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Research: Large-scale investigation of species-specific orphan genes in the human gut microbiome elucidates their evolutionary origins
- Nikolaos Vakirlis and
- Anne Kupczok
Genome Res. June 2024 34: 888-903; Published in Advance July 8, 2024, doi:10.1101/gr.278977.124
...: In this window In a new window Figure 2. Large scale-identification of species-specific orphan genes (SSOGs) in the human gut microbiome. (A) The main steps of the computational workflow of similarity searches. (B) Distribution of the SSOG proportion in a given species’ pan. The red dashed line denotes...
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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
.... Nonetheless, bacteria offer several unique avenues for research into the process and mechanics of gene birth at a resolution not feasible in other organisms. Both their amenability to experimental evolutionary analysis and their strain-level variation in gene content foster investigations of how noncoding...
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Research: The chromatin landscape of the histone-possessing Bacteriovorax bacteria
- Georgi K. Marinov,
- Benjamin Doughty,
- Anshul Kundaje,
- and William J. Greenleaf
Genome Res. January 2025 35: 109-123; Published in Advance November 21, 2024, doi:10.1101/gr.279418.124
...be associated with replication initiation.Chromatin accessibility correlates with transcriptional activity in BacteriovoraxOur next step was to characterize the relationship between chromatin accessibility and transcriptional activity in Bacteriovorax as well as their dynamics upon large-scale gene expression...
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Review: A systematic guide for identifying transcription factors that directly regulate the expression of a gene of interest
- Andrew D. Bates,
- Dawid Grzela,
- Maciej Studzian,
- Louise Brennan,
- Moli Williams,
- Conor Fawcett,
- Beth Hammond,
- Manreen Grewal,
- Marcin Ratajewski,
- Lukasz Pulaski,
- and Urszula L. McClurg
Genome Res. March 2026 36: 433-459; Published in Advance February 17, 2026, doi:10.1101/gr.281154.125
...explain the transcriptional regulation of your GOI, this does not mean that you have to do all of the “wet-laboratory” experiments yourself: Data mining is a crucial step in developing your hypotheses. Proliferation of easily accessible, large-scale, high-throughput studies provides fertile ground...
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Method: Genealogical inference and more flexible sequence clustering using iterative PopPUNK
- Bin Zhao,
- John A. Lees,
- Hongjin Wu,
- Chao Yang,
- and Daniel Falush
Genome Res. May 30, 2023 gr.277395.122; Published in Advance May 30, 2023, doi:10.1101/gr.277395.122
...to represent strains from a sequence type or clonal group. Population geneticists usually 97 require clusters of population or sub-population level to conduct species-level studies. 98 99 Two state-of-the-art pipelines for large-scale datasets that allow multi-level 100 clustering are Fastbaps (Tonkin-Hill et...
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Method: Accurate and fast graph-based pangenome annotation and clustering with ggCaller
- Samuel T. Horsfield,
- Gerry Tonkin-Hill,
- Nicholas J. Croucher,
- and John A. Lees
Genome Res. September 2023 33: 1622-1637; Published in Advance August 24, 2023, doi:10.1101/gr.277733.123
...a population must be predicted, functionally annotated, and clustered, representing the “pan.” Despite the volume of data available, gene prediction and annotation are currently conducted in isolation on individual s, which is computationally inefficient and frequently inconsistent across s. Here, we introduce...
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Research: Large-scale genomic sequencing of extraintestinal pathogenic Escherichia coli strains
- Stephen J. Salipante,
- David J. Roach,
- Jacob O. Kitzman,
- Matthew W. Snyder,
- Bethany Stackhouse,
- Susan M. Butler-Wu,
- Choli Lee,
- Brad T. Cookson,
- and Jay Shendure
Genome Res. January 2015 25: 119-128; Published in Advance November 4, 2014, doi:10.1101/gr.180190.114
...of Washington, Seattle, Washington 98195, USA Large-scale bacterial sequencing efforts to date have provided limited information on the most prevalent category of disease: sporadically acquired infections caused by common pathogenic bacteria. Here, we performed whole- sequencing and de novo assembly of 312...
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Research: Timescale and genetic linkage explain the variable impact of defense systems on horizontal gene transfer
- Yang Liu,
- João Botelho,
- and Jaime Iranzo
Genome Res. February 2025 35: 268-278; Published in Advance January 10, 2025, doi:10.1101/gr.279300.124
..., against which bacteria have evolved an elaborate repertoire of defense systems (Doron et al. 2018; Botelho et al. 2023; Georjon and Bernheim 2023; Mayo-Muñoz et al. 2023; Shaw et al. 2023). As a result, large-scale patterns of HGT are shaped by an interplay of ecological and genetic variables...
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Research: Large-scale genome analysis of bovine commensal Escherichia coli reveals that bovine-adapted E. coli lineages are serving as evolutionary sources of the emergence of human intestinal pathogenic strains
- Yoko Arimizu,
- Yumi Kirino,
- Mitsuhiko P. Sato,
- Koichi Uno,
- Toshio Sato,
- Yasuhiro Gotoh,
- Frédéric Auvray,
- Hubert Brugere,
- Eric Oswald,
- Jacques G. Mainil,
- Kelly S. Anklam,
- Dörte Döpfer,
- Shuji Yoshino,
- Tadasuke Ooka,
- Yasuhiro Tanizawa,
- Yasukazu Nakamura,
- Atsushi Iguchi,
- Tomoko Morita-Ishihara,
- Makoto Ohnishi,
- Koichi Akashi,
- Tetsuya Hayashi,
- and Yoshitoshi Ogura
Genome Res. September 2019 29: 1495-1505; Published in Advance August 22, 2019, doi:10.1101/gr.249268.119
...Large-scale analysis of bovine commensal Escherichia coli reveals that bovine-adapted E. coli lineages are serving as evolutionary sources of the emergence of human intestinal pathogenic strains Yoko Arimizu1,2, Yumi Kirino3, Mitsuhiko P. Sato1, Koichi Uno4, Toshio Sato4, Yasuhiro Gotoh1, Frédéric...
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Perspective: Half dozen of one, six billion of the other: What can small- and large-scale molecular systems biology learn from one another?
- Ian A. Mellis and
- Arjun Raj
Genome Res. October 2015 25: 1466-1472; doi:10.1101/gr.190579.115
..., showing that the SNP changed expression of a particular gene, Small- and large-scale systems biology Genome Research 1469 www..org which then altered lipid levels in the blood (Musunuru et al. 2010). This example and others like it provides a beautiful arc from discovery to mechanism and is in many ways...
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