URMC / Microbiology & Immunology / Research

Research Areas

SARS-CoV-2/COVID-19

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is the causative agent of the ongoing COVID-19. Faculty research on SARS-CoV-2/COVID-19 includes studies on: genetic analysis of SARS-CoV-2 genome; virus-host interactions; immune response of SARS-CoV-2 infection; development of new drugs and vaccines.

Active Research Laboratories

Dewhurst Lab - Influenza Viruses; Virus Polymerase HIV Vaccine Development; NeuroAIDS Research
Serra-Moreno Lab - Understanding how HIV overcomes the innate immune barriers in its target cells to establish a chronic infection, with the goal of using this information to find new avenues for therapeutic intervention
Singh Lab - Focused on immune-pathogenesis of viral infections such as Human Immunodeficiency Virus (HIV) and SARS-CoV-2.
Munger Lab - Mechanisms of Pathogenic Metabolic Manipulation
Yan Sun Lab - Mechanisms of Defective Viral Genome Generation
Takimoto Lab - Host-virus interaction of Influenza and Paramyxoviruses
Topham Lab - Respiratory Virus Immunity
Yarovinsky Lab - Immune regulation
Yiping Zhu Lab - Working with retroviruses (HIV-1, MLV, etc.) and focuses on identifying new host antiviral factors and deciphering viral antagonism of host defense

Anti-infectives & Drug Discovery

Identification of new genetic targets for antimicrobial drugs, development and early-phase testing of new anti-infectives for hard-to-treat organisms such as Methicillin Resistant Staphylococcus Aureus (MRSA) and Acinetobacter baumanii, as well as TB and fungal pathogens that afflict immunocompromised persons.

Active Research Laboratories

Dewhurst Lab - Influenza Viruses; Virus Polymerase HIV Vaccine Development; NeuroAIDS Research
Dunman Lab - Using S. aureus and A. baumannii as Model Organisms for Antibacterial Development and to Study Bacterial Pathogenesis
Minsoo Kim Lab - Cancer immunotherapy/Host immune response to influenza infection/ Inflammation biology of sepsis
Munger Lab - Mechanisms of Pathogenic Metabolic Manipulation
Pavelka Lab - Cell envelopes of pathogenic bacteria
Program for Advanced Immune Bioimaging

Autoimmune Disease

A critical component of the immune system is tight regulation; ensuring appropriate termination of immune responses following pathogen clearance and avoiding the inappropriate activation of immune responses to self tissues resulting in autoimmunity.

Active Research Laboratories

Anolik Lab - B Cells and Immune Diseases
Fowell Lab - Regulation of Immunity
Minsoo Kim Lab - Cancer immunotherapy/Host immune response to influenza infection/ Inflammation biology of sepsis
Mosmann Lab - Th1 and Th2 Subsets of CD4+ T Cells
Program for Advanced Immune Bioimaging
Sant Lab - Immunodominance in CD4 T Cell Responses
Schwarz Lab - Bone Loss Research
Yarovinsky Lab - Immune regulation

Biodefense

Faculty research focuses on a range of Category A, B and C Priority Pathogens. Studies include analysis of the pathogenesis of important bacterial and viral biodefense agents, comparative genomic studies on Vibrio species, genetic analysis of Francisella tularensis, analysis of immune responses to such viruses as influenza virus, Respiratory Syncytial Virus (RSV) and human arenaviruses such as Lassa and Junin, and the development and testing of new vaccines for pathogens that include human arenaviruses and influenza.

Active Research Laboratories

Frelinger Lab - T cell immunity to tumors and pathogens
Lawrence Lab - Environmental signaling, immune function, and cellular development
Munger Lab - Mechanisms of Pathogenic Metabolic Manipulation
Pavelka Lab - Cell envelopes of pathogenic bacteria
Sant Lab - Immunodominance in CD4 T Cell Responses
Takimoto Lab - Host-virus interaction of Influenza and Paramyxoviruses
Ward Lab - Mechanisms of Poxvirus Envelope Formation
Yarovinsky Lab - Host Resistance in Parasitic Infection

Cancer

Oncogenically transformed cells arise through a multistep process, and are normally subject to immune surveillance and elimination by the immune system. Cluster research focuses understanding of the immune mechanisms involved in tumor recognition and rejection, as well as fundamental mechanisms of cellular transformation and the role of microbial agents in oncogenic disease of the gastrointestinal (GI) tract. Studies include translational research aimed at improved cancer therapeutics and/or cancer vaccines, as well as studies into the basic mechanisms of cell transformation.

Active Research Laboratories

Frelinger Lab - T cell immunity to tumors and pathogens
Gill Lab - Microbial Pathogens and the Impact of Human Microbial Flora on Human Health and Disease
Lord Lab - Cell Mediated Immunity to Tumors
Munger Lab - Mechanisms of Pathogenic Metabolic Manipulation
Robert Lab - Evolution of Immune Surveillance, Tumor and Viral Immunity
Yarovinsky Lab - Inflammation and Cancer

Cell Biology

Microbes and viruses interact with host cells to induce alterations in cellular phenotype and function, thereby subverting host cell metabolism to meet their own needs. In addition, many microbes and viruses exert effects on the host immune response, so as to evade host immune control. Knowledge of the interplay between infectious pathogens and their host cells is therefore important, in order to identify potential new targets for drug therapy and as a basis for understanding microbial pathogenesis. Research focuses on various aspects of mammalian and amphibian cell biology including, cell to cell interactions, cell cycle control, intracellular signaling, differentiation and subcellular organelles.

Active Research Laboratories

Fowell Lab - Regulation of Immunity
Lawrence Lab - Environmental signaling, immune function, and cellular development
Minsoo Kim Lab - Cancer immunotherapy/Host immune response to influenza infection/ Inflammation biology of sepsis
Munger Lab - Mechanisms of Pathogenic Metabolic Manipulation
Program for Advanced Immune Bioimaging
Singh Lab - Focused on immune-pathogenesis of viral infections such as Human Immunodeficiency Virus (HIV) and SARS-CoV-2.
Ward Lab - Mechanisms of Poxvirus Envelope Formation
Yarovinsky Lab - Dendritic Cell Biology

ESKAPE Pathogens, Hard-To-Treat Infections & Drug Resistant Organisms

The ESKAPE pathogens comprise the 6 bacterial pathogens considered to be of greatest healthcare concern by the Infectious Diseases Society of America, because of their high burden of disease and frequent ability to evade currently used antibiotics. Chief among these is Staphylococcus aureus, which is the focus of several faculty laboratories, interested in establishing bacterial determinants of virulence as well as new targets for antimicrobial therapy. Other ESKAPE pathogens under investigation include Acinetobacter baumanii, Pseudomonas aeruginosa and enterobacterial species. Additional research focuses on Mycobacterium tuberculosis, as well as fungal species that a major cause of disease among medically immune suppressed persons, and polymicrobial infection.

Active Research Laboratories

Dunman Lab - Using S. aureus and A. baumannii as Model Organisms for Antibacterial Development and to Study Bacterial Pathogenesis
Gill Lab - Microbial Pathogens and the Impact of Human Microbial Flora on Human Health and Disease
Pavelka Lab - Cell envelopes of pathogenic bacteria
Schwarz Lab - Bone Loss Research

Genetics, Genomics & Metagenomics

Microbes and viruses interact with their immediate environment and in doing so alter the expression of their own genes or those of the host. Faculty study the regulation of gene expression at all levels, including global changes in bacterial gene expression in biofilms and dental caries, cytokine and gene expression changes associated with immune cell differentiation, and the comparative genomics of Vibrio cholerae species. These studies are enhanced by the University of Rochester's state of the art Functional Genomics Center, and other recent upgrades in the Core Facilities of the Medical Center.

Active Research Laboratories

Dziejman Lab - Type Three Secretion System Mediated Pathogenesis of V. cholerae
Gill Lab - Microbial Pathogens and the Impact of Human Microbial Flora on Human Health and Disease
Munger Lab - Mechanisms of Pathogenic Metabolic Manipulation
Pavelka Lab - Cell envelopes of pathogenic bacteria
Program for Advanced Immune Bioimaging
Robert Lab - Evolution of Immune Surveillance, Tumor and Viral Immunity
Topham Lab - Respiratory Virus Immunity
Yarovinsky Lab - Intestinal Microbiota

HIV/AIDS

HIV/AIDS remains a major cause of death both in the U.S. and internationally. Faculty research on HIV/AIDS includes studies on: viral transmission and pathogenesis, including HIV-associated neurologic disease; development of novel therapeutic and preventive approaches – including new drugs and vaccines; and studies on the opportunistic pathogens that are a major cause of morbidity and mortality in persons with HIV/AIDS. The University of Rochester Center for AIDS Research provides a central hub for campus research on the virus.

Active Research Laboratories

Dewhurst Lab - Influenza Viruses; Virus Polymerase HIV Vaccine Development; NeuroAIDS Research
Munger Lab - Mechanisms of Pathogenic Metabolic Manipulation
Serra-Moreno Lab - Understanding how HIV overcomes the innate immune barriers in its target cells to establish a chronic infection, with the goal of using this information to find new avenues for therapeutic intervention
Singh Lab - Focused on immune-pathogenesis of viral infections such as Human Immunodeficiency Virus (HIV) and SARS-CoV-2.
Yarovinsky Lab - Toxoplasmosis
Yiping Zhu Lab - Working with retroviruses (HIV-1, MLV, etc.) and focuses on identifying new host antiviral factors and deciphering viral antagonism of host defense

Immune Regulation & Immunologic Mechanisms

Research into immunological mechanisms includes studies in diverse research areas in immunology, including: antigen presentation and processing; B cell subsets and regulation of B cell responses; T cell activation and differentiation; T cell memory and homing; immune responses to pathogenic organisms; comparative immunology using the frog Xenopus as a model system; mechanisms of autoimmunity; and the identification and analysis of gene expression signatures associated with immune responses to infection and immunization. These varied research programs seek to dissect key regulatory events that control protective and pathogenic immune responses.

Active Research Laboratories

Fowell Lab - Regulation of Immunity
Frelinger Lab - T cell immunity to tumors and pathogens
Lawrence Lab - Environmental signaling, immune function, and cellular development
Lord Lab - Cell Mediated Immunity to Tumors
Minsoo Kim Lab - Cancer immunotherapy/Host immune response to influenza infection/ Inflammation biology of sepsis
Program for Advanced Immune Bioimaging
Robert Lab - Evolution of Immune Surveillance, Tumor and Viral Immunity
Sant Lab - Immunodominance in CD4 T Cell Responses
Singh Lab - Focused on immune-pathogenesis of viral infections such as Human Immunodeficiency Virus (HIV) and SARS-CoV-2.
Thakar Lab - Delineation the effects of age, immunogenicity of the antigens, host genotype and host’s immune history using bioinformatics, systems biology and dynamic modeling tools
Yarovinsky Lab - Intestinal Homeostasis and Inflammation

Molecular Basis of Microbial Pathogenesis

An important weapon in the battle of infectious diseases is a basic understanding of the mechanisms of pathogenesis of infectious agents and the interaction of the pathogen with the host. A major research goal of the faculty is therefore to examine the mechanisms by which pathogenic microorganisms cause disease, using an interdisciplinary approach that involves scientists trained in microbiology, virology, molecular biology, and host defense.

Active Research Laboratories

Dewhurst Lab - Influenza Viruses; Virus Polymerase HIV Vaccine Development; NeuroAIDS Research
Dunman Lab - Using S. aureus and A. baumannii as Model Organisms for Antibacterial Development and to Study Bacterial Pathogenesis
Dziejman Lab - Type Three Secretion System Mediated Pathogenesis of V. cholerae
Fowell Lab - Regulation of Immunity
Frelinger Lab - T cell immunity to tumors and pathogens
Gill Lab - Microbial Pathogens and the Impact of Human Microbial Flora on Human Health and Disease
Munger Lab - Mechanisms of Pathogenic Metabolic Manipulation
Pavelka Lab - Cell envelopes of pathogenic bacteria
Program for Advanced Immune Bioimaging
Robert Lab - Evolution of Immune Surveillance, Tumor and Viral Immunity
Singh Lab - Focused on immune-pathogenesis of viral infections such as Human Immunodeficiency Virus (HIV) and SARS-CoV-2.
Yan Sun Lab - Mechanisms of Defective Viral Genome Generation
Takimoto Lab - Host-virus interaction of Influenza and Paramyxoviruses
Thakar Lab - Delineation the effects of age, immunogenicity of the antigens, host genotype and host’s immune history using bioinformatics, systems biology and dynamic modeling tools
Ward Lab - Mechanisms of Poxvirus Envelope Formation
Yarovinsky Lab - Innate immunity and Immune Regulation in Parasitic Infection

Opportunistic Pathogens

Opportunistic pathogens are microorganisms that usually do not cause disease in healthy hosts. However, they are often the source of opportunistic infections in hosts who are immunocompromised or when they bypass host defenses as a result of tissue damage caused by cuts, burns or surgery. Faculty research is focused on bacterial and fungal opportunistic pathogens, including Staphylococcus aureus, Acinetobacter baumanii, Enterococcus faecalis, Pneumocystis carinii, Candida albicans and Cryptococcus neoformans. Investigators use biochemical, genetic and genomic approaches to study mechanisms of pathogenesis and interactions with the host.

Active Research Laboratories

Gill Lab - Microbial Pathogens and the Impact of Human Microbial Flora on Human Health and Disease
Yarovinsky Lab - Toxoplasmosis

Respiratory Pathogens

Interactions of respiratory pathogens with the host respiratory environment can lead to severe life-threatening infections or chronic debilitating infections that persist for years. Severe infections are often the result of synergistic interactions between bacterial and viral pathogens such as Staphylococcus aureus and Respiratory Syncytial Virus (RSV). Chronic lung infections such as Cystic Fibrosis are often polymicrobial infections of multiple bacteria, including Pseudomonas aeruginosa, Hemophilus influenzae and Staphylococcus aureus. Multiple faculty study RSV, influenza virus, Staphylococcus aureus, Pseudomonas aeruginosa, Mycobacterium tuberculosis and Pneumocystis carinii. Investigators are exploring mechanisms of virulence as well as development of vaccines.

Active Research Laboratories

Dewhurst Lab - Influenza Viruses; Virus Polymerase HIV Vaccine Development; NeuroAIDS Research
Gill Lab - Microbial Pathogens and the Impact of Human Microbial Flora on Human Health and Disease
Pavelka Lab - Cell envelopes of pathogenic bacteria
Yan Sun Lab - Mechanisms of Defective Viral Genome Generation
Takimoto Lab - Host-virus interaction of Influenza and Paramyxoviruses
Thakar Lab - Delineation the effects of age, immunogenicity of the antigens, host genotype and host’s immune history using bioinformatics, systems biology and dynamic modeling tools.

Vaccine Biology

Vaccines represent perhaps the most cost-effective approach to improving human health and well-being, saving tens of millions of lives each year. Moreover, the UR has an impressive track record of contributing to the development of important human vaccines, including the Hemophilus influenza b (Hib) vaccine and the recently developed Human Papillomavirus (HPV) vaccine. Research focuses on basic mechanisms involved in the generation of pathogen-specific immune responses as well as translationally-oriented studies that involve the derivation and testing of novel vaccines and/or vaccine delivery systems.

Active Research Laboratories

Dewhurst Lab - Influenza Viruses; Virus Polymerase HIV Vaccine Development; NeuroAIDS Research
Dunman Lab - Using S. aureus and A. baumannii as Model Organisms for Antibacterial Development and to Study Bacterial Pathogenesis
Frelinger Lab - T cell immunity to tumors and pathogens
Lord Lab - Cell Mediated Immunity to Tumors
Robert Lab - Evolution of Immune Surveillance, Tumor and Viral Immunity
Sant Lab - Immunodominance in CD4 T Cell Responses
Schwarz Lab - Bone Loss Research
Thakar Lab - Delineation the effects of age, immunogenicity of the antigens, host genotype and host’s immune history using bioinformatics, systems biology and dynamic modeling tools