Showing 14 of 14 results

• 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

  Cis-regulatory architecture of human ESC-derived hypothalamic neuron differentiation aids in variant-to-gene mapping of relevant complex traits

  Matthew C. Pahl, Claudia A. Doege, Kenyaita M. Hodge, et al.

  Nat Commun. 2021-11-19;12(1):6749.

  • doi:10.1038/s41467-021-27001-4
  • PMID:34799566
  • PMCID:PMC8604959

• 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

  Joint disease-specificity at the regulatory base-pair level

  Pushpanathan Muthuirulan, Dewei Zhao, Mariel Young, et al.

  Nat Commun. 2021-07-06;12(1):4161.

  • doi:10.1038/s41467-021-24345-9
  • PMID:34230488
  • PMCID:PMC8260791

• Publication

  released

  Common schizophrenia risk variants are enriched in open chromatin regions of human glutamatergic neurons

  Mads E. Hauberg, Jordi Creus-Muncunill, Jaroslav Bendl, et al.

  Nat Commun. 2020-11-04;11(1):5581.

  • doi:10.1038/s41467-020-19319-2
  • PMID:33149216
  • PMCID:PMC7643171

• 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

  Regulatory sites for splicing in human basal ganglia are enriched for disease-relevant information

  Sebastian Guelfi, Karishma D’Sa, Juan A. Botía, et al.

  Nat Commun. 2020-02-25;11(1):1041.

  • doi:10.1038/s41467-020-14483-x
  • PMID:32098967
  • PMCID:PMC7042265

• 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

  ATAC-Seq analysis reveals a widespread decrease of chromatin accessibility in age-related macular degeneration

  Jie Wang, Cristina Zibetti, Peng Shang, et al.

  Nat Commun. 2018-04-10;9(1):1364.

  • doi:10.1038/s41467-018-03856-y
  • PMID:29636475
  • PMCID:PMC5893535

• Publication

  released

  Re-analysis of public genetic data reveals a rare X-chromosomal variant associated with type 2 diabetes

  Sílvia Bonàs-Guarch, Marta Guindo-Martínez, Irene Miguel-Escalada, et al.

  Nat Commun. 2018-01-22;9(1):321.

  • doi:10.1038/s41467-017-02380-9
  • PMID:29358691
  • PMCID:PMC5778074

• Publication

  released

  Single-cell Transcriptomes Identify Human Islet Cell Signatures And Reveal Cell-type–specific Expression Changes In Type 2 Diabetes

  Nathan Lawlor, Joshy George, Mohan Bolisetty, et al.

  Genome Research. 2017-02-01;27(2):208-222.

  • doi:10.1101/gr.212720.116
  • PMID:27864352

• Publication

  released

  Prepatterning Of Differentiation-driven Nuclear Lamin A/C-associated Chromatin Domains By GlcNAcylated Histone H2B

  Torunn Rønningen, Akshay Shah, Anja R. Oldenburg, et al.

  Genome Research. 2015-12;25(12):1825-1835.

  • doi:10.1101/gr.193748.115
  • PMID:26359231

• Publication

  released

  Acute TNF-induced Repression Of Cell Identity Genes Is Mediated By NFκB-directed Redistribution Of Cofactors From Super-enhancers

  Søren Fisker Schmidt, Bjørk Ditlev Larsen, Anne Loft, et al.

  Genome Research. 2015-09;25(9):1281-1294.

  • doi:10.1101/gr.188300.114
  • PMID:26113076

• Publication

  released

  Genome-wide Analysis Of Histone Modifications In Human Pancreatic Islets

  Reena Bhandare, Jonathan Schug, John Le Lay, et al.

  Genome Research. 2010-04;20(4):428-433.

  • doi:10.1101/gr.102038.109
  • PMID:20181961