Search Publications

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
Trifonov V, Pasqualucci L, Dalla-Favera R, Rabadan R.  2011.  Fractal-like distributions over the rational numbers in high-throughput biological and clinical data. Sci Rep. 1:191. 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
Anastassiou D, Rumjantseva V, Cheng W-Y, Huang J, Canoll P, Yamashiro DJ, Kandel JJ.  2011.  Human cancer cells express Slug-based epithelial-mesenchymal transition gene expression signature obtained in vivo. BMC Cancer. 11:529. Go to Pubmed
Chard K, Russell M, Lussier YA, Mendonça EA, Silverstein JC.  2011.  A cloud-based approach to medical NLP. AMIA Annu Symp Proc. 2011:207-16. 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
Lussier YA, H Xing R, Salama JK, Khodarev NN, Huang Y, Zhang Q, Khan SA, Yang X, Hasselle MD, Darga TE et al.  2011.  MicroRNA expression characterizes oligometastasis(es). PLoS One. 6(12):e28650. Go to Pubmed
Raj A, Dewar M, Palacios G, Rabadan R, Wiggins CH.  2011.  Identifying hosts of families of viruses: a machine learning approach. PLoS One. 6(12):e27631. 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
Slattery M, Riley T, Liu P, Abe N, Gomez-Alcala P, Dror I, Zhou T, Rohs R, Honig B, Bussemaker H et al.  2011.  Cofactor binding evokes latent differences in DNA binding specificity between Hox proteins. Cell. 147(6):1270-82. 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
Luan B, Martyna G, Stolovitzky G.  2011.  Characterizing and controlling the motion of ssDNA in a solid-state nanopore. Biophys J. 101(9):2214-22. Go to Pubmed
Rossi D, Bruscaggin A, Spina V, Rasi S, Khiabanian H, Messina M, Fangazio M, Vaisitti T, Monti S, Chiaretti S et al.  2011.  Mutations of the SF3B1 splicing factor in chronic lymphocytic leukemia: association with progression and fludarabine-refractoriness. Blood. 118(26):6904-8. Go to Pubmed
Amini S, Hottes AK, Smith LE, Tavazoie S.  2011.  Fitness landscape of antibiotic tolerance in Pseudomonas aeruginosa biofilms. PLoS Pathog. 7(10):e1002298. Go to Pubmed
Sumazin P, Yang X, Chiu H-S, Chung W-J, Iyer A, Llobet-Navas D, Rajbhandari P, Bansal M, Guarnieri P, Silva J et al.  2011.  An extensive microRNA-mediated network of RNA-RNA interactions regulates established oncogenic pathways in glioblastoma. Cell. 147(2):370-81. Go to Pubmed
Kuziemko A, Honig B, Petrey D.  2011.  Using structure to explore the sequence alignment space of remote homologs. PLoS Comput Biol. 7(10):e1002175. Go to Pubmed
Birsoy K, Berry R, Wang T, Ceyhan O, Tavazoie S, Friedman JM, Rodeheffer MS.  2011.  Analysis of gene networks in white adipose tissue development reveals a role for ETS2 in adipogenesis. Development. 138(21):4709-19. Go to Pubmed
Shen Y, Gu Y, Pe'er I.  2011.  A hidden Markov model for copy number variant prediction from whole genome resequencing data. BMC Bioinformatics. 12 Suppl 6:S4. Go to Pubmed
Basso K, Mussolin L, Lettieri A, Brahmachary M, Lim WKeat, 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. 50(12):1063-75. 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
Califano A.  2011.  Striking a balance between feasible and realistic biological models. Sci Transl Med. 3(103):103ps39. Go to Pubmed
Bishop EP, Rohs R, Parker SCJ, West SM, Liu P, Mann RS, Honig B, Tullius TD.  2011.  A map of minor groove shape and electrostatic potential from hydroxyl radical cleavage patterns of DNA. ACS Chem Biol. 6(12):1314-20. Go to Pubmed
Vilar S, Harpaz R, Chase H, 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. 18 Suppl 1:i73-80. 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
Meyer P, Alexopoulos LG, Bonk T, Califano A, Cho CR, de la Fuente A, de Graaf D, Hartemink AJ, Hoeng J, Ivanov NV et al.  2011.  Verification of systems biology research in the age of collaborative competition. Nat Biotechnol. 29(9):811-5. Go to Pubmed
Prill RJ, Saez-Rodriguez J, Alexopoulos LG, Sorger PK, Stolovitzky G.  2011.  Crowdsourcing network inference: the DREAM predictive signaling network challenge. Sci Signal. 4(189):mr7. Go to Pubmed
Wolpaw AJ, Shimada K, Skouta R, Welsch ME, Akavia UDavid, Pe'er D, Shaik F, J Bulinski C, Stockwell BR.  2011.  Modulatory profiling identifies mechanisms of small molecule-induced cell death. Proc Natl Acad Sci U S A. 108(39):E771-80. Go to Pubmed
Wingler LM, Cornish VW.  2011.  Reiterative Recombination for the in vivo assembly of libraries of multigene pathways. Proc Natl Acad Sci U S A. 108(37):15135-40. Go to Pubmed
de Julio MKruithof-, Alvarez M, Galli A, Chu J, Price SM, Califano A, Shen MM.  2011.  Regulation of extra-embryonic endoderm stem cell differentiation by Nodal and Cripto signaling. Development. 138(18):3885-95. Go to Pubmed
Amini S, Tavazoie S.  2011.  Antibiotics and the post-genome revolution. Curr Opin Microbiol. 14(5):513-8. Go to Pubmed
Hottes AK, Tavazoie S.  2011.  Microarray-based genetic footprinting strategy to identify strain improvement genes after competitive selection of transposon libraries. Methods Mol Biol. 765:83-97. Go to Pubmed
Pasqualucci L, Trifonov V, Fabbri G, Ma J, Rossi D, Chiarenza A, Wells VA, Grunn A, Messina M, Elliot O et al.  2011.  Analysis of the coding genome of diffuse large B-cell lymphoma. Nat Genet. 43(9):830-7. Go to Pubmed
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. 475(7357):510-3. 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
Holmes A, Hawson A, Liu F, Friedman C, Khiabanian H, Rabadan R.  2011.  Discovering disease associations by integrating electronic clinical data and medical literature. PLoS One. 6(6):e21132. Go to Pubmed
Patwa LG, Fan T-J, Tchaptchet S, Liu Y, Lussier YA, R Sartor B, Hansen JJ.  2011.  Chronic intestinal inflammation induces stress-response genes in commensal Escherichia coli. Gastroenterology. 141(5):1842-51.e1-10. Go to Pubmed
Mathew B, Jacobson JR, Berdyshev E, Huang Y, Sun X, Zhao Y, Gerhold LM, Siegler J, Evenoski C, Wang T et al.  2011.  Role of sphingolipids in murine radiation-induced lung injury: protection by sphingosine 1-phosphate analogs. FASEB J. 25(10):3388-400. Go to Pubmed
Fischer M, Zhang QCliff, Dey F, Chen BY, Honig B, Petrey D.  2011.  MarkUs: a server to navigate sequence-structure-function space. Nucleic Acids Res. 39(Web Server issue):W357-61. Go to Pubmed
Chen JL, Li J, Stadler WM, Lussier YA.  2011.  Protein-network modeling of prostate cancer gene signatures reveals essential pathways in disease recurrence. J Am Med Inform Assoc. 18(4):392-402. Go to Pubmed
Fabbri G, Rasi S, Rossi D, Trifonov V, Khiabanian H, Ma J, Grunn A, Fangazio M, Capello D, Monti S et al.  2011.  Analysis of the chronic lymphocytic leukemia coding genome: role of NOTCH1 mutational activation. J Exp Med. 208(7):1389-401. Go to Pubmed
Tiacci E, Trifonov V, Schiavoni G, Holmes A, Kern W, Martelli MPaola, Pucciarini A, Bigerna B, Pacini R, Wells VA et al.  2011.  BRAF mutations in hairy-cell leukemia. N Engl J Med. 364(24):2305-15. Go to Pubmed
Gilman SR, 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. 70(5):898-907. Go to Pubmed
Zhu J, Yu Y, Ulbrich MH, Li M-hui, Isacoff EY, 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. 108(25):10133-8. Go to Pubmed
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. 27(14):1995-7. Go to Pubmed
Gusev A, Kenny EE, Lowe JK, Salit J, Saxena R, Kathiresan S, Altshuler D, Friedman JM, Breslow J, Pe'er I.  2011.  DASH: a method for identical-by-descent haplotype mapping uncovers association with recent variation. Am J Hum Genet. 88(6):706-17. Go to Pubmed
Zhang QCliff, Deng L, Fisher M, Guan J, Honig B, Petrey D.  2011.  PredUs: a web server for predicting protein interfaces using structural neighbors. Nucleic Acids Res. 39(Web Server issue):W283-7. Go to Pubmed
Harrer S, Waggoner PS, Luan B, Afzali-Ardakani A, Goldfarb DL, Peng H, Martyna G, Rossnagel SM, Stolovitzky G.  2011.  Electrochemical protection of thin film electrodes in solid state nanopores. Nanotechnology. 22(27):275304. 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
Vendome J, Posy S, Jin X, Bahna F, Ahlsen G, Shapiro L, Honig B.  2011.  Molecular design principles underlying β-strand swapping in the adhesive dimerization of cadherins. Nat Struct Mol Biol. 18(6):693-700. Go to Pubmed
Xie X, Ho JWK, Murphy C, Kaiser G, Xu B, Chen TYueh.  2011.  Testing and Validating Machine Learning Classifiers by Metamorphic Testing. J Syst Softw. 84(4):544-558. Go to Pubmed
Dai H, Murphy C, Kaiser G.  2010.  Configuration Fuzzing for Software Vulnerability Detection. Proc Int Conf Availab Reliab Secur. :525-530. Go to Pubmed
Kim H, Watkinson J, Anastassiou D.  2011.  Biomarker discovery using statistically significant gene sets. J Comput Biol. 18(10):1329-38. Go to Pubmed
Yang X, Li J, Lee Y, Lussier YA.  2011.  GO-Module: functional synthesis and improved interpretation of Gene Ontology patterns. Bioinformatics. 27(10):1444-6. Go to Pubmed
Pe'er D, Hacohen N.  2011.  Principles and strategies for developing network models in cancer. Cell. 144(6):864-73. Go to Pubmed
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. Science. 331(6022):1289-95. Go to Pubmed
Pasqualucci L, Dominguez-Sola D, Chiarenza A, Fabbri G, Grunn A, Trifonov V, Kasper LH, Lerach S, Tang H, Ma J et al.  2011.  Inactivating mutations of acetyltransferase genes in B-cell lymphoma. Nature. 471(7337):189-95. Go to Pubmed
Lee Y, Li J, Gamazon E, Chen JL, Tikhomirov A, Cox NJ, Lussier YA.  2010.  Biomolecular Systems of Disease Buried Across Multiple GWAS Unveiled by Information Theory and Ontology. AMIA Jt Summits Transl Sci Proc. 2010:31-5. Go to Pubmed
Borlawsky TB, Li J, Shagina L, Crowson MG, Liu Y, Friedman C, Lussier YA.  2010.  Evaluation of an Ontology-anchored Natural Language-based Approach for Asserting Multi-scale Biomolecular Networks for Systems Medicine. AMIA Jt Summits Transl Sci Proc. 2010:6-10. Go to Pubmed
Yang X, Lee Y, Fan H, Sun X, Lussier YA.  2010.  Identification of common microRNA-mRNA regulatory biomodules in human epithelial cancers. Chin Sci Bull. 55(31):3576-3589. Go to Pubmed
Harrison O, Jin X, Hong S, Bahna F, Ahlsen G, Brasch J, Wu Y, Vendome J, Felsovalyi K, Hampton CM et al.  2011.  The extracellular architecture of adherens junctions revealed by crystal structures of type I cadherins. Structure. 19(2):244-56. Go to Pubmed
Ross KAndrew.  2011.  Evidence for somatic gene conversion and deletion in bipolar disorder, Crohn's disease, coronary artery disease, hypertension, rheumatoid arthritis, type-1 diabetes, and type-2 diabetes. BMC Med. 9:12. Go to Pubmed
Brasch J, Harrison O, Ahlsen G, Carnally SM, Henderson RM, Honig B, Shapiro L.  2011.  Structure and binding mechanism of vascular endothelial cadherin: a divergent classical cadherin. J Mol Biol. 408(1):57-73. Go to Pubmed
Shechtman CF, Henneberry AL, Seimon TA, Tinkelenberg AH, Wilcox LJ, Lee E, Fazlollahi M, Munkacsi AB, Bussemaker H, Tabas I et al.  2011.  Loss of subcellular lipid transport due to ARV1 deficiency disrupts organelle homeostasis and activates the unfolded protein response. J Biol Chem. 286(14):11951-9. Go to Pubmed
Yao L, Divoli A, Mayzus I, Evans JA, Rzhetsky A.  2011.  Benchmarking ontologies: bigger or better? PLoS Comput Biol. 7(1):e1001055. Go to Pubmed
Xie X, Ho J, Murphy C, Kaiser G, Xu B, Chen TYueh.  2010.  Application of Metamorphic Testing to Supervised Classifiers. Proc Int Conf Qual Softw. 2009(2009):135-144. 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
Murphy C, Vaughan M, Ilahi W, Kaiser G.  2010.  Automatic Detection of Previously-Unseen Application States for Deployment Environment Testing and Analysis. Proc Int Workshop Autom Softw Test. 2010:16-23. Go to Pubmed
Harpaz R, Perez H, Chase H, Rabadan R, Hripcsak G, Friedman C.  2011.  Biclustering of adverse drug events in the FDA's spontaneous reporting system. Clin Pharmacol Ther. 89(2):243-50. Go to Pubmed
Mugler A, Grinshpun B, Franks R, Wiggins C.  2011.  Statistical method for revealing form-function relations in biological networks. Proc Natl Acad Sci U S A. 108(2):446-51. Go to Pubmed

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