Showing 25 of 44 results

• Publication

  released

  Identification of target genes and regulatory networks for bone mineral density GWAS loci through systematic targeting and inhibition

  Mohammadjavad Kahlani, Larry Mesner, Vedavathi Madhu, et al.

  bioRxiv. 2026-02-16;(Preprint)

  • PMID:41757073
  • PMCID:PMC12934652
  • doi:10.64898/2026.02.11.705362

• Publication

  released

  Genetic effects on chromatin accessibility uncover mechanisms of liver gene regulation and quantitative traits

  Kevin W Currin, Hannah J Perrin, Gautam K Pandey, et al.

  Genome Res. 2025-05-20;

  • doi:10.1101/gr.279741.124
  • PMID:40393811

• Publication

  released

  Response splicing QTLs in primary human chondrocytes identifies putative osteoarthritis risk genes

  Seyoun Byun, Philip Coryell, Nicole Kramer, et al.

  bioRxiv. 2024-11-12;

  • doi:10.1101/2024.11.11.622754

• 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

  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

  Loss of RREB1 in pancreatic beta cells reduces cellular insulin content and affects endocrine cell gene expression

  Katia K. Mattis, Nicole A. J. Krentz, Christoph Metzendorf, et al.

  Diabetologia. 2023-01-12;

  • doi:10.1007/s00125-022-05856-6
  • PMID:36633628

• Publication

  released

  Single-cell gene expression and chromatin accessibility profiling of human pancreatic islets at basal and stimulatory conditions nominates mechanisms of type 1 diabetes genetic risk

  Ricardo D’Oliveira Albanus, Xuming Tang, Henry J. Taylor, et al.

  bioRxiv. 2022-11-14;

  • doi:10.1101/2022.11.12.516291

• Publication

  released

  Systematic evaluation of chromosome conformation capture assays

  Betul Akgol Oksuz, Liyan Yang, Sameer Abraham, et al.

  Nat Methods. 2021-09-03;18(9):1046-1055.

  • doi:10.1038/s41592-021-01248-7
  • PMID:34480151
  • PMCID:PMC8446342

  Data summary: Data are available at GEO under accession number GSE163666. Supplementary Table 1 lists datasets…See more

  Available supplemental data: website

  URL: https://github.com/dekkerlab/matrix_paper

  Data summary: Scripts and notebooks used in this paper can be accessed at…See more

• Publication

  released

  Cardiac cell type-specific gene regulatory programs and disease risk association

  James D Hocker, Olivier B Poirion, Fugui Zhu, et al.

  Sci Adv.. 2021-05-14;7(20):eabf1444.

  • doi:10.1126/sciadv.abf1444
  • PMID:33990324
  • PMCID:PMC8121433

• 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

  Rationale and design of the Kidney Precision Medicine Project

  Ian H de Boer, Charles E Alpers, Evren U Azeloglu, et al.

  Kidney International. 2021-03-01;99(3):498-510.

  • PMID:33637194
  • doi:10.1016/j.kint.2020.08.039
  • PMCID:PMC8330551

  Available supplemental data: website

  URL: https://www.kpmp.org

  Data summary: The Kidney Precision Medicine Project (KPMP) is an ambitious, multi-year project funded by the…See more

  Available supplemental data: website

  URL: https://www.kpmp.org/doi-collection/10-48698-92nk-e805

  Data summary: Aggregated, clustered single-cell RNA-seq data used in the KPMP Atlas Explorer v1.3 - Dataset…See more

• Publication

  released

  A human cell atlas of fetal chromatin accessibility

  Silvia Domcke, Andrew J Hill, Riza M Daza, et al.

  Science. 2020-11-13;370(6518):eaba7612.

  • doi:10.1126/science.aba7612
  • PMID:33184180
  • PMCID:PMC7785298

  Available supplemental data: website

  File format: other format

  URL: https://descartes.brotmanbaty.org/bbi/human-chromatin-during-development/

  Data summary: sci-ATAC-seq data of human fetal tissues:…See more

• Publication

  released

  Single-cell multiomic profiling of human lungs reveals cell-type-specific and age-dynamic control of SARS-CoV2 host genes

  Allen Wang, Joshua Chiou, Olivier B Poirion, et al.

  eLife. 2020-11-09;9:e62522.

  • doi:10.7554/eLife.62522
  • PMID:33164753

  Available supplemental data: website

  File format: other format

  URL: https://www.ncbi.nlm.nih.gov/projects/gap/cgi-bin/study.cgi?study_id=phs001961.v1.p1

  Data summary: sci-ATAC-seq data of human lung samples: dbGaP: phs001961

• 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

  Landscape of stimulation-responsive chromatin across diverse human immune cells

  Diego Calderon, Michelle L. T. Nguyen, Anja Mezger, et al.

  Nature Genetics. 2019-9-30;51:1494–1505.

  • doi:10.1038/s41588-019-0505-9
  • PMID:31570894
  • PMCID:PMC6858557

• Publication

  released

  Methylome and transcriptome maps of human visceral and subcutaneous adipocytes reveal key epigenetic differences at developmental genes

  Stephen T. Bradford, Shalima S. Nair, Aaron L. Statham, et al.

  Scientific Reports. 2019-07-02;1(9):9511.

  • doi:10.1038/s41598-019-45777-w
  • PMID:31266983
  • PMCID:PMC6606599

• Publication

  released

  Human Pancreatic Islet Three-dimensional Chromatin Architecture Provides Insights into The Genetics of Type 2 Diabetes

  Irene Miguel-Escalada, Silvia Bonàs-Guarch, Inês Cebola, et al.

  Nature Genetics. 2019-06-28;51:1137-1148.

  • doi:10.1038/s41588-019-0457-0
  • PMID:31253982

  URL: https://www.nature.com/articles/s41588-019-0457-0

• 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

  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

  Extensive Heterogeneity and Intrinsic Variation in Spatial Genome Organization

  Elizabeth H Finn, Gianluca Pegoraro, Hugo B Brandão, et al.

  Cell. 2019-03-07;176(6):1502-1515.e10.

  • doi:10.1016/j.cell.2019.01.020
  • PMID:30799036
  • PMCID:PMC6408223

  Data summary: The Hi-C data has been deposited in GEO under ID code GSE107051, and in the 4D Nucleome data…See more

• Publication

  released

  Single-Cell Transcriptome Analysis Maps the Developmental Track of the Human Heart

  Yueli Cui, Yuxuan Zheng, Xixi Liu, et al.

  Cell Rep. 2019-02-12;26(7):1934-1950.e5.

  • doi:10.1016/j.celrep.2019.01.079
  • PMID:30759401

• Publication

  released

  Retinal transcriptome and eQTL analyses identify genes associated with age-related macular degeneration

  Rinki Ratnapriya, Olukayode A. Sosina, Margaret R. Starostik, et al.

  Nature Genetics. 2019-02-11;51:606–610.

  • doi:10.1038/s41588-019-0351-9
  • PMID:30742112

• Publication

  released

  Integration of Human Adipocyte Chromosomal Interactions with Adipose Gene Expression Prioritizes Obesity-related Genes from GWAS

  David Z. Pan, Kristina M. Garske, Marcus Alvarez, et al.

  Nature Communicationsvolume. 2018-4-17;9(1):1512.

  • doi:10.1038/s41467-018-03554-9
  • PMID:30135520
  • PMCID:PMC5904163

  URL: https://www.nature.com/articles/s41467-018-03554-9

• Publication

  released

  Genetic variant at coronary artery disease and ischemic stroke locus 1p32.2 regulates endothelial responses to hemodynamics

  Matthew D Krause, Ru-Ting Huang, David Wu, et al.

  Proc Natl Acad Sci U S A .. 2018-11-27;115(48):E11349-E11358.

  • doi:10.1073/pnas.1810568115
  • PMID:30429326
  • PMCID:PMC6275533

  URL: https://pubmed.ncbi.nlm.nih.gov/30429326/