Searching journal content for articles similar to Gentles and Karlin 11 (4): 540.

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  1. Method: High-throughput and genome-scale targeted mutagenesis using CRISPR in a nonmodel multicellular organism, Bombyx mori
    • Sanyuan Ma,
    • Tong Zhang,
    • Ruolin Wang,
    • Pan Wang,
    • Yue Liu,
    • Jiasong Chang,
    • Aoming Wang,
    • Xinhui Lan,
    • Le Sun,
    • Hao Sun,
    • Run Shi,
    • Wei Lu,
    • Dan Liu,
    • Na Zhang,
    • Wenbo Hu,
    • Xiaogang Wang,
    • Weiqing Xing,
    • Ling Jia,
    • and Qingyou Xia
    Genome Res. January 2024 34: 134-144; Published in Advance January 8, 2024, doi:10.1101/gr.278297.123
    ..., the most efficient germline transformation platform is piggyBac system, which has been proved and widely used for over 20 years (Ma et al. 2014a; Chang et al. 2020a). piggyBac transposon can drive gene delivery in a wide range of eukaryotes, so our strategy and results also lay the foundation for applying...
  2. Research: Genome-scale analysis of metazoan replication origins reveals their organization in specific but flexible sites defined by conserved features
    • Christelle Cayrou,
    • Philippe Coulombe,
    • Alice Vigneron,
    • Slavica Stanojcic,
    • Olivier Ganier,
    • Isabelle Peiffer,
    • Eric Rivals,
    • Aurore Puy,
    • Sabine Laurent-Chabalier,
    • Romain Desprat,
    • and Marcel Méchali
    Genome Res. September 2011 21: 1438-1449; Published in Advance July 12, 2011, doi:10.1101/gr.121830.111
    ...results demonstrate thatmetazoanOris are in large excess relative to their standard use, and computational simulations suggest that flexible Oris are clustered in groups that define the replicons, where activation of one Ori silences the others in the same group. Results Genome-scale mapping of DNA...
  3. LETTER: Genome-scale analysis of Streptomyces coelicolor A3(2) metabolism
    • Irina Borodina,
    • Preben Krabben,
    • and Jens Nielsen
    Genome Res. June 2005 15: 820-829; doi:10.1101/gr.3364705
    ...Genome-scale analysis of Streptomyces coelicolor A3(2) metabolism Irina Borodina 1 , Preben Krabben 2 , and Jens Nielsen 1 , 3 1 Center for Microbial Biotechnology, BioCentrum-DTU, Technical University of Denmark, DK-2800 Lyngby, Denmark...
  4. LETTER: Genome-Scale Reconstruction of the Saccharomyces cerevisiae Metabolic Network
    • Jochen Förster,
    • Iman Famili,
    • Patrick Fu,
    • Bernhard Ø. Palsson,
    • and Jens Nielsen
    Genome Res. February 1, 2003 13: 244-253; doi:10.1101/gr.234503
    ...Genome-Scale Reconstruction of the Saccharomyces cerevisiae Metabolic Network Jochen Förster 1 , 3 , 4 , Iman Famili 2 , 4 , Patrick Fu 2 , Bernhard Ø. Palsson 2 , and Jens Nielsen 1 , 5 1Center for Process...
  5. LETTER: Reconstruction and Validation of Saccharomyces cerevisiae iND750, a Fully Compartmentalized Genome-Scale Metabolic Model
    • Natalie C. Duarte,
    • Markus J. Herrgård,
    • and Bernhard Ø. Palsson
    Genome Res. July 2004 14: 1298-1309; Published in Advance June 14, 2004, doi:10.1101/gr.2250904
    ...Reconstruction and Validation of Saccharomyces cerevisiae iND750, a Fully Compartmentalized Genome-Scale Metabolic Model Natalie C. Duarte 1 , 3 , Markus J. Herrgård 1 , 2 , 3 , and Bernhard Ø. Palsson 1 , 4 1 Department...
  6. 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
    ...sitesA eukaryotic gene typically consists of regulatory elements such as distal enhancers, which can act over long distances; a proximal promoter containing key TF binding sites; a core promoter surrounding the transcription start site (TSS) where the preinitiation complex assembles, followed...
    OPEN ACCESS ARTICLE
  7. Research: Synergistic regulation by H3K36 and H3K27 methylation defines the chromatin landscape to control virulence and secondary metabolism in a fungal pathogen
    • Xingmin Han,
    • Chenghui Xu,
    • Yiyi Ren,
    • Meiling Guo,
    • Jiayue Yan,
    • Xuan Wang,
    • Chao Liu,
    • Qin Gu,
    • Xing-Xing Shen,
    • Zhonghua Ma,
    • and Yun Chen
    Genome Res. November 2025 35: 2472-2487; Published in Advance October 14, 2025, doi:10.1101/gr.280560.125
    ...: chenyun0927@zju.edu.cnAbstractHistone methylation, catalyzed by SET domain-containing lysine methyltransferases, is a conserved epigenetic mechanism regulating gene expression in eukaryotes. However, the evolutionary dynamics of SET domain proteins and their functional interplay in fungi remain poorly...
  8. Research: Atypical epigenetic and small RNA control of degenerated transposons and their fragments in clonally reproducing Spirodela polyrhiza
    • Rodolphe Dombey,
    • Daniel Buendía-Ávila,
    • Verónica Barragán-Borrero,
    • Laura Diezma-Navas,
    • Arturo Ponce-Mañe,
    • José Mario Vargas-Guerrero,
    • Rana Elias,
    • and Arturo Marí-Ordóñez
    Genome Res. March 2025 35: 522-544; Published in Advance March 4, 2025, doi:10.1101/gr.279532.124
    ...of silencing mechanisms that exist in plants and the importance of using disparate model species to discover these mechanisms.Transposable elements (TEs), or transposons, are mobile genetic elements that can change location and generate new copies in their host s. As a result, TEs populate eukaryotic s and can...
    OPEN ACCESS ARTICLE
  9. Method: Inferring and comparing metabolism across heterogeneous sets of annotated genomes using AuCoMe
    • Arnaud Belcour,
    • Jeanne Got,
    • Méziane Aite,
    • Ludovic Delage,
    • Jonas Collén,
    • Clémence Frioux,
    • Catherine Leblanc,
    • Simon M. Dittami,
    • Samuel Blanquart,
    • Gabriel V. Markov,
    • and Anne Siegel
    Genome Res. June 2023 33: 972-987; Published in Advance July 19, 2023, doi:10.1101/gr.277056.122
    ...distant algae, underlining the potential of AuCoMe to accelerate the broad exploration of metabolic evolution across the tree of life.The comparison of genomic data gave rise to today's view of the three domains of life: bacteria, archaea, and eukaryotes, which are divided into several supergroups (Burki...
  10. Research: Global characterization of somatic mutations and DNA methylation changes during vegetative propagation in strawberries
    • Shaoqiang Hu,
    • Xiangguo Zeng,
    • Yuguo Liu,
    • Yongping Li,
    • Minghao Qu,
    • Wen-Biao Jiao,
    • Yongchao Han,
    • and Chunying Kang
    Genome Res. October 2024 34: 1582-1594; Published in Advance October 15, 2024, doi:10.1101/gr.279378.124
    ..., and the mutation frequency varies among the subs. Our study has systematically characterized the genetic and epigenetic variants in regenerated woodland strawberry plants and different individuals of the same strawberry cultivar, providing an accurate assessment of somatic mutations at the genomic scale...
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