Searching journal content for articles similar to Kato-Maeda et al. 11 (4): 547.

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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
...emerged transcription of a pre-existing ORF. (B) De novo gene emergence from a frameshifted gene sequence. (Created with BioRender; https://www.biorender.com/.)Merging comparative genomic and transcriptomic data allow detection of both the lineage-specific transcripts and the mutations responsible...
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Method: A high-throughput screening method for selecting feature SNPs to evaluate breed diversity and infer ancestry
- Meilin Zhang,
- Heng Du,
- Yu Zhang,
- Yue Zhuo,
- Zhen Liu,
- Yahui Xue,
- Lei Zhou,
- Sixuan Zhou,
- Wanying Li,
- and Jian-Feng Liu
Genome Res. August 2025 35: 1875-1886; Published in Advance July 15, 2025, doi:10.1101/gr.280176.124
..., the evaluation of the breed diversity and ancestries of the population directly based on genomics has gradually been used instead of statistical inferences based on pedigree information.Various marker-based techniques are available for analyzing the breed diversity and ancestries of populations (Yaro et al. 2017...
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Research: Oxygen-induced stress reveals context-specific gene regulatory effects in human brain organoids
- Benjamin D. Umans and
- Yoav Gilad
Genome Res. August 2025 35: 1689-1700; Published in Advance June 2, 2025, doi:10.1101/gr.280219.124
...correspondingly, 2855 hyperoxia-responsive genes) exhibited a greater than 1.5-fold change in expression compared to baseline. As expected, we detected far more DE genes in abundant cell types (Supplemental Fig. S2C), within which 76%–92% of hypoxia-evoked transcriptional effects and 84%–93% of hyperoxia...
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Method: Optimizing nanopore adaptive sampling for pneumococcal serotype surveillance in complex samples using the graph-based GNASTy algorithm
- Samuel T. Horsfield,
- Basil C.T. Fok,
- Yuhan Fu,
- Paul Turner,
- John A. Lees,
- and Nicholas J. Croucher
Genome Res. April 2025 35: 1025-1040; Published in Advance March 4, 2025, doi:10.1101/gr.279435.124
...Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton CB10 1SA, United Kingdom; 3Centre for Tropical Medicine and Global Health, University of Oxford, Oxford OX3 7LG, United Kingdom ↵4 These authors contributed equally to this work. Corresponding author: shorsfield...
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Method: Seamless, rapid, and accurate analyses of outbreak genomic data using split k-mer analysis
- Romain Derelle,
- Johanna von Wachsmann,
- Tommi Mäklin,
- Joel Hellewell,
- Timothy Russell,
- Ajit Lalvani,
- Leonid Chindelevitch,
- Nicholas J. Croucher,
- Simon R. Harris,
- and John A. Lees
Genome Res. October 2024 34: 1661-1673; Published in Advance October 15, 2024, doi:10.1101/gr.279449.124
...track of k-mer counts, even in relatively small sequencing experiments, takes >90% of the runtime, so filtering on the minimum observation count is an important optimization target. For simulated 150 bp paired-end reads from Mycobacterium tuberculosis at 60× coverage, a baseline of keeping counts...
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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
...from annotation errors, because they are typically detected by comparative genomics approaches. These in turn rely on the automatic prediction of protein-coding open reading frames (ORFs) and sequence similarity searches between species, both potential sources of artifacts in the form of spurious ORFs...
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Research: Dynamic DNA N⁶-adenine methylation (6mA) governs the encystment process, showcased in the unicellular eukaryote Pseudocohnilembus persalinus
- Yongqiang Liu,
- Junhua Niu,
- Fei Ye,
- Therese Solberg,
- Borong Lu,
- Chundi Wang,
- Mariusz Nowacki,
- and Shan Gao
Genome Res. February 2024 34: 256-271; Published in Advance March 12, 2024, doi:10.1101/gr.278796.123
...in various biological studies including epigenetics, cell biology, and genomics (Nowacki et al. 2008; Cheng et al. 2019; Liu et al. 2021; Zhao et al. 2021; Zheng et al. 2021; Tian et al. 2022; Wei et al. 2022; Jin et al. 2023; Solberg et al. 2023; Zhang et al. 2023). A characteristic feature of ciliates...
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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
....ggCaller accurately represents pans of bacterial species with varying levels of diversityTo benchmark ggCaller on real-world data, we analyzed sequences from three bacterial species with varying patterns of pan diversity. Mycobacterium tuberculosis is a slow-replicating respiratory pathogen with a low mutation rate...
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Research: Genetic control of the dynamic transcriptional response to immune stimuli and glucocorticoids at single-cell resolution
- Justyna A. Resztak,
- Julong Wei,
- Samuele Zilioli,
- Edward Sendler,
- Adnan Alazizi,
- Henriette E. Mair-Meijers,
- Peijun Wu,
- Xiaoquan Wen,
- Richard B. Slatcher,
- Xiang Zhou,
- Francesca Luca,
- and Roger Pique-Regi
Genome Res. June 2023 33: 839-856; Published in Advance July 13, 2023, doi:10.1101/gr.276765.122
...–environment interaction effects have a major role in immunological phenotypes (Martin et al. 2021). Genome-wide association studies (GWAS) have successfully identified hundreds of variants associated with autoimmune and allergic disease risk. For example, genetic associations from GWAS explain up to 33...
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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
...2005). Genes are also frequently duplicated and lost vertically upon cell division (Arnold et al. 2022). The influence of these sources of variation varies by species. Clonal species such as Mycobacterium tuberculosis (Mtb) typically accumulate variation nearly entirely through point mutations, whereas...
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