Searching journal content for articles similar to Roberts et al. 34 (4): 620.

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  1. Resource: Interspecies regulatory landscapes and elements revealed by novel joint systematic integration of human and mouse blood cell epigenomes
    • Guanjue Xiang,
    • Xi He,
    • Belinda M. Giardine,
    • Kathryn J. Isaac,
    • Dylan J. Taylor,
    • Rajiv C. McCoy,
    • Camden Jansen,
    • Cheryl A. Keller,
    • Alexander Q. Wixom,
    • April Cockburn,
    • Amber Miller,
    • Qian Qi,
    • Yanghua He,
    • Yichao Li,
    • Jens Lichtenberg,
    • Elisabeth F. Heuston,
    • Stacie M. Anderson,
    • Jing Luan,
    • Marit W. Vermunt,
    • Feng Yue,
    • Michael E.G. Sauria,
    • Michael C. Schatz,
    • James Taylor,
    • Berthold Göttgens,
    • Jim R. Hughes,
    • Douglas R. Higgs,
    • Mitchell J. Weiss,
    • Yong Cheng,
    • Gerd A. Blobel,
    • David M. Bodine,
    • Yu Zhang,
    • Qunhua Li,
    • Shaun Mahony,
    • and Ross C. Hardison
    Genome Res. July 2024 34: 1089-1105; Published in Advance July 1, 2024, doi:10.1101/gr.277950.123
    ...and functions of different cell types are determined by the expression of distinctive sets of genes in each. This differential gene expression is regulated by the interplay of transcription factors (TFs) binding to cis-regulatory elements (CREs) in the genomic DNA, such as promoters and enhancers, forging...
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  2. Research: Cohesin regulates tissue-specific expression by stabilizing highly occupied cis-regulatory modules
    • Andre J. Faure,
    • Dominic Schmidt,
    • Stephen Watt,
    • Petra C. Schwalie,
    • Michael D. Wilson,
    • Huiling Xu,
    • Robert G. Ramsay,
    • Duncan T. Odom,
    • and Paul Flicek
    Genome Res. November 2012 22: 2163-2175; Published in Advance July 10, 2012, doi:10.1101/gr.136507.111
    ...Cohesin regulates tissue-specific expression by stabilizing highly occupied cis -regulatory modules Andre J. Faure 1 , 7 , Dominic Schmidt 2 , 3 , 7 , Stephen Watt 2 , 3 , Petra C. Schwalie 1 , Michael D. Wilson 2 , 3 , 8...
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  3. Method: Identification of regulatory elements from nascent transcription using dREG
    • Zhong Wang,
    • Tinyi Chu,
    • Lauren A. Choate,
    • and Charles G. Danko
    Genome Res. February 2019 29: 293-303; Published in Advance December 20, 2018, doi:10.1101/gr.238279.118
    ...to detect the location of transcriptional regulatory elements from GRO/PRO/ChRO-seq data (dREG). The basic idea behind dREG is to differentiate between two types of regions that show high levels of RNA polymerase: (1) positions where new RNA polymerase initiates; and (2) positions where RNA polymerase...
  4. Methods: Footer: A quantitative comparative genomics method for efficient recognition of cis-regulatory elements
    • David L. Corcoran,
    • Eleanor Feingold,
    • Jessica Dominick,
    • Marietta Wright,
    • Jo Harnaha,
    • Massimo Trucco,
    • Nick Giannoukakis,
    • and Panayiotis V. Benos
    Genome Res. June 2005 15: 840-847; doi:10.1101/gr.2952005
    ...Footer: A quantitative comparative genomics method for efficient recognition of cis -regulatory elements David L. Corcoran 1 , 2 , Eleanor Feingold 1 , 2 , Jessica Dominick 2 , Marietta Wright 4 , Jo Harnaha 4 , Massimo Trucco 4...
  5. Methods: Cross-species de novo identification of cis-regulatory modules with GibbsModule: Application to gene regulation in embryonic stem cells
    • Dan Xie,
    • Jun Cai,
    • Na-Yu Chia,
    • Huck H. Ng,
    • and Sheng Zhong
    Genome Res. August 2008 18: 1325-1335; Published in Advance May 15, 2008, doi:10.1101/gr.072769.107
    ....107 . ↵ 8 Although we use the term ‘‘upstream sequence’’ to describe the method, in practice, the method should be applied to any regions that may contain cis -regulatory elements. ↵ 9 Throughout this article we use 1, −0.33, −1, −0.33, and 10 as match score, mismatch penalty, gap open penalty...
  6. Method: Recovering gene regulatory networks in single-cell multi-omics data with PRISM-GRN
    • Wenhao Zhang,
    • Lan Cao,
    • Xiaoxuan Gu,
    • Yongyu Long,
    • and Ying Wang
    Genome Res. January 2026 36: 142-158; Published in Advance October 9, 2025, doi:10.1101/gr.280757.125
    ...) introduces the concept of cis-regulatory potential to infer subpopulation-specific GRNs, achieving significantly higher accuracy compared with correlation-based methods. CellOracle (Kamimoto et al. 2023) enables GRN inference by integrating single-cell multi-omics data with prior regulatory knowledge...
  7. Research: Analyzing super-enhancer temporal dynamics reveals potential critical enhancers and their gene regulatory networks underlying skeletal muscle development
    • Song Zhang,
    • Chao Wang,
    • Shenghua Qin,
    • Choulin Chen,
    • Yongzhou Bao,
    • Yuanyuan Zhang,
    • Lingna Xu,
    • Qingyou Liu,
    • Yunxiang Zhao,
    • Kui Li,
    • Zhonglin Tang,
    • and Yuwen Liu
    Genome Res. December 2024 34: 2190-2202; Published in Advance October 21, 2024, doi:10.1101/gr.278344.123
    ...regulatory factor (MRF) family (MYOD1, MYOG, MYF5, and MYF6) and myocyte enhancer factor 2 (MEF2) family (MEF2A, MEF2B, MEF2C, and MEF2D) (Hernández-Hernández et al. 2017). These TFs bind cis-regulatory elements (CREs), such as enhancers, to spatiotemporally regulate gene expression (Yan et al. 2019; Zhao et...
  8. Method: Integration of transcriptomics and long-read genomics prioritizes structural variants in rare disease
    • Tanner D. Jensen,
    • Bohan Ni,
    • Chloe M. Reuter,
    • John E. Gorzynski,
    • Sarah Fazal,
    • Devon Bonner,
    • Rachel A. Ungar,
    • Pagé C. Goddard,
    • Archana Raja,
    • Euan A. Ashley,
    • Jonathan A. Bernstein,
    • Stephan Zuchner,
    • Undiagnosed Diseases Network,
    • Michael D. Greicius,
    • Stephen B. Montgomery,
    • Michael C. Schatz,
    • Matthew T. Wheeler,
    • and Alexis Battle
    Genome Res. April 2025 35: 914-928; Published in Advance March 20, 2025, doi:10.1101/gr.279323.124
    ...conserved cis-regulatory elements, or high-scoring CADD variants. These 519 nonregulatory rare SVs were not enriched proximal to expression outliers (LOR 0.33, adj. P-value = 1.00) (Fig. 3C). We then sought to validate these ABC-element enrichments in a larger sample size from GTEx. Notably, enhancer...
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  9. Method: Accurate allocation of multimapped reads enables regulatory element analysis at repeats
    • Alexis Morrissey,
    • Jeffrey Shi,
    • Daniela Q. James,
    • and Shaun Mahony
    Genome Res. June 2024 34: 937-951; Published in Advance July 10, 2024, doi:10.1101/gr.278638.123
    ...Alexis Morrissey, Jeffrey Shi, Daniela Q. James and Shaun Mahony Center for Eukaryotic Gene Regulation, Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, Pennsylvania 16802, USA Corresponding author: mahony@psu.eduAbstractTransposable elements...
  10. Method: Aggregation of recount3 RNA-seq data improves inference of consensus and tissue-specific gene coexpression networks
    • Prashanthi Ravichandran,
    • Princy Parsana,
    • Rebecca Keener,
    • Kasper D. Hansen,
    • and Alexis Battle
    Genome Res. September 2025 35: 2087-2103; Published in Advance July 17, 2025, doi:10.1101/gr.280808.125
    ...quintiles of network centrality (Supplemental Figs. S22 and S23; Supplemental Table S9). We observed that peripheral genes (Quintile 1) and central genes (Quintile 5) of consensus networks exhibited an excess overlap > 1 of eQTL-deficient genes (those which lacked significant cis-regulatory variants...
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