Showing 16 of 16 results

• Publication

  released

  Multimodal cell atlas of the ageing human skeletal muscle

  Yiwei Lai, Ignacio Ramírez-Pardo, Joan Isern, et al.

  Nature. 2024-04-22;

  • PMID:38649488
  • doi:10.1038/s41586-024-07348-6

  Data summary: All raw data have been deposited to CNGB Nucleotide Sequence Archive (CNP0004394, CNP0004395,…See more

  URL: https://db.cngb.org/cdcp/hlma/

  Data summary: All processed data are available at the Human Muscle Ageing Cell Atlas database.

  URL: https://github.com/MGI-tech-bioinformatics/DNBelab_C_Series_HT_scRNA-analysis-software

  Data summary: All data were analysed using standard programs and packages, as described in the Methods. Custom…See more

  URL: https://github.com/123anjuan/HMA

  Data summary: Analysis of the generated data82.

• 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

  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

  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

  Single-cell ATAC-Seq in human pancreatic islets and deep learning upscaling of rare cells reveals cell- specific type 2 diabetes regulatory signatures

  Vivek Rai, Daniel X Quang, Michael R Erdos, et al.

  Mol Metab. 2019-12-20;32:109-121.

  • doi:10.1016/j.molmet.2019.12.006
  • PMID:32029221
  • PMCID:PMC6961712

  URL: https://theparkerlab.med.umich.edu/data/vivekrai/sci-ATAC-seq/single-cells-ataqv/

  Data summary: Ataqv: single-nuclei

  URL: https://theparkerlab.med.umich.edu/data/vivekrai/2017_bulk-islets_atacseq_nih/ataqv_subset/

  Data summary: Ataqv: Bulk Islets

  URL: https://github.com/ParkerLab/PillowNet

  Data summary: PillowNet

  URL: http://epigenomegateway.wustl.edu/browser/?bundle=c9c33400-8b18-11e9-bcd4-cf4d247bba10

  Data summary: Epigenome Browser

• 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

  Genome-wide analysis of PDX1 target genes in human pancreatic progenitors

  Xianming Wang, Michael Sterr, Ingo Burtscher, et al.

  Mol Metab. 2018-03-01;9:57-68.

  • doi:10.1016/j.molmet.2018.01.011
  • PMCID:PMC5870105
  • PMID:29396371

• 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

  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