Searching journal content for articles similar to Bacolla et al. 18 (10): 1545.

Displaying results 1-10 of 838

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
...Institute, Kansas City, Missouri 64108, USA; 4Victor Phillip Dahdaleh Institute of Genomic Medicine at McGill University, Montréal, Québec H3A 0G1, Canada Corresponding authors: david.lougheed@mail.mcgill.ca, guil.bourque@mcgill.caAbstractVariation in short tandem repeats (STRs) is implicated in Mendelian...
Select this article
Method: Accurate detection of tandem repeats from error-prone sequences with EquiRep
- Zhezheng Song,
- Tasfia Zahin,
- Xiang Li,
- and Mingfu Shao
Genome Res. December 2025 35: 2714-2721; Published in Advance August 21, 2025, doi:10.1101/gr.280750.125
...realistic simulated reads.Evaluation using simulated sequences with recurring k-mers in a unitGenomic sequences are not purely random, often containing recurring substrings. We compared different methods on this scenario with simulations in which the repeat unit itself contains recurring structures...
OPEN ACCESS ARTICLE
Select this article
Research: Dynamic evolution of satellite DNAs drastically differentiates the genomes of Tribolium sibling species
- Damira Veseljak,
- Evelin Despot-Slade,
- Marin Volarić,
- Lucija Horvat,
- Tanja Vojvoda Zeljko,
- Nevenka Meštrović,
- and Brankica Mravinac
Genome Res. November 2025 35: 2445-2460; Published in Advance September 16, 2025, doi:10.1101/gr.280516.125
...Zagreb, Croatia Corresponding author: Brankica.Mravinac@irb.hrAbstractTandemly repeated satellite DNAs (satDNAs) are among the most abundant and fastest-evolving eukaryotic sequences, but the way they model s is still elusive. Here, we investigate the evolutionary dynamics of satDNAs in the extremely sat...
Select this article
Resource: Quadrupia provides a comprehensive catalog of G-quadruplexes across genomes from the tree of life
- Nikol Chantzi,
- Akshatha Nayak,
- Fotis A. Baltoumas,
- Eleni Aplakidou,
- Shiau Wei Liew,
- Jesslyn Elvaretta Galuh,
- Michail Patsakis,
- Austin Montgomery,
- Camille Moeckel,
- Ioannis Mouratidis,
- Saiful Arefeen Sazed,
- Wilfried Guiblet,
- Panagiotis Karmiris-Obratański,
- Guliang Wang,
- Apostolos Zaravinos,
- Karen M. Vasquez,
- Chun Kit Kwok,
- Georgios A. Pavlopoulos,
- and Ilias Georgakopoulos-Soares
Genome Res. November 2025 35: 2578-2600; Published in Advance August 26, 2025, doi:10.1101/gr.279790.124
...↵11 These authors contributed equally to this work. Corresponding authors: pavlopoulos@fleming.gr, izg5139@psu.eduAbstractG-quadruplex DNA structures exhibit a profound influence on essential biological processes, including transcription, replication, telomere maintenance, and genomic stability...
OPEN ACCESS ARTICLE
Select this article
Method: Uncovering methylation-dependent genetic effects on regulatory element function in diverse genomes
- Rachel M. Petersen,
- Christopher M. Vockley,
- and Amanda J. Lea
Genome Res. August 2025 35: 1781-1793; Published in Advance July 14, 2025, doi:10.1101/gr.279957.124
...of identifying methylation-dependent regulatory activity at many thousands of genomic regions simultaneously and allows for the testing of causal relationships between DNA methylation and gene expression on a region-by-region basis. Here, we develop a multiplexed mSTARR-seq protocol to assay naturally occurring...
OPEN ACCESS ARTICLE
Select this article
Research: Diverse evolutionary trajectories of mitocoding DNA in mammalian and avian nuclear genomes
- Yu-Chi Chen,
- David L.J. Vendrami,
- Maximilian L. Huber,
- Luisa E.Y. Handel,
- Christopher R. Cooney,
- Joseph I. Hoffman,
- and Toni I. Gossmann
Genome Res. June 2025 35: 1313-1324; Published in Advance March 31, 2025, doi:10.1101/gr.279428.124
...and introgression (Gabaldón 2020; Setter et al. 2020; Popadin et al. 2022). Although it is known that an organism's genomic architecture is fundamental to whether hybridization/introgression occurs successfully, we have limited knowledge of the extent to which lateral gene transfer, hybridization, and introgression...
Select this article
Research: Candida albicans isolates contain frequent heterozygous structural variants and transposable elements within genes and centromeres
- Ursula Oggenfuss,
- Robert T. Todd,
- Natthapon Soisangwan,
- Bailey Kemp,
- Alison Guyer,
- Annette Beach,
- and Anna Selmecki
Genome Res. April 2025 35: 824-838; Published in Advance October 22, 2024, doi:10.1101/gr.279301.124
...). These two centromeres contain long inverted repeat sequences that are likely involved in nonallelic homologous recombination resulting in the isochromosome structure (Sanyal et al. 2004; Burrack et al. 2013; Todd et al. 2019).Centromeres faithfully segregate chromosomes during cell division. Within...
Select this article
Research: Natural variation in C. elegans short tandem repeats
- Gaotian Zhang,
- Ye Wang,
- and Erik C. Andersen
Genome Res. October 2022 32: 1852-1861; Published in Advance October 4, 2022, doi:10.1101/gr.277067.122
...9691 polymorphic STRs (pSTRs) with missing calls in <10% of all strains (Table 1; Supplemental Table S1). The composition of STR sequences was found to be more complicated than simple repeats of motifs (Urquhart et al. 1994). Here, we classified STRs into six groups based on the reference STR sequences...
OPEN ACCESS ARTICLE
Select this article
Research: The motif composition of variable number tandem repeats impacts gene expression
- Tsung-Yu Lu,
- Paulina N. Smaruj,
- Geoffrey Fudenberg,
- Nicholas Mancuso,
- and Mark J.P. Chaisson
Genome Res. April 2023 33: 511-524; Published in Advance April 10, 2023, doi:10.1101/gr.276768.122
...(Desseyn et al. 2000), the distance between gene and gene regulators (Sun et al. 2018), the number of regulator binding sites (Tsuge et al. 2005), and the number of CpG sites (DeJesus-Hernandez et al. 2011; Renton et al. 2011). Abundant associations between repeat copy number and human traits have been...
OPEN ACCESS ARTICLE
Select this article
Resource: Structural variants in 3000 rice genomes
- Roven Rommel Fuentes,
- Dmytro Chebotarov,
- Jorge Duitama,
- Sean Smith,
- Juan Fernando De la Hoz,
- Marghoob Mohiyuddin,
- Rod A. Wing,
- Kenneth L. McNally,
- Tatiana Tatarinova,
- Andrey Grigoriev,
- Ramil Mauleon,
- and Nickolai Alexandrov
Genome Res. May 2019 29: 870-880; Published in Advance April 16, 2019, doi:10.1101/gr.241240.118
...contributing to phenotypic differences, and structural variants also play an important role (Saxena et al. 2014; Francia et al. 2015).Detection and characterization of structural variants (SVs) has revolutionized the understanding of the landscape of genomic variation in different species. A structural variant...
OPEN ACCESS ARTICLE

For checked items

view abstracts
download to citation manager

Searching journal content for articles similar to Bacolla et al. 18 (10): 1545.

Search Results

Modify Results

This search

Preprint Server

Current Issue

In This Issue

Citation format:
Results / page:
Results order: