Searching journal content for articles similar to Ayala 19 (5): 693.

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  1. Method: De novo reconstruction of satellite repeat units from sequence data
    • Yujie Zhang,
    • Justin Chu,
    • Haoyu Cheng,
    • and Heng Li
    Genome Res. November 2023 33: 1994-2001; Published in Advance November 2, 2023, doi:10.1101/gr.278005.123
    .... A monomer “B” could range from a few base pairs (bp) to thousands of bp in length and an entire SatDNA could span megabases in large s. Several percent of the human , or a couple of hundred megabases in total, is composed of SatDNA (Altemose et al. 2022). Monomers in a SatDNA array are similar in sequence...
  2. Review: k-mer approaches for biodiversity genomics
    • Katharine M. Jenike,
    • Lucía Campos-Domínguez,
    • Marilou Boddé,
    • José Cerca,
    • Christina N. Hodson,
    • Michael C. Schatz,
    • and Kamil S. Jaron
    Genome Res. February 2025 35: 219-230; Published in Advance January 31, 2025, doi:10.1101/gr.279452.124
    ...-free techniques for species assignment as well as detection of horizontal gene transfer candidates (for review, see Ren et al. 2018).For most applications we need to select a k long enough so that most k-mers in the will be found only once. The proportion of k-mers corresponding to a unique position...
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  3. Method: Enabling efficient and robust analysis of tandem repeats in genomic data using wavefront-based string decomposer
    • Junhai Qi,
    • Zhidong Yang,
    • Ting Yu,
    • and Guojun Li
    Genome Res. April 8, 2026 gr.281346.125; Published in Advance April 8, 2026, doi:10.1101/gr.281346.125
    ...16 TRs are genomic sequences composed of tandemly arranged DNA repeat units. TRs are broadly categorized into short17 tandem repeats (STRs) and long tandem repeats (LTRs) based on repeat unit length. STRs typically consist of 1–6 base18 pair (bp) repeat units, whereas LTRs can span hundreds of base...
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  4. Research: Fusion, fission, and scrambling of the bilaterian genome in Bryozoa
    • Thomas D. Lewin,
    • Isabel Jiah-Yih Liao,
    • Mu-En Chen,
    • John D.D. Bishop,
    • Peter W.H. Holland,
    • and Yi-Jyun Luo
    Genome Res. January 2025 35: 78-92; Published in Advance January 6, 2025, doi:10.1101/gr.279636.124
    ...in each lineage, plus a surprising degree of large-scale organizational similarity. Many groups of orthologous genes have been retained on the same chromosome for hundreds of millions of years and remain together in diverse and highly divergent lineages (Putnam et al. 2007, 2008; Simakov et al. 2013, 2022...
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  5. Research: A-to-I RNA editing occurs at over a hundred million genomic sites, located in a majority of human genes
    • Lily Bazak,
    • Ami Haviv,
    • Michal Barak,
    • Jasmine Jacob-Hirsch,
    • Patricia Deng,
    • Rui Zhang,
    • Farren J. Isaacs,
    • Gideon Rechavi,
    • Jin Billy Li,
    • Eli Eisenberg,
    • and Erez Y. Levanon
    Genome Res. March 2014 24: 365-376; Published in Advance December 17, 2013, doi:10.1101/gr.164749.113
    ...A-to-I RNA editing occurs at over a hundred million genomic sites, located in a majority of human genes Lily Bazak 1 , Ami Haviv 1 , Michal Barak 1 , Jasmine Jacob-Hirsch 1 , 2 , Patricia Deng 3 , Rui Zhang 3 , Farren J...
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  6. Method: Optimizing nanopore adaptive sampling for pneumococcal serotype surveillance in complex samples using the graph-based GNASTy algorithm
    • Samuel T. Horsfield,
    • Basil C.T. Fok,
    • Yuhan Fu,
    • Paul Turner,
    • John A. Lees,
    • and Nicholas J. Croucher
    Genome Res. April 2025 35: 1025-1040; Published in Advance March 4, 2025, doi:10.1101/gr.279435.124
    .... As observed in Martin et al. (2022), targets at low concentration produce more variable enrichment values due to the low numbers of reads detected by both NAS and control channels. Overall, the slower read alignment speed of graph pseudoalignment compared to minimap2 did not have a large enough effect...
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  7. Method: Phased nanopore assembly with Shasta and modular graph phasing with GFAse
    • Ryan Lorig-Roach,
    • Melissa Meredith,
    • Jean Monlong,
    • Miten Jain,
    • Hugh E. Olsen,
    • Brandy McNulty,
    • David Porubsky,
    • Tessa G. Montague,
    • Julian K. Lucas,
    • Chris Condon,
    • Jordan M. Eizenga,
    • Sissel Juul,
    • Sean K. McKenzie,
    • Sara E. Simmonds,
    • Jimin Park,
    • Mobin Asri,
    • Sergey Koren,
    • Evan E. Eichler,
    • Richard Axel,
    • Bruce Martin,
    • Paolo Carnevali,
    • Karen H. Miga,
    • and Benedict Paten
    Genome Res. March 2024 34: 454-468; Published in Advance April 16, 2024, doi:10.1101/gr.278268.123
    ...the need for parental sequencing (Selvaraj et al. 2013). Sequencing technologies like Hi-C and Pore-C exploit the physical packing of chromatin in the nucleus to ligate proximal regions of DNA molecules, which can be hundreds of millions of base pairs apart along the chromosome (Lieberman-Aiden et al. 2009...
  8. Preface: On the origin of Darwinism
    • Hillary E. Sussman
    Genome Res. May 2009 19: 691-692; doi:10.1101/gr.094458.109
    ...here? Genome Res. (this issue). doi: 10.1101/gr.086652.108. Ayala, F.J. 2009. One hundred fifty years without Darwin are enough! Genome Res. (this issue). doi: 10.1101/gr.084285.108. Darwin, C. 1859. On the origin of species by means of natural selection, or the preservation of favoured races...
  9. Research: Candida albicans isolates contain frequent heterozygous structural variants and transposable elements within genes and centromeres
    • Ursula Oggenfuss,
    • Robert T. Todd,
    • Natthapon Soisangwan,
    • Bailey Kemp,
    • Alison Guyer,
    • Annette Beach,
    • and Anna Selmecki
    Genome Res. April 2025 35: 824-838; Published in Advance October 22, 2024, doi:10.1101/gr.279301.124
    .... albicans) (Goodwin and Poulter 2000; Goodwin et al. 2001; Fig. 2E). One hundred and fifty-three of the full-length TEs belonged to the superfamily Ty1, followed by unclassified retrotransposons (n = 94), Ty3 (n = 30), LINE (n = 20), and DNA transposons (n = 19) (Fig. 2F). One hundred and sixty-four TE...
  10. Research: Extreme genome scrambling in marine planktonic Oikopleura dioica cryptic species
    • Charles Plessy,
    • Michael J. Mansfield,
    • Aleksandra Bliznina,
    • Aki Masunaga,
    • Charlotte West,
    • Yongkai Tan,
    • Andrew W. Liu,
    • Jan Grašič,
    • María Sara del Río Pisula,
    • Gaspar Sánchez-Serna,
    • Marc Fabrega-Torrus,
    • Alfonso Ferrández-Roldán,
    • Vittoria Roncalli,
    • Pavla Navratilova,
    • Eric M. Thompson,
    • Takeshi Onuma,
    • Hiroki Nishida,
    • Cristian Cañestro,
    • and Nicholas M. Luscombe
    Genome Res. March 2024 34: 426-440; Published in Advance April 15, 2024, doi:10.1101/gr.278295.123
    ...ancestor of metazoans (Simakov et al. 2022). The most famous example of conserved microsynteny in animals is the Hox cluster, which contains genes that regulate axial patterning during embryogenesis and whose ancestry can be traced back to the origin of bilaterian animals hundreds of millions of years ago...
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