Searching journal content for articles similar to Kumar et al. 14 (10a): 1975.

Displaying results 1-10 of 6311

For checked items

view abstracts
download to citation manager

Select this article
Research: APOBEC3A drives deaminase mutagenesis in human gastric epithelium
- Yohan An,
- Ji-Hyun Lee,
- Joonoh Lim,
- Jeonghwan Youk,
- Seongyeol Park,
- Ji-Hyung Park,
- Kijong Yi,
- Taewoo Kim,
- Chang Hyun Nam,
- Won Hee Lee,
- Soo A Oh,
- Yoo Jin Bae,
- Thomas M. Klompstra,
- Haeun Lee,
- Jinju Han,
- Junehwak Lee,
- Jung Woo Park,
- Jie-Hyun Kim,
- Hyunki Kim,
- Hugo Snippert,
- Bon-Kyoung Koo,
- and Young Seok Ju
Genome Res. October 2025 35: 2158-2172; Published in Advance August 26, 2025, doi:10.1101/gr.280338.124
...cassettes into the of gastric organoids (1) expressing rtTA and hygromycin B resistance protein (CMV-rtTA-HygR), and (2) expressing APOBEC enzymes and fluorescence protein (TRE-APOBEC (A3A or A3B)-IRES-mCherry) using the piggyBac transposon system (Fig. 1A; Woodard and Wilson 2015; Wilson et al. 2007...
OPEN ACCESS ARTICLE
Select this article
Method: ScisTree2 enables large-scale inference of cell lineage trees and genotype calling using efficient local search
- Haotian Zhang,
- Yiming Zhang,
- Teng Gao,
- and Yufeng Wu
Genome Res. December 2025 35: 2781-2791; Published in Advance September 3, 2025, doi:10.1101/gr.280542.125
...analyses in cancer genomics.The ability of ScisTree2 to analyze a large number of cells may be useful in large-scale cancer genomics analyses. One such analysis is identifying rare cancer subclones, which can drive disease recurrence and therapy resistance. For example, relapse of acute myeloid leukemia...
OPEN ACCESS ARTICLE
Select this article
Method: High-fidelity, large-scale targeted profiling of microsatellites
- Caitlin A. Loh,
- Danielle A. Shields,
- Adam Schwing,
- and Gilad D. Evrony
Genome Res. July 2024 34: 1008-1026; Published in Advance July 16, 2024, doi:10.1101/gr.278785.123
...tools enables high-fidelity, large-scale profiling of microsatellites, which may find utility in diverse applications such as lineage tracing, population genetics, ecology, and forensics.Microsatellites, also known as short tandem repeats, are genomic sequences composed of tandem repeats of short (1...
Select this article
Research: Large-scale investigation of species-specific orphan genes in the human gut microbiome elucidates their evolutionary origins
- Nikolaos Vakirlis and
- Anne Kupczok
Genome Res. June 2024 34: 888-903; Published in Advance July 8, 2024, doi:10.1101/gr.278977.124
...; and they are more aggregation-prone, have a higher biosynthetic cost, and a higher isoelectric point (the latter was also observed for de novo genes in yeast and fly) (Blevins et al. 2021; Montañés et al. 2023). All these differences hold when considering each taxonomic class individually (Supplemental Fig. S8...
Select this article
Method: High-throughput and genome-scale targeted mutagenesis using CRISPR in a nonmodel multicellular organism, Bombyx mori
- Sanyuan Ma,
- Tong Zhang,
- Ruolin Wang,
- Pan Wang,
- Yue Liu,
- Jiasong Chang,
- Aoming Wang,
- Xinhui Lan,
- Le Sun,
- Hao Sun,
- Run Shi,
- Wei Lu,
- Dan Liu,
- Na Zhang,
- Wenbo Hu,
- Xiaogang Wang,
- Weiqing Xing,
- Ling Jia,
- and Qingyou Xia
Genome Res. January 2024 34: 134-144; Published in Advance January 8, 2024, doi:10.1101/gr.278297.123
...a large-scale mutant library using a nonmodel organism. Furthermore, because we used piggyBac transposon, which can drive gene delivery in a wide range of eukaryotes and has the largest reported cargo capacity (Wu et al. 2007; Chang et al. 2019; Li et al. 2020) as the delivery strategy, the results...
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
...in shaping evolution of retroelement-associated TE-CRE landscapes in Atlantic salmon.Although retroelements dominate the salmon TE-CRE landscape, the role of DNA transposons such as DTA and DTT elements in TE-CRE evolution cannot be neglected owing to their high genomic copy numbers (Figs. 1, 3A). Indeed...
Select this article
Method: Genome-wide maps of CPD deamination in yeast reveal the impact of DNA sequence context and nucleosome architecture on cytosine deamination rates
- Marian F. Laughery,
- Bastian Stark,
- Benjamin Morledge-Hampton,
- Steven A. Roberts,
- and John J. Wyrick
Genome Res. January 2026 36: 183-196; Published in Advance December 9, 2025, doi:10.1101/gr.280384.124
...to UV mutagenesis. However, the impact of genomic context and chromatin architecture on CPD deamination rates in cells remains poorly understood. Here, we develop a method known as dCPD-seq to map deaminated CPDs (dCPDs) across the of repair-deficient yeast cells at single-nucleotide resolution. Our d...
OPEN ACCESS ARTICLE
Select this article
Method: Secure discovery of genetic relatives across large-scale and distributed genomic data sets
- Matthew M. Hong,
- David Froelicher,
- Ricky Magner,
- Victoria Popic,
- Bonnie Berger,
- and Hyunghoon Cho
Genome Res. September 2024 34: 1312-1323; Published in Advance August 7, 2024, doi:10.1101/gr.279057.124
...-Relate on the UK Biobank and All of Us data sets. On a data set of 200,000 individuals split between two parties, SF-Relate detects 97% of third-degree or closer relatives within 15 h of runtime. Our work enables secure identification of relatives across large-scale genomic data sets.Collaborative studies that aim...
OPEN ACCESS ARTICLE
Select this article
Mini-Review: Large-scale genomic analysis of the domestic dog informs biological discovery
- Reuben M. Buckley and
- Elaine A. Ostrander
Genome Res. June 2024 34: 811-821; Published in Advance July 2, 2024, doi:10.1101/gr.278569.123
...this gene could provide a viable therapeutic target in dogs (Urick and Bell 2020; Kawaguchi et al. 2021; Urick et al. 2021).Sequencing strategies for large-scale genomic analysesIn the past 10 years, there has been a steady decrease in the cost of short-read whole- sequencing (WGS) (Cullen and Friedenberg...
OPEN ACCESS ARTICLE
Select this article
Resource: CGC1, a new reference genome for Caenorhabditis elegans
- Kazuki Ichikawa,
- Massa J. Shoura,
- Karen L. Artiles,
- Dae-Eun Jeong,
- Chie Owa,
- Haruka Kobayashi,
- Yoshihiko Suzuki,
- Manami Kanamori,
- Yu Toyoshima,
- Yuichi Iino,
- Ann E. Rougvie,
- Lamia Wahba,
- Andrew Z. Fire,
- Erich M. Schwarz,
- and Shinichi Morishita
Genome Res. August 2025 35: 1902-1918; Published in Advance July 15, 2025, doi:10.1101/gr.280274.124
...of ribosomal RNA genes are observed in other species such as budding yeast and humans (Hori et al. 2023), we investigated how the 45S rDNA array of CGC1 differs from arrays in other C. elegans strains. For this, we analyzed publicly available PacBio HiFi read data sets from two strains “DLW N2 Bristol...
OPEN ACCESS ARTICLE

For checked items

view abstracts
download to citation manager

Searching journal content for articles similar to Kumar et al. 14 (10a): 1975.

Search Results

Modify Results

This search

Preprint Server

Current Issue

In This Issue

Citation format:
Results / page:
Results order: