Searching journal content for articles similar to Lucas et al. 29 (8): 1250.

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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
...with annotations of accessible chromatin regions identified using ATAC-seq data from the liver and brain. Analysis of the overlap between TEs and accessible chromatin revealed a large depletion of TEs in accessible chromatin. Although TEs represent ∼52% of the sequence, TE insertions only represent <20...
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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
...years has revolutionized our ability to catalog cancer risk variants and understand the genomic landscape of cancer. Early studies relied on targeted sequencing and microarrays to detect genomic and transcriptomic variations enriched in cancer patients, revealing, for example, the prevalence...
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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
...-mer-spectra analysis revealed a similar size across all four sequenced individuals (mean size across k-mer sizes 20, 30, and 40: 800–817 Mb) and pointed toward lower estimates of -wide heterozygosity in both offspring (mean heterozygosity across k-mer sizes 20, 30, and 40; wildI: 0.097%, parent: 0.119%, offspring1: 0...
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Method: Genotyping of selected germline adaptive immune system loci using short-read sequencing data
- Michael K.B. Ford,
- Ananth Hari,
- Meredith Yeager,
- Lisa Mirabello,
- Stephen Chanock,
- Ibrahim Numanagić,
- COVNET Consortium,
- and S. Cenk Sahinalp
Genome Res. September 2025 35: 2076-2086; Published in Advance August 5, 2025, doi:10.1101/gr.280314.124
...diagnoses and treatments based on patients’ genetic and environmental circumstances. A critical component of a person's physiological makeup is their immune system, but individual genetic variation in many immune system genes has remained resistant to analysis using classical whole- or targeted sequencing...
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Method: High-resolution genotype-free mapping of genetic variation with CRI-SPA-Map
- Sheila Lutz,
- Megan Lawler,
- Samuel Amidon,
- and Frank W Albert
Genome Res. March 23, 2026 gr.281514.125; Published in Advance March 23, 2026, doi:10.1101/gr.281514.125
...a small effect on the trait, but due to the large number of 39 causal variants, they contribute substantially to trait variation. 40 Two main experimental designs are used to dissect genetic variation in complex traits. Genetic 41 mapping by linkage analysis involves crossing genetically different...
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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
...) technologies continue to make whole- sequencing more complete, affordable, and accurate. LRS provides significant advantages over short-read sequencing approaches, including phased de novo assembly, access to previously excluded genomic regions, and discovery of more complex structural variants (SVs...
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Research: Long-read sequencing reveals HBV integration patterns and oncogenic impact on early-onset hepatocellular carcinoma
- Yao Wang,
- Dong Yu,
- Yue Mei,
- ZhiDa Fu,
- Jian Lin,
- Di Wu,
- Yuan Yang,
- and Hongli Yan
Genome Res. November 2025 35: 2389-2405; Published in Advance September 16, 2025, doi:10.1101/gr.279889.124
...and transcriptomic levels, along with their regulatory effects on structural variations (SVs) and gene expression. Functional validation is performed using dual-luciferase assays and cell-based experiments. Our findings reveal that integrated HBV sequences form long concatemers, mediating inter- and intrachromosomal...
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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
...be used to identify crossovers from family sequencing data.As whole- sequencing (WGS) becomes ubiquitous, large family-based cohorts are now available, which have the potential to reveal more about how genetic material is transmitted within families and about how shared genetic material contributes...
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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
..., such as single-nucleotide variation (SNV), copy number alteration (CNA), and structural variation (SV). The high-throughput sequencing (HTS) technology has revolutionized the way we look at many human diseases, particularly cancer. With its constantly improved capacity and reduced cost, HTS is enabling...
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Method: Parallel analysis of replication timing, gene expression, and copy number with PARTAGE
- Lakshana Sruthi Sadu Murari,
- Quinn Dickinson,
- Silvia Meyer-Nava,
- and Juan Carlos Rivera-Mulia
Genome Res. March 19, 2026 ; Published in Advance March 19, 2026, doi:10.1101/gr.281532.125
...of RT and transcriptomes from independent batches of samples, which obscures the complex coregulation between the epi and transcriptome. Here, we present PARTAGE, a multiomics approach that enables joint profiling of copy number variation (CNV), RT, and gene expression from the same sample, providing...
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