Searching journal content for articles similar to Giraudeau et al. 9 (7): 647.

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  1. Method: Partitioned multi-MUM finding for scalable pangenomics with MumemtoM
    • Vikram S. Shivakumar and
    • Ben Langmead
    Genome Res. February 2026 36: 397-404; Published in Advance November 7, 2025, doi:10.1101/gr.280940.125
    ...into multi-MUMs (Treangen 2008; Treangen et al. 2014), our method generalizes to merging across arbitrary initial collections of sequences, including multiway merging. This yields a highly parallelizable and easily updateable multi-MUM-finding workflow that scales to hundreds of human s.MumemtoM comprises...
  2. Method: A simple method for finding related sequences by adding probabilities of alternative alignments
    • Martin C. Frith
    Genome Res. August 2024 34: 1165-1173; Published in Advance August 16, 2024, doi:10.1101/gr.279464.124
    ...: mcfrith@edu.k.u-tokyo.ac.jpAbstractThe main way of analyzing genetic sequences is by finding sequence regions that are related to each other. There are many methods to do that, usually based on this idea: Find an alignment of two sequence regions, which would be unlikely to exist between unrelated...
  3. Method: Identification of the shortest species-specific oligonucleotide sequences
    • Ioannis Mouratidis,
    • Maxwell A. Konnaris,
    • Nikol Chantzi,
    • Candace S.Y. Chan,
    • Michail Patsakis,
    • Kimonas Provatas,
    • Austin Montgomery,
    • Fotis A. Baltoumas,
    • Congzhou M. Sha,
    • Manvita Mareboina,
    • Georgios A. Pavlopoulos,
    • Dionysios V. Chartoumpekis,
    • and Ilias Georgakopoulos-Soares
    Genome Res. February 2025 35: 279-295; Published in Advance January 2, 2025, doi:10.1101/gr.280070.124
    ...-primes to identify regions that have evolved in a specific taxonomy. We also investigated if the proportion of mammalian taxonomic quasi-prime sequences shared between species enabled their clustering based on their evolutionary relatedness. We find that closely related species share a larger proportion of mammalian...
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  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
    ..., USA ↵3 These authors contributed equally to this work. Corresponding author: mxs2589@psu.eduAbstractA tandem repeat is a sequence of nucleotides that appear as multiple contiguous, near-identical copies arranged consecutively. Tandem repeats are widespread across natural s, play critical roles...
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  5. Method: k-mer manifold approximation and projection for visualizing DNA sequences
    • Chengbo Fu,
    • Einari A. Niskanen,
    • Gong-Hong Wei,
    • Zhirong Yang,
    • Marta Sanvicente-García,
    • Marc Güell,
    • and Lu Cheng
    Genome Res. May 2025 35: 1234-1246; Published in Advance April 10, 2025, doi:10.1101/gr.279458.124
    ...between ETV6 and FLI1. Moreover, KMAP identifies four prevalent patterns in gene editing data of the AAVS1 locus, aligning with findings reported in the literature. These applications underscore that KMAP can be a valuable tool across various biological contexts.DNA sequence serve as the primary carrier...
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  6. Method: Reference-informed prediction of alternative splicing and splicing-altering mutations from sequences
    • Chencheng Xu,
    • Suying Bao,
    • Ye Wang,
    • Wenxing Li,
    • Hao Chen,
    • Yufeng Shen,
    • Tao Jiang,
    • and Chaolin Zhang
    Genome Res. July 2024 34: 1052-1065; Published in Advance July 26, 2024, doi:10.1101/gr.279044.124
    ...are located in the vicinities of human gene sequences in the high-dimensional space, they are especially helpful in learning the impact of splicing-altering mutations, which also represent small perturbations in the human gene sequences. In our study, we designed a dual-sequence mode to optimize the learning...
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  7. Method: Aligning distant sequences to graphs using long seed sketches
    • Amir Joudaki,
    • Alexandru Meterez,
    • Harun Mustafa,
    • Ragnar Groot Koerkamp,
    • André Kahles,
    • and Gunnar Rätsch
    Genome Res. July 2023 33: 1208-1217; Published in Advance April 18, 2023, doi:10.1101/gr.277659.123
    ....Our work focuses on sequence-to-graph alignment, defined as aligning a query sequence to a sequence graph (Garrison et al. 2018; Ghaffaari and Marschall 2019; Rautiainen and Marschall 2020). Sequence-to-graph alignment involves finding the minimal number of editing operations to transform the query...
  8. Review: Advancing genomic technologies and clinical awareness accelerates discovery of disease-associated tandem repeat sequences
    • Terence Gall-Duncan,
    • Nozomu Sato,
    • Ryan K.C. Yuen,
    • and Christopher E. Pearson
    Genome Res. January 2022 32: 1-27; Published in Advance December 29, 2021, doi:10.1101/gr.269530.120
    ...% of them had at least one repeat sequence that was not present in the reference . These findings were bolstered by another recent publication which also identified TRs associated within a separate cohort of ASD individuals, using a novel bioinformatic tool called MonSTR (Mitra et al. 2021).Given...
  9. LETTER: Predicting Human Minisatellite Polymorphism
    • France Denoeud,
    • Gilles Vergnaud,
    • and Gary Benson
    Genome Res. May 1, 2003 13: 856-867; Published in Advance April 14, 2003, doi:10.1101/gr.574403
    ...below, would preclude finding both highly polymorphic and hypermutable repeats. The purpose of this report is to define inexpensive strategies to accelerate the search for highly polymorphic minisatellites. The goal has been the development of sequence-based predictive criteria for polymorphism. Results...
  10. Method: Localizing unmapped sequences with families to validate the Telomere-to-Telomere assembly and identify new hotspots for genetic diversity
    • Brianna Chrisman,
    • Chloe He,
    • Jae-Yoon Jung,
    • Nate Stockham,
    • Kelley Paskov,
    • Peter Washington,
    • Juli Petereit,
    • and Dennis P. Wall
    Genome Res. October 2023 33: 1734-1746; Published in Advance October 25, 2023, doi:10.1101/gr.277175.122
    ...: brianna.chrisman@gmail.comAbstractAlthough it is ubiquitous in genomics, the current human reference (GRCh38) is incomplete: It is missing large sections of heterochromatic sequence, and as a singular, linear reference , it does not represent the full spectrum of human genetic diversity. To characterize...
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