Searching journal content for articles similar to Zhou et al. 29 (3): 472.

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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
...sequence that is assigned to the four genomic contexts.Active CREs in tissues and cells are associated with increased chromatin accessibility (Keene et al. 1981; McGhee et al. 1981; Buenrostro et al. 2013). Thus, to study the contribution of TEs to the salmon CRE landscape, we integrated our TE annotation...
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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
..., Illumina, ONT, and PacBio) will be required to develop a more comprehensive truth set of indels for benchmarking. Resources such as the Platinum pedigree (CEPH pedigree 1463) by Illumina will be particularly useful as they enable studying phased assemblies and variant calling in the context of transmission...
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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
..., and the special inheritance status of the X Chromosome presents challenges. We have developed a hidden Markov model that addresses these issues by modeling the inheritance of variants in families in the presence of error-prone regions and inherited deletions. We call our method PhasingFamilies. We validate...
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Research: Comprehensive analysis of indels in whole-genome microsatellite regions and microsatellite instability across 21 cancer types
- Akihiro Fujimoto,
- Masashi Fujita,
- Takanori Hasegawa,
- Jing Hao Wong,
- Kazuhiro Maejima,
- Aya Oku-Sasaki,
- Kaoru Nakano,
- Yuichi Shiraishi,
- Satoru Miyano,
- Go Yamamoto,
- Kiwamu Akagi,
- Seiya Imoto,
- and Hidewaki Nakagawa
Genome Res. March 2020 30: 334-346; Published in Advance March 24, 2020, doi:10.1101/gr.255026.119
...in microsatellites for 2913 International Cancer Genome Consortium (ICGC) pan-cancer samples from 21 tissues (The International Cancer Genome Consortium 2010; The ICGC/TCGA Pan-Cancer Analysis of Whole Genomes Consortium 2020) to reveal the whole- mutational landscape of microsatellite regions. We developed a method...
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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
...clusters in sequential models to, for example, infer local ancestry and IBD tracts in hidden Markov models, as well as investigate its potential integration into imputation based on haplotype reconstruction and association studies.MethodsThe method is based on phased haplotype data from diallelic markers...
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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
...and two offspring at the full genomic level. We also integrated data from a presumed unrelated individual caught in the wild from the same source population at the same time as the parental individual and kept under the same conditions.ResultsOne wild-caught individual of the species B. nigrodorsalis...
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Method: Whole-genome bisulfite sequencing with improved accuracy and cost
- Masako Suzuki,
- Will Liao,
- Frank Wos,
- Andrew D. Johnston,
- Justin DeGrazia,
- Jennifer Ishii,
- Toby Bloom,
- Michael C. Zody,
- Soren Germer,
- and John M. Greally
Genome Res. September 2018 28: 1364-1371; Published in Advance August 9, 2018, doi:10.1101/gr.232587.117
...enough coverage to represent cytosines at CG dinucleotides and elsewhere in the , the amount of sequencing required has been too costly for most research budgets. The decision has therefore been made to sacrifice comprehensiveness and to survey the instead, attempting to focus on the loci believed...
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Research: Cell cycle arrest explains the observed bulk 3D genomic alterations in response to long-term heat shock in K562 cells
- Bingxiang Xu,
- Xiaomeng Gao,
- Xiaoli Li,
- Yan Jia,
- Feifei Li,
- and Zhihua Zhang
Genome Res. July 2022 32: 1285-1297; Published in Advance July 14, 2022, doi:10.1101/gr.276554.122
...and chromatin accessibility respond differently in short- and long-term heat shock in human K562 cells. We found that chromatin conformation in K562 cells was largely stable in response to short-term heat shock, whereas it showed clear and characteristic changes after long-term heat treatment with little...
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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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Method: DNA-m6A calling and integrated long-read epigenetic and genetic analysis with fibertools
- Anupama Jha,
- Stephanie C. Bohaczuk,
- Yizi Mao,
- Jane Ranchalis,
- Benjamin J. Mallory,
- Alan T. Min,
- Morgan O. Hamm,
- Elliott Swanson,
- Danilo Dubocanin,
- Connor Finkbeiner,
- Tony Li,
- Dale Whittington,
- William Stafford Noble,
- Andrew B. Stergachis,
- and Mitchell R. Vollger
Genome Res. November 2024 34: 1976-1986; Published in Advance June 7, 2024, doi:10.1101/gr.279095.124
...and epigenetic analyses of long-read data within structurally and somatically variable genomic regions.Highly accurate long-read single-molecule DNA sequencing has revolutionized the comprehensive assembly of phased genetic architectures, enabling the first complete human assemblies (Wenger et al. 2019; Vollger...

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