Searching journal content for articles similar to Zhang et al. 31 (7): 1290.

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  1. 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
    ...disease and complex traits but can be difficult to resolve with short-read sequencing. We present STRkit, a software package for genotyping STRs using long-read sequencing (LRS) that uses proximate single-nucleotide variants to improve genotyping accuracy without a priori haplotype information. We show...
  2. 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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  3. Method: Rapid and accurate demultiplexing of direct RNA nanopore sequencing data with SeqTagger
    • Leszek P. Pryszcz,
    • Gregor Diensthuber,
    • Laia Llovera,
    • Rebeca Medina,
    • Anna Delgado-Tejedor,
    • Luca Cozzuto,
    • Julia Ponomarenko,
    • and Eva Maria Novoa
    Genome Res. April 2025 35: 956-966; Published in Advance January 29, 2025, doi:10.1101/gr.279290.124
    ...Tagger is a rapid and accurate demultiplexing program that is robust across different sequencing chemistries (RNA002, RNA004), devices (MinION, PromethION), and RNA species (mRNA, tRNA), supporting both FAST5 and POD5 file formats. It achieves very high precision and recall on both smaller (4) and larger (96...
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  4. Review: Leveraging the power of long reads for targeted sequencing
    • Shruti V. Iyer,
    • Sara Goodwin,
    • and William Richard McCombie
    Genome Res. November 2024 34: 1701-1718; doi:10.1101/gr.279168.124
    ...with short reads has largely been eliminated. Long-range PCR-based approaches for characterizing single genes are now more tenable without the added cost of additional short-read data. Paired with low-cost Flongles from ONT, rapid screening for amplicon targets from pathogens like the monkeypox virus...
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  5. Method: Fast sequence alignment for centromeres with RaMA
    • Pinglu Zhang,
    • Yanming Wei,
    • Qinzhong Tian,
    • Quan Zou,
    • and Yansu Wang
    Genome Res. May 2025 35: 1209-1218; Published in Advance February 12, 2025, doi:10.1101/gr.279763.124
    ...and sequence alignment, resulting in rapid and accurate alignments.Comparison of RaMA and other methods on repetitive sequencesDue to the arrangement of consecutive alpha satellite repeats into HOR units, which are repeated hundreds or thousands of times in each centromere, and the sequence identity between...
  6. Research: Accurate genotyping of three major respiratory bacterial pathogens with ONT R10.4.1 long-read sequencing
    • Nora Zidane,
    • Carla Rodrigues,
    • Valérie Bouchez,
    • Martin Rethoret-Pasty,
    • Virginie Passet,
    • Sylvain Brisse,
    • and Chiara Crestani
    Genome Res. August 2025 35: 1758-1766; Published in Advance June 2, 2025, doi:10.1101/gr.279829.124
    ...when multiplexing) (Sanderson et al. 2024), and the ability to circularize chromosomes and plasmids owing to its long-read nature (Lerminiaux et al. 2024). It also provides options for real-time sequencing and rapid library preparation, essential for quick outbreak responses (Wagner et al. 2023). Early...
  7. Method: Nanopore-based consensus sequencing enables accurate multimodal tumor cell-free DNA profiling
    • Li-Ting Chen,
    • Myrthe Jager,
    • Dàmi Rebergen,
    • Geertruid J. Brink,
    • Tom van den Ende,
    • Willem Vanderlinden,
    • Pauline Kolbeck,
    • Marc Pagès-Gallego,
    • Ymke van der Pol,
    • Nicolle Besselink,
    • Norbert Moldovan,
    • Nizar Hami,
    • Wigard P. Kloosterman,
    • Hanneke van Laarhoven,
    • Florent Mouliere,
    • Ronald Zweemer,
    • Jan Lipfert,
    • Sarah Derks,
    • Alessio Marcozzi,
    • and Jeroen de Ridder
    Genome Res. April 2025 35: 886-899; Published in Advance January 13, 2025, doi:10.1101/gr.279144.124
    ...are essential for detecting TFs below 3%. NanoRCS provides an opportunity for cost-effective and rapid sample processing, which aligns well with clinical needs, particularly in settings where quick and accurate cancer monitoring is essential for personalized treatment strategies.A recent advancement in cancer...
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  8. Method: Highly accurate assembly polishing with DeepPolisher
    • Mira Mastoras,
    • Mobin Asri,
    • Lucas Brambrink,
    • Prajna Hebbar,
    • Alexey Kolesnikov,
    • Daniel E. Cook,
    • Maria Nattestad,
    • Julian Lucas,
    • Taylor S. Won,
    • Pi-Chuan Chang,
    • Andrew Carroll,
    • Benedict Paten,
    • Kishwar Shafin,
    • and and the Human Pangenome Reference Consortium
    Genome Res. July 2025 35: 1595-1608; Published in Advance May 19, 2025, doi:10.1101/gr.280149.124
    ...of polishing edits applied (5586 for HG002 and 8795 for HG005) (Supplemental Table 15).DiscussionRapid advancements in long-read sequencing and assembly algorithms in recent years are ushering in a new era of population-scale, T2T assembly projects (Ebert et al. 2021; Rhie et al. 2021; Liao et al. 2023). Many...
  9. Method: Seamless, rapid, and accurate analyses of outbreak genomic data using split k-mer analysis
    • Romain Derelle,
    • Johanna von Wachsmann,
    • Tommi Mäklin,
    • Joel Hellewell,
    • Timothy Russell,
    • Ajit Lalvani,
    • Leonid Chindelevitch,
    • Nicholas J. Croucher,
    • Simon R. Harris,
    • and John A. Lees
    Genome Res. October 2024 34: 1661-1673; Published in Advance October 15, 2024, doi:10.1101/gr.279449.124
    ...this growing volume of bacterial data, providing rapid results, but that remain simple so they can be used without highly trained bioinformaticians, expensive data analysis, and long-term storage and processing of large files. Here we describe split k-mer analysis (SKA2), a method that supports both reference...
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  10. Method: Accurate bacterial outbreak tracing with Oxford Nanopore sequencing and reduction of methylation-induced errors
    • Mara Lohde,
    • Gabriel E. Wagner,
    • Johanna Dabernig-Heinz,
    • Adrian Viehweger,
    • Sascha D. Braun,
    • Stefan Monecke,
    • Celia Diezel,
    • Claudia Stein,
    • Mike Marquet,
    • Ralf Ehricht,
    • Mathias W. Pletz,
    • and Christian Brandt
    Genome Res. November 2024 34: 2039-2047; Published in Advance October 23, 2024, doi:10.1101/gr.278848.123
    ...Table 3). Consequently, when using ONT-based sequence data from open public databases or when analyzing outbreaks, one should test for read ambiguity by using, for example, the provided MPOA workflow before further analysis.Based on our in-depth investigation, we recommend using the Nanopore rapid PCR...
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