Searching journal content for articles similar to Gitter et al. 23 (2): 365.

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  1. Research: Meta-analysis of activated neurons reveals dynamic regulation of diverse classes of alternative splicing
    • Keegan S. Krick,
    • Marissa Maroni,
    • Erica Korb,
    • Kristen W. Lynch,
    • and Elizabeth A. Heller
    Genome Res. June 2025 35: 1301-1312; Published in Advance April 24, 2025, doi:10.1101/gr.280082.124
    ..., and it functions by initiating conserved calcium-dependent signaling cascades to activate activity-dependent gene networks (West et al. 2001; Rienecker et al. 2020, 2022). Despite this, the paradigm cannot recapitulate the temporal kinetics of variable stimuli or uncouple localized depolarization, for example...
  2. Research: Kinetic networks identify TWIST2 as a key regulatory node in adipogenesis
    • Arun B. Dutta,
    • Daniel S. Lank,
    • Roza K. Przanowska,
    • Piotr Przanowski,
    • Lixin Wang,
    • Bao Nguyen,
    • Ninad M. Walavalkar,
    • Fabiana M. Duarte,
    • and Michael J. Guertin
    Genome Res. March 2023 33: 314-331; Published in Advance February 21, 2023, doi:10.1101/gr.277559.122
    ...potential upstream REs and regulatory TFs. Only by combining multiple approaches can one fully capture the signaling dynamics driving transcription regulatory cascades.Differential TF activity defines cell identity and drives cellular responses to environmental stimuli by enforcing gene regulatory programs...
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  3. Research: Linking the dynamics of chromatin occupancy and transcription with predictive models
    • Trung Q. Tran,
    • Heather K. MacAlpine,
    • Vinay Tripuraneni,
    • Sneha Mitra,
    • David M. MacAlpine,
    • and Alexander J. Hartemink
    Genome Res. June 2021 31: 1035-1046; Published in Advance April 23, 2021, doi:10.1101/gr.267237.120
    ...configurations. Understanding how changing chromatin configurations associate with transcription remains a fundamental research problem. We sought to characterize at high spatiotemporal resolution the dynamic interplay between transcription and chromatin in response to cadmium stress. Whereas gene regulatory...
  4. Research: Snake venom gene expression is coordinated by novel regulatory architecture and the integration of multiple co-opted vertebrate pathways
    • Blair W. Perry,
    • Siddharth S. Gopalan,
    • Giulia I.M. Pasquesi,
    • Drew R. Schield,
    • Aundrea K. Westfall,
    • Cara F. Smith,
    • Ivan Koludarov,
    • Paul T. Chippindale,
    • Mark W. Pellegrino,
    • Edward B. Chuong,
    • Stephen P. Mackessy,
    • and Todd A. Castoe
    Genome Res. June 2022 32: 1058-1073; Published in Advance June 1, 2022, doi:10.1101/gr.276251.121
    ...by venom depletion (ERK signaling) and further enhanced by cellular stress responses (UPR signaling). This overarching regulatory network involves many TFs previously speculated to be involved in venom regulation in different gene families and species, and links preliminary findings from independent...
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  5. Research: A KMT2A-AFF1 gene regulatory network highlights the role of core transcription factors and reveals the regulatory logic of key downstream target genes
    • Joe R. Harman,
    • Ross Thorne,
    • Max Jamilly,
    • Marta Tapia,
    • Nicholas T. Crump,
    • Siobhan Rice,
    • Ryan Beveridge,
    • Edward Morrissey,
    • Marella F.T.R. de Bruijn,
    • Irene Roberts,
    • Anindita Roy,
    • Tudor A. Fulga,
    • and Thomas A. Milne
    Genome Res. July 2021 31: 1159-1173; Published in Advance June 4, 2021, doi:10.1101/gr.268490.120
    ...: thomas.milne@imm.ox.ac.ukAbstractRegulatory interactions mediated by transcription factors (TFs) make up complex networks that control cellular behavior. Fully understanding these gene regulatory networks (GRNs) offers greater insight into the consequences of disease-causing perturbations than can...
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  6. Research: Genome-wide analysis of plant miRNA action clarifies levels of regulatory dynamics across developmental contexts
    • Xiaoli Ma,
    • Tom Denyer,
    • Marie Javelle,
    • Antje Feller,
    • and Marja C.P. Timmermans
    Genome Res. May 2021 31: 811-822; Published in Advance April 16, 2021, doi:10.1101/gr.270918.120
    ...decisions, carefully coordinated in space and time by complex networks of transcription factors (TFs) that convert inputs from positional signals into differential patterns of gene expression. The expression of central TF network components is itself dynamic and precisely regulated to ensure robustness...
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  7. Research: Transcriptional regulatory dynamics drive coordinated metabolic and neural response to social challenge in mice
    • Michael C. Saul,
    • Christopher H. Seward,
    • Joseph M. Troy,
    • Huimin Zhang,
    • Laura G. Sloofman,
    • Xiaochen Lu,
    • Patricia A. Weisner,
    • Derek Caetano-Anolles,
    • Hao Sun,
    • Sihai Dave Zhao,
    • Sriram Chandrasekaran,
    • Saurabh Sinha,
    • and Lisa Stubbs
    Genome Res. June 2017 27: 959-972; Published in Advance March 29, 2017, doi:10.1101/gr.214221.116
    ...transcription and the enrichment of TFs and chromatin modifiers in the L cluster imply that transcriptional regulation is a core component of the network, a prediction examined further below. Transcriptional regulatory dynamics underlie the transcriptomic response to intruder Transcriptional regulatory network...
  8. Research: Temporal mapping of CEBPA and CEBPB binding during liver regeneration reveals dynamic occupancy and specific regulatory codes for homeostatic and cell cycle gene batteries
    • Janus Schou Jakobsen,
    • Johannes Waage,
    • Nicolas Rapin,
    • Hanne Cathrine Bisgaard,
    • Fin Stolze Larsen,
    • and Bo Torben Porse
    Genome Res. April 2013 23: 592-603; Published in Advance February 12, 2013, doi:10.1101/gr.146399.112
    ...Temporal mapping of CEBPA and CEBPB binding during liver regeneration reveals dynamic occupancy and specific regulatory codes for homeostatic and cell cycle gene batteries Janus Schou Jakobsen 1 , 2 , 3 , 7 , Johannes Waage 1 , 2 , 3 , 4 , Nicolas Rapin...
  9. Method: Model-driven mapping of transcriptional networks reveals the circuitry and dynamics of virulence regulation
    • Ezekiel J. Maier,
    • Brian C. Haynes,
    • Stacey R. Gish,
    • Zhuo A. Wang,
    • Michael L. Skowyra,
    • Alyssa L. Marulli,
    • Tamara L. Doering,
    • and Michael R. Brent
    Genome Res. May 2015 25: 690-700; Published in Advance February 2, 2015, doi:10.1101/gr.184101.114
    ...Model-driven mapping of transcriptional networks reveals the circuitry and dynamics of virulence regulation Ezekiel J. Maier 1 , 2 , 5 , Brian C. Haynes 1 , 2 , 5 , 6 , Stacey R. Gish 3 , Zhuo A. Wang 3 , Michael L. Skowyra 3...
  10. Research: Complex expression dynamics and robustness in C. elegans insulin networks
    • Ashlyn D. Ritter,
    • Yuan Shen,
    • Juan Fuxman Bass,
    • Sankarganesh Jeyaraj,
    • Bart Deplancke,
    • Arnab Mukhopadhyay,
    • Jian Xu,
    • Monica Driscoll,
    • Heidi A. Tissenbaum,
    • and Albertha J.M. Walhout
    Genome Res. June 2013 23: 954-965; Published in Advance March 28, 2013, doi:10.1101/gr.150466.112
    ...Complex expression dynamics and robustness in C. elegans insulin networks Ashlyn D. Ritter 1 , 2 , 3 , Yuan Shen 2 , 3 , 5 , Juan Fuxman Bass 1 , 3 , Sankarganesh Jeyaraj 2 , 3 , 6 , Bart Deplancke 2 , 3 , 7 , Arnab...
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