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Showing 1–11 of 11 results
Advanced filters: Author: Siddarth Selvaraj Clear advanced filters

  • The Vertebrate Genome Project has used an optimized pipeline to generate high-quality genome assemblies for sixteen species (representing all major vertebrate classes), which have led to new biological insights.

    • Arang Rhie
    • Shane A. McCarthy
    • Erich D. Jarvis
    ResearchOpen Access
    Nature
    Volume: 592, P: 737-746

  • It is currently unclear how quantitative changes in chromatin loop propensity contribute to differential gene regulation. Here, the authors use phased Hi-C, RNA-seq, and ChIP-seq to show that subtle changes in loop propensity associate with differential gene regulation across cell types and haplotypes.

    • William W. Greenwald
    • He Li
    • Kelly A. Frazer
    ResearchOpen Access
    Nature Communications
    Volume: 10, P: 1-17

  • An analysis of genome-wide chromatin interactions during human embryonic stem cell differentiation reveals changes in chromatic organization and simultaneously identifies allele-resolved chromatin structure and differences in gene expression during differentiation.

    • Jesse R. Dixon
    • Inkyung Jung
    • Bing Ren
    ResearchOpen Access
    Nature
    Volume: 518, P: 331-336

  • The three-dimensional organization of the human and mouse genomes in embryonic stem cells and terminally differentiated cell types is investigated, revealing that large, megabase-sized chromatin interaction domains are a pervasive and conserved structural feature of genome organization.

    • Jesse R. Dixon
    • Siddarth Selvaraj
    • Bing Ren
    Research
    Nature
    Volume: 485, P: 376-380

  • A novel approach to analyse high-depth Hi-C data provides a comprehensive chromatin interaction map at approximately 5–10 kb resolution in human fibroblasts; this reveals that TNF-α-responsive enhancers are already in contact with target promoters before signalling and that this chromatin looping is a strong predictor of gene induction.

    • Fulai Jin
    • Yan Li
    • Bing Ren
    Research
    Nature
    Volume: 503, P: 290-294

  • High-coverage, ultra-long-read nanopore sequencing is used to create a new human genome assembly that improves on the coverage and accuracy of the current reference (GRCh38) and includes the gap-free, telomere-to-telomere sequence of the X chromosome.

    • Karen H. Miga
    • Sergey Koren
    • Adam M. Phillippy
    ResearchOpen Access
    Nature
    Volume: 585, P: 79-84

  • As part of the Epigenome Roadmap project, this study uses a chromosome-spanning haplotype reconstruction strategy to construct haplotype-resolved epigenomic maps for a diverse set of human tissues; the maps reveal extensive allelic biases in chromatin state and transcription, which vary across individuals due to genetic backgrounds.

    • Danny Leung
    • Inkyung Jung
    • Bing Ren
    ResearchOpen Access
    Nature
    Volume: 518, P: 350-354

  • As part of the Epigenome Roadmap Project, genome-wide maps of DNA methylation and transcriptomes together with genomic DNA sequencing of 18 different primary human tissue types from 4 individuals are presented; analysis reveals widespread differential methylation of CG sites between tissues, and the presence of non-CG methylation in adult tissues.

    • Matthew D. Schultz
    • Yupeng He
    • Joseph R. Ecker
    ResearchOpen Access
    Nature
    Volume: 523, P: 212-216