Searching journal content for articles similar to Lougheed et al. 36 (3): 578.

Displaying results 1-10 of 6046
For checked items
  1. Method: Estimating the size of long tandem repeat expansions from short reads with ScatTR
    • Rashid Al-Abri and
    • Gamze Gürsoy
    Genome Res. December 2025 35: 2701-2713; Published in Advance August 21, 2025, doi:10.1101/gr.280563.125
    ...copy number. A lower RMSE indicates that a method produces more accurate predictions. We sampled a subset of 30 TR loci identified by Tandem Repeats Finder (TRF) with motif lengths between 2 and 20 bp (Benson 1999) and simulated and reference-aligned short-read paired-end WGS samples with expansions...
    OPEN ACCESS ARTICLE
  2. Method: Multisample motif discovery and visualization for tandem repeats
    • Yaran Zhang,
    • Marc Hulsman,
    • Alex Salazar,
    • Niccolò Tesi,
    • Lydian Knoop,
    • Sven van der Lee,
    • Sanduni Wijesekera,
    • Jana Krizova,
    • Erik-Jan Kamsteeg,
    • and Henne Holstege
    Genome Res. April 2025 35: 850-862; Published in Advance November 13, 2024, doi:10.1101/gr.279278.124
    ...). With MotifScope, we can examine these different classes of variations between reads while annotating them with a consistent motif set. MotifScope also uses grayscale to color single-nucleotide motifs to visually separate them from multibase motifs.Alignment of sequences can further facilitate repeat sequence...
    OPEN ACCESS ARTICLE
  3. Method: Enabling efficient and robust analysis of tandem repeats in genomic data using wavefront-based string decomposer
    • Junhai Qi,
    • Zhidong Yang,
    • Ting Yu,
    • and Guojun Li
    Genome Res. April 8, 2026 gr.281346.125; Published in Advance April 8, 2026, doi:10.1101/gr.281346.125
    ...University5 of Science and Technology, Hong Kong S.A.R., China, 9990776 ∗Correspondence to: tingy@sdu.edu.cn and gjli@sdu.edu.cn7 Abstract8 Tandem repeats (TRs) analysis is crucial for understanding structure and variation. However, string de-9 composition, a key challenge in TRs analysis, remains...
    OPEN ACCESS ARTICLEACCEPTED MANUSCRIPT
  4. 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
    ...designed to detect small repeat units from relatively low-error-rate data such as short-read sequencing data. They often do not perform well with higher repeat lengths and/or lower frequencies. Other tools like DeepRepeat (Fang et al. 2022), tandem-genotypes (Mitsuhashi et al. 2019), and Expansion...
    OPEN ACCESS ARTICLE
  5. 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
    ...variation rates between ART-derived and natural-born miceThe rate of de novo structural variants (SVs) is predicted to be at least one order of magnitude lower than the single-nucleotide mutation rate (Belyeu et al. 2021a), a consideration that limits our power to detect small or modest differences in SV...
  6. 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
    ...610081, P.R. China Corresponding author: erik.andersen@gmail.com, erik.andersen@northwestern.eduAbstractShort tandem repeats (STRs) represent an important class of genetic variation that can contribute to phenotypic differences. Although millions of single nucleotide variants (SNVs) and short indels have...
    OPEN ACCESS ARTICLE
  7. 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
    ...duplication, structural variation, and high sequence similarity between gene copies, has historically made them challenging targets for genotyping studies using standard short-read WGS approaches. Despite their critical functional role in adaptive immunity and their documented associations with various...
    OPEN ACCESS ARTICLE
  8. Resource: Visualization and analysis of medically relevant tandem repeats in nanopore sequencing of control cohorts with pathSTR
    • Wouter De Coster,
    • Ida Höijer,
    • Inge Bruggeman,
    • Svenn D'Hert,
    • Malin Melin,
    • Adam Ameur,
    • and Rosa Rademakers
    Genome Res. November 2024 34: 2074-2080; Published in Advance August 15, 2024, doi:10.1101/gr.279265.124
    ...intensive, and do not fully describe all repeat properties. Short-read sequencing technologies have difficulty in correctly determining the allele size, especially as the repeat length gets longer than the read length, but some specialized methods have enabled population-wide tandem repeat genotyping...
    OPEN ACCESS ARTICLE
  9. 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 precision medicine (Romero et al. 2016; Montserrat et al. 2020; Dominguez Mantes et al. 2023). Here, we explore the use of variational autoencoders (VAEs), a type of neural network used to learn a low-dimensional representation of the data, to analyze sequences of single nucleotide polymorphisms (SNPs...
    OPEN ACCESS ARTICLE
  10. Resource: Genome-wide identification of tandem repeats associated with splicing variation across 49 tissues in humans
    • Kohei Hamanaka,
    • Daisuke Yamauchi,
    • Eriko Koshimizu,
    • Kei Watase,
    • Kaoru Mogushi,
    • Kinya Ishikawa,
    • Hidehiro Mizusawa,
    • Naomi Tsuchida,
    • Yuri Uchiyama,
    • Atsushi Fujita,
    • Kazuharu Misawa,
    • Takeshi Mizuguchi,
    • Satoko Miyatake,
    • and Naomichi Matsumoto
    Genome Res. March 2023 33: 435-447; Published in Advance March 27, 2023, doi:10.1101/gr.277335.122
    ...independently of nearby variantsThese 58,290 TR–splicing associations might be attributable to nearby true causal variants in linkage disequilibrium (LD) with the TRs. To address this issue, we determined whether TRs could explain splicing variation independently of nearby variants such as single-nucleotide...
For checked items

Search Results

Next 10 » New Search

Modify Results

Citation format:
Results / page:
Results order:

This search

  • Alert me when new articles matching this search are published
  • Download all citations on this page to my citation manager

Preprint Server



Current Issue

  1. April 2026, 36 (4)
  1. Current Issue
  1. Alert me to new issues of Genome Research