| QIIME 2: Reproducible, interactive, scalable, and extensible microbiome data science E Bolyen, JR Rideout, MR Dillon, NA Bokulich, C Abnet, GA Al-Ghalith, ... PeerJ Preprints, 2018 | 15948* | 2018 |
| DRAM for distilling microbial metabolism to automate the curation of microbiome function M Shaffer, MA Borton, BB McGivern, AA Zayed, SL La Rosa, LM Solden, ... Nucleic Acids Research 48 (16), 8883-8900, 2020 | 543 | 2020 |
| Differences in fecal microbial metabolites and microbiota of children with autism spectrum disorders DW Kang, ZE Ilhan, NG Isern, DW Hoyt, DP Howsmon, M Shaffer, ... Anaerobe 49, 121-131, 2018 | 334 | 2018 |
| An exploration of Prevotella-rich microbiomes in HIV and men who have sex with men AJS Armstrong, M Shaffer, NM Nusbacher, C Griesmer, S Fiorillo, ... Microbiome 6 (1), 1-16, 2018 | 142 | 2018 |
| Diverse Intestinal Bacteria Contain Putative Zwitterionic Capsular Polysaccharides with Anti-inflammatory Properties CP Neff, ME Rhodes, KL Arnolds, CB Collins, J Donnelly, N Nusbacher, ... Cell Host & Microbe 20 (4), 535-547, 2016 | 129 | 2016 |
| Complexities of gut microbiome dysbiosis in the context of HIV infection and antiretroviral therapy SX Li, AJS Armstrong, CP Neff, M Shaffer, CA Lozupone, BE Palmer Clinical Pharmacology & Therapeutics 99 (6), 600-611, 2016 | 84 | 2016 |
| Gut microbiota from high-risk men who have sex with men drive immune activation in gnotobiotic mice and in vitro HIV infection SX Li, S Sen, JM Schneider, KN Xiong, NM Nusbacher, N Moreno-Huizar, ... PLoS pathogens 15 (4), e1007611, 2019 | 77 | 2019 |
| Microbiome and metabolome data integration provides insight into health and disease M Shaffer, AJS Armstrong, VV Phelan, N Reisdorph, CA Lozupone Translational Research 189, 51-64, 2017 | 77 | 2017 |
| AMON: annotation of metabolite origins via networks to integrate microbiome and metabolome data M Shaffer, K Thurimella, K Quinn, K Doenges, X Zhang, S Bokatzian, ... BMC bioinformatics 20 (1), 1-11, 2019 | 45 | 2019 |
| Prevalence and Source of Fecal and Oral Bacteria on Infant, Child, and Adult Hands M Shaffer, C Lozupone mSystems 3 (1), e00192-17, 2018 | 37 | 2018 |
| SCNIC: Sparse correlation network investigation for compositional data M Shaffer, K Thurimella, JD Sterrett, CA Lozupone Molecular Ecology Resources 23 (1), 312-325, 2023 | 27 | 2023 |
| Genome-resolved metaproteomics decodes the microbial and viral contributions to coupled carbon and nitrogen cycling in river sediments JA Rodríguez-Ramos, MA Borton, BB McGivern, GJ Smith, LM Solden, ... Msystems 7 (4), e00516-22, 2022 | 15 | 2022 |
| Optimization of proteomics sample preparation for identification of host and bacterial proteins in mouse feces M Baniasad, Y Kim, M Shaffer, A Sabag-Daigle, I Leleiwi, RA Daly, ... Analytical and Bioanalytical Chemistry 414 (7), 2317-2331, 2022 | 12 | 2022 |
| Where does Neisseria acquire foreign DNA from: an examination of the source of genomic and pathogenic islands and the evolution of the Neisseria genus C Putonti, B Nowicki, M Shaffer, Y Fofanov, S Nowicki BMC evolutionary biology 13 (1), 1-12, 2013 | 11 | 2013 |
| ORT: A workflow linking genome-scale metabolic models with reactive transport codes RL Rubinstein, MA Borton, H Zhou, M Shaffer, DW Hoyt, J Stegen, ... Bioinformatics 38 (3), 778-784, 2022 | 7 | 2022 |
| Human-gut phages harbor sporulation genes D Schwartz, J Rodriguez-Ramos, M Shaffer, R Flynn, RA Daly, K Wrighton, ... bioRxiv, 2023.01. 19.524802, 2023 | 5 | 2023 |
| Targeted curation of the gut microbial gene content modulating human cardiovascular disease MA Borton, M Shaffer, DW Hoyt, R Jiang, J Ellenbogen, SO Purvine, ... bioRxiv, 2022.06. 20.496735, 2022 | 4 | 2022 |
| Exposing New Taxonomic Variation with Inflammation-A Murine Model-Specific Genome Database for Gut Microbiome Researchers I Leleiwi, J Rodriguez-Ramos, M Shaffer, A Sabag-Daigle, K Kokkinias, ... bioRxiv, 2022.10. 24.513540, 2022 | 2 | 2022 |
| kb_DRAM: Annotating and functional profiling of genomes with DRAM in KBase M Shaffer, MA Borton, B Bolduc, P Ghadermazi, J Edirisinghe, JP Faria, ... bioRxiv, 2022.03. 13.484145, 2022 | 2* | 2022 |
| Microbial Genome-Resolved Metaproteomic Analyses Frame Intertwined Carbon and Nitrogen Cycles in River Hyporheic Sediments JA Rodríguez-Ramos, MA Borton, BB McGivern, GJ Smith, LM Solden, ... | 1 | 2021 |
Catherine LozuponeAssociate Professor of Medicine, University of Colorado, Denver在 ucdenver.edu 的电子邮件经过验证
Catherine LozuponeAssociate Professor of Medicine, University of Colorado, Denver在 ucdenver.edu 的电子邮件经过验证
Abigail JS ArmstrongRutgers University在 cabm.rutgers.edu 的电子邮件经过验证