Publications

Beyond Antimicrobial Use: A Framework for Prioritizing Antimicrobial Resistance Interventions

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

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

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

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?

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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.

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

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

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

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

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