Searching journal content for articles similar to Yu et al. 34 (2): 326.

Displaying results 1-7 of 7
For checked items
  1. Research: Turnover of ribosome-associated transcripts from de novo ORFs produces gene-like characteristics available for de novo gene emergence in wild yeast populations
    • Éléonore Durand,
    • Isabelle Gagnon-Arsenault,
    • Johan Hallin,
    • Isabelle Hatin,
    • Alexandre K. Dubé,
    • Lou Nielly-Thibault,
    • Olivier Namy,
    • and Christian R. Landry
    Genome Res. June 2019 29: 932-943; Published in Advance May 31, 2019, doi:10.1101/gr.239822.118
    ...resistance to MTX (Tarassov et al. 2008) in-frame, as well as out-of-frame as a control. Dhfr along with a HPH-resistance module (on a pAG32-DHFR1,2-3; synthesized by Synbio Tech) were PCR amplified (Kapa HiFi DNA polymerase, Kapa Biosystems) using primers that, at each end, added homology regions flanking...
    OPEN ACCESS ARTICLE
  2. Review: k-mer approaches for biodiversity genomics
    • Katharine M. Jenike,
    • Lucía Campos-Domínguez,
    • Marilou Boddé,
    • José Cerca,
    • Christina N. Hodson,
    • Michael C. Schatz,
    • and Kamil S. Jaron
    Genome Res. February 2025 35: 219-230; Published in Advance January 31, 2025, doi:10.1101/gr.279452.124
    ...reference. However, it does require high-accuracy reads (such as Illumina or PacBio HiFi) as a reference point, and ideally, these reference reads would be orthogonal to those used for the assembly.Comparison of sequencing libraries using k-mersk-mers can also be used to identify genomic differences between...
    OPEN ACCESS ARTICLE
  3. Resource: High-quality assembly of the Chinese white truffle genome and recalibrated divergence time estimate provide insight into the evolutionary dynamics of Tuberaceae
    • Jacopo Martelossi,
    • Jacopo Vujovic,
    • Yue Huang,
    • Alessia Tatti,
    • Kaiwei Xu,
    • Federico Puliga,
    • Yuanxue Chen,
    • Omar Rota Stabelli,
    • Fabrizio Ghiselli,
    • Xiaoping Zhang,
    • and Alessandra Zambonelli
    Genome Res. November 2025 35: 2601-2616; Published in Advance August 21, 2025, doi:10.1101/gr.280368.124
    ...–associated microorganisms. To obtain coverage information, we mapped HiFi reads back to the assembly with minimap2 v2.24-r1122 (-ax map-hifi) (Li 2018), whereas for taxonomic annotation, we blasted all contigs against the NCBI nt database (BLASTN -max_target_seqs 10 -max_hsps 1 -evalue 1 × 10−25). Reads mapped...
  4. Mini-Review: A Hitchhiker's Guide to long-read genomic analysis
    • Medhat Mahmoud,
    • Daniel P. Agustinho,
    • and Fritz J. Sedlazeck
    Genome Res. April 2025 35: 545-558; doi:10.1101/gr.279975.124
    ...methods.Two leading long-read sequencing technologies currently dominate the market and have significantly impacted the genomics field (Fig. 1A): Pacific Biosciences (PacBio) HiFi and Oxford Nanopore Technologies (ONT) sequencing. While both technologies produce continuous long reads, they present...
  5. Research: The grasshopper genome reveals long-term gene content conservation of the X Chromosome and temporal variation in X Chromosome evolution
    • Xinghua Li,
    • Judith E. Mank,
    • and Liping Ban
    Genome Res. July 2024 34: 997-1007; Published in Advance August 5, 2024, doi:10.1101/gr.278794.123
    ...that using the highly accurate long-read PacBio HiFi sequencing is an effective assembly strategy for highly repetitive s. During the repeat annotation, we constructed a de novo repeat library based on our assembly using RepeatModeler (Flynn et al. 2020). Combining our custom repeat library, the Dfam...
  6. 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
    ...DNA isolation.Genome assembly and refinement of the CGC1 We first assembled HiFi reads into 602 contigs with HiCanu 2.1.1 (Nurk et al. 2020), consolidated them to 80 nonredundant contigs (Supplemental Table S2A) with purge_dups 1.2.5 (Guan et al. 2020), and further reduced them to 61 nonredundant contigs...
    OPEN ACCESS ARTICLE
  7. 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
    ...Enrichment method that uses the C-terminal 6-Histidine tag present on the HiFi Cas9 nuclease to pull down Cas9-bound nontarget fragments from the sequencing pool. Through HisTag-based isolation and pulldown of Cas9-bound nontarget DNA after the Cas9 cleavage step, ACME physically reduces background DNA...
    OPEN ACCESS ARTICLE
For checked items

Search Results

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. March 2026, 36 (3)
  1. Current Issue
  1. Alert me to new issues of Genome Research