About

Susan Holmes is a Professor of Statistics, Emerita, at Stanford University. She has been working in non-parametric multivariate statistics applied to Biology since 1985. Holmes trained in the French school of Data Analysis in Montpellier and has taught at MIT, Harvard, and was an Associate Professor of Biometry at Cornell before moving to Stanford in 1998. She created the Thinking Matters class: Breaking Codes and Finding Patterns and enjoys working on big messy data sets, primarily from the areas of Immunology, Cancer Biology, and Microbial Ecology. Her theoretical interests include applied probability, Monte Carlo Markov chains (MCMC), Graph Limit Theory, Differential Geometry, and the topology of the space of Phylogenetic Trees. Holmes co-authored the book Modern Statistics for Modern Biology with Wolfgang Huber from EMBL and teaches this material as a crash course (BIOS221) regularly every year. Her current research focus is on improving the statistical analyses and reproducibility of data in perturbation studies of the Human Microbiome. She holds numerous honors and awards, including fellowships at the Fields Institute and the Center for the Advanced Study of the Behavioral Sciences, and has served on various scientific advisory boards and research institutes.

Research topics

• Computer Science
• Medicine
• Biology
• Immunology
• Data Mining
• Internal medicine
• Data science
• Pathology
• Mathematics
• Mathematical analysis
• Psychology
• Pediatrics
• Geometry
• Pure mathematics
• Bioinformatics
• Computational science
• Programming language
• Algorithm
• Environmental health
• Cell biology
• Anesthesia
• Intensive care medicine
• Virology
• Computational biology

Selected publications

• Vaginal microbiota impacts of a Lactobacillus crispatus live biotherapeutic and predictors of colonization in randomized controlled trial

  Cell Host & Microbe · 2026-03-27 · 2 citations

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  PublisherDOI

• VIBRANT: A phase 1 randomized trial of multi-strain vaginal L. crispatus live biotherapeutic products in people with bacterial vaginosis

  Cell Host & Microbe · 2026-03-18 · 3 citations

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  PublisherDOI

• Guidelines for preventing and reporting contamination in low-biomass microbiome studies

  Nature Microbiology · 2025-06-20 · 67 citations

  reviewOpen access
  PublisherOA PDFDOI

• Prior vaccination prevents overactivation of innate immune responses during COVID-19 breakthrough infection

  Science Translational Medicine · 2025-01-29 · 18 citations

  articleOpen access

  At this stage in the COVID-19 pandemic, most infections are "breakthrough" infections that occur in individuals with prior severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) exposure. To refine long-term vaccine strategies against emerging variants, we examined both innate and adaptive immunity in breakthrough infections. We performed single-cell transcriptomic, proteomic, and functional profiling of primary and breakthrough infections to compare immune responses from unvaccinated and vaccinated individuals during the SARS-CoV-2 Delta wave. Breakthrough infections were characterized by a less activated transcriptomic profile in monocytes and natural killer cells, with induction of pathways limiting monocyte migratory potential and natural killer cell proliferation. Furthermore, we observed a female-specific increase in transcriptomic and proteomic activation of multiple innate immune cell subsets during breakthrough infections. These insights suggest that prior SARS-CoV-2 vaccination prevents overactivation of innate immune responses during breakthrough infections with discernible sex-specific patterns and underscore the potential of harnessing vaccines in mitigating pathologic immune responses resulting from overactivation.

  PublisherOA PDFDOI

• Randomized Trial of Multi-Strain Lactobacillus crispatus Vaginal Live Biotherapeutic Products after Antibiotic Therapy for Bacterial Vaginosis: Study Protocol for VIBRANT (Vaginal Live Biotherapeutic RANdomized Trial)

  SSRN Electronic Journal · 2025-01-01 · 2 citations

  preprintOpen access
  PublisherDOI

• Estimating the size of a set using cascading exclusion

  ArXiv.org · 2025-08-07

  preprintOpen accessSenior author

  Let $S$ be a finite set, and $X_1,\ldots,X_n$ an i.i.d. uniform sample from $S$. To estimate the size $|S|$, without further structure, one can wait for repeats and use the birthday problem. This requires a sample size of the order $|S|^\frac{1}{2}$. On the other hand, if $S=\{1,2,\ldots,|S|\}$, the maximum of the sample blown up by $n/(n-1)$ gives an efficient estimator based on any growing sample size. This paper gives refinements that interpolate between these extremes. A general non-asymptotic theory is developed. This includes estimating the volume of a compact convex set, the unseen species problem, and a host of testing problems that follow from the question `Is this new observation a typical pick from a large prespecified population?' We also treat regression style predictors. A general theorem gives non-parametric finite $n$ error bounds in all cases.

  PublisherOA PDFDOI

• Author Correction: Community-wide hackathons to identify central themes in single-cell multi-omics

  UNC Libraries · 2025-05-13

  articleOpen access
  PublisherDOI

• Community-wide hackathons to identify central themes in single-cell multi-omics

  UNC Libraries · 2025-05-13

  articleOpen access
  PublisherDOI

• Microbiota effects and predictors of <i>Lactobacillus crispatu</i> s colonization after treatment with a vaginal live biotherapeutic: results from a randomized, double-blinded, placebo-controlled trial

  medRxiv · 2025-08-21

  preprintOpen access

  Abstract Bacterial vaginosis (BV) affects &gt;25% of women worldwide and often recurs after standard-of-care metronidazole (MTZ) treatment. LACTIN-V, a live biotherapeutic product (LBP) containing Lactobacillus crispatus strain CTV-05, reduced recurrent BV in a Phase 2b clinical trial, but efficacy was incomplete. We characterized microbiota and immune effects and correlates of treatment success in trial samples. By week 12, L. crispatus -dominant microbiota was achieved in 30% of LBP recipients compared to 9% of placebo (benefit ratio: 3.31; p&lt;0.005). This effect was mostly due to CTV-05, but native L. crispatus strains were also present and increased over time. Inflammatory cytokines decreased in both arms after MTZ, but returned to baseline in placebo recipients. L. crispatus colonization was associated with pre-MTZ microbiota, baseline cytokine profiles, post-MTZ bacterial load, and clinical and behavioral variables. These findings elucidate LBP microbiota effects and identify predictors of treatment success, informing improved intervention strategies to advance women’s health.

  PublisherOA PDFDOI

• NKp30 and NKG2D contribute to natural killer cell-mediated recognition of HIV-infected cells

  iScience · 2025-09-13 · 2 citations

  articleOpen access

  . We characterized the patterns of NK cell ligand expression on CD4 T cells at baseline and after infection with a panel of transmitted/founder HIV-1 strains to identify key receptor-ligand pairings. CRISPR editing of CD4 T cells to knock out the NKp30 ligand B7-H6, or the NKG2D ligand MICB reduced NK cell responses to HIV-infected cells in some donors. Blockade of NKp30 or NKG2D on NK cells compromised their specificity of killing HIV-infected cells. Collectively, we identified receptor-ligand pairs including NKp30:B7-H6 and NKG2D:MICB that contribute to NK cell recognition of HIV-infected cells.

  PublisherDOI

Recent grants

• EMSW21-VIGRE: Vertical Integration of Mathematics, Statistics and Applied Mathematics.

  NSF · $2.7M · 2005–2014

• NIH Grant R03AI063576

  NIH · $149k · 2010

• Hierarchical Testing

  NSF · $300k · 2012–2015

• NIH Grant R01AI112401

  NIH · $6.2M · 2020

• NIH Grant R01GM086884

  NIH · $895k · 2015

Frequent coauthors

• Catherine A. Blish

  Chan Zuckerberg Initiative (United States)

  85 shared

• David A. Relman

  Stanford University

  67 shared

• Heather B. Jaspan

  University of Cape Town

  48 shared

• Persi Diaconis

  48 shared

• Christof Seiler

  Maastricht University

  45 shared

• Clive M. Gray

  University of Cape Town

  44 shared

• Anna‐Ursula Happel

  University of Cape Town

  37 shared

• Jonathan M. Blackburn

  University of Cape Town

  37 shared

Labs

• Susan HolmesPI

Awards & honors

• CASBS Fellow, Center for the Advanced study of the Behaviora…
• Breiman Lecturer, N(eur)IPS (December, 2016)
• Fellow, Fields Institute in Mathematical Sciences, Toronto,…
• Director's Transformative Research Award, NIH (2013)
• John Henry Samter University Fellow in Undergraduate Educati…