Searching journal content for articles similar to Yeh et al. 29 (8): 1343.

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  1. Method: Accurate short-read alignment through r-index-based pangenome indexing
    • Rahul Varki,
    • Massimiliano Rossi,
    • Eddie Ferro,
    • Marco Oliva,
    • Erik Garrison,
    • Ben Langmead,
    • and Christina Boucher
    Genome Res. July 2025 35: 1609-1620; Published in Advance June 12, 2025, doi:10.1101/gr.279858.124
    ...Accurate short-read alignment through r-index-based pan indexing Rahul Varki1,4, Massimiliano Rossi1,4, Eddie Ferro1, Marco Oliva1, Erik Garrison2, Ben Langmead3 and Christina Boucher1 1Department of Computer and Information Science and Engineering, University of Florida, Gainesville, Florida 32611...
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  2. 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
    ...-than-read-length allele-calling methods similar to those used by short-read STR genotyping tools like GangSTR (Mousavi et al. 2019) or ExpansionHunter (Dolzhenko et al. 2019). Finally, STRkit, like most of the other tools tested, is a catalog-based genotyper; it requires a list of loci with reference coordinates...
  3. Method: Discovering human transcription factor physical interactions with genetic variants, novel DNA motifs, and repetitive elements using enhanced yeast one-hybrid assays
    • Shaleen Shrestha,
    • Jared Allan Sewell,
    • Clarissa Stephanie Santoso,
    • Elena Forchielli,
    • Sebastian Carrasco Pro,
    • Melissa Martinez,
    • and Juan Ignacio Fuxman Bass
    Genome Res. September 2019 29: 1533-1544; doi:10.1101/gr.248823.119
    ...experimental methods, such as chromatin immunoprecipitation, generally test one TF at a time, and computational motif algorithms often lead to false-positive and -negative predictions. To address these limitations, we developed an experimental approach based on enhanced yeast one-hybrid assays. The first...
  4. Method: Scalable cell-specific coexpression networks for granular regulatory pattern discovery with NeighbourNet
    • Yidi Deng,
    • Jiadong Mao,
    • Jarny Choi,
    • and Kim-Anh Le Cao
    Genome Res. March 5, 2026 gr.281171.125; Published in Advance March 5, 2026, doi:10.1101/gr.281171.125
    ...1Scalable cell-specific coexpression networks for granular regulatory 2 pattern discovery with NeighbourNet 3 Yidi Deng1,2, Jiadong Mao1,† & Jarny Choi3,† & Kim-Anh Lê Cao1,*,† 4 1Melbourne Integrative Genomics, School of Mathematics and Statistics, The University of Melbourne, 5 3010, Australia 6...
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  5. 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
    ...; Gadala-Maria et al. 2019; Rodriguez et al. 2020; for graphical depictions of the locus organization, see Lefranc and Lefranc 2001a,b). These features make germline genotyping with classic array or short-read-based approaches very challenging.Although short-read WGS approaches for IG-like genotyping...
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  6. 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
    ...also a need for tools to characterize and analyze TRs using long-read data across multiple samples. In this study, we present MotifScope, a novel algorithm for the characterization and visualization of TRs based on a de novo k-mer approach for motif discovery. Comparative analysis against established...
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  7. Method: A versatile type VI CRISPR-based approach for targeted m6A demethylation in mRNAs
    • Panagiotis G. Adamopoulos,
    • Konstantina Athanasopoulou,
    • and Andreas Scorilas
    Genome Res. January 2026 36: 169-182; Published in Advance December 11, 2025, doi:10.1101/gr.280476.125
    ...dedicated to develop targeted methylation and/or demethylation approaches based on the dCas13 system, aiming to disclose the complex roles of m6A in major cellular processes (Li et al. 2020; Cao et al. 2021).Despite the progress made by the recent incorporation of fused dCas13 constructs in modern...
  8. 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
    ...has historically been hindered by the lack of tools. Many genomic studies utilize short-read-based whole- sequencing (WGS) but exclude half of the data with RepeatMasker, a tool that identifies repetitive DNA sequences for removal. Currently, >56% of the human is removed with RepeatMasker (Nishimura...
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  9. Method: Genome-wide maps of CPD deamination in yeast reveal the impact of DNA sequence context and nucleosome architecture on cytosine deamination rates
    • Marian F. Laughery,
    • Bastian Stark,
    • Benjamin Morledge-Hampton,
    • Steven A. Roberts,
    • and John J. Wyrick
    Genome Res. January 2026 36: 183-196; Published in Advance December 9, 2025, doi:10.1101/gr.280384.124
    ...deamination in yeast cells. Our data indicate that CPD deamination is elevated at minor-in rotational positions where the DNA minor groove faces the histone octamer, likely owing to increased solvent accessibility of the C4 position of the cytosine base. Moreover, we also observe strand-specific enrichment...
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  10. Method: Delineating yeast cleavage and polyadenylation signals using deep learning
    • Emily Kunce Stroup and
    • Zhe Ji
    Genome Res. July 2024 34: 1066-1080; Published in Advance June 24, 2024, doi:10.1101/gr.278606.123
    ....ji@northwestern.eduAbstract3′-end cleavage and polyadenylation is an essential process for eukaryotic mRNA maturation. In yeast species, the polyadenylation signals that recruit the processing machinery are degenerate and remain poorly characterized compared with the well-defined regulatory elements in mammals. Here we...
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