Icahn School of Medicine at Mount Sinai
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Research Papers

Research Papers

Gang Fang, John Beaulaurier, Shijia Zhu, et al. (2015) Single molecule-level detection and long read-based phasing of epigenetic variations in bacterial methylomes. Nature Communications 6 Read paper

Sanderson S, Linderman M, Suckiel S, Diaz G, Zinberg R, Ferryman K, Wasserstein M, Kasarskis A, Schadt E (2015) Motivations, concerns and preferences of personal genome sequencing research participants: Baseline findings from the HealthSeq project. EJHG 10.1038 Read paper

Tu Z, Zhang B, Zhu J, Huang T, et al. contributed to the network analysis in the project The Genotype-Tissue Expression (GTEx) pilot analysis: Multi-tissue gene regulation in humans. Science Read paper

Jose Clemente, et al. (2015) The Microbiome of Uncontacted Amerindians. Science Advances Read paper

Harm Van Bakel, Ivan Marazzi, Christopher Basler, Ana Fernandez-Sesma, et al. (2015) Senataxin suppresses the antiviral transcriptional response and controls vital biogenesis. Nature Immunology Read paper

Brown B, Evans M, Israelow B, Mullokandov G, Agudo J, Sourisseau M, Bashir A, Maldonado A, Dar A, et al. (2014) Hepatitis C virus genetics affects miR-122 requirements and response to miR-122 inhibitors. Nat Commun 5. Read paper

Zhu J, Huynh JL, Yoo S, Zhang B, Schadt E, Casaccia P, et al. (2014) Common dysregulation network in the human prefrontal cortex underlies two neurodegenerative diseases. Mol Syst Biol 10:743. Read paper

Brahmachary M, Guilmatre A, Quilez J, Hasson D, Borel C, Warburton P, Sharp AJ, et al. (2014) Digital genotyping of macrosatellites and multicopy genes reveals novel biological functions associated with copy number variation of large tandem repeats. PloS Genet 10 : e1004418 Read paper

Houten S, Denis S, te Brinke H, Jongejan A, van Kampen AHC, et al. (2014) Mitochondrial NADP(H) deficiency due to a mutation in NADK2 causes dienoyl-CoA reductase deficiency with hyperlysinemia. Hum Mol Genet 23(11) Read paper

Pinto D, Delaby E, Merico D, Barbosa M, Merikangas A, et al. (2014) Convergence of Genes and Cellular Pathways Dysregulated in Autism Spectrum Disorders. Cell Press. Read paper

Briese T, Mishra N, Jain K, Zalmout I, Jabado O, et al. (2014) Middle East Respiratory Syndrome Coronavirus Quasispecies That Include Homologues of Human Isolates Revealed through Whole-Genome Analysis and Virus Cultured from Dromedary Camels in Saudi Arabia. mBio 5(3) Read paper

Auer P, Teumer A, Schick U, O’Shaughnessy A, Lo K, et al. (2014) Rare and low-frequency coding variants in CXCR2 and other genes are associated with hematological traits. Nat Genet. (2014) Read paper

Dhandapany P, Razzaque M, Muthusami U, Kunnoth S, Edwards J, et al. (2014) RAF1 mutations in childhood-onset dilated cardiomyopathy. Nat. Genet. Read paper

Sivendran S, Chang R, Pham L, Phelps R, Harcharik S et al. (2014) Dissection of Immune Gene Networks in Primary Melanoma Tumors Critical for Anti-Tumor Surveillance of Patients with Stage II-III Resectable Disease. J Invest Dermatol. Read paper

Björkegren JLM, Hägg S, Talukdar HA, Foroughi Asl H, Jain RK, et al. (2014) Plasma Cholesterol-Induced Lesion Networks Activated before Regression of Early, Mature, and Advanced Atherosclerosis. PLoS Genet 10(2) Read paper

Fromer M, Pocklington A, Kavanagh D, Williams H, Dwyer S et al. (2014) De novo mutations in schizophrenia implicate synaptic networks. Nature. Read paper

Kidd B, Peters L, Schadt E, Dudley J (2014) Unifying immunology with informatics and multiscale biology. Nat Immunol 15(2):118-27 Read paper

Purcell S, Moran J, Fromer M, Ruderfer D, Solovieff N et al. (2014) A polygenic burden of rare disruptive mutations in schizophrenia. Nature. Read paper

Parikh A, Lee C, Perinne J, Marchini S, Baccarini A et al. (2014) microRNA-181a has a critical role in ovarian cancer progression through the regulation of the epithelial-mesenchymal transition. Nat Commun 5. Read paper

Martignetti J, Camacho-Vanegas O, Priedigkeit N, Camacho C, Pereira E, et al. (2014) Personalized Ovarian Cancer Disease Surveillance and Detection of Candidate Therapeutic Drug Target in Circulating Tumor DNA. Neoplasia 16(1). Read paper

Sanderson S, Linderman M, Kasarskis A, Bashir A, Diaz G et al. (2013) Informed decision-making among students analyzing their personal genomes on a whole genome sequencing course: a longitudinal cohort study. Genome Med 5(12). Read paper

Agudo J, Ruzo A, Tung N, Salmon H, Leboeuf M, et al. (2014) The miR-126-VEGFR2 axis controls the innate response to pathogen-associated nucleic acids. Nat Immunol 15(1):54-62 Read paper

Huynh J, Garg P, Thin T, Yoo S, Dutta R et al. (2014) Epigenome-wide differences in pathology-free regions of multiple sclerosis?affected brains. Nat Neurosci 17(1):121-130 Read paper

Ripke S, O'Dushlaine C, Chambert K, Moran J , Kähler A, et al. (2013) Genome-wide association analysis identifies 13 new risk loci for schizophrenia. Nat Genet 2013 Aug 25. doi: 10.1038/ng.2742 Read paper

Zhang B, Gaiteri C, Bodea LG, Wang Z, McElwee J, et al. (2013) Integrated Systems Approach Identifies Genetic Nodes and Networks in Late-Onset Alzheimer's Disease. Cell 153(3):707-720 Read paper

Schadt EE, Banerjee O, Fang G, Feng Z, Wong WH, et al. (2013) Modeling kinetic rate variation in third generation DNA sequencing data to detect putative modifications to DNA bases. Genome Res. 23: 129-141 Read paper

Gargis AS, Kalman L, Berry MW, Bick DP, Dimmock DP, et al. (2012). Assuring the quality of next-generation sequencing in clinical laboratory practice. Nat Biotechnol. 30(11):1033-6. Read paper

Fang G, Munera D, Friedman DI, Mandlik A, Chao MC, et al. (2012) Genome-wide mapping of methylated adenine residues in pathogenic Escherichia coli using single-molecule real-time sequencing. Nat Biotechnol. 30: 1232-1239 Read paper

Bashir A, Klammer AA, Robins WP, Chin CS, Webster D, et al. (2012) A hybrid approach for the automated finishing of bacterial genomes. Nat Biotechnol. 30, 701-707 Read paper

Schadt EE, Woo S, Hao K (2012) Bayesian method to predict individual SNP genotypes from gene expression data. Nat Genet 44: 603-608 Read paper

Smith CC, Wang Q, Chin C, Salerno S,Damon LE, et al. (2012) Validation of ITD mutations in FLT3 as a therapeutic target in human acute myeloid leukaemia. Nature 485, 260-263 Read paper

Brunner JI, Gotter AL, Millstein J, Garson S, Binns J, et al. (2011) Pharmacological validation of candidate causal sleep genes identified in an N2 cross. J Neurogenet. 25(4):167-81. Read paper

Millstein J, Winrow CJ, Kasarskis A, Owens JR, Zhou L, et al. (2011) Identification of causal genes, networks, and transcriptional regulators of REM sleep and wake. Sleep. 34(11):1469-77 Read paper

Rasko DA, Webster DR, Sahl JW, Bashir A, Boisen N, et al. (2011) Origins of the E. coli strain causing an outbreak of hemolytic-uremic syndrome in Germany. N Engl J Med 365: 709-717. Read paper

Su WL, Kleinhanz RR, Schadt EE (2011) Characterizing the role of miRNAs within gene regulatory networks using integrative genomics techniques. Mol Syst Biol 7: 490. Read paper

Chin CS, Sorenson J, Harris JB, Robins WP, Charles RC, et al. (2011) The origin of the Haitian cholera outbreak strain. N Engl J Med 364: 33-42. Read paper

Wontakal SN, Guo X, Will B, Shi M, Raha D, et al. (2011) A large gene network in immature erythroid cells is controlled by the myeloid and B cell transcriptional regulator PU.1. PLoS Genet 7: e1001392.9 Read paper

Karmakar S, Mahajan MC, Schulz V, Boyapaty G, Weissman SM (2010) A multiprotein complex necessary for both transcription and DNA replication at the β-globin locus. EMBO J 29: 3260-3271. Read paper

Schadt EE, Linderman MD, Sorenson J, Lee L, Nolan GP (2010) Computational solutions to large-scale data management and analysis. Nat Rev Genet 11: 647-657. Read paper

Pandey G, Zhang B, Chang AN, Myers CL, Zhu J, et al. (2010) An integrative multi-network and multi-classifier approach to predict genetic interactions. PLoS Comput Biol 6. Read paper

Yang X, Zhang B, Molony C, Chudin E, Hao K, et al. (2010) Systematic genetic and genomic analysis of cytochrome P450 enzyme activities in human liver. Genome Res 20: 1020-1036 Read paper

Schadt EE, Turner S, Kasarskis A (2010) A window into third-generation sequencing. Hum Mol Genet 19: R227-240. Read paper

Zhang W, Zhu J, Schadt EE, Liu JS (2010) A Bayesian partition method for detecting pleiotropic and epistatic eQTL modules. PLoS Comput Biol 6: e1000642 Read paper

Wang K, Narayanan M, Zhong H, Tompa M, Schadt EE, et al. (2009) Meta-analysis of inter-species liver co-expression networks elucidates traits associated with common human diseases. PLoS Comput Biol 5: e1000616 Read paper

Mahajan MC, Karmakar S, Newburger PE, Krause DS, Weissman SM (2009) Dynamics of alpha-globin locus chromatin structure and gene expression during erythroid differentiation of human CD34( ) cells in culture. Exp Hematol 37: 1143-1156.e1143 Read paper

Schadt EE (2009) Molecular networks as sensors and drivers of common human diseases. Nature 461: 218-223 Read paper

Pandey G, Myers CL, Kumar V (2009) Incorporating functional inter-relationships into protein function prediction algorithms. BMC Bioinformatics 10: 142 Read paper

Yang X, Deignan JL, Qi H, Zhu J, Qian S, et al. (2009) Validation of candidate causal genes for obesity that affect shared metabolic pathways and networks. Nat Genet 41: 415-423 Read paper

Schadt EE, Friend SH, Shaywitz DA (2009) A network view of disease and compound screening. Nat Rev Drug Discov 8: 286-295 Read paper

Schadt EE, Molony C, Chudin E, Hao K, Yang X, et al. (2008) Mapping the genetic architecture of gene expression in human liver. PLoS Biol 6: e107 Read paper

Chen Y, Zhu J, Lum PY, Yang X, Pinto S, et al. (2008) Variations in DNA elucidate molecular networks that cause disease. Nature 452: 429-435 Read paper

Zhu J, Zhang B, Smith EN, Drees B, Brem RB, et al. (2008) Integrating large-scale functional genomic data to dissect the complexity of yeast regulatory networks. Nat Genet 40: 854-861 Read paper

Emilsson V, Thorleifsson G, Zhang B, Leonardson AS, Zink F, et al. (2008) Genetics of gene expression and its effect on disease. Nature 452: 423-428 Read paper