Searching journal content for articles similar to Reid et al. 21 (3): 477.

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  1. Method: Integration of high-throughput proteomic data and complementary omics layers with PriOmics
    • Robin Kosch,
    • Katharina Limm,
    • Annette M. Staiger,
    • Nadine S. Kurz,
    • Nicole Seifert,
    • Bence Oláh,
    • Stefan Solbrig,
    • Viola Poeschel,
    • Gerhard Held,
    • Marita Ziepert,
    • Norbert Schmitz,
    • Emil Chteinberg,
    • Reiner Siebert,
    • Rainer Spang,
    • Helena U. Zacharias,
    • German Ott,
    • Peter J. Oefner,
    • and Michael Altenbuchinger
    Genome Res. January 2026 36: 197-213; Published in Advance November 18, 2025, doi:10.1101/gr.279487.124
    ...differentiate both ABC and GCB with the same edge sign from unclassified DLBCL, is a peptide proteotypic for DNA methyltransferase 1 (DNMT1). DNMT1, which belongs to a family of DNA methyltransferases that catalyze the transfer of the methyl moiety from S-adenosylmethionine to DNA, plays an important role...
  2. Method: A high-throughput screening method for selecting feature SNPs to evaluate breed diversity and infer ancestry
    • Meilin Zhang,
    • Heng Du,
    • Yu Zhang,
    • Yue Zhuo,
    • Zhen Liu,
    • Yahui Xue,
    • Lei Zhou,
    • Sixuan Zhou,
    • Wanying Li,
    • and Jian-Feng Liu
    Genome Res. August 2025 35: 1875-1886; Published in Advance July 15, 2025, doi:10.1101/gr.280176.124
    ...; Eusebi et al. 2020). Many studies compare and utilize different types of marker techniques, including mitochondrial DNA barcoding (mtDNA) (Guo et al. 2006), the Y-Chromosome technique (Bruford et al. 2003), minisatellite and microsatellite markers (Ćurković et al. 2016), and single...
    OPEN ACCESS ARTICLE
  3. Method: High-throughput and genome-scale targeted mutagenesis using CRISPR in a nonmodel multicellular organism, Bombyx mori
    • Sanyuan Ma,
    • Tong Zhang,
    • Ruolin Wang,
    • Pan Wang,
    • Yue Liu,
    • Jiasong Chang,
    • Aoming Wang,
    • Xinhui Lan,
    • Le Sun,
    • Hao Sun,
    • Run Shi,
    • Wei Lu,
    • Dan Liu,
    • Na Zhang,
    • Wenbo Hu,
    • Xiaogang Wang,
    • Weiqing Xing,
    • Ling Jia,
    • and Qingyou Xia
    Genome Res. January 2024 34: 134-144; Published in Advance January 8, 2024, doi:10.1101/gr.278297.123
    ...(Supplemental Fig. S2). We tested the sgRNA of the two lines through simple genomic PCR and found that both phenotypes were theoretically related to their predicted functions (Paine et al. 2019; Schimmel et al. 2021). The target regions of Peanuts (KWMTBOMO05973) and DNA primase large subunit (KWMTBOMO01805...
  4. Resource: A systems view on DNA damage response kinetics in Tetrahymena
    • Emily Nischwitz,
    • Vivien Schoonenberg,
    • Rachel Mullner,
    • Albert Fradera-Sola,
    • Susanne Zimbelmann,
    • Joshua J Smith,
    • and Falk Butter
    Genome Res. January 28, 2026 gr.281000.125; Published in Advance January 28, 2026, doi:10.1101/gr.281000.125
    ...) identifies and subsequently repairs damaged DNA (Ciccia 40 and Elledge 2010; Molinaro et al. 2021). Primary DNA repair pathways include nucleotide 41 excision repair (NER), base excision repair (BER), mismatch repair (MMR), homologous 42 recombination (HR), non-homologous end joining (NHEJ), and interstrand...
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  5. 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
    ...between scRNA-seq and scATAC-seq pose challenges for identifying different cell types, which hinders the discovery of novel types. In this study, we propose a new label transfer tool scSHEFT, which simultaneously considers gene expression count data, peak count data, and Gene Activity Scores as inputs...
  6. Research: Colibactin leads to a bacteria-specific mutation pattern and self-inflicted DNA damage
    • Emily Lowry,
    • Yiqing Wang,
    • Tal Dagan,
    • and Amir Mitchell
    Genome Res. August 2024 34: 1154-1164; Published in Advance August 16, 2024, doi:10.1101/gr.279517.124
    ...damage (Vollmer et al. 1997), and a CFP under control of a constitutive promoter into a low-copy plasmid (Fig. 4A). The CFP tag allowed us to identify reporter cell colonies and normalize DNA damage–induced fluorescence (YFP) to cell numbers in reporter colonies.View larger version: In this window...
    OPEN ACCESS ARTICLE
  7. Method: CRISPR-Cas9-based repeat depletion for high-throughput genotyping of complex plant genomes
    • Marzia Rossato,
    • Luca Marcolungo,
    • Luca De Antoni,
    • Giulia Lopatriello,
    • Elisa Bellucci,
    • Gaia Cortinovis,
    • Giulia Frascarelli,
    • Laura Nanni,
    • Elena Bitocchi,
    • Valerio Di Vittori,
    • Leonardo Vincenzi,
    • Filippo Lucchini,
    • Kirstin E. Bett,
    • Larissa Ramsay,
    • David James Konkin,
    • Massimo Delledonne,
    • and Roberto Papa
    Genome Res. May 2023 33: 787-797; Published in Advance May 1, 2023, doi:10.1101/gr.277628.122
    .... This could be achieved by using enzymes that enable target enrichment by depleting unwanted sequences from HTS libraries. For example, the duplex-specific nuclease (DSN) selectively digests double-stranded DNA molecules, and can be used to eliminate highly abundant sequences in a controlled denaturation...
    OPEN ACCESS ARTICLE
  8. Method: EnDeep4mC predicts DNA N4-methylcytosine sites using a dual-adaptive feature encoding framework in deep ensembles
    • Shuyu Zhang,
    • Quan Zou,
    • Mengting Niu,
    • Zhibin Lv,
    • Antony Stalin,
    • and Ximei Luo
    Genome Res. March 2026 36: 589-599; Published in Advance February 17, 2026, doi:10.1101/gr.280977.125
    ..., and the complete training protocol, enabling exact replication of the model architectures and experimental results.Feature encoding schemesMore than 24 common feature encoding schemes are widely used in epigenetic site prediction. In the work of EpiTEAmDNA, Li et al. (2023) demonstrated that 10 feature encoding...
    OPEN ACCESS ARTICLE
  9. Research: Genomic epidemiology of carbapenem-resistant Enterobacterales at a New York City hospital over a 10-year period reveals complex plasmid-clone dynamics and evidence for frequent horizontal transfer of blaKPC
    • Angela Gomez-Simmonds,
    • Medini K. Annavajhala,
    • Dwayne Seeram,
    • Todd W. Hokunson,
    • Heekuk Park,
    • and Anne-Catrin Uhlemann
    Genome Res. November 2024 34: 1895-1907; Published in Advance October 4, 2024, doi:10.1101/gr.279355.124
    ...than one carbapenem-resistant bacterial species. All isolates underwent Illumina sequencing as previously described (Gomez-Simmonds et al. 2018b). Briefly, genomic DNA was extracted from bacterial broth cultures using the QIAamp DNA Blood Mini Kit or QIAamp 96 QIAcube HT DNA isolation Kit (Qiagen...
    OPEN ACCESS ARTICLE
  10. Method: High-throughput single-molecule telomere characterization
    • Jennifer McCaffrey,
    • Eleanor Young,
    • Katy Lassahn,
    • Justin Sibert,
    • Steven Pastor,
    • Harold Riethman,
    • and Ming Xiao
    Genome Res. November 2017 27: 1904-1915; Published in Advance October 12, 2017, doi:10.1101/gr.222422.117
    .... An in vitro CRISPR/Cas9 RNA-directed nickase system directs the specific labeling of human (TTAGGG)n DNA tracts in s that have also been barcoded using a separate nickase enzyme that recognizes a 7bp motif -wide. High-throughput imaging and analysis of large DNA single molecules from s labeled in this fashion...
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