Microbiology, Virology, and Parasitology Faculty

The University of Pennsylvania has a very collaborative and integrated research program in microbiology involving approximately 75 faculty throughout the campus. The program provides the best graduate training available in the molecular and cellular biology of viral and bacterial pathogenesis and parasitology. Faculty throughout the Perelman School of Medicine, the School of Veterinary Medicine, the School of Dental Medicine, the School of Arts and Sciences, Children's Hospital, and the Wistar Institute participate.

Microbiology, Virology and Parasitology Members

Current Members

Microbiology, Virology and Parasitology

Click the faculty member's name to see more detailed information.

Faculty

Mohamed Abdel-Mohsen, PhD	Hyun Koo
Michael C. Abt, PhD	Daniel W. Kulp, PhD
Jorge Ivan Alvarez, PhD	Maayan Levy, Ph.D.
Will Bailis, Ph.D.	Paul M Lieberman, Ph.D.
Katie Barott, PhD	Michela Locci, Ph.D.
Paul F. Bates, PhD	James B. Lok, Ph.D.
Edward M Behrens, MD	Carolina B. Lopez, Ph.D.
Daniel P. Beiting, Ph.D.	Thomas J. Nolan, Ph.D.
Jeffrey M. Bergelson, MD	Una O'Doherty, M.D.Ph.D.
Michael R. Betts, PhD	Paula M Oliver, PhD
Andrew N. Binns	Yvonne J. Paterson, Ph.D.
Jacob S Brenner, MD, PhD	Paul J Planet, Ph.D, M.D.
Dustin Brisson, PhD	Joshua B Plotkin, Phd
Igor E. Brodsky, PhD	Mechthild Pohlschroder
Frederic D. Bushman, Ph.D.	Michael Povelones, PhD
Kyong-Mi Chang, MD	Robert P. Ricciardi, Ph.D.
Sara Cherry, Ph.D.	James L. Riley, Ph.D.
Gary H Cohen, Ph.D.	David S. Roos, Ph.D.
Ronald G. Collman, MD	Dieter M. Schifferli, Dr. med. vet., Ph. D.
M. Fevzi Daldal	Phillip Scott, Ph.D.
Cesar de la Fuente-Nunez, Ph.D.	George M. Shaw, M.D., Ph.D.
Laurence C Eisenlohr VMD/PhD	Hao Shen, Ph.D.
Joseph A. Fraietta, Ph.D.	Sunny Shin, Ph.D.
Harvey M. Friedman, MD	Michael Silverman, MD, PhD
Glen N. Gaulton, Ph.D.	Gary Smith, MA, MA, D.Phil, Cert. Ed.
Mark D Goulian, Ph D	Joseph W. St. Geme, III, MD
Robert M. Greenberg, PhD	Boris Striepen, PhD
Elizabeth A Grice, Ph.D.	Flavia R Teles
Beatrice H. Hahn, M.D.	Christoph Thaiss, Ph.D.
Ronald N Harty, Ph.D.	Susan R. Weiss, Ph.D.
Sarah Henrickson, M.D., Ph.D.	Drew Weissman, M.D., Ph.D.
Scott Hensley, PhD	Matthew D. Weitzman, Ph.D.
De'Broski R. Herbert, PhD	E. John Wherry, PhD
James A. Hoxie, M.D.	Elizabeth A. White, Ph.D.
Christopher A. Hunter, Ph.D.	Jianxin You, Ph.D.
Stuart N. Isaacs, M.D.	Yan Yuan
Kellie Ann Jurado, PhD	Joseph P. Zackular, Ph.D.
Rahul M. Kohli, M.D., Ph.D	Jun (Jay) Zhu, Ph.D.
Dennis L. Kolson, M.D., Ph.D.

The current research interests of the faculty in microbiology and virology encompass a broad range of disciplines including:

Bacteriology

Faculty	Brief Research Description
Jorge Alvarez	Research in the Alvarez lab is aiming to understand the biology of the Central Nervous System (CNS) barriers under homeostatic and inflammatory conditions. These barriers selectively restrict the molecular and cellular trafficking between the periphery and the CNS, but also serve as a signaling interface that actively regulates exchanges between both compartments. They are composed of the blood-brain barrier (BBB), the blood-meningeal barrier (BMB) and the blood cerebrospinal fluid barrier (BCB).
Andrew Binns	Agrobacterum tumefaciens; host-pathogen interaction; type IV secretion
Dustin Brisson	Disease ecology, molecular evolution, microbial ecology/ evolution, host-pathogen interaction
Igor Brodsky	Host-pathogen interactions; bacterial pathogenesis; Yersinia; innate immunity
Frederic Bushman	Metagenomic analysis of bacterial communities
Fevzi Daldal	Photosynthetic and respiratory electron transfer pathways and structure, function and biogenesis of cytochrome complexes
Mark Goulian	Bacterial regulatory networks; two-component signaling; antimicrobial peptides
Elizabeth Grice	microbial genomics, metagenomics, wound healing, innate immunity, microbiome of skin in health and disease
Rahul Kohli	Antimicrobial resistance; SOS pathway
Hyun (Michel) Koo	Assembly principles and the virulence determinants of oral biofilms, as well as developing novel therapeutic approaches to prevent biofilm-dependent oral infectious diseases such as dental caries
Michael S. Marks	Cell biology of host-pathogen interactions; innate immunity; phagocytosis; dendritic cell responses to bacteria; primary immunodeficiency disorders
Yvonne Paterson	Tumor immunology; Listeria monocytogenes; vaccines against infectious and neoplastic disease
Paul Planet	Evolution and ecology of bacterial pathogens.
Mechthild Pohlschroder	Protein secretion; membrane protein insertion; archaea
Dieter Schifferli	Escherichia coli and Salmonella pathogenesis; fimbriae; vaccines
Phillip Scott	T helper cell subsets; IL-12; T cell memory; Leishmania
Hao Shen	Bacterial pathogenesis and mechanisms of immune evasion; Listeria monocytogenes; Bacillus anthracis
Sunny Shin	Immunnity against bacterial pathogens; bacterial pathogenesis; Legionella pneumophila
Joseph St. Geme, III	Molecular and cellular determinants of bacterial pathogenicity, with a particular focus on Haemophilus influenzae and Kingella kingae
Joseph Zackular	Clostridium difficile; Enterococcus; Gut microbiome; Host-pathogen interactions; Pathogen-microbiota interactions; Inflammatory Bowel DIsease; Colorectal cancer.
Jun (Jay) Zhu	Quorum sensing; bacterial pathogenesis; Vibrio cholerae and virulence gene regulation; biofilms

Emerging Infectious Disease

Faculty	Brief Research Description
Paul Bates	Ebola virus; hepatitis C; SARS
Dustin Brisson	Disease ecology, molecular evolution, microbial ecology/ evolution, host-pathogen interaction
Frederic Bushman	Poxvirus topoisomerases
Sara Cherry	West Nile Virus; Dengue Virus; Rift Valley Fever Virus; Venezuealan Equine Encephalitis virus; Poxvirus
Gary Cohen	Smallpox glycoproteins; vaccinia virus
Ronald Harty	Ebola virus; VSV; Matrix Proteins; Budding; Reverse-Genetics; Virus-Host Interactions
Stuart Isaacs	Vaccinia virus, Recombinant vaccines, poxvirus , pathogenesis, smallpox, smallpox therapeutics
Paul Planet	Evolution and ecology of bacterial pathogens
Robert Ricciardi	Smallpox and vaccinia processivity factors
Erle Robertson	oncogenesis, viruses and cancer, viral oncology, Tumor Virology, Gene therapy, Kaposi's Sarcoma, Epstein-Barr Virus, Lymphoproliferative disease, Lymphomas
David Roos	Molecular parasitology, drug resistance, organellar targeting, eukaryotic evolution, pathogen genomics, database mining, computational biology, Toxoplasma, Plasmodium, malaria
Dieter Schifferli	Yersinia pestis, Salmonella, Escherichia coli, fimbriae, adhesion, plague
Hao Shen	Listeria, Ebola, T lymphocyte, bacterial pathogenesis, vaccine
David Weiner	DNA Vaccines, HIV, Viral Protein R., Vaccines
Susan Weiss	murine coronavirus, SARS associated coronavirus, viral pathogenesis
James Wilson	adenovirus, adeno-associated virus (AAV), gene therapy, gene transfer, lentivirus
Yan Yuan	Kaposi's sarcoma-associated herpesvirus, virus-host interaction, microRNAs.
Jun (Jay) Zhu	Genomics, Genetics, host-pathogen interaction, cell-cell signaling.

Immune Responses

Faculty	Brief Research Description
Michael Betts	HIV; T cell; Immune Response
Igor Brodsky	Host-pathogen interactions; bacterial pathogenesis; Yersinia; innate immunity
Kyong-Mi Chang	HCV, HBV, liver disease, HIV/HCV coinfection, alcohol, viral pathogenesis, viral persistence, immune regulation, T cell exhaustion, transplant tolerance, epitope mapping, immunogenetics
Sara Cherry	Virus, genomics, RNAi, genetics, Drosophila, innate, immunity
Hildegund Ertl	HIV Vaccine, HPV vaccines, Rabies Virus vaccines
Harvey Friedman	HSV immune evasion, glycoprotein gC, glycoprotein gE, complement, pathogenesis.
Glen Gaulton	Lymphocyte Development, Retrovirus Pathology, HIV-1, Imaging, Diagnostics
Elizabeth Grice	microbial genomics, metagenomics, wound healing, innate immunity, microbiome of skin in health and disease
Scott Hensley	Influenza virus, antigenic drift, viral pathogenesis, viral receptors, antibody specificity, vaccines
James Hoxie	AIDS, CD4, chemokine receptors, HIV, SIV, envelope glycoproteins, viral entry, neutralization, vaccine
Christopher Hunter	Innate and adaptive immunity to infection; immune pathology; cytokine biology; cell biology of intracellular parasites; neuroimmunology
Stuart Isaacs	Vaccinia virus, Recombinant vaccines, poxvirus , pathogenesis, smallpox, smallpox therapeutics
Carl June	T cells, human, gene therapy, genetic engineering, signal transduction
Rahul Kohli	Antibody diversity; innate immune retroviral restriction resistance
Carolina Lopez	Virus-host interaction, innate immunity, respiratory viruses, lung immunity.
Michael S. Marks	Cell biology of host-pathogen interactions; innate immunity; phagocytosis; dendritic cell responses to bacteria; primary immunodeficiency disorders
Luis Montaner	HIV immunopathogenesis; innate immunity; cytokines
Paula Oliver	Lymphocyte activation and tolerance; T cell response to pathogen infection; HECT-type E3 ubiquitin ligases
Yvonne Paterson	Immune regulation, antigen design, vaccine development, cancer immunotherapy, HIV, HPV
Paul Planet	Evolution and ecology of bacterial pathogen
Michael Povelones	Mosquito immunity to malaria parasites; Innate recognition of pathogens; Regulation of the immune response
Robert Ricciardi	Adenovirus; Human Kaposi’s Sarcoma Virus; immune escape
James Riley	T cell activation, Tumor Specific T cells, HIV specific T cells, expression profiles
David Roos	Molecular parasitology, drug resistance, organellar targeting, eukaryotic evolution, pathogen genomics, database mining, computational biology, Toxoplasma, Plasmodium, malaria
Dieter Schifferli	Yersinia pestis, Salmonella, Escherichia coli, fimbriae, adhesion, plague
Phillip Scott	Parasites, Leishmania, T cells, Th1 cells, Th2 cells, memory T cells
Hao Shen	Listeria, Ebola, T lymphocyte, bacterial pathogenesis, vaccine
Sunny Shin	Immunnity against bacterial pathogens; bacterial pathogenesis; Legionella pneumophila
David Weiner	DNA Vaccines, HIV, Viral Protein R., Vaccines.
Susan Weiss	murine coronavirus, SARS associated coronavirus, viral pathogenesis
Drew Weissman	HIV, Immunopathogenesis, RNAi, DMBT1, dendritic cell, siRNA, antigen presentation
E. John Wherry	Immunological memory, T cell memory, Chronic infection, T cell dysfunction, Memory T cell differentiation
James Wilson	adenovirus, adeno-associated virus (AAV), gene therapy, gene transfer, lentivirus
Yan Yuan	Kaposi's sarcoma-associated herpesvirus, virus-host interaction, microRNAs

Microbial Genomics and Evolution

Faculty	Brief Research Description
Dustin Brisson	I am interested in the interactions between pathogenic microbes and their hosts and how specifically those interactions shape the ecology and evolution of both the microbe and the host populations. Additionally, I am interested in the causes and consequences of molecular evolution and population genetics of pathogens. Methods from field ecology (including chicken-wire and cargo pants!), advanced molecular techniques, mathematical modeling, and computational analysis are commonly used in my lab to address relevant hypotheses.
Frederic Bushman	HIV, integration, integrase, poxvirus, DNA modifying enzyme, virology, variola, RNA interference, interferon
Sara Cherry	Virus, genomics, RNAi, genetics, Drosophila, innate, immunity
M. Fevzi Daldal	Rhodobacter, cytochrome
Elizabeth Grice	microbial genomics, metagenomics, wound healing, innate immunity, microbiome of skin in health and disease
Scott Hensley	Influenza virus, antigenic drift, viral pathogenesis, viral receptors, antibody specificity, vaccine
Rahul Kohli	Our laboratory focuses on the enzymatic generation of genomic diversity. We utilize a broad array of approaches, including biochemical characterization of enzyme mechanisms, chemical synthesis of enzyme probes, and biological assays spanning immunology and virology to study this central tactic in the constant battle between our immune system and pathogens.
Paul Planet	Evolution and ecology of bacterial pathogens
Joshua Plotkin	I am broadly interested in molecular population genetics and evolution. My research is based largely on computation and mathematical theory. A primary goal is to develop statistical methods for inferring the action of natural selection from intra-specific polymorphism data and from inter-specific sequence variation. Of particular interest are applications to the genomes of pathogens, whose proteins experience a wide range of selective pressures determined by interactions with their hosts.
Mechthild Pohlschroder	Archaea, protein secretion, porkaryotes, haloarchaea, type IV pili, flagella, biofilm.
David Roos	Molecular parasitology, drug resistance, organellar targeting, eukaryotic evolution, pathogen genomics, database mining, computational biology, Toxoplasma, Plasmodium, malaria
Joseph Zackular	Clostridium difficile; Enterococcus; Gut microbiome; Host-pathogen interactions; Pathogen-microbiota interactions; Inflammatory Bowel DIsease; Colorectal cancer.
Jun (Jay) Zhu	Genomics, Genetics, host-pathogen interaction, cell-cell signaling.

Parasitology

Faculty	Brief Research Description
Daniel Beiting	Immunology, microbiology, genomics
Dustin Brisson	Disease ecology, molecular evolution, microbial ecology/ evolution, host-pathogen interaction
De'Broski Herbert	Regulatory networks, immunity, inflammation, tissue repair, mucosal interface
Christopher Hunter	Immunity to Toxoplasma gondii; innate immunity; immunopathology
James Lok	Strongyloides, Caenorhabditis, Dirofilaria, transcription factor, dauer, G protein, TGF beta, parasite, nematode.
Thomas Nolan	Strongyloides stercoralis, parasite behavior, canine and feline parasites, Parasitology.
Michael Povelones	Mosquito immunity to malaria parasites; Innate recognition of pathogens; Regulation of the immune response
David Roos	Molecular parasitology, drug resistance, organellar targeting, eukaryotic evolution, pathogen genomics, database mining, computational biology, Toxoplasma, Plasmodium, malaria.
Phillip Scott	Parasites, Leishmania, T cells, Th1 cells, Th2 cells, memory T cells
Hao Shen	Listeria, Ebola, T lymphocyte, bacterial pathogenesis, vaccine

Tumor Virology

Faculty	Brief Research Description
Paul Bates	Ebola, Virus entry, glycoproteins, viral assembly, SARS, retrovirus, gene therapy.
Jeffrey Bergelson	Virus entry, adenovirus, coxsackievirus, viral pathogenesis, virus receptor, vaccine delivery
Kyong-Mi Chang	HCV immune pathogenesis, HCV persistence, Viral escape, Viral persistence, Epitope mapping, Liver disease, T cell suppression, HIV/HCV coinfection, Alcohol
Ronald Collman	HIV, virus, tropism, signal transduction, gp120, viral envelope, macrophage
Laurence Eisenlohr	Cell biology of MHC class I-restricted antigen processing and presentation, MHD class II-restricted antigen processing and presentation, "Cryptic" MHC Class I-Restricted Epitopes, Cancer immunotherapy and autoimmunity
Harvey Freidman	HSV immune evasion, glycoprotein gC, glycoprotein gE, complement, pathogenesis
Glen Gaulton	Lymphocyte Development, Retrovirus Pathology, HIV-1, Gene Therapy
James Hoxie	AIDS, CD4, chemokine receptors, HIV, SIV, envelope glycoproteins, viral entry, neutralization, vaccine
Dennis Kolson	Neuron, hippocampus, apoptosis, gene expression, single-cell mRNA, HIV, chemokine receptor, NMDA receptor
Paul Lieberman	Viral latency, chromatin, DNA replication, transcription, cancer
Ronen Marmorstein	Transcription, Chromatin regulation, Protein-DNA recognition, Posttranslational modification, Tumor Suppressors, Viral oncoproteins, X-ray Crystallography, Enzymology, Structure, Biophysics
Robert Ricciardi	Mechanisms by which oncogenic proteins of human viruses exploit cellular functions and regulate gene expression to produce disease and cancer
Erle Robertson	Oncogenesis, viruses and cancer, viral oncology, Tumor Virology, Gene therapy, Kaposi's Sarcoma, Epstein-Barr Virus, Lymphoproliferative disease, Lymphomas
Andrei Thomas-Tikhonenko	Myc, p53, microRNA, angiogenesis, colon cancer, B-lymphoma, interferons, infection
David Weiner	DNA Vaccines, HIV, Viral Protein R., Vaccines
Susan Weiss	Murine coronavirus, SARS associated coronavirus, viral pathogenesis
Drew Weissman	HIV, Immunopathogenesis, RNAi, gp-340, dendritic cell, siRNA, antigen presentation, HIV vaccine
Matthew D. Weitzman	Virology, Virus Replication, DNA Damage and Repair, Genome Instability, Viral Vectors
Elizabeth White	Human Papillomavirus, tumor virus, cancer virology, transformation, innate immunity, HPV
Jianxin You	DNA tumor viruses, Host targets, Persistent virl latent infection, Viral oncogenesis, Tumor virology, Bromodomain protein BRD4 and cancer
Yan Yuan	Kaposi's sarcoma-associated herpesvirus, virus-host interaction, the external guide sequence technique

Virology

Faculty	Brief Research Description
Paul Bates	Ebola, Virus entry, glycoproteins, viral assembly, SARS, retrovirus, gene therapy
Jeffrey Bergelson	Virus entry, adenovirus, coxsackievirus, viral pathogenesis, virus receptor
Michael Betts	HIV; T cell; Immune Response
Frederic Bushman	HIV, integration, integrase, poxvirus, DNA modifying enzyme, virology, variola, RNA interference, interferon
Kyong-Mi Chang	HCV, HBV, liver disease, HIV/HCV coinfection, alcohol, viral pathogenesis, viral persistence, immune regulation, T cell exhaustion, transplant tolerance, epitope mapping, immunogenetics
Sara Cherry	Virus, genomics, RNAi, genetics, Drosophila, innate, immunity
Gary Cohen	Herpes, HSV, virology, glycoproteins, virus entry
Ronald Collman	HIV, virus, tropism, signal transduction, gp120, viral envelope, macrophage
Laurence Eisenlohr	Cell biology of MHC class I-restricted antigen processing and presentation, MHD class II-restricted antigen processing and presentation, "Cryptic" MHC Class I-Restricted Epitopes, Cancer immunotherapy and autoimmunity
Harvey Friedman	HSV immune evasion, glycoprotein gC, glycoprotein gE, complement, pathogenesis
Glen Gaulton	Lymphocyte Development, Retrovirus Pathology, HIV-1, Imaging, Diagnostics
Beatrice Hahn	HIV-1 transmission, ape Plasmodium infections, SIVcpz infection of wild chimpanzee, HIV vaccine development
Ronald Harty	Ebola virus; VSV; Matrix Proteins; Budding; Reverse-Genetics; Virus-Host Interactions.
Scott Hensley	Influenza virus, antigenic drift, viral pathogenesis, viral receptors, antibody specificity, vaccines
James Hoxie	AIDS, CD4, chemokine receptors, HIV, SIV, envelope glycoproteins, viral entry, neutralization, vaccine
Stuart Isaacs	Vaccinia virus, Recombinant vaccines, poxvirus , pathogenesis, smallpox, smallpox therapeutics.
Kelly Jordan-Sciutto	Cell Cycle, Oxidative Stress Response, Antioxidant Response, Neurodegeneration, Transcription, Primary Culture, HIV encephalitis, Alzheimer Disease, Parkinson disease, Retinoblastoma, E2F1
Rahul Kohli	Our laboratory focuses on the enzymatic generation of genomic diversity. We utilize a broad array of approaches, including biochemical characterization of enzyme mechanisms, chemical synthesis of enzyme probes, and biological assays spanning immunology and virology to study this central tactic in the constant battle between our immune system and pathogens.
Dennis Kolson	Neuron, hippocampus, apoptosis, gene expression, single-cell mRNA, HIV, chemokine receptor, NMDA receptor.
Paul Lieberman	Viral latency, telomeres, chromatin, DNA replication, transcription regulation, herpesvirus.
Carolina Lopez	Virus-host interaction, innate immunity, respiratory viruses, lung immunity.
Luis Montaner	Innate Immunity & HIV-1 Infection: Dendritic cells & Natural Killer Cells Direct or indirect interactions of viral particles with innate and specific adaptive immunity effector cells affects the cross talk between antigen presenting cells (APCs), NK cells and the antigen specific T and B-lymphocytes, and may contribute to regulate HIV disease progression. Specifically, we are pursuing analysis of the effects of HIV infection in macrophages, dendritic cells and Natural Killer cells
Una O'Doherty	HIV, latency, reservoirs, dendritic cells, viral pathogenesis, proviral integration, retrovirus, virology, T cell activation, resting T cells.
Yvonne Paterson	Immune regulation, antigen design, vaccine development, cancer immunotherapy, HIV, HPV
Robert Ricciardi	Our laboratory is interested in the mechanisms by which oncogenic proteins of human viruses exploit cellular functions and regulate gene expression to produce disease and cancer.
James Riley	T cell activation, Tumor Specific T cells, HIV specific T cells, expression profiles.
Erle Robertson	oncogenesis, viruses and cancer, viral oncology, Tumor Virology, Gene therapy, Kaposi's Sarcoma, Epstein-Barr Virus, Lymphoproliferative disease, Lymphomas.
George Shaw	Molecular studies of HIV-1 transmission, persistence and pathogenesis, SIV transmission, persistence and pathogenesis, HCV transmission, persistence and pathogenesis
David Weiner	DNA Vaccines, HIV, Viral Protein R., Vaccines.
Susan Weiss	Murine coronavirus, SARS associated coronavirus, viral pathogenesis.
Drew Weissman	HIV, Immunopathogenesis, RNAi, DMBT1, dendritic cell, siRNA, antigen presentation.
Matthew D. Weitzman	Virology, Virus Replication, DNA Damage and Repair, Genome Instability, Viral Vectors
E. John Wherry	Immunological memory, T cell memory, Chronic infection, T cell dysfunction, Memory T cell differentiation.
Elizabeth White	Human Papillomavirus, tumor virus, cancer virology, transformation, innate immunity, HPV
James Wilson	Adenovirus, adeno-associated virus (AAV), gene therapy, gene transfer, lentivirus.
Jianxin You	DNA tumor viruses, Host targets, Persistent latent infection, Episome maintenance, Oncogenesis, Tumor virology, Gene therapy,
Yan Yuan	Kaposi's sarcoma-associated herpesvirus, virus-host interaction, microRNAs.

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