Holmes, Susan P.

DADA2: High–resolution sample inference from Illumina amplicon data

Callahan, B. J., McMurdie, P. J., Rosen, M. J., Han, A. W., Johnson, A. J. A., & Holmes, S. P. (2016) · Nature Methods

Genomics and Phylogenetic StudiesMicrobial Community Ecology and Physiology

Cited by 35,698

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

Bolyen, E., Rideout, J. R., Dillon, M. R., Bokulich, N. A., Abnet, C. C., Al-Ghalith, G. A., Alexander, H., Alm, E. J., Arumugam, M., Asnicar, F., et al. (2019) · Nature Biotechnology

Scientific Computing and Data ManagementGut microbiota and health

Cited by 23,742

Simple statistical identification and removal of contaminant sequences in marker-gene and metagenomics data

Davis, N. M., Proctor, D. M., Holmes, S. P., Relman, D. A., & Callahan, B. J. (2018) · Microbiome

Genomics and Phylogenetic StudiesMicrobial Community Ecology and Physiology

Cited by 3,493

Temporal and spatial variation of the human microbiota during pregnancy

DiGiulio, D. B., Callahan, B. J., McMurdie, P. J., Costello, E. K., Lyell, D. J., Robaczewska, A., Sun, C. L., Goltsman, D. S. A., Wong, R. J., Shaw, G., et al. (2015) · Proceedings of the National Academy of Sciences

Reproductive tract infections researchGut microbiota and health

Cited by 1,129

Profiling the human intestinal environment under physiological conditions

Shalon, D., Culver, R. N., Grembi, J. A., Folz, J., Treit, P. V., Shi, H., Rosenberger, F. A., Dethlefsen, L., Meng, X., Yaffe, E., et al. (2023) · Nature

Gut microbiota and healthGastrointestinal motility and disorders

Cited by 484

Interpreting prevotella and bacteroides as biomarkers of diet and lifestyle

Gorvitovskaia, A., Holmes, S. P., & Huse, S. M. (2016) · Microbiome

Gut microbiota and healthOral microbiology and periodontitis research

Cited by 461

Replication and refinement of a vaginal microbial signature of preterm birth in two racially distinct cohorts of US women

Callahan, B. J., DiGiulio, D. B., Goltsman, D. S. A., Sun, C. L., Costello, E. K., Jeganathan, P., Biggio, J. R., Wong, R. J., Druzin, M. L., Shaw, G. M., et al. (2017) · Proceedings of the National Academy of Sciences

Reproductive tract infections researchPreterm Birth and Chorioamnionitis

Cited by 391

Nasal Microenvironments and Interspecific Interactions Influence Nasal Microbiota Complexity and S. aureus Carriage

Yan, M., Pamp, S. J., Fukuyama, J., Hwang, P. H., Cho, D.-Y., Holmes, S., & Relman, D. A. (2013) · Cell Host & Microbe

Antimicrobial Resistance in StaphylococcusGut microbiota and health

Cited by 351

Genetically dictated change in host mucus carbohydrate landscape exerts a diet-dependent effect on the gut microbiota

Kashyap, P. C., Marcobal, A., Ursell, L. K., Smits, S. A., Sonnenburg, E. D., Costello, E. K., Higginbottom, S. K., Domino, S. E., Holmes, S. P., Relman, D. A., et al. (2013) · Proceedings of the National Academy of Sciences

Gut microbiota and healthMicrobial Metabolites in Food Biotechnology

Cited by 285

A spatial gradient of bacterial diversity in the human oral cavity shaped by salivary flow

Proctor, D. M., Fukuyama, J. A., Loomer, P. M., Armitage, G. C., Lee, S. A., Davis, N. M., Ryder, M. I., Holmes, S. P., & Relman, D. A. (2018) · Nature Communications

Oral microbiology and periodontitis researchMicrobial Community Ecology and Physiology

Cited by 115

REPRODUCIBLE RESEARCH WORKFLOW IN R FOR THE ANALYSIS OF PERSONALIZED HUMAN MICROBIOME DATA

CALLAHAN, B., PROCTOR, D., RELMAN, D., FUKUYAMA, J., & HOLMES, S. (2016) · Biocomputing 2016

Scientific Computing and Data ManagementGenomics and Phylogenetic Studies

Cited by 35

Learning Weighted Submanifolds With Variational Autoencoders and Riemannian Variational Autoencoders

Miolane, N., & Holmes, S. (2020) · 2020 IEEE/CVF Conference on Computer Vision and Pattern Recognition (CVPR)

Neural Networks and ApplicationsTopological and Geometric Data Analysis

Cited by 16