Searching journal content for articles similar to Gouliouris et al. 29 (4): 626.

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Method: Secure phasing of private genomes in a trusted execution environment with TX-Phase
- Natnatee Dokmai,
- Kaiyuan Zhu,
- S. Cenk Sahinalp,
- and Hyunghoon Cho
Genome Res. December 2025 35: 2626-2636; Published in Advance November 12, 2025, doi:10.1101/gr.280558.125
...Secure phasing of private s in a trusted execution environment with TX-Phase Natnatee Dokmai1, Kaiyuan Zhu2, S. Cenk Sahinalp3 and Hyunghoon Cho1,4 1Department of Biomedical Informatics and Data Science, Yale School of Medicine, New Haven, Connecticut 06510, USA; 2Department of Computer Science...
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Research: Widespread natural selection on metabolite levels in humans
- Yanina Timasheva,
- Kaido Lepik,
- Orsolya Liska,
- Balázs Papp,
- and Zoltán Kutalik
Genome Res. August 2024 34: 1121-1129; Published in Advance August 16, 2024, doi:10.1101/gr.278756.123
.... First, evolutionarily distant species show substantial similarities in metabolite levels, indicating widespread evolutionary conservation of the metabolome (Ma et al. 2015; Park et al. 2016). Second, the levels of central metabolites obey simple optimality principles, indicating that metabolite levels...
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Research: A decade of genomic history for healthcare-associated Enterococcus faecium in the United Kingdom and Ireland
- Kathy E. Raven,
- Sandra Reuter,
- Rosy Reynolds,
- Hayley J. Brodrick,
- Julie E. Russell,
- M. Estée Török,
- Julian Parkhill,
- and Sharon J. Peacock
Genome Res. October 2016 26: 1388-1396; Published in Advance August 15, 2016, doi:10.1101/gr.204024.116
...hospital-adapted clonal lineage CC17 of Enterococcus faecium. J Clin Microbiol 44: 1059–1064. Lebreton F, van Schaik W, Mcguire AM, Godfrey P, Griggs A, Corander J, Cheng L, Saif S, Young S, Zeng Q, et al. 2013. Emergence of epidemic multidrug-resistant Enterococcus faecium from animal and commensal...
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Research: Widespread specific intron retention events in nuclear RNA complexes identified by sedimentation analysis of pluripotent cellular extracts
- Isabela T. Pereira,
- Izabela Mamede,
- Paulo P. Amaral,
- Gloria R. Franco,
- and John L. Rinn
Genome Res. October 2025 35: 2189-2198; Published in Advance August 26, 2025, doi:10.1101/gr.280431.125
...exported and translated. Now, our study has identified hundreds more GETs with specific retained introns in the nucleus—perhaps indicating this phenomenon of intron retention and “storage” is more widespread. This could also explain why GET-RIs are more resistant to degradation to ensure proper “storage...
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Research: Major impacts of widespread structural variation on sorghum
- Zhihai Zhang,
- Joao Paulo Gomes Viana,
- Bosen Zhang,
- Kimberly K.O. Walden,
- Hans Müller Paul,
- Stephen P. Moose,
- Geoffrey P. Morris,
- Chris Daum,
- Kerrie W. Barry,
- Nadia Shakoor,
- and Matthew E. Hudson
Genome Res. February 2024 34: 286-299; Published in Advance March 13, 2024, doi:10.1101/gr.278396.123
...associations between SVs and sorghum traits. The addition of SVs to GWAS substantially increased heritability estimates for some traits, indicating their important contribution to functional allelic variation at the level. Our discovery of the widespread impacts of SVs on heritable gene expression variation...
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Method: Accurate detection of tandem repeats from error-prone sequences with EquiRep
- Zhezheng Song,
- Tasfia Zahin,
- Xiang Li,
- and Mingfu Shao
Genome Res. December 2025 35: 2714-2721; Published in Advance August 21, 2025, doi:10.1101/gr.280750.125
..., USA ↵3 These authors contributed equally to this work. Corresponding author: mxs2589@psu.eduAbstractA tandem repeat is a sequence of nucleotides that appear as multiple contiguous, near-identical copies arranged consecutively. Tandem repeats are widespread across natural s, play critical roles...
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Method: Statistically rigorous and computationally efficient chromatin stripe detection with Quagga
- Fan Feng,
- Sean Moran,
- Anders S. Hansen,
- Xiaotian Zhang,
- and Jie Liu
Genome Res. January 2026 36: 159-168; Published in Advance November 12, 2025, doi:10.1101/gr.280132.124
...features in which a singular loop anchor interacts with a contiguous region of DNA so, at the bulk sequencing level, it appears as a long stripe on chromatin contact matrices. Stripes are thought to play an important role in gene regulation and have been implicated in regulating a cell's lineage...
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Method: Nanopore strand-specific mismatch enables de novo detection of bacterial DNA modifications
- Xudong Liu,
- Ying Ni,
- Lianwei Ye,
- Zhihao Guo,
- Lu Tan,
- Jun Li,
- Mengsu Yang,
- Sheng Chen,
- and Runsheng Li
Genome Res. November 2024 34: 2025-2038; Published in Advance October 2, 2024, doi:10.1101/gr.279012.124
...species, namely, Acinetobacter pittii (Liu et al. 2022), Bacillus cereus (Cui et al. 2016), Enterococcus faecium (Zheng et al. 2007), Escherichia coli (Chen et al. 2017), Klebsiella pneumoniae (Yang et al. 2019), Pseudomonas aeruginosa (Zhao et al. 2023), Salmonella enterica (Chen et al. 2020...
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Method: Rapid SARS-CoV-2 surveillance using clinical, pooled, or wastewater sequence as a sensor for population change
- Apurva Narechania,
- Dean Bobo,
- Kevin Deitz,
- Rob DeSalle,
- Paul J. Planet,
- and Barun Mathema
Genome Res. October 2024 34: 1651-1660; Published in Advance September 25, 2024, doi:10.1101/gr.278594.123
...into a variant sweep (Supplemental Fig. 11).The fact that we could not detect the transition between Alpha and Delta in San Diego wastewater indicates that real-time detection from complex sequence mixtures requires further study. The main issue is coverage. Our KHILL metric functions best with reads spread...
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Research: T2T-CHM13 improves read mapping and detection of clinically relevant genetic variation in the Swedish population
- Daniel Schmitz,
- Adam Ameur,
- and Åsa Johansson
Genome Res. November 2025 35: 2377-2388; Published in Advance September 16, 2025, doi:10.1101/gr.279320.124
...for the detection of many novel variants, especially in the previously unresolved regions. They also found that their novel reference reduces the number of false-positive calls mainly in protein-coding genes, and they highlight the increased sensitivity for detection of rare variants and singletons (Aganezov et al...
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