Publications
Beyond Antimicrobial Use: A Framework for Prioritizing Antimicrobial Resistance Interventions
Noyes NR, Slizovskiy IB, Singer RS
Impact 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
Fernandes LM, Guimaraes I, Noyes NR, Caixeta L, Machado, V
Exploring Prediction of Antimicrobial Resistance Based on Protein Solvent Accessibility Variation
Marini S, Slizovskiy IB, Noyes NR, Boucher C, Prosperi M.
Investigating the cow skin and teat canal microbiomes of the bovine udder using different sampling and sequencing approaches
C.J.Dean, I.B.Slizovskiy, K.K.Crone, A.X.Pfennig, B.J.Heins, L.S.Caixeta, N.R.Noyes
Mobilization of Antibiotic Resistance: Are Current Approaches for Colocalizing Resistomes and Mobilomes Useful?
Ilya B. Slizovskiy, Kingshuk Mukherjee, Christopher J. Dean, Christina Boucher, Noelle R. Noyes
Metagenome SNP Calling via Read Colored de Bruijn Graphs
Bahar Alipanahi, Martin D Muggli, Musa Jundi, Noelle R Noyes, Christina A Boucher
MEGARes 2.0: a database for classification of antimicrobial drug, biocide and metal resistance determinants in metagenomic sequence data
Enrique Doster, Steven M. Lakin, Christopher J. Dean, Cory Wolfe, Jared G. Young, Christina Boucher, Keith E Belk, Noelle R Noyes, Paul S Morley
A Cautionary Report for Pathogen Identification Using Shotgun Metagenomics; A Comparison to Aerobic Culture and Polymerase Chain Reaction for Salmonella enterica Identification
Enrique Doster, Pablo Rovira, , Noelle R. Noyes, Brandy A. Burgess, Xiang Yang, Maggie D. Weinroth, Lyndsey Linke, Roberta Magnuson, Christina Boucher, Keith E Belk, Paul S Morley
Characterization of the Microbial Resistome in Conventional and “Raised Without Antibiotics” Beef and Dairy Production Systems
Pablo Rovira, Tim McAllister, Steven Michael Lakin, Shaun R. Cook, Enrique Doster, Noelle R. Noyes, Maggie D. Weinroth, Xiang Yang, Jennifer K. Parker, Christina Boucher, Calvin W. Booker, Dale R Woerner, Keith E Belk, Paul S Morley
Metagenomics of Meat and Poultry
Margaret D. Weinroth, Noelle R. Noyes, Paul S. Morley, Keith E. Belk
Hierarchical Hidden Markov models enable accurate and diverse detection of antimicrobial resistance sequences
Steven M. Lakin, Alan Kuhnle, Bahar Alipanahi, Noelle R. Noyes, Chris Dean, Martin Muggli, Rob Raymond, Zaid Abdo, Mattia Prosperi, Keith E. Belk, Paul S. Morley & Christina Boucher
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
Circulation of plasmids harboring resistance genes to quinolones and/or extended spectrum cephalosporins in multiple Salmonella enterica serotypes from swine in the United States
1. 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
A Comparative Study of Serum Biochemistry, Metabolome and Microbiome Parameters of Clinically Healthy, Normal Weight, Overweight, and Obese Companion Dogs
Forster GM, Stockman J, Noyes NR, Heuberger AL, Broeckling CD, Bantle CM, Ryan EP
Investigating effects of tulathromycin metaphylaxis on the fecal resistome and microbiome of feedlot cattle early in the feeding period using shotgun metagenomic sequencing
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.
Effects of Ceftiofur and Chlortetracycline on the Resistome of Feedlot Cattle
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
Impact of sequencing depth on the characterization of the microbiome and resistome
Rahat Zaheer, Noelle Noyes, Rodrigo Ortega Polo, Shaun R. Cook, Eric Marinier, Gary Van Domselaar, Keith E. Belk, Paul S. Morley & Tim A. McAllister
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
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
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
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
MEGARes: an antimicrobial resistance database for high throughput sequencing
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
Characterization of the resistome in manure, soil and wastewater from dairy and beef production systems
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
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