Richard H. Scheuermann, PhD

Director, La Jolla Campus

Richard H. Scheuermann is Director of Informatics, Director of JCVI’s La Jolla Campus and an adjunct professor of pathology at U.C. San Diego. After completing his doctoral research, he accepted an independent research position at the Basel Institute for Immunology in Basel, Switzerland. In 1992, he joined the faculty in the Department of Pathology at the University of Texas Southwestern Medical Center in Dallas where he rose to the rank of Professor with tenure. In 2001, he made a career shift into the discipline of bioinformatics, initiated with a sabbatical year at the San Diego Supercomputer Center. In 2012, Dr. Scheuermann moved to San Diego to become the Director of Informatics at JCVI, and in 2016 was promoted to Director of the La Jolla Campus.

Dr. Scheuermann has applied his deep knowledge in molecular immunology and infectious disease toward the development of novel computational data mining methods and knowledge representation approaches, including the development of biomedical ontologies and their use in data mining, novel methods for the analysis of gene expression, protein network and flow cytometry data, and novel comparative genomics methods. These computational methods have been made available through several public database and analysis resources, including the Influenza Research Database (IRD), the Virus Pathogen Resource (ViPR), and the Immunology Database and Analysis Portal (ImmPort) supported by the U.S. National Institutes of Health.

He received a BS in Life Sciences from the Massachusetts Institute of Technology, and a PhD in Molecular Biology from the University of California, Berkeley.

Research Priorities

Informatics database resources and knowledge representation standards
  • Principle investigator on the Influenza Research Database (IRD), the Virus Pathogen Resource (ViPR) and the Immunology Database and Analysis Portal (ImmPort) development projects.
  • Development of biomedical ontologies and other knowledge representation standards through the Open Biomedical Ontology (OBO) Foundry, including the Cell Ontology (CL), the Ontology for General Medical Sciences (OGMS), the Ontology for Biomedical Investigations (OBI), and the Minimum Information about a Flow Cytometry Experiment (MIFlowCyt).
Flow cytometry analysis methods
  • Development of a suite of cytometry data processing and analysis methods, including FLOCK, FlowMap-FR, FCSTrans, and DAFi.
  • Co-founder of the FlowCAP Consortium for the critical evaluation of cytometry analysis methods using benchmark datasets and objective performance metrics.
  • Development of the FlowGate resource for user-friendly access to cytometry analysis methods.
  • Application of computational cytometry analysis methods to study immunological responses to vaccination, respiratory pathogen infection, autoimmunity, and leukemia and lymphoma.
Systems biology analysis methods
  • Identification of functional modules within gene/protein networks based on their topological properties using MoNet and dMoNet.
  • Dissemination of systems biology of infectious diseases data through the IRD and ViPR resources.
Transcriptomics and single cell genomics
  • Development of a suite of gene expression microarray analysis methods, including DFW, DFCM, CLASSIFI, and GO-Bayes.
  • Use of single cell RNA sequencing (scRNAseq) to study the cellular complexity of the human cerebral cortex, vaccine responses, and the development of multiple sclerosis.
  • Application of machine learning methods for scRNAseq analysis, including quality control procedures and marker gene feature selection.


FastMix: a versatile data integration pipeline for cell type-specific biomarker inference.
Bioinformatics (Oxford, England). 2022-10-14; 38.20: 4735-4744.
PMID: 36018232
A novel vaccine based on SARS-CoV-2 CD4+ and CD8+ T cell conserved epitopes from variants Alpha to Omicron.
Scientific reports. 2022-10-06; 12.1: 16731.
PMID: 36202985
Machine learning for cell type classification from single nucleus RNA sequencing data.
PloS one. 2022-09-23; 17.9: e0275070.
PMID: 36149937
Animal Models of Enterovirus D68 Infection and Disease.
Journal of virology. 2022-08-10; 96.15: e0083322.
PMID: 35852353
Cell type matching in single-cell RNA-sequencing data using FR-Match.
Scientific reports. 2022-06-15; 12.1: 9996.
PMID: 35705694
Genomic evolution of the Coronaviridae family.
Virology. 2022-05-01; 570.123-133.
PMID: 35398776
Defining the risk of SARS-CoV-2 variants on immune protection.
Nature. 2022-05-01; 605.7911: 640-652.
PMID: 35361968
Antibodies elicited by SARS-CoV-2 infection or mRNA vaccines have reduced neutralizing activity against Beta and Omicron pseudoviruses.
Science translational medicine. 2022-03-02; 14.634: eabn7842.
PMID: 35025672
The genome and preliminary single-nuclei transcriptome of Lemna minuta reveals mechanisms of invasiveness.
Plant physiology. 2022-02-04; 188.2: 879-897.
PMID: 34893913
Corticosteroid treatment in COVID-19 modulates host inflammatory responses and transcriptional signatures of immune dysregulation.
Journal of leukocyte biology. 2021-12-01; 110.6: 1225-1239.
PMID: 34730254
Machine Learning-Based Single Cell and Integrative Analysis Reveals That Baseline mDC Predisposition Correlates With Hepatitis B Vaccine Antibody Response.
Frontiers in immunology. 2021-10-29; 12.690470.
PMID: 34777332
A machine learning method for the discovery of minimum marker gene combinations for cell type identification from single-cell RNA sequencing.
Genome research. 2021-10-01; 31.10: 1767-1780.
PMID: 34088715
Impact of SARS-CoV-2 variants on the total CD4+ and CD8+ T cell reactivity in infected or vaccinated individuals.
Cell reports. Medicine. 2021-07-20; 2.7: 100355.
PMID: 34230917
FR-Match: robust matching of cell type clusters from single cell RNA sequencing data using the Friedman-Rafsky non-parametric test.
Briefings in bioinformatics. 2021-07-20; 22.4:
PMID: 33249453
Standardization of assay representation in the Ontology for Biomedical Investigations.
Database : the journal of biological databases and curation. 2021-07-09; 2021.
PMID: 34244718
A system-view of Bordetella pertussis booster vaccine responses in adults primed with whole-cell versus acellular vaccine in infancy.
JCI insight. 2021-04-08; 6.7:
PMID: 33690224
Multi-Omic Data Integration Allows Baseline Immune Signatures to Predict Hepatitis B Vaccine Response in a Small Cohort.
Frontiers in immunology. 2020-11-30; 11.578801.
PMID: 33329547
Epidemiology and Sequence-Based Evolutionary Analysis of Circulating Non-Polio Enteroviruses.
Microorganisms. 2020-11-25; 8.12:
PMID: 33255654
A Sequence Homology and Bioinformatic Approach Can Predict Candidate Targets for Immune Responses to SARS-CoV-2.
Cell host & microbe. 2020-04-08; 27.4: 671-680.e2.
PMID: 32183941
Machine Learning of Discriminative Gate Locations for Clinical Diagnosis.
Cytometry. Part A : the journal of the International Society for Analytical Cytology. 2020-03-01; 97.3: 296-307.
PMID: 31691488
A survey of known immune epitopes in the enteroviruses strains associated with acute flaccid myelitis.
Human immunology. 2019-11-01; 80.11: 923-929.
PMID: 31451291
Differential transcriptome and development of human peripheral plasma cell subsets.
JCI insight. 2019-05-02; 4.9:
PMID: 31045577
Classification of human Herpesviridae proteins using Domain-architecture Aware Inference of Orthologs (DAIO).
Virology. 2019-03-01; 529.29-42.
PMID: 30660046
DAFi: A directed recursive data filtering and clustering approach for improving and interpreting data clustering identification of cell populations from polychromatic flow cytometry data.
Cytometry. Part A : the journal of the International Society for Analytical Cytology. 2018-06-01; 93.6: 597-610.
PMID: 29665244
Fast and accurate HLA typing from short-read next-generation sequence data with xHLA.
Proceedings of the National Academy of Sciences of the United States of America. 2017-07-25; 114.30: 8059-8064.
PMID: 28674023
Pacific Symposium on Biocomputing. Pacific Symposium on Biocomputing. 2016-01-01; 22.564-575.
PMID: 27897007
Mapping cell populations in flow cytometry data for cross-sample comparison using the Friedman-Rafsky test statistic as a distance measure.
Cytometry. Part A : the journal of the International Society for Analytical Cytology. 2016-01-01; 89.1: 71-88.
PMID: 26274018
Strengthening the influenza vaccine virus selection and development process: Report of the 3rd WHO Informal Consultation for Improving Influenza Vaccine Virus Selection held at WHO headquarters, Geneva, Switzerland, 1-3 April 2014.
Vaccine. 2015-08-26; 33.36: 4368-82.
PMID: 26148877
Critical assessment of automated flow cytometry data analysis techniques.
Nature methods. 2013-03-01; 10.3: 228-38.
PMID: 23396282
Ontologies for clinical and translational research: Introduction.
Journal of biomedical informatics. 2011-02-01; 44.1: 3-7.
PMID: 21241822
Towards Viral Genome Annotation Standards, Report from the 2010 NCBI Annotation Workshop.
Viruses. 2010-10-13; 2.10: 2258-2268.
PMID: 21994619
Elucidation of seventeen human peripheral blood B-cell subsets and quantification of the tetanus response using a density-based method for the automated identification of cell populations in multidimensional flow cytometry data.
Cytometry. Part B, Clinical cytometry. 2010-01-01; 78 Suppl 1.S69-82.
PMID: 20839340
Toward an ontological treatment of disease and diagnosis.
Summit on translational bioinformatics. 2009-03-01; 2009.116-20.
PMID: 21347182
An improved ontological representation of dendritic cells as a paradigm for all cell types.
BMC bioinformatics. 2009-02-25; 10.70.
PMID: 19243617
Newly Discovered Human Brain Cell: Rosehip Neurons
Tracking Enterovirus D68, Cause of a Polio-like Illness in Some Patients
SynBioBeta COVID-19 Town Hall - JCVI’s Richard Scheuermann on coronavirus immune epitopes
Lecture at UC San Diego - Application of single-cell genomics
Human Vaccines Project - Machine Learning and Single Cell Genomics
CBIM Summer School - Automatic flow cytometry gating methods/figcaption>
AFM First Virtual Symposium Part III - Introduction
AFM First Virtual Symposium Part III - Looking at pathogenesis: The virus and the immune system
Bioinformatics Open Source Conference (BOSC) 2019 - Archaeopteryx js, Web based Visualization and Exploration of Annotated Phylogenetic Trees

Top scientists join forces to study leading theory behind long COVID

Several JCVI scientists will be contributing to the newly launched Long Covid Research Initiative — a collaboration of researchers, clinicians, and patients working to rapidly study and treat long Covid.


SARS-CoV-2 Mutation Tracking

The San Diego Union Tribune

Scientists rush to determine if mutant strain of coronavirus will deepen pandemic

U.S. researchers have been slow to perform the genetic sequencing that will help clarify the situation

Collaborator Release

LJI Scientists Identify Potential Targets for Immune Responses to Novel Coronavirus

The research, which includes comparative genomics analysis by JCVI scientists Yun Zhang and Richard Scheuermann, provides essential information about the human immune response to coronavirus infection that will guide the design and evaluation of diagnostics and vaccine candidates

Asia Times

How AI can help us decode immunity

Artificial intelligence and machine learning will be the keys to unraveling how the human immune system prevents and controls disease


Fighting Back Against Flu

Collaborator Release

Scientists identify a new kind of human brain cell

‘Rosehip’ neurons not found in rodents, may be involved in fine-level control between regions of the human brain

Collaborator Release

S2 Genomics Awarded $280,000 Phase I STTR Grant from the National Institutes of Health

S2 Genomics will develop the Singulator™ system for automated preparation of single cells or nuclei from solid tissue samples