Searching journal content for articles similar to Chang et al. 16 (3): 405.

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  1. Research: Transcription and potential functions of a novel XIST isoform in male peripheral glia
    • Kevin S. O'Leary,
    • Meng-Yen Li,
    • Kevyn Jackson,
    • Lijie Shi,
    • Elena Ezhkova,
    • Bernice E. Morrow,
    • and Deyou Zheng
    Genome Res. February 2026 36: 257-274; Published in Advance December 12, 2025, doi:10.1101/gr.280832.125
    ..., SOX10, TCF4, ETS1, SREBF1, CEBPB, KLF2, and ETV5) were higher in either skeletal muscle or heart nonmyelinating Schwann cells. Analysis of the transcription regulatory programs by the SCENIC software predicted that FOXO1 (and YY1) could regulate XIST in heart and skeletal muscle Schwann cells...
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  2. Research: Mapping multitissue regulatory variants reveals a liver-centric coexpression network associated with duck egg-laying performance
    • Yang Xi,
    • Jingjing Qi,
    • Zhao Yang,
    • Yutian Zeng,
    • Huicong Zhang,
    • Qiuyu Tao,
    • Mengru Xu,
    • Anqi Huang,
    • Shenqiang Hu,
    • Chunchun Han,
    • Lili Bai,
    • Jiwei Hu,
    • Jiwen Wang,
    • Liang Li,
    • Lingzhao Fang,
    • and Hehe Liu
    Genome Res. October 2025 35: 2211-2225; Published in Advance September 10, 2025, doi:10.1101/gr.280345.124
    ...an individual in the test set. The x- and y-axes represent standardized actual and predicted egg production, respectively. (D) Feature importance ranking in the predictive model based on multilayer regulatory features. The x-axis indicates feature contribution (gain), and the y-axis shows the molecular...
  3. Research: Genomic origin, fragmentomics, and transcriptional properties of long cell-free DNA molecules in human plasma
    • Huiwen Che,
    • Peiyong Jiang,
    • L.Y. Lois Choy,
    • Suk Hang Cheng,
    • Wenlei Peng,
    • Rebecca W.Y. Chan,
    • Jing Liu,
    • Qing Zhou,
    • W.K. Jacky Lam,
    • Stephanie C.Y. Yu,
    • So Ling Lau,
    • Tak Y. Leung,
    • John Wong,
    • Vincent Wai-Sun Wong,
    • Grace L.H. Wong,
    • Stephen L. Chan,
    • K.C. Allen Chan,
    • and Y.M. Dennis Lo
    Genome Res. February 2024 34: 189-200; Published in Advance February 26, 2024, doi:10.1101/gr.278556.123
    ...different genomic elements, including euchromatin and heterochromatin. We aggregated cfDNA data generated by SMRT or ONT sequencing to profile the genomic representations and studied the correlation between long cfDNA molecules and gene transcriptional activity. We examined end frequencies of long molecules...
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  4. Research: Joint actions of diverse transcription factor families establish neuron-type identities and promote enhancer selectivity
    • Angela Jimeno-Martín,
    • Erick Sousa,
    • Rebeca Brocal-Ruiz,
    • Noemi Daroqui,
    • Miren Maicas,
    • and Nuria Flames
    Genome Res. March 2022 32: 459-473; Published in Advance January 24, 2022, doi:10.1101/gr.275623.121
    ...de la Salud, Universidad San Jorge, 50830, Villanueva de Gállego, Zaragoza, Spain Corresponding author: nflames@ibv.csic.esAbstractTo systematically investigate the complexity of neuron specification regulatory networks, we performed an RNA interference (RNAi) screen against all 875 transcription...
  5. Research: Sense–antisense miRNA pairs constitute an elaborate reciprocal regulatory circuit
    • Yulong Song,
    • Lishi Li,
    • Wenbing Yang,
    • Qiang Fu,
    • Wanying Chen,
    • Zeng Fang,
    • Wen Li,
    • Nannan Gu,
    • and Rui Zhang
    Genome Res. May 2020 30: 661-672; Published in Advance May 18, 2020, doi:10.1101/gr.257121.119
    ...targets hundreds of protein-coding genes via partially complementary base pairing (Bushati and Cohen 2007; Bartel 2009). Despite the importance of miRNAs, their antisense transcription has not been systematically investigated. Stranded RNA-seq, which preserves transcript strandedness information, has been...
  6. Research: Global regulatory features of alternative splicing across tissues and within the nervous system of C. elegans
    • Bina Koterniak,
    • Pallavi P. Pilaka,
    • Xicotencatl Gracida,
    • Lisa-Marie Schneider,
    • Iva Pritišanac,
    • Yun Zhang,
    • and John A. Calarco
    Genome Res. December 2020 30: 1766-1780; Published in Advance October 30, 2020, doi:10.1101/gr.267328.120
    ...value measurements. (Right) The log2-transformed fold change over median ratios for the same genes with splicing differences, ordered according to panel on the left. (C) Gene Ontology (GO) enrichment analysis of genes with steady-state transcript level differences from heatmap in A. Overrepresentation...
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  7. Resource: Systematic detection of brain protein-coding genes under positive selection during primate evolution and their roles in cognition
    • Guillaume Dumas,
    • Simon Malesys,
    • and Thomas Bourgeron
    Genome Res. March 2021 31: 484-496; Published in Advance January 13, 2021, doi:10.1101/gr.262113.120
    ...author: guillaume.dumas@centraliens.netAbstractThe human brain differs from that of other primates, but the genetic basis of these differences remains unclear. We investigated the evolutionary pressures acting on almost all human protein-coding genes (N = 11,667; 1:1 orthologs in primates) based...
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  8. Method: A novel k-mer set memory (KSM) motif representation improves regulatory variant prediction
    • Yuchun Guo,
    • Kevin Tian,
    • Haoyang Zeng,
    • Xiaoyun Guo,
    • and David Kenneth Gifford
    Genome Res. June 2018 28: 891-900; Published in Advance April 13, 2018, doi:10.1101/gr.226852.117
    ...consists of four steps (Fig. 2A): Step 1: KMAC selects a set of enriched k-mers and clusters them. K-mers with k exact bases and from 0 to g gapped bases are KSM motif model for regulatory variant prediction Genome Research 893 www..org considered. Themaximumnumber of gaps g, which can be specified...
  9. Method: Predictive regulatory models in Drosophila melanogaster by integrative inference of transcriptional networks
    • Daniel Marbach,
    • Sushmita Roy,
    • Ferhat Ay,
    • Patrick E. Meyer,
    • Rogerio Candeias,
    • Tamer Kahveci,
    • Christopher A. Bristow,
    • and Manolis Kellis
    Genome Res. July 2012 22: 1334-1349; Published in Advance March 28, 2012, doi:10.1101/gr.127191.111
    ...Predictive regulatory models in Drosophila melanogaster by integrative inference of transcriptional networks Daniel Marbach 1 , 2 , 7 , Sushmita Roy 1 , 2 , 3 , 7 , Ferhat Ay 1 , 2 , 4 , 5 , Patrick E. Meyer 1 , 2 , 6...
  10. Method: Uncovering cis-regulatory sequence requirements for context-specific transcription factor binding
    • J. Omar Yáñez-Cuna,
    • Huy Q. Dinh,
    • Evgeny Z. Kvon,
    • Daria Shlyueva,
    • and Alexander Stark
    Genome Res. October 2012 22: 2018-2030; Published in Advance April 25, 2012, doi:10.1101/gr.132811.111
    ...Uncovering cis -regulatory sequence requirements for context-specific transcription factor binding J. Omar Yáñez-Cuna 1 , Huy Q. Dinh 2 , 3 , 4 , Evgeny Z. Kvon 1 , 4 , Daria Shlyueva 1 , 4 and Alexander Stark 1 , 5...
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