Zobrazeno 1 - 10
of 113
pro vyhledávání: '"Todd J. Treangen"'
Autor:
Michael X. Wang, Esther G. Lou, Nicolae Sapoval, Eddie Kim, Prashant Kalvapalle, Bryce Kille, R. A. Leo Elworth, Yunxi Liu, Yilei Fu, Lauren B. Stadler, Todd J. Treangen
Publikováno v:
Nature Communications, Vol 15, Iss 1, Pp 1-12 (2024)
Abstract Tiled amplicon sequencing has served as an essential tool for tracking the spread and evolution of pathogens. Over 15 million complete SARS-CoV-2 genomes are now publicly available, most sequenced and assembled via tiled amplicon sequencing.
Externí odkaz:
https://doaj.org/article/c670d790ce214a17bb6d50275f486f82
Autor:
Yilei Fu, Sergey Aganezov, Medhat Mahmoud, John Beaulaurier, Sissel Juul, Todd J. Treangen, Fritz J. Sedlazeck
Publikováno v:
Nature Communications, Vol 15, Iss 1, Pp 1-12 (2024)
Abstract The assignment of variants across haplotypes, phasing, is crucial for predicting the consequences, interaction, and inheritance of mutations and is a key step in improving our understanding of phenotype and disease. However, phasing is limit
Externí odkaz:
https://doaj.org/article/1dd83e9f61f048f28d406eb4b606a3d9
Autor:
Yunxi Liu, Nicolae Sapoval, Pilar Gallego-García, Laura Tomás, David Posada, Todd J. Treangen, Lauren B. Stadler
Publikováno v:
Nature Communications, Vol 15, Iss 1, Pp 1-13 (2024)
Abstract Wastewater surveillance for SARS-CoV-2 provides early warnings of emerging variants of concerns and can be used to screen for novel cryptic linked-read mutations, which are co-occurring single nucleotide mutations that are rare, or entirely
Externí odkaz:
https://doaj.org/article/a7a3cb7b38de45c7a44e934759d246c0
Autor:
Nicolae Sapoval, Yunxi Liu, Esther G. Lou, Loren Hopkins, Katherine B. Ensor, Rebecca Schneider, Lauren B. Stadler, Todd J. Treangen
Publikováno v:
Nature Communications, Vol 14, Iss 1, Pp 1-7 (2023)
Abstract As clinical testing declines, wastewater monitoring can provide crucial surveillance on the emergence of SARS-CoV-2 variant of concerns (VoCs) in communities. In this paper we present QuaID, a novel bioinformatics tool for VoC detection base
Externí odkaz:
https://doaj.org/article/a04f1d64bced465dbcfc4f13cac50f51
Autor:
Nidia S. Trovao, Vincent Pan, Chirag Goel, Pilar Gallego-García, Yunxi Liu, Christopher Barbara, Rebecca Borg, Mark Briffa, Chanelle Cilia, Laura Grech, Mario Vassallo, Todd J. Treangen, David Posada, Afshin Beheshti, Joseph Borg, Graziella Zahra
Publikováno v:
Microbiology Spectrum, Vol 11, Iss 6 (2023)
ABSTRACT Genomic surveillance and epidemiology have shed light on the viral diversity driving coronavirus disease 2019 (COVID-19) outbreaks and are important during waves of highly transmissible and immune-escaping variants of interest or of concern
Externí odkaz:
https://doaj.org/article/f1a6cc6482d84decbe6fa32d3afad560
Publikováno v:
Nature Communications, Vol 13, Iss 1, Pp 1-14 (2022)
Contaminant sequences in metagenomic samples can potentially impact the interpretation of findings reported in microbiome studies, especially in low biomass environments. Here the authors describe Squeegee, a computational approach designed to detect
Externí odkaz:
https://doaj.org/article/b0c2ddaf39714c43a59d88919f452807
Publikováno v:
Genome Biology, Vol 23, Iss 1, Pp 1-22 (2022)
Abstract With the arrival of telomere-to-telomere (T2T) assemblies of the human genome comes the computational challenge of efficiently and accurately constructing multiple genome alignments at an unprecedented scale. By identifying nucleotides acros
Externí odkaz:
https://doaj.org/article/b2a401aad2964ff08eb9603fc8d322b1
SeqScreen: accurate and sensitive functional screening of pathogenic sequences via ensemble learning
Autor:
Advait Balaji, Bryce Kille, Anthony D. Kappell, Gene D. Godbold, Madeline Diep, R. A. Leo Elworth, Zhiqin Qian, Dreycey Albin, Daniel J. Nasko, Nidhi Shah, Mihai Pop, Santiago Segarra, Krista L. Ternus, Todd J. Treangen
Publikováno v:
Genome Biology, Vol 23, Iss 1, Pp 1-29 (2022)
Abstract The COVID-19 pandemic has emphasized the importance of accurate detection of known and emerging pathogens. However, robust characterization of pathogenic sequences remains an open challenge. To address this need we developed SeqScreen, which
Externí odkaz:
https://doaj.org/article/9c83eebfad2b4b72a204629a4c57f43d
Autor:
Gene D. Godbold, F. Curtis Hewitt, Anthony D. Kappell, Matthew B. Scholz, Stacy L. Agar, Todd J. Treangen, Krista L. Ternus, Jonas B. Sandbrink, Gregory D. Koblentz
Publikováno v:
Frontiers in Bioengineering and Biotechnology, Vol 11 (2023)
Regulation of research on microbes that cause disease in humans has historically been focused on taxonomic lists of ‘bad bugs’. However, given our increased knowledge of these pathogens through inexpensive genome sequencing, 5 decades of research
Externí odkaz:
https://doaj.org/article/8cde06eb4d7146ef84f939180732ecf0
Autor:
Nicolae Sapoval, Amirali Aghazadeh, Michael G. Nute, Dinler A. Antunes, Advait Balaji, Richard Baraniuk, C. J. Barberan, Ruth Dannenfelser, Chen Dun, Mohammadamin Edrisi, R. A. Leo Elworth, Bryce Kille, Anastasios Kyrillidis, Luay Nakhleh, Cameron R. Wolfe, Zhi Yan, Vicky Yao, Todd J. Treangen
Publikováno v:
Nature Communications, Vol 13, Iss 1, Pp 1-12 (2022)
Deep learning has enabled advances in understanding biology. In this review, the authors outline advances, and limitations of deep learning in five broad areas and the future challenges for the biosciences.
Externí odkaz:
https://doaj.org/article/14e0a06b00c7444c9c738a631681c526