Searching journal content for articles similar to Doolittle and Zhaxybayeva 19 (5): 744.

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  1. Method: Robust analysis of prokaryotic pangenome gene gain and loss rates with Panstripe
    • Gerry Tonkin-Hill,
    • Rebecca A. Gladstone,
    • Anna K. Pöntinen,
    • Sergio Arredondo-Alonso,
    • Stephen D. Bentley,
    • and Jukka Corander
    Genome Res. January 2023 33: 129-140; Published in Advance January 20, 2023, doi:10.1101/gr.277340.122
    ...Robust analysis of prokaryotic pan gene gain and loss rates with Panstripe Gerry Tonkin-Hill1,2, Rebecca A. Gladstone1, Anna K. Pöntinen1, Sergio Arredondo-Alonso1,2, Stephen D. Bentley2 and Jukka Corander1,2,3 1Department of Biostatistics, University of Oslo, 0372 Blindern, Norway; 2Parasites...
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  2. Research: Evolutionary assembly patterns of prokaryotic genomes
    • Maximilian O. Press,
    • Christine Queitsch,
    • and Elhanan Borenstein
    Genome Res. June 2016 26: 826-833; Published in Advance April 14, 2016, doi:10.1101/gr.200097.115
    ...Evolutionary assembly patterns of prokaryotic s Maximilian O. Press1, Christine Queitsch1 and Elhanan Borenstein1,2,3 1Department of Genome Sciences, University of Washington, Seattle, Washington 98195, USA; 2Department of Computer Science and Engineering, University of Washington, Seattle...
  3. Method: An integrative strategy to identify the entire protein coding potential of prokaryotic genomes by proteogenomics
    • Ulrich Omasits,
    • Adithi R. Varadarajan,
    • Michael Schmid,
    • Sandra Goetze,
    • Damianos Melidis,
    • Marc Bourqui,
    • Olga Nikolayeva,
    • Maxime Québatte,
    • Andrea Patrignani,
    • Christoph Dehio,
    • Juerg E. Frey,
    • Mark D. Robinson,
    • Bernd Wollscheid,
    • and Christian H. Ahrens
    Genome Res. December 2017 27: 2083-2095; Published in Advance November 15, 2017, doi:10.1101/gr.218255.116
    ...of completely sequenced s, the large majority of which (>90%) originate from prokaryotes (Reddy et al. 2015). The accurate annotation of all protein-coding genes (interchangeably used with CDSs from here on) is essential to exploit this genomic information at multiple levels: from small, focused experiments, up...
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  4. Research: Origin and domestication of papaya Yh chromosome
    • Robert VanBuren,
    • Fanchang Zeng,
    • Cuixia Chen,
    • Jisen Zhang,
    • Ching Man Wai,
    • Jennifer Han,
    • Rishi Aryal,
    • Andrea R. Gschwend,
    • Jianping Wang,
    • Jong-Kuk Na,
    • Lixian Huang,
    • Lingmao Zhang,
    • Wenjing Miao,
    • Jiqing Gou,
    • Jie Arro,
    • Romain Guyot,
    • Richard C. Moore,
    • Ming-Li Wang,
    • Francis Zee,
    • Deborah Charlesworth,
    • Paul H. Moore,
    • Qingyi Yu,
    • and Ray Ming
    Genome Res. April 2015 25: 524-533; Published in Advance March 11, 2015, doi:10.1101/gr.183905.114
    ...Origin and domestication of papaya Y h chromosome Robert VanBuren 1 , 2 , 9 , Fanchang Zeng 2 , 9 , Cuixia Chen 2 , 9 , Jisen Zhang 1 , 9 , Ching Man Wai 2 , Jennifer Han 2 , Rishi Aryal 2 , Andrea R...
  5. Method: Directed shotgun proteomics guided by saturated RNA-seq identifies a complete expressed prokaryotic proteome
    • Ulrich Omasits,
    • Maxime Quebatte,
    • Daniel J. Stekhoven,
    • Claudia Fortes,
    • Bernd Roschitzki,
    • Mark D. Robinson,
    • Christoph Dehio,
    • and Christian H. Ahrens
    Genome Res. November 2013 23: 1916-1927; Published in Advance July 22, 2013, doi:10.1101/gr.151035.112
    ....4% protein-coding genes were missed in the original annotations (Venter et al. 2011), justifying our focus on the reference . Our strategy to achieve as complete as possible coverage of the expressed proteome of a prokaryote consists of three stages. In a first stage, RNA and proteins are extracted from...
  6. Method: EnDeep4mC predicts DNA N4-methylcytosine sites using a dual-adaptive feature encoding framework in deep ensembles
    • Shuyu Zhang,
    • Quan Zou,
    • Mengting Niu,
    • Zhibin Lv,
    • Antony Stalin,
    • and Ximei Luo
    Genome Res. March 2026 36: 589-599; Published in Advance February 17, 2026, doi:10.1101/gr.280977.125
    ...confirms its robust transferability from animal to microbe groups. Evolutionary analysis further uncovers the functional differentiation of 4mC sequences in biological evolution: Prokaryotic 4mC relies on stable patterns, whereas eukaryotes achieve regulatory plasticity through dynamic sequence...
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  7. 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
    ...sequence origins.Benchmarking EukRep, Tiara, and GutEukTo benchmark the performance of GutEuk against Tiara and EukRep, we filtered out the s originally used for training Tiara and EukRep in the testing set (2995, 93, and 43 s for prokaryotes, fungi, and protozoa, respectively, of diverse taxonomic origins...
  8. Preface: On the origin of Darwinism
    • Hillary E. Sussman
    Genome Res. May 2009 19: 691-692; doi:10.1101/gr.094458.109
    ....) J. of the Proc. of the Linnean Soc. of London. Zoology 3: 45–62. Doolittle, W.F. and Zhaxybayeva, O. 2009. On the origin of prokaryotic species. Genome Res. (this issue). doi: 10.1101/gr.086645.108. Flint, J. and Mackay, T.F.C. 2009. Genetic architecture of quantitative traits in mice, flies...
  9. LETTER: Prokaryotic phylogenies inferred from protein structural domains
    • Eric J. Deeds,
    • Hooman Hennessey,
    • and Eugene I. Shakhnovich
    Genome Res. March 2005 15: 393-402; doi:10.1101/gr.3033805
    ...Prokaryotic phylogenies inferred from protein structural domains Eric J. Deeds 1 , Hooman Hennessey 2 , and Eugene I. Shakhnovich 3 , 4 1 Department of Molecular and Cellular Biology, Harvard University, Cambridge, Massachusetts 02138, USA...
  10. Review: De novo gene birth and the conundrum of ORFan genes in bacteria
    • Md. Hassan uz-Zaman and
    • Howard Ochman
    Genome Res. August 2025 35: 1679-1688; Published in Advance July 10, 2025, doi:10.1101/gr.280157.124
    ...postulated to originate from either horizontal transfer, rapid divergence from pre-existing genes, or de novo emergence from noncoding sequences. We assess the body of research that explores each of these hypotheses and demonstrate that the mystery of the origin of bacterial ORFans still remains unresolved...
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