Showing 25 of 26 results

• Publication

  released

  Deconstruction of rheumatoid arthritis synovium defines inflammatory subtypes

  Fan Zhang, Anna Helena Jonsson, Aparna Nathan, et al.

  Nature. 2023-11-08;623(7987):616-624.

  • doi:10.1038/s41586-023-06708-y
  • PMID:37938773
  • PMCID:PMC10651487

  URL: https://doi.org/10.7303/syn52297840

  Data summary: CITE-seq single-cell expression matrices and sequencing and bulk expression matrices are available…See more

  URL: https://arkportal.synapse.org/Explore/Datasets/DetailsPage?id=syn52297840

  Data summary: Associated genotype and clinical data are available through the Arthritis and Autoimmune and…See more

  URL: https://immunogenomics.io/ampra2/

  Data summary: A cell browser website is available to visualize our data and results.

  Data summary: AMP Phase 1 single-cell data from ref. 8 are available on Immport (SDY998). PEAC clinical trial…See more

  URL: https://github.com/Immunogenomics/RA_Atlas_CITEseq/

  Data summary: The source code for the analyses is available at GitHub

  URL: https://zenodo.org/record/8118599

  Data summary: The source code for the analyses is available at zenodo

• Publication

  released

  Cohesin-mediated loop anchors confine the locations of human replication origins

  Daniel J Emerson # 1 2 3 , Peiyao A Zhao # 4 , Ashley L Cook # 1 2 3 , et al.

  Nature. 2022-06-08;606(7915):812-819.

  • doi:10.1038/s41586-022-04803-0
  • PMID:35676475
  • PMCID:PMC9217744

  Data summary: All new raw data created in this manuscript have been uploaded to the 4D Nucleome portal and will…See more

• Publication

  released

  Chromatin accessibility and gene expression during adipocyte differentiation identify context-dependent effects at cardiometabolic GWAS loci

  Hannah J Perrin, Kevin W Currin, Swarooparani Vadlamudi, et al.

  PLoS Genet. 2021-10-26;17(10):e1009865.

  • doi:10.1371/journal.pgen.1009865
  • PMID:34699533
  • PMCID:PMC8570510

• Publication

  released

  Systematic analysis of binding of transcription factors to noncoding variants

  Jian Yan, Yunjiang Qiu, André M. Ribeiro dos Santos, et al.

  Nature. 2021-1-27;

  • doi:10.1038/s41586-021-03211-0
  • PMID:33505025

• Publication

  released

  Large-scale genetic association and single cell accessible chromatin mapping defines cell type-specific mechanisms of type 1 diabetes risk

  Joshua Chiou, Ryan J Geusz, Mei-Lin Okino, et al.

  Nature. 2021-05-19;594(7863):398-402.

  • doi:10.1038/s41586-021-03552-w
  • PMID:34012112

• Publication

  released

  Glucocorticoid signaling in pancreatic islets modulates gene regulatory programs and genetic risk of type 2 diabetes

  Anthony Aylward, Mei-Lin Okino, Paola Benaglio, et al.

  PLoS Genet. 2021-05-13;17(5):e1009531.

  • doi:10.1371/journal.pgen.1009531
  • PMID:33983929
  • PMCID:PMC8183998

• Publication

  released

  Genome-wide enhancer maps link risk variants to disease genes

  Joseph Nasser, Drew T. Bergman, Charles P. Fulco, et al.

  Nature. 2021-04-07;593:238–243.

  • doi:10.1038/s41586-021-03446-x

• Publication

  released

  Regulatory genomic circuitry of human disease loci by integrative epigenomics

  Carles A Boix, Benjamin T James, Yongjin P Park, et al.

  Nature. 2021-02-03;590(7845):300-307.

  • doi:10.1038/s41586-020-03145-z
  • PMID:33536621
  • PMCID:PMC7875769

• Publication

  released

  Expanded encyclopaedias of DNA elements in the human and mouse genomes

  The ENCODE Project Consortium, Jill E. Moore, Michael J. Purcaro, et al.

  Nature. 2020-07-29;583(7818):699–710.

  • doi:10.1038/s41586-020-2493-4
  • PMID:32728249
  • PMCID:PMC7410828

• Publication

  released

  Index and biological spectrum of human DNase I hypersensitive sites

  Wouter Meuleman, Alexander Muratov, Eric Rynes, et al.

  Nature. 2020-07-29;584(7820):244–251.

  • doi:10.1038/s41586-020-2559-3
  • PMCID:PMC7422677
  • PMID:32728217

• Publication

  released

  Integrative analysis of gene expression, DNA methylation, physiological traits, and genetic variation in human skeletal muscle

  D. Leland Taylor, Anne U. Jackson, Narisu Narisu, et al.

  PNAS. 2019-05-28;116(22):10883-10888.

  • doi:10.1073/pnas.1814263116
  • PMID:31076557
  • PMCID:PMC6561151

  URL: https://www.ebi.ac.uk/birney-srv/FUSION/

• Publication

  released

  Charting cellular identity during human in vitro β-cell differentiation

  Adrian Veres, Aubrey L Faust, Henry L Bushnell, et al.

  Nature. 2019-05-01;569(7756):368-373.

  • doi:10.1038/s41586-019-1168-5
  • PMCID:PMC6903417
  • PMID:31068696

• Publication

  released

  Genetic regulation of the placental transcriptome underlies birth weight and risk of childhood obesity

  Shouneng Peng, Maya A. Deyssenroth, Antonio F. Di Narzo, et al.

  PLoS Genet. 2018-12-31;14(12):e1007799.

  • doi:10.1371/journal.pgen.1007799
  • PMID:30596636
  • PMCID:PMC6329610

• Publication

  released

  Identification and functional analysis of glycemic trait loci in the China Health and Nutrition Survey

  Cassandra N Spracklen, Jinxiu Shi, Swarooparani Vadlamudi, et al.

  PLoS Genet. 2018-04-05;14(4):e1007275.

  • doi:10.1371/journal.pgen.1007275
  • PMID:29621232
  • PMCID:PMC5886383

• Publication

  released

  Genetic Regulatory Signatures Underlying Islet Gene Expression And Type 2 Diabetes

  Arushi Varshney, Laura J. Scott, Ryan P. Welch, et al.

  PNAS. 2017-02-28;114(9):2301-2306.

  • doi:10.1073/pnas.1621192114
  • PMID:28193859
  • PMCID:PMC5338551

• Publication

  released

  Mapping Of Histone Modifications In Episomal HBV cccDNA Uncovers An Unusual Chromatin Organization Amenable To Epigenetic Manipulation

  Philipp Tropberger, Alexandre Mercier, Margaret Robinson, et al.

  PNAS. 2015-10-20;112(42):E5715-E5724.

  • doi:10.1073/pnas.1518090112
  • PMID:26438841

• Publication

  released

  Characterization of TCF21 Downstream Target Regions Identifies a Transcriptional Network Linking Multiple Independent Coronary Artery Disease Loci

  Olga Sazonova, Yuqi Zhao, Sylvia Nürnberg, et al.

  PLoS Genet. 2015-05-28;11(5):e1005202.

  • doi:10.1371/journal.pgen.1005202
  • PMID:26020271
  • PMCID:PMC4447360

  URL: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE61369

• Publication

  released

  Integrative analysis of haplotype-resolved epigenomes across human tissues

  Danny Leung, Inkyung Jung, Nisha Rajagopal, et al.

  Nature. 2015-02-19;518(7539):350-354.

  • doi:10.1038/nature14217
  • PMID:25693566
  • PMCID:PMC4449149

• Publication

  released

  Global Genomic And Transcriptomic Analysis Of Human Pancreatic Islets Reveals Novel Genes Influencing Glucose Metabolism

  João Fadista, Petter Vikman, Emilia Ottosson Laakso, et al.

  PNAS. 2014-09-23;111(38):13924-13929.

  • doi:10.1073/pnas.1402665111
  • PMID:25201977

• Publication

  released

  A common Greenlandic TBC1D4 variant confers muscle insulin resistance and type 2 diabetes

  Ida Moltke, Niels Grarup, Marit E Jørgensen, et al.

  Nature. 2014-08-14;512(7513):190-3.

  • doi:10.1038/nature13425
  • PMID:25043022

• Publication

  released

  Chromatin Stretch Enhancer States Drive Cell-specific Gene Regulation And Harbor Human Disease Risk Variants

  Stephen C. J. Parker, Michael L. Stitzel, D. Leland Taylor, et al.

  PNAS. 2013-10-29;110(44):17921-17926.

  • doi:10.1073/pnas.1317023110
  • PMID:24127591

• Publication

  released

  Transcriptome and genome sequencing uncovers functional variation in humans

  Tuuli Lappalainen, Michael Sammeth, Marc R Friedländer, et al.

  Nature. 2013-09-26;501(7468):506-11.

  • doi:10.1038/nature12531
  • PMID:24037378
  • PMCID:PMC3918453

• Publication

  released

  Identification, replication, and functional fine-mapping of expression quantitative trait loci in primary human liver tissue

  Federico Innocenti, Gregory M Cooper, Ian B Stanaway, et al.

  PLoS Genet. 2011-05-26;7(5):e1002078.

  • doi:10.1371/journal.pgen.1002078
  • PMID:21637794
  • PMCID:PMC3102751

• Publication

  released

  Biological, clinical and population relevance of 95 loci for blood lipids

  Tanya M Teslovich, Kiran Musunuru, Albert V Smith, et al.

  Nature. 2010-08-05;466(7307):707-13.

  • doi:10.1038/nature09270
  • PMID:20686565
  • PMCID:PMC3039276

  URL: http://csg.sph.umich.edu/willer/public/lipids2010/

• Publication

  released

  Parental origin of sequence variants associated with complex diseases

  Augustine Kong, Valgerdur Steinthorsdottir, Gisli Masson, et al.

  Nature. 2009-12-17;462(7275):868-74.

  • doi:10.1038/nature08625
  • PMID:20016592
  • PMCID:PMC3746295