Searching journal content for articles similar to Zhang et al. 32 (10): 1852.

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  1. Method: Accurate detection of tandem repeats from error-prone sequences with EquiRep
    • Zhezheng Song,
    • Tasfia Zahin,
    • Xiang Li,
    • and Mingfu Shao
    Genome Res. December 2025 35: 2714-2721; Published in Advance August 21, 2025, doi:10.1101/gr.280750.125
    ..., et al. 2019. ExpansionHunter: a sequence-graph-based tool to analyze variation in short tandem repeat regions. Bioinformatics 35: 4754–4756. doi:10.1093/bioinformatics/btz431 ↵Fang L, Liu Q, Monteys AM, Gonzalez-Alegre P, Davidson BL, Wang K. 2022. DeepRepeat: direct quantification of short tandem...
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  2. Research: Natural diversity of telomere length distributions across 100 Saccharomyces cerevisiae strains
    • Clotilde Garrido,
    • Cintia Gómez-Muñoz,
    • Etienne Kornobis,
    • Nicolas Agier,
    • Oana Ilioaia,
    • Gilles Fischer,
    • and Zhou Xu
    Genome Res. March 2026 36: 522-533; Published in Advance January 16, 2026, doi:10.1101/gr.281132.125
    ...al. 2009). More recently, larger variations in TL across natural isolates have been reported (D'Angiolo et al. 2023; O'Donnell et al. 2023). Using short-read whole- sequencing data, D'Angiolo and colleagues (2023) found that wild strains display shorter telomeres than strains from domesticated...
  3. Resource: CGC1, a new reference genome for Caenorhabditis elegans
    • Kazuki Ichikawa,
    • Massa J. Shoura,
    • Karen L. Artiles,
    • Dae-Eun Jeong,
    • Chie Owa,
    • Haruka Kobayashi,
    • Yoshihiko Suzuki,
    • Manami Kanamori,
    • Yu Toyoshima,
    • Yuichi Iino,
    • Ann E. Rougvie,
    • Lamia Wahba,
    • Andrew Z. Fire,
    • Erich M. Schwarz,
    • and Shinichi Morishita
    Genome Res. August 2025 35: 1902-1918; Published in Advance July 15, 2025, doi:10.1101/gr.280274.124
    ...when assembling VC2010. Alternatively, it might reflect real genetic change: Tandem repeat lengths at the rDNA locus of C. elegans can vary dynamically over time (Wahba et al. 2021), and such variation might at least partially account for differences between our earlier VC2010 and later CGC1 assemblies...
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  4. Method: Accurate allocation of multimapped reads enables regulatory element analysis at repeats
    • Alexis Morrissey,
    • Jeffrey Shi,
    • Daniela Q. James,
    • and Shaun Mahony
    Genome Res. June 2024 34: 937-951; Published in Advance July 10, 2024, doi:10.1101/gr.278638.123
    ...(TEs) and other repetitive regions have been shown to contain gene regulatory elements, including transcription factor binding sites. However, regulatory elements harbored by repeats have proven difficult to characterize using short-read sequencing assays such as ChIP-seq or ATAC-seq. Most regulatory...
  5. 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
    ...Science and Engineering, Pennsylvania State University, University Park, Pennsylvania 16802, USA Short tandem repeats (STRs) are implicated in dozens of human genetic diseases and contribute significantly to variation and instability. Yet profiling STRs from short-read sequencing data is challenging...
  6. Research: Transposons contribute to the functional diversification of the head, gut, and ovary transcriptomes across Drosophila natural strains
    • Marta Coronado-Zamora and
    • Josefa González
    Genome Res. September 2023 33: 1541-1553; Published in Advance October 4, 2023, doi:10.1101/gr.277565.122
    ...assembly that minimizes the potential sources of errors while identifying a comprehensive set of gene–TE chimeras. We applied this method to the head, gut, and ovary dissected from five Drosophila melanogaster natural strains, with individual reference s available. We found that ∼19% of body part...
  7. Resource: The fine-scale recombination rate variation and associations with genomic features in a butterfly
    • Aleix Palahí i Torres,
    • Lars Höök,
    • Karin Näsvall,
    • Daria Shipilina,
    • Christer Wiklund,
    • Roger Vila,
    • Peter Pruisscher,
    • and Niclas Backström
    Genome Res. May 2023 33: 810-823; Published in Advance June 12, 2023, doi:10.1101/gr.277414.122
    ...is known for natural populations. A broader taxonomic sampling is hence necessary to get a more complete picture of what drives recombination rate variation within s and between lineages. This applies not the least to holocentric organisms without localized centromeres (Suomalainen 1953...
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  8. Resource: Recompleting the Caenorhabditis elegans genome
    • Jun Yoshimura,
    • Kazuki Ichikawa,
    • Massa J. Shoura,
    • Karen L. Artiles,
    • Idan Gabdank,
    • Lamia Wahba,
    • Cheryl L. Smith,
    • Mark L. Edgley,
    • Ann E. Rougvie,
    • Andrew Z. Fire,
    • Shinichi Morishita,
    • and Erich M. Schwarz
    Genome Res. June 2019 29: 1009-1022; Published in Advance May 23, 2019, doi:10.1101/gr.244830.118
    ...assembly has 99.98% identity to N2 but with an additional 1.8 Mb including tandem repeat expansions and duplications. For 116 structural discrepancies between N2 and VC2010, 97 structures matching VC2010 (84%) were also found in two outgroup strains, implying deficiencies in N2. Over 98% of N2 genes...
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  9. Research: Natural selection drives the accumulation of amino acid tandem repeats in human proteins
    • Loris Mularoni,
    • Alice Ledda,
    • Macarena Toll-Riera,
    • and M. Mar Albà
    Genome Res. June 2010 20: 745-754; Published in Advance March 24, 2010, doi:10.1101/gr.101261.109
    ...Natural selection drives the accumulation of amino acid tandem repeats in human proteins Loris Mularoni 1 , 2 , 5 , Alice Ledda 1 , 5 , Macarena Toll-Riera 1 , 3 and M. Mar Albà 1 , 3 , 4 , 6 1 Biomedical Informatics...
  10. Research: Natural genetic variation in yeast longevity
    • Stefan W. Stumpferl,
    • Sue E. Brand,
    • James C. Jiang,
    • Boguslawa Korona,
    • Anurag Tiwari,
    • Jianliang Dai,
    • Jae-Gu Seo,
    • and S. Michal Jazwinski
    Genome Res. October 2012 22: 1963-1973; Published in Advance September 5, 2012, doi:10.1101/gr.136549.111
    ...results have been obtained in the Caenorhabditis elegans model system ( Jenkins et al. 2004). The othermajor geneticmodels used in aging research,Drosophila melanogaster andMusmusculus, are also inbred and adapted to the laboratory, raising identical concerns, while the focus on natural genetic variation...
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