Searching journal content for articles similar to Peters et al. 25 (3): 426.

Displaying results 1-10 of 6194

For checked items

view abstracts
download to citation manager

Select this article
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...
OPEN ACCESS ARTICLE
Select this article
Method: De novo detection of somatic variants in high-quality long-read single-cell RNA sequencing data
- Arthur Dondi,
- Nico Borgsmüller,
- Pedro F. Ferreira,
- Brian J. Haas,
- Francis Jacob,
- Viola Heinzelmann-Schwarz,
- Tumor Profiler Consortium,
- and Niko Beerenwinkel
Genome Res. April 2025 35: 900-913; Published in Advance March 19, 2025, doi:10.1101/gr.279281.124
...identified by comparing variants from tumor biopsies with those from matched normal biopsies derived from respective healthy tissue. However, as matched normals are rarely available, methods to detect somatic variants de novo were developed for bulk sequencing, mainly relying on germline variant allele...
OPEN ACCESS ARTICLE
Select this article
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...
Select this article
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
..., which can be explained either by parthenogenesis or by self-fertilization. Because classic microsatellite analyses are insufficient to differentiate between the different forms of automictic parthenogenesis and selfing (Svendsen et al. 2015), we applied a whole- sequencing approach to compare the parent...
Select this article
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
...of the platinum NA12878. This three-generation family has been sequenced using two sequencing technologies and six variant calling pipelines (Eberle et al. 2017) to eliminate variant calling errors and to detect crossovers. We ran PhasingFamilies on one generation of the family, composed of NA12878, her husband...
Select this article
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
..., USA; 2NVIDIA Corporation, Santa Clara, California 95051, USA Corresponding author: wwang7@mdanderson.orgAbstractAccurate detection of somatic mutations in DNA sequencing data is a fundamental prerequisite for cancer research. Previous analytical challenges were overcome by consensus mutation calling...
OPEN ACCESS ARTICLE
Select this article
Research: Modest increase in the de novo single-nucleotide mutation rate in house mice born by assisted reproduction
- Laura Blanco-Berdugo,
- Alexis Garretson,
- and Beth L. Dumont
Genome Res. January 2026 36: 50-60; Published in Advance November 13, 2025, doi:10.1101/gr.281180.125
...found no evidence for an increased point mutation rate in animals born via in vitro fertilization (IVF) (Caperton et al. 2007), a retrospective comparative analysis in humans uncovered a significantly higher de novo point mutation rate in IVF-born children (Wang et al. 2021). However, the underlying...
Select this article
Method: Nanopore strand-specific mismatch enables de novo detection of bacterial DNA modifications
- Xudong Liu,
- Ying Ni,
- Lianwei Ye,
- Zhihao Guo,
- Lu Tan,
- Jun Li,
- Mengsu Yang,
- Sheng Chen,
- and Runsheng Li
Genome Res. November 2024 34: 2025-2038; Published in Advance October 2, 2024, doi:10.1101/gr.279012.124
...advancements over traditional bisulfite sequencing (Liu et al. 2023). However, the challenge of detecting bacterial DNA modifications persists, primarily due to their unique and diverse motifs (Roberts et al. 2023).Significant advancements have also been made in developing methods for detecting bacterial DNA...
Select this article
Research: Deciphering the largest disease-associated transcript isoforms in the human neural retina with advanced long-read sequencing approaches
- Merel Stemerdink,
- Tabea Riepe,
- Nick Zomer,
- Renee Salz,
- Michael Kwint,
- Jaap Oostrik,
- Raoul Timmermans,
- Barbara Ferrari,
- Stefano Ferrari,
- Alfredo Dueñas Rey,
- Emma Delanote,
- Suzanne E. de Bruijn,
- Hannie Kremer,
- Susanne Roosing,
- Frauke Coppieters,
- Alexander Hoischen,
- Frans P.M. Cremers,
- Peter A.C. ‘t Hoen,
- Erwin van Wijk,
- and Erik de Vrieze
Genome Res. April 2025 35: 725-739; Published in Advance March 4, 2025, doi:10.1101/gr.280060.124
...Bio) long-read mRNA isoform sequencing (Iso-Seq) technology (Wang et al. 2016) provides deeper insights into the transcriptome complexity caused by alternative splicing events. This technology eliminates the need for de novo transcript assembly, and consequently provides greater certainty...
Select this article
Research: The rate and spectrum of new mutations in mice inferred by long-read sequencing
- Eugenio López-Cortegano,
- Jobran Chebib,
- Anika Jonas,
- Anastasia Vock,
- Sven Künzel,
- Peter D. Keightley,
- and Diethard Tautz
Genome Res. January 2025 35: 43-54; Published in Advance December 2, 2024, doi:10.1101/gr.279982.124
...of de novo structural variation in mammals (e.g., Kloosterman et al. 2015; Belyeu et al. 2021; Steensma et al. 2023), but these studies have employed short-read technology, which limits the SMs detected primarily to copy-number variants and hinders the discovery of mutations within repetitive sequences...
OPEN ACCESS ARTICLE

For checked items

view abstracts
download to citation manager

Searching journal content for articles similar to Peters et al. 25 (3): 426.

Search Results

Modify Results

This search

Preprint Server

Current Issue

In This Issue

Citation format:
Results / page:
Results order: