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Showing 1–17 of 17 results
Advanced filters: Author: Andrew B. Stergachis Clear advanced filters

  • Large-effect variants in autism remain elusive. Here, the authors use long-read sequencing to assemble phased genomes for 189 individuals, identifying pathogenic variants in TBL1XR1, MECP2, and SYNGAP1, plus nine candidate structural variants missed by short-read methods.

    • Yang Sui
    • Jiadong Lin
    • Evan E. Eichler
    ResearchOpen Access
    Nature Communications
    Volume: 17, P: 1-16

  • Mouse genomic footprinting reveals conservation of transcription factor (TF) recognition repertoires and trans-regulatory circuitry despite massive turnover of DNA elements that contact TFs in vivo.

    • Andrew B. Stergachis
    • Shane Neph
    • John A. Stamatoyannopoulos
    ResearchOpen Access
    Nature
    Volume: 515, P: 365-370

  • Long-read chromatin assay reveals (1) a novel class of accessible chromatin regions, (2) accessibility within individual LTR retrotransposons and (3) the relationship between diffuse accessibility, gene body methylation and hAT transposon insertion.

    • Kerry L. Bubb
    • Morgan O. Hamm
    • Christine Queitsch
    Research
    Nature Plants
    Volume: 11, P: 1181-1192

  • An empirical approach for identifying optimal proteotypic peptides and fragmentation patterns from in vitro–synthesized proteins, for targeted proteomics applications, is described.

    • Andrew B Stergachis
    • Brendan MacLean
    • Michael J MacCoss
    Research
    Nature Methods
    Volume: 8, P: 1041-1043

  • The Somatic Mosaicism across Human Tissues Network aims to create a reference catalogue of somatic mosaicism across different tissues and cells within individuals.

    • Tim H. H. Coorens
    • Ji Won Oh
    • Yuqing Wang
    Reviews
    Nature
    Volume: 643, P: 47-59

  • An extensive map of human DNase I hypersensitive sites, markers of regulatory DNA, in 125 diverse cell and tissue types is described; integration of this information with other ENCODE-generated data sets identifies new relationships between chromatin accessibility, transcription, DNA methylation and regulatory factor occupancy patterns.

    • Robert E. Thurman
    • Eric Rynes
    • John A. Stamatoyannopoulos
    ResearchOpen Access
    Nature
    Volume: 489, P: 75-82

  • Isaac et al. present mtFiber-seq, a method that measures individual mitochondrial genome packaging at nucleotide resolution. They show that most nucleoids are in an inaccessible state, modulated by the abundance of the DNA-binding protein TFAM.

    • R. Stefan Isaac
    • Thomas W. Tullius
    • L. Stirling Churchman
    Research
    Nature Structural & Molecular Biology
    Volume: 31, P: 568-577

  • Simultaneous profiling of the genome, methylome, epigenome and transcriptome using single-molecule chromatin fiber sequencing and multiplexed arrays isoform sequencing identifies the genetic and molecular basis of an undiagnosed Mendelian disease case with an X;13-balanced translocation.

    • Mitchell R. Vollger
    • Jonas Korlach
    • Andrew B. Stergachis
    Research
    Nature Genetics
    Volume: 57, P: 469-479

  • This overview of the ENCODE project outlines the data accumulated so far, revealing that 80% of the human genome now has at least one biochemical function assigned to it; the newly identified functional elements should aid the interpretation of results of genome-wide association studies, as many correspond to sites of association with human disease.

    • Ian Dunham
    • Anshul Kundaje
    • Ewan Birney
    ResearchOpen Access
    Nature
    Volume: 489, P: 57-74

  • The GREGoR consortium provides foundational resources and substrates for the future of rare disease genomics.

    • Moez Dawood
    • Ben Heavner
    • Gabrielle C. Villard
    Reviews
    Nature
    Volume: 647, P: 331-342

  • John Stamatoyannopoulos, John Mattick and colleagues use DNase I–hypersensitive site maps from 86 diverse cell types to identify a subset of exons that have DNase I hypersensitivity and are accompanied by 'phantom' signals in chromatin immunoprecipitation and sequencing (ChIP-seq) resulting from cross-linking with proximal promoter- or enhancer-bound factors.

    • Tim R Mercer
    • Stacey L Edwards
    • John A Stamatoyannopoulos
    Research
    Nature Genetics
    Volume: 45, P: 852-859