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Showing 1–19 of 19 results
Advanced filters: Author: Alon Goren Clear advanced filters

  • The molecular mechanisms underlying tumour initiation remain elusive. Here, the authors use spatiotemporally controlled oncogene activation and tumour suppressor inhibition with multi-omics to unveil the role of YAP-mediated oral epithelial progenitor cell reprogramming into tumour-initiating cells.

    • Farhoud Faraji
    • Sydney I. Ramirez
    • J. Silvio Gutkind
    ResearchOpen Access
    Nature Communications
    Volume: 16, P: 1-20

  • Single-cell RNA sequencing is used to investigate the transcriptional response of 18 mouse bone-marrow-derived dendritic cells after lipopolysaccharide stimulation; many highly expressed genes, such as key immune genes and cytokines, show bimodal variation in both transcript abundance and splicing patterns. This variation reflects differences in both cell state and usage of an interferon-driven pathway involving Stat2 and Irf7.

    • Alex K. Shalek
    • Rahul Satija
    • Aviv Regev
    Research
    Nature
    Volume: 498, P: 236-240

  • The amount of genome-scale data on covalent histone modification patterns is rapidly increasing. This Review brings together current knowledge on how modification 'signatures' relate to the structure and function of chromatin, from regulatory elements and gene structure to organization in the nucleus.

    • Vicky W. Zhou
    • Alon Goren
    • Bradley E. Bernstein
    Reviews
    Nature Reviews Genetics
    Volume: 12, P: 7-18

  • Here the authors show that a large fraction of the tissue-specific methylation pattern is generated postnatally. These changes, which occur in response to hormone signaling, appear to play a major role in the regulation of gene expression and tissue maturation in the liver.

    • Yitzhak Reizel
    • Ofra Sabag
    • Howard Cedar
    ResearchOpen Access
    Nature Communications
    Volume: 9, P: 1-11

  • Keith Ligon, Adam Resnick, Rameen Beroukhim and colleagues identify MYB-QKI fusions in angiocentric gliomas and show that these rearrangements promote tumorigenesis through activation of MYB by truncation, enhancer translocation driving aberrant MYB-QKI expression and hemizygous loss of QKI.

    • Pratiti Bandopadhayay
    • Lori A Ramkissoon
    • Adam C Resnick
    Research
    Nature Genetics
    Volume: 48, P: 273-282

  • 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

    • Alon Goren
    • Howard Cedar
    Reviews
    Nature Reviews Molecular Cell Biology
    Volume: 4, P: 25-32

  • 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

  • Analysis of whole-genome sequencing and expression data for 17 tissues identifies short tandem repeats whose repeat number is associated with gene expression (eSTRs). Specific eSTRs are implicated in different complex traits through colocalization analysis with known genome-wide association study signals.

    • Stephanie Feupe Fotsing
    • Jonathan Margoliash
    • Melissa Gymrek
    Research
    Nature Genetics
    Volume: 51, P: 1652-1659

  • The proper use of spike-in normalization in ChIP-seq improves sensitivity for detecting genome-wide changes between conditions, but improper use is common, calling some biological conclusions into question. A survey of public datasets generates guidelines for implementation of spike-in normalization for future ChIP-seq experiments.

    • Lauren A. Patel
    • Yuwei Cao
    • Alon Goren
    Comments & Opinion
    Nature Biotechnology
    Volume: 42, P: 1343-1349

  • 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