Searching journal content for articles similar to Clowney et al. 21 (8): 1249.

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  1. Research: Oxygen-induced stress reveals context-specific gene regulatory effects in human brain organoids
    • Benjamin D. Umans and
    • Yoav Gilad
    Genome Res. August 2025 35: 1689-1700; Published in Advance June 2, 2025, doi:10.1101/gr.280219.124
    ...studies of neurological disorders and provide new insights into the hidden regulatory mechanisms influenced by environmental factors in the brain.Understanding how gene regulatory variants function across different cellular and environmental contexts is essential for interpreting genetic associations...
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  2. Research: Gene by environment interaction mouse model reveals a functional role for 5-hydroxymethylcytosine in neurodevelopmental disorders
    • Ligia A. Papale,
    • Andy Madrid,
    • Qi Zhang,
    • Kailei Chen,
    • Lara Sak,
    • Sündüz Keleş,
    • and Reid S. Alisch
    Genome Res. February 2022 32: 266-279; Published in Advance December 23, 2021, doi:10.1101/gr.276137.121
    .... Genomic profiling revealed disruptions in hippocampal and striatal 5hmC levels that are correlated to altered transcript levels of genes linked to these phenotypes (e.g., Reln, Dst, Trio, and Epha5). Chromatin immunoprecipitation coupled with high-throughput sequencing and hippocampal nuclear lysate pull...
  3. Method: Pooled analysis of radiation hybrids identifies loci for growth and drug action in mammalian cells
    • Arshad H. Khan,
    • Andy Lin,
    • Richard T. Wang,
    • Joshua S. Bloom,
    • Kenneth Lange,
    • and Desmond J. Smith
    Genome Res. October 2020 30: 1458-1467; Published in Advance September 2, 2020, doi:10.1101/gr.262204.120
    ..., having fewer literature citations in the GeneRIF and Reactome databases (Supplemental Fig. S28). Of the 442 coding region RH growth genes, 148 had neither literature citations in GeneRIF nor entries in the Reactome database. Study of these little understood genes may provide insights into mammalian cell...
  4. Research: Promoter architecture of mouse olfactory receptor genes
    • Charles Plessy,
    • Giovanni Pascarella,
    • Nicolas Bertin,
    • Altuna Akalin,
    • Claudia Carrieri,
    • Anne Vassalli,
    • Dejan Lazarevic,
    • Jessica Severin,
    • Christina Vlachouli,
    • Roberto Simone,
    • Geoffrey J. Faulkner,
    • Jun Kawai,
    • Carsten O. Daub,
    • Silvia Zucchelli,
    • Yoshihide Hayashizaki,
    • Peter Mombaerts,
    • Boris Lenhard,
    • Stefano Gustincich,
    • and Piero Carninci
    Genome Res. March 2012 22: 486-497; Published in Advance December 22, 2011, doi:10.1101/gr.126201.111
    ...Promoter architecture of mouse olfactory receptor genes Charles Plessy 1 , 14 , Giovanni Pascarella 2 , 3 , 12 , 14 , Nicolas Bertin 1 , 14 , Altuna Akalin 4 , 10 , 14 , Claudia Carrieri 2 , Anne Vassalli 5 , 11...
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  5. Research: Pangolin genomes and the evolution of mammalian scales and immunity
    • Siew Woh Choo,
    • Mike Rayko,
    • Tze King Tan,
    • Ranjeev Hari,
    • Aleksey Komissarov,
    • Wei Yee Wee,
    • Andrey A. Yurchenko,
    • Sergey Kliver,
    • Gaik Tamazian,
    • Agostinho Antunes,
    • Richard K. Wilson,
    • Wesley C. Warren,
    • Klaus-Peter Koepfli,
    • Patrick Minx,
    • Ksenia Krasheninnikova,
    • Antoinette Kotze,
    • Desire L. Dalton,
    • Elaine Vermaak,
    • Ian C. Paterson,
    • Pavel Dobrynin,
    • Frankie Thomas Sitam,
    • Jeffrine J. Rovie-Ryan,
    • Warren E. Johnson,
    • Aini Mohamed Yusoff,
    • Shu-Jin Luo,
    • Kayal Vizi Karuppannan,
    • Gang Fang,
    • Deyou Zheng,
    • Mark B. Gerstein,
    • Leonard Lipovich,
    • Stephen J. O'Brien,
    • and Guat Jah Wong
    Genome Res. October 2016 26: 1312-1322; Published in Advance August 10, 2016, doi:10.1101/gr.203521.115
    ...adaptations was evident from positively selected genes involving immunity-related pathways, inflammation, energy storage and metabolism, muscular and nervous systems, and scale/hair development. Olfactory receptor gene families are significantly expanded in pangolins, reflecting their well-developed olfaction...
  6. Method: Characterizing spatial gene expression heterogeneity in spatially resolved single-cell transcriptomic data with nonuniform cellular densities
    • Brendan F. Miller,
    • Dhananjay Bambah-Mukku,
    • Catherine Dulac,
    • Xiaowei Zhuang,
    • and Jean Fan
    Genome Res. October 2021 31: 1843-1855; Published in Advance May 25, 2021, doi:10.1101/gr.271288.120
    ...on spatially resolved RNA capture followed by sequencing, such as spatial transcriptomics and Slide-seq, provide spatially resolved untargeted transcriptomic profiling at the pixel level, with pixel size of 10–100 µm (Larsson et al. 2021). Such high throughput data generation, both in terms of the number...
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  7. Method: Identification of human silencers by correlating cross-tissue epigenetic profiles and gene expression
    • Di Huang,
    • Hanna M. Petrykowska,
    • Brendan F. Miller,
    • Laura Elnitski,
    • and Ivan Ovcharenko
    Genome Res. April 2019 29: 657-667; Published in Advance March 18, 2019, doi:10.1101/gr.247007.118
    ...toward understanding gene regulatory mechanisms (Maston et al. 2006).High-throughput sequencing techniques have provided a wealth of -wide landscapes of various epigenetic modifications and transcription factor (TF) binding sites. These data, together with the increasing knowledge of histone modification...
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  8. Resource: A lacZ reporter gene expression atlas for 313 adult KOMP mutant mouse lines
    • David B. West,
    • Ravi K. Pasumarthi,
    • Brian Baridon,
    • Esi Djan,
    • Amanda Trainor,
    • Stephen M. Griffey,
    • Eric K. Engelhard,
    • Jared Rapp,
    • Bowen Li,
    • Pieter J. de Jong,
    • and K.C. Kent Lloyd
    Genome Res. April 2015 25: 598-607; Published in Advance January 15, 2015, doi:10.1101/gr.184184.114
    ...methods. After careful annotation, LacZ staining patterns in a high percentage of mutants revealed a unique structure-function not previously reported for many of these genes. The validation of methods for LacZ staining, annotation, and expression analysis reported here provides unique insights...
  9. LETTER: Comparative analysis of chicken chromosome 28 provides new clues to the evolutionary fragility of gene-rich vertebrate regions
    • Laurie Gordon,
    • Shan Yang,
    • Mary Tran-Gyamfi,
    • Dan Baggott,
    • Mari Christensen,
    • Aaron Hamilton,
    • Richard Crooijmans,
    • Martien Groenen,
    • Susan Lucas,
    • Ivan Ovcharenko,
    • and Lisa Stubbs
    Genome Res. November 2007 17: 1603-1613; Published in Advance October 5, 2007, doi:10.1101/gr.6775107
    ...solidly assembled mammalian and nonmammalian s as anchor points. The chicken sequence provides an excellent candidate for this comparison. However, chicken whole shotgun (wgs) assembly was particularly challenging in the most gene-rich segments, including chicken DNA segments related to most...
  10. Letter: Comparison of diverse developmental transcriptomes reveals that coexpression of gene neighbors is not evolutionarily conserved
    • Itai Yanai and
    • Craig P. Hunter
    Genome Res. December 2009 19: 2214-2220; Published in Advance September 10, 2009, doi:10.1101/gr.093815.109
    ...that play known roles in the patterning of the embryo show remarkable expression similarity between orthologs (median R = 0.9, P < 0.005). In contrast, we find significantly lower levels of expression similarity among groups of genes not expected to function in early embryogenesis: olfactory receptors...
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