Z, Gusev A, Cho J, Pe'er I.  2012.  Detecting identity by descent and homozygosity mapping in whole-exome sequencing data. PLoS One. 7(10):e47618. Go to Pubmed
Zhang QCliff, Petrey D, Deng L, Qiang L, Shi Y, Thu CAye, Bisikirska B, Lefebvre C, Accili D, Hunter T et al.  2012.  Structure-based prediction of protein-protein interactions on a genome-wide scale. Nature. 490(7421):556-60. Go to Pubmed
Urban TJ, Shen Y, Stolz A, Chalasani N, Fontana RJ, Rochon J, Ge D, Shianna KV, Daly AK, M Lucena I et al.  2012.  Limited contribution of common genetic variants to risk for liver injury due to a variety of drugs. Pharmacogenet Genomics. 22(11):784-95. Go to Pubmed
Plata G, Fuhrer T, Hsiao T-L, Sauer U, Vitkup D.  2012.  Global probabilistic annotation of metabolic networks enables enzyme discovery. Nat Chem Biol. 8(10):848-54. Go to Pubmed
Yang Y, Wu J, Demir A, Castillo-Martin M, Melamed R, Zhang G, Fukunaga-Kanabis M, Perez-Lorenzo R, Zheng B, Silvers DN et al.  2012.  GAB2 induces tumor angiogenesis in NRAS-driven melanoma. Oncogene. Go to Pubmed
Harrison O, Vendome J, Brasch J, Jin X, Hong S, Katsamba PS, Ahlsen G, Troyanovsky RB, Troyanovsky SM, Honig B et al.  2012.  Nectin ectodomain structures reveal a canonical adhesive interface. Nat Struct Mol Biol. 19(9):906-15. Go to Pubmed
Rossi D, Trifonov V, Fangazio M, Bruscaggin A, Rasi S, Spina V, Monti S, Vaisitti T, Arruga F, Famà R et al.  2012.  The coding genome of splenic marginal zone lymphoma: activation of NOTCH2 and other pathways regulating marginal zone development. J Exp Med. 209(9):1537-51. Go to Pubmed
Campbell CL, Palamara PFrancesco, Dubrovsky M, Botigué LR, Fellous M, Atzmon G, Oddoux C, Pearlman A, Hao L, Henn BM et al.  2012.  North African Jewish and non-Jewish populations form distinctive, orthogonal clusters. Proc Natl Acad Sci U S A. 109(34):13865-70. Go to Pubmed
Anthony SJ, St Leger JA, Pugliares K, Ip HS, Chan JMinhow, Carpenter Z, Navarrete-Macias I, Sanchez-Leon M, Saliki JT, Pedersen J et al.  2012.  Emergence of fatal avian influenza in New England harbor seals. MBio. 3(4):e00166-12. Go to Pubmed
Singh D, Chan JMinhow, Zoppoli P, Niola F, Sullivan R, Castano A, Liu EMinwei, Reichel J, Porrati P, Pellegatta S et al.  2012.  Transforming fusions of FGFR and TACC genes in human glioblastoma. Science. 337(6099):1231-5. Go to Pubmed
Wang J, Kobayashi T, Floc'h N, Kinkade CWaugh, Aytes A, Dankort D, Lefebvre C, Mitrofanova A, Cardiff RD, McMahon M et al.  2012.  B-Raf activation cooperates with PTEN loss to drive c-Myc expression in advanced prostate cancer. Cancer Res. 72(18):4765-76. Go to Pubmed
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. Nat Genet. 44(8):841-7. Go to Pubmed
Silverstein SC, Rabadan R.  2012.  How many neutrophils are enough (redux, redux)? J Clin Invest. 122(8):2776-9. Go to Pubmed
Freddolino PL, Tavazoie S.  2012.  The dawn of virtual cell biology. Cell. 150(2):248-50. Go to Pubmed
Floc'h N, Kinkade CWaugh, 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. Cancer Res. 72(17):4483-93. Go to Pubmed
Girgis HS, Harris K, Tavazoie S.  2012.  Large mutational target size for rapid emergence of bacterial persistence. Proc Natl Acad Sci U S A. 109(31):12740-5. Go to Pubmed
Marbach D, Costello JC, Küffner R, Vega NM, Prill RJ, Camacho DM, Allison KR, Kellis M, Collins JJ, Stolovitzky G.  2012.  Wisdom of crowds for robust gene network inference. Nat Methods. 9(8):796-804. Go to Pubmed
Prabhu S, Pe'er I.  2012.  Ultrafast genome-wide scan for SNP-SNP interactions in common complex disease. Genome Res. 22(11):2230-40. Go to Pubmed
R McIsaac S, Petti AA, Bussemaker H, Botstein D.  2012.  Perturbation-based analysis and modeling of combinatorial regulation in the yeast sulfur assimilation pathway. Mol Biol Cell. 23(15):2993-3007. Go to Pubmed
Petti AA, R McIsaac S, Ho-Shing O, Bussemaker H, Botstein D.  2012.  Combinatorial control of diverse metabolic and physiological functions by transcriptional regulators of the yeast sulfur assimilation pathway. Mol Biol Cell. 23(15):3008-24. Go to Pubmed
Freddolino PL, Goodarzi H, Tavazoie S.  2012.  Fitness landscape transformation through a single amino acid change in the rho terminator. PLoS Genet. 8(5):e1002744. Go to Pubmed
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. 19(6):1066-74. Go to Pubmed
Iliadis A, Anastassiou D, Wang X.  2012.  A unified framework for haplotype inference in nuclear families. Ann Hum Genet. 76(4):312-25. Go to Pubmed
Shan Y, Eastwood MP, Zhang X, Kim ET, Arkhipov A, Dror RO, Jumper J, Kuriyan J, Shaw DE.  2012.  Oncogenic mutations counteract intrinsic disorder in the EGFR kinase and promote receptor dimerization. Cell. 149(4):860-70. Go to Pubmed
Dror RO, Dirks RM, Grossman JP, Xu H, Shaw DE.  2012.  Biomolecular simulation: a computational microscope for molecular biology. Annu Rev Biophys. 41:429-52. Go to Pubmed
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. 11:61-75. Go to Pubmed
Freddolino PL, Tavazoie S.  2012.  Beyond homeostasis: a predictive-dynamic framework for understanding cellular behavior. Annu Rev Cell Dev Biol. 28:363-84. Go to Pubmed
Brasch J, Harrison O, Honig B, Shapiro L.  2012.  Thinking outside the cell: how cadherins drive adhesion. Trends Cell Biol. 22(6):299-310. Go to Pubmed
Dapito DH, Mencin A, Gwak G-Y, Pradere J-P, Jang M-K, Mederacke I, Caviglia JM, Khiabanian H, Adeyemi A, Bataller R et al.  2012.  Promotion of hepatocellular carcinoma by the intestinal microbiota and TLR4. Cancer Cell. 21(4):504-16. Go to Pubmed
Raval A, Piana S, Eastwood MP, Dror RO, Shaw DE.  2012.  Refinement of protein structure homology models via long, all-atom molecular dynamics simulations. Proteins. 80(8):2071-9. Go to Pubmed
Henn BM, Hon L, J Macpherson M, Eriksson N, Saxonov S, Pe'er I, Mountain JL.  2012.  Cryptic distant relatives are common in both isolated and cosmopolitan genetic samples. PLoS One. 7(4):e34267. Go to Pubmed
Jensen MØ, Jogini V, Borhani DW, Leffler AE, Dror RO, Shaw DE.  2012.  Mechanism of voltage gating in potassium channels. Science. 336(6078):229-33. Go to Pubmed
Goodarzi H, Najafabadi HS, Oikonomou P, Greco TM, Fish L, Salavati R, Cristea IM, Tavazoie S.  2012.  Systematic discovery of structural elements governing stability of mammalian messenger RNAs. Nature. 485(7397):264-8. Go to Pubmed
Cheng W-Y, Kandel JJ, Yamashiro DJ, Canoll P, Anastassiou D.  2012.  A multi-cancer mesenchymal transition gene expression signature is associated with prolonged time to recurrence in glioblastoma. PLoS One. 7(4):e34705. Go to Pubmed
Tan AY, Riley T, Coady T, Bussemaker H, Manley JL.  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. 109(16):6030-5. Go to Pubmed
Kreimer A, Litvin O, Hao K, Molony C, Pe'er D, Pe'er I.  2012.  Inference of modules associated to eQTLs. Nucleic Acids Res. 40(13):e98. Go to Pubmed
Chen Y, Sheng R, Källberg M, Silkov A, Tun MP, Bhardwaj N, Kurilova S, Hall RA, Honig B, Lu H et al.  2012.  Genome-wide functional annotation of dual-specificity protein- and lipid-binding modules that regulate protein interactions. Mol Cell. 46(2):226-37. Go to Pubmed
Meyer P, Hoeng J, J Rice J, Norel R, Sprengel J, Stolle K, Bonk T, Corthesy S, Royyuru A, Peitsch M et al.  2012.  Industrial methodology for process verification in research (IMPROVER): toward systems biology verification. Bioinformatics. 28(9):1193-201. Go to Pubmed
Kenny EE, Pe'er I, Karban A, Ozelius L, Mitchell AA, Ng SMeng, Erazo M, Ostrer H, Abraham C, Abreu MT et al.  2012.  A genome-wide scan of Ashkenazi Jewish Crohn's disease suggests novel susceptibility loci. PLoS Genet. 8(3):e1002559. Go to Pubmed
Lindorff-Larsen K, Maragakis P, Piana S, Eastwood MP, Dror RO, Shaw DE.  2012.  Systematic validation of protein force fields against experimental data. PLoS One. 7(2):e32131. Go to Pubmed
Gatta GDella, Palomero T, Perez-Garcia A, Ambesi-Impiombato A, Bansal M, Carpenter Z, De Keersmaecker K, Sole X, Xu L, Paietta E et al.  2012.  Reverse engineering of TLX oncogenic transcriptional networks identifies RUNX1 as tumor suppressor in T-ALL. Nat Med. 18(3):436-40. Go to Pubmed
Kruse AC, Hu J, Pan AC, Arlow DH, Rosenbaum DM, Rosemond E, Green HF, Liu T, Chae PSeok, Dror RO et al.  2012.  Structure and dynamics of the M3 muscarinic acetylcholine receptor. Nature. 482(7386):552-6. Go to Pubmed
Lindorff-Larsen K, Trbovic N, Maragakis P, Piana S, Shaw DE.  2012.  Structure and dynamics of an unfolded protein examined by molecular dynamics simulation. J Am Chem Soc. 134(8):3787-91. Go to Pubmed
Greenbaum BD, Li OTW, Poon LLM, Levine AJ, Rabadan R.  2012.  Viral reassortment as an information exchange between viral segments. Proc Natl Acad Sci U S A. 109(9):3341-6. Go to Pubmed
Martínez MRodríguez, Corradin A, Klein U, Alvarez M, Toffolo GM, di Camillo B, Califano A, Stolovitzky G.  2012.  Quantitative modeling of the terminal differentiation of B cells and mechanisms of lymphomagenesis. Proc Natl Acad Sci U S A. 109(7):2672-7. Go to Pubmed
Califano A, Kellis M, Stolovitzky G.  2012.  Preface: RECOMB Systems Biology, Regulatory Genomics, and DREAM 2011 special issue. J Comput Biol. 19(2):101. Go to Pubmed
Yang X, Regan K, Huang Y, Zhang Q, Li J, Seiwert TY, Cohen EEW, H Xing R, Lussier YA.  2012.  Single sample expression-anchored mechanisms predict survival in head and neck cancer. PLoS Comput Biol. 8(1):e1002350. Go to Pubmed
Guha S, Rosenfeld J, Malhotra AK, Lee AT, Gregersen PK, Kane JM, Pe'er I, Darvasi A, Lencz T.  2012.  Implications for health and disease in the genetic signature of the Ashkenazi Jewish population. Genome Biol. 13(1):R2. Go to Pubmed
Nicoletti P, Cartsos VM, Palaska PK, Shen Y, Floratos A, Zavras AI.  2012.  Genomewide pharmacogenetics of bisphosphonate-induced osteonecrosis of the jaw: the role of RBMS3. Oncologist. 17(2):279-87. Go to Pubmed
Ferreira CM, Chen JL, Li J, Shimomura K, Yang X, Lussier YA, Pinto LH, Solway J.  2012.  Genetic interactions between chromosomes 11 and 18 contribute to airway hyperresponsiveness in mice. PLoS One. 7(1):e29579. Go to Pubmed
Lefebvre C, Rieckhof G, Califano A.  2012.  Reverse-engineering human regulatory networks. Wiley Interdiscip Rev Syst Biol Med. 4(4):311-25. Go to Pubmed
Ntziachristos P, Tsirigos A, Van Vlierberghe P, Nedjic J, Trimarchi T, Flaherty MSol, Ferres-Marco D, da Ros V, Tang Z, Siegle J et al.  2012.  Genetic inactivation of the polycomb repressive complex 2 in T cell acute lymphoblastic leukemia. Nat Med. 18(2):298-301. Go to Pubmed
Eletsky A, Petrey D, Zhang QCliff, Lee H-W, Acton T, Xiao R, Everett JK, Prestegard JH, Honig B, Montelione G et al.  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. 13(1):1-7. Go to Pubmed
Borhani DW, Shaw DE.  2012.  The future of molecular dynamics simulations in drug discovery. J Comput Aided Mol Des. 26(1):15-26. Go to Pubmed
Jin X, Walker MA, 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 Ca²+-free interdomain linkers. Proc Natl Acad Sci U S A. 109(3):E127-34. Go to Pubmed
Gusev A, Shah MJ, Kenny EE, Ramachandran A, Lowe JK, Salit J, Lee CC, Levandowsky EC, Weaver TN, Doan QC et al.  2012.  Low-pass genome-wide sequencing and variant inference using identity-by-descent in an isolated human population. Genetics. 190(2):679-89. Go to Pubmed
Dewal N, Hu Y, Freedman ML, Laframboise T, Pe'er I.  2012.  Calling amplified haplotypes in next generation tumor sequence data. Genome Res. 22(2):362-74. Go to Pubmed
Freddolino PL, Amini S, Tavazoie S.  2012.  Newly identified genetic variations in common Escherichia coli MG1655 stock cultures. J Bacteriol. 194(2):303-6. Go to Pubmed
Floratos A, Honig B, Pe'er D, Califano A.  2012.  Using systems and structure biology tools to dissect cellular phenotypes. J Am Med Inform Assoc. 19(2):171-5. Go to Pubmed
Luan B, Stolovitzky G, Martyna G.  2012.  Slowing and controlling the translocation of DNA in a solid-state nanopore. Nanoscale. 4(4):1068-77. Go to Pubmed
Rossi D, Rasi S, Fabbri G, Spina V, Fangazio M, Forconi F, Marasca R, Laurenti L, Bruscaggin A, Cerri M et al.  2012.  Mutations of NOTCH1 are an independent predictor of survival in chronic lymphocytic leukemia. Blood. 119(2):521-9. Go to Pubmed
Iñigo S, Alvarez M, Strasser B, Califano A, Cerdán PD.  2012.  PFT1, the MED25 subunit of the plant Mediator complex, promotes flowering through CONSTANS dependent and independent mechanisms in Arabidopsis. Plant J. 69(4):601-12. Go to Pubmed
Gusev A, Palamara PFrancesco, Aponte G, Zhuang Z, Darvasi A, Gregersen P, Pe'er I.  2012.  The architecture of long-range haplotypes shared within and across populations. Mol Biol Evol. 29(2):473-86. Go to Pubmed
Bansal M, Califano A.  2012.  Genome-wide dissection of posttranscriptional and posttranslational interactions. Methods Mol Biol. 786:131-49. Go to Pubmed
Velez C, Palamara PFrancesco, Guevara-Aguirre J, Hao L, Karafet T, Guevara-Aguirre M, Pearlman A, Oddoux C, Hammer M, Burns E et al.  2012.  The impact of Converso Jews on the genomes of modern Latin Americans. Hum Genet. 131(2):251-63. Go to Pubmed
Rudin C, Waltz D, Anderson RN, Boulanger A, Salleb-Aouissi A, Chow M, Dutta H, Gross PN, Huang B, Ierome S et al.  2012.  Machine learning for the New York City power grid. IEEE Trans Pattern Anal Mach Intell. 34(2):328-45. Go to Pubmed
Shen Y, Nicoletti P, Floratos A, Pirmohamed M, Molokhia M, Geppetti P, Benemei S, Giomi B, Schena D, Vultaggio A et al.  2012.  Genome-wide association study of serious blistering skin rash caused by drugs. Pharmacogenomics J. 12(2):96-104. Go to Pubmed