Search Publications

2015 Publications

Polubriaginof F, Tatonetti NP, Vawdrey DK.  2015.  An Assessment of Family History Information Captured in an Electronic Health Record. AMIA Annu Symp Proc. 2015:2035-42. Go to Pubmed
Gallego-Perez D, Otero JJ, Czeisler C, Ma J, Ortiz C, Gygli P, Catacutan FPatsy, Gokozan HNuman, Cowgill A, Sherwood T et al.  2015.  Deterministic transfection drives efficient nonviral reprogramming and uncovers reprogramming barriers. Nanomedicine. Go to Pubmed
Pereira L, Kratsios P, Serrano-Saiz E, Sheftel H, Mayo AE, Hall DH, White JG, LeBoeuf B, L Garcia R, Alon U et al.  2015.  A cellular and regulatory map of the cholinergic nervous system of C.elegans. Elife. 4 Go to Pubmed
Hart MP, Hobert O.  2015.  Sexual Dimorphism: Mystery Neurons Control Sex-Specific Behavioral Plasticity. Curr Biol. 25(24):R1170-2. Go to Pubmed
Riley TR, Lazarovici A, Mann RS, Bussemaker HJ.  2015.  Building accurate sequence-to-affinity models from high-throughput in vitro protein-DNA binding data using FeatureREDUCE. Elife. 4 Go to Pubmed
Hoffman KB, Dimbil M, Kyle RF, Tatonetti NP, Erdman CB, Demakas A, Chen D, Overstreet BM.  2015.  A Drug Safety Rating System Based on Postmarketing Costs Associated with Adverse Events and Patient Outcomes. J Manag Care Spec Pharm. 21(12):1134-43. Go to Pubmed
Zhang H, Zheng T, Chua CWai, Shen M, Gelmann EP.  2015.  Nkx3.1 controls the DNA repair response in the mouse prostate. Prostate. Go to Pubmed
Yang WSeok, Stockwell BR.  2015.  Ferroptosis: Death by Lipid Peroxidation. Trends Cell Biol. Go to Pubmed
Khare A, Tavazoie S.  2015.  Multifactorial Competition and Resistance in a Two-Species Bacterial System. PLoS Genet. 11(12):e1005715. Go to Pubmed
Lee AK, Kulcsar KA, Elliott O, Khiabanian H, Nagle ER, Jones MEB, Amman BR, Sanchez-Lockhart M, Towner JS, Palacios G et al.  2015.  De novo transcriptome reconstruction and annotation of the Egyptian rousette bat. BMC Genomics. 16:1033. Go to Pubmed
Putcha P, Yu J, Rodriguez-Barrueco R, Saucedo-Cuevas L, Villagrasa P, Murga-Penas E, Quayle SN, Yang M, Castro V, Llobet-Navas D et al.  2015.  HDAC6 activity is a non-oncogene addiction hub for inflammatory breast cancers. Breast Cancer Res. 17(1):149. Go to Pubmed
Gymrek M, Willems T, Guilmatre A, Zeng H, Markus B, Georgiev S, Daly MJ, Price AL, Pritchard JK, Sharp AJ et al.  2015.  Abundant contribution of short tandem repeats to gene expression variation in humans. Nat Genet. Go to Pubmed
Shen MM.  2015.  Illuminating the Properties of Prostate Luminal Progenitors. Cell Stem Cell. 17(6):644-6. Go to Pubmed
Morton ER, Lynch J, Froment A, Lafosse S, Heyer E, Przeworski M, Blekhman R, Segurel L.  2015.  Variation in Rural African Gut Microbiota Is Strongly Correlated with Colonization by Entamoeba and Subsistence. PLoS Genet. 11(11):e1005658. Go to Pubmed
Kidd BA, Wroblewska A, Boland MR, Agudo J, Merad M, Tatonetti NP, Brown BD, Dudley JT.  2015.  Mapping the effects of drugs on the immune system. Nat Biotechnol. Go to Pubmed
Romano JD, Tatonetti NP.  2015.  VenomKB, a new knowledge base for facilitating the validation of putative venom therapies. Sci Data. 2:150065. Go to Pubmed
Del Giudice I, Marinelli M, Wang J, Bonina S, Messina M, Chiaretti S, Ilari C, Cafforio L, Raponi S, Mauro FR et al.  2015.  Inter- and intra-patient clonal and subclonal heterogeneity of chronic lymphocytic leukaemia: evidences from circulating and lymph nodal compartments. Br J Haematol. Go to Pubmed
Arlotta P, Hobert O.  2015.  Homeotic Transformations of Neuronal Cell Identities. Trends Neurosci. Go to Pubmed
Bisikirska B, Bansal M, Shen Y, Teruya-Feldstein J, Chaganti R, Califano A.  2015.  Elucidation and pharmacological targeting of novel molecular drivers of follicular lymphoma progression. Cancer Res. Go to Pubmed
Singhal S, Leffler EM, Sannareddy K, Turner I, Venn O, Hooper DM, Strand AI, Li Q, Raney B, Balakrishnan CN et al.  2015.  Stable recombination hotspots in birds. Science. 350(6263):928-32. Go to Pubmed
Palamara PFrancesco, Francioli LC, Wilton PR, Genovese G, Gusev A, Finucane HK, Sankararaman S, Sunyaev SR, de Bakker PIW, Wakeley J et al.  2015.  Leveraging Distant Relatedness to Quantify Human Mutation and Gene-Conversion Rates. Am J Hum Genet. Go to Pubmed
Almeida ACarolina d, Abate F, Khiabanian H, Martinez-Escala E, Guitart J, Tensen CP, Vermeer MH, Rabadan R, Ferrando A, Palomero T.  2015.  The mutational landscape of cutaneous T cell lymphoma and Sézary syndrome. Nat Genet. Go to Pubmed
Sun J, Wang J, Pefanis E, Chao J, Rothschild G, Tachibana I, Chen JKui, Ivanov II, Rabadan R, Takeda Y et al.  2015.  Transcriptomics Identify CD9 as a Marker of Murine IL-10-Competent Regulatory B Cells. Cell Rep. Go to Pubmed
Clarke OB, Tomasek D, Jorge CD, Dufrisne MBelcher, Kim M, Banerjee S, Rajashankar KR, Shapiro L, Hendrickson WA, Santos H et al.  2015.  Structural basis for phosphatidylinositol-phosphate biosynthesis. Nat Commun. 6:8505. Go to Pubmed
Liu X, Hernandez N, Kisselev S, Floratos A, Sawle A, Ionita-Laza I, Ottman R, Louis ED, Clark LN.  2015.  Identification of candidate genes for familial early-onset essential tremor. Eur J Hum Genet. Go to Pubmed
Lee SHyung, Shen MM.  2015.  Cell types of origin for prostate cancer. Curr Opin Cell Biol. 37:35-41. Go to Pubmed
Pivovarov R, Perotte AJ, Grave E, Angiolillo J, Wiggins CH, Elhadad N.  2015.  Learning probabilistic phenotypes from heterogeneous EHR data. J Biomed Inform. Go to Pubmed
Jung Y, Ji HY, Chen Z, Chan HFai, Atchison L, Klitzman B, Truskey G, Leong KW.  2015.  Scaffold-free, Human Mesenchymal Stem Cell-Based Tissue Engineered Blood Vessels. Sci Rep. 5:15116. Go to Pubmed
Jacunski A, Dixon SJ, Tatonetti NP.  2015.  Connectivity Homology Enables Inter-Species Network Models of Synthetic Lethality. PLoS Comput Biol. 11(10):e1004506. Go to Pubmed
Barrows D, Schoenfeld SM, Hodakoski C, Silkov A, Honig B, Couvillon A, Shymanets A, Nuernberg B, Asara JM, Parsons R.  2015.  PAK kinases mediate the phosphorylation of PREX2 to initiate feedback inhibition of Rac1. J Biol Chem. Go to Pubmed
O'Connell NE, Lelli K, Mann RS, Palmer AG.  2015.  Asparagine deamidation reduces DNA-binding affinity of the Drosophila melanogaster Scr homeodomain. FEBS Lett. Go to Pubmed
Klauzinska M, McCurdy D, Rangel C, Vaidyanath A, Castro N, Shen MM, Gonzales M, Bertolette D, Bianco C, Callahan R et al.  2015.  Cripto-1 Ablation Disrupts Alveolar Development in the Mouse Mammary Gland through a Progesterone Receptor-Mediated Pathway. Am J Pathol. Go to Pubmed
Ellis P, Burbridge S, Soubes S, Ohyama K, Ben-Haim N, Chen C, Dale K, Shen MM, Constam D, Placzek M.  2015.  ProNodal acts via FGFR3 to govern duration of Shh expression in the prechordal mesoderm. Development. Go to Pubmed
Yu J, Silva J, Califano A.  2015.  ScreenBEAM: a Novel Meta-Analysis Algorithm for Functional Genomics Screens via Bayesian Hierarchical Modeling. Bioinformatics. Go to Pubmed
Qiu W, Tang SM, Lee S, Turk AT, Sireci AN, Qiu A, Rose C, Xie C, Kitajewski J, Wen H-J et al.  2015.  Loss of Activin Receptor Type 1B Accelerates Development of Intraductal Papillary Mucinous Neoplasms in Mice With Activated KRAS. Gastroenterology. Go to Pubmed
Mitrofanova A, Aytes A, Zou M, Shen MM, Abate-Shen C, Califano A.  2015.  Predicting Drug Response in Human Prostate Cancer from Preclinical Analysis of In Vivo Mouse Models. Cell Rep. Go to Pubmed
Guo Y, Ding X, Shen Y, Lyon GJ, Wang K.  2015.  SeqMule: automated pipeline for analysis of human exome/genome sequencing data. Sci Rep. 5:14283. Go to Pubmed
Castel SE, Levy-Moonshine A, Mohammadi P, Banks E, Lappalainen T.  2015.  Tools and best practices for data processing in allelic expression analysis. Genome Biol. 16(1):195. Go to Pubmed
Venere M, Horbinski C, Crish JF, Jin X, Vasanji A, Major J, Burrows AC, Chang C, Prokop J, Wu Q et al.  2015.  The mitotic kinesin KIF11 is a driver of invasion, proliferation, and self-renewal in glioblastoma. Sci Transl Med. 7(304):304ra143. Go to Pubmed
Katz FS, Pecic S, Tran TH, Trakht I, Schneider L, Zhu Z, Ton-That L, Luzac M, Zlatanic V, Damera S et al.  2015.  Discovery of New Classes of Compounds that Reactivate Acetylcholinesterase Inhibited by Organophosphates. Chembiochem. Go to Pubmed
Shibata M, Shen M.  2015.  Stem cells in genetically-engineered mouse models of prostate cancer. Endocr Relat Cancer. Go to Pubmed
Alqadah A, Hsieh Y-W, Vidal B, Chang C, Hobert O, Chuang C-F.  2015.  Postmitotic diversification of olfactory neuron types is mediated by differential activities of the HMG-box transcription factor SOX-2. EMBO J. Go to Pubmed
Alvarez MJ, Chen JC, Califano A.  2015.  DIGGIT: A Bioconductor package to infer genetic variants driving cellular phenotypes. Bioinformatics. Go to Pubmed
Baskovich B, Hiraki S, Upadhyay K, Meyer P, Carmi S, Barzilai N, Darvasi A, Ozelius L, Peter I, Cho JH et al.  2015.  Expanded genetic screening panel for the Ashkenazi Jewish population. Genet Med. Go to Pubmed
Alarcón CR, Goodarzi H, Lee H, Liu X, Tavazoie S, Tavazoie SF.  2015.  HNRNPA2B1 Is a Mediator of m(6)A-Dependent Nuclear RNA Processing Events. Cell. Go to Pubmed
Stockwell BR, Stockwell MS, Cennamo M, Jiang E.  2015.  Blended Learning Improves Science Education. Cell. 162(5):933-6. Go to Pubmed
Jiang K, Sun X, Chen Y, Shen Y, Jarvis JN.  2015.  RNA sequencing from human neutrophils reveals distinct transcriptional differences associated with chronic inflammatory states. BMC Med Genomics. 8(1):55. Go to Pubmed
Yahi A, Tatonetti NP.  2015.  A knowledge-based, automated method for phenotyping in the EHR using only clinical pathology reports. AMIA Jt Summits Transl Sci Proc. 2015:64-8. Go to Pubmed
Ingram JR, Knockenhauer KE, Markus BM, Mandelbaum J, Ramek A, Shan Y, Shaw DE, Schwartz TU, Ploegh HL, Lourido S.  2015.  Allosteric activation of apicomplexan calcium-dependent protein kinases. Proc Natl Acad Sci U S A. Go to Pubmed
Gut G, Tadmor MD, Pe'er D, Pelkmans L, Liberali P.  2015.  Trajectories of cell-cycle progression from fixed cell populations. Nat Methods. Go to Pubmed
Stefanakis N, Carrera I, Hobert O.  2015.  Regulatory Logic of Pan-Neuronal Gene Expression in C. elegans. Neuron. 87(4):733-50. Go to Pubmed
Biswas KH, Hartman KL, Yu C-H, Harrison OJ, Song H, Smith AW, Huang WYC, Lin W-C, Guo Z, Padmanabhan A et al.  2015.  E-cadherin junction formation involves an active kinetic nucleation process. Proc Natl Acad Sci U S A. 112(35):10932-7. Go to Pubmed
Chen B-J, Litvin O, Ungar L, Pe'er D.  2015.  Context Sensitive Modeling of Cancer Drug Sensitivity. PLoS One. 10(8):e0133850. Go to Pubmed
L Y Fan R, Valkenburg SA, Wong CKS, Li OTW, Nicholls JM, Rabadan R, Peiris JSMalik, Poon LLM.  2015.  Generation of Live Attenuated Influenza Virus by Using Codon Usage Bias. J Virol. 89(21):10762-73. Go to Pubmed
Raval A, Piana S, Eastwood MP, Shaw DE.  2015.  Assessment of the utility of contact-based restraints in accelerating the prediction of protein structure using molecular dynamics simulations. Protein Sci. Go to Pubmed
Zhang J, Lieu YK, Ali AM, Penson A, Reggio KS, Rabadan R, Raza A, Mukherjee S, Manley JL.  2015.  Disease-associated mutation in SRSF2 misregulates splicing by altering RNA-binding affinities. Proc Natl Acad Sci U S A. Go to Pubmed
Chen C-S, Hong S, Indra I, Sergeeva AP, Troyanovsky RB, Shapiro L, Honig B, Troyanovsky SM.  2015.  α-Catenin-mediated cadherin clustering couples cadherin and actin dynamics. J Cell Biol. Go to Pubmed
Goodwin M, Mohan A, Batra R, Lee K-Y, Charizanis K, Gómez FJosé Fern, Eddarkaoui S, Sergeant N, Buée L, Kimura T et al.  2015.  MBNL Sequestration by Toxic RNAs and RNA Misprocessing in the Myotonic Dystrophy Brain. Cell Rep. Go to Pubmed
Alizadeh AA, Aranda V, Bardelli A, Blanpain C, Bock C, Borowski C, Caldas C, Califano A, Doherty M, Elsner M et al.  2015.  Toward understanding and exploiting tumor heterogeneity. Nat Med. 21(8):846-53. Go to Pubmed
Feng H, Zhang X, Zhang C.  2015.  mRIN for direct assessment of genome-wide and gene-specific mRNA integrity from large-scale RNA-sequencing data. Nat Commun. 6:7816. Go to Pubmed
Rodriguez-Barrueco R, Yu J, Saucedo-Cuevas LP, Olivan M, Llobet-Navas D, Putcha P, Castro V, Murga-Penas EM, Collazo-Lorduy A, Castillo-Martin M et al.  2015.  Inhibition of the autocrine IL-6-JAK2-STAT3-calprotectin axis as targeted therapy for HR-/HER2+ breast cancers. Genes Dev. 29(15):1631-48. Go to Pubmed
Tasoff J, Mee MT, Wang HH.  2015.  An Economic Framework of Microbial Trade. PLoS One. 10(7):e0132907. Go to Pubmed
Liu X, Jia Y, Stoopler MB, Shen Y, Cheng H, Chen J, Mansukhani M, Koul S, Halmos B, Borczuk AC.  2015.  Next-Generation Sequencing of Pulmonary Sarcomatoid Carcinoma Reveals High Frequency of Actionable MET Gene Mutations. J Clin Oncol. Go to Pubmed
Brichta L, Shin W, Jackson-Lewis V, Blesa J, Yap E-L, Walker Z, Zhang J, Roussarie J-P, Alvarez MJ, Califano A et al.  2015.  Identification of neurodegenerative factors using translatome-regulatory network analysis. Nat Neurosci. Go to Pubmed
Puente XS, Beà S, Valdés-Mas R, Villamor N, Gutiérrez-Abril J, Martín-Subero JI, Munar M, Rubio-Pérez C, Jares P, Aymerich M et al.  2015.  Non-coding recurrent mutations in chronic lymphocytic leukaemia. Nature. Go to Pubmed
Meyer WK, Venkat A, Kermany AR, van de Geijn B, Zhang S, Przeworski M.  2015.  Evolutionary history inferred from the de novo assembly of a non-model organism, the blue-eyed black lemur. Mol Ecol. Go to Pubmed
Mendes CS, Bartos I, Márka Z, Akay T, Márka S, Mann RS.  2015.  Quantification of gait parameters in freely walking rodents. BMC Biol. 13:50. Go to Pubmed
Woo JHoon, Shimoni Y, Yang WSeok, Subramaniam P, Iyer A, Nicoletti P, Martínez MRodríguez, Lopez G, Mattioli M, Realubit R et al.  2015.  Elucidating Compound Mechanism of Action by Network Perturbation Analysis. Cell. 162(2):441-51. Go to Pubmed
Hayano M, Yang WS, Corn CK, Pagano NC, Stockwell BR.  2015.  Loss of cysteinyl-tRNA synthetase (CARS) induces the transsulfuration pathway and inhibits ferroptosis induced by cystine deprivation. Cell Death Differ. Go to Pubmed
Lu X-J, Bussemaker HJ, Olson WK.  2015.  DSSR: an integrated software tool for dissecting the spatial structure of RNA. Nucleic Acids Res. Go to Pubmed
Hwang H, Petrey D, Honig B.  2015.  A hybrid method for protein-protein interface prediction. Protein Sci. Go to Pubmed
Goodwin JF, Kothari V, Drake JM, Zhao S, Dylgjeri E, Dean JL, Schiewer MJ, McNair C, Jones JK, Aytes A et al.  2015.  DNA-PKcs-Mediated Transcriptional Regulation Drives Prostate Cancer Progression and Metastasis. Cancer Cell. 28(1):97-113. Go to Pubmed
Freedberg DE, Toussaint NC, Chen SP, Ratner AJ, Whittier S, Wang TC, Wang HH, Abrams JA.  2015.  Proton Pump Inhibitors Alter Specific Taxa in the Human Gastrointestinal Microbiome: A Crossover Trial. Gastroenterology. Go to Pubmed
Vidal B, Santella A, Serrano-Saiz E, Bao Z, Chuang C-F, Hobert O.  2015.  C. elegans SoxB genes are dispensable for embryonic neurogenesis but required for terminal differentiation of specific neuron types. Development. 142(14):2464-77. Go to Pubmed
Ikiz B, Alvarez MJ, Ré DB, Le Verche V, Politi K, Lotti F, Phani S, Pradhan R, Yu C, Croft GF et al.  2015.  The Regulatory Machinery of Neurodegeneration in In Vitro Models of Amyotrophic Lateral Sclerosis. Cell Rep. Go to Pubmed
Rabadan R.  2015.  WE-D-BRB-03: Geometrization of Tumor Evolution. Med Phys. 42(6):3666. Go to Pubmed
Nicoletti P, Bansal M, Lefebvre C, Guarnieri P, Shen Y, Pe'er I, Califano A, Floratos A.  2015.  ABC Transporters and the Proteasome Complex Are Implicated in Susceptibility to Stevens-Johnson Syndrome and Toxic Epidermal Necrolysis across Multiple Drugs. PLoS One. 10(6):e0131038. Go to Pubmed
Rao S, Machado ACarolina D, Zhou T, Rastogi C, Bussemaker HJ, Rohs R.  2015.  22 Evolving insights on how cytosine methylation affects protein-DNA binding. J Biomol Struct Dyn. 33 Suppl 1:12. Go to Pubmed
Zhou T, Shen N, Yang L, Abe N, Horton J, Mann RS, Bussemaker HJ, Gordân R, Rohs R.  2015.  14 Quantitative modeling of transcription factor binding specificities using DNA shape. J Biomol Struct Dyn. 33 Suppl 1:8-9. Go to Pubmed
Kwon YDo, Pancera M, Acharya P, Georgiev IS, Crooks ET, Gorman J, M Joyce G, Guttman M, Ma X, Narpala S et al.  2015.  Crystal structure, conformational fixation and entry-related interactions of mature ligand-free HIV-1 Env. Nat Struct Mol Biol. Go to Pubmed
Gordon PM, Hobert O.  2015.  A Competition Mechanism for a Homeotic Neuron Identity Transformation in C. elegans. Dev Cell. Go to Pubmed
Levine JH, Simonds EF, Bendall SC, Davis KL, Amir E-AD, Tadmor MD, Litvin O, Fienberg HG, Jager A, Zunder ER et al.  2015.  Data-Driven Phenotypic Dissection of AML Reveals Progenitor-like Cells that Correlate with Prognosis. Cell. Go to Pubmed
Howell K, White JG, Hobert O.  2015.  Spatiotemporal control of a novel synaptic organizer molecule. Nature. Go to Pubmed
Murgan S, Kari W, Rothbächer U, Iché-Torres M, Mélénec P, Hobert O, Bertrand V.  2015.  Atypical Transcriptional Activation by TCF via a Zic Transcription Factor in C. elegans Neuronal Precursors. Dev Cell. 33(6):737-45. Go to Pubmed
Vilar S, Lorberbaum T, Hripcsak G, Tatonetti NP.  2015.  Improving Detection of Arrhythmia Drug-Drug Interactions in Pharmacovigilance Data through the Implementation of Similarity-Based Modeling. PLoS One. 10(6):e0129974. Go to Pubmed
Pitt LA, Tikhonova AN, Hu H, Trimarchi T, King B, Gong Y, Sanchez-Martin M, Tsirigos A, Littman DR, Ferrando AA et al.  2015.  CXCL12-Producing Vascular Endothelial Niches Control Acute T Cell Leukemia Maintenance. Cancer Cell. 27(6):755-68. Go to Pubmed
Lee H-O, He X, Mookerjee-Basu J, Zhongping D, Hua X, Nicolas E, Sulis MLuisa, Ferrando AA, Testa JR, Kappes DJ.  2015.  Disregulated expression of the transcription factor ThPOK during T-cell development leads to high incidence of T-cell lymphomas. Proc Natl Acad Sci U S A. Go to Pubmed
Ostrowski EA, Shen Y, Tian X, Sucgang R, Jiang H, Qu J, Katoh-Kurasawa M, Brock DA, Dinh C, Lara-Garduno F et al.  2015.  Genomic Signatures of Cooperation and Conflict in the Social Amoeba. Curr Biol. 25(12):1661-5. Go to Pubmed
Bose S, Wan Z, Carr A, Rizvi AH, Vieira G, Pe'er D, Sims PA.  2015.  Scalable microfluidics for single cell RNA printing and sequencing. Genome Biol. 16(1):120. Go to Pubmed
Boland MRegina, Shahn Z, Madigan D, Hripcsak G, Tatonetti NP.  2015.  Birth Month Affects Lifetime Disease Risk: A Phenome-Wide Method. J Am Med Inform Assoc. Go to Pubmed
Bansal M, Mendiratta G, Anand S, Kushwaha R, Kim R, Kustagi M, Iyer A, Chaganti RSk, Califano A, Sumazin P.  2015.  Direct ChIP-Seq significance analysis improves target prediction. BMC Genomics. 16 Suppl 5:S4. Go to Pubmed
Yu L, Sawle AD, Wynn J, Aspelund G, Stolar CJ, Arkovitz MS, Potoka D, Azarow KS, Mychaliska GB, Shen Y et al.  2015.  Increased burden of de novo predicted deleterious variants in complex congenital diaphragmatic hernia. Hum Mol Genet. Go to Pubmed
Nascimento CS, Barbosa LT, Brito C, Fernandes RPM, Mann RS, Pinto APaula G, Oliveira HC, Dodson MV, Guimarães SEF, Duarte MS.  2015.  Identification of Suitable Reference Genes for Real Time Quantitative Polymerase Chain Reaction Assays on Pectoralis major Muscle in Chicken (Gallus gallus ). PLoS One. 10(5):e0127935. Go to Pubmed
DiGiuseppe JA, Tadmor MD, Pe'er D.  2015.  Detection of Minimal Residual Disease in B Lymphoblastic Leukemia Using viSNE. Cytometry B Clin Cytom. Go to Pubmed
Dixon SJ, Winter GE, Musavi LS, Lee E, Snijder B, Rebsamen M, Superti-Furga G, Stockwell BR.  2015.  Human haploid cell genetics reveals roles for lipid metabolism genes in non-apoptotic cell death. ACS Chem Biol. Go to Pubmed
Enriquez J, Venkatasubramanian L, Baek M, Peterson M, Aghayeva U, Mann RS.  2015.  Specification of individual adult motor neuron morphologies by combinatorial transcription factor codes. Neuron. Go to Pubmed
Pefanis E, Wang J, Rothschild G, Lim J, Kazadi D, Sun J, Federation A, Chao J, Elliott O, Liu Z-P et al.  2015.  RNA exosome-regulated long non-coding RNA transcription controls super-enhancer activity. Cell. 161(4):774-89. Go to Pubmed
Rivas MA, Pirinen M, Conrad DF, Lek M, Tsang EK, Karczewski KJ, Maller JB, Kukurba KR, DeLuca DS, Fromer M et al.  2015.  Human genomics. Effect of predicted protein-truncating genetic variants on the human transcriptome. Science. 348(6235):666-9. Go to Pubmed
Melé M, Ferreira PG, Reverter F, DeLuca DS, Monlong J, Sammeth M, Young TR, Goldmann JM, Pervouchine DD, Sullivan TJ et al.  2015.  Human genomics. The human transcriptome across tissues and individuals. Science. 348(6235):660-5. Go to Pubmed
GTEx Consortium.  2015.  Human genomics. The Genotype-Tissue Expression (GTEx) pilot analysis: multitissue gene regulation in humans. Science. 348(6235):648-60. Go to Pubmed
GTEx Consortium.  2015.  Human genomics. The Genotype-Tissue Expression (GTEx) pilot analysis: multitissue gene regulation in humans. Science. 348(6235):648-60. Go to Pubmed
Baran Y, Subramaniam M, Biton A, Tukiainen T, Tsang EK, Rivas MA, Pirinen M, Gutierrez-Arcelus M, Smith KS, Kukurba KR et al.  2015.  The landscape of genomic imprinting across diverse adult human tissues. Genome Res. Go to Pubmed
Trampush JW, Lencz T, Knowles E, Davies G, Guha S, Pe'er I, Liewald DC, Starr JM, Djurovic S, Melle I et al.  2015.  Independent evidence for an association between general cognitive ability and a genetic locus for educational attainment. Am J Med Genet B Neuropsychiatr Genet. Go to Pubmed
Melamed RD, Wang J, Iavarone A, Rabadan R.  2015.  An information theoretic method to identify combinations of genomic alterations that promote glioblastoma. J Mol Cell Biol. Go to Pubmed
T Chen S, Petrey D, Garzón JIgnacio, Honig B.  2015.  Predicting peptide-mediated interactions on a genome-wide scale. PLoS Comput Biol. 11(5):e1004248. Go to Pubmed
Melamed RD, Emmett KJ, Madubata C, Rzhetsky A, Rabadan R.  2015.  Genetic similarity between cancers and comorbid Mendelian diseases identifies candidate driver genes. Nat Commun. 6:7033. Go to Pubmed
Englander MT, Avins JL, Fleisher RC, Liu B, Effraim PR, Wang J, Schulten K, Leyh TS, Gonzalez RL, Cornish VW.  2015.  The ribosome can discriminate the chirality of amino acids within its peptidyl-transferase center. Proc Natl Acad Sci U S A. 112(19):6038-43. Go to Pubmed
Ayvaz S, Horn J, Hassanzadeh O, Zhu Q, Stan J, Tatonetti NP, Vilar S, Brochhausen M, Samwald M, Rastegar-Mojarad M et al.  2015.  Toward a complete dataset of drug-drug interaction information from publicly available sources. J Biomed Inform. Go to Pubmed
Kratsios P, Pinan-Lucarré B, Kerk SYen, Weinreb A, Bessereau J-L, Hobert O.  2015.  Transcriptional Coordination of Synaptogenesis and Neurotransmitter Signaling. Curr Biol. Go to Pubmed
Emmett KJ, Rosenstein JK, van de Meent J-W, Shepard KL, Wiggins CH.  2015.  Statistical inference for nanopore sequencing with a biased random walk model. Biophys J. 108(8):1852-5. Go to Pubmed
Repunte-Canonigo V, Shin W, Vendruscolo LF, Lefebvre C, van der Stap L, Kawamura T, Schlosburg JE, Alvarez M, Koob GF, Califano A et al.  2015.  Identifying candidate drivers of alcohol dependence-induced excessive drinking by assembly and interrogation of brain-specific regulatory networks. Genome Biol. 16(1):68. Go to Pubmed
Causton HC, Feeney KA, Ziegler CA, O'Neill JS.  2015.  Metabolic Cycles in Yeast Share Features Conserved among Circadian Rhythms. Curr Biol. 25(8):1056-62. Go to Pubmed
Wu X, Zhang Z, Schramm CA, M Joyce G, Kwon YDo, Zhou T, Sheng Z, Zhang B, O'Dell S, McKee K et al.  2015.  Maturation and Diversity of the VRC01-Antibody Lineage over 15 Years of Chronic HIV-1 Infection. Cell. Go to Pubmed
Boland MR, Tatonetti NP, Hripcsak G.  2015.  Development and validation of a classification approach for extracting severity automatically from electronic health records. J Biomed Semantics. 6:14. Go to Pubmed
Kaplan A, Gaschler MM, Dunn DE, Colligan R, Brown LM, Palmer AG, Lo DC, Stockwell BR.  2015.  Small molecule-induced oxidation of protein disulfide isomerase is neuroprotective. Proc Natl Acad Sci U S A. Go to Pubmed
Califano A, Kellis M, Stolovitzky G.  2015.  Preface: RECOMB/ISCB Systems Biology, Regulatory Genomics, and DREAM 2014 Special Issue. J Comput Biol. 22(4):251-2. Go to Pubmed
Abe N, Dror I, Yang L, Slattery M, Zhou T, Bussemaker HJ, Rohs R, Mann RS.  2015.  Deconvolving the Recognition of DNA Shape from Sequence. Cell. Go to Pubmed
Shen MM.  2015.  Cancer: The complex seeds of metastasis. Nature. Go to Pubmed
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