Searching journal content for articles similar to Sapoval et al. 31 (4): 635.

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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
...highlighted the critical role of genomic surveillance for guiding policy and control. Timeliness is key, but sequence alignment and phylogeny slow most surveillance techniques. Millions of SARS-CoV-2 s have been assembled. Phylogenetic methods are ill equipped to handle this sheer scale. We introduce...
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Research: Global loss of cellular m⁶A RNA methylation following infection with different SARS-CoV-2 variants
- Roshan Vaid,
- Akram Mendez,
- Ketan Thombare,
- Rebeca Burgos-Panadero,
- Rémy Robinot,
- Barbara F. Fonseca,
- Nikhil R. Gandasi,
- Johan Ringlander,
- Mohammad Hassan Baig,
- Jae-June Dong,
- Jae Yong Cho,
- Björn Reinius,
- Lisa A. Chakrabarti,
- Kristina Nystrom,
- and Tanmoy Mondal
Genome Res. March 2023 33: 299-313; Published in Advance March 1, 2023, doi:10.1101/gr.276407.121
...2 (SARS-CoV-2). Since 2019, the virus has spread over the world, and novel variants have emerged in succession, associated with changes in transmissibility and disease severity capacity (Tao et al. 2021). The SARS-CoV-2 consists of a single-stranded positive genomic RNA of approximately 30...
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Method: Subgenomic RNA identification in SARS-CoV-2 genomic sequencing data
- Matthew D. Parker,
- Benjamin B. Lindsey,
- Shay Leary,
- Silvana Gaudieri,
- Abha Chopra,
- Matthew Wyles,
- Adrienn Angyal,
- Luke R. Green,
- Paul Parsons,
- Rachel M. Tucker,
- Rebecca Brown,
- Danielle Groves,
- Katie Johnson,
- Laura Carrilero,
- Joe Heffer,
- David G. Partridge,
- Cariad Evans,
- Mohammad Raza,
- Alexander J. Keeley,
- Nikki Smith,
- Ana Da Silva Filipe,
- James G. Shepherd,
- Chris Davis,
- Sahan Bennett,
- Vattipally B. Sreenu,
- Alain Kohl,
- Elihu Aranday-Cortes,
- Lily Tong,
- Jenna Nichols,
- Emma C. Thomson,
- The COVID-19 Genomics UK (COG-UK) Consortium,
- Dennis Wang,
- Simon Mallal,
- and Thushan I. de Silva
Genome Res. April 2021 31: 645-658; Published in Advance March 15, 2021, doi:10.1101/gr.268110.120
...: t.desilva@sheffield.ac.ukAbstractWe have developed periscope, a tool for the detection and quantification of subgenomic RNA (sgRNA) in SARS-CoV-2 genomic sequence data. The translation of the SARS-CoV-2 RNA for most open reading frames (ORFs) occurs via RNA intermediates termed “subgenomic RNAs.” sg...
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Research: Mapping genome variation of SARS-CoV-2 worldwide highlights the impact of COVID-19 super-spreaders
- Alberto Gómez-Carballa,
- Xabier Bello,
- Jacobo Pardo-Seco,
- Federico Martinón-Torres,
- and Antonio Salas
Genome Res. October 2020 30: 1434-1448; Published in Advance September 2, 2020, doi:10.1101/gr.266221.120
...of variable geographical origins worldwide, revealing a rather uniform mutation occurrence along branches that could have implications for diagnostics and the design of future vaccines. Identification of the root of SARS-CoV-2 s is not without problems, owing to conflicting interpretations derived from either...
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Research: Sequencing identifies multiple early introductions of SARS-CoV-2 to the New York City region
- Matthew T. Maurano,
- Sitharam Ramaswami,
- Paul Zappile,
- Dacia Dimartino,
- Ludovic Boytard,
- André M. Ribeiro-dos-Santos,
- Nicholas A. Vulpescu,
- Gael Westby,
- Guomiao Shen,
- Xiaojun Feng,
- Megan S. Hogan,
- Manon Ragonnet-Cronin,
- Lily Geidelberg,
- Christian Marier,
- Peter Meyn,
- Yutong Zhang,
- John Cadley,
- Raquel Ordoñez,
- Raven Luther,
- Emily Huang,
- Emily Guzman,
- Carolina Arguelles-Grande,
- Kimon V. Argyropoulos,
- Margaret Black,
- Antonio Serrano,
- Melissa E. Call,
- Min Jae Kim,
- Brendan Belovarac,
- Tatyana Gindin,
- Andrew Lytle,
- Jared Pinnell,
- Theodore Vougiouklakis,
- John Chen,
- Lawrence H. Lin,
- Amy Rapkiewicz,
- Vanessa Raabe,
- Marie I. Samanovic,
- George Jour,
- Iman Osman,
- Maria Aguero-Rosenfeld,
- Mark J. Mulligan,
- Erik M. Volz,
- Paolo Cotzia,
- Matija Snuderl,
- and Adriana Heguy
Genome Res. December 2020 30: 1781-1788; Published in Advance October 22, 2020, doi:10.1101/gr.266676.120
...(SARS-CoV), and of possible bat origin (Andersen et al. 2020; Zhou et al. 2020). Building on infrastructure from past outbreaks (Carroll et al. 2015; Park et al. 2015), genomic epidemiology has been applied to track the worldwide spread of SARS-CoV-2 using mutations in viral s to link otherwise...
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Review: Artificial intelligence and machine learning in cell-free-DNA-based diagnostics
- W.H. Adrian Tsui,
- Spencer C. Ding,
- Peiyong Jiang,
- and Y.M. Dennis Lo
Genome Res. January 2025 35: 1-19; doi:10.1101/gr.278413.123
...@cuhk.edu.hkAbstractThe discovery of circulating fetal and tumor cell-free DNA (cfDNA) molecules in plasma has opened up tremendous opportunities in noninvasive diagnostics such as the detection of fetal chromosomal aneuploidies and cancers and in posttransplantation monitoring. The advent of high-throughput sequencing...
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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
...understanding of genomic structure and function, with broad implications for personalized medicine (Wojcik et al. 2023) and evolutionary biology (Stergachis et al. 2020).Despite its revolutionary potential, long-read sequencing still faces several challenges. Compared to short-read technologies, it requires...
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Research: Genomic regulatory landscape underlying the antiviral response of Atlantic salmon
- Shahmir Naseer,
- Thomas C Clark,
- Bertrand Collet,
- Pooran Dewari,
- Damir Baranasic,
- Daniel J Macqueen,
- Pierre Boudinot,
- and Samuel A.M. Martin
Genome Res. October 22, 2025 gr.280579.125; Published in Advance October 22, 2025, doi:10.1101/gr.280579.125
...provides novel insights into the genomic regulatory landscape underlying antiviral 33 immunity in a farmed fish with a complex . 34 Introduction 35 The innate immune response to viral infection, which is mainly based on the type I interferon 36 (type I IFN) pathway is crucial to both disease progression...
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Method: A spectral component approach leveraging identity-by-descent graphs to address recent population structure in genomic analysis
- Ruhollah Shemirani,
- Gillian M. Belbin,
- Sinead Cullina,
- Christa Caggiano,
- Christopher R. Gignoux,
- Noah Zaitlen,
- and Eimear E. Kenny
Genome Res. March 2026 36: 534-546; Published in Advance December 23, 2025, doi:10.1101/gr.280659.125
...these approaches show promise, they currently have some limitations, such as implicating large genomic regions in variant association and requiring methodological improvements to LMM scalability. Future work could explore the use of PCs, ARGs, and SPCs in tandem as a powerful tool for addressing the challenges...
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Method: Autoencoders for genomic variation analysis
- Margarita Geleta,
- Daniel Mas Montserrat,
- Xavier Giro-i-Nieto,
- and Alexander G. Ioannidis
Genome Res. February 2026 36: 348-360; Published in Advance January 20, 2026, doi:10.1101/gr.280086.124
..., Barcelona 08034, Spain; 3Department of Electrical Engineering and Computer Science, University of California, Berkeley, Berkeley, California 94720, USA; 4Genomics Institute, University of California, Santa Cruz, Santa Cruz, California 95060, USA; 5Institute for Computational and Mathematical Engineering...
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