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Showing 1–19 of 19 results
Advanced filters: Author: Kyle Farh Clear advanced filters

  • The Human Development Multiomic Atlas catalogues single-cell accessibility and gene expression data from human fetal cells across 12 organs, enabling the inference of syntactic rules for motifs that govern cell-type-specific transcription factor binding and chromatin accessibility during human development.

    • Betty B. Liu
    • Selin Jessa
    • William J. Greenleaf
    ResearchOpen Access
    Nature
    P: 1-14

  • WGS data were used from 347,630 individuals with European ancestry in the UK Biobank to obtain high-precision estimates of coding and non-coding rare variant heritability for 34 complex traits and diseases.

    • Pierrick Wainschtein
    • Yuanxiang Zhang
    • Loic Yengo
    ResearchOpen Access
    Nature
    Volume: 649, P: 1219-1227

  • This study describes the integrative analysis of 111 reference human epigenomes, profiled for histone modification patterns, DNA accessibility, DNA methylation and RNA expression; the results annotate candidate regulatory elements in diverse tissues and cell types, their candidate regulators, and the set of human traits for which they show genetic variant enrichment, providing a resource for interpreting the molecular basis of human disease.

    • Anshul Kundaje
    • Wouter Meuleman
    • Manolis Kellis
    ResearchOpen Access
    Nature
    Volume: 518, P: 317-330

  • A global network of researchers was formed to investigate the role of human genetics in SARS-CoV-2 infection and COVID-19 severity; this paper reports 13 genome-wide significant loci and potentially actionable mechanisms in response to infection.

    • Mari E. K. Niemi
    • Juha Karjalainen
    • Chloe Donohue
    ResearchOpen Access
    Nature
    Volume: 600, P: 472-477

  • Analysis of the genomes of 50 species of Lemuriformes shows high levels of genomic diversity, likely due to allele sharing, as well as population declines and inbreeding patterns resulting from ecological factors and human impacts in Madagascar.

    • Joseph D. Orkin
    • Lukas F. K. Kuderna
    • Tomas Marques Bonet
    Research
    Nature Ecology & Evolution
    Volume: 9, P: 42-56

  • Genome-wide association studies combined with data from epigenomic maps for immune cells have been used to fine-map causal variants for 21 autoimmune diseases; disease risk tends to be linked to single nucleotide polymorphisms in cell-type-specific enhancers, often in regions adjacent to transcription factor binding motifs.

    • Kyle Kai-How Farh
    • Alexander Marson
    • Bradley E. Bernstein
    Research
    Nature
    Volume: 518, P: 337-343

  • There is a genetic component to the risk of severe COVID-19, but the genetic effects are difficult to separate from social constructs that covary with genetic ancestry. To address this, the authors identify determinants of COVID-19 severity using admixture mapping, viral phylodynamics, and host immune and metagenomic sequencing.

    • Victoria N. Parikh
    • Alexander G. Ioannidis
    • Euan A. Ashley
    ResearchOpen Access
    Nature Communications
    Volume: 13, P: 1-10

  • Hilary Finucane, Brendan Bulik-Sullivan, Benjamin Neale, Alkes Price and colleagues introduce a new method, called stratified LD score regression, for partitioning heritability by functional category using genome-wide association study summary statistics. They observe a substantial enrichment of heritability in conserved regions and illustrate how this approach can provide insights into the biological basis of disease and direction for functional follow-up.

    • Hilary K Finucane
    • Brendan Bulik-Sullivan
    • Alkes L Price
    Research
    Nature Genetics
    Volume: 47, P: 1228-1235

  • With ultra-deep RNA sequencing, Zhang et al. report increased usage of alternative promoters driven by AR, FOXA1 and MYC during prostate cancer progression and suggest altered DNA methylation as a potential underlying mechanism.

    • Meng Zhang
    • Martin Sjöström
    • David A. Quigley
    Research
    Nature Cell Biology
    Volume: 26, P: 1176-1186

  • Whole-genome alignment of 239 primate species reveals noncoding regulatory elements that are under selective constraint in primates but not in other placental mammals, that are enriched for variants that affect human gene expression and complex traits in diseases.

    • Lukas F. K. Kuderna
    • Jacob C. Ulirsch
    • Kyle Kai-How Farh
    ResearchOpen Access
    Nature
    Volume: 625, P: 735-742

  • Whole-genome bisulfite sequencing along with whole-genome and transcriptome sequencing of 100 prostate cancer metastases identifies genomic regions that are differentially methylated during disease progression and a novel epigenomic subtype.

    • Shuang G. Zhao
    • William S. Chen
    • Felix Y. Feng
    Research
    Nature Genetics
    Volume: 52, P: 778-789

  • In this study, the authors describe the subset of activity-regulated enhancers that modulate transcription in cultured neurons and that participate in the regulation of synaptic maturation. In addition, they demonstrate Fos binding to these enhancers is essential for this activity-dependent regulation of transcription.

    • Athar N Malik
    • Thomas Vierbuchen
    • Michael E Greenberg
    Research
    Nature Neuroscience
    Volume: 17, P: 1330-1339

  • Using common variants in six non-human primate species, the authors train a deep neural network that identifies pathogenic mutations in patients with rare disease with 88% accuracy and enables the discovery of 14 new candidate genes in intellectual disability.

    • Laksshman Sundaram
    • Hong Gao
    • Kyle Kai-How Farh
    Research
    Nature Genetics
    Volume: 50, P: 1161-1170

  • This Review explores the genetic basis of diversification and adaptation in non-human primates, including their responses to ecological and environmental changes.

    • Christian Roos
    • Lakshmi Seshadri
    • Jeffrey Rogers
    Reviews
    Nature Reviews Biodiversity
    Volume: 1, P: 353-370

  • The authors use tiled CRISPR activation for functional enhancer discovery across two autoimmunity risk loci, CD69 and IL2RA, and identify elements with features of stimulus-responsive enhancers, including an IL2RA enhancer that harbours a fine-mapped autoimmunity risk variant.

    • Dimitre R. Simeonov
    • Benjamin G. Gowen
    • Alexander Marson
    Research
    Nature
    Volume: 549, P: 111-115