Searching journal content for articles similar to Viñuela et al. 20 (7): 929.

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  1. Research: Genome-wide patterns of selection–drift variation strongly associate with organismal traits across the green plant lineage
    • Kavitha Uthanumallian,
    • Andrea Del Cortona,
    • Susana M. Coelho,
    • Olivier De Clerck,
    • Sebastian Duchene,
    • and Heroen Verbruggen
    Genome Res. August 2024 34: 1130-1139; Published in Advance August 29, 2024, doi:10.1101/gr.279002.124
    ...Genome-wide patterns of selection–drift variation strongly associate with organismal traits across the green plant lineage Kavitha Uthanumallian1, Andrea Del Cortona2, Susana M. Coelho3, Olivier De Clerck2, Sebastian Duchene4,5 and Heroen Verbruggen1,6 1Melbourne Integrative Genomics, School of Bio...
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  2. Research: Genome-wide profiling reveals functional interplay of DNA sequence composition, transcriptional activity, and nucleosome positioning in driving DNA supercoiling and helix destabilization in C. elegans
    • Kristina Krassovsky,
    • Rajarshi P. Ghosh,
    • and Barbara J. Meyer
    Genome Res. July 2021 31: 1187-1202; Published in Advance June 24, 2021, doi:10.1101/gr.270082.120
    ...overwind or underwind DNA, creating DNA supercoils (Kouzine and Levens 2007). Supercoils can, in turn, induce formation of single-stranded DNA (ssDNA, hereafter SS DNA) or other non-B DNA structures.Genome-wide mapping of alternative DNA structures in cell lines and computational predictions in s suggested...
  3. Research: A low-abundance class of Dicer-dependent siRNAs produced from a variety of features in C. elegans
    • Thiago L. Knittel,
    • Brooke E. Montgomery,
    • Alex J. Tate,
    • Ennis W. Deihl,
    • Anastasia S. Nawrocki,
    • Frederic J. Hoerndli,
    • and Taiowa A. Montgomery
    Genome Res. December 2024 34: 2203-2216; Published in Advance December 2, 2024, doi:10.1101/gr.279083.124
    ...). Nonetheless, even at low abundance, they could have important roles in gene regulation and thus their identification would be an important step toward a more complete understanding of the small RNA landscape of C. elegans. In this study, our aim was to identity and characterize these siRNAs in the context...
  4. Research: Natural variation in C. elegans short tandem repeats
    • Gaotian Zhang,
    • Ye Wang,
    • and Erik C. Andersen
    Genome Res. October 2022 32: 1852-1861; Published in Advance October 4, 2022, doi:10.1101/gr.277067.122
    ...across wild C. elegans strains.ResultsGenome-wide profiling of STR variation in C. elegansTo investigate the natural variation of C. elegans STRs, we first identified 31,991 reference STRs in the C. elegans reference (Table 1; Supplemental Table S1). These STRs comprise motif lengths of 1–6 bp...
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  5. Research: A genome-wide transcriptome and translatome analysis of Arabidopsis transposons identifies a unique and conserved genome expression strategy for Ty1/Copia retroelements
    • Stefan Oberlin,
    • Alexis Sarazin,
    • Clément Chevalier,
    • Olivier Voinnet,
    • and Arturo Marí-Ordóñez
    Genome Res. September 2017 27: 1549-1562; Published in Advance August 7, 2017, doi:10.1101/gr.220723.117
    ...and transcriptionally active transposons in A. thaliana is illustrated by our comprehensive analysis of the cotranscriptional and translational features of Ty1/Copia elements, a family of young and active retroelements in plant s, and how such features impact their biology. Genome-wide transcript profiling revealed...
  6. Method: Accurate typing of short tandem repeats from genome-wide sequencing data and its applications
    • Arkarachai Fungtammasan,
    • Guruprasad Ananda,
    • Suzanne E. Hile,
    • Marcia Shu-Wei Su,
    • Chen Sun,
    • Robert Harris,
    • Paul Medvedev,
    • Kristin Eckert,
    • and Kateryna D. Makova
    Genome Res. May 2015 25: 736-749; Published in Advance March 30, 2015, doi:10.1101/gr.185892.114
    ...STRs with consecutive repeat numbers. Applying our model and pipeline to Illumina sequencing data with 100-bp reads, we could confidently genotype several disease-related long trinucleotide STRs. Utilizing this pipeline, for the first time we determined the genome-wide STR germline mutation rate from...
  7. Method: Genome-wide nucleosome map and cytosine methylation levels of an ancient human genome
    • Jakob Skou Pedersen,
    • Eivind Valen,
    • Amhed M. Vargas Velazquez,
    • Brian J. Parker,
    • Morten Rasmussen,
    • Stinus Lindgreen,
    • Berit Lilje,
    • Desmond J. Tobin,
    • Theresa K. Kelly,
    • Søren Vang,
    • Robin Andersson,
    • Peter A. Jones,
    • Cindi A. Hoover,
    • Alexei Tikhonov,
    • Egor Prokhortchouk,
    • Edward M. Rubin,
    • Albin Sandelin,
    • M. Thomas P. Gilbert,
    • Anders Krogh,
    • Eske Willerslev,
    • and Ludovic Orlando
    Genome Res. March 2014 24: 454-466; Published in Advance December 3, 2013, doi:10.1101/gr.163592.113
    ...Genome-wide nucleosome map and cytosine methylation levels of an ancient human genome Jakob Skou Pedersen 1 , 14 , 15 , Eivind Valen 2 , 3 , 14 , Amhed M. Vargas Velazquez 4 , Brian J. Parker 3 , Morten Rasmussen 4 , 5 , Stinus...
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  8. Method: Characterization of meiotic recombination intermediates through gene knockouts in founder hybrid mice
    • Benjamin Davies,
    • Gang Zhang,
    • Daniela Moralli,
    • Samy Alghadban,
    • Daniel Biggs,
    • Chris Preece,
    • Peter Donnelly,
    • and Anjali Gupta Hinch
    Genome Res. November 2023 33: 2018-2027; Published in Advance November 17, 2023, doi:10.1101/gr.278024.123
    ...phenotype (Fig. 2B). Furthermore, no sperm could be isolated from their caudal epididymides (Fig. 2C).Genome-wide maps of RAD51 and RPA binding in Dmc1−/− mouse testesUsing this pipeline of optimized mutagenesis via CRISPR-Cas9 electroporation, followed by verification of absence of DMC1 at the protein...
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  9. Resource: A large-scale zebrafish gene knockout resource for the genome-wide study of gene function
    • Gaurav K. Varshney,
    • Jing Lu,
    • Derek E. Gildea,
    • Haigen Huang,
    • Wuhong Pei,
    • Zhongan Yang,
    • Sunny C. Huang,
    • David Schoenfeld,
    • Nam H. Pho,
    • David Casero,
    • Takashi Hirase,
    • Deborah Mosbrook-Davis,
    • Suiyuan Zhang,
    • Li-En Jao,
    • Bo Zhang,
    • Ian G. Woods,
    • Steven Zimmerman,
    • Alexander F. Schier,
    • Tyra G. Wolfsberg,
    • Matteo Pellegrini,
    • Shawn M. Burgess,
    • and Shuo Lin
    Genome Res. April 2013 23: 727-735; Published in Advance February 4, 2013, doi:10.1101/gr.151464.112
    ...A large-scale zebrafish gene knockout resource for the genome-wide study of gene function Gaurav K. Varshney 1 , 8 , Jing Lu 2 , 3 , 8 , Derek E. Gildea 4 , Haigen Huang 3 , Wuhong Pei 1 , Zhongan Yang 3 , Sunny C. Huang...
  10. Research: Pangenome analysis reveals families of ubiquitin-ligase adaptors as key genomic divergence drivers that lead to hybrid incompatibility
    • Dongying Xie,
    • Pohao Ye,
    • Yiming Ma,
    • and Zhongying Zhao
    Genome Res. March 2026 36: 506-521; Published in Advance February 17, 2026, doi:10.1101/gr.280885.125
    ...nematode (C. elegans, C. remanei, and Caenorhabditis brenneri; see Methods), only 5% (294 out of 5426) and 2.5% (60 out of 2393) of C. nigoni–specific and C. briggsae–specific dispensable genes, respectively, are shared with these outgroups (Fig. 3B; Supplemental Table S4). This suggests that these gene...
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