Program Director/Principal Investigator (Last, First, Middle):
BIOGRAPHICAL SKETCH
Provide the following information for the Senior/key personnel and other significant contributors in the order listed on Form Page 2.
Follow this format for each person. DO NOT EXCEED FOUR PAGES.
NAME
POSITION TITLE
Richard H. Scheuermann
Professor and Director of Informatics
eRA COMMONS USER NAME (credential, e.g., agency login)
rscheuermann
EDUCATION/TRAINING (Begin with baccalaureate or other initial professional education, such as nursing, include postdoctoral training and
residency training if applicable.)
DEGREE
INSTITUTION AND LOCATION
MM/YY
FIELD OF STUDY
(if applicable)
Massachusetts Institute of Technology,
Cambridge, MA
B.S.
1977-1981
Life Sciences
Ph.D.
1981-1986
Molecular Biology
-
1986-1991
Immunology
Sabbatical
2002
Bioinformatics
University of California, Berkeley, CA
Basel Institute for Immunology, Basel, Switzerland
University of California, San Diego, CA
A. Personal Statement
Dr. Scheuermann has an active research program in bioinformatics and computational biology, which includes
innovative research in computational algorithm development for gene expression microarray, HLA genetic and
flow cytometry data analysis, and in knowledge representation of clinical and laboratory experiment data using
minimum information standards and ontologies, as applied to cancer, immunology and infectious disease
research. During his tenure on the faculty in Pathology at U.T. Southwestern he served as the Director of the
Immunology Graduate Program and was involved in infectious disease molecular diagnostic test development.
B.
Positions and Honors
Employment History
1980-1981
Massachusetts Institute of Technology, Department of Biology.
Research with
Annamaria Torriani-Gorini on the regulation of E.coli alkaline phosphatase synthesis using an
in vitro transcription-translation system. Teaching Assistant in Introductory Biology lab course.
1981-1986
University of California, Berkeley, Department of Molecular Biology. Graduate research
with Harrison Echols on the identification and purification of the -subunit of Escherichia coli
DNA polymerase III: an editing exonuclease for DNA replication. T.A. in Advanced Molecular
Biology.
1986-1991
Basel Institute for Immunology, Basel, Switzerland. Research Member. The regulation of
mouse immunoglobulin heavy chain synthesis: cis- and trans-acting elements involved in
enhancer function. Molecular aspects of hematopoiesis and tumorigenesis using c-myc
transgenic mice.
Jan-Sep 2002 University of California, San Diego, San Diego Supercomputer Center. Visiting Scholar
(sabbatical). Development of a relational database to integrate results obtained from multiple
experimental approaches, and development of clustering and connectivity models for the
computational analysis of the data generated in conjunction with the Alliance for Cellular
Signaling (AFCS).
1992-2012
University of Texas Southwestern Medical Center, Department of Pathology. Assistant
Professor (1992-1998); Associate Professor (1998-2004); Professor (2004-2012). Signal
transduction in lymphoma cell cycle arrest, apoptosis & tumor dormancy. Data mining
algorithm and database development for computational immunology and infectious disease
research. Instructor in medical school Pathology and graduate school Tumor Immunology and
Bioinformatics courses. Infectious disease molecular diagnostics development.
PHS 398/2590 (Rev. 06/09)
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Program Director/Principal Investigator (Last, First, Middle):
2012-present
J. Craig Venter Institute, San Diego. Professor and Director of Informatics. Bioinformatics
and computational biology applied to infectious disease, immunology and genomics
translational research.
Academic Appointments
Professor w/tenure
Chief
Research Professor II
Director
Member
Development Specialist
Director
Department of Pathology (2004-2012)
Division of Biomedical Informatics (2006-2012)
Department of Statistical Science, SMU (2012-present)
U.T. Southwestern Tissue Procurement Resource (2003-2010)
Simmons Comprehensive Cancer Center (2003-2012)
Molecular Diagnostics Laboratory (1994-2006)
Immunology Graduate Program (1998-2002)
Advisory Positions
Scientific Advisory Board
Scientific Advisory Board
Scientific Advisory Board
Bioinformatics Advisory Board
Coordinating Committee
Coordinating Editor
Gene Ontology Consortium, Bar Harbor, ME (2008-present)
Biomind, LLC, Rockville, MD (2005-present)
Lead Horse Technologies, Aurora, CO (2006-present)
Immune Tolerance Network, San Francisco, CA (2006-2010)
Ontology for Biomedical Investigations - OBI (2006-present)
Open Biomedical Ontologies Foundry (2007-present)
Honors, Awards and Professional Activities (partial list)
 James A. Shannon Director's Award (NIH) (1994)
 Associate Editor, Journal of Immunology (1995 - 2001)
 Patents No. 5,686,072 "Epitope-specific monoclonal antibodies and immunotoxins and uses thereof"
SN 08/202,042; issued 11/11/97; "Anti-erbB2 antibodies" SN 08/731,794; filed 10/18/96 (with
Genentech)
 NIH ZRG1 SSS-N, fellowship (1997-2007); panel chair (2001, 2003, 2005)
 Association for Molecular Pathology (AMP) - including Nominations Committee Representative (19971999), Program Committee Chair (2001), Executive Council Member (2000-2002)
 Appointment as Research Assistant Professor in the Department of Statistical Science at Southern
Methodist University (2012-present)
C.
Selected Peer-reviewed Publications (15 selected from 119 publications total)
Most relevant to the current application
1. Bai X, Rogers BB, Harkins PC, Sommerauer J, Squires R,Rotondo K, Quan A, Dawson DB & Scheuermann
RH (2000) " Predictive value of quantitative PCR-based viral burden analysis for eight human herpesviruses
in pediatric solid organ transplant patients", J. Mol. Diagn. 2: 191-201. PMCID: PMC1906918
2. Scheuermann RH, Domiati-Saad R, and Rogers BB (2004) " DNA Virus Detection " pg 429 – 440 in
Diagnostic Molecular Microbiology, 2nd Edition, D. Persing, Ed., American Society for Microbiology Press.
3. Karp DR, Carlin S, Cook-Deegan R, Ford DE, Geller G, Glass DN, Greely H, Guthridge J, Kahn J, Kaslow
R, Kraft C, MacQuenn K, Malin B, Scheuermann RH, Sugarman J. (2008) “Ethical and Practical Issues
Associated with Aggregating Databases”, PLoSMedicine, 5:e190. PMCID: PMC2553818
4. Scheuermann RH, Ceusters W and Smith B (2009) “Toward an Ontological Treatment of Disease and
Diagnosis”, AMIA 2009 Summit on Translational Bioinformatics Proceedings 116-120. PMCID:
PMC3041577.
5. Ligocki AJ, Lovato L, Xiang D, Guidry P, Scheuermann RH, ……, Monson NL (2010) “A unique antibody
gene signature is prevalent in the central nervous system of patients with multiple sclerosis” Journal of
Neuroimmunology, 226:192-193. PMCID: PMC2937103
6. Thomson G, Marthandan N, Hollenbach JA, Mack SJ, Erlich HA, et al. (2010) “Sequence Feature Variant
Type (SFVT) Analysis of the HLA Genetic Association in Juvenile Idiopathic Arthritis” Pacific Symposium on
Biocomputing 2010:359-370. PMCID: PMC2958177
7. Malin B, Karp D, and Scheuermann RH (2010) “Technical and Policy Approaches to Balancing Patient
Privacy and Data Sharing in Clinical and Translational Research”, Journal of Investigative Medicine 58: 1118. PMCID: PMC2836827
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Program Director/Principal Investigator (Last, First, Middle):
8. Karp DR, Marthandan N, Marsh SGE, Feolo M, Ahn C, Arnett FC, Ashburner M, Cowell L, DeLuca D, Diehl
AD, ….., and Scheuermann RH (2010) “Novel sequence feature variant type analysis of the HLA genetic
association in systemic sclerosis”, Human Mol. Genet. 19: 707-19. PMCID: PMC2807365
9. Qian Y, Wei C, Lee FE, Campbell J, ….. Mosmann T, Sanz I and Scheuermann RH(2010) “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, 78B:S69-S82. PMCID: PMC3084630
10. Kong M, Dahlke C, Xiang D, Karp D, Scheuermann RH (2011) “Toward an Ontology-Based Framework for
Clinical Research Databases”, Journal of Biomedical Informatics 44: 48-58. PMCID: PMC2953614
Additional recent publications of importance to the field (in chronological order)
1.Smith B, Ashburner M, Rosse C, Bard J, Bug W, Ceusters W, Goldberg LJ, Eilbeck K, Ireland A, Mungall CJ,
the OBI Consortium, Leontis N, Rocca-Serra P, Ruttenberg A, Sansone SA, Scheuermann RH, Shah N,
Whetzel PL, Lewis S. (2007) “The OBO Foundry: coordinated evolution of ontologies to support biomedical
data integration”, Nature Biotechnology 25:1251-1255; doi:10.1038/nbt1346. PMCID: PMC2814061
2. Luo F, Yang Y, Chen C-F, Chang R, Zhou J, Scheuermann RH. (2007) “Modular organization of protein
interaction networks”, Bioinformatics 23:207-214.
3. Zhang S, Cao J, Kong YM, Scheuermann RH (2010) “GO-Bayes: Gene Ontology-based overrepresentation analysis using a Bayesian approach”, Bioinformatics 26(7): 905-11. PMCID: PMC2913669
4. Squires RB, Noronha J, Hunt V,Garcia-Sastre A, Macken C, Baumgarth N, Scheuermann RH (2012)
“Influenza Research Database: an integrated bioinformatics resource for influenza research and
surveillance” Influenza and Other Respiratory Viruses, doi: 10.1111/j.1750-2659.2011.00331.x. [Epub
ahead of print]. PMID: 22260278
5. Huang J, Mirel D, Pugh E, Xing C, Robinson PN, Pertsemlidis A, Ding LH, Kozlitina J, Maher J, Rios J,
Story M, Marthandan N, Scheuermann RH (2011) “Minimum Information About a Genotyping Experiment”
Standards in Genomic Sciences, 5:224-229. PMID: 22180825; PMCID: PMC3235517
D. Research Support
Ongoing Research Support
Influenza Research Database
N01-AI40041
(Scheuermann RH, PI)
10/01/09-09/30/14
The goal of this project is to modify the BioHealthBase Bioinformatics Resource Center into a bioinformatics
resource solely focused on the support of influenza virus research data, including genome sequence, animal
and human surveillance, vaccine clinical trials, and laboratory experiment data, and related analytical and
visualization tools.
Virus Pathogen Database and Analysis Resource (ViPR)
N01-AI2008038
(Scheuermann RH, PI)
10/01/09-09/30/14
The goal of this project is to develop the Virus Pathogen Database and Analysis Resource (ViPR), a state-ofthe-art database and analysis infrastructure for gene and protein structure and function data focused on all
Category A - C priority viral pathogens chosen for their dual importance as potential agents of bioterrorism and
as endemic or re-emerging public health concerns in the United States and around the world, including West
Nile Virus, Hepatitis C Virus, Dengue Virus, Chikungunya Virus, Variola Major, Ebola Virus and related viruses.
Bioinformatics Approach to Influenza A/H1N1 Vaccine Immune Profiling
U01-AI089859
(Gottardo R, PI; Scheuermann RH, co-I)
07/01/12-06/30/14
The goal of this project is to increase reproducibility of assays and aid in the within- and between-laboratory
comparison of results for the standardization of flow cytometry (FCM). Standardized data analysis pipelines
would allow Human Immunology Project Consortium (HIPC) investigators, and eventually non-HIPC
investigators, to perform reproducible analyses that would open the door to novel cross-center studies, which
would not be possible otherwise. HIPC will generate a set of highly standardized data across 9 centers
(including 5 HIPC labs) using lyophilized antibody plates (lyoplate) and standard (FITMaN) marker panels.
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Program Director/Principal Investigator (Last, First, Middle):
Using these FITMaN lyoplate data, we propose to identify and implement optimized analysis strategies for
FCM data.
The Statistical and Computational Analysis of Flow Cytometry Data
R01-EB008400
(Gottardo R, PI; Scheuermann RH, co-I)
05/01/11-04/30/16
The goal of this project is to develop a comprehensive analytical infrastructure for the processing and
interpretation of flow cytometry (FCM) and mass cytometry (MCM) data. The primary focus will be the
development of statistical methods and computational tools for comprehensively identifying, matching and
semantically labeling cell populations across samples. Strategies will then be developed for deriving
quantitative and qualitative cellular characteristics from cell populations defined by automated population
identification algorithms. These characteristics are then used to semantically query the Cell Onotolgy to
automatically map algorithmically defined cell populations with standardized cell type representations. In
collaboration with the British Columbia Cancer Research Center, computational methods to match similar cell
populations across multiple samples will be developed.
Respiratory Pathogens Research Center (RPRC) Data Management and Modeling HA Evolution
HHSN272201200005C
(Topham D, PI; Scheuermann RH, co-I)
05/01/12-12/12/18
The goal of this project is to provide advice and guidance regarding the management and analysis of the data
resulting from the Rochester RPRC project both from a bioinformatics and an information technology
perspective. Additionally, expertise will be provided in the development and implementation of methods for
balancing patient privacy and data sharing in clinical and translational research. Development of novel
analytical methods for biomedical data will be supported, including the analysis of flow cytometry, gene
expression, and HLA genetic data.
Completed Research Support (selected)
Bioinformatics Integration Support Contract (BISC)
N01-AI40076
(Scheuermann RH, PI)
06/01/04-09/30/12
The goal of this project is to develop the Immunology Database and Analysis Portal (ImmPort). ImmPort
combines an extensive knowledgebase of information about proteins and gene structure and function with
platform for primary experimental data submission and analysis. This goal will be achieved through the
development of experimental data standards, biomedical ontologies, and novel analytical algorithms utilizing
state-of-the-art bioinformatics and computational biology approaches. ImmPort is designed to support all
NIAID-funded investigators.
North and Central Texas Clinical and Translational Science Initiative (CTSA)
UL1-RR023468
(Toto, PI; Scheuermann RH, Bioinformatics Lead)
09/01/07-08/31/12
To develop a fully integrated, multidisciplinary and multidimensional partnership of several academic and
clinical institutions, committed to promoting the new discipline of clinical and translational science, in order to
accelerate the translation of advances in biomedical research to patients and the community.
Integrative Immunology Training Grant
T32-AI005284
(Scheuermann RH, PI)
09/01/03-08/31/08
The purpose of the Advanced Immunology Training Program at UT Southwestern was to provide
comprehensive training of predoctoral and postdoctoral fellows in modern immunology. The goal was to
produce sophisticated and highly trained research scientists who are capable of developing experimental
approaches to investigate the normal functioning of the immune system and the defects in normal immune
system function that contribute to human disease. This goal was achieved through an integrated combination
of training activities that includes: 1) required graduate-level coursework composed of didactic instruction and
discussion sessions (predocs only); 2) fellowship proposal preparation and oral defense as part of the
qualifying exam process (predocs only); 3) annual Works-in-Progress and other oral presentations for each
trainee; 4) teaching opportunities in medical school and graduate school courses; 5) journal club participation;
6) either dissertation research leading to the Ph.D. degree (predocs) or advanced research training (postdocs);
and 7) practical training in other career-related activities, especially for postdoctoral fellows.
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