# Publications and Presentations

During my time in academia, I have amassed a few notable accomplishments. Of course, as the old saying goes, “if it isn’t published, then it never happened,” so here is a list of everything that actually happened.

Academia is not the be-all and end-all of life (contrary to what your professor might have told you). I’ve found the side-effects to be similar to this guy’s:

> I have spent too long in school and not enough time in the middle of nowhere, and it has inhibited my ability to learn the simple things.

Baxter Black, DVM
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### Genetic analysis of bovine papillomas

19 Sep 2024
Thomas A. Christensen II
Rachel Palinski
Bob Gentry

Bovine papillomavirus (BPV) is a major cause of reproductive failure in cattle. In bulls, penile papillomas caused by BPV may cause reluctance to breed, and is always a cause to fail an animal on a breeding soundness exam. Historically, it has been thought that BPV was transmitted via direct contact and could be controlled by managing clinically presenting animals in the herd, but more recent evidence suggests alternative modes of transmission. BPV has been found repeatably in clinically healthy …

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### Got Warts? Bovine Papillomavirus Pathogenesis, Transmission, and Vaccination

19 Sep 2024
Bob Gentry
Thomas A. Christensen II

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### YAVSAP: versatile viral quasispecies analysis for veterinary samples

05 Mar 2024
Thomas A. Christensen II
Steven Stancic
Andrea Lu
Dana Mitzel
William Wilson
Rachel Palinski

Viral populations within an infected host are composed of viral particles with a spectrum of genetic mutations rather than a unified genome. This phenomenon is referred to as viral “quasispecies,” and has been useful for the understanding of viral transmission and early detection of new viral variants. Next generation sequencing (NGS) has enabled the study of these quasispecies for many viral species, notably Influenza A and B, Human Immunodeficiency Virus (HIV), Foot and Mouth …

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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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