Institutions
University of Pittsburgh
SAPPHGenE is collaborating with several labs at the University of Pittsburgh, depending on qualified candidates’ training needs. Unless otherwise indicated, labs are located in Scaife Hall, which is adjacent to UPMC Presbyterian Hospital in the Oakland neighborhood of Pittsburgh.
Lee Harrison, MD
Harrison Laboratory
Microbial Genomic Epidemiology Laboratory (MiGEL)
The Harrison laboratory combines epidemiology and hospital epidemiology, molecular biology, and public health-related research, providing the opportunity for cross discipline research. The laboratory houses an extensive global collection of bacterial pathogens, along with associated epidemiologic and clinical data. The Infectious Diseases division has numerous faculty engaged in research, who provide valuable intellectual interaction and contribute to collaborations on project development. This provides an excellent multidisciplinary research training environment.
The lab is fully equipped to perform whole genome sequencing and other molecular characterization of bacterial pathogens. It has its own Illumina MiSeq DNA sequencer, and through collaboration with the University of Pittsburgh Genomics and Proteomics Core Laboratories (GPCL), access to Agilent Tapestation to size DNA libraries for whole genome sequencing.
Cornelius Clancy, MD
Clancy Laboratory
The Clancy laboratory studies the molecular pathogenesis of invasive infections caused by Candida albicans.
Dr. Clancy’s research has identified several novel genes that contribute to the pathogenesis of candidiasis and aspergillosis. Biological processes related to these genes that are studied in the lab include histone methylation and transcriptional regulation, DNA damage responses, and phosphoinositide regulation.
In addition, he and Dr. Minh-Hong Nguyen collaborate on research on mechanisms of antimicrobial resistance in bacteria and fungi, as well as their clinical relevance.
Yohei Doi, MD, PhD
Doi Laboratory
The mission of Dr. Doi’s laboratory is to identify and investigate antimicrobial resistance of clinical concern among gram-negative bacterial pathogens.
The areas of research include the genetic and molecular basis of emerging antimicrobial resistance mechanisms; the rapid diagnosis of resistance using phenotypic, genetic, and lipidomic approaches; and inhibitor-based drug discovery. Current efforts are focused on colistin resistance in Acinetobacter baumannii, a problematic healthcare-associated pathogen, and fosfomycin resistance in Escherichia coli, the predominant cause of urinary tract infection in both healthcare and community settings. The latter work has expanded into drug discovery effort aimed at reversing resistance using an inhibitor-based approach.
In addition, Dr. Doi is the Director of the Department of Medicine’s Center for Innovative Antimicrobial Therapy.
Alison Morris, MD, MS
Morris Laboratory
Division of Pulmonary, Allergy, & Critical Care Medicine, Department of Medicine, University of Pittsburgh School of Medicine
Dr. Morris’ laboratory is in the University of Pittsburgh HIV Lung Research Center, which is located in the Biomedical Science Tower. It offers advanced resources for biomedical computing software and biological specimen storage and tracking. Additionally, there are at least four flow cytometry facilities in the institution that support both clinical and research activities. All facilities have state-of-the-art cytometers for cell sorting and cell population analysis, including standardized clinical screening and flow imaging capabilities. Each facility has highly trained staff and faculty.
Dr. Morris’ research interests focus in several overlapping areas:
- Role of the microbiome in HIV-associated lung disease
- Understanding and manipulating the respiratory and gut microbiota in the ICU
- The role of nitrate-reducing bacteria in pulmonary hypertension
- HIV-associated emphysema and pulmonary hypertension
- Role of Pneumocystis and other fungi in COPD and HIV
In addition, Dr. Morris is the Director of the Center for Medicine and the Microbiome.
Vaughn Cooper, PhD
Cooper Laboratory
Department of Microbiology and Molecular Genetics, University of Pittsburgh School of Medicine, Bridgeside Point II Building
The primary goal of Dr. Cooper’s laboratory is to understand how bacterial populations evolve and adapt to colonize hosts and cause disease. By studying evolution-in-action, both in experimental populations and in ongoing infections, and using the latest methods in genomic sequencing, he and his team seek to identify mechanisms of bacterial adaptation in vitro and in vivo. He is particularly focused on how bacterial populations form complex communities within biofilms and how cells perceive cues to attach or disperse. He is also developing genome-based diagnostics for bacterial infections.
In addition to research on complex scientific problems, MMG also emphasizes training the next generation of talented young scientists, providing outstanding mentoring to junior and midlevel faculty, students and postdoctoral fellows.
For more information, please visit Dr. Cooper’s lab page here: http://www.mmg.pitt.edu/lab/cooper-lab
Mark Roberts, MD, MPP
Public Health Dynamics Laboratory
Dr. Roberts directs the Public Health Dynamics Laboratory (PHDL), which maintains computer laboratories in PPH to support of modeling and simulation in public health.
PHDL is an interdisciplinary activity at Pitt Public Health at the University of Pittsburgh focused on the development of computational methods to improve the theory and the practice of public health. The PHDL includes over 40 faculty and staff, including epidemiologists, biostatisticians, behavioral scientists, public health policy experts and computational scientists to produce the next generation of analysis tools for the exploration of critical public health problems. Areas of active research include:
- Infectious disease dynamics
- Spatial epidemiology
- Global open access public health databases
- Vaccine distribution in developing countries
- Public health response to epidemics and other emergencies
- Social networks and effects on obesity, smoking, and other health behaviors
- Dynamics of community violence
The PHDL is on the vanguard of public health research and computational modeling, and takes an active role in the development of open source computational tools for the analysis of public health issues. It provides an invigorating research environment for faculty, students and post-doctoral fellows interested in advancing computational approaches to problems in public health.
Daria Van Tyne, PhD
Van Tyne Laboratory
Division of Infectious Diseases, Department of Medicine, University of Pittsburgh School of Medicine
The Van Tyne Lab studies how bacteria evolve during human infection to resist antibiotics and the host immune system, using comparative genomics and functional approaches. The lab sequences bacterial strains from human infections and uses functional genomics to identify and characterize novel resistance mechanisms. These include the ability of bacteria to resist the host immune system, or to persist in the face of antibiotic pressure. The lab also works with other research groups to develop new antibiotics that can treat drug-resistant bacterial infections. The lab helps characterize new types of antimicrobial molecules and understands how novel compounds kill bacteria. The lab is also developing bacteriophages as novel therapeutics.
Barbara Methé, PhD
Center for Medicine and the Microbiome (CMM)
University of Pittsburgh School of Medicine
The University of Pittsburgh Center for Medicine and the Microbiome was established to foster innovative basic, translational, and clinical research in the microbiome. The Center is comprised of MD and PhD researchers in multiple disciplines who will work together to understand the role of the microbiome in health and disease and to apply this knowledge to develop novel diagnostic and therapeutic strategies. The center provides a home for interdisciplinary studies of the microbiome and integrating work of basic and clinical scientists with access to large clinical cohorts in order to efficiently test new ideas and rapidly disseminate pioneering treatments.