Searching journal content for articles similar to Li et al. 34 (11): 2081.

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  1. Method: Minimizing reference bias with an imputed personalized reference
    • Kavya Vaddadi,
    • Mao-Jan Lin,
    • Sina Majidian,
    • Taher Mun,
    • and Ben Langmead
    Genome Res. March 5, 2026 ; Published in Advance March 5, 2026, doi:10.1101/gr.280989.125
    ...a personalized reference, for example, a diploid human reference constructed to match a donor individual’s alleles. Here, we present a new impute-first alignment framework that combines elements of genotype imputation and read alignment. We first genotype the individual using a subsample of the input reads...
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  2. Resource: CGC1, a new reference genome for Caenorhabditis elegans
    • Kazuki Ichikawa,
    • Massa J. Shoura,
    • Karen L. Artiles,
    • Dae-Eun Jeong,
    • Chie Owa,
    • Haruka Kobayashi,
    • Yoshihiko Suzuki,
    • Manami Kanamori,
    • Yu Toyoshima,
    • Yuichi Iino,
    • Ann E. Rougvie,
    • Lamia Wahba,
    • Andrew Z. Fire,
    • Erich M. Schwarz,
    • and Shinichi Morishita
    Genome Res. August 2025 35: 1902-1918; Published in Advance July 15, 2025, doi:10.1101/gr.280274.124
    ...derivative of the N2 strain. We use improved long-read sequencing and manual assembly of 43 recalcitrant genomic regions to overcome deficiencies of prior N2 and VC2010 assemblies and to assemble tandem repeat loci, including a 772 kb sequence for the 45S rRNA genes. Although many differences from earlier...
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  3. Method: Verkko2 integrates proximity-ligation data with long-read De Bruijn graphs for efficient telomere-to-telomere genome assembly, phasing, and scaffolding
    • Dmitry Antipov,
    • Mikko Rautiainen,
    • Sergey Nurk,
    • Brian P. Walenz,
    • Steven J. Solar,
    • Adam M. Phillippy,
    • and Sergey Koren
    Genome Res. July 2025 35: 1583-1594; Published in Advance May 19, 2025, doi:10.1101/gr.280383.124
    ...-C chromosome conformation capture data for both phasing and scaffolding of the assembly graph and supports both short-read Hi-C as well as Nanopore-based Pore-C (Deshpande et al. 2022) sequencing data. Critically, Verkko integrates this long-range linkage information directly with the assembly graph, improving...
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  4. Method: spRefine denoises and imputes spatial transcriptomic data 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 ; Published in Advance February 3, 2026, doi:10.1101/gr.281001.125
    ...that are further compounded by the higher cost of spatial data compared to traditional single-cell data. To overcome this challenge, we introduce spRefine, a deep learning framework that leverages genomic language models to jointly denoise and impute spatial transcriptomic data. Our results demonstrate that sp...
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  5. Method: Complete genetic and epigenetic architecture of D4Z4 macrosatellites in FSHD, BAMS, and reference cohorts with D4Z4End2End
    • Lucinda C. Xiao,
    • Ayush Semwal,
    • Brianna St John,
    • Kathleen Zeglinski,
    • Shian Su,
    • James Lancaster,
    • Shifeng Xue,
    • Bruno Reversade,
    • Matthew E. Ritchie,
    • Frédérique Magdinier,
    • Marnie E. Blewitt,
    • and Quentin Gouil
    Genome Res. March 23, 2026 ; Published in Advance March 23, 2026, doi:10.1101/gr.280907.125
    ...from two controls, four FSHD1 patients, four FSHD2 patients, and two patients with Bosma arhinia microphthalmia syndrome (BAMS) caused by SMCHD1 variants, as well as publicly available data from 30 B-lymphoblastoid cell lines from the 1000 Genomes Project and Human Pan Reference Consortium. We attain...
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  6. Research: Ultra-long-range interactions between active regulatory elements
    • Elias T. Friman,
    • Ilya M. Flyamer,
    • Davide Marenduzzo,
    • Shelagh Boyle,
    • and Wendy A. Bickmore
    Genome Res. August 2023 33: 1269-1283; Published in Advance July 14, 2023, doi:10.1101/gr.277567.122
    ...for long-range (>1 Mb) interactions represented by rare colocalization events, a stripe pattern, no requirement for homotypic binding, and a correlation with the number of nearby active sites.DiscussionOverall, our results indicate that active CREs interact across large genomic distances, and the level...
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  7. Research: Stable genome structures in living fossil fishes
    • Cheng Wang,
    • Chase D. Brownstein,
    • Wenjun Chen,
    • Zufa Ding,
    • Dan Yu,
    • Yu Deng,
    • Chenguang Feng,
    • Thomas J. Near,
    • Shunping He,
    • and Liandong Yang
    Genome Res. February 2026 36: 318-329; Published in Advance January 13, 2026, doi:10.1101/gr.280800.125
    ...(ONT), Hi-C, and RNA sequencing. For details, see the Supplemental Methods.Genome assembly and evaluationHigh-throughput Illumina data were employed for k-mer-based size estimation. PacBio HiFi and ONT ultralong reads were used to generate draft assemblies, whereas Hi-C data anchored contigs...
  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
    ...TR uses a maximum likelihood framework to evaluate alignments of reads to reference sequences with variable TR copy numbers and applies a combination of Monte Carlo–based simulated annealing and golden section search (GSS). The goal of this study is to provide a method that enables accurate copy number...
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  9. Research: Long-range promoter–enhancer contacts are conserved during evolution and contribute to gene expression robustness
    • Alexandre Laverré,
    • Eric Tannier,
    • and Anamaria Necsulea
    Genome Res. February 2022 32: 280-296; Published in Advance December 20, 2021, doi:10.1101/gr.275901.121
    ...conformation capture techniques, which identify pairs of genomic segments found in physical proximity in the nucleus (Dekker et al. 2002; Zhao et al. 2006; Schoenfelder et al. 2015). These techniques revealed numerous long-range chromatin contacts between promoters and distal regulatory elements (de Laat...
  10. 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
    ...× coverage, ONT R10 simplex reads that we subsetted to ∼32× coverage, and ONT R10 duplex reads at ∼12× coverage for the Genome-in-a-Bottle (GIAB) HG002 individual from the GIAB Ashkenazi trio. We then aligned these reads to the GRCh38 (hg38) reference (see Methods). Next, we genotyped about 900,000 STR...
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