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  1. Research: Strong bias in long-read sequencing prevents assembly of Drosophila melanogaster Y-linked genes
    • A. Bernardo Carvalho,
    • Bernard Y. Kim,
    • and Fabiana Uno
    Genome Res. January 2026 36: 71-82; Published in Advance October 1, 2025, doi:10.1101/gr.280604.125
    ...), using the shallower and equally biased PacBio CLR data set from Kim et al. (2014), had to manually fill the gaps in Y-linked genes by integrating CDS sequences from FlyBase (Larkin et al. 2021).The bias primarily affects read initiation but also impairs read extension and basecalling, with read...
  2. Method: Extremely fast construction and querying of compacted and colored de Bruijn graphs with GGCAT
    • Andrea Cracco and
    • Alexandru I. Tomescu
    Genome Res. July 2023 33: 1198-1207; Published in Advance May 30, 2023, doi:10.1101/gr.277615.122
    ...Bruijn graphs are one of the most fundamental data structures in computational genomics. Colored compacted de Bruijn graphs are a variant built on a collection of sequences and associate to each k-mer the sequences in which it appears. We present GGCAT, a tool for constructing both types of graphs, based...
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  3. Method: Robust 16S rRNA classification based on a compressed LCA index
    • Omar Ahmed,
    • Christina Boucher,
    • and Ben Langmead
    Genome Res. December 2025 35: 2650-2660; Published in Advance August 25, 2025, doi:10.1101/gr.279846.124
    .... 2024) and (2) full-text approaches that create a full-text index to query with substrings of any length or perform alignments to determine the likely origin of a read (Altschul et al. 1990; Matsen et al. 2010; Kim et al. 2016; Menzel et al. 2016; Ahmed et al. 2023b; Song and Langmead 2024).A k-mer-based...
  4. 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
    ...to share any sensitive information (Fig. 1). The input data set for each party includes phased haplotype sequences from individuals within that party's cohort. We consider the parties to be honest-but-curious, meaning that they follow our analysis protocol faithfully but might try to infer information...
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  5. 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
    ...by counting k-mers/motifs (with the motif length k determined by the tandem repeat finder annotation of the locus) in the repeat sequence according to the forward strand of the reference , splitting sequences based on the known repeat motif length but unbiased to which motifs can be found. Each k-mer...
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  6. Research: Targeted and complete genomic sequencing of the major histocompatibility complex in haplotypic form of individual heterozygous samples
    • Taishan Hu,
    • Timothy L. Mosbruger,
    • Nikolaos G. Tairis,
    • Amalia Dinou,
    • Pushkala Jayaraman,
    • Mahdi Sarmady,
    • Kingham Brewster,
    • Yang Li,
    • Tristan J. Hayeck,
    • Jamie L. Duke,
    • and Dimitri S. Monos
    Genome Res. October 2024 34: 1500-1513; Published in Advance September 26, 2024, doi:10.1101/gr.278588.123
    ...resources. In the past, we used RSE to show proof-of-concept that targeting and sequencing the MHC of a homozygous sample (PGF) with short-read Illumina technology was feasible. However, the short reads of the Illumina platform and the limited set of oligos designed to capture the MHC of the homozygous PGF...
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  7. Method: Optimizing nanopore adaptive sampling for pneumococcal serotype surveillance in complex samples using the graph-based GNASTy algorithm
    • Samuel T. Horsfield,
    • Basil C.T. Fok,
    • Yuhan Fu,
    • Paul Turner,
    • John A. Lees,
    • and Nicholas J. Croucher
    Genome Res. April 2025 35: 1025-1040; Published in Advance March 4, 2025, doi:10.1101/gr.279435.124
    ...uses a seed-and-extend approach between a query and reference sequence, and has been used previously in metagenomic read classification (Mäklin et al. 2021; Alanko et al. 2023). We implemented graph psuedoalignment using Bifrost (Holley and Melsted 2020), which builds colored compacted DBGs, whereby k-mers...
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  8. Method: Accurate and fast graph-based pangenome annotation and clustering with ggCaller
    • Samuel T. Horsfield,
    • Gerry Tonkin-Hill,
    • Nicholas J. Croucher,
    • and John A. Lees
    Genome Res. September 2023 33: 1622-1637; Published in Advance August 24, 2023, doi:10.1101/gr.277733.123
    ...). Nonbranching paths of k-mers are merged into unitigs (from here referred to as “nodes”). These nodes are “colored” based on the input s they are found in, enabling calculation of the population frequency of all sequences greater than k bases in length.View larger version: In this window In a new window Figure...
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  9. Resource: Genome sequencing of C. elegans balancer strains reveals previously unappreciated complex genomic rearrangements
    • Tatiana Maroilley,
    • Stephane Flibotte,
    • Francesca Jean,
    • Victoria Rodrigues Alves Barbosa,
    • Andrew Galbraith,
    • Afiya Razia Chida,
    • Filip Cotra,
    • Xiao Li,
    • Larisa Oncea,
    • Mark Edgley,
    • Don Moerman,
    • and Maja Tarailo-Graovac
    Genome Res. January 2023 33: 154-167; Published in Advance December 5, 2022, doi:10.1101/gr.276988.122
    ...described in the literature. For most of these, we are reporting for the first time the exact genomic location, at base-pair resolution, of the breakpoints of each rearrangement and the structure at the junction of the breakpoints: strict, microduplications, or inserted sequence (Fig. 4B).View larger...
  10. Method: Sequencing Illumina libraries at high accuracy on the ONT MinION using R2C2
    • Alexander Zee,
    • Dori Z.Q. Deng,
    • Matthew Adams,
    • Kayla D. Schimke,
    • Russell Corbett-Detig,
    • Shelbi L. Russell,
    • Xuan Zhang,
    • Robert J. Schmitz,
    • and Christopher Vollmers
    Genome Res. November/December 2022 32: 2092-2106; Published in Advance November 9, 2022, doi:10.1101/gr.277031.122
    ...technology has revolutionized biological, biomedical, and clinical research. Hundreds of sequencing-based methods exist today to query gene expression (RNA-seq) (Mortazavi et al. 2008), chromatin state (chromatin immunoprecipitation [ChIP]-seq and ATAC-seq) (Barski et al. 2007; Buenrostro et al. 2013...
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