Search Results - "Ryan, R. R"

Polypolish: Short-read polishing of long-read bacterial genome assemblies by Wick, Ryan R, Holt, Kathryn E

“…Long-read-only bacterial genome assemblies usually contain residual errors, most commonly homopolymer-length errors. Short-read polishing tools can use short…”
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Performance of neural network basecalling tools for Oxford Nanopore sequencing by Wick, Ryan R, Judd, Louise M, Holt, Kathryn E

“…Basecalling, the computational process of translating raw electrical signal to nucleotide sequence, is of critical importance to the sequencing platforms…”
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Unicycler: Resolving bacterial genome assemblies from short and long sequencing reads by Wick, Ryan R, Judd, Louise M, Gorrie, Claire L, Holt, Kathryn E

“…The Illumina DNA sequencing platform generates accurate but short reads, which can be used to produce accurate but fragmented genome assemblies. Pacific…”
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Assembling the perfect bacterial genome using Oxford Nanopore and Illumina sequencing by Wick, Ryan R, Judd, Louise M, Holt, Kathryn E

“…A perfect bacterial genome assembly is one where the assembled sequence is an exact match for the organism's genome-each replicon sequence is complete and…”
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Do DNA Double-Strand Breaks Drive Aging? by White, Ryan R., Vijg, Jan

“…DNA double-strand breaks (DSBs) are rare, but highly toxic, lesions requiring orchestrated and conserved machinery to prevent adverse consequences, such as…”
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Emergence of healing in the Antarctic ozone layer by Solomon, Susan, Ivy, Diane J., Kinnison, Doug, Mills, Michael J., Neely, Ryan R., Schmidt, Anja

“…Industrial chlorofluorocarbons that cause ozone depletion have been phased out under the Montreal Protocol. A chemically driven increase in polar ozone (or…”
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Goal Setting and Action Planning for Health Behavior Change by Bailey, Ryan R.

“…Health behavior change is challenging for most individuals, but there are many strategies that individuals can use to facilitate their behavior change efforts…”
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Bandage: interactive visualization of de novo genome assemblies by Wick, Ryan R, Schultz, Mark B, Zobel, Justin, Holt, Kathryn E

“…Although de novo assembly graphs contain assembled contigs (nodes), the connections between those contigs (edges) are difficult for users to access. Bandage (a…”
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A genomic surveillance framework and genotyping tool for Klebsiella pneumoniae and its related species complex by Lam, Margaret M. C., Wick, Ryan R., Watts, Stephen C., Cerdeira, Louise T., Wyres, Kelly L., Holt, Kathryn E.

“…Klebsiella pneumoniae is a leading cause of antimicrobial-resistant (AMR) healthcare-associated infections, neonatal sepsis and community-acquired liver…”
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Wavelength-Selective, IR Light-Driven Hinges Based on Liquid Crystalline Elastomer Composites by Kohlmeyer, Ryan R., Chen, Jian

“…An uphill climb: The title systems show fast, reversible bending with a large strain. Such hinges can power remote‐controlled soft robots, including foldable…”
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Distinct evolutionary dynamics of horizontal gene transfer in drug resistant and virulent clones of Klebsiella pneumoniae by Wyres, Kelly L, Wick, Ryan R, Judd, Louise M, Froumine, Roni, Tokolyi, Alex, Gorrie, Claire L, Lam, Margaret M C, Duchêne, Sebastián, Jenney, Adam, Holt, Kathryn E

“…Klebsiella pneumoniae has emerged as an important cause of two distinct public health threats: multi-drug resistant (MDR) healthcare-associated infections and…”
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A human memory circuit derived from brain lesions causing amnesia by Ferguson, Michael A., Lim, Chun, Cooke, Danielle, Darby, R. Ryan, Wu, Ona, Rost, Natalia S., Corbetta, Maurizio, Grafman, Jordan, Fox, Michael D.

“…Human memory is thought to depend on a circuit of connected brain regions, but this hypothesis has not been directly tested. We derive a human memory circuit…”
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Kaptive Web: User-Friendly Capsule and Lipopolysaccharide Serotype Prediction for Klebsiella Genomes by Wick, Ryan R, Heinz, Eva, Holt, Kathryn E, Wyres, Kelly L

“…As whole-genome sequencing becomes an established component of the microbiologist's toolbox, it is imperative that researchers, clinical microbiologists, and…”
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Trycycler: consensus long-read assemblies for bacterial genomes by Wick, Ryan R, Judd, Louise M, Cerdeira, Louise T, Hawkey, Jane, Méric, Guillaume, Vezina, Ben, Wyres, Kelly L, Holt, Kathryn E

“…While long-read sequencing allows for the complete assembly of bacterial genomes, long-read assemblies contain a variety of errors. Here, we present Trycycler,…”
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Microbiome and Exudates of the Root and Rhizosphere of Brachypodium distachyon, a Model for Wheat by Kawasaki, Akitomo, Donn, Suzanne, Ryan, Peter R, Mathesius, Ulrike, Devilla, Rosangela, Jones, Amanda, Watt, Michelle

“…The rhizosphere microbiome is regulated by plant genotype, root exudates and environment. There is substantial interest in breeding and managing crops that…”
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Catalytic Applications of Vanadium: A Mechanistic Perspective by Langeslay, Ryan R, Kaphan, David M, Marshall, Christopher L, Stair, Peter C, Sattelberger, Alfred P, Delferro, Massimiliano

“…The chemistry of vanadium has seen remarkable activity in the past 50 years. In the present review, reactions catalyzed by homogeneous and supported vanadium…”
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Peptide Radicals and Cation Radicals in the Gas Phase by Tureček, František, Julian, Ryan R

“…The authors discuss the use of electron impact localization of closed shell organic molecules to obtain cation radicals…”
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Lesion network localization of criminal behavior by Darby, R. Ryan, Horn, Andreas, Cushman, Fiery, Fox, Michael D.

“…Following brain lesions, previously normal patients sometimes exhibit criminal behavior. Although rare, these cases can lend unique insight into the…”
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Understanding fibroblast heterogeneity in the skin by Driskell, Ryan R, Watt, Fiona M

“…Highlights • Fibroblasts are functionally heterogeneous. • Heterogeneity is attributable to distinct lineages. • Fibroblasts are regulated by epidermal Wnt…”
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Benchmarking of long-read assemblers for prokaryote whole genome sequencing [version 1; peer review: 4 approved] by Wick, Ryan R, Holt, Kathryn E

“…Background: Data sets from long-read sequencing platforms (Oxford Nanopore Technologies and Pacific Biosciences) allow for most prokaryote genomes to be…”
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