Searching journal content for articles similar to Parey et al. 32 (9): 1685.

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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
...regulatory phenotypes have been partly linked to divergent TE insertions in promoters of gene duplicates (Gillard et al. 2021; Sahlström et al. 2023), but the link between WGD and TE-CRE evolution has remained elusive. One hypothesis is that WGDs induce a genomic shock that results in bursts of TE activity...
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Method: Gene duplication is associated with gene diversification and potential neofunctionalization in lung cancer evolution
- Paul Ashford,
- Alexander M. Frankell,
- Zofia Piszka,
- Camilla S.M. Pang,
- Mahnaz Abbasian,
- Maise Al Bakir,
- Mariam Jamal-Hanjani,
- Nicholas McGranahan,
- Charles Swanton,
- and Christine A. Orengo
Genome Res. March 2026 36: 561-577; Published in Advance February 19, 2026, doi:10.1101/gr.278663.123
...; and neofunctionalization, in which duplicates evolve new functions (Taylor and Raes 2004; Hahn 2009; Kondrashov 2012; Kuzmin et al. 2022). Genome sequencing has supported the view that whole- duplication (WGD) events frequently occur during evolution across all domains of life, with many plant species retaining polyploid...
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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: 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
...of species reveals unique insights into centromere evolution. Genome Biol 14: R10. doi:10.1186/gb-2013-14-1-r10 ↵Meuthen D, Baldauf SA, Bakker TCM, Thünken T. 2016. Conspecific alarm cues affect interspecific aggression in cichlid fishes. Hydrobiologia 767: 37–49. doi:10.1007/s10750-015-2473-0 ↵Neaves WB...
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Mini-Review: Evolution of genome-wide methylation profiling technologies
- Carolina Montano and
- Winston Timp
Genome Res. April 2025 35: 572-582; doi:10.1101/gr.278407.123
...in particular genes (Grafodatskaya et al. 2013; Barbosa et al. 2018). Illumina's Infinium MethylationEPIC array, which targets nearly a million methylation sites, is the most widely used platform for this analysis. Microarray methylation data, e.g., The Cancer Genome Atlas (TCGA) Research Network...
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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
.... Eichler1,8 1Department of Genome Sciences, University of Washington School of Medicine, Seattle, Washington 98195-5065, USA; 2Institute for Medical Biometry and Bioinformatics, Medical Faculty, Heinrich Heine University, 40225 Düsseldorf, Germany; 3Core Unit Bioinformatics, Medical Faculty, Heinrich Heine...
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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
...multiple family members at high rates (Paskov et al. 2021). Large structural variants such as deletions and duplications may also hinder attempts to identify crossovers in families by producing genomic regions with unusual, non-Mendelian variant patterns (Roach et al. 2010).Several approaches have been...
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Research: Stable genome structures in living fossil fishes
- Cheng Wang,
- Chase D. Brownstein,
- Wenjun Chen,
- Zufa Ding,
- Dan Yu,
- Yu Deng,
- Chenguang Feng,
- Thomas J. Near,
- Shunping He,
- and Liandong Yang
Genome Res. February 2026 36: 318-329; Published in Advance January 13, 2026, doi:10.1101/gr.280800.125
...contributed equally to this work. Corresponding authors: thomas.near@yale.edu, clad@ihb.ac.cn, yangliandong1987@163.comAbstractGenomic evolution can propel and restrict species diversification. Rapid molecular evolution and genomic rearrangement is often associated with increased species diversification...
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Research: Whole-genome resequencing of temporally stratified samples reveals substantial loss of haplotype diversity in the highly inbred Scandinavian wolf population
- Agnese Viluma,
- Øystein Flagstad,
- Mikael Åkesson,
- Camilla Wikenros,
- Håkan Sand,
- Petter Wabakken,
- and Hans Ellegren
Genome Res. March 2022 32: 449-458; Published in Advance February 8, 2022, doi:10.1101/gr.276070.121
...of Scandinavian wolvesDiscussionBy analyzing 76 whole s from temporal subsamples of Scandinavian wolves, we illustrate the possibility of direct quantification of genomic erosion in a highly inbred natural population (Fig. 6). Our data reveal considerable loss of large haplotype segments, sometimes spanning...
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Resource: Generation and analysis of a mouse multitissue genome annotation atlas
- Matthew Adams and
- Christopher Vollmers
Genome Res. November 2024 34: 2108-2117; Published in Advance October 23, 2024, doi:10.1101/gr.279217.124
...DNA consensus reads—averaging 5.4 million reads per tissue for a dozen tissues. Using the Mandalorion tool, we processed these reads to generate the Tissue-level Atlas of Mouse Isoforms which is available as a trackhub for the UCSC Genome Browser and contains at least one full-length isoform for the vast...
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