Showing 24 of 24 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

  Genome-wide analysis of the interplay between chromatin-associated RNA and 3D genome organization in human cells

  Riccardo Calandrelli, Xingzhao We, John Lalith Charles Richard, et al.

  Nat Commun. 2023-10-16;14(1):6519.

  • doi:10.1038/s41467-023-42274-7
  • PMID:37845234
  • PMCID:PMC10579264

  Available supplemental data: website

  URL: https://data.4dnucleome.org

  Data summary: All high-throughput data supporting the current study have been deposited on the 4D Nucleome Data…See more

  Available supplemental data: website

  URL: https://github.com/Zhong-Lab-UCSD/RNA3Dgenome-code-repository

  Data summary: The codes used for the analysis have been deposited and made publicly available on GitHub at…See more

• 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

  Cis-regulatory architecture of human ESC-derived hypothalamic neuron differentiation aids in variant-to-gene mapping of relevant complex traits

  Matthew C. Pahl, Claudia A. Doege, Kenyaita M. Hodge, et al.

  Nat Commun. 2021-11-19;12(1):6749.

  • doi:10.1038/s41467-021-27001-4
  • PMID:34799566
  • PMCID:PMC8604959

• 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

  Functional characterization of T2D-associated SNP effects on baseline and ER stress-responsive β cell transcriptional activation

  Shubham Khetan, Susan Kales, Romy Kursawe, et al.

  Nat Commun. 2021-09-02;12(1):5242.

  • doi:10.1038/s41467-021-25514-6
  • PMID:34475398
  • PMCID:PMC8413311

  URL: https://cmdga.org/publications/63f879cd-f426-4495-a12d-103fdac5867c/

  URL: https://zenodo.org/record/4974390#.YzHqHi-B39A

  Data summary: Linked to Zenodo

• Publication

  released

  Joint disease-specificity at the regulatory base-pair level

  Pushpanathan Muthuirulan, Dewei Zhao, Mariel Young, et al.

  Nat Commun. 2021-07-06;12(1):4161.

  • doi:10.1038/s41467-021-24345-9
  • PMID:34230488
  • PMCID:PMC8260791

• 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

  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

  Common schizophrenia risk variants are enriched in open chromatin regions of human glutamatergic neurons

  Mads E. Hauberg, Jordi Creus-Muncunill, Jaroslav Bendl, et al.

  Nat Commun. 2020-11-04;11(1):5581.

  • doi:10.1038/s41467-020-19319-2
  • PMID:33149216
  • PMCID:PMC7643171

• Publication

  released

  Genetic variant effects on gene expression in human pancreatic islets and their implications for T2D

  Ana Viñuela, Arushi Varshney, Martijn van de Bunt, et al.

  Nat Commun. 2020-09-30;11(1):4912.

  • doi:10.1038/s41467-020-18581-8
  • PMID:32999275
  • PMCID:PMC7528108

  URL: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7528108/

• 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

  Regulatory sites for splicing in human basal ganglia are enriched for disease-relevant information

  Sebastian Guelfi, Karishma D’Sa, Juan A. Botía, et al.

  Nat Commun. 2020-02-25;11(1):1041.

  • doi:10.1038/s41467-020-14483-x
  • PMID:32098967
  • PMCID:PMC7042265

• Publication

  released

  Functional testing of thousands of osteoarthritis-associated variants for regulatory activity

  Jason C Klein, Aidan Keith, Sarah J Rice, et al.

  Nat Commun. 2019-06-04;10(1):2434.

  • doi:10.1038/s41467-019-10439-y
  • PMID:31164647
  • PMCID:PMC6547687

• 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

  ATAC-Seq analysis reveals a widespread decrease of chromatin accessibility in age-related macular degeneration

  Jie Wang, Cristina Zibetti, Peng Shang, et al.

  Nat Commun. 2018-04-10;9(1):1364.

  • doi:10.1038/s41467-018-03856-y
  • PMID:29636475
  • PMCID:PMC5893535

• Publication

  released

  Re-analysis of public genetic data reveals a rare X-chromosomal variant associated with type 2 diabetes

  Sílvia Bonàs-Guarch, Marta Guindo-Martínez, Irene Miguel-Escalada, et al.

  Nat Commun. 2018-01-22;9(1):321.

  • doi:10.1038/s41467-017-02380-9
  • PMID:29358691
  • PMCID:PMC5778074

• 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

  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

  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

  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