Searching journal content for articles similar to Narlikar et al. 20 (3): 381.

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  1. Resource: Genome-wide identification of tandem repeats associated with splicing variation across 49 tissues in humans
    • Kohei Hamanaka,
    • Daisuke Yamauchi,
    • Eriko Koshimizu,
    • Kei Watase,
    • Kaoru Mogushi,
    • Kinya Ishikawa,
    • Hidehiro Mizusawa,
    • Naomi Tsuchida,
    • Yuri Uchiyama,
    • Atsushi Fujita,
    • Kazuharu Misawa,
    • Takeshi Mizuguchi,
    • Satoko Miyatake,
    • and Naomichi Matsumoto
    Genome Res. March 2023 33: 435-447; Published in Advance March 27, 2023, doi:10.1101/gr.277335.122
    ...map spl-TRs in a -wide manner across tissues throughout the whole body by using the Genotype-Tissue expression (GTEx) v8 data set, a population-scale resource of whole- sequencing (WGS) and RNA sequencing (RNA-seq).ResultsGenome-wide identification of spl-TRs across 49 tissuesWe discovered cis spl...
  2. Research: Genome-wide evaluation of the effect of short tandem repeat variation on local DNA methylation
    • Alejandro Martin-Trujillo,
    • Paras Garg,
    • Nihir Patel,
    • Bharati Jadhav,
    • and Andrew J. Sharp
    Genome Res. February 2023 33: 184-196; Published in Advance December 28, 2022, doi:10.1101/gr.277057.122
    ...these questions, we first analyzed two independent data sets comprising PCR-free whole- sequencing (WGS) and -wide DNA methylation levels derived from whole-blood samples in 245 (discovery cohort) and 484 individuals (replication cohort). Using genotypes for 131,635 polymorphic STRs derived from WGS using Hip...
  3. Method: Genome-wide dynamics of RNA synthesis, processing, and degradation without RNA metabolic labeling
    • Mattia Furlan,
    • Eugenia Galeota,
    • Nunzio Del Gaudio,
    • Erik Dassi,
    • Michele Caselle,
    • Stefano de Pretis,
    • and Mattia Pelizzola
    Genome Res. October 2020 30: 1492-1507; Published in Advance September 25, 2020, doi:10.1101/gr.260984.120
    ...under specific conditions. Genes altered in T cell samples were associated with the regulation of T cell number and proliferation and with immunodeficiency. Genes altered in heart samples were associated with cardiac hypertrophy, abnormal contractility, and cardiomyopathy. Indeed, a subset...
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  4. Research: Genome-wide analysis of polymerase III–transcribed Alu elements suggests cell-type–specific enhancer function
    • Xiao-Ou Zhang,
    • Thomas R. Gingeras,
    • and Zhiping Weng
    Genome Res. September 2019 29: 1402-1414; Published in Advance August 14, 2019, doi:10.1101/gr.249789.119
    ...window Figure 1. Genome-wide identification of expressed Alu elements using RAMPAGE data. (A) A computational pipeline to call RAMPAGE peaks and annotate expressed Alu elements. Paired-end RAMPAGE reads (R1 and R2, black; N, read pairs in total) with uniquely mapping R2 reads were first clustered to call...
  5. Research: Enhancers display constrained sequence flexibility and context-specific modulation of motif function
    • Franziska Reiter,
    • Bernardo P. de Almeida,
    • and Alexander Stark
    Genome Res. March 2023 33: 346-358; Published in Advance March 20, 2023, doi:10.1101/gr.277246.122
    ...Vienna, Austria; 3Medical University of Vienna, Vienna BioCenter, 1030 Vienna, Austria ↵4 These authors contributed equally to this work. Corresponding author: stark@starklab.orgAbstractThe information about when and where each gene is to be expressed is mainly encoded in the DNA sequence of enhancers...
  6. Resource: Genome-wide identification and characterization of transcription start sites and promoters in the tunicate Ciona intestinalis
    • Rui Yokomori,
    • Kotaro Shimai,
    • Koki Nishitsuji,
    • Yutaka Suzuki,
    • Takehiro G. Kusakabe,
    • and Kenta Nakai
    Genome Res. January 2016 26: 140-150; Published in Advance December 14, 2015, doi:10.1101/gr.184648.114
    ...Genome-wide identification and characterization of transcription start sites and promoters in the tunicate Ciona intestinalis Rui Yokomori 1 , Kotaro Shimai 2 , Koki Nishitsuji 3 , Yutaka Suzuki 1 , Takehiro G. Kusakabe 2 , 4...
  7. Research: Genome-wide specificity of DNA binding, gene regulation, and chromatin remodeling by TALE- and CRISPR/Cas9-based transcriptional activators
    • Lauren R. Polstein,
    • Pablo Perez-Pinera,
    • D. Dewran Kocak,
    • Christopher M. Vockley,
    • Peggy Bledsoe,
    • Lingyun Song,
    • Alexias Safi,
    • Gregory E. Crawford,
    • Timothy E. Reddy,
    • and Charles A. Gersbach
    Genome Res. August 2015 25: 1158-1169; Published in Advance May 29, 2015, doi:10.1101/gr.179044.114
    ...-based activators (Fig. 2D).View larger version: In this window In a new window Figure 2. Genome-wide specificity of TALE-VP64 and dCas9-VP64-mediated gene activation. RNA-seq was performed on samples co-transfected with a set of four TALE-VP64 expression plasmids targeting either IL1RN (A) or HBG1/2 (C...
  8. Research: Genome-wide phosphoacetylation of histone H3 at Drosophila enhancers and promoters
    • Wendy A. Kellner,
    • Edward Ramos,
    • Kevin Van Bortle,
    • Naomi Takenaka,
    • and Victor G. Corces
    Genome Res. June 2012 22: 1081-1088; Published in Advance April 16, 2012, doi:10.1101/gr.136929.111
    ...Genome-wide phosphoacetylation of histone H3 at Drosophila enhancers and promoters Wendy A. Kellner , Edward Ramos , Kevin Van Bortle , Naomi Takenaka and Victor G. Corces 1 Department of Biology, Emory University, Atlanta...
  9. Review: Advancing genomic technologies and clinical awareness accelerates discovery of disease-associated tandem repeat sequences
    • Terence Gall-Duncan,
    • Nozomu Sato,
    • Ryan K.C. Yuen,
    • and Christopher E. Pearson
    Genome Res. January 2022 32: 1-27; Published in Advance December 29, 2021, doi:10.1101/gr.269530.120
    ...to begin to enhance identifying disease-causing TR expansions (Fig. 1).Bioinformatic algorithms are unleashing the potential of NGS for repeat disease discoveryApplication of NGS approaches in this field was first published in 2011 in one of two papers that reported the discovery of the GGGGCC repeat...
  10. Method: Genome-wide identification of conserved regulatory function in diverged sequences
    • Leila Taher,
    • David M. McGaughey,
    • Samantha Maragh,
    • Ivy Aneas,
    • Seneca L. Bessling,
    • Webb Miller,
    • Marcelo A. Nobrega,
    • Andrew S. McCallion,
    • and Ivan Ovcharenko
    Genome Res. July 2011 21: 1139-1149; Published in Advance May 31, 2011, doi:10.1101/gr.119016.110
    ...Genome-wide identification of conserved regulatory function in diverged sequences Leila Taher 1 , David M. McGaughey 2 , Samantha Maragh 2 , 3 , Ivy Aneas 4 , Seneca L. Bessling 2 , Webb Miller 5 , Marcelo A. Nobrega 4...
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