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Showing 1–27 of 27 results
Advanced filters: Author: Noam Bernstein Clear advanced filters

  • The authors summarize the data produced by phase III of the Encyclopedia of DNA Elements (ENCODE) project, a resource for better understanding of the human and mouse genomes.

    • Federico Abascal
    • Reyes Acosta
    • Zhiping Weng
    ResearchOpen Access
    Nature
    Volume: 583, P: 699-710

  • A critical goal in functional genomics is evaluating which non-coding elements contribute to gene expression, cellular function, and disease. Here the authors present a CRISPRi-based method using truncated guides disrupts transcription factor binding and enhancer activity across thousands of sites, expanding CRISPRi targeting scope for functional genomics and enabling efficient screening of repeated genomic elements

    • Molly M. Moore
    • Siddarth Wekhande
    • Fadi J. Najm
    ResearchOpen Access
    Nature Communications
    Volume: 16, P: 1-12

  • 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

  • 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

  • Nanopore sequencing is used to profile chromatin accessibility and DNA methylation on DNA molecules over 100 kb. Phasing analysis at the H19/IGF2 locus identifies a primate-specific enhancer driving biallelic IGF2 expression in specific cellular contexts.

    • Sofia Battaglia
    • Kevin Dong
    • Bradley E. Bernstein
    Research
    Nature Genetics
    Volume: 54, P: 1504-1513

  • Parallelized analysis in clinical genomics can lead to sample or data mislabelling, and could have serious downstream consequences. Here the authors present a tool to quantify sample genetic relatedness and detect such mistakes, and apply it to thousands of datasets from the ENCODE consortium.

    • Nauman Javed
    • Yossi Farjoun
    • Noam Shoresh
    ResearchOpen Access
    Nature Communications
    Volume: 11, P: 1-8

  • Machine learning models enable atomistic simulations of phase transitions in amorphous silicon, predict electronic fingerprints, and show that the pressure-induced crystallization occurs over three distinct stages.

    • Volker L. Deringer
    • Noam Bernstein
    • Stephen R. Elliott
    Research
    Nature
    Volume: 589, P: 59-64

  • 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

  • Synthetic materials tend to excel in either stiffness or extensibility, whereas a combination of the two is necessary to exceed the performance of natural biomaterials. Here the authors present a bioinspired polymer consisting of cyclic β-peptide rings that is capable of transitioning between rigid and unfolded conformations on demand.

    • Kenan P. Fears
    • Manoj K. Kolel-Veetil
    • Thomas D. Clark
    ResearchOpen Access
    Nature Communications
    Volume: 9, P: 1-8

  • The lowest-energy exciton state in caesium lead halide perovskite nanocrystals is shown to be a bright triplet state, contrary to expectations that lowest-energy excitons should always be dark.

    • Michael A. Becker
    • Roman Vaxenburg
    • Alexander L. Efros
    Research
    Nature
    Volume: 553, P: 189-193

  • A large collection of new modENCODE and ENCODE genome-wide chromatin data sets from cell lines and developmental stages in worm, fly and human are analysed; this reveals many conserved features of chromatin organization among the three organisms, as well as notable differences in the composition and locations of repressive chromatin.

    • Joshua W. K. Ho
    • Youngsook L. Jung
    • Peter J. Park
    ResearchOpen Access
    Nature
    Volume: 512, P: 449-452

  • The authors summarize the history of the ENCODE Project, the achievements of ENCODE 1 and ENCODE 2, and how the new data generated and analysed in ENCODE 3 complement the previous phases.

    • Federico Abascal
    • Reyes Acosta
    • Richard M. Myers
    Reviews
    Nature
    Volume: 583, P: 693-698

  • The Impact of Genomic Variation on Function Consortium is combining single-cell mapping, genomic perturbations and predictive modelling to investigate relationships between human genomic variation, genome function and phenotypes and will provide an open resource to the community.

    • Jesse M. Engreitz
    • Heather A. Lawson
    • Ella K. Samer
    Reviews
    Nature
    Volume: 633, P: 47-57

  • Nested sampling is an algorithm for computing Bayesian inference and high-dimensional integrals. This Primer introduces the nested sampling algorithm and variations, highlighting its use across various areas of physical science, from cosmology to particle physics.

    • Greg Ashton
    • Noam Bernstein
    • David Yallup
    Reviews
    Nature Reviews Methods Primers
    Volume: 2, P: 1-22