Showing 23 of 268 results

• Publication

  released

  An encyclopedia of human enhancer-gene regulatory interactions

  Andreas R. Gschwind, Kristy S. Mualim, Alireza Karbalayghareh, et al.

  Nature. 2026-07-15;

  • PMID:42457959
  • doi:10.1038/s41586-026-10781-4

• 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

  GWAS-informed data integration and non-coding CRISPRi screen illuminate genetic etiology of bone mineral density

  Mitchell Conery, James A. Pippin, Yadav Wagley, et al.

  Genome Biology. 2025-10-03;26(1):331.

  • PMID:41044600
  • doi:10.1186/s13059-025-03802-4
  • PMCID:PMC12492525

• 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

  Variant-to-function analysis of the childhood obesity chr12q13 locus implicates rs7132908 as a causal variant within the 3' UTR of FAIM2

  Sheridan H Littleton, Khanh B Trang, Christina M Volpe, et al.

  Cell Genomics. 2024-05-08;

  • doi:10.1101/2023.08.21.553157
  • PMID:37662342
  • PMCID:PMC10473629

  Data summary: Hi-C, RNA-seq, ATAC-seq, single-nucleus RNA-seq, and single-nucleus ATAC-seq data have been…See more

  URL: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE241592

  Data summary: Raw and processed Hi-C data GEO: GSE241592

  URL: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE241050

  Data summary: Raw and processed RNA-seq data GEO: GSE241050

  URL: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE241591

  Data summary: Raw and processed ATAC-seq data GEO: GSE241591

  URL: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE241594

  Data summary: Raw and processed single-nucleus RNA-seq data GEO: GSE241594

  URL: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE241593

  Data summary: Raw and processed single-nucleus ATAC-seq data GEO: GSE241593;

• Publication

  released

  Response eQTLs, chromatin accessibility, and 3D chromatin structure in chondrocytes provide mechanistic insight into osteoarthritis risk

  Nicole E Kramer, Philip Coryell, Susan D'Costa, et al.

  bioRvix. 2024-05-05;

  • doi:10.1101/2024.05.05.592567

• 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

  Human skeletal muscle aging atlas

  Veronika R. Kedlian, Yaning Wang, Tianliang Liu, et al.

  Nature Aging. 2024-04-15;

  • PMID:38622407
  • doi:10.1038/s43587-024-00613-3

  URL: https://www.muscleageingcellatlas.org

  Data summary: The processed data objects generated within this study are available for browsing

  URL: https://doi.org/10.7272/Q65X273X

  Data summary: Raw sequencing data for the newly generated libraries have been deposited to ArrayExpress…See more

  Data summary: Mouse datasets were obtained from GSE110878, GSE138707, GSE134540, GSE143476, GSE149590 and…See more

  Data summary: All other data supporting the findings of this study are available from the corresponding authors…See more

  URL: https://github.com/Teichlab/SKM_ageing_atlas

  Data summary: Code availability: All custom notebooks and scripts used in this study have been deposited to

• Publication

  released

  Primary osteoarthritis chondrocyte map of chromatin conformation reveals novel candidate effector genes

  Norbert Bittner, Chenfu Shi, Danyun Zhao, et al.

  Ann Rheum Dis. 2024-03-13;:ard-2023-224945.

  • PMID:38479789
  • doi:10.1136/ard-2023-224945

• Publication

  released

  An integrated map of cell type-specific gene expression in pancreatic islets

  Ruth M Elgamal, Parul Kudtarkar, Rebecca L Melton, et al.

  Diabetes. 2023-15-08;(db230130)

  • PMID:37582230
  • doi:10.2337/db23-0130

• Publication

  released

  Population-scale skeletal muscle single-nucleus multi-omic profiling reveals extensive context specific genetic regulation

  Arushi Varshney Arushi Varshney, Nandini Manickam, Peter Orchard, et al.

  bioRxiv. 2023-12-15;

  • PMID:38168419
  • PMCID:PMC10760134
  • doi:10.1101/2023.12.15.571696

  URL: https://www.biorxiv.org/content/10.1101/2023.12.15.571696v2

• 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

  Cell-Type Composition Affects Adipose Gene Expression Associations With Cardiometabolic Traits

  Sarah M Brotman, Anniina Oravilahti, Jonathan D Rosen, et al.

  Diabetes. 2023-11-01;72(11):1707-1718.

  • doi:10.2337/db23-0365
  • PMID:37647564
  • PMCID:PMC10588284

• 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

  A comparative atlas of single-cell chromatin accessibility in the human brain

  Yang Eric Li, Sebastian Preissl, Michael Miller, et al.

  Science. 2023-10-13;382(6667)

  • doi:10.1126/science.adf7044
  • PMID:37824643
  • PMCID:PMC10852054

• Publication

  released

  Plasma proteomic associations with genetics and health in the UK Biobank

  Benjamin B Sun, Joshua Chiou, Matthew Traylor, et al.

  Nature. 2023-10-04;622(7982):329-338.

  • doi:10.1038/s41586-023-06592-6
  • PMID:37794186
  • PMCID:PMC10567551

  URL: http://ukb-ppp.gwas.eu

  Data summary: Proteo-genomic results and summary association data are available through an interactive portal.

  URL: https://www.ukbiobank.ac.uk/enable-your-research

  Data summary: Underlying NPX measures are available through the UK Biobank Research Analysis Portal.

  URL: https://biobank.ndph.ox.ac.uk/showcase/label.cgi?id=1839

  Data summary: UKB has catalogued the dataset in Category 1839, under ‘Field 30900’, described in greater detail…See more

• Publication

  released

  Dynamic network-guided CRISPRi screen identifies CTCF-loop-constrained nonlinear enhancer gene regulatory activity during cell state transitions

  Renhe Luo, Jielin Yan, Jin Woo Oh, et al.

  at Genet. 2023-07-24;55(8):1336-1346.

  • doi:10.1038/s41588-023-01450-7
  • PMID:37488417

  Available supplemental data: website

  Data summary: The parental HUES8 hESC line was obtained from Harvard University under a material transfer…See more

• Publication

  released

  An atlas of healthy and injured cell states and niches in the human kidney

  Blue B. Lake, Rajasree Menon, Seth Winfree, et al.

  Nature. 2023-07-19;619(7970):585-594.

  • doi:10.1038/s41586-023-05769-3
  • PMID:37468583
  • PMCID:PMC10356613

  URL: https://www.nature.com/articles/s41586-023-05769-3

• Publication

  released

  Increased body mass index is linked to systemic inflammation through altered chromatin co-accessibility in human preadipocytes

  Kristina M. Garske, Asha Kar, Caroline Comenho, et al.

  Nat Commun. 2023-07-14;14(1):4214.

  • doi:10.1038/s41467-023-39919-y
  • PMID:37452040
  • PMCID:PMC10349101

• Publication

  released

  Gene expression in African Americans, Puerto Ricans and Mexican Americans reveals ancestry-specific patterns of genetic architecture

  Linda Kachuri, Angel C. Y. Mak, Donglei Hu, et al.

  Nat Genet. 2023-05-25;55(6):952-963.

  • PMID:37231098
  • doi:10.1038/s41588-023-01377-z
  • PMCID:PMC10260401

• 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

  Dynamic chromatin organization and regulatory interactions in human endothelial cell differentiation

  Kris G Alavattam, Katie A Mitzelfelt, Giancarlo Bonora, et al.

  Stem Cell Reports. 2023-01-10;18(1):159-174.

  • doi:10.1016/j.stemcr.2022.11.003
  • PMID:36493778
  • PMCID:PMC9860068

  Available supplemental data: website

  URL: https://data.4dnucleome.org/Alavattam-Mitzelfelt-endothelial-differentiation-chromatin

  Data summary: Data have been deposited in the 4DN data portal and are publicly available at…See more

  Available supplemental data: website

  Data summary: Previously published CM differentiation data are available from GEO: GSE106690 (Bertero et al.,…See more

  Available supplemental data: website

  URL: https://github.com/Noble-Lab/

  Data summary: Source code for analyses performed in this study is available at…See more