Searching journal content for articles similar to Carlson et al. 25 (8): 1244.

Displaying results 1-10 of 5626

For checked items

view abstracts
download to citation manager

Select this article
Method: Read-level genotyping of short tandem repeats using long reads and single-nucleotide variation with STRkit
- David R. Lougheed,
- Tomi Pastinen,
- and Guillaume Bourque
Genome Res. March 2026 36: 578-588; Published in Advance January 15, 2026, doi:10.1101/gr.280766.125
...(Horton et al. 2023). Direct STR genotyping at a scale is thus valuable; STRs cannot always be imputed using SNVs (Gymrek et al. 2016; Saini et al. 2018), as SNV–STR linkage disequilibrium (LD) is lower than SNV–SNV pair LD (Willems et al. 2014; Press et al. 2018). Examination of STR variation...
Select this article
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
...) and clique enumeration to resolve ambiguous read assignments across highly similar gene sequences. Our previous work employed a similar framework to genotype germline IG heavy-chain variable (IGHV) genes using long-read WGS (Ford et al. 2020) and short-read WGS (Ford et al. 2022), implemented in the Immuno...
OPEN ACCESS ARTICLE
Select this article
Method: MIPSTR: a method for multiplex genotyping of germline and somatic STR variation across many individuals
- Keisha D. Carlson,
- Peter H. Sudmant,
- Maximilian O. Press,
- Evan E. Eichler,
- Jay Shendure,
- and Christine Queitsch
Genome Res. May 2015 25: 750-761; Published in Advance February 6, 2015, doi:10.1101/gr.182212.114
...-of-principle experiments, we use MIPSTR to determine germline STR genotypes for 102 STR loci with high accuracy across diverse populations of the plant A. thaliana. We show that putatively functional STRs may be identified by deviation from predicted STR variation and by association with quantitative phenotypes. Using DNA...
Select this article
Method: Nanopore sequencing identifies high-frequency somatic structural variations in laryngeal squamous cell carcinoma genomes
- Xuyan Liu,
- Lin Xia,
- Yixin Qiao,
- Yang Li,
- Yan Huang,
- Bingyan Yue,
- Xi Liang,
- Xin Yang,
- Honghui Zhang,
- Jiaxun Zhang,
- Xiao Chen,
- Dan Xie,
- and Jifeng Liu
Genome Res. April 8, 2026 gr.281046.125; Published in Advance April 8, 2026, doi:10.1101/gr.281046.125
.... Although somatic structural variations (SVs) have been documented in LSCC, 23 conventional short-read sequencing lacks the sensitivity to effectively detect high-frequency 24 SVs shared across multiple samples—variants that play a crucial role in tumorigenesis. Here, 25 we present SomaGauss-SV, a somatic...
- Abstract
- Full Text (PDF)
OPEN ACCESS ARTICLEACCEPTED MANUSCRIPT
Select this article
Research: Confounding factors in assessing the enriched expression of somatic mutant alleles in bulk tumor samples
- Kohei Hagiwara,
- Andrew Thrasher,
- Nadezhda V. Terekhanova,
- and Jinghui Zhang
Genome Res. March 4, 2026 ; Published in Advance March 4, 2026, doi:10.1101/gr.281003.125
.... The confounding effect is particularly pronounced in low-purity tumor samples. These findings serve to caution the interpretation of allelic imbalance characterized by somatic mutation alone, which suggests the inclusion of germline heterozygous SNPs for detecting bona fide ASE. A comprehensive assessment of ASE...
OPEN ACCESS ARTICLE
Select this article
Method: Autoencoders for genomic variation analysis
- Margarita Geleta,
- Daniel Mas Montserrat,
- Xavier Giro-i-Nieto,
- and Alexander G. Ioannidis
Genome Res. February 2026 36: 348-360; Published in Advance January 20, 2026, doi:10.1101/gr.280086.124
..., and contrast several metrics (including the LD structure and the SNP entropy) of the simulated sequences with that of real sequences as a genotype simulation quality assessment.MethodsVariational autoencodersRepresentation learning, also known as feature learning, attempts to recover a compact set of so...
OPEN ACCESS ARTICLE
Select this article
Research: Extensive variation in germline de novo mutations in Poecilia reticulata
- Yuying Lin,
- Iulia Darolti,
- Wouter van der Bijl,
- Jake Morris,
- and Judith E. Mank
Genome Res. August 2023 33: 1317-1324; Published in Advance July 13, 2023, doi:10.1101/gr.277936.123
...DNMs. By applying the same individual-level and site-level filtering criteria, and intersecting the results from the two genotype callers, we obtained an average number of 5.20, 24.90, and 4.80 DNMs across each pedigree (Fam1, Fam2, Fam3) (Table 1; Supplemental Table S1). To calculate the germline...
Select this article
Research: T2T-CHM13 improves read mapping and detection of clinically relevant genetic variation in the Swedish population
- Daniel Schmitz,
- Adam Ameur,
- and Åsa Johansson
Genome Res. November 2025 35: 2377-2388; Published in Advance September 16, 2025, doi:10.1101/gr.279320.124
...as described in the original SweGen paper (Ameur et al. 2017). The majority of SweGen comprises 942 unrelated individuals from the Swedish Twin Register (STR) who were selected to mirror the overall distribution of genetic principal components (PCs) of all 10,000 STR individuals that underwent SNV genotyping...
OPEN ACCESS ARTICLE
Select this article
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
...High-resolution, genotype-free mapping of genetic 1 variation with CRI-SPA-Map 2 3 Sheila Lutz*, Megan Lawler†, Samuel Amidon†, Frank W. Albert* 4 Department of Genetics, Cell Biology, & Development, 5 University of Minnesota, 6 6-160 Jackson Hall, 321 Church St SE 7 Minneapolis, MN 55455, USA 8...
- Abstract
- Full Text (PDF)
OPEN ACCESS ARTICLEACCEPTED MANUSCRIPT
Select this article
Research: Accurate genotyping of three major respiratory bacterial pathogens with ONT R10.4.1 long-read sequencing
- Nora Zidane,
- Carla Rodrigues,
- Valérie Bouchez,
- Martin Rethoret-Pasty,
- Virginie Passet,
- Sylvain Brisse,
- and Chiara Crestani
Genome Res. August 2025 35: 1758-1766; Published in Advance June 2, 2025, doi:10.1101/gr.279829.124
...when multiplexing) (Sanderson et al. 2024), and the ability to circularize chromosomes and plasmids owing to its long-read nature (Lerminiaux et al. 2024). It also provides options for real-time sequencing and rapid library preparation, essential for quick outbreak responses (Wagner et al. 2023). Early...

For checked items

view abstracts
download to citation manager

Searching journal content for articles similar to Carlson et al. 25 (8): 1244.

Search Results

Modify Results

This search

Preprint Server

Current Issue

In This Issue

Citation format:
Results / page:
Results order: