Showing 25 of 146 results

• Publication

  released

  Systematic Functional Characterization of Candidate Causal Genes for Type 2 Diabetes Risk Variants

  Thomsen SK, Ceroni A, van de Bunt M, et al.

  December 2016;(65(12)):3805-3811.

  • PMID:27554474
  • doi:10.2337/db16-0361

• 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

  A comprehensive spatio-cellular map of the human hypothalamus

  John A. Tadross, Lukas Steuernagel, Georgina K. C. Dowsett, et al.

  Nature. 2025-02-05;639(8055):708-716.

  • doi:10.1038/s41586-024-08504-8
  • PMID:39910307
  • PMCID:PMC11922758

  URL: https://www.nature.com/articles/s41586-024-08504-8

• 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

  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

  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

  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

• 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

  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

  Human prefrontal cortex gene regulatory dynamics from gestation to adulthood at single-cell resolution

  Charles A Herring, Rebecca K Simmons, Saskia Freytag, et al.

  Cell. 2022-10-31;185(23):4428-4447.

  • doi:10.1016/j.cell.2022.09.039
  • PMID:36318921

  Available supplemental data: website

  File format: other format

  URL: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE168408

  Data summary: Single-nuclei RNA-seq and single-nuclei ATAC-seq data have been deposited at GEO under accession…See more

  Available supplemental data: website

  URL: http://brain.listerlab.org/

  Data summary: Accompanying interactive browsers for this study are available at http://brain.listerlab.org.

  Available supplemental data: website

  URL: http://development.psychencode.org/

  Data summary: All data for the Velmeshev et al. study is publicly available through the Sequence Read Archive,…See more

  Available supplemental data: website

  URL: https://www.sciencedirect.com/science/article/pii/S0092867422012582?via%3Dihub#sec4.1

  Data summary: All original code has been deposited at Zenodo and is publicly available as of the date of…See more

  Available supplemental data: website

  URL: https://www.sciencedirect.com/science/article/pii/S0092867422012582?via%3Dihub#sec4.2.1

  Data summary: Any additional information required to reanalyze the data reported in this work paper is available…See more

• Publication

  released

  Proper acquisition of cell class identity in organoids allows definition of fate specification programs of the human cerebral cortex

  Ana Uzquiano, Amanda J Kedaigle, Martina Pigoni, et al.

  Cell. 2022-09-29;185(20):3770-3788.e27.

  • doi:10.1016/j.cell.2022.09.010
  • PMID:36179669
  • PMCID:PMC9990683

  Available supplemental data: website

  URL: https://www.synapse.org

  Data summary: Read-level data from scRNA-seq, scATAC-seq, SHARE-seq, and Slide-seq data, supporting the findings…See more

  Available supplemental data: website

  URL: https://singlecell.broadinstitute.org/single_cell/study/SCP1756

  Data summary: The count-level data and meta-data have been deposited at the Single Cell Portal.

  Available supplemental data: website

  URL: https://doi.org/10.17632/7cxccpv4hg.1

  Data summary: Supplemental data related to Figures 1, ​,3,3, ​,4,4, ​,5,5, ​,6,6, and ​and77 has been deposited…See more

  Available supplemental data: website

  URL: https://github.com/AmandaKedaigle/OrganoidAtlas

  Data summary: Code used during data analysis is available at GitHub. d Any additional information required to…See more

  Available supplemental data: website

  URL: http://solo.bmap.ucla.edu/shiny/webapp/

  Data summary: Data from previous publications that was used in this study can be found at the Gene Expression…See more

• Publication

  released

  Genetic regulation of RNA splicing in human pancreatic islets

  Goutham Atla, Silvia Bonàs-Guarch, Mirabai Cuenca-Ardura, et al.

  Genome Biol. 2022-09-15;23(1):196.

  • doi:10.1186/s13059-022-02757-0
  • PMID:36109769
  • PMCID:PMC9479353

  URL: https://genomebiology.biomedcentral.com/articles/10.1186/s13059-022-02757-0#Sec36

  Available supplemental data: website

  File format: text

  URL: https://zenodo.org/record/6546807#.Y-wbZi-B39B

• Publication

  released

  The developmental impacts of natural selection on human pelvic morphology

  Mariel Young, Daniel Richard, Mark Grabowski, et al.

  Sci Adv. 2022-08-19;8(33):eabq4884.

  • doi:10.1126/sciadv.abq4884
  • PMID:35977020
  • PMCID:PMC9385149

• 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

  Combining SNP-to-gene linking strategies to identify disease genes and assess disease omnigenicity

  Steven Gazal, Omer Weissbrod, Farhad Hormozdiari, et al.

  Nature Genetics. 2022-06-06;(2022)

  • doi:10.1101/2021.08.02.21261488

  URL: https://doi.org/10.5281/zenodo.6354007

  Data summary: The list of 19,995 genes, summary statistics of the 63 independent traits, training and validation…See more

  Data summary: Links for all data sets used to create S2G strategies are provided in Supplementary Table 26.

  URL: http://www.ukbiobank.ac.uk/

  Data summary: Access to the UK Biobank resource is available via application

  URL: https://www.ebi.ac.uk/gwas/api/search/downloads/full

  Data summary: The GWAS Catalog is available

  URL: https://raw.githubusercontent.com/opentargets/genetics-gold-standards/master/gold_standards/processed/gwas_gold_standards.191108.tsv

  Data summary: Open Targets SNP–gene pairs are available

  URL: https://www.dropbox.com/s/kz2c49rpm2yanf5/all_byCS_rev1.txt?dl=0

  Data summary: SNP–gene pairs from ref48 are available

  URL: https://alkesgroup.broadinstitute.org/cS2G/code

  Data summary: The code to estimate precision and recall of S2G strategies and the code to create combined S2G…See more

  URL: https://doi.org/10.5281/zenodo.6415925

  Data summary: The code to estimate precision and recall of S2G strategies and the code to create combined S2G…See more

• Publication

  released

  Single-nucleus chromatin accessibility profiling highlights regulatory mechanisms of coronary artery disease risk

  Adam W Turner, Shengen Shawn Hu, Jose Verdezoto Mosquera, et al.

  Nat Genet.. 2022-06-01;54(6):804-816.

  • doi:10.1038/s41588-022-01069-0
  • PMID:35590109
  • PMCID:PMC9203933

  File format: TSV

  URL: https://static-content.springer.com/esm/art%3A10.1038%2Fs41588-022-01069-0/MediaObjects/41588_2022_1069_MOESM10_ESM.xlsx

  Data summary: Supplementary Data 6 Chromatin accessibility QTLs within individual coronary artery cell types,…See more

  File format: TSV

  URL: https://static-content.springer.com/esm/art%3A10.1038%2Fs41588-022-01069-0/MediaObjects/41588_2022_1069_MOESM11_ESM.xlsx

  Data summary: Supplementary Data 7 Chromatin accessibility QTLs from bulk coronary artery ATAC-seq data,…See more

• Publication

  released

  The Tabula Sapiens: A multiple-organ, single-cell transcriptomic atlas of humans

  Tabula Sapiens Consortium*; Robert C Jones, Jim Karkanias, Mark A Krasnow, et al.

  Science. 2022-05-13;376(6594):eabl4896.

  • doi:10.1126/science.abl4896
  • PMID:35549404

  Available supplemental data: website

  URL: http://tabula-sapiens-portal.ds.czbiohub.org/

  Data summary: The entire dataset can be explored interactively at http://tabula-sapiens-portal.ds.czbiohub.org/.

  Available supplemental data: website

  URL: https://doi.org/10.5281/zenodo.6069683

  Data summary: The code used for the analysis is available from Zenodo (https://doi.org/10.5281/zenodo.6069683).

  Available supplemental data: website

  URL: https://doi.org/10.6084/m9.figshare.14267219

  Data summary: Gene counts and metadata are available from figshare…See more

  Available supplemental data: website

  URL: https://registry.opendata.aws/tabula-sapiens/

  Data summary: The raw data files are available from a public AWS S3 bucket…See more

  Available supplemental data: website

  URL: https://doi.org/10.6084/m9.figshare.14962947

  Data summary: The histology images are available from figshare (https://doi.org/10.6084/m9.figshare.14962947).

  Available supplemental data: website

  URL: https://doi.org/10.6084/m9.figshare.14977281

  Data summary: SpliZ scores are available from figshare (https://doi.org/10.6084/m9.figshare.14977281).

• Publication

  released

  A chromatin accessibility landscape during early adipogenesis of human adipose-derived stem cells

  Sen Li, Xiaolin Zong, Liheng Zhang, et al.

  Adipocyte. 2022-04-17;11(1):239-249.

  • doi:10.1080/21623945.2022.2063015
  • PMID:35435105
  • PMCID:PMC9037556

• Publication

  released

  Non-cell-autonomous disruption of nuclear architecture as a potential cause of COVID-19-induced anosmia

  Marianna Zazhytska, Albana Kodra, Daisy A Hoagland, et al.

  Cell. 2022-03-17;185(6):1052-1064.e12.

  • doi:10.1016/j.cell.2022.01.024
  • PMID:35180380
  • PMCID:PMC8808699

  Available supplemental data: website

  URL: https://doi.org/10.1101/2021.02.09.430314

  Data summary: Human and hamster RNAseq, scRNAseq, in situ HiC, supplemental spreadsheets and detailed…See more

  Data summary: This study did not generate custom computer code. Any additional information is available from…See more

• Publication

  released

  Single nucleus multi-omics identifies human cortical cell regulatory genome diversity

  Chongyuan Luo, Hanqing Liu, Fangming Xie, et al.

  Cell Genom. 2022-03-09;2(3):100107.

  • doi:10.1016/j.xgen.2022.100107
  • PMID:35419551
  • PMCID:PMC9004682

  Available supplemental data: website

  URL: http://neomorph.salk.edu/Human_cells_snmCT-seq.php

  Data summary: Raw and processed data included in this study were deposited to NCBI GEO/SRA with accession number…See more

  Available supplemental data: website

  URL: http://neomorph.salk.edu/human_frontal_cortex_ensemble.php

  Data summary: snmCAT-seq generated from brain tissues can be visualized at…See more

  Available supplemental data: website

  URL: https://assets.nemoarchive.org/dat-s3creyz

  Data summary: snRNA-seq data is available for download from the Neuroscience Multi-omics Archive…See more

  Available supplemental data: website

  URL: https://github.com/mukamel-lab/SingleCellFusion

  Data summary: The code for SingleCellFusion is available from https://github.com/mukamel-lab/SingleCellFusion.

  Available supplemental data: website

  URL: https://github.com/lhqing/snmCAT-seq_integration

  Data summary: The code benchmarking computational integration methods are available from…See more

  Available supplemental data: website

  URL: https://github.com/FangmingXie/mctseq_over_under_splitting/blob/master/over-under-splitting-analysis.ipynb

  Data summary: The code reproducing the over- and under-splitting analysis are available from…See more

  Available supplemental data: website

  URL: https://www.protocols.io/view/snmcat-v1-bwubpesn

  Data summary: A detailed bench protocol for snmCAT-seq and future updates to the method can be found at…See more