Searching journal content for articles similar to Fiddes et al. 28 (7): 1029.

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  1. Method: Combining DNA and protein alignments to improve genome annotation with LiftOn
    • Kuan-Hao Chao,
    • Jakob M. Heinz,
    • Celine Hoh,
    • Alan Mao,
    • Alaina Shumate,
    • Mihaela Pertea,
    • and Steven L. Salzberg
    Genome Res. February 2025 35: 311-325; Published in Advance December 27, 2024, doi:10.1101/gr.279620.124
    ...by the Liftoff (Shumate and Salzberg 2021) and CAT (Fiddes et al. 2018) programs, which were used to create the initial annotation of the human T2T-CHM13 (Nurk et al. 2022) based on the annotation of the human reference , GRCh38. However, in cases in which the DNA sequence of a newly assembled deviates...
  2. Resource: Building better genome annotations across the tree of life
    • Adam H. Freedman and
    • Timothy B. Sackton
    Genome Res. May 2025 35: 1261-1276; Published in Advance April 15, 2025, doi:10.1101/gr.280377.124
    ...initio prediction, assembly from RNA-seq reads, and annotation transfer); they are highly cited, commonly used; and they have publicly accessible code repositories, most of which show recent contributions by developers. We initially sought to include the Comparative Annotation Toolkit (Fiddes et al. 2018...
  3. 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
    ...of skimming in epidemiology, conservation, and comparative genomics.MethodsDNA extractionDNA from primate buffy coat samples was extracted Qiagen DNA mini kit (cat. 51306) by the Southwest National Primate Center (SNPRC) and treated with Qiagen RNase A. DNA from mouse tissues and all vertebrate muscle samples...
  4. Method: Highly accurate assembly polishing with DeepPolisher
    • Mira Mastoras,
    • Mobin Asri,
    • Lucas Brambrink,
    • Prajna Hebbar,
    • Alexey Kolesnikov,
    • Daniel E. Cook,
    • Maria Nattestad,
    • Julian Lucas,
    • Taylor S. Won,
    • Pi-Chuan Chang,
    • Andrew Carroll,
    • Benedict Paten,
    • Kishwar Shafin,
    • and and the Human Pangenome Reference Consortium
    Genome Res. July 2025 35: 1595-1608; Published in Advance May 19, 2025, doi:10.1101/gr.280149.124
    ...Mira Mastoras1, Mobin Asri1, Lucas Brambrink2, Prajna Hebbar1, Alexey Kolesnikov2, Daniel E. Cook2, Maria Nattestad2, Julian Lucas1, Taylor S. Won1, Pi-Chuan Chang2, Andrew Carroll2, Benedict Paten1, Kishwar Shafin2, and the Human Pan Reference Consortium3 1UC Santa Cruz Genomics Institute...
  5. Method: Genetic complexity of killer-cell immunoglobulin-like receptor genes in human pangenome assemblies
    • Tsung-Kai Hung,
    • Wan-Chi Liu,
    • Sheng-Kai Lai,
    • Hui-Wen Chuang,
    • Yi-Che Lee,
    • Hong-Ye Lin,
    • Chia-Lang Hsu,
    • Chien-Yu Chen,
    • Ya-Chien Yang,
    • Jacob Shujui Hsu,
    • and Pei-Lung Chen
    Genome Res. August 2024 34: 1211-1223; Published in Advance September 9, 2024, doi:10.1101/gr.278358.123
    ...alleles (Fig. 3B; Supplemental Table S2). By annotating IPD-KIR alleles to 94 HPRC haplotypes, 115 CDS-only alleles were complemented with the full genomic sequences derived from HPRC assemblies.View larger version: In this window In a new window Figure 3. Representation of typical and atypical haplotype...
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  6. Research: Evaluating recovery potential of the northern white rhinoceros from cryopreserved somatic cells
    • Tate Tunstall,
    • Richard Kock,
    • Jiri Vahala,
    • Mark Diekhans,
    • Ian Fiddes,
    • Joel Armstrong,
    • Benedict Paten,
    • Oliver A. Ryder,
    • and Cynthia C. Steiner
    Genome Res. June 2018 28: 780-788; Published in Advance May 24, 2018, doi:10.1101/gr.227603.117
    ...S, Kronenberg ZN, Underwood JG, Gordon D, Earl D, Keane T, Eichler EE, et al. 2018. Comparative Annotation Toolkit (CAT) - simultaneous clade and personal annotation. bioRxiv doi: 10.1101/231118. Folch J, Cocero M, Chesné P, Alabart J, Domínguez V, Cognié Y, Roche A, Fernández-Arias A,Martí J...
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