Searching journal content for articles similar to Thompson et al. 14 (10a): 1967.

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  1. Method: Decoding ChIP-seq with a double-binding signal refines binding peaks to single-nucleotides and predicts cooperative interaction
    • Antonio L.C. Gomes,
    • Thomas Abeel,
    • Matthew Peterson,
    • Elham Azizi,
    • Anna Lyubetskaya,
    • Luís Carvalho,
    • and James Galagan
    Genome Res. October 2014 24: 1686-1697; Published in Advance July 14, 2014, doi:10.1101/gr.161711.113
    ...to unveil the complexity of the resulting regulatory circuits. A modified version of our method could also, in principle, predict cooperative interaction between different TFs. In order to predict interaction between different TFs, however, studies that immunoprecipitatemultiple TFs in the same...
  2. Review: A systematic guide for identifying transcription factors that directly regulate the expression of a gene of interest
    • Andrew D. Bates,
    • Dawid Grzela,
    • Maciej Studzian,
    • Louise Brennan,
    • Moli Williams,
    • Conor Fawcett,
    • Beth Hammond,
    • Manreen Grewal,
    • Marcin Ratajewski,
    • Lukasz Pulaski,
    • and Urszula L. McClurg
    Genome Res. March 2026 36: 433-459; Published in Advance February 17, 2026, doi:10.1101/gr.281154.125
    ..., hinging on the precise binding of transcription factors (TFs) and cofactors to gene regulatory elements such as promoters and enhancers. Although it is relatively routine to profile -wide DNA binding landscapes of proteins, identifying the specific proteins that bind to, and regulate the transcription of...
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  3. Method: A network-based analysis of colon cancer splicing changes reveals a tumorigenesis-favoring regulatory pathway emanating from ELK1
    • Dror Hollander,
    • Maya Donyo,
    • Nir Atias,
    • Keren Mekahel,
    • Zeev Melamed,
    • Sivan Yannai,
    • Galit Lev-Maor,
    • Asaf Shilo,
    • Schraga Schwartz,
    • Iris Barshack,
    • Roded Sharan,
    • and Gil Ast
    Genome Res. April 2016 26: 541-553; Published in Advance February 9, 2016, doi:10.1101/gr.193169.115
    ...A network-based analysis of colon cancer splicing changes reveals a tumorigenesis-favoring regulatory pathway emanating from ELK1 Dror Hollander 1 , Maya Donyo 1 , 7 , Nir Atias 2 , 7 , Keren Mekahel 1 , Zeev Melamed 1 , 8 , Sivan...
  4. 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
    ...regulatory genes (Narang et al. 2015), determine changes in regulatory mechanisms that are key to cellular identity (Wang et al. 2021), and prioritize genes that drive phenotypic variability (van Dam et al. 2017).Despite the utility of GCNs in understanding biological systems, network inference is still...
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  5. Method: Dissecting multilayer cell–cell communications with signaling feedback loops from spatial transcriptomics data
    • Lulu Yan,
    • Jinyu Cheng,
    • Qing Nie,
    • and Xiaoqiang Sun
    Genome Res. June 2025 35: 1400-1414; Published in Advance April 22, 2025, doi:10.1101/gr.279857.124
    ...for dissecting multilayer ligand/receptor-target regulation and multicellular signaling circuits from ST data, which can advance understanding of the mechanistic and functional roles of spatial CCC.The coordinated activities of cells serve as fundamental building blocks for achieving the fate and function...
  6. Methods: Ab initio identification of functionally interacting pairs of cis-regulatory elements
    • Brad A. Friedman,
    • Michael B. Stadler,
    • Noam Shomron,
    • Ye Ding,
    • and Christopher B. Burge
    Genome Res. October 2008 18: 1643-1651; Published in Advance September 17, 2008, doi:10.1101/gr.080085.108
    ...Ab initio identification of functionally interacting pairs of cis -regulatory elements Brad A. Friedman 1 , 2 , 4 , 6 , Michael B. Stadler 1 , 5 , Noam Shomron 1 , Ye Ding 2 , and Christopher B. Burge 1 , 3 , 6 1...
  7. Methods: Genome-wide computational prediction of transcriptional regulatory modules reveals new insights into human gene expression
    • Mathieu Blanchette,
    • Alain R. Bataille,
    • Xiaoyu Chen,
    • Christian Poitras,
    • Josée Laganière,
    • Céline Lefèbvre,
    • Geneviève Deblois,
    • Vincent Giguère,
    • Vincent Ferretti,
    • Dominique Bergeron,
    • Benoit Coulombe,
    • and François Robert
    Genome Res. May 2006 16: 656-668; Published in Advance April 10, 2006, doi:10.1101/gr.4866006
    ...Genome-wide computational prediction of transcriptional regulatory modules reveals new insights into human gene expression Genome-wide cis -regulatory module predictions Mathieu Blanchette 1 , 5 , Alain R. Bataille 2 , Xiaoyu Chen 1 , Christian Poitras 2...
  8. Resource: Streamlined spatial and environmental expression signatures characterize the minimalist duckweed Wolffia australiana
    • Tom Denyer,
    • Pin-Jou Wu,
    • Kelly Colt,
    • Bradley W. Abramson,
    • Zhili Pang,
    • Pavel Solansky,
    • Allen Mamerto,
    • Tatsuya Nobori,
    • Joseph R. Ecker,
    • Eric Lam,
    • Todd P. Michael,
    • and Marja C.P. Timmermans
    Genome Res. July 2024 34: 1106-1120; Published in Advance July 1, 2024, doi:10.1101/gr.279091.124
    .... 2011), is specifically expressed in cells of this supercluster (Fig. 1D). Further, select basic helix–loop–helix (bHLH) and MYB TF genes linked to drought-stress responses are uniquely expressed in cells of the CA supercluster. These include MYB41 and MYB49, which are part of a regulatory circuit...
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  9. Method: ESICCC as a systematic computational framework for evaluation, selection, and integration of cell-cell communication inference methods
    • Jiaxin Luo,
    • Minghua Deng,
    • Xuegong Zhang,
    • and Xiaoqiang Sun
    Genome Res. October 2023 33: 1788-1805; Published in Advance October 12, 2023, doi:10.1101/gr.278001.123
    ...signaling pathways from databases to infer cell-cell communication, whereas MISTy and HoloNet deduce regulatory relationships between intracellular target genes and ligands or receptors without taking regulatory pathways into account. In addition, most of the L/R-target inference methods require...
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  10. Research: AP-1 subunits converge promiscuously at enhancers to potentiate transcription
    • Jungkyun Seo,
    • D. Dewran Koçak,
    • Luke C. Bartelt,
    • Courtney A. Williams,
    • Alejandro Barrera,
    • Charles A. Gersbach,
    • and Timothy E. Reddy
    Genome Res. April 2021 31: 538-550; Published in Advance March 5, 2021, doi:10.1101/gr.267898.120
    ...in vitro have suggested differences in TRE or CRE affinity (Isakova et al. 2017). Massively parallel reporter assay (MPRA) analyses have also shown that AP-1-mediated cis-regulatory activity depends on sequences beyond the core TRE (Chaudhari and Cohen 2018). It remains unresolved whether AP-1 subunits...
    OPEN ACCESS ARTICLE
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