Searching journal content for articles similar to Thill et al. 16 (6): 776.

Displaying results 1-10 of 3179
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  1. Resource: Exploration of fine-scale recombination rate variation in the domestic horse
    • Samantha K. Beeson,
    • James R. Mickelson,
    • and Molly E. McCue
    Genome Res. October 2019 29: 1744-1752; Published in Advance August 21, 2019, doi:10.1101/gr.243311.118
  2. Method: Spark: A navigational paradigm for genomic data exploration
    • Cydney B. Nielsen,
    • Hamid Younesy,
    • Henriette O'Geen,
    • Xiaoqin Xu,
    • Andrew R. Jackson,
    • Aleksandar Milosavljevic,
    • Ting Wang,
    • Joseph F. Costello,
    • Martin Hirst,
    • Peggy J. Farnham,
    • and Steven J.M. Jones
    Genome Res. November 2012 22: 2262-2269; Published in Advance September 7, 2012, doi:10.1101/gr.140665.112
    ...Spark: A navigational paradigm for genomic data exploration Cydney B. Nielsen 1 , 9 , Hamid Younesy 2 , Henriette O'Geen 3 , Xiaoqin Xu 3 , Andrew R. Jackson 4 , Aleksandar Milosavljevic 4 , Ting Wang 5 , Joseph F...
  3. Method: Quality assessment of long read data in multisample lrRNA-seq experiments using SQANTI-reads
    • Netanya Keil,
    • Carolina Monzó,
    • Lauren McIntyre,
    • and Ana Conesa
    Genome Res. April 2025 35: 987-998; Published in Advance March 3, 2025, doi:10.1101/gr.280021.124
    ...-read technology applied (Fig. 2A). Specifically, PC1, which explains 56% of the variance, distinguished cDNA ONT samples from those generated by the other two technologies, while PC2, accounting for 35% of the variance, highlighted differences between dRNA ONT and cDNA PacBio. To further explore these differences...
  4. Method: Kinetic measurement of gene-specific RNA polymerase II transcription elongation rates
    • Haiyue Liu and
    • Lea H. Gregersen
    Genome Res. November 2025 35: 2550-2562; Published in Advance October 22, 2025, doi:10.1101/gr.280852.125
    ...II (RNAPII) speed, RNAPII elongation rate studies have been limited to a relatively small number of long genes or to velocity estimates inferred indirectly from RNAPII occupancy data. Here, we present DRB/TTchem-seq2, a modified version of the DRB/TTchem-seq method, to directly measure gene...
    OPEN ACCESS ARTICLE
  5. Method: Partitioned multi-MUM finding for scalable pangenomics with MumemtoM
    • Vikram S. Shivakumar and
    • Ben Langmead
    Genome Res. February 2026 36: 397-404; Published in Advance November 7, 2025, doi:10.1101/gr.280940.125
    ...the primates in 842 GB of memory and 37.4 h of running time.To further explore this new multi-MUM data set, we studied the most conserved sequences across the primate species. Similar to ultraconserved elements (UCEs) (Bejerano et al. 2004; Hecker and Hiller 2020; Cummins et al. 2024), multi-MUMs across...
  6. 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
    ...trends in response to the damaging agents. These networks reveal both 28 a core and specific global dynamic response to the different genotoxic stressors, highlighting 29 unexpected pathway crosstalk. In addition to the comprehensive analysis presented here, the 30 2 data can be explored via...
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  7. Method: Real-time analysis and visualization of nanopore metagenomic samples with MARTi
    • Ned Peel,
    • Samuel Martin,
    • Darren Heavens,
    • Douglas W. Yu,
    • Matthew D. Clark,
    • and Richard M. Leggett
    Genome Res. November 2025 35: 2488-2500; Published in Advance October 27, 2025, doi:10.1101/gr.280550.125
    ..., visualization, and exploration of metagenomic data. MARTi supports various classification methods, including BLAST, Centrifuge, and Kraken2, letting users customize parameters and utilize their own databases for taxonomic classification and antimicrobial resistance analysis. With a user-friendly, browser...
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  8. Method: Automated interpretable artificial intelligence genomic prediction with AIGP
    • Lei Wei,
    • Ziqin Jiang,
    • Baoliang Fan,
    • Yidan Yan,
    • Zhenqiang Xu,
    • Xiaoxiang Hu,
    • and Yuzhe Wang
    Genome Res. March 5, 2026 gr.281006.125; Published in Advance March 5, 2026, doi:10.1101/gr.281006.125
    ..., model construction, speed optimization, 96 parameter adjustment, and weight evaluation, providing user-friendly solutions for 97 cross-disciplinary genetics based on artificial intelligence. 98 Results 99 Trait classification of different genetic architecture 100 We analyzed 20 traits in six animal...
    ACCEPTED MANUSCRIPT
  9. Research: Characterization of the role of spatial proximity of DNA double-strand breaks in the formation of CRISPR-Cas9-induced large structural variations
    • Mikkel Dahl-Jessen,
    • Thorkild Terkelsen,
    • Rasmus O. Bak,
    • and Uffe Birk Jensen
    Genome Res. February 2025 35: 231-241; Published in Advance January 13, 2025, doi:10.1101/gr.278575.123
    ...in K562 cells and normalized to the end point SV frequency for each sgRNA pair as a measure of SV formation speed. (A) Formation speed of deletions for sgRNA pairs AB, CD, EF, and GX (n = 6 sgRNA pairs in each group; six chromosome loci with one sgRNA pair). (B) Formation speed of deletions...
  10. Method: An optimized toolkit for high-molecular-weight DNA extraction and ultra-long-read nanopore sequencing using glass beads and hexamminecobalt(III) chloride
    • Inswasti Cahyani,
    • John Tyson,
    • Nadine Holmes,
    • Josh Quick,
    • Chris Moore,
    • Nick Loman,
    • and Matthew Loose
    Genome Res. May 2025 35: 1154-1166; Published in Advance March 24, 2025, doi:10.1101/gr.279943.124
    .... However, different sample types often require tailored extractions to provide optimal DNA for sequencing, so we sought to use a wide range of sample extraction protocols to obtain UL reads on ONT platforms. We also explored reducing both sample input requirements and the total time for library preparation...
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