Searching journal content for articles similar to Gardiner et al. 4 (5): 288.

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  1. Method: Accurate typing of short tandem repeats from genome-wide sequencing data and its applications
    • Arkarachai Fungtammasan,
    • Guruprasad Ananda,
    • Suzanne E. Hile,
    • Marcia Shu-Wei Su,
    • Chen Sun,
    • Robert Harris,
    • Paul Medvedev,
    • Kristin Eckert,
    • and Kateryna D. Makova
    Genome Res. May 2015 25: 736-749; Published in Advance March 30, 2015, doi:10.1101/gr.185892.114
    ...Accurate typing of short tandem repeats from genome-wide sequencing data and its applications Arkarachai Fungtammasan 1 , 2 , 3 , 4 , 8 , Guruprasad Ananda 1 , 3 , 4 , 5 , 8 , 9 , Suzanne E. Hile 3 , 6 , Marcia Shu-Wei Su 2 , 3...
  2. ARTICLES: Generation of entire human papillomavirus genomes by long PCR: frequency of errors produced during amplification.
    • A C Stewart,
    • P E Gravitt,
    • S Cheng,
    • and C M Wheeler
    Genome Res. August 1995 5: 79-88; doi:10.1101/gr.5.1.79
    ...Generation of entire human papillomavirus genomes by long PCR: frequency of errors produced during amplification. A C Stewart , P E Gravitt , S Cheng , and C M Wheeler University of New Mexico Cancer Research and Treatment Center, Department...
  3. Method: Optimizing nanopore adaptive sampling for pneumococcal serotype surveillance in complex samples using the graph-based GNASTy algorithm
    • Samuel T. Horsfield,
    • Basil C.T. Fok,
    • Yuhan Fu,
    • Paul Turner,
    • John A. Lees,
    • and Nicholas J. Croucher
    Genome Res. April 2025 35: 1025-1040; Published in Advance March 4, 2025, doi:10.1101/gr.279435.124
    ...in the presence of nonpathogenic streptococci, the method was both specific and sensitive when targeting the capsular biosynthetic locus (CBL), the operon that determines S. pneumoniae serotype. NAS significantly improved coverage and yield of the CBL relative to sequencing without NAS and accurately quantified...
    OPEN ACCESS ARTICLE
  4. METHODS: Homogeneous Assays for Single-Nucleotide Polymorphism Typing Using AlphaScreen
    • Lucille Beaudet,
    • Julie Bédard,
    • Billy Breton,
    • Roberto J. Mercuri,
    • and Marcia L. Budarf
    Genome Res. April 1, 2001 11: 600-608; doi:10.1101/gr.1725501
    ...Homogeneous Assays for Single-Nucleotide Polymorphism Typing Using AlphaScreen Lucille Beaudet 1 , 3 , Julie Bédard 1 , Billy Breton 1 , Roberto J. Mercuri 1 , and Marcia L. Budarf 2 1BioSignal Packard Inc., Montréal, Québec...
  5. Research: Timescale and genetic linkage explain the variable impact of defense systems on horizontal gene transfer
    • Yang Liu,
    • João Botelho,
    • and Jaime Iranzo
    Genome Res. February 2025 35: 268-278; Published in Advance January 10, 2025, doi:10.1101/gr.279300.124
    ...:1 for size and MGE abundance; 1.75:1 and 1.5:1 with statistical significance). The analysis also reveals differences regarding the association between defense systems and distinct types of MGEs (Fig. 1A, middle rows). In all defense systems, negative associations with prophages are more frequent than were...
    OPEN ACCESS ARTICLE
  6. Method: Detecting m6A RNA modification from nanopore sequencing using a semisupervised learning framework
    • Haotian Teng,
    • Marcus Stoiber,
    • Ziv Bar-Joseph,
    • and Carl Kingsford
    Genome Res. November 2024 34: 1987-1999; Published in Advance October 15, 2024, doi:10.1101/gr.278960.124
    ...wild-type Arabidopsis (Col-0), mutants (vir-1) defective in m6A writer, and VIR-complemented lines. We used the three replicates of the wild-type line to evaluate the method.Xron accurately identifies m6A sitesTo evaluate the performance of Xron, we applied Xron that is fine-tuned on yeast data...
    OPEN ACCESS ARTICLE
  7. Method: scSHEFT enables multiomics label transfer from scRNA-seq to scATAC-seq through dual alignment
    • Zhitao Huang,
    • Ruiqing Zheng,
    • Pengzhen Jia,
    • Xuhua Yan,
    • Jinmiao Chen,
    • and Min Li
    Genome Res. February 2026 36: 387-396; Published in Advance January 20, 2026, doi:10.1101/gr.280410.125
    ...labels are transferred from well-annotated scRNA-seq data to less-annotated omics data, such as scATAC-seq. This approach leverages the gene expression profiles available in scRNA-seq to help annotate common cell types and even novel cell types for other omics data. However, the heterogeneous features...
  8. LETTER: Sequence Diversity and Large-Scale Typing of SNPs in the Human Apolipoprotein E Gene
    • Deborah A. Nickerson,
    • Scott L. Taylor,
    • Stephanie M. Fullerton,
    • Kenneth M. Weiss,
    • Andrew G. Clark,
    • Jari H. Stengård,
    • Veikko Salomaa,
    • Eric Boerwinkle,
    • and Charles F. Sing
    Genome Res. October 1, 2000 10: 1532-1545; doi:10.1101/gr.146900
    ...Sequence Diversity and Large-Scale Typing of SNPs in the Human Apolipoprotein E Gene Deborah A. Nickerson 1 , 7 , Scott L. Taylor 1 , Stephanie M. Fullerton 2 , 3 , Kenneth M. Weiss 2 , Andrew G. Clark 3 , Jari H. Stengård 4...
  9. METHODS: Evaluation of Single Nucleotide Polymorphism Typing with Invader on PCR Amplicons and Its Automation
    • Charles A. Mein,
    • Bryan J. Barratt,
    • Michael G. Dunn,
    • Thorsten Siegmund,
    • Annabel N. Smith,
    • Laura Esposito,
    • Sarah Nutland,
    • Helen E. Stevens,
    • Amanda J. Wilson,
    • Michael S. Phillips,
    • Nancy Jarvis,
    • Scott Law,
    • Monika de Arruda,
    • and John A. Todd
    Genome Res. March 1, 2000 10: 330-343; doi:10.1101/gr.10.3.330
    ...Evaluation of Single Nucleotide Polymorphism Typing with Invader on PCR Amplicons and Its Automation Charles A. Mein 1 , Bryan J. Barratt 1 , Michael G. Dunn 1 , Thorsten Siegmund 1 , Annabel N. Smith 1 , Laura Esposito 1...
  10. Method: Optimal marker genes for c-separated cell types with SepSolve
    • Bartol Borozan,
    • Tomislav Prusina,
    • Luka Borozan,
    • Domagoj Ševerdija,
    • Francisca Rojas Ringeling,
    • Domagoj Matijević,
    • and Stefan Canzar
    Genome Res. December 2025 35: 2770-2780; Published in Advance October 9, 2025, doi:10.1101/gr.280637.125
    ..., 93053 Regensburg, Germany Corresponding authors: domagoj@mathos.hr, stefan.canzar@ur.deAbstractThe identification of cell types in single-cell RNA-seq studies relies on the distinct expression signature of marker genes. A small set of target genes is also needed to design probes for targeted spatial...
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