Searching journal content for articles similar to Moles et al. 13 (11): 2467.

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  1. Method: Genome skimming with nanopore sequencing precisely determines global and transposon DNA methylation in vertebrates
    • Christopher Faulk
    Genome Res. June 2023 33: 948-956; Published in Advance July 13, 2023, doi:10.1101/gr.277743.123
    ...used for mitochondrial recovery and species identification. Long-read nanopore sequencers enable simultaneous reading of both DNA sequence and methylation and can multiplex samples for low-cost skimming. Here I present nanopore sequencing as a highly precise platform for global DNA methylation...
  2. Research: Global analyses of the dynamics of mammalian microRNA metabolism
    • Elena R. Kingston and
    • David P. Bartel
    Genome Res. November 2019 29: 1777-1790; Published in Advance September 13, 2019, doi:10.1101/gr.251421.119
    ...fit the isoform model to data from the dividing MEFs. The parameters fit to these data revealed that global trends in isoform dynamics resembled those observed for contact-inhibited MEFs; in particular, conversion to the U-tailed isoform generally proceeded with the fastest rates, and these U...
  3. Research: Global regulatory features of alternative splicing across tissues and within the nervous system of C. elegans
    • Bina Koterniak,
    • Pallavi P. Pilaka,
    • Xicotencatl Gracida,
    • Lisa-Marie Schneider,
    • Iva Pritišanac,
    • Yun Zhang,
    • and John A. Calarco
    Genome Res. December 2020 30: 1766-1780; Published in Advance October 30, 2020, doi:10.1101/gr.267328.120
    .... 2011). We used hypergeometric optimization of motif enrichment (HOMER) (Heinz et al. 2010), which can detect enriched motifs in a given list of sequences relative to a background list of sequences. We first compared sequences spanning alternative cassette exons and flanking introns to equivalent...
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  4. Research: Nascent RNA sequencing reveals a dynamic global transcriptional response at genes and enhancers to the natural medicinal compound celastrol
    • Noah Dukler,
    • Gregory T. Booth,
    • Yi-Fei Huang,
    • Nathaniel Tippens,
    • Colin T. Waters,
    • Charles G. Danko,
    • John T. Lis,
    • and Adam Siepel
    Genome Res. November 2017 27: 1816-1829; Published in Advance October 12, 2017, doi:10.1101/gr.222935.117
    ...replicates per time point (Fig. 1A). To ensure that we could normalize read counts even in the presence of global changes in transcription,we spiked the samenumber of permeable Drosophila cells into each sample prior to run-on (Booth et al. 2016). Samples were sequenced to a total combined depth of 334.3 M...
  5. Resource: A biochemical landscape of A-to-I RNA editing in the human brain transcriptome
    • Masayuki Sakurai,
    • Hiroki Ueda,
    • Takanori Yano,
    • Shunpei Okada,
    • Hideki Terajima,
    • Toutai Mitsuyama,
    • Atsushi Toyoda,
    • Asao Fujiyama,
    • Hitomi Kawabata,
    • and Tsutomu Suzuki
    Genome Res. March 2014 24: 522-534; Published in Advance January 9, 2014, doi:10.1101/gr.162537.113
    ...set of A-to-I editing sites validated by the ICE method must be isolated for optimization of several ICE-seq parameters. As an extension of our previous analysis (Sakurai et al. 2010), we analyzed 1686 regions in human brain cDNA by the ICE method and identified 13,884 editing sites (Supplemental...
  6. Method: Pangenome-based genome inference using integer programming
    • Ghanshyam Chandra,
    • Md Helal Hossen,
    • Stephan Scholz,
    • Alexander T. Dilthey,
    • Daniel Gibney,
    • and Chirag Jain
    Genome Res. December 2025 35: 2661-2670; Published in Advance August 21, 2025, doi:10.1101/gr.280567.125
    ...by default based on our empirical observations on the MHC pan graph. But on other pan graphs, users may need to tune the parameter using the procedure described in the Results (see section “Effect of parameter c”).Further refinement of the proposed optimization framework is necessary to align...
  7. Method: Mapping and quantifying nascent transcript start sites using TT-TSS-seq
    • Eleanor Elgood Hunt,
    • Claudia Vivori,
    • Richard Mitter,
    • Vedis Agnadottir,
    • and Folkert J. van Werven
    Genome Res. March 2026 36: 600-610; Published in Advance February 17, 2026, doi:10.1101/gr.280726.125
    ...optimize the TSS-seq protocol to enhance sensitivity and accuracy. Specifically, we refine enzymatic reactions for decapping and RNA ligation and incorporate 5′ oligonucleotides containing unique molecular identifiers (UMIs) and barcodes to enable accurate quantification and sample multiplexing. The TT...
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  8. Method: Deep structural clustering reveals hidden systematic biases in RNA sequencing data
    • Qiang Su,
    • Yi Long,
    • Deming Gou,
    • Junmin Quan,
    • Xiaoming Zhou,
    • and Qizhou Lian
    Genome Res. November 2025 35: 2563-2577; Published in Advance September 19, 2025, doi:10.1101/gr.280713.125
    ...distribution to derive mean and standard deviation parameters (Fig. 3A, left). We then applied this parameterized model to the aggregated sequencing counts (Supplemental Fig. S6); discrepancies between the predicted and observed data revealed GC-content-related biases (Fig. 3A, right). We repeated this process...
  9. Methods: Design optimization methods for genomic DNA tiling arrays
    • Paul Bertone,
    • Valery Trifonov,
    • Joel S. Rozowsky,
    • Falk Schubert,
    • Olof Emanuelsson,
    • John Karro,
    • Ming-Yang Kao,
    • Michael Snyder,
    • and Mark Gerstein
    Genome Res. February 2006 16: 271-281; Published in Advance December 19, 2005, doi:10.1101/gr.4452906
    ...Design optimization methods for genomic DNA tiling arrays Paul Bertone 1 , 3 , Valery Trifonov 2 , Joel S. Rozowsky 3 , Falk Schubert 2 , Olof Emanuelsson 3 , John Karro 3 , Ming-Yang Kao 4 , Michael Snyder 1 , 3...
  10. Method: Robust and efficient annotation of cell states through gene signature scoring
    • Laure Ciernik,
    • Agnieszka Kraft,
    • Florian Barkmann,
    • Josephine Yates,
    • and Valentina Boeva
    Genome Res. March 2026 36: 630-644; Published in Advance February 18, 2026, doi:10.1101/gr.280926.125
    ...of constructing a valid control gene set. Overall, ANS induced the smallest bias, confirming the proposed strategy for control gene selection as the optimal one.The influence of cell-type proportions, batch effects, signature length, and inclusion of irrelevant genes on gene signature scoringThe mean control...
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