Searching journal content for articles similar to Zheng et al. 32 (8): 1573.

Displaying results 1-10 of 4318
For checked items
  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. Research: Modest increase in the de novo single-nucleotide mutation rate in house mice born by assisted reproduction
    • Laura Blanco-Berdugo,
    • Alexis Garretson,
    • and Beth L. Dumont
    Genome Res. January 2026 36: 50-60; Published in Advance November 13, 2025, doi:10.1101/gr.281180.125
    ...transfer) affects stability. Age-matched cohorts of 12 ART-derived and 16 naturally conceived C57BL/6J inbred mice were reared in a controlled setting and whole--sequenced to ∼50× coverage. Using a rigorous pipeline for de novo single-nucleotide variant (dnSNV) discovery, we observe a ∼30% (95% CI: 4...
  3. Perspective: Functional assays in Drosophila facilitate classification of variants of uncertain significance associated with rare diseases
    • Jung-Wan Mok,
    • Shelley B. Gibson,
    • Haley A. Dostalik,
    • and Shinya Yamamoto
    Genome Res. July 2025 35: 1473-1484; Published in Advance June 4, 2025, doi:10.1101/gr.278291.123
    .../AMP) guidelines to classify genetic variants into five categories: pathogenic, likely pathogenic, benign, likely benign, and variant(s) of uncertain significance (VUS) (Richards et al. 2015). Whereas the first four classifications could be useful in interpreting rare variants that are found in genes that have...
  4. 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
    ..., Gainesville, Florida 32611, USA Corresponding author: langmea@cs.jhu.eduAbstractTaxonomic sequence classification is a computational problem central to the study of metagenomics and evolution. Advances in compressed indexing with the r-index enable full-text pattern matching against large sequence collections...
  5. Method: Fast decoding cell type–specific transcription factor binding landscape at single-nucleotide resolution
    • Hongyang Li and
    • Yuanfang Guan
    Genome Res. April 2021 31: 721-731; Published in Advance March 19, 2021, doi:10.1101/gr.269613.120
    ...Hongyang Li and Yuanfang Guan Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, Michigan 48109, USA Corresponding author: gyuanfan@umich.eduAbstractDecoding the cell type–specific transcription factor (TF) binding landscape at single-nucleotide resolution...
  6. Method: De novo detection of somatic variants in high-quality long-read single-cell RNA sequencing data
    • Arthur Dondi,
    • Nico Borgsmüller,
    • Pedro F. Ferreira,
    • Brian J. Haas,
    • Francis Jacob,
    • Viola Heinzelmann-Schwarz,
    • Tumor Profiler Consortium,
    • and Niko Beerenwinkel
    Genome Res. April 2025 35: 900-913; Published in Advance March 19, 2025, doi:10.1101/gr.279281.124
    ...high-quality LR scRNA-seq data to call de novo somatic single-nucleotide variants (SNVs), including in mitochondria (mtSNVs), copy number alterations (CNAs), and gene fusions, to reconstruct the tumor clonal heterogeneity. Before somatic variant calling, LongSom reannotates marker gene-based cell types...
    OPEN ACCESS ARTICLE
  7. Method: Exon Nomenclature And Classification of Transcripts (ENACT) provides a systematic framework to annotate exon attributes
    • Paras Verma,
    • Deeksha Thakur,
    • Deepanshi Awasthi,
    • and Shashi Bhushan Pandit
    Genome Res. June 2025 35: 1440-1455; Published in Advance May 7, 2025, doi:10.1101/gr.279878.124
    ...@iisermohali.ac.inAbstractIsoform diversity is known to enhance a gene's functional repertoire by producing protein variants with distinct functional implications. Despite numerous studies on transcriptome diversifying processes (alternative splicing/transcription), understanding their extent and correlated impact on proteome diversity...
  8. Method: Three-dimensional missense tolerance ratio analysis
    • Riley E. Perszyk,
    • Anders S. Kristensen,
    • Polina Lyuboslavsky,
    • and Stephen F. Traynelis
    Genome Res. August 2021 31: 1447-1461; Published in Advance July 22, 2021, doi:10.1101/gr.275528.121
    ...of Medicine, Atlanta, Georgia 30322, USA Corresponding author: rperszy@emory.eduAbstractA wealth of genetic information is available describing single-nucleotide variants in the human population that appear to be well-tolerated and in and of themselves do not confer disease. These variant data sets contain...
  9. Research: Common cis-regulatory variation modifies the penetrance of pathogenic SHROOM3 variants in craniofacial microsomia
    • Hao Zhu,
    • Jiao Zhang,
    • Soumya Rao,
    • Matthew D. Durbin,
    • Ying Li,
    • Ruirui Lang,
    • Jiqiang Liu,
    • Baichuan Xiao,
    • Hailin Shan,
    • Ziqiu Meng,
    • Jinmo Wang,
    • Xiaokai Tang,
    • Zhenni Shi,
    • Liza L. Cox,
    • Shouqin Zhao,
    • Stephanie M. Ware,
    • Tiong Y. Tan,
    • Michelle de Silva,
    • Lyndon Gallacher,
    • Ting Liu,
    • Jie Mi,
    • Changqing Zeng,
    • Hou-Feng Zheng,
    • Qingguo Zhang,
    • Stylianos E. Antonarakis,
    • Timothy C. Cox,
    • and Yong-Biao Zhang
    Genome Res. May 2025 35: 1065-1079; Published in Advance April 15, 2025, doi:10.1101/gr.280047.124
    ...by numbered brown circles. Variants emphasized in red denote those predicted as pathogenic by the ESM1b and AlphaMissense algorithm. Likely pathogenic variants determined using combination patterns are marked by bold in CFM patients. (B) Manhattan plot of CFM-associated variants in SHROOM3. This plot...
  10. Research: Analysis of canine gene constraint identifies new variants for orofacial clefts and stature
    • Reuben M. Buckley,
    • Nüket Bilgen,
    • Alexander C. Harris,
    • Peter Savolainen,
    • Cafer Tepeli,
    • Metin Erdoğan,
    • Aitor Serres Armero,
    • Dayna L. Dreger,
    • Frank G. van Steenbeek,
    • Marjo K. Hytönen,
    • Heidi G. Parker,
    • Jessica Hale,
    • Hannes Lohi,
    • Bengi Çınar Kul,
    • Adam R. Boyko,
    • and Elaine A. Ostrander
    Genome Res. May 2025 35: 1080-1093; Published in Advance March 24, 2025, doi:10.1101/gr.280092.124
    ..., S2; Supplemental Tables S1–S3). Throughout the coding sequence (CDS) and splice sites, we captured 611,644 single-nucleotide variants (SNVs), 28,970 small deletions, and 28,123 small insertions, including multiallelic variants (Methods; Supplemental Fig. S3; Supplemental Table S4).Three separate...
    OPEN ACCESS ARTICLE
For checked items

Search Results

Next 10 » New Search

Modify Results

Citation format:
Results / page:
Results order:

This search

  • Alert me when new articles matching this search are published
  • Download all citations on this page to my citation manager

Preprint Server



Current Issue

  1. April 2026, 36 (4)
  1. Current Issue
  1. Alert me to new issues of Genome Research