Searching journal content for articles similar to Swinnen et al. 22 (5): 975.

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Research: The role of transposon activity in shaping cis-regulatory element evolution after whole-genome duplication
- Øystein Monsen,
- Lars Grønvold,
- Alex Datsomor,
- Thomas Harvey,
- James Kijas,
- Alexander Suh,
- Torgeir R. Hvidsten,
- and Simen Rød Sandve
Genome Res. March 2025 35: 475-488; Published in Advance February 12, 2025, doi:10.1101/gr.278931.124
...) and tissues (Fig. 3D–G). We find that in promoters the proportion of TEs in open chromatin decreases toward a transcription start site (TSS) and the gene body, probably reflecting increased purifying selection pressure (less tolerance for TE insertions) inside the gene body.Furthermore, we find that close...
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Research: Evidence for selfing in a vertebrate from whole-genome sequencing
- Astrid Böhne,
- Zeynep Oğuzhan,
- Ioannis Chrysostomakis,
- Simon Vitt,
- Denis Meuthen,
- Sebastian Martin,
- Sandra Kukowka,
- and Timo Thünken
Genome Res. December 2023 33: 2133-2142; Published in Advance December 7, 2023, doi:10.1101/gr.277368.122
..., the Nile tilapia O. niloticus (assembly version GCF_001858045.2), which was previously determined as a suitable reference for analyzing cichlid whole- sequencing Illumina data, including the genus Benitochromis (Matschiner et al. 2020).Variant identificationThe resulting alignments (average read mapping...
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Research: Whole-genome long-read sequencing downsampling and its effect on variant-calling precision and recall
- William T. Harvey,
- Peter Ebert,
- Jana Ebler,
- Peter A. Audano,
- Katherine M. Munson,
- Kendra Hoekzema,
- David Porubsky,
- Christine R. Beck,
- Tobias Marschall,
- Kiran Garimella,
- and Evan E. Eichler
Genome Res. December 2023 33: 2029-2040; Published in Advance December 7, 2023, doi:10.1101/gr.278070.123
....9] (Kolmogorov et al. 2019).We set out to determine how variant-calling performance differs depending on the platform, depth of sequence coverage (×), and computational method. For this assessment, we generated downsampled sets of HiFi and both standard and ultra-long ONT (UL-ONT) sequence data at depths of 5, 8...
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Method: Accelerated somatic mutation calling for whole-genome and whole-exome sequencing data from heterogenous tumor samples
- Shuangxi Ji,
- Tong Zhu,
- Ankit Sethia,
- and Wenyi Wang
Genome Res. April 2024 34: 633-641; Published in Advance April 8, 2024, doi:10.1101/gr.278456.123
...as a major contributing caller to reach final consensus calls by The Cancer Genome Atlas (TCGA) PanCanAtlas project (Ellrott et al. 2018), across approximately 13,000 tumor samples, and the International Cancer Genome Consortium Pan-Cancer Analysis of Whole Genomes (ICGC-PCAWG) initiative (The ICGC/TCGA Pan...
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Research: An atlas of fish genome evolution reveals delayed rediploidization following the teleost whole-genome duplication
- Elise Parey,
- Alexandra Louis,
- Jérôme Montfort,
- Yann Guiguen,
- Hugues Roest Crollius,
- and Camille Berthelot
Genome Res. September 2022 32: 1685-1697; Published in Advance August 12, 2022, doi:10.1101/gr.276953.122
..., and physiological genomics, illuminating processes such as environmental adaptation, species diversification, social behavior, or sex determination (Rittschof et al. 2014; Capel 2017; Salzburger 2018; Kim et al. 2019; Xie et al. 2019; Greenway et al. 2020). Around two hundred fish species have reference assemblies...
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Method: Genome-wide maps of CPD deamination in yeast reveal the impact of DNA sequence context and nucleosome architecture on cytosine deamination rates
- Marian F. Laughery,
- Bastian Stark,
- Benjamin Morledge-Hampton,
- Steven A. Roberts,
- and John J. Wyrick
Genome Res. January 2026 36: 183-196; Published in Advance December 9, 2025, doi:10.1101/gr.280384.124
...and human melanomas are elevated at fast-deaminating TCG sequences, occurring about three- to fivefold more frequently than expected from the levels of damage formation (Fig. 3H).CPD deamination is suppressed near the transcription start and end sites of yeast genesTo determine how CPD deamination...
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Research: Copy number variation alters local and global mutational tolerance
- Grace Avecilla,
- Pieter Spealman,
- Julia Matthews,
- Elodie Caudal,
- Joseph Schacherer,
- and David Gresham
Genome Res. August 2023 33: 1340-1353; Published in Advance August 31, 2023, doi:10.1101/gr.277625.122
..., and mitotic stress (Zhu et al. 2018). These effects may also be background dependent as one study mapped differences in aneuploidy tolerance between W303 and wild yeast strains to a single gene, SSD1, which has a truncating mutation in W303 (Hose et al. 2020). SSD1 is an RNA-binding translational regulator...
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Method: Identifying crossovers and shared genetic material in whole genome sequencing data from families
- Kelley Paskov,
- Brianna Chrisman,
- Nathaniel Stockham,
- Peter Yigitcan Washington,
- Kaitlyn Dunlap,
- Jae-Yoon Jung,
- and Dennis P. Wall
Genome Res. October 2023 33: 1747-1756; Published in Advance October 25, 2023, doi:10.1101/gr.277172.122
...sequencing data is spurious crossover calls caused by variant calling errors. This issue is exacerbated in WGS owing to its higher error rate compared with microarray data, paired with the existence of error-prone regions of the (low complexity regions, microsatellites, etc.) where errors occur across...
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Method: Haplotype and population structure inference using neural networks in whole-genome sequencing data
- Jonas Meisner and
- Anders Albrechtsen
Genome Res. August 2022 32: 1542-1552; Published in Advance July 6, 2022, doi:10.1101/gr.276813.122
..., we capture structure that does not reflect population structure but instead captures variation that could be owing to SNP ascertainment or strong LD structure as previously observed for the UK Biobank (Privé et al. 2020). The signal is caused by a single genomic region as shown by the SNP loadings...
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Method: TraDIS-Xpress: a high-resolution whole-genome assay identifies novel mechanisms of triclosan action and resistance
- Muhammad Yasir,
- A. Keith Turner,
- Sarah Bastkowski,
- David Baker,
- Andrew J. Page,
- Andrea Telatin,
- Minh-Duy Phan,
- Leigh Monahan,
- George M. Savva,
- Aaron Darling,
- Mark A. Webber,
- and Ian G. Charles
Genome Res. February 2020 30: 239-249; Published in Advance February 12, 2020, doi:10.1101/gr.254391.119
.... Differences in insertion sites when grown in different conditions identify genes involved in survival of any given test condition. However, traditional TraDIS protocols have been limited by being unable to assay essential genes that do not tolerate any insertions within them, as well as by being costly...
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