Publications
The K-mer antibiotic resistance gene
variant analyzer (KARGVA)
Frontiers in Microbiology
Marini, S., Boucher, C., Noyes, N., & Prosperi, M.
Elucidation of genomic conjugative features and associated cargo genes across bacterial genera using genus-genus mobilization networks
Frontiers in Genetics
Nayar, G., Terrizzano, I., Seabolt, E., Agarwal, A., Boucher, C., Ruiz, J., Slizovskiy, I., Kaufman, J., & Noyes, N.
Advancing antimicrobial resistance monitoring in surface waters with metagenomic and quasimetagenomic methods
PLOS Water
Ottesen, A., Kocurek, B., Ramachandran, P., Reed, E., Commichaux, S., Engelbach, G., Nannekm M., Fleurant, S.S., Zhao, S., Kabera, C., Merrill, A., Bonin, N., Worley, H., Noyes, N.R., Boucher, C., McDermott, P., & Strain, E.,
Target-enriched long-read sequencing (TELSeq) contextualizes antimicrobial resistance genes in metagenomes
Microbiome
Slizovskiy, I., Oliva, M., Settle, J., Zyskina, L., Prosperi, M., Boucher, C., & Noyes, N.
The impacts of viral infection and subsequent antimicrobials on the microbiome-resistome of growing pigs
Microbiome
Gaire, T., Odland, C., Zhang, B., Ray, T., Doster, E., Nerem, J., Dee, S., Davies, P., & Noyes, N.R.
Syotti: Scalable bait design for DNA enrichment
Bioinformatics
Alanko, J., Slizovskiy, I., Lokshtanov, D., Gagle, T., Noyes, N., & Boucher, C.
Cow-related factors associated with intramammary infections during the 1st week postpartum in primiparous dairy cows in certified organic herds
The Veterinary Journal
Fernandes, L., Celestino, M.L., Menta, P.R., Silva, T.H., Paiva, D., Ribeiro, T.L., Caixeta, L.S., Noyes, N.R., & Machado, V.S.
Towards routine employment of computational tools for antimicrobial resistance determination via high-throughput sequencing
Briefings in Bioinformatics
Marini, S., Mora, R., Boucher, C., Noyes, N.R., & Prosperi, M.
AMR-meta: a k-mer and metafeature approach to classify antimicrobial resistance from high-throughput short-read metagenomics data
Gigascience
Marini, S., Olivia, M., Slizovskiy, I. B., Das, R.A., Noyes, N. R., Kahveci, T., Boucher, C.A., & Prosperi, M.
Evaluation of the impact of
antimicrobial use protocols in PRRS virus infected swine on phenotypic
antimicrobial resistance
patterns.
Applied and Environmental Microbiology
Odland, C., Elder R., Noyes, N.R., Dee, S., Nerem, J., & Davies, P.
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
Metagenome SNP calling via read dolored de Bruijn Graphs
Bioinformatics
Bahar Alipanahi, Martin D Muggli, Musa Jundi, Noelle R Noyes, Christina A Boucher
PrPC knockdown by liposome-siRNA-peptide complexes (LSPCs) prolongs survival and normal behavior of prion-infected mice immunotolerant to treatment
PLOS ONE
Heather Bender, Noelle Noyes, Jessica L. Annis, Amanda Hitpas, Luke Mollnow, Kendra Croak, Sarah Kane, Kaitlyn Wagner, Steven Dow, Mark Zabel
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.
Metagenomics of meat and poultry
Food Microbiology: Fundamentals and Frontiers, 5th Ed.
Weinroth MD, Noyes NR, Morley PS, Belk KE.
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
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.
Enrichment allows identification of diverse, rare elements in metagenomic resistome-virulome sequencing
Microbiome
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
Bioinformatics
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
Use of metagenomic shotgun sequencing technology to detect foodborne pathogens within the microbiome of the beef production chain
Applied and Environmental Microbiology
Yang, X., Noyes, N., Doster, E., Martin, J., Linke, L., Magnuson, R., Yang, H., Geornaras, I., Woener, D., Jones, K.L., Boucher, C., Morley, P.S., & Belk, K.
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.
Rapid Salmonella detection in experimentally inoculated equine faecal and veterinary hospital environmental samples using commercially available lateral flow immunoassays
Equine Veterinary Journal
Burgess, B. A., Noyes, N. R., Bolte, D. S., Hyatt, D. R., van Metre, D. C., & Morley, P. S.
Age influences the temporal dynamics of microbiome and antimicrobial resistance genes among fecal bacteria in a cohort of production pigs
Animal Microbiome
Gaire, T., Scott, H., Noyes, N., Ericsson, A., Tokach, M., Menegat, M., Vinasco, J., Roenne, B., Ray, T., Nagaraja, T.G., & Volkova, V.
MEGARes and AMR++, v3.0 an updated comprehensive database of antimicrobial resistance determinants and an improved software pipeline for classification using high-throughput sequencing
Nucleic Acid Research
Nathalie Bonin, Enrique Doster, Hannah Worley, Lee J Pinnel, Jonathan E Bravo, Peter Ferm, Simone Marini, Mattia Prosperi, Noelle Noyes, Paul S Morley, Christina Boucher
Evaluating the effects of antimicrobial drug use on the ecology of antimicrobial resistance and microbial community structure in beef feedlot cattle
Microbiology
Doster, E., Pinnell, L., Noyes, N., Parker, J., Anderson, C., Booker, C., Hannon, S.J., McAllister, T.A., Gow, S.P,, Belk K.E., & . Morley, P.
Factors influencing usage of antimicrobial drugs among pastoralists in Kenya
Tropical Animal Health and Production
Makau, D., Slizovskiy, I., Obanda, V., Noyes, N., Johnson, J., Oakes, M., Travis, D., VanderWaal, K., & Omondi, G
A longitudinal investigation of the effects of age, dietary fiber type and level, and injectable antimicrobials on the fecal microbiome and antimicrobial resistance of finisher pigs
Journal of Animal Science
Gaire, T., Noyes, N.R., Scott, H.M., Nagaraja, T.G., & Volkova, V.
Evaluation of contamination in milk samples pooled from independently collected quarters within a laboratory setting
Frontiers in Microbiology
Dean, C., Fernandes, L.M., Mosca, F., Caixeta, L., Machado, V., & Noyes, N.R.
Challenges in large-scale life science projects and implications for training
Humanities and Social Sciences Communication
Morrison-Smith, S., Noyes, N.R., Boucher, C.A., & Ruiz, J.
The microbiome of common bedding materials before and after use on commercial dairy farms
Animal Microbiome
Ray, T., Gaire, T.N., Dean, C.J., Rowe, S., Godden, S.W., & Noyes, N.R.
Considerations and best practices for animal science 16S ribosomal RNA gene sequencing microbiome studies
Journal of Animal Science
Weinroth, M.D., Belk, A.D., Dean, C.J., Noyes, N.R., Dittoe, D.K., Rothrock, M.J., Jr., Rickie, S.C., Myer, P.R., Henniger, M.T., Ramirez, G.A., Oakley, B.B., Summers, K.L., Miles, A.M., Ault-Seay, T.B., Yu, Z., Metcalf, J., & Wells, J.
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.
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
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
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.
Associations between sexual habits, menstrual hygiene practices, demographics and the vaginal microbiome as revealed by Bayesian network analysis
PLOS ONE
Noelle Noyes, Kyu-Chul Cho, Jacques Ravel, Larry J. Forney, Zaid Abdo
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
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
Whole-genome sequencing and concordance between antimicrobial susceptibility genotypes and phenotypes of bacterial isolates associated with bovine respiratory disease
G3
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
eLife
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
Antimicrobial resistance in Escherichia coli recovered from feedlot cattle and associations with antimicrobial Use
PLOS ONE
Benedict, K.M., Gow, S.P., McAllister, T.A., Booker, C.W., Hannon, S.J., Checkley, S.L., Noyes, N.R., & Morley, P.S.
Mannheimia haemolytica in heedlot 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.