DEPARTMENT OF PATHOLOGY

 

Richard H. Scheuermann, Ph.D.

Richard H. Scheuermann, Ph.D.

  • Professor
  • Director, Surgical Pathology
  • Ph.D. — University of California, Berkeley, 1986
  • Director of Informatics: J. Craig Venter Institute
  • Research Professor II: Southern Methodist University

Research Interests

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. 

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.

Representative Publications

  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. PMCID: PMC2814061
  2. Chen Z, McGee M, Liu Q, Scheuermann RH (2007) “A distribution free summarization method for Affymetrix GeneChip arrays”. Bioinformatics 23:321-7. PubMed PMID: 17148508.
  3. Luo F, Yang Y, Chen CF, Chang R, Zhou J, Scheuermann RH (2007) “Modular organization of protein interaction networks”. Bioinformatics 23:207-14. PubMed PMID: 17092991.
  4. Taylor CF, Field D, Sansone SA, Aerts J, Apweiler R, Ashburner M, Ball CA, …..Scheuermann RH, Schober D, Smith B, Snape J, Stoeckert CJ Jr, Tipton K, Sterk P, Untergasser A, Vandesompele J, Wiemann S (2008) “Promoting coherent minimum reporting guidelines for biological and biomedical investigations: the MIBBI project”, Nat Biotechnol. 26:889-96. PMCID: PMC2771753.
  5. Lee JA, Spidlen J, Boyce K, ……. Wilson C, Scheuermann RH, Brinkman RR (2008) “MIFlowCyt: the minimum information about a Flow Cytometry Experiment”. Cytometry A. 73:926-30. PMCID: PMC2773297.
  6. Scheuermann RH, Ceusters W and Smith B (2009) “Toward an Ontological Treatment of Disease and Diagnosis”, AMIA 2009 Summit on Translational Bioinformatics Proc. 116-120. PMCID: PMC3041577.
  7. Zhang S, Cao J, Kong YM, Scheuermann RH (2010) “GO-Bayes: Gene Ontology-based over-representation analysis using a Bayesian approach”, Bioinformatics 26: 905-11. PMCID: PMC2913669
  8. 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
  9. Spidlen J, Barsky A, Breuer K, Carr P, Nazaire MD, Hill BA, Qian Y, Liefeld T, Reich M, Mesirov JP, Wilkinson P, Scheuermann RH, Sekaly RP, Brinkman RR (2013) “GenePattern flow cytometry suite”. Source Code Biol Med. 8:14. PMCID: PMC3717030.
  10. Aghaeepour N, Finak G, The FlowCAP Consortium, The DREAM Consortium, Hoos HH, Mosmann TR, Gottardo R, Brinkman RR, Scheuermann RH (2013) “Critical Assessment of Cell Population Identification Techniques in Flow Cytometry” Nature Methods 10: 228-238. PubMed PMID: 23396282.
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Biography

Dr. Scheuermann received his B.S. degree in Life Sciences from the Massachusetts Institute of Technology and his Ph.D. degree 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 and holder of the John H. Childers Professorship in Pathology.  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 UCSD.  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 the J. Craig Venter Institute.  Dr. Scheuermann currently leads two large database development projects funded by the U.S. National Institutes of Health – the Influenza Research Database (www.fludb.org) and the Virus Pathogen Bioinformatics Resource Center (www.viprbrc.org), and previously served as the PI on the Immunology Database and Analysis Portal (https://immport.niaid.nih.gov/) project and as the Biomedical Informatics Key Function Lead for UT Southwestern’s Clinical and Translational Science Award (CTSA).

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