Searching journal content for articles similar to Dai and Guan 30 (9): 1364.

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  1. Method: spRefine denoises and imputes spatial transcriptomics with a reference-free framework powered by genomic language model
    • Tianyu Liu,
    • Tinglin Huang,
    • Wengong Jin,
    • Tinyi Chu,
    • Rex Ying,
    • and Hongyu Zhao
    Genome Res. February 3, 2026 gr.281001.125; Published in Advance February 3, 2026, doi:10.1101/gr.281001.125
    ...this integration as a promising457 paradigm for combining sequence-level priors with reference-free spatial modeling,458 supported by ablation studies.459 Finally, we note that the performance of spRefine may be affected by the choices460 of models to generate the gene embeddings, and thus a better model can...
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  2. Method: Strain-level metagenomic profiling using pangenome graphs with PanTax
    • Wenhai Zhang,
    • Yuansheng Liu,
    • Guangyi Li,
    • Jialu Xu,
    • Enlian Chen,
    • Alexander Schönhuth,
    • and Xiao Luo
    Genome Res. February 2026 36: 405-420; Published in Advance January 14, 2026, doi:10.1101/gr.280858.125
    ..., inevitably miss large parts of the genetic material one seeks to analyze. High-throughput sequencing or short-read sequencing (SRS), such as Illumina sequencing, has been routinely used in reference-based taxonomic classification of metagenomic data, which explains the development of many related tools...
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  3. 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...
  4. Method: Real-time analysis and visualization of nanopore metagenomic samples with MARTi
    • Ned Peel,
    • Samuel Martin,
    • Darren Heavens,
    • Douglas W. Yu,
    • Matthew D. Clark,
    • and Richard M. Leggett
    Genome Res. November 2025 35: 2488-2500; Published in Advance October 27, 2025, doi:10.1101/gr.280550.125
    .... (2024), who demonstrated that incorporating read length information can improve abundance estimation accuracy for ONT data sets.For real-time metagenomic applications, analysis rate should be greater than or equal to sequencing rate to keep up. We demonstrated that MARTi can analyze ∼1 Gbp every 3.5 min...
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  5. 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
    ...Shruti V. Iyer, Sara Goodwin and William Richard McCombie Cold Spring Harbor Laboratory, Cold Spring Harbor, New York 11724, USA Corresponding author: mccombie@cshl.eduAbstractLong-read sequencing technologies have improved the contiguity and, as a result, the quality of assemblies by generating...
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  6. Method: Minerva: an alignment- and reference-free approach to deconvolve Linked-Reads for metagenomics
    • David C. Danko,
    • Dmitry Meleshko,
    • Daniela Bezdan,
    • Christopher Mason,
    • and Iman Hajirasouliha
    Genome Res. January 2019 29: 116-124; Published in Advance December 6, 2018, doi:10.1101/gr.235499.118
    ...of taxonomic assignments and of k-mer-based clustering. To the best of our knowledge, we are the first to address the problem of barcode deconvolution in metagenomics.Recently, long-read sequencing technologies (e.g., Pacific Biosciences, Oxford Nanopore) have become commercially available. These techniques...
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  7. 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
    ..., especially when their expansions are larger than the fragment sizes used in standard short-read sequencing. Here, we introduce ScatTR, a novel computational method that leverages a maximum likelihood framework to estimate the copy number of large TR expansions from short-read sequencing data. Scat...
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  8. Method: Analysis of coding gene expression from small RNA sequencing
    • Aygun Azadova,
    • Anthonia Ekperuoh,
    • Greg N. Brooke,
    • and Antonio Marco
    Genome Res. March 2026 36: 611-618; Published in Advance February 10, 2026, doi:10.1101/gr.281364.125
    ...of the analyzed reads (Sun et al. 2022). In addition, given the potential impact of repeated sequences, we also investigated the relative role of read complexity in the sequencing libraries. To do so, we computed the normalized Shannon entropy based in the uniqueness of sequencing reads (ranging from zero if all...
  9. Method: Accurate estimation of intraspecific microbial gene content variation in metagenomic data with MIDAS v3 and StrainPGC
    • Byron J. Smith,
    • Chunyu Zhao,
    • Veronika Dubinkina,
    • Xiaofan Jin,
    • Liron Zahavi,
    • Saar Shoer,
    • Jacqueline Moltzau-Anderson,
    • Eran Segal,
    • and Katherine S. Pollard
    Genome Res. May 2025 35: 1247-1260; Published in Advance April 10, 2025, doi:10.1101/gr.279543.124
    ...the causes and consequences of this intraspecific diversity. The enormous size of pan references, strain mixing within samples, and inconsistent sequencing depth present challenges for existing tools that analyze samples one at a time. To address this gap, we updated the MIDAS pan profiler, now released...
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  10. Method: Contrasting and combining transcriptome complexity captured by short and long RNA sequencing reads
    • Seong Woo Han,
    • San Jewell,
    • Andrei Thomas-Tikhonenko,
    • and Yoseph Barash
    Genome Res. October 2024 34: 1624-1635; Published in Advance September 25, 2024, doi:10.1101/gr.278659.123
    ...These authors contributed equally to this work. Corresponding author: yosephb@upenn.eduAbstractMapping transcriptomic variations using either short- or long-read RNA sequencing is a staple of genomic research. Long reads are able to capture entire isoforms and overcome repetitive regions, whereas short reads...
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