JCVI: About / Bios / Richard H. Scheuermann
 
 
Section Banner

About

Biographies

Richard H. Scheuermann, Ph.D.
Director of Informatics
Professor

Research Interests and Accomplishments

Richard H. Scheuermann, Ph.D., Director of Informatics at JCVI, received a B.S. in Life Sciences from the Massachusetts Institute of Technology, and a Ph.D. in Molecular Biology from the University of California, Berkeley.  After completing his doctoral research on bacterial replication fidelity at U.C. Berkeley, he accepted an independent research position at the Basel Institute for Immunology in Switzerland, where he identified the CDP protein as a critical regulator of immunoglobulin gene expression and the role of nuclear matrix attachment in transcription regulation.  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 2012, after 20 years on the faculty of U.T. Southwestern, Dr. Scheuermann pulled up his roots and moved to San Diego to become the Director of Informatics at JCVI.

While at U.T. Southwestern, Dr. Scheuermann established a productive research program investigating signal transduction pathways that regulate normal lymphocyte development and function and that induce cell cycle arrest and apoptosis in lymphomas, supported through numerous research grants from the National Institutes of Health, the American Cancer Society, the Texas Higher Education Coordinating Board, and other granting agencies.  In the Pathology Department, he also worked on the development and validation of novel diagnostic methods for viruses that mediate chronic infectious disease and for chromosomal translocations that drive leukemia and lymphoma development.  In 2001 he made a dramatic career shift into the discipline of bioinformatics, initiated with a sabbatical year at the San Diego Supercomputer Center on the campus of the University of California, San Diego.

Since 2001, 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 knowledge representation approaches and computational methods have been made available to the research community through several public database and analysis resources, including the Influenza Research Database (IRD; www.fludb.org), the Virus Pathogen Resource (ViPR; www.viprbrc.org) and the Immunology Database and Analysis Portal (ImmPort; www.immport.org) supported by the National Institutes of Health.  At JCVI he is also expanding his bioinformatics research program into the area of human genomics.

Select Publications

Kong YM, Dahlke C, et al.
Toward an Ontology-based Framework for Clinical Research Databases.

Journal of biomedical informatics. 2011 Feb 01; 44: 48-58.[more]

Qian Y, Wei C, et al.
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 Oct 01; 78: S69-82.[more]

Zhang S, Cao J, et al.
GO-Bayes: Gene Ontology-based Overrepresentation Analysis Using a Bayesian Approach.

Bioinformatics (Oxford, England). 2010 Apr 01; 26: 905-11.[more]

Karp DR, Marthandan N, et al.
Novel Sequence Feature Variant Type Analysis of the HLA Genetic Association In Systemic Sclerosis.

Human molecular genetics. 2010 Feb 15; 19: 707-19.[more]

Masci AM, Arighi CN, et al.
An Improved Ontological Representation of Dendritic Cells as a Paradigm for All Cell Types.

BMC bioinformatics. 2009 May 01; 10: 70.[more]

Scheuermann RH, Ceusters W, et al.
Toward an Ontological Treatment of Disease and Diagnosis.

Summit on translational bioinformatics. 2009 May 01; 2009: 116-20.[more]

Smith B, Ashburner M, et al.
The OBO Foundry: Coordinated Evolution of Ontologies to Support Biomedical Data Integration.

Nature biotechnology. 2007 Nov 01; 25: 1251-5.[more]

Chen Z, McGee M, et al.
A Distribution Free Summarization Method for Affymetrix GeneChip Arrays.

Bioinformatics (Oxford, England). 2007 Feb 01; 23: 321-7.[more]

Luo F, Yang Y, et al.
Modular Organization of Protein Interaction Networks.

Bioinformatics (Oxford, England). 2007 Jan 15; 23: 207-14.[more]

Bai X, Hosler G, et al.
Quantitative Polymerase Chain Reaction for Human Herpesvirus Diagnosis and Measurement of Epstein-Barr Virus Burden In Posttransplant Lymphoproliferative Disorder.

Clinical chemistry. 1997 Oct 01; 43: 1843-9.[more]

Uhr JW, Scheuermann RH, et al.
Cancer Dormancy: Opportunities for New Therapeutic Approaches.

Nature medicine. 1997 May 01; 3: 505-9.[more]