# Category: Paper

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### nf-core/taxprofiler: highly parallelised and flexible pipeline for metagenomic taxonomic classification and profiling

23 Oct 2023
Sofia Stamouli
Moritz E. Beber
Tanja Normark
Thomas A. Christensen II
Lili Andersson-Li
Maxime Borry
Mahwash Jamy
Nf-Core Community
James A. Fellows Yates

Metagenomic classification tackles the problem of characterising the taxonomic source of all DNA sequencing reads in a sample. A common approach to address the differences and biases between the many different taxonomic classification tools is to run metagenomic data through multiple classification tools and databases. This, however, is a very time-consuming task when performed manually - particularly when combined with the appropriate preprocessing of sequencing reads before the classification. …

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### Investigation of Hydronium Diffusion in Poly(vinyl alcohol) Hydrogels: A Critical First Step to Describe Acid Transport for Encapsulated Bioremediation

02 Sep 2022
Carson J. Silsby
Jonathan R. Counts
Thomas A. Christensen II
Mark F. Roll
Kristopher v. Waynant
James G. Moberly

Bioremediation of chlorinated aliphatic hydrocarbon-contaminated aquifers can be hindered by high contaminant concentrations and acids generated during remediation. Encapsulating microbes in hydrogels may provide a protective, tunable environment from inhibiting compounds; however, current approaches to formulate successful encapsulated systems rely on trial and error rather than engineering approaches because fundamental information on mass-transfer coefficients is lacking. To address this …

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### Assessment of Porcine Rotavirus-associated virome variations in pigs with enteric disease

27 Apr 2022
Tyler Doerksen
Thomas A. Christensen II
Andrea Lu
Lance Noll
Jianfa Bai
Jamie Henningson
Rachel Palinski

Enteric disease is the predominant cause of morbidity and mortality in young mammals including pigs. Viral species involved in porcine enteric disease complex (PEDC) include rotaviruses, coronaviruses, picornaviruses, astroviruses and pestiviruses among others. The virome of three groups of swine samples submitted to the Kansas State University Veterinary Diagnostic Laboratory for routine testing were assessed, namely, a Rotavirus A positive (RVA) group, a Rotavirus co-infection (RV) group and a …

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