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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
...or declines to extinction at the leading edge of the COVID-19 pandemic.The COVID-19 pandemic has been fueled by the repeated emergence of SARS-CoV-2 variants, a few of which have propelled worldwide, asynchronous waves of infection (Koelle et al. 2022). First arising in late 2019 in Wuhan, China, the spread...
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Resource: The SynMall resource for characterizing the functional impact of synonymous variation
- Chen Ye,
- Xiaoyan Li,
- Na Cheng,
- Yansen Su,
- and Junfeng Xia
Genome Res. February 2026 36: 421-431; Published in Advance December 17, 2025, doi:10.1101/gr.281257.125
..., Kaur K, Liu C, et al. 2020. ClinVar: improvements to accessing data. Nucleic Acids Res 48: D835–D844. doi:10.1093/nar/gkz972 ↵Li C, Tian D, Tang B, Liu X, Teng X, Zhao W, Zhang Z, Song S. 2021. Genome Variation Map: a worldwide collection of variations across multiple species. Nucleic Acids Res 49: D...
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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
...are needed in order to properly capture the genetic composition of populations. Here, we explore deep learning techniques, namely, variational autoencoders (VAEs), to process genomic data from a population perspective. We show the power of VAEs for a variety of tasks relating to the interpretation...
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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
..., Gothenburg 41345, Sweden ↵9 These authors contributed equally to this work. Corresponding author: tanmoy.mondal@gu.seAbstractInsights into host–virus interactions during SARS-CoV-2 infection are needed to understand COVID-19 pathogenesis and may help to guide the design of novel antiviral therapeutics. N6...
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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
...COVID-19 samples worldwide to provide comprehensive analysis of SARS-CoV-2 sgRNA.Understanding variation within subgenomic RNA (sgRNA) synthesis within the human host may have important implications for the study of SARS-CoV-2 biology and evolution. Owing to advances in sequencing technology...
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Research: Genetic variation in recalcitrant repetitive regions of the Drosophila melanogaster genome
- Harsh G. Shukla,
- Mahul Chakraborty,
- and J.J. Emerson
Genome Res. September 2025 35: 2023-2040; Published in Advance July 16, 2025, doi:10.1101/gr.280728.125
...the Drosophila Genome Nexus (DGN) (Lack et al. 2015). We employed this sample population because it is derived from haploid embryos, thereby mitigating issues related to genotyping. Moreover, the Zambian strains show high levels of interstrain variation. Ignoring the stocks with the In(2L)t inversion, 147 of 197...
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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
...SNVs observed are U > C and C > U (Fig. 2B). We also note that A > G, G > A, and G > U iSNVs are common. These findings, specific to the iSNV mutational profile and frequency, are highly concordant with the recent intra-host SARS-CoV-2 genomic analyses from COVID-19 positive patients in Austria (Popa et al...
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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
...of outbreak trajectory.ResultsTo assess the spread of SARS-CoV-2 within the NYULH COVID-19 inpatient and outpatient population, we deployed and optimized a viral sequencing, quality control (QC), and analysis pipeline by repurposing existing genomics infrastructure. Samples from unique individuals were...
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Research: Stable genome structures in living fossil fishes
- Cheng Wang,
- Chase D. Brownstein,
- Wenjun Chen,
- Zufa Ding,
- Dan Yu,
- Yu Deng,
- Chenguang Feng,
- Thomas J. Near,
- Shunping He,
- and Liandong Yang
Genome Res. February 2026 36: 318-329; Published in Advance January 13, 2026, doi:10.1101/gr.280800.125
...the new s, we show that gars have the slowest rates of genomic structural and sequence evolution of all vertebrates. In species of the two living gar genera Atractosteus and Lepisosteus, 83.35% of the s remain identical even though they diverged over 100 million years ago. Genome size variation among gars...
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Method: Read-level genotyping of short tandem repeats using long reads and single-nucleotide variation with STRkit
- David R. Lougheed,
- Tomi Pastinen,
- and Guillaume Bourque
Genome Res. March 2026 36: 578-588; Published in Advance January 15, 2026, doi:10.1101/gr.280766.125
...Institute, Kansas City, Missouri 64108, USA; 4Victor Phillip Dahdaleh Institute of Genomic Medicine at McGill University, Montréal, Québec H3A 0G1, Canada Corresponding authors: david.lougheed@mail.mcgill.ca, guil.bourque@mcgill.caAbstractVariation in short tandem repeats (STRs) is implicated in Mendelian...

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