Integrative Genetic and Epigenetic Analysis Uncovers Regulatory Mechanisms of Autoimmune Disease.

[1]  Nikolaos A Patsopoulos,et al.  Limited statistical evidence for shared genetic effects of eQTLs and autoimmune disease-associated loci in three major immune cell types , 2017, Nature Genetics.

[2]  Adam R. Johnson,et al.  Resolving TYK2 locus genotype-to-phenotype differences in autoimmunity , 2016, Science Translational Medicine.

[3]  Søren Brunak,et al.  Analysis of five chronic inflammatory diseases identifies 27 new associations and highlights disease-specific patterns at shared loci , 2016, Nature Genetics.

[4]  James Y. Zou Analysis of protein-coding genetic variation in 60,706 humans , 2015, Nature.

[5]  Dariusz M Plewczynski,et al.  CTCF-Mediated Human 3D Genome Architecture Reveals Chromatin Topology for Transcription , 2015, Cell.

[6]  Y. Fujimoto,et al.  Interleukin 19 reduces inflammation in chemically induced experimental colitis. , 2015, International immunopharmacology.

[7]  Eric Haugen,et al.  Large-scale identification of sequence variants impacting human transcription factor occupancy in vivo , 2015, Nature Genetics.

[8]  Masa Umicevic Mirkov,et al.  Association mapping of inflammatory bowel disease loci to single variant resolution , 2015, bioRxiv.

[9]  Calliope A. Dendrou,et al.  Class II HLA interactions modulate genetic risk for multiple sclerosis , 2015, Nature Genetics.

[10]  Casey S. Greene,et al.  International genome-wide meta-analysis identifies new primary biliary cirrhosis risk loci and targetable pathogenic pathways , 2015, Nature Communications.

[11]  Yakir A Reshef,et al.  Partitioning heritability by functional annotation using genome-wide association summary statistics , 2015, Nature Genetics.

[12]  Judy H. Cho,et al.  Association analyses identify 38 susceptibility loci for inflammatory bowel disease and highlight shared genetic risk across populations , 2015, Nature Genetics.

[13]  Ayal B. Gussow,et al.  The Intolerance of Regulatory Sequence to Genetic Variation Predicts Gene Dosage Sensitivity , 2015, PLoS genetics.

[14]  B. Pasaniuc,et al.  Leveraging Functional-Annotation Data in Trans-ethnic Fine-Mapping Studies. , 2015, American journal of human genetics.

[15]  Buhm Han,et al.  Disentangling the Effects of Colocalizing Genomic Annotations to Functionally Prioritize Non-coding Variants within Complex-Trait Loci , 2014, bioRxiv.

[16]  Bethany B. Parks,et al.  Immune cell-based screening assay for response to anticancer agents: applications in pharmacogenomics , 2015, Pharmacogenomics and personalized medicine.

[17]  Manolis Kellis,et al.  Fine mapping of type 1 diabetes susceptibility loci and evidence for colocalization of causal variants with lymphoid gene enhancers , 2015, Nature Genetics.

[18]  Raphael Gottardo,et al.  Orchestrating high-throughput genomic analysis with Bioconductor , 2015, Nature Methods.

[19]  Michael Q. Zhang,et al.  Integrative analysis of 111 reference human epigenomes , 2015, Nature.

[20]  M. Daly,et al.  Genetic and Epigenetic Fine-Mapping of Causal Autoimmune Disease Variants , 2014, Nature.

[21]  M. Daly,et al.  LD Score regression distinguishes confounding from polygenicity in genome-wide association studies , 2014, Nature Genetics.

[22]  Han Xu,et al.  Partitioning heritability of regulatory and cell-type-specific variants across 11 common diseases. , 2014, American journal of human genetics.

[23]  G. Fonseca-Camarillo,et al.  Expression of interleukin (IL)‐19 and IL‐24 in inflammatory bowel disease patients: a cross‐sectional study , 2014, Clinical and experimental immunology.

[24]  B. Ren,et al.  The 3D genome in transcriptional regulation and pluripotency. , 2014, Cell stem cell.

[25]  J. Shendure,et al.  A general framework for estimating the relative pathogenicity of human genetic variants , 2014, Nature Genetics.

[26]  Jun S. Liu,et al.  Genetics of rheumatoid arthritis contributes to biology and drug discovery , 2013 .

[27]  M. Lupien,et al.  Combinatorial effects of multiple enhancer variants in linkage disequilibrium dictate levels of gene expression to confer susceptibility to common traits , 2014, Genome research.

[28]  M. Pirinen,et al.  Analysis of immune-related loci identifies 48 new susceptibility variants for multiple sclerosis , 2013, Nature Genetics.

[29]  Miles Parkes,et al.  Genetic insights into common pathways and complex relationships among immune-mediated diseases , 2013, Nature Reviews Genetics.

[30]  D. Goldstein,et al.  Genic Intolerance to Functional Variation and the Interpretation of Personal Genomes , 2013, PLoS genetics.

[31]  S. Purcell,et al.  Pleiotropy in complex traits: challenges and strategies , 2013, Nature Reviews Genetics.

[32]  Kimberly R. Kukurba,et al.  Systematic functional regulatory assessment of disease-associated variants , 2013, Proceedings of the National Academy of Sciences.

[33]  Sampath Prahalad,et al.  Dense genotyping of immune-related disease regions identifies 14 new susceptibility loci for juvenile idiopathic arthritis , 2013, Nature Genetics.

[34]  Boris Lenhard,et al.  Patterns of regulatory activity across diverse human cell types predict tissue identity, transcription factor binding, and long-range interactions , 2013, Genome research.

[35]  Buhm Han,et al.  Chromatin marks identify critical cell types for fine mapping complex trait variants , 2012 .

[36]  Jake K. Byrnes,et al.  Bayesian refinement of association signals for 14 loci in 3 common diseases , 2012, Nature Genetics.

[37]  James T. Elder,et al.  Identification of fifteen new psoriasis susceptibility loci highlights the role of innate immunity , 2012, Nature Genetics.

[38]  David C. Wilson,et al.  Host-microbe interactions have shaped the genetic architecture of inflammatory bowel disease , 2012, Nature.

[39]  Shane J. Neph,et al.  Systematic Localization of Common Disease-Associated Variation in Regulatory DNA , 2012, Science.

[40]  Nathan C. Sheffield,et al.  The accessible chromatin landscape of the human genome , 2012, Nature.

[41]  J. Todd,et al.  Seven newly identified loci for autoimmune thyroid disease , 2012, Human molecular genetics.

[42]  Daniel J. Gaffney,et al.  Dense fine-mapping study identifies new susceptibility loci for primary biliary cirrhosis , 2012, Nature Genetics.

[43]  Manolis Kellis,et al.  ChromHMM: automating chromatin-state discovery and characterization , 2012, Nature Methods.

[44]  Nicola K. Wilson,et al.  Long-range DNA looping and gene expression analyses identify DEXI as an autoimmune disease candidate gene , 2011, Human molecular genetics.

[45]  Matti Pirinen,et al.  Identification of 15 new psoriasis susceptibility loci highlights the role of innate immunity , 2012 .

[46]  S. Batzoglou,et al.  Linking disease associations with regulatory information in the human genome , 2012, Genome research.

[47]  P. D. de Bakker,et al.  Genome‐wide meta‐analysis identifies novel multiple sclerosis susceptibility loci , 2011, Annals of neurology.

[48]  H. Nakajima,et al.  IL-19 as a potential therapeutic in autoimmune and inflammatory diseases. , 2011, Current pharmaceutical design.

[49]  Sarah Edkins,et al.  Dense genotyping identifies and localizes multiple common and rare variant association signals in celiac disease , 2011, Nature Genetics.

[50]  Kasper Lage,et al.  Pervasive Sharing of Genetic Effects in Autoimmune Disease , 2011, PLoS genetics.

[51]  J. Harrow,et al.  A conditional knockout resource for the genome-wide study of mouse gene function , 2011, Nature.

[52]  M. Brown,et al.  Promise and pitfalls of the Immunochip , 2011, Arthritis research & therapy.

[53]  J. Stamatoyannopoulos,et al.  Chromatin accessibility pre-determines glucocorticoid receptor binding patterns , 2011, Nature Genetics.

[54]  D. Altshuler,et al.  A map of human genome variation from population-scale sequencing , 2010, Nature.

[55]  T. Mikkelsen,et al.  The NIH Roadmap Epigenomics Mapping Consortium , 2010, Nature Biotechnology.

[56]  A. Murphy,et al.  Interleukin‐19 protects mice from innate‐mediated colonic inflammation , 2010, Inflammatory bowel diseases.

[57]  Judy H. Cho,et al.  Unraveling the Genetics of Autoimmunity , 2010, Cell.

[58]  Margaret A. Pericak-Vance,et al.  The role of the CD58 locus in multiple sclerosis , 2009, Proceedings of the National Academy of Sciences.

[59]  A. Zhernakova,et al.  Detecting shared pathogenesis from the shared genetics of immune-related diseases , 2009, Nature Reviews Genetics.

[60]  S. Tsaih,et al.  Genetic influence on immune phenotype revealed strain-specific variations in peripheral blood lineages. , 2008, Physiological genomics.

[61]  Anton J. Enright,et al.  An efficient algorithm for large-scale detection of protein families. , 2002, Nucleic acids research.

[62]  T. Cremer,et al.  Chromosome territories, nuclear architecture and gene regulation in mammalian cells , 2001, Nature Reviews Genetics.

[63]  Y. Benjamini,et al.  Controlling the false discovery rate: a practical and powerful approach to multiple testing , 1995 .