Showing 25 of 29 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

  A genome-wide CRISPR screen identifies CALCOCO2 as a regulator of beta cell function influencing type 2 diabetes risk

  Antje K Rottner, Yingying Ye, Elena Navarro-Guerrero, et al.

  Nat Genet. 2022-12-21;55(1):54-65.

  • doi:10.1038/s41588-022-01261-2
  • PMID:36543916
  • PMCID:PMC9839450

  URL: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9839450/

  Available supplemental data: website

  File format: text

  URL: https://hugeamp.org:8000/research.html?pageid=beta_cell_249

  Data summary: Pancreatic beta cell function and type 2 diabetes predicted effector genes (Rottner AK et al., 2023)

• 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

  Prioritization of autoimmune disease-associated genetic variants that perturb regulatory element activity in T cells

  Kousuke Mouri, Michael H. Guo, Carl G. de Boer, et al.

  Nat Genet. 2022-05-01;54(5):603-612.

  • doi:10.1038/s41588-022-01056-5
  • PMID:35513721

• 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

  A map of transcriptional heterogeneity and regulatory variation in human microglia

  Adam M. H. Young, Natsuhiko Kumasaka, Fiona Calvert, et al.

  Nat Genet. 2021-06-03;53(6):861-868.

  • doi:10.1038/s41588-021-00875-2
  • PMID:34083789
  • PMCID:PMC7610960

• 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

  Single-cell chromatin accessibility identifies pancreatic islet cell type- and state-specific regulatory programs of diabetes risk

  Joshua Chiou, Chun Zeng, Zhang Cheng, et al.

  Nat Genet. 2021-04-01;53(4):455-466.

  • doi:10.1038/s41588-021-00823-0
  • PMID:33795864

• Publication

  released

  Liquid chromatin Hi-C characterizes compartment-dependent chromatin interaction dynamics

  Houda Belaghzal, Tyler Borrman, Andrew D Stephens, et al.

  Nat Genet. 2021-02-11;53(3):367-378.

  • doi:10.1038/s41588-021-00784-4
  • PMID:33574602
  • PMCID:PMC7946813

  Data summary: All sequencing data have been submitted to a public data repository (GEO; accession number…See more

• 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

  Single-cell epigenomic analyses implicate candidate causal variants at inherited risk loci for Alzheimer’s and Parkinson’s diseases

  M Ryan Corces, Anna Shcherbina, Soumya Kundu, et al.

  Nat Genet. 2020 Oct 26;52(11):1158-1168.

  • doi:10.1038/s41588-020-00721-x
  • PMID:33106633
  • PMCID:PMC7606627

• Publication

  released

  Transcriptionally active HERV-H retrotransposons demarcate topologically associating domains in human pluripotent stem cells

  Yanxiao Zhang, Ting Li, Sebastian Preissl, et al.

  Nat Genet. 2019-08-19;51(9):1380-1388.

  • doi:10.1038/s41588-019-0479-7
  • PMID:31427791
  • PMCID:PMC6722002

  Available supplemental data: website

  Data summary: All sequencing datasets have been deposited on GEO with the accession number GSE116862.

• 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

  Fine-mapping type 2 diabetes loci to single-variant resolution using high-density imputation and islet-specific epigenome maps

  Anubha Mahajan, Daniel Taliun, Matthias Thurner, et al.

  Nat Genet. 2018-10-08;50(11):1505-1513.

  • doi:10.1038/s41588-018-0241-6
  • PMID:30297969
  • PMCID:PMC6287706

• Publication

  released

  Type 2 diabetes risk alleles in PAM impact insulin release from human pancreatic β-cells

  Soren K Thomsen, Anne Raimondo, Benoit Hastoy, et al.

  Nat Genet. 2018-07-27;50(8):1122-1131.

  • doi:10.1038/s41588-018-0173-1
  • PMID:30054598
  • PMCID:PMC6237273

• Publication

  released

  Regulatory variants at KLF14 influence type 2 diabetes risk via a female-specific effect on adipocyte size and body composition

  Kerrin S Small, Marijana Todorčević, Mete Civelek, et al.

  Nat Genet. 2018-04-09;50(4):572-580.

  • doi:10.1038/s41588-018-0088-x
  • PMID:29632379
  • PMCID:PMC5935235

• Publication

  released

  Shared genetic effects on chromatin and gene expression indicate a role for enhancer priming in immune response

  Kaur Alasoo, Julia Rodrigues, Subhankar Mukhopadhyay, et al.

  Nat Genet. 2018-01-29;50(3):424-431.

  • doi:10.1038/s41588-018-0046-7
  • PMID:29379200
  • PMCID:PMC6548559

• Publication

  released

  Molecular and functional variation in iPSC-derived sensory neurons

  Jeremy Schwartzentruber, Stefanie Foskolou, Helena Kilpinen, et al.

  Nat Genet. 2017-12-11;50(1):54-61.

  • doi:10.1038/s41588-017-0005-8
  • PMID:29229984
  • PMCID:PMC5742539

• Publication

  released

  Variation in the glucose transporter gene SLC2A2 is associated with glycemic response to metformin

  Kaixin Zhou, Sook Wah Yee, Eric L Seiser, et al.

  Nat Genet. 2016-08-08;48(9):1055-1059.

  • doi:10.1038/ng.3632
  • PMID:27500523
  • PMCID:PMC5007158

• 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

  Gene-gene and gene-environment interactions detected by transcriptome sequence analysis in twins

  Alfonso Buil, Andrew Anand Brown, Tuuli Lappalainen, et al.

  Nat Genet. 2014-12-01;47(1):88-91.

  • doi:10.1038/ng.3162
  • PMID:25436857
  • PMCID:PMC4643454

• 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