Cargando…

Towards increased accuracy and reproducibility in SARS-CoV-2 next generation sequence analysis for public health surveillance

During the COVID-19 pandemic, SARS-CoV-2 surveillance efforts integrated genome sequencing of clinical samples to identify emergent viral variants and to support rapid experimental examination of genome-informed vaccine and therapeutic designs. Given the broad range of methods applied to generate ne...

Descripción completa

Detalles Bibliográficos
Autores principales:	Connor, Ryan, Yarmosh, David A., Maier, Wolfgang, Shakya, Migun, Martin, Ross, Bradford, Rebecca, Brister, J. Rodney, Chain, Patrick SG, Copeland, Courtney A., di Iulio, Julia, Hu, Bin, Ebert, Philip, Gunti, Jonathan, Jin, Yumi, Katz, Kenneth S., Kochergin, Andrey, LaRosa, Tré, Li, Jiani, Li, Po-E, Lo, Chien-Chi, Rashid, Sujatha, Maiorova, Evguenia S., Xiao, Chunlin, Zalunin, Vadim, Pruitt, Kim D.
Formato:	Online Artículo Texto
Lenguaje:	English
Publicado:	Cold Spring Harbor Laboratory 2022
Materias:	Article
Acceso en línea:	https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9645426/ https://www.ncbi.nlm.nih.gov/pubmed/36380755 http://dx.doi.org/10.1101/2022.11.03.515010

Ejemplares similares

Advances and Challenges in Metatranscriptomic Analysis
por: Shakya, Migun, et al.
Publicado: (2019)

Intrahost SARS-CoV-2 k-mer identification method (iSKIM) for rapid detection of mutations of concern reveals emergence of global mutation patterns
por: Thommana, Ashley, et al.
Publicado: (2022)

Standardized phylogenetic and molecular evolutionary analysis applied to species across the microbial tree of life
por: Shakya, Migun, et al.
Publicado: (2020)

Intrahost SARS-CoV-2 k-mer Identification Method (iSKIM) for Rapid Detection of Mutations of Concern Reveals Emergence of Global Mutation Patterns
por: Thommana, Ashley, et al.
Publicado: (2022)

Insights into origin and evolution of α-proteobacterial gene transfer agents
por: Shakya, Migun, et al.
Publicado: (2017)

A Gene Cluster That Encodes Histone Deacetylase Inhibitors Contributes to Bacterial Persistence and Antibiotic Tolerance in Burkholderia thailandensis
por: Micheva-Viteva, Sofiya N., et al.
Publicado: (2020)

dtoolAI: Reproducibility for Deep Learning
por: Hartley, Matthew, et al.
Publicado: (2020)

App Savvy: Turning Ideas into iPad and iPhone Apps Customers Really Want
por: Yarmosh, Ken
Publicado: (2010)

Reproducible determination of transpulmonary pressures
por: De Meyer, G.R.A., et al.
Publicado: (2022)

Propagation of SARS-CoV-2 in Calu-3 Cells to Eliminate Mutations in the Furin Cleavage Site of Spike
por: Baczenas, John James, et al.
Publicado: (2021)

EDGE COVID-19: a web platform to generate submission-ready genomes from SARS-CoV-2 sequencing efforts
por: Lo, Chien-Chi, et al.
Publicado: (2022)

A public website for the automated assessment and validation of SARS-CoV-2 diagnostic PCR assays
por: Li, Po-E, et al.
Publicado: (2020)

Machine-Learning Classification Suggests That Many Alphaproteobacterial Prophages May Instead Be Gene Transfer Agents
por: Kogay, Roman, et al.
Publicado: (2019)

Omnidirectional optical filters
por: Kochergin, Vladimir
Publicado: (2003)

Repeatability and Reproducibility of Decisions by Latent Fingerprint Examiners
por: Ulery, Bradford T., et al.
Publicado: (2012)

Remdesivir and GS-441524 Retain Antiviral Activity against Delta, Omicron, and Other Emergent SARS-CoV-2 Variants
por: Pitts, Jared, et al.
Publicado: (2022)

Coming Full Circle: Reflections and Inspirations from a Cystic Fibrosis Patient Scientist Panel
por: Nowakowski, Alexandra “Xan” C. H., et al.
Publicado: (2022)

Improved Yield of High Molecular Weight DNA Coincides with Increased Microbial Diversity Access from Iron Oxide Cemented Sub-Surface Clay Environments
por: Hurt, Richard A., et al.
Publicado: (2014)

Error, reproducibility and sensitivity: a pipeline for data processing of Agilent oligonucleotide expression arrays
por: Chain, Benjamin, et al.
Publicado: (2010)

An Image Analysis Solution For Quantification and Determination of Immunohistochemistry Staining Reproducibility
por: Chlipala, Elizabeth A., et al.
Publicado: (2020)

Experimental evidence for the impact of soil viruses on carbon cycling during surface plant litter decomposition
por: Albright, Michaeline B. N., et al.
Publicado: (2022)

Soft palate perforation from Glidescope® intubation: A case report
por: Oh, Matthew W., et al.
Publicado: (2021)

Stop Reproducing the Reproducibility Crisis
por: Bernard, Christophe
Publicado: (2023)

NCBI’s Virus Discovery Hackathon: Engaging Research Communities to Identify Cloud Infrastructure Requirements
por: Connor, Ryan, et al.
Publicado: (2019)

Epigenetic regulation of gene expression in Shiga toxin-producing Escherichia coli: Transcriptomic data
por: Carter, Michelle Qiu, et al.
Publicado: (2021)

Remedial Treatment of Corroded Iron Objects by Environmental Aeromonas Isolates
por: Kooli, Wafa M., et al.
Publicado: (2019)

Genetic conservation of SARS-CoV-2 RNA replication complex in globally circulating isolates and recently emerged variants from humans and minks suggests minimal pre-existing resistance to remdesivir
por: Martin, Ross, et al.
Publicado: (2021)

Solving the Problem: Genome Annotation Standards before the Data Deluge
por: Klimke, William, et al.
Publicado: (2011)

Mesoporous Silica-gold Films for Straightforward, Highly Reproducible Monitoring of Mercury Traces in Water
por: Mutschler, Anna, et al.
Publicado: (2018)

4549 Reproducible Informatics for Reproducible Translational Research
por: Gouripeddi, Ram, et al.
Publicado: (2020)

The Gut Microbiome and Alcoholic Liver Disease: Ethanol Consumption Drives Consistent and Reproducible Alteration in Gut Microbiota in Mice
por: LeBrun, Erick S., et al.
Publicado: (2020)

NCBI’s Virus Discovery Codeathon: Building “FIVE” —The Federated Index of Viral Experiments API Index
por: Martí-Carreras, Joan, et al.
Publicado: (2020)

A comprehensive benchmarking study of protocols and sequencing platforms for 16S rRNA community profiling
por: D’Amore, Rosalinda, et al.
Publicado: (2016)

STAT: a fast, scalable, MinHash-based k-mer tool to assess Sequence Read Archive next-generation sequence submissions
por: Katz, Kenneth S., et al.
Publicado: (2021)

A Multifactor Analysis of Fungal and Bacterial Community Structure in the Root Microbiome of Mature Populus deltoides Trees
por: Shakya, Migun, et al.
Publicado: (2013)

The incidence of hypersensitivity reactions to non-steroidal anti-inflammatory drugs in patients with chronic urticaria
por: Kolkhir, Pavel, et al.
Publicado: (2014)

Reproducibility in research
por: Siegel, Vivian
Publicado: (2011)

SPS Reproducibility
por: Faugier, A
Publicado: (1991)

Reproducibility of LEP
por: Bohl, T
Publicado: (1991)

The quest for reproducibility
por: Kitamura, Felipe, et al.
Publicado: (2021)

Cannot write session to /tmp/vufind_sessions/sess_jumap0uij0kupjqvt5dafbotr6