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Alexander                      Diehl

Alexander D. Diehl PhD

Department of Neurology

Assistant Professor

Specialty/Research Focus

Autoimmunity; Bioinformatics; Genomics and proteomics; Immunology; Infectious Disease; Molecular and Cellular Biology; Molecular genetics; Neurobiology

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Professional Summary:

My primary research is in the field of biomedical ontology development. An ontology is a controlled, structured vocabulary intended to represent knowledge within a particular domain. Terms in an ontology have logical relationships to each other and to terms in other ontologies, to allow for reasoning and inference across the ontology. Biomedical ontologies allow annotation and integration of scientific data within particular fields of science and medicine, and their careful curation and logical structure facilitate data analysis. My work in biomedical ontology is strongly informed by my earlier experience in laboratory research in immunology, genetics, molecular biology and virology.

My research group works on ontologies for both basic and clinical applications, in collaboration with researchers both at UB and other institutions. I led efforts to revise and extend the Cell Ontology, which is intended to represent in vivo cell types from across biology. We worked extensively to bring it up to community-accepted standards in ontology development, placing particular emphasis on improving the representation of hematopoietic cells and neurons. We are developing the Cell Ontology as a metadata standard for annotation and analysis of experimental data in immunology in support of the National Institute of Allergy and Infectious Diseases (NIAID) ImmPort Immunology Database and Analysis Portal and Human Immunology Project Consortium. We have also developed ways to use the Cell Ontology in support of the analysis of gene expression data linked to cell types and have contributed to the Functional Annotation of the Mammalian Genome (FANTOM) 5 Consortium‘s work on identifying gene transcription start sites across multiple cell types and tissues.

My research team is also developing the Neurological Disease Ontology to represent clinical and basic aspects of neurological diseases in order to support translational research in this area. In collaboration with clinical colleagues at UB, we are initially focusing on Alzheimer’s disease and dementia, multiple sclerosis and stroke. We have as well developed a companion ontology, the Neuropsychological Testing Ontology, to aid in the annotation and analysis of neuropsychological testing results used as part of the diagnosis of Alzheimer‘s disease and other neurological diseases.

I am a long-term member of the Gene Ontology (GO) Consortium and have a particular interest in the representation of immunology and neuroscience in the GO. I am also involved in UB’s contribution to the Protein Ontology and contribute as well to the work of the Infectious Disease Ontology Consortium, Immunology Ontology Consortium and Vaccine Ontology Consortium.

I teach and mentor students at the master’s and doctoral levels, and advise undergraduate, graduate, and medical students in summer research projects as well.

Education and Training:
  • PhD, Molecular Cell Biology, Washington University (1995)
  • BS, Molecular Biophysics and Biochemistry, Yale University (1986)
  • Research Assistant Professor, Biomedical Informatics, University at Buffalo (2014-present)
  • Assistant Professor, University at Buffalo (2010-present)
  • Research Scientist, Mouse Genome Informatics, The Jackson Laboratory (2009–2010)
  • Senior Scientific Curator, Mouse Genome Informatics, The Jackson Laboratory (2006–2009)
  • Scientific Curator, Mouse Genome Informatics, The Jackson Laboratory (2003–2006)
  • Research Scientist, Drug Discovery, Decode Genetics, Iceland (2000–2002)
  • Post Doctoral Fellow, Microbiology and Tumor Biology Center, Karolinska Institute, Sweden (1996–2000)
Awards and Honors:
  • Wenner-Gren Samfundet Post-Doctoral Fellowship (1997)
  • Howard Hughes Medical Institute Pre-Doctoral Fellowship (1990)
  • Associate Member of Sigma Xi Scientific Honor Society (1986)

Research Expertise:
  • Biomedical ontology development: Experienced biomedical ontology developer for the Gene Ontology, Cell Ontology, Protein Ontology, Vaccine Ontology, Infectious Disease Ontology, and Neurological Disease Ontology.
Research Centers:
  • Jacobs Neurological Institute
  • Center of Excellence in Bioinformatics and Life Sciences
UB 2020 Strategic Strengths:
  • Health and Wellness Across the Lifespan
Grants and Sponsored Research:
  • September 2011–June 2015
    PRO: A Protein Ontology in OBO Foundry for Integration of Biomedical Knowledge
    Role: Co-Investigator
  • December 2010–August 2011
    ARRA: Revision and Extension of the Cell Ontology
    The Jackson Laboratory
    Role: Principal Investigator
  • June 2010–August 2010
    Importation of Neuron Types from the BAMS and NeuronDB Resources to the Cell Ontology
    International Neuroinformatics Coordinating Facility
    Role: Principal Investigator

Journal Articles:
See All (24 Total) >

Professional Memberships:
  • International Society for Biocuration (2014)
  • International Association for Ontology and Its Applications (2014)
  • "Principles of Ontology Development" ICBO: International Conference on Biomedical Ontology (2011)
  • "The Neurological Disease Ontology" BFO 2011 (Basic Formal Ontology Editorial Meeting) (2011)
  • "The Neurological Disease Ontology" Alzforum / Protein Ontology Kick-Off Meeting (2011)
  • "Development of the Cell Ontology via Logical Definition of Cell Types" , The Biocomplexity Institute, Indiana University (2011)
  • "Comprehensive Annotation System for Infectious Disease Data" IDO (Infectious Disease Ontology) Workshop 2010 (2010)
  • "Cross-Product Development of the Cell Ontology" Skeletal Anatomy Jamboree, NESCent (2010)
  • "Restructuring of the Cell Ontology: Focus on Hematopoietic Cells" , The Jackson Laboratory, Genetics Interest Group (2010)
  • "Hematopoietic Cell Types: Prototype for a Revised Cell Ontology" International Conference on Biomedical Ontology (2009)
  • "Introduction to the Gene Ontology" Cell Behavior Ontology Workshop (2009)
  • "Improvements in the Representation of Immune Cells in the Cell Ontology" DAIT Bioinformatics Summit 2008 (2008)
  • "Gene Ontology for Immunology: an Overview" 94th Annual Meeting of the American Association of Immunologists (2008)
  • "Representing Immunology in the GO: Ontology Development and Annotation" DAIT Bioinformatics Summit 2007 (2007)
  • "Representation of Immunology in the GO" Ontology Workshop: Focus on Immunology (NIAID) (2006)
  • "Requirement for MHC Class II Expression for Influenza Infection of Mouse and Human Cell Lines" Keystone Symposium on the Cell Biology of Viral Entry, Replication, and Pathogenesis (2000)
  • "Molecular Pathogenesis of Viral Infection" Keystone Symposium on Molecular Aspects of Viral Immunity (1995)
  • "Generation and analysis of mutant cells deficient in expression of MHC Class II molecules" XXVth Annual Meeting of the Scandinavian Society for Immunology (1994)
See All (16 Total) >
Service Activities:
  • Ad-hoc Journal Reviewer; Bioinformatics, Database, Journal of Biomedical Semantics, Neuroinformatics, Trends in Microbiology; Peer Reviewer (2009–2012)

Clinical Specialties:
Clinical Offices:
Insurance Accepted:

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Contact Information

B2-165 NYS Center Of Excellence in Bioinformatics and Life Sciences
701 Ellicott Street
Buffalo, NY 14203
Phone: 716-881-8975

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