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Research

Research Papers

Research Papers

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).

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)

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.

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

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

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

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.

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

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

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).

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

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

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

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

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

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.

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

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

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.

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.

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.

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

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.

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

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.

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.

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

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.

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.

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

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

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

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.

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

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.

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.

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.

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.

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.

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.


Research Papers

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