Searching journal content for articles similar to Yanai and Hunter 19 (12): 2214.

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  1. Resource: A chromosome-scale epigenetic map of the Hydra genome reveals conserved regulators of cell state
    • Jack F. Cazet,
    • Stefan Siebert,
    • Hannah Morris Little,
    • Philip Bertemes,
    • Abby S. Primack,
    • Peter Ladurner,
    • Matthias Achrainer,
    • Mark T. Fredriksen,
    • R. Travis Moreland,
    • Sumeeta Singh,
    • Suiyuan Zhang,
    • Tyra G. Wolfsberg,
    • Christine E. Schnitzler,
    • Andreas D. Baxevanis,
    • Oleg Simakov,
    • Bert Hobmayer,
    • and Celina E. Juliano
    Genome Res. February 2023 33: 283-298; Published in Advance January 13, 2023, doi:10.1101/gr.277040.122
    ...and Martindale 2017b); and the target genes of developmentally significant TFs are at least partially conserved across the two clades (Münder et al. 2010; Gufler et al. 2018; Hartl et al. 2019). However, beyond these general similarities, little is known about cnidarian gene regulatory networks...
  2. Research: Independent evolution of transcript abundance and gene regulatory dynamics
    • Gat Krieger,
    • Offir Lupo,
    • Avraham A. Levy,
    • and Naama Barkai
    Genome Res. July 2020 30: 1000-1011; Published in Advance July 22, 2020, doi:10.1101/gr.261537.120
    ...of coexpression vectors within each species to define the nearest neighbors (NN), namely, pairs of genes with the most similar coexpression vector (Fig. 2D, bottom). As expected, these two control measures are highly correlated (R = 0.91) (Supplemental Fig. S2A). Thus, although in the between-species comparison...
  3. Resource: Transcription initiation mapping in 31 bovine tissues reveals complex promoter activity, pervasive transcription, and tissue-specific promoter usage
    • Daniel E. Goszczynski,
    • Michelle M. Halstead,
    • Alma D. Islas-Trejo,
    • Huaijun Zhou,
    • and Pablo J. Ross
    Genome Res. April 2021 31: 732-744; Published in Advance March 15, 2021, doi:10.1101/gr.267336.120
    ...with protein-coding and lncRNA genes. The diversity of analyzed tissues captured the expression of 18,312 previously annotated genes. However, no expression was detected for 5016 genes, likely reflecting the absence of embryonic/fetal developmental genes in our collection of tissues from juvenile/adult animals...
  4. Resource: An atlas of alternative splicing profiles and functional associations reveals new regulatory programs and genes that simultaneously express multiple major isoforms
    • Javier Tapial,
    • Kevin C.H. Ha,
    • Timothy Sterne-Weiler,
    • André Gohr,
    • Ulrich Braunschweig,
    • Antonio Hermoso-Pulido,
    • Mathieu Quesnel-Vallières,
    • Jon Permanyer,
    • Reza Sodaei,
    • Yamile Marquez,
    • Luca Cozzuto,
    • Xinchen Wang,
    • Melisa Gómez-Velázquez,
    • Teresa Rayon,
    • Miguel Manzanares,
    • Julia Ponomarenko,
    • Benjamin J. Blencowe,
    • and Manuel Irimia
    Genome Res. October 2017 27: 1759-1768; Published in Advance August 30, 2017, doi:10.1101/gr.220962.117
    ...profiles of AS events assembled to date. VastDB provides readily accessible quantitative information on the inclusion levels and functional associations of AS events detected in RNA-seq data from diverse vertebrate cell and tissue types, as well as developmental stages. The VastDB profiles reveal extensive...
  5. Resource: Genome-wide annotation of microRNA primary transcript structures reveals novel regulatory mechanisms
    • Tsung-Cheng Chang,
    • Mihaela Pertea,
    • Sungyul Lee,
    • Steven L. Salzberg,
    • and Joshua T. Mendell
    Genome Res. September 2015 25: 1401-1409; Published in Advance August 19, 2015, doi:10.1101/gr.193607.115
    .... 2009. MicroRNAs: target recognition and regulatory functions. Cell 136: 215–233. Baskerville S, Bartel DP. 2005.Microarray profiling ofmicroRNAs reveals frequent coexpression with neighboring miRNAs and host genes. RNA 11: 241–247. Cai X, Hagedorn CH, Cullen BR. 2004. Human microRNAs are processed from...
  6. Method: Discovery and assessment of conserved Pax6 target genes and enhancers
    • Pedro Coutinho,
    • Sofia Pavlou,
    • Shipra Bhatia,
    • Kevin J. Chalmers,
    • Dirk A. Kleinjan,
    • and Veronica van Heyningen
    Genome Res. August 2011 21: 1349-1359; Published in Advance May 26, 2011, doi:10.1101/gr.124115.111
    ...conserved direct targets of pax6. The procedure to identify pax6 target enhancers and associated genes is based on the screen of evolutionarily conserved noncoding genomic sequences from orthologous loci in zebrafish and human (ormouse). (B) The screens were performed usingmodels based on pax6 binding sites...
  7. Review: The superpowers of imprinting control regions
    • Bertille Montibus,
    • Franck Court,
    • and Philippe Arnaud
    Genome Res. January 2026 36: 1-19; Published in Advance December 10, 2025, doi:10.1101/gr.281215.125
    ...then, between 150 and 200 imprinted genes have been identified in humans and mice, with almost one-third of them conserved between these two species (Babak et al. 2008, 2015; Perez et al. 2015; Andergassen et al. 2017; Tucci et al. 2019). Most of these imprinted genes are organized in evolutionarily...
  8. Research: Core promoter T-blocks correlate with gene expression levels in C. elegans
    • Vladislav Grishkevich,
    • Tamar Hashimshony,
    • and Itai Yanai
    Genome Res. May 2011 21: 707-717; Published in Advance March 2, 2011, doi:10.1101/gr.113381.110
    ...conserved element identified byMEME is a periodic occurrence of three to five thymines (Fig. 1A). We named a single group of these neighboring thymines a ‘‘T-block.’’ T-blocks are widely distributed in the ; ;42% of C. elegans genes contain the motif (Supplemental Table S1). The five motifs identified in C...
  9. Method: Polyomino reconstructs spatial transcriptomic profiles with single-cell resolution via a region-allocation method
    • Quanyou Cai,
    • Lihui Lin,
    • Xin Liu,
    • and Jiekai Chen
    Genome Res. November 2025 35: 2513-2526; Published in Advance October 22, 2025, doi:10.1101/gr.280532.125
    ...in reconstructing spatial transcriptomic profiles in comparison with deconvolution-based approaches such as cell2location (Kleshchevnikov et al. 2022) and RCTD (Cable et al. 2022). Based on the high-resolution seqFISH+ data set, we simulated spatial spot data by aggregating gene expression profiles from neighboring...
    OPEN ACCESS ARTICLE
  10. 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
    ...that these TFBSs in the 3′ region of genes could give rise to antisense transcription that would interfere with sense transcription ( Katayama et al. 2005 ). Recent analysis of the transcriptome of mammalian s revealed that a large proportion of all transcripts detected represent noncoding transcription ( Kapranov...
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