Searching journal content for articles similar to Lewin et al. 19 (11): 1925.

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  1. Method: Pangenome-based genome inference using integer programming
    • Ghanshyam Chandra,
    • Md Helal Hossen,
    • Stephan Scholz,
    • Alexander T. Dilthey,
    • Daniel Gibney,
    • and Chirag Jain
    Genome Res. December 2025 35: 2661-2670; Published in Advance August 21, 2025, doi:10.1101/gr.280567.125
    ...: chirag@iisc.ac.inAbstractAffordable genotyping methods are essential in genomics. Commonly used genotyping methods primarily support single-nucleotide variants and short indels but neglect structural variants. Additionally, accuracy of read alignments to a reference is unreliable in highly polymorphic...
  2. Method: OMKar automates genome karyotyping using optical maps to identify constitutional abnormalities
    • Siavash Raeisi Dehkordi,
    • Zhaoyang Jia,
    • Joey Estabrook,
    • Jen Hauenstein,
    • Neil Miller,
    • Naz Güleray-Lafci,
    • Jürgen Neesen,
    • Alex Hastie,
    • Alka Chaubey,
    • Andy Wing Chun Pang,
    • Paul Dremsek,
    • and Vineet Bafna
    Genome Res. December 2025 35: 2671-2681; Published in Advance November 14, 2025, doi:10.1101/gr.280536.125
    ...on microscopic chromosome examination, a complex and expertise-dependent process with megabase-scale resolution. Optical mapping (OGM) technology offers an efficient approach to detect large-scale genomic lesions. Here, we introduce OMKar, a computational method that generates virtual karyotypes from OGM data...
    OPEN ACCESS ARTICLE
  3. Method: Geometric deep learning framework for de novo genome assembly
    • Lovro Vrček,
    • Xavier Bresson,
    • Thomas Laurent,
    • Martin Schmitz,
    • Kenji Kawaguchi,
    • and Mile Šikić
    Genome Res. April 2025 35: 839-849; Published in Advance October 29, 2024, doi:10.1101/gr.279307.124
    ...to those of the state-of-the-art tools across several species. With every new assembled telomere-to-telomere, the amount of reliable training data at our disposal increases. Combining the straightforward generation of abundant simulated data for diverse genomic structures with the AI approach makes...
  4. Resource: Chromosome-level subgenome-aware de novo assembly provides insight into Saccharomyces bayanus genome divergence after hybridization
    • Cory Gardner,
    • Junhao Chen,
    • Christina Hadfield,
    • Zhaolian Lu,
    • David Debruin,
    • Yu Zhan,
    • Maureen J. Donlin,
    • Tae-Hyuk Ahn,
    • and Zhenguo Lin
    Genome Res. November 2024 34: 2133-2146; Published in Advance September 17, 2024, doi:10.1101/gr.279364.124
    ...for the identification of major genomic events that have occurred since hybridization, such as recombination, chromosomal rearrangements, and LOH (see Methods). Our first approach used nonoverlapping blocks of 5000 bp for every chromosome in a BLAST search against the s of S. eubayanus and S. uvarum, with the origin...
  5. Research: Evidence for selfing in a vertebrate from whole-genome sequencing
    • Astrid Böhne,
    • Zeynep Oğuzhan,
    • Ioannis Chrysostomakis,
    • Simon Vitt,
    • Denis Meuthen,
    • Sebastian Martin,
    • Sandra Kukowka,
    • and Timo Thünken
    Genome Res. December 2023 33: 2133-2142; Published in Advance December 7, 2023, doi:10.1101/gr.277368.122
    ...assessed the final mapping rate with the flagstat command of SAMtools v1.8, which was >90% for all samples and in the range of previously reported mapping rates for cichlid s used in population genomic analyses (individual mapping rates; wildI: 91.46%, parent: 91.43, offspring1: 91.96%, offspring2: 91...
  6. Method: Ultrafast genome-wide inference of pairwise coalescence times
    • Regev Schweiger and
    • Richard Durbin
    Genome Res. July 2023 33: 1023-1031; Published in Advance August 10, 2023, doi:10.1101/gr.277665.123
    ...and 1000 Genomes data with θ = 0.00075 and ρ = 0.0006, a cache of size 10 kbp, and output every 1-kbp sites.Selection simulation studyWe simulated two sets of samples. First, we used the cosi2 (Shlyakhter et al. 2014) simulator to generate 100 replicates of 100 haploid sequences of length 10 Mbp, where...
    OPEN ACCESS ARTICLE
  7. Method: Accelerated somatic mutation calling for whole-genome and whole-exome sequencing data from heterogenous tumor samples
    • Shuangxi Ji,
    • Tong Zhu,
    • Ankit Sethia,
    • and Wenyi Wang
    Genome Res. April 2024 34: 633-641; Published in Advance April 8, 2024, doi:10.1101/gr.278456.123
    ..., Wysoker A, Fennell T, Ruan J, Homer N, Marth G, Abecasis G, Durbin R, 1000 Genome Project Data Processing Subgroup. 2009. The Sequence Alignment/Map format and SAMtools. Bioinformatics 25: 2078–2079. doi:10.1093/bioinformatics/btp352 ↵McLaren W, Gil L, Hunt SE, Riat HS, Ritchie GRS, Thormann A, Flicek P...
    OPEN ACCESS ARTICLE
  8. Method: Genome skimming with nanopore sequencing precisely determines global and transposon DNA methylation in vertebrates
    • Christopher Faulk
    Genome Res. June 2023 33: 948-956; Published in Advance July 13, 2023, doi:10.1101/gr.277743.123
    ...: 3094–3100. doi:10.1093/bioinformatics/bty191 ↵Li H, Handsaker B, Wysoker A, Fennell T, Ruan J, Homer N, Marth G, Abecasis G, Durbin R, 1000 Genome Project Data Processing Subgroup. 2009. The Sequence Alignment/Map format and SAMtools. Bioinformatics 25: 2078–2079. doi:10.1093/bioinformatics/btp352 ↵Li...
  9. Research: Genome-wide oscillations in G + C density and sequence conservation
    • Zarmik Moqtaderi,
    • Susan Brown,
    • and Welcome Bender
    Genome Res. November 2021 31: 2050-2057; Published in Advance October 14, 2021, doi:10.1101/gr.274332.120
    ...seemed likely to reflect mobile element insertions. Because mobile elements have not been cataloged in the T. confusum , we simply assessed genomic copy number for sequences in this region. We scanned across this region in each species with 18-base windows (displaced every nine bases) and counted...
  10. 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
    ...encoded unchanged products in VC2010; moreover, we predicted ≥53 new genes in VC2010. The recompleted of C. elegans should be a valuable resource for genetics, genomics, and systems biology.The usefulness of model organisms in modern biology partly comes from their having reference assemblies...
    OPEN ACCESS ARTICLE
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