Showing 25 of 30 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

  Human and rat skeletal muscle single-nuclei multi-omic integrative analyses nominate causal cell types, regulatory elements, and SNPs for complex traits

  Peter Orchard, Nandini Manickam, Christa Ventresca, et al.

  Genome Res. 2021-11-23;31(12):2258-2275.

  • doi:10.1101/gr.268482.120
  • PMID:34815310
  • PMCID:PMC8647829

  URL: https://zenodo.org/search?page=1&size=20&q=5009200

  URL: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE178735

• 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

  A molecular quantitative trait locus map for osteoarthritis

  Julia Steinberg, Lorraine Southam, Theodoros I. Roumeliotis, et al.

  Nature Communications. 2021-02-26;12(1):1309.

  • doi:10.1038/s41467-021-21593-7
  • PMID:33637762

  URL: https://msk.hugeamp.org/downloads.html

  URL: https://hmgubox.helmholtz-muenchen.de/d/fc1fcf65a6724152b7f9/

• 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

  An integrated multi-omics approach identifies the landscape of interferon-α-mediated responses of human pancreatic beta cells

  Maikel L. Colli, Mireia Ramos-Rodríguez, Ernesto S. Nakayasu, et al.

  Nature Communications. 2020-05-22;11(1):2584.

  • doi:10.1038/s41467-020-16327-0
  • PMID:32444635
  • PMCID:PMC7244579

• Publication

  released

  A Single-nucleus RNA-sequencing Pipeline to Decipher the Molecular Anatomy and Pathophysiology of Human Kidneys

  Blue B. Lake, Song Chen, Masato Hoshi, et al.

  Nature Communications. 2019-06-27;10(2832(2019))

  • doi:10.1038/s41467-019-10861-2
  • PMID:31249312

  URL: https://www.nature.com/articles/s41467-019-10861-2

• Publication

  released

  Pancreatic Islet Chromatin Accessibility and Conformation Reveals Distal Enhancer Networks of Type 2 Diabetes Risk

  William W Greenwald, Joshua Chiou, Jian Yan, et al.

  Nature Communications. 2019-05-07;10, Article number: 2078 (2019)

  • doi:10.1101/299388
  • PMID:31064983

  URL: https://www.nature.com/articles/s41467-019-09975-4

• Publication

  released

  Defining inflammatory cell states in rheumatoid arthritis joint synovial tissues by integrating single-cell transcriptomics and mass cytometry

  Fan Zhang#, Kevin Wei#, Kamil Slowikowski#, et al.

  Nat Immunol. 2019-05-06;20(7):928-942.

  • doi:10.1038/s41590-019-0378-1
  • PMID:31061532
  • PMCID:PMC6602051

  URL: https://www.immport.org/shared/study/SDY998

  Data summary: The single-cell RNA-seq data, bulk RNA-seq data, mass cytometry data, flow cytometry data, and the…See more

  URL: https://www.ncbi.nlm.nih.gov/projects/gap/cgi-bin/study.cgi?study_id=phs001457.v1.p1

  Data summary: The raw single-cell RNA-seq data are deposited in dbGaP.

  URL: https://github.com/immunogenomics/amp_phase1_ra

  Data summary: The source code repository of the computational and statistical analysis is located at…See more

  URL: https://immunogenomics.io/ampra

  Data summary: Data can also be viewed on three different websites 1/3.

  URL: https://immunogenomics.io/cellbrowser/

  Data summary: Data can also be viewed on three different websites 2/3.

  URL: https://portals.broadinstitute.org/single_cell/study/amp-phase-1

  Data summary: Data can also be viewed on three different websites 3/3.

• 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

  Dynamics of Genome Reorganization During Human Cardiogenesis Reveal an RBM20-dependent Splicing Factory

  Alessandro Bertero, Paul A. Fields, Vijay Ramani, et al.

  Nature Communications. 2019-04-04;10(1):1538.

  • doi:10.1038/s41467-019-09483-5
  • PMID:30948719
  • PMCID:PMC6449405

  URL: https://www.nature.com/articles/s41467-019-09483-5

• Publication

  released

  Genome-scale Capture C promoter interactions implicate effector genes at GWAS loci for bone mineral density

  Alessandra Chesi, Yadav Wagley, Matthew E. Johnson, et al.

  Nature Communications. 2019-03-19;10(1):1260.

  • PMID:30890710
  • doi:10.1038/s41467-019-09302-x
  • PMCID:PMC6425012

  URL: https://www.nature.com/articles/s41467-019-09302-x

• Publication

  released

  Cardiomyocyte Gene Programs Encoding Morphological and Functional Signatures in Cardiac Hypertrophy and Failure

  Seitaro Nomura, Masahiro Satoh, Takanori Fujita, et al.

  Nature Communications. 2018-10-30;9(4435(2018))

  • doi:10.1038/s41467-018-06639-7
  • PMID:30375404

  URL: https://www.nature.com/articles/s41467-018-06639-7

• Publication

  released

  Single Cell RNA Sequencing of Human Liver Reveals Distinct Intrahepatic Macrophage Populations

  Sonya A. MacParland, Jeff C. Liu, Xue-Zhong Ma, et al.

  Nature Communications. 2018-10-22;9(4383)

  • doi:10.1038/s41467-018-06318-7
  • PMID:30348985

  URL: https://www.nature.com/articles/s41467-018-06318-7#content

• Publication

  released

  High-throughput characterization of genetic effects on DNA-protein binding and gene transcription

  Cynthia A Kalita, Christopher D Brown, Andrew Freiman, et al.

  Genome Res. 2018-09-25;28(11):1701-1708.

  • doi:10.1101/gr.237354.118
  • PMID:30254052
  • PMCID:PMC6211638

• Publication

  released

  Protein quantitative trait locus study in obesity during weight-loss identifies a leptin regulator

  Jérôme Carayol, Christian Chabert, Alessandro Di Cara, et al.

  Nature Communications. 2017-12-12;8(1):2084.

  • doi:10.1038/s41467-017-02182-z
  • PMCID:PMC5727191
  • PMID:29234017

• Publication

  released

  Disease-specific biases in alternative splicing and tissue-specific dysregulation revealed by multitissue profiling of lymphocyte gene expression in type 1 diabetes

  Jeremy R B Newman, Ana Conesa, Matthew Mika, et al.

  Genome Res. 2017-11-01;27(11):1807-1815.

  • doi:10.1101/gr.217984.116
  • PMCID:PMC5668939
  • PMID:29025893

• Publication

  released

  Bivariate genome-wide association meta-analysis of pediatric musculoskeletal traits reveals pleiotropic effects at the SREBF1/TOM1L2 locus

  Carolina Medina-Gomez, John P. Kemp, Niki L. Dimou, et al.

  Nature Communications. 2017-07-25;8(1):121.

  • doi:10.1038/s41467-017-00108-3
  • PMID:28743860
  • PMCID:PMC5527106

• Publication

  released

  The Genetic Regulatory Signature Of Type 2 Diabetes In Human Skeletal Muscle

  Laura J. Scott, Michael R. Erdos, Jeroen R. Huyghe, et al.

  Nature Communications. 2016-06-29;7:Article number: 11764 (2016).

  • doi:10.1038/ncomms11764
  • PMID:27353450