Searching journal content for articles similar to Leshchiner et al. 22 (8): 1541.

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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
...-Cancer Analysis of Whole Genomes Consortium 2020), across approximately 2700 tumor samples.One major limitation of MuSE 1, like many other mutation callers (Koboldt et al. 2012; Larson et al. 2012; Cibulskis et al. 2013), is the computational speed. It takes 2–3 d to finish running the WGS data of a tumor...
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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
...elements, but that this association is not driven by higher transposition activities of CRE-superspreader TE subfamilies.Coexpression analysis support TE-CRE driven regulatory network evolutionIf TEs are spreading CREs with sequences that either have a potent TF binding motif or are prone to mutate...
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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
...Whole- long-read sequencing downsampling and its effect on variant-calling precision and recall William T. Harvey1, Peter Ebert2,3,4, Jana Ebler2,4, Peter A. Audano5, Katherine M. Munson1, Kendra Hoekzema1, David Porubsky1, Christine R. Beck5,6, Tobias Marschall2,4, Kiran Garimella7 and Evan E...
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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
.... A uniform recombination rate of 1.0 × 10−8 has been assumed in all simulations as well as a mutation rate of 2.36 × 10−8 (Tennessen et al. 2012) for a sequence of 1.0 × 109 bases.Simulation 1 has the following population split times: t1 = 100, t2 = 60, t3 = 40, and t4 = 20 with an assumed constant...
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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
...in their nuclear organization and topological features, which prevented rediploidization, whereas sequence exchanges at LORe loci on other homeologs may have been locally maintained as a result of selection, for example by removing deleterious mutations or transferring favorable alleles at all gene loci...
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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
..., including loss of segregating variants. However, there is a shortage of quantitative studies of how genetic diversity changes over time in natural populations, especially on -wide scales. Here, we analyzed whole- sequences from 76 wolves of a highly inbred Scandinavian population, founded by only one female...
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Perspective: Unraveling the hidden complexity of cancer through long-read sequencing
- Qiuhui Li,
- Ayse G. Keskus,
- Justin Wagner,
- Michal B. Izydorczyk,
- Winston Timp,
- Fritz J. Sedlazeck,
- Alison P. Klein,
- Justin M. Zook,
- Mikhail Kolmogorov,
- and Michael C. Schatz
Genome Res. April 2025 35: 599-620; Published in Advance March 20, 2025, doi:10.1101/gr.280041.124
...leading to the clonal evolution of cancer cells (Qing et al. 2020; Chakravarty and Solit 2021). Somatic mutations in key genes and their regulatory sequences, especially oncogenes, tumor suppressors, and DNA repair genes, are frequently found in cancers and contribute to tumor progression and therapeutic...
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Research: Low-frequency somatic copy number alterations in normal human lymphocytes revealed by large-scale single-cell whole-genome profiling
- Lu Liu,
- He Chen,
- Cheng Sun,
- Jianyun Zhang,
- Juncheng Wang,
- Meijie Du,
- Jie Li,
- Lin Di,
- Jie Shen,
- Shuang Geng,
- Yuhong Pang,
- Yingying Luo,
- Chen Wu,
- Yusi Fu,
- Zhe Zheng,
- Jianbin Wang,
- and Yanyi Huang
Genome Res. January 2022 32: 44-54; Published in Advance December 28, 2021, doi:10.1101/gr.275453.121
...and robust method to perform uniform single-cell whole- amplification (WGA) is the main challenge to improving the accuracy and precision of somatic CNA identification.In this report, we present a high-throughput single-cell WGA and sequencing method: Tn5-transposase–assisted single-cell whole- sequencing...
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Method: Whole-genome analysis of noncoding genetic variations identifies multiscale regulatory element perturbations associated with Hirschsprung disease
- Alexander Xi Fu,
- Kathy Nga-Chu Lui,
- Clara Sze-Man Tang,
- Ray Kit Ng,
- Frank Pui-Ling Lai,
- Sin-Ting Lau,
- Zhixin Li,
- Maria-Mercè Garcia-Barcelo,
- Pak-Chung Sham,
- Paul Kwong-Hang Tam,
- Elly Sau-Wai Ngan,
- and Kevin Y. Yip
Genome Res. November 2020 30: 1618-1632; Published in Advance September 18, 2020, doi:10.1101/gr.264473.120
...@hku.hk, engan@hku.hk, kevinyip@cse.cuhk.edu.hkAbstractIt is widely recognized that noncoding genetic variants play important roles in many human diseases, but there are multiple challenges that hinder the identification of functional disease-associated noncoding variants. The number of noncoding variants can...

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