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Microbiology, Virology, and Parasitology Faculty

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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

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Faculty

Flavia R Teles

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

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

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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
Jonathan Miner Zika virus, West Nile virus, chikungunya virus, Mayaro virus, La Crosse virus, Powassan virus
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.

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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
Chengcheng Jin Understanding how immune responses are initiated and evolve over time as tumors arise de novo and progress in the native TME; Defining the molecular and cellular mechanisms by which the immune system senses and responds to microbiota-derived or tumor-intrinsic signals in the TME to regulate tumor growth and responses to therapies.
Carl June T cells, human, gene therapy, genetic engineering, signal transduction
Rahul Kohli Antibody diversity; innate immune retroviral restriction resistance
Leyuan Ma Genetic, chemistry, engineering, and computational tools to decode the molecular and cellular crosstalk between immune cells and their microenvironment. Engineering novel biomaterials, protein, and cell-based precision immunotherapies.
Michael S. Marks Cell biology of host-pathogen interactions; innate immunity; phagocytosis; dendritic cell responses to bacteria; primary immunodeficiency disorders
Jonathan Miner host-pathogen interactions, interferon, innate immunity, STING, cGAS, TREX1, RIG-I, nucleic acid sensors
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
Warren Pear Tumor Biology, Development, Stem Cells, Hematopoiesis, Immune Function
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
Shaon Sangupta

circadian regulation of the Host-pathogen interaction, tissue clocks, circadian rhythms, influenza, neonatal lung, lung inflammation, NK cells 

 
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

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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
Chengcheng Jin Understanding how immune responses are initiated and evolve over time as tumors arise de novo and progress in the native TME; Defining the molecular and cellular mechanisms by which the immune system senses and responds to microbiota-derived or tumor-intrinsic signals in the TME to regulate tumor growth and responses to therapies.
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.

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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

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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

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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.
Leyuan Ma Using genetic, chemistry, engineering, and computational tools to decode the molecular and cellular crosstalk between immune cells and their microenvironment. Engineering novel biomaterials, protein, and cell-based precision immunotherapies.
Jonathan Miner

flavivirus, alphavirus, herpesvirus, bunyavirus, immune response, gene therapy, viral pathogenesis
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.
Shaon Sangupta circadian regulation of the Host-pathogen interaction, tissue clocks, circadian rhythms, influenza, neonatal lung, lung inflammation, NK cells 
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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