Searching journal content for articles similar to Gabriel et al. 34 (5): 769.

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  1. Method: GeneMark-ETP significantly improves the accuracy of automatic annotation of large eukaryotic genomes
    • Tomáš Brůna,
    • Alexandre Lomsadze,
    • and Mark Borodovsky
    Genome Res. May 2024 34: 757-768; Published in Advance June 12, 2024, doi:10.1101/gr.278373.123
    ...comparisons with the transcript-supported BRAKER1 (Hoff et al. 2016) and protein-supported BRAKER2 (Brůna et al. 2021), we ran BRAKER1 and BRAKER2 with the same RNA-seq libraries and the same protein databases, respectively, as the ones used in experiments with GeneMark-ETP. Also, we ran TSEBRA (Gabriel et al...
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  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
    ...from the three major approaches to the annotation problem. At the core of six of these—MAKER (Cantarel et al. 2008) with both protein and RNA-seq evidence; BRAKER1 (RNA-seq evidence only); BRAKER2 (protein evidence only); BRAKER3 (protein and RNA-seq evidence); CGP using protein evidence; and CGP...
  3. 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
    ...) Saccoglossus kowalevskii, (Sma) Schistosoma mansoni, (Sme) Schmidtea mediterranea, (Sro) Symsagittifera roscoffensis, (Tad) Trichoplax adhaerens, (Tca) Tribolium castaneum, and (Xtr) Xenopus tropicalis.We performed comprehensive gene prediction using the BRAKER3 pipeline (Gabriel et al. 2024), utilizing...
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  4. Research: Contiguous and complete assemblies of Blastocystis gut microbiome–associated protists reveal evolutionary diversification to host ecology
    • Abigail L. Lind,
    • Nathan A. McDonald,
    • Elias R. Gerrick,
    • Ami S. Bhatt,
    • and Katherine S. Pollard
    Genome Res. June 2025 35: 1377-1390; Published in Advance April 22, 2025, doi:10.1101/gr.279080.124
    ...GCA_002245135.1. As no predicted proteins or RNA-seq data were available for P. lacertae, genes were predicted from this using the BRAKER3 pipeline, using OrthoDB11 Eukaryota protein sequences as evidence. Proteins from all Blastocystis assemblies, C. burkhardae, and P. lacertae were annotated using...
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  5. Research: Transposable elements contribute to the evolution of host shift–related genes in cactophilic Drosophila species
    • Daniel Siqueira de Oliveira,
    • Anaïs Larue,
    • William Vilas Boas Nunes,
    • Francois Sabot,
    • Alejandra Bodelón,
    • María Pilar García Guerreiro,
    • Cristina Vieira,
    • and Claudia Marcia Aparecida Carareto
    Genome Res. March 2026 36: 487-505; Published in Advance February 10, 2026, doi:10.1101/gr.280463.125
    ...species.ResultsGenome assemblies and gene annotationTo investigate the potential role of TEs in host shift of cactophilic Drosophila species, we performed Oxford Nanopore Technologies (ONT) long-read sequencing on species that have different preferential cacti as hosts: D. buzzatii (Opuntia sp.), D...
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