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Our Research Center

Brings together Investigators with multidisciplinary backgrounds, including microbiology, immunology, genetics, epigenetics, next generation sequencing, metabolomics, microbiome research, computational biology and bioinformatics, to elucidate host-pathogen interactions underlying various infectious diseases.

The Team


Petros C. Karakousis


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Dr. Karakousis is a Professor of Medicine at the Johns Hopkins University School of Medicine, with a joint appointment in International Health at the Johns Hopkins Bloomberg School of Public Health. He has clinical expertise in infectious diseases and tuberculosis. His research interests include the use of systems biology-based approaches to study Mycobacterium tuberculosis persistence and antibiotic tolerance, as well as to identify biosignatures for TB diagnosis and assessment of treatment response. His laboratory is actively investigating novel approaches to target M. tuberculosis persisters and adjunctive, host-directed therapies to shorten curative TB treatment and improve lung inflammation.


Dr. Karakousis received his undergraduate degree in 1994 from the Johns Hopkins University and his medical degree in 1998 from Washington University School of Medicine in St. Louis. He completed residency training in internal medicine in 2001 at the Hospital of the University of Pennsylvania. After completing fellowship training in infectious diseases at Johns Hopkins, he joined the Department of Medicine faculty in 2005. He has editorial responsibilities at Journal of Infectious Diseases, Microbiology Spectrum, Frontiers in Microbiology, and PLoS One and is a standing member of the NIH Bacterial Pathogenesis study section. for PLoS One and is on the editorial advisory board of the Journal of Infectious Diseases. He is a Fellow of the Infectious Diseases Society of America and a member of the American Society of Clinical Investigation.

Joel Bader


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Dr. Bader is a Professor of Biomedical Engineering and Computer Science at Johns Hopkins University. He also serves as interim Director of the High Throughput Biology Center in the Institute for Basic Biomedical Sciences. He holds faculty positions in the Institute for Computational Medicine and the Institute for Genetic Medicine. A physicist and mathematician with a strong interest in genomics and proteomics, Dr. Bader is collaborating with his colleagues on interpreting the complex map of gene-gene and protein-protein interactions in yeast. In the field of infectious diseases, his lab has developed new computational methods and joint wet-lab approaches to understand host-pathogen interactions underlying TB pathogenesis and M. tuberculosis persistence, with the goal of developing new therapies.


Dr. Bader received his bachelor’s degree in biochemistry from Lehigh University and Ph.D. in theoretical chemistry from the University of California, Berkeley. He completed a postdoctoral fellowship in theoretical chemistry from Columbia University and worked as director of bioinformatics at the CuraGen Corporation before joining the Johns Hopkins faculty in 2003. Dr. Bader also serves on the editorial board of PLoS Computational Biology, PLoS ONE, Plant Cell and the American Journal of Pharmacogenomics.

Akshay Gupte


Dr. Gupte’s research is focused on the intersection of infectious and chronic lung diseases in low- and middle-income settings. He leads several Indo-US collaborative studies to describe the epidemiology and pathogenesis of lung impairment in TB/HIV/diabetes, measure its impact on poor clinical outcomes, and identify therapeutic and programmatic interventions to improve post-TB lung health and longevity. Dr. Gupte is an active member of several multi-national TB/HIV research consortia such as the TB Transformative Science Working Group of the ACTG, the TB and Lung Health Working Group of the IeDEA network, and is the US Chair of the Clinical and Epidemiology Working Group of the RePORT-India TB Research consortium. Dr. Gupte is a 2017 Fogarty Fellow and recipient of the Arthur M. Dannenberg, Jr., Award for excellence in TB research. Dr. Gupte completed his medical training in India and received his Master’s and Doctoral training in Global Disease Epidemiology and Control from the Johns Hopkins Bloomberg School of Public Health.


Alison Hill

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Dr. Hill is an Assistant Professor of Biomedical Engineering at Johns Hopkins University, and a core faculty member at the Johns Hopkins Institute for Computational Medicine and Infectious Disease Dynamics Group. Dr. Hill’s team has developed mathematical models and computational tools to help understand, predict, and treat infectious diseases, with a particular focus on human viral infections including HIV/AIDS. She also works on drug resistant infections, bed bugs infestations, anti-viral immune responses, and SARS-CoV-2/COVID-19. Her research spans infection dynamics both within individual hosts and across populations. Her group also studies on general evolutionary theory of infectious diseases. 

Dr. Hill received her B.S. in 2007 from Queen's University in Kingston, ON, and her Ph.D. from the joint Harvard-MIT Division of Health-Sciences and Technology (HST)’s Medical Engineering and Medical Physics Program in 2013. She received her M.P.H from the Harvard T.H. Chan School of Public Health in 2020.

Cynthia Sears

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Dr. Sears is a Professor of Medicine and Oncology at the Johns Hopkins University School of Medicine and a Professor of Molecular Microbiology and Immunology at the Bloomberg School of Public Health. She is the microbiome program leader of the Bloomberg-Kimmel Institute for Cancer Immunotherapy at Johns Hopkins and is director of the Johns Hopkins Germ-free Murine Facility. Dr. Sear is an Infectious Disease expert, with a clinical focus on foodborne and intestinal infections. In the laboratory, her group studies how microbes impact the pathogenesis of colon cancer. Specific carcinogenic bacteria of interest include enterotoxigenic Bacteroides fragilis (ETBF), Fusobacterium subspp, pks+ Escherichia coli and Clostridioides difficile. The Sears laboratory integrates studies in humans and mouse models, employing microbiology, bioinformatics and immunological methods.

Dr. Sears received her medical degree from Thomas Jefferson Medical College, and completed residency training in internal medicine at The New York Hospital of Cornell Medical School. She trained as a fellow in Infectious Diseases at the the University of Virginia and Memorial Sloan Kettering Cancer Institute. Dr. Sears joined the faculty at the Johns Hopkins University School of Medicine in 1988. Dr. Sears has held many leadership positions, including as President of the Infectious Diseases Society of America (IDSA), and as Associate Editor of Clinical Infectious Diseases from 2000 to 2016.

David Dowdy


Dr. Dowdy is an Associate Professor of Epidemiology at Johns Hopkins Bloomberg School of Public Health. His interdisciplinary research lies at the nexus of infectious disease modeling, health economics, operational and implementation science, and classical epidemiology. His primary interests are dynamic modeling and economic evaluation of TB and TB/HIV, including evaluating the implementation and scale-up of TB and HIV control interventions, especially diagnostic and case-finding strategies. He is currently working with collaborators on projects based in Malawi, South Africa, Uganda, India, Zambia, Brazil, Canada, and the United States. 

Dr. Dowdy received his Bachelor degree from Duke University in 1999. He received his medical degree from Johns Hopkins University and Ph.D. from Johns Hopkins Bloomberg School of Public Health in 2008.

Jeffrey Tornheim

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Dr. Tornheim is an Assistant Professor of Medicine in the Division of Infectious Diseases at Johns Hopkins University School of Medicine. His research explores the application of new diagnostic technologies to improved health outcomes in the treatment of drug-resistant tuberculosis among both adult and pediatric patients in India. In particular, his focus is on the use of whole genome sequencing of M. tuberculosis isolates to detect antibiotic resistance and guide clinical management, and various high-throughput approaches, including whole blood transcriptomics and plasma metabolomics, for the diagnosis of TB and assessment of treatment response.

Dr. Tornheim received his MD/MPH degrees from Mount Sinai University School of Medicine, and completed residency training in Internal Medicine and Pediatrics at Yale University School of Medicine. He completed his clinical fellowship in Infectious Diseases at Johns Hopkins University School of Medicine in 2017 and joined the Infectious Diseases faculty.

Stuart C. Ray

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Dr. Ray is a Professor of Medicine and Oncology and serves as Vice-Chair of Medicine for Data Integrity and Analytics at the Johns Hopkins University School of Medicine He is a virologist and clinical investigator in the Center for Viral Hepatitis Research, and a faculty member of the Janeway Firm of the Osler Medical Service. Dr. Ray’s laboratory has focused on the evolution of hepatitis C virus (HCV) during acute and chronic infection, developing and applying computational and molecular biology tools to underlying mechanisms, including stochastic variation, immune selection, and viral fitness.

Dr. Ray received his M.D. from Vanderbilt University School of Medicine in 1990. After an internship and residency at Johns Hopkins Hospital, he continued there as an Assistant Chief of Service. He completed his Infectious Diseases fellowship training under the mentorship of Dr. Robert Bollinger, and joined the Johns Hopkins faculty in 1997.

Winston Timp

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Dr. Timp is an Associate Professor of Biomedical Engineering at Johns Hopkins University. He has expertise in the development and application of sequencing technologies to gain a deeper understanding of biology and a more accurate set of clinical tools for human disease. His research integrates the principles of biophysics, molecular biology and computational biology to create new tools for exploring the epigenomes and genomes of different lifeforms ranging in size from the influenza to hummingbirds to California redwoods.

Dr. Timp received Bachelor degrees in biochemistry, chemistry, physics and electrical engineering from the University of Illinois at Urbana. He then earned his Master degree and Ph.D. in electrical engineering from the Massachusetts Institute of Technology, where he worked at the Whitehead Institute, focusing his thesis work on the study of cellular communication in a 3-D microenvironment. After receiving his doctorate, he trained as a postdoctoral fellow at Johns Hopkins, studying the epigenetics of cancer. He joined the faculty of the Whiting School of Engineering in 2013. Dr. Timp is a member of the Biophysical Society, Institute of Electrical and Electronics Engineers, and the American Society of Genetics, and sits on the editorial board for Epigenetic Insights and is a bioRxiv Affiliate.


Marc K. Halushka

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The Halushka laboratory is interested in the overarching question of expression localization in tissues. To address this, the laboratory has set out upon several avenues of discovery in the areas of microRNA (miRNA) expression, proteomics and tissue gene expression. Many of these queries relate to the cardiovascular field. as Dr. Halushka is a cardiovascular pathologist. Recently, Dr. Halushka has been collaborating with Dr. Karakousis on miRNA and tRNA-derived fragment (tRF) expression in M. tuberculosis-infected macrophages.

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