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Evaluation of the impact of
antimicrobial use protocols in PRRS virus infected swine on phenotypic
antimicrobial resistance


Applied and Environmental Microbiology

Noyes NR, Slizovskiy IB, Singer RS

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Beyond Antimicrobial Use: A Framework for Prioritizing Antimicrobial Resistance Interventions


Annual Review of Animal Biosciences

Noyes NR, Slizovskiy IB, Singer RS


Investigating the cow skin and teat canal microbiomes of the bovine udder using different sampling and sequencing approaches

Journal of Dairy Science

C.J.Dean, I.B.Slizovskiy, K.K.Crone, A.X.Pfennig, B.J.Heins, L.S.Caixeta, N.R.Noyes

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Metagenome SNP Calling via Read Colored de Bruijn Graphs



Bahar Alipanahi, Martin D Muggli, Musa Jundi, Noelle R Noyes, Christina A Boucher


A Cautionary Report for Pathogen Identification Using Shotgun Metagenomics; A Comparison to Aerobic Culture and Polymerase Chain Reaction for Salmonella enterica Identification

Frontiers in Microbiology

Doster E, Rovira P, Noyes NR, Burgess BA, Yang X, Weinroth MD, Linke L, Magnuson R, Boucher CA, Belk KE, Morley PS.


Characterization of the Microbial Resistome in Conventional and “Raised Without Antibiotics” Beef and Dairy Production Systems

Frontiers in Microbiology

Rovira, P, McAllister TA, Lakin SM, Cook SR, Doster E, Noyes NR, Weinroth MD, Yang X, Parker JK, Boucher CA, Booker CW, Woerner DR, Belk KE, Morley PS.

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PrPC knockdown by liposome-siRNA-peptide complexes (LSPCs) prolongs survival and normal behavior of prion-infected mice immunotolerant to treatment


Heather Bender, Noelle Noyes, Jessica L. Annis, Amanda Hitpas, Luke Mollnow, Kendra Croak, Sarah Kane, Kaitlyn Wagner, Steven Dow, Mark Zabel

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Circulation of plasmids harboring resistance genes to quinolones and/or extended spectrum cephalosporins in multiple Salmonella enterica serotypes from swine in the United States

Antimicrobial Agents and Chemotherapy

Elnekave E, Hong SL, Lim S, Hayer SS, Boxrud D, Taylor AJ, Lappi V, Noyes NR, Johnson TJ, Rovira A, Davies P, Perez A, Alvarez J

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Investigating effects of tulathromycin metaphylaxis on the fecal resistome and microbiome of feedlot cattle early in the feeding period using shotgun metagenomic sequencing

Frontiers in Microbiology

Doster E*, Rovira P, Noyes NR*, Burgess BA, Yang X, Weinroth MD, Lakin SM, Dean CJ, Linke L, Magnuson R, Jones KI, Boucher C, Ruiz J, Belk KE**, Morley PS**. *,** Authors contributed equally.

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Impact of sequencing depth on the characterization of the microbiome and resistome

Scientific Reports

Rahat Zaheer, Noelle Noyes, Rodrigo Ortega Polo, Shaun R. Cook, Eric Marinier, Gary Van Domselaar, Keith E. Belk, Paul S. Morley & Tim A. McAllister


Enrichment allows identification of diverse, rare elements in metagenomic resistome-virulome sequencing


Noelle R. Noyes, Maggie D. Weinroth, Jennifer K. Parker, Chris J. Dean, Steven M. Lakin, Robert A. Raymond, Pablo Rovira, Enrique Doster, Zaid Abdo, Jennifer N. Martin, Kenneth L. Jones, Jaime Ruiz, Christina A. Boucher, Keith E. Belk, and Paul S. Morley


Succinct Colored de Bruijn Graphs



Martin D. Muggli, Alexander Bowe, Noelle R. Noyes, Paul S. Morley, Keith E. Belk, Robert Raymond, Travis Gagie, Simon J. Puglisi, Christina Boucher


Characterization of the resistome in manure, soil and wastewater from dairy and beef production systems

Scientific Reports

Noelle R. Noyes, Xiang Yang, Lyndsey M. Linke, Roberta J. Magnuson, Shaun R. Cook, Rahat Zaheer, Hua Yang, Dale R. Woerner, Ifigenia Geornaras, Jessica A. McArt, Sheryl P. Gow, Jaime Ruiz, Kenneth L. Jones, Christina A. Boucher, Tim A. McAllister, Keith E. Belk & Paul S. Morley

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Mannheimia haemolytica in Feedlot Cattle: Prevalence of Recovery and Associations with Antimicrobial Use, Resistance, and Health Outcomes

Journal of Veterinary Internal Medicine

Noyes, N. R., Benedict, K. M., Gow, S. P., Booker, C. W., Hannon, S. J., McAllister, T. A., & Morley, P. S. 

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Antimicrobial Resistance in Escherichia coli Recovered from Feedlot Cattle and Associations with Antimicrobial Use


Benedict, K.M., Gow, S.P., McAllister, T.A., Booker, C.W., Hannon, S.J., Checkley, S.L., Noyes, N.R., & Morley, P.S.

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Effect of subclinical mastitis
detected in the first month of lactation on somatic cell count linear scores, milk yield, fertility, and culling of dairy cows
in certified organic herds.


Journal of Dairy Science

Fernandes LM, Guimaraes I, Noyes NR, Caixeta L, Machado, V.


Exploring Prediction of Antimicrobial
Resistance Based on Protein Solvent Accessibility Variation


Frontiers in Genetics

Marini S, Slizovskiy IB, Noyes NR, Boucher C, Prosperi M.

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Mobilization of Antibiotic Resistance: Are Current Approaches for Colocalizing Resistomes and Mobilomes Useful?

Frontiers in Microbiology

Ilya B. Slizovskiy, Kingshuk Mukherjee, Christopher J. Dean, Christina Boucher, Noelle R. Noyes


MEGARes 2.0: a database for classification of antimicrobial drug, biocide and metal resistance determinants in metagenomic sequence data

Nucleic Acids Research

Enrique Doster, Steven M. Lakin, Christopher J. Dean, Cory Wolfe, Jared G. Young, Christina Boucher, Keith E Belk, Noelle R Noyes, Paul S Morley

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Genome sequence of Listeria innocua
strain MEZLIS26 isolated from a goat in South Africa


Microbiology Resource Announcements

Zowalaty ME, Hickman R, Zishiri O, Noyes NR, Järhult J.

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Metagenomics of Meat and Poultry


Food Microbiology: Fundamentals and Frontiers, 5th Ed.

Weinroth MD, Noyes NR, Morley PS, Belk KE.

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Hierarchical Hidden Markov models enable accurate and diverse detection of antimicrobial resistance sequences


Communications Biology

Lakin SM, Kuhnle A, Alipanahi B, Noyes NR, Dean C, Martin M, Raymond RE, Zaid A, Prosperi

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A Comparative Study of Serum Biochemistry, Metabolome and Microbiome Parameters of Clinically Healthy, Normal Weight, Overweight, and Obese Companion Dogs

Topics in Companion Animal Medicine

Forster GM, Stockman J, Noyes NR, Heuberger AL, Broeckling CD, Bantle CM, Ryan EP.


Effects of Ceftiofur and Chlortetracycline on the Resistome of Feedlot Cattle

Applied and Environmental Microbiology

Margaret D. Weinroth, H. Morgan Scott, Bo Norby, Guy H. Loneragan, Noelle R. Noyes, Pablo Rovira, Enrique Doster, Xiang Yang, Dale R. Woerner, Paul S. Morley and Keith E. Belk


Associations between sexual habits, menstrual hygiene practices, demographics and the vaginal microbiome as revealed by Bayesian network analysis


Noelle Noyes, Kyu-Chul Cho, Jacques Ravel, Larry J. Forney, Zaid Abdo


Whole-Genome Sequencing and Concordance Between Antimicrobial Susceptibility Genotypes and Phenotypes of Bacterial Isolates Associated with Bovine Respiratory Disease


Owen JR, Noyes N, Young AE, Prince DJ, Blanchard PC, Lehenbauer TW, Aly SS, Davis JH, O'Rourke SM, Abdo Z, Belk K, Miller MR, Morley P, Van Eenennaam AL


MEGARes: an antimicrobial resistance database for high throughput sequencing


Nucleic Acids Research

Steven M. Lakin, Chris Dean, Noelle R. Noyes, Adam Dettenwanger, Anne Spencer Ross, Enrique Doster, Pablo Rovira, Zaid Abdo, Kenneth L. Jones, Jaime Ruiz, Keith E. Belk, Paul S. Morley, Christina Boucher


Resistome diversity in cattle and the environment decreases during beef production


Noelle R Noyes, Xiang Yang, Lyndsey M Linke, Roberta J Magnuson, Adam Dettenwanger, Shaun Cook, Ifigenia Geornaras, Dale E Woerner, Sheryl P Gow, Tim A McAllister, Hua Yang, Jaime Ruiz, Kenneth L Jones, Christina A Boucher, Paul S Morley, Keith E Belk

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Modelling considerations in the analysis of associations between antimicrobial use and resistance in beef feedlot cattle

Epidemiology and Infection

Noyes, N. R., Benedict, K. M., Gow, S. P.,  Waldner, C.L., Reid-Smith, R.J., Booker, C. W., McAllister, T. A., & Morley, P. S.