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  1. Method: Overcoming limitations to customize DeepVariant for domesticated animals with TrioTrain
    • Jenna Kalleberg,
    • Jacob Rissman,
    • and Robert D. Schnabel
    Genome Res. August 2025 35: 1859-1874; Published in Advance June 2, 2025, doi:10.1101/gr.279542.124
    ...that standardized methods for population-based analyses with cattle (Hayes and Daetwyler 2019). Three runs were produced after the release of the current reference : ARS-UCD1.2 (Rosen et al. 2020), with Run7 in 2019 (N = 3818), Run8 in 2020 (N = 4931), and Run9 in 2021 (N = 6191). Over time, detection power...
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  2. Perspective: Challenges in identifying mRNA transcript starts and ends from long-read sequencing data
    • Ezequiel Calvo-Roitberg,
    • Rachel F. Daniels,
    • and Athma A. Pai
    Genome Res. November 2024 34: 1719-1734; doi:10.1101/gr.279559.124
    ...are depictions of the varying adapter ligation and sequencing for ONT (top) and PacBio (bottom) methods.Although advances in LRS methods have improved accuracy and consistency in sequencing of full-length molecules in recent years, these techniques still face technical and computational hurdles, which vary...
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  3. Perspective: The first five years of single-cell cancer genomics and beyond
    • Nicholas E. Navin
    Genome Res. October 2015 25: 1499-1507; doi:10.1101/gr.191098.115
    ...@mdanderson.org Abstract Single-cell sequencing (SCS) is a powerful new tool for investigating evolution and diversity in cancer and understanding the role of rare cells in tumor progression. These methods have begun to unravel key questions in cancer biology that have been difficult to address with bulk tumor...
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  4. Method: Ultraconserved elements are novel phylogenomic markers that resolve placental mammal phylogeny when combined with species-tree analysis
    • John E. McCormack,
    • Brant C. Faircloth,
    • Nicholas G. Crawford,
    • Patricia Adair Gowaty,
    • Robb T. Brumfield,
    • and Travis C. Glenn
    Genome Res. April 2012 22: 746-754; Published in Advance December 29, 2011, doi:10.1101/gr.125864.111
    ...of coalescent stochasticity by integrating data from individual loci into recently developed phylogenetic algorithms for estimating species histories from collections of discordant gene histories (Liu et al. 2009). One of the major hurdles to estimating species trees from phylogenomic data has been the reliance...
  5. RESOURCE: Assembly, Annotation, and Integration of UNIGENE Clusters into the Human Genome Draft
    • Degen Zhuo,
    • Wei D. Zhao,
    • Fred A. Wright,
    • Hee-Yung Yang,
    • Jian-Ping Wang,
    • Russell Sears,
    • Troy Baer,
    • Do-Hun Kwon,
    • David Gordon,
    • Solomon Gibbs,
    • Dean Dai,
    • Qing Yang,
    • Joe Spitzner,
    • Ralf Krahe,
    • Don Stredney,
    • Al Stutz,
    • and Bo Yuan
    Genome Res. May 1, 2001 11: 904-918; Published in Advance April 11, 2001, doi:10.1101/gr.164501
    ...Abstract The recent release of the first draft of the human genome provides an unprecedented opportunity to integrate human genes and their functions in a complete positional context. However, at least three significant technical hurdles remain: first, to assemble a complete and nonredundant human...
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