| MEGARes: an antimicrobial resistance database for high throughput sequencing SM Lakin, C Dean, NR Noyes, A Dettenwanger, AS Ross, E Doster, ... Nucleic acids research 45 (D1), D574-D580, 2017 | 330 | 2017 |
| MEGARes 2.0: a database for classification of antimicrobial drug, biocide and metal resistance determinants in metagenomic sequence data E Doster, SM Lakin, CJ Dean, C Wolfe, JG Young, C Boucher, KE Belk, ... Nucleic acids research 48 (D1), D561-D569, 2020 | 298 | 2020 |
| Impact of sequencing depth on the characterization of the microbiome and resistome R Zaheer, N Noyes, R Ortega Polo, SR Cook, E Marinier, ... Scientific reports 8 (1), 5890, 2018 | 200 | 2018 |
| Use of metagenomic shotgun sequencing technology to detect foodborne pathogens within the microbiome of the beef production chain X Yang, NR Noyes, E Doster, JN Martin, LM Linke, RJ Magnuson, H Yang, ... Applied and environmental microbiology 82 (8), 2433-2443, 2016 | 145 | 2016 |
| Succinct colored de Bruijn graphs MD Muggli, A Bowe, NR Noyes, PS Morley, KE Belk, R Raymond, T Gagie, ... Bioinformatics 33 (20), 3181-3187, 2017 | 127 | 2017 |
| Resistome diversity in cattle and the environment decreases during beef production NR Noyes, X Yang, LM Linke, RJ Magnuson, A Dettenwanger, S Cook, ... elife 5, e13195, 2016 | 126 | 2016 |
| Characterization of the resistome in manure, soil and wastewater from dairy and beef production systems NR Noyes, X Yang, LM Linke, RJ Magnuson, SR Cook, R Zaheer, H Yang, ... Scientific reports 6 (1), 24645, 2016 | 125 | 2016 |
| Associations between sexual habits, menstrual hygiene practices, demographics and the vaginal microbiome as revealed by Bayesian network analysis N Noyes, KC Cho, J Ravel, LJ Forney, Z Abdo PloS one 13 (1), e0191625, 2018 | 122 | 2018 |
| Mannheimia haemolytica in Feedlot Cattle: Prevalence of Recovery and Associations with Antimicrobial Use, Resistance, and Health Outcomes NR Noyes, KM Benedict, SP Gow, CW Booker, SJ Hannon, TA McAllister, ... Journal of veterinary internal medicine 29 (2), 705-713, 2015 | 81 | 2015 |
| A comparative study of serum biochemistry, metabolome and microbiome parameters of clinically healthy, normal weight, overweight, and obese companion dogs GM Forster, J Stockman, N Noyes, AL Heuberger, CD Broeckling, ... Topics in companion animal medicine 33 (4), 126-135, 2018 | 72 | 2018 |
| Enrichment allows identification of diverse, rare elements in metagenomic resistome-virulome sequencing NR Noyes, ME Weinroth, JK Parker, CJ Dean, SM Lakin, RA Raymond, ... Microbiome 5, 1-13, 2017 | 72 | 2017 |
| Characterization of the microbial resistome in conventional and “raised without antibiotics” beef and dairy production systems P Rovira, T McAllister, SM Lakin, SR Cook, E Doster, NR Noyes, ... Frontiers in microbiology 10, 1980, 2019 | 67 | 2019 |
| Antimicrobial Resistance in Escherichia coli Recovered from Feedlot Cattle and Associations with Antimicrobial Use KM Benedict, SP Gow, TA McAllister, CW Booker, SJ Hannon, ... PloS one 10 (12), e0143995, 2015 | 66 | 2015 |
| Investigating effects of tulathromycin metaphylaxis on the fecal resistome and microbiome of commercial feedlot cattle early in the feeding period E Doster, P Rovira, NR Noyes, BA Burgess, X Yang, MD Weinroth, ... Frontiers in microbiology 9, 1715, 2018 | 59 | 2018 |
| Considerations and best practices in animal science 16S ribosomal RNA gene sequencing microbiome studies MD Weinroth, AD Belk, C Dean, N Noyes, DK Dittoe, MJ Rothrock Jr, ... Journal of animal science 100 (2), skab346, 2022 | 52 | 2022 |
| Mobilization of antibiotic resistance: are current approaches for colocalizing resistomes and mobilomes useful? IB Slizovskiy, K Mukherjee, CJ Dean, C Boucher, NR Noyes Frontiers in microbiology 11, 1376, 2020 | 40 | 2020 |
| MEGARes and AMR++, v3. 0: an updated comprehensive database of antimicrobial resistance determinants and an improved software pipeline for classification using high-throughput … N Bonin, E Doster, H Worley, LJ Pinnell, JE Bravo, P Ferm, S Marini, ... Nucleic acids research 51 (D1), D744-D752, 2023 | 39 | 2023 |
| Effects of ceftiofur and chlortetracycline on the resistomes of feedlot cattle MD Weinroth, HM Scott, B Norby, GH Loneragan, NR Noyes, P Rovira, ... Applied and environmental microbiology 84 (13), e00610-18, 2018 | 37 | 2018 |
| Whole-genome sequencing and concordance between antimicrobial susceptibility genotypes and phenotypes of bacterial isolates associated with bovine respiratory disease JR Owen, N Noyes, AE Young, DJ Prince, PC Blanchard, TW Lehenbauer, ... G3: Genes, Genomes, Genetics 7 (9), 3059-3071, 2017 | 34 | 2017 |
| Hierarchical Hidden Markov models enable accurate and diverse detection of antimicrobial resistance sequences SM Lakin, A Kuhnle, B Alipanahi, NR Noyes, C Dean, M Muggli, ... Communications biology 2 (1), 294, 2019 | 29 | 2019 |
