Searching journal content for articles similar to Maurano et al. 30 (12): 1781.

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  1. Method: Rapid SARS-CoV-2 surveillance using clinical, pooled, or wastewater sequence as a sensor for population change
    • Apurva Narechania,
    • Dean Bobo,
    • Kevin Deitz,
    • Rob DeSalle,
    • Paul J. Planet,
    • and Barun Mathema
    Genome Res. October 2024 34: 1651-1660; Published in Advance September 25, 2024, doi:10.1101/gr.278594.123
    ....88 ↵Gonzalez-Reiche AS, Hernandez MM, Sullivan MJ, Ciferri B, Alshammary H, Obla A, Fabre S, Kleiner G, Polanco J, Khan Z, et al. 2020. Introductions and early spread of SARS-CoV-2 in the New York city area. Science 369: 297–301. doi:10.1126/science.abc1917 ↵Grenfell BT, Pybus OG, Gog JR, Wood JLN, Daly JM...
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  2. Research: SARS-CoV-2 genomic diversity and the implications for qRT-PCR diagnostics and transmission
    • Nicolae Sapoval,
    • Medhat Mahmoud,
    • Michael D. Jochum,
    • Yunxi Liu,
    • R.A. Leo Elworth,
    • Qi Wang,
    • Dreycey Albin,
    • Huw A. Ogilvie,
    • Michael D. Lee,
    • Sonia Villapol,
    • Kyle M. Hernandez,
    • Irina Maljkovic Berry,
    • Jonathan Foox,
    • Afshin Beheshti,
    • Krista Ternus,
    • Kjersti M. Aagaard,
    • David Posada,
    • Christopher E. Mason,
    • Fritz J. Sedlazeck,
    • and Todd J. Treangen
    Genome Res. April 2021 31: 635-644; Published in Advance February 18, 2021, doi:10.1101/gr.268961.120
    ..., Westby G, Shen G, Feng X, et al. 2020. Sequencing identifies multiple early introductions of SARS-CoV-2 to the New York City region. Genome Res 30: 1781–1788. doi:10.1101/gr.266676.120 ↵Muth D, Corman VM, Roth H, Binger T, Dijkman R, Gottula LT, Gloza-Rausch F, Balboni A, Battilani M, Rihtarič D, et al...
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  3. Method: An optimized protocol for quality control of gene therapy vectors using nanopore direct RNA sequencing
    • Kathleen Zeglinski,
    • Christian Montellese,
    • Matthew E. Ritchie,
    • Monther Alhamdoosh,
    • Cédric Vonarburg,
    • Rory Bowden,
    • Monika Jordi,
    • Quentin Gouil,
    • Florian Aeschimann,
    • and Arthur Hsu
    Genome Res. November 2024 34: 1966-1975; Published in Advance October 28, 2024, doi:10.1101/gr.279405.124
    ...for precise identification of truncated vector sequences. As such, it has proven successful during the recent pandemic, with the high-throughput sequencing of the SARS-CoV-2 viral (Bull et al. 2020; Pater et al. 2021; Barbé et al. 2022). Other long-read approaches such as ONT and PacBio also have...
  4. Method: Accurate bacterial outbreak tracing with Oxford Nanopore sequencing and reduction of methylation-induced errors
    • Mara Lohde,
    • Gabriel E. Wagner,
    • Johanna Dabernig-Heinz,
    • Adrian Viehweger,
    • Sascha D. Braun,
    • Stefan Monecke,
    • Celia Diezel,
    • Claudia Stein,
    • Mike Marquet,
    • Ralf Ehricht,
    • Mathias W. Pletz,
    • and Christian Brandt
    Genome Res. November 2024 34: 2039-2047; Published in Advance October 23, 2024, doi:10.1101/gr.278848.123
    ...graphics for data analysis. Springer-Verlag, New York. ↵Wyres KL, Lam MMC, Holt KE. 2020. Population genomics of Klebsiella pneumoniae. Nat Rev Microbiol 18: 344–359. doi:10.1038/s41579-019-0315-1 Mara Lohde 1 , Gabriel E. Wagner 2 , Johanna Dabernig-Heinz 2 , Adrian Viehweger 3 , Sascha D. Braun 4 , 5...
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  5. Perspective: Challenges in identifying mRNA transcript starts and ends from long-read sequencing data
    • Ezequiel Calvo-Roitberg,
    • Rachel F. Daniels,
    • and Athma A. Pai
    Genome Res. November 2024 34: 1719-1734; doi:10.1101/gr.279559.124
    ...DNAs during library preparation allows for multiple rounds of terminal adapter and target molecule sequencing.Computational approaches to identify and quantify full-length isoformsDespite the development of experimental approaches to more accurately sequence full-length RNA molecules, there are still...
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  6. Research: Enhanced detection of RNA modifications and read mapping with high-accuracy nanopore RNA basecalling models
    • Gregor Diensthuber,
    • Leszek P. Pryszcz,
    • Laia Llovera,
    • Morghan C. Lucas,
    • Anna Delgado-Tejedor,
    • Sonia Cruciani,
    • Jean-Yves Roignant,
    • Oguzhan Begik,
    • and Eva Maria Novoa
    Genome Res. November 2024 34: 1865-1877; Published in Advance September 13, 2024, doi:10.1101/gr.278849.123
    ...contributed equally to this work. Corresponding authors: oguzhan.begik@crg.eu, eva.novoa@crg.euAbstractIn recent years, nanopore direct RNA sequencing (DRS) became a valuable tool for studying the epitranscriptome, owing to its ability to detect multiple modifications within the same full-length native RNA...
  7. Perspective: Diversifying the genomic data science research community
    • The Genomic Data Science Community Network
    Genome Res. July 2022 32: 1231-1241; Published in Advance July 20, 2022, doi:10.1101/gr.276496.121
    ..., Washington, DC 20560, USA; 13Guttman Community College, New York, NY 10018, USA; 14Department of Microbiology and Biomedical Sciences, Dine College, Tuba City, AZ 86045, USA; 15Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA; 16Department of Biology, Johns Hopkins University, Baltimore, MD...
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  8. Review: A systematic guide for identifying transcription factors that directly regulate the expression of a gene of interest
    • Andrew D. Bates,
    • Dawid Grzela,
    • Maciej Studzian,
    • Louise Brennan,
    • Moli Williams,
    • Conor Fawcett,
    • Beth Hammond,
    • Manreen Grewal,
    • Marcin Ratajewski,
    • Lukasz Pulaski,
    • and Urszula L. McClurg
    Genome Res. March 2026 36: 433-459; Published in Advance February 17, 2026, doi:10.1101/gr.281154.125
    ..., and the PTM profile of regulatory proteins. To investigate direct DNA–protein interactions, scientists can either isolate a protein of interest and identify all of the DNA sequences capable of binding to it or, conversely, use a DNA sequence of interest to identify proteins that are capable of binding to it...
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  9. Research: Integration site-dependent HIV-1 promoter activity shapes host chromatin conformation
    • Jack A. Collora and
    • Ya-Chi Ho
    Genome Res. June 9, 2023 gr.277698.123; Published in Advance June 9, 2023, doi:10.1101/gr.277698.123
    ...cells (Jiang et al. 2020; Huang et al. 2021). Our study identified transcription factors that may regulate HIV-1 7 chromatin accessibility and HIV-1-host interactions at the integration site. 8 9 10 DISCUSSIONS 11 Viral infection, such as influenza and SARS-CoV-2, can disrupt chromatin structure...
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  10. Method: Analyzing rare mutations in metagenomes assembled using long and accurate reads
    • Marcus W. Fedarko,
    • Mikhail Kolmogorov,
    • and Pavel A. Pevzner
    Genome Res. November/December 2022 32: 2119-2133; Published in Advance November 23, 2022, doi:10.1101/gr.276917.122
    ...for the FDR-controlled identification and analysis of rare mutations in MAGs assembled using HiFi reads. We show that deep HiFi sequencing has the potential to reveal and phase tens of thousands of rare mutations in a single MAG, identify hotspots and coldspots of these mutations, and detail MAGs’ growth...
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