Searching journal content for articles similar to Vaid et al. 33 (3): 299.

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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
...near-complete sweep to dominance.At the pandemic's outset, epidemiological work was focused on transmission networks, but SARS-CoV-2's high rates of infection quickly outstripped our ability to trace it (Li et al. 2020). When it became clear that even focused global efforts would only characterize...
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Method: A versatile type VI CRISPR-based approach for targeted m⁶A demethylation in mRNAs
- Panagiotis G. Adamopoulos,
- Konstantina Athanasopoulou,
- and Andreas Scorilas
Genome Res. January 2026 36: 169-182; Published in Advance December 11, 2025, doi:10.1101/gr.280476.125
...(Li et al. 2017). The significance of m6A for cellular homeostasis has prompted many studies to focus on the development of methodologies for the efficient manipulation of this modification in mRNAs. Nevertheless, the investigation of specific RNA methylated sites is an extremely challenging task...
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Research: Single-cell discovery of m⁶A RNA modifications in the hippocampus
- Shuangshuang Feng,
- Maitena Tellaetxe-Abete,
- Yujie Zhang,
- Yan Peng,
- Han Zhou,
- Mingjie Dong,
- Erika Larrea,
- Liang Xue,
- Li Zhang,
- and Magdalena J. Koziol
Genome Res. June 2024 34: 822-836; Published in Advance July 15, 2024, doi:10.1101/gr.278424.123
..., this work provides new insights into the molecular mechanisms underlying hippocampal physiology and lays the foundation for future studies investigating the dynamic nature of m6A RNA methylation in the healthy and diseased brain.The hippocampus, crucial for learning and memory (Bird and Burgess 2008...
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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
...RNA sequencing of cultured cells infected with SARS-CoV-2 (Davidson et al. 2020; Kim et al. 2020; Taiaroa et al. 2020) or more traditional total poly(A) RNA-seq (Finkel et al. 2020). We hypothesized that we could detect and quantify the levels of sgRNA to both identify novel noncanonical sgRNA...
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Method: Detecting m6A RNA modification from nanopore sequencing using a semisupervised learning framework
- Haotian Teng,
- Marcus Stoiber,
- Ziv Bar-Joseph,
- and Carl Kingsford
Genome Res. November 2024 34: 1987-1999; Published in Advance October 15, 2024, doi:10.1101/gr.278960.124
...@cs.cmu.eduAbstractDirect nanopore-based RNA sequencing can be used to detect posttranscriptional base modifications, such as N6-methyladenosine (m6A) methylation, based on the electric current signals produced by the distinct chemical structures of modified bases. A key challenge is the scarcity of adequate training data...
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Research: Epigenetic drift score captures directional methylation variability and links aging to transcriptional, metabolic, and genetic alterations
- Xiu Fan,
- Qili Qian,
- Wenran Li,
- Tianzi Liu,
- Changqing Zeng,
- Peilin Jia,
- Huandong Lin,
- Xin Gao,
- Li Jin,
- Mingfeng Xia,
- Sijia Wang,
- and Fan Liu
Genome Res. October 2025 35: 2173-2188; Published in Advance August 1, 2025, doi:10.1101/gr.280155.124
...aging. These include changes in DNA methylation, histone modifications, chromatin remodeling, and noncoding RNAs. Collectively, such alterations disrupt gene regulatory networks, leading to transcriptional dysregulation, loss of cellular homeostasis, and increased vulnerability to age-related diseases...
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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
...the intra-host diversity of SARS-CoV-2 by conducting a broad evaluation of (1) intra-host single nucleotide variants (iSNV), (2) consensus-level single nucleotide polymorphisms (SNPs), and (3) structural variants (SVs), across consensus s and RNA-seq data sets totaling over 7000 samples.ResultsWe analyzed...
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Research: Global characterization of somatic mutations and DNA methylation changes during vegetative propagation in strawberries
- Shaoqiang Hu,
- Xiangguo Zeng,
- Yuguo Liu,
- Yongping Li,
- Minghao Qu,
- Wen-Biao Jiao,
- Yongchao Han,
- and Chunying Kang
Genome Res. October 2024 34: 1582-1594; Published in Advance October 15, 2024, doi:10.1101/gr.279378.124
...al. 2015). Genome-wide increases in DNA methylation levels, particularly at CHH sites, were detected in cultured samples during somatic embryogenesis in soybean (Ji et al. 2019). In sweet orange, the global CHH methylation levels were significantly decreased at the callus induction stage...
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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
...a ribodepletion strategy starting from total RNA from nasopharyngeal swabs. Hybridization capture with custom biotinylated baits targeting the full SARS-CoV-2 sequence was used to enrich RNA-seq libraries before sequencing (Methods; Supplemental Fig. S2). Of 1107 libraries generated and sequenced, fully 78...
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Method: Uncovering methylation-dependent genetic effects on regulatory element function in diverse genomes
- Rachel M. Petersen,
- Christopher M. Vockley,
- and Amanda J. Lea
Genome Res. August 2025 35: 1781-1793; Published in Advance July 14, 2025, doi:10.1101/gr.279957.124
...is functionally negligible, having little to no effect on TF binding or downstream mRNA production (Hu et al. 2013; Pacis et al. 2015; Kribelbauer et al. 2020; Kreibich et al. 2023). In addition to many regions of the being functionally insensitive to methylation, others display DNAm-expression relationships...
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