Searching journal content for articles similar to West et al. 28 (4): 569.

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  1. Method: Transcriptome reconstruction and functional analysis of eukaryotic marine plankton communities via high-throughput metagenomics and metatranscriptomics
    • Alexey Vorobev,
    • Marion Dupouy,
    • Quentin Carradec,
    • Tom O. Delmont,
    • Anita Annamalé,
    • Patrick Wincker,
    • and Eric Pelletier
    Genome Res. April 2020 30: 647-659; Published in Advance March 23, 2020, doi:10.1101/gr.253070.119
    ...are expected to provide results similar to those achieved for bacteria or archaea. Recently, a semisupervised method based on a model trained with a set of diverse references allowed eukaryotic reconstruction from complex natural environments (West et al. 2018; Olm et al. 2019).Novel reference...
  2. 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
    ...that different lineages of Blastocystis have varied ecological roles in the host gut.The vertebrate gut is host to a diverse ecosystem of bacteria, archaea, viruses, and microbial eukaryotes. This diverse microbial community has broad impacts on the physiology and development of the host. Gut microbes can...
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  3. Method: Probing the eukaryotic microbes of ruminants with a deep-learning classifier and comprehensive protein databases
    • Ming Yan,
    • Thea O. Andersen,
    • Phillip B. Pope,
    • and Zhongtang Yu
    Genome Res. February 2025 35: 368-378; Published in Advance December 27, 2024, doi:10.1101/gr.279825.124
    ...lineages by accurately differentiating fungi and protozoa from other ecosystems. Because eukaryotic communities are less diverse in the gut than in aquatic and terrestrial environments, and there is minimal overlap in eukaryotic microbial diversity among these ecosystems (Parfrey et al. 2014), Gut...
  4. Review: Accurate and complete genomes from metagenomes
    • Lin-Xing Chen,
    • Karthik Anantharaman,
    • Alon Shaiber,
    • A. Murat Eren,
    • and Jillian F. Banfield
    Genome Res. March 2020 30: 315-333; Published in Advance March 18, 2020, doi:10.1101/gr.258640.119
    ..., the bottleneck imposed by the requirement for isolates precluded genomic insights for the vast majority of microbial life. Shotgun sequencing of microbial communities, referred to initially as community genomics and subsequently as -resolved metagenomics, can circumvent this limitation by obtaining meta...
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  5. Research: Complete genomes of Asgard archaea reveal diverse integrated and mobile genetic elements
    • Luis E. Valentin-Alvarado,
    • Ling-Dong Shi,
    • Kathryn E. Appler,
    • Alexander Crits-Christoph,
    • Valerie De Anda,
    • Benjamin A. Adler,
    • Michael L. Cui,
    • Lynn Ly,
    • Pedro Leão,
    • Richard J. Roberts,
    • Rohan Sachdeva,
    • Brett J. Baker,
    • David F. Savage,
    • and Jillian F. Banfield
    Genome Res. October 2024 34: 1595-1609; Published in Advance October 15, 2024, doi:10.1101/gr.279480.124
    ...Sachdeva1, Brett J. Baker3,4, David F. Savage1,7,8 and Jillian F. Banfield1,4,9,10 1Innovative Genomics Institute, University of California, Berkeley, California 94720, USA; 2Department of Plant and Microbial Biology, University of California, Berkeley, California 94720, USA; 3Department of Marine Science...
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