M. Shaffer

发表

An exploration of Prevotella-rich microbiomes in HIV and men who have sex with men

B. Palmer, C. Lozupone, Abigail J. S. Armstrong, 2018, Microbiome.

Differences in fecal microbial metabolites and microbiota of children with autism spectrum disorders.

Dae-Wook Kang, Michael Shaffer, Rosa Krajmalnik-Brown, 2018, Anaerobe.

DRAM for distilling microbial metabolism to automate the curation of microbiome function

M. Sullivan, B. Bolduc, Pengfei Liu, 2020, bioRxiv.

DRAM for distilling microbial metabolism to automate the curation of microbiome function

M. Sullivan, B. Bolduc, Pengfei Liu, 2020, Nucleic acids research.

Targeted curation of the gut microbial gene content modulating human cardiovascular disease

Elizabeth K. Eder, D. Hoyt, M. Lipton, 2022, bioRxiv.

Microbial Genome-Resolved Metaproteomic Analyses Frame Intertwined Carbon and Nitrogen Cycles in River Hyporheic Sediments

Elizabeth K. Eder, D. Hoyt, M. Lipton, 2021 .

Draft Metagenome-Assembled Genome Sequences of Three Novel Ammonia-Oxidizing Nitrososphaera Strains Recovered from Agricultural Soils in Western Colorado

K. Wrighton, R. Daly, M. Shaffer, 2022, Microbiology resource announcements.

Resource Diverse Intestinal Bacteria Contain Putative Zwitterionic Capsular Polysaccharides with Anti-inflammatory Properties Graphical Abstract Highlights

M. McCarter, B. Palmer, S. Mazmanian, 2022 .

Exposing new taxonomic variation with inflammation — a murine model-specific genome database for gut microbiome researchers

B. Ahmer, K. Wrighton, R. Daly, 2022, bioRxiv.

Reproducible, interactive, scalable and extensible microbiome data science using QIIME 2

Francesco Asnicar, Mingxun Wang, Yang Bai, 2019, Nature Biotechnology.

Reproducible, interactive, scalable and extensible microbiome data science using QIIME 2

William A. Walters, Ahmad Turan Naimey, Lasse Buur Rasmussen, 2019, Nature Biotechnology.

QIIME 2: Reproducible, interactive, scalable, and extensible microbiome data science

Francesco Asnicar, Mingxun Wang, Pieter C. Dorrestein, 2018 .

Complexities of Gut Microbiome Dysbiosis in the Context of HIV Infection and Antiretroviral Therapy

C. Lozupone, M. Shaffer, S X Li, 2016, Clinical pharmacology and therapeutics.

Diverse Intestinal Bacteria Contain Putative Zwitterionic Capsular Polysaccharides with Anti-inflammatory Properties.

Michael Shaffer, M. McCarter, B. Palmer, 2016, Cell host & microbe.

SCNIC: Sparse correlation network investigation for compositional data

Michael Shaffer, Catherine A. Lozupone, Kumar Thurimella, 2020, bioRxiv.

Draft Metagenome-Assembled Genome Sequence of a Novel Citricoccus Species from Agricultural Soil in Western Colorado

K. Wrighton, R. Daly, M. Shaffer, 2023, Microbiology resource announcements.

kb_DRAM: annotation and metabolic profiling of genomes with DRAM in KBase

José P. Faria, C. Henry, S. H. Chan, 2022, bioRxiv.

ORT: A workflow linking genome-scale metabolic models with reactive transport codes

D. Hoyt, C. Henry, R. Versteeg, 2021, bioRxiv.

Manuscript title: DRAM for distilling microbial metabolism to automate the curation of microbiome

M. Sullivan, K. Wrighton, Rosa, 2022 .

Prevalence and Source of Fecal and Oral Bacteria on Infant, Child, and Adult Hands

C. Lozupone, M. Shaffer, Michael Shaffer, 2018, mSystems.

Author Correction: Reproducible, interactive, scalable and extensible microbiome data science using QIIME 2

Francesco Asnicar, Mingxun Wang, Yang Bai, 2019, Nature Biotechnology.

Genome-Resolved Metaproteomics Decodes the Microbial and Viral Contributions to Coupled Carbon and Nitrogen Cycling in River Sediments

Elizabeth K. Eder, D. Hoyt, M. Lipton, 2022, bioRxiv.

AMON: annotation of metabolite origins via networks to integrate microbiome and metabolome data

M. Shaffer, K. Thurimella, K. Quinn, 2019, BMC Bioinformatics.

AMON: Annotation of metabolite origins via networks to better integrate microbiome and metabolome data

C. Lozupone, M. Shaffer, N. Reisdorph, 2018, bioRxiv.

Microbiome and metabolome data integration provides insight into health and disease.

Nichole Reisdorph, Michael Shaffer, C. Lozupone, 2017, Translational research : the journal of laboratory and clinical medicine.

AMON: annotation of metabolite origins via networks to integrate microbiome and metabolome data

C. Lozupone, M. Shaffer, N. Reisdorph, 2019, BMC Bioinformatics.

Gut microbiota from high-risk men who have sex with men drive immune activation in gnotobiotic mice and in vitro HIV infection

M. McCarter, B. Palmer, C. Lozupone, 2019, PLoS pathogens.

Optimization of proteomics sample preparation for identification of host and bacterial proteins in mouse feces

B. Ahmer, V. Wysocki, K. Wrighton, 2022, Analytical and Bioanalytical Chemistry.

Human-Gut Phages Harbor Sporulation Genes

J. Lennon, K. Wrighton, R. Daly, 2023, bioRxiv.

Spatial and temporal metagenomics of river compartments reveals viral community dynamics in an urban impacted stream

K. Wrighton, A. Oliverio, J. Stegen, 2023, bioRxiv.

Diverse Intestinal Bacteria Contain Putative Zwitterionic Capsular Polysaccharides with Anti-inflammatory Properties.

M. McCarter, B. Palmer, S. Mazmanian, 2016, Cell host & microbe.

kb_DRAM: annotation and metabolic profiling of genomes with DRAM in KBase

José P. Faria, Janaka N. Edirisinghe, C. Henry, 2023, Bioinformatics.