Searching journal content for articles similar to Tena et al. 24 (7): 1075.

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  1. Research: Functional genomics analysis of developing zebrafish and human endoderm reveals highly conserved cis-regulatory modules acting during vertebrate organogenesis
    • Daniela M Riley,
    • Randa Elsayed,
    • Mark D Walsh,
    • Simaran Johal,
    • Ying Lin,
    • Harry Walton,
    • Till Bretschneider,
    • Sascha Ott,
    • and Andrew C Nelson
    Genome Res. March 4, 2026 gr.280838.125; Published in Advance March 4, 2026, doi:10.1101/gr.280838.125
    ...2 functional genomics approaches to identify highly conserved endodermal cis-regulatory 30 modules (CRMs) functioning across the 400 million years of evolution separating zebrafish 31 and humans. Our analyses suggest that there are few endoderm-specific CRMs, with many 32 CRMs governing pancreas...
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  2. Resource: Modeling transcriptional regulation of model species with deep learning
    • Evan M. Cofer,
    • João Raimundo,
    • Alicja Tadych,
    • Yuji Yamazaki,
    • Aaron K. Wong,
    • Chandra L. Theesfeld,
    • Michael S. Levine,
    • and Olga G. Troyanskaya
    Genome Res. June 2021 31: 1097-1105; Published in Advance April 22, 2021, doi:10.1101/gr.266171.120
    ...for separate sequences, we can identify how sequence differences may lead to regulatory differences. As a consequence, we can predict whether a variant might increase or decrease regulatory activity for any of DeepArk's 6562 regulatory features. This ability to predict the cis-regulatory effects of genomic...
    OPEN ACCESS ARTICLE
  3. Resource: Dynamic transcriptional and chromatin accessibility landscape of medaka embryogenesis
    • Yingshu Li,
    • Yongjie Liu,
    • Hang Yang,
    • Ting Zhang,
    • Kiyoshi Naruse,
    • and Qiang Tu
    Genome Res. June 2020 30: 924-937; Published in Advance June 26, 2020, doi:10.1101/gr.258871.119
    ...-read RNA-seq, short-read RNA-seq, and ATAC-seq. By integrating these data sets, we constructed a much-improved gene model set including about 17,000 novel isoforms and identified 1600 transcription factors, 1100 long noncoding RNAs, and 150,000 potential cis-regulatory elements as well. Time-series data...
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