Henrik Salje

Core Faculty

Henrik Salje established the Pathogen Dynamics Group in 2020. He and his team were previously at Institut Pasteur in Paris, France. His research combines the development of analytical approaches with empirical research to better understand the transmission dynamics of different infectious diseases with the ultimate goal of helping guide control efforts. In particular, this involves working with genetic, antigenic, and epidemiological data alongside information on how populations behave, interact with their environment. He has an undergraduate degree in Biochemistry from Oxford University, a Master's degree in Biostatistics from Johns Hopkins Bloomberg School of Public Health, and a PhD in Epidemiology, also from Johns Hopkins. 

Lab Management

Theodora Anderson

Lab Manager

Theodora is the Lab Manager and a Research Assistant for the group. She has extensive experience in academic administration and research. Theodora has an academic background in Biology, Anthropology and Forensics, and has obtained her PGDip in Bioinformatics from the University of Edinburgh. She has previously investigated genetic traits in human mixed ancestry populations, the existence of MRSA in fish, as well as host switching in Staphylococcus aureus using phylogenetic distances as driver. Theodora is currently working on understanding the factors influencing the spread of SARS-CoV-2.


Rachel Sippy

Dr. Sippy's research focuses on the role of climate and the environment in driving vector borne illness, at the level of pathogen, vector, and host. She completed her BSc in Genetics from Iowa State University in 2007, and an MPH from the University of Utah in 2013. She received a T32 training fellowship to complete her PhD in Epidemiology at the University of Wisconsin-Madison, finishing in 2018. Dr. Sippy studied the role of the indoor built environment on exposure risk to Aedes aegypti vectors during her postdoctoral training with SUNY Upstate Medical University and the University of Florida.

Lin Wang


Research Associate in the Pathogen Dynamics Group. He is studying the role of antigenic and genetic diversity of dengue virus in driving the transmission and population risk in Thailand. He is interested in system immunology, metagenomics, serology, statistical epidemiology, and mathematical modeling, with applications in arbovirus (e.g. dengue) and emerging diseases (e.g. A/H1N1, COVID-19). He was a chargé de recherche in the Mathematical Modelling of Infectious Disease Unit, Institut Pasteur, and postdoc fellow in the School of Public Health, The University of Hong Kong. He has a PhD in Electronic Engineering from Fudan University, MSc, and BSc in Physics from Nankai University and Southeast University

PhD Students

Sophie Belman

PhD student

Sophie is a PhD student co-supervised by Stephen Bentley at the Wellcome Sanger Institute and Henrik Salje at the University of Cambridge. She is working towards understanding global spatiotemporal dynamics of Streptococcus pneumoniae (pneumococcal) populations. The migratory pathways and connectivity of pneumococcal populations has implications for vaccine implementation and development.  Sophie obtained her MSc in Medical Microbiology from the London School of Hygiene and Tropical Medicine.

Noémie Lefrancq

PhD student

Noemie is a PhD student working on the integration of genetic and spatial data to better understand the spread, maintenance, and control of pathogens. She is working with datasets of Bordetella pertussis genomes from throughout France as well as other European countries in a collaborative project with the national reference center for Pertussis in France. She also works with Listeria and dengue virus.


Megan O'Driscoll

PhD student

Megan's work focuses on the development and application of mathematical models to better understand arboviral immune dynamics. She is interested in how complex immunological interactions can shape pathogen transmission dynamics in a population. Megan obtained her MSc in Epidemiology from the London School of Hygiene and Tropical Medicine and she previously worked in the Department of Infectious Disease Epidemiology at Imperial College London.

Gabriel Ribeiro dos Santos

PhD student
PhD student in the Pathogen Dynamics Group, Gabriel is interested in public health policies. He focuses on developing tools to better understand the impact of interventions on the transmission of arboviruses. He is also studying the contribution of different data types (geolocated case data, virus genetic sequences, serology data, etc.) to these methods. He previously worked at the Institut Pasteur on the same topics.

Nayantara Wijayanandana

PhD student
Nayantara is a visiting student in the Pathogen Dynamics Group, co-supervised by Henrik Salje. She is doing her PhD at the London School of Hygiene and Tropical Medicine on transmission dynamics of dengue in Sri Lanka, applying statistical and mathematical models to geolocated case data to understand the spatio-temporal heterogeneity of transmission. She is also interested in incorporating genetic and mobility data in her research to describe transmission patterns. Her experience is in vector-borne diseases - specifically dengue and malaria - and she has previously done field surveys and established sentinel surveillance to describe malaria transmission in distinct endemic settings in Nigeria, Uganda, Southern Sudan, and Zambia.

Master's Students

Raina Jia

MPhil Student

Raina is an MPhil student in genetics. She is interested in accessing the evolutionary relationships of pathogen strains. Her work looks at the pattern of transmission and spread of human infectious diseases using phylogenetic analysis. She previously had an academic background in biomedical sciences and worked in the pharmaceutical industry.



Oscar Cortés Azuero

Master's student

Oscar Felipe Cortes Azuero is a Master's student at Ecole Centrale de Lille. His interests are in integrating mathematics into applied biological questions. He conducted an internship in the Pathogen Dynamics Groups, where he worked on a Nipah virus project exploring how pathogen genomes could be used to infer viral dynamics in bat populations.

Undergraduate Students

Zheyuan Yang

Part III Student

Zheyuan is a fourth-year undergraduate student in Systems Biology. With a background in biological natural sciences, he is working on a Part III research project exploring the role of human movement in the transmission of arbovirus in South Asia. He is also interested in using media analytics to understand the viral spread of misinformation through social networks, especially in the context of public health issues.


Simon Cauchemez

Simon Cauchemez heads the Mathematical Modelling of Infectious Diseases Unit at Institut Pasteur. The main research objective of his unit is to develop state-of-the-art statistical and mathematical methods to address these challenges, with the aim to increase the understanding of how pathogens spread in human populations as well as the impact of interventions, to support policymaking and optimize control strategies. His approach is highly multidisciplinary, looking at infectious diseases through multiple perspectives (statistics, modeling, epidemiology, surveillance, Public Health, policymaking, microbiology), multiple scales, and multiple data streams. Before joining Institut Pasteur, Simon Cauchemez was working in the Department of Infectious Disease Epidemiology at Imperial College London

Amy Wesolowski

Amy is an Assistant Professor in the department of Epidemiology at Johns Hopkins University. She is interested in understanding how human behavior can impact infectious disease dynamics. She uses a range of statistical and dynamical models to better understand disease transmission and control. She also works to use novel data sources to describe human populations. She primarily works in Africa and Asia supporting both field and modeling studies. She completed her PhD in Engineering and Public Policy from Carnegie Mellon University in 2014.

Justin Lessler

Justin Lessler is an Associate Professor in the department of Epidemiology at Johns Hopkins University researching the dynamics and control of infectious disease, with particular interest in influenza, measles, cholera and dengue. Justin works on the development and application of statistics, dynamic models and novel study designs to better understand and control infectious disease. In particular, he is interested in creating synergies between infection control practice, data collection and infectious disease dynamics.

Derek Cummings

Derek is an infectious disease epidemiologist at the University of Florida and engaged in theoretical and field studies of disease transmission. The goal of his research is to understand the temporal and spatial dynamics of the spread of infectious diseaess in order to inform interventions to control their spread. He is specifically interested in the dynamics of dengue, influenza, measles, and chikungunya. He currently leads field studies of influenza in the US and China, and dengue and chikungunya in Thailand and India. 

Emily Gurley

Emily is an Associate Scientist in the Department of Epidemiology at Johns Hopkins University and leads multi-disciplinary studies on the transmission and prevention of emerging and vaccine preventable diseases, such as Nipah virus, hepatitis E virus, and arboviruses. She has worked in Bangladesh for more than a decade and her interests include improving the communication and collaboration between field epidemiologists and infectious disease modelers and development of novel surveillance strategies. Her research adopts a One Health approach to the study and prevention of infectious disease, taking into account the ecological context in which human disease occurs. Emily is the Co-Director for the Child Health and Mortality Prevention Surveillance (CHAMPS) site in Bangladesh, aiming to determine the etiology of and prevent child deaths. She also works closely with the US Centers for Disease Control and Prevention’s Global Disease Detection program.

Isabel Rodriguez-Barraquer

Isabel is an Assistant Professor in the Division of HIV, ID and Global Medicine at University of California, San Francisco. She is interested in applying novel epidemiological and statistical methods to understand the dynamics of infectious diseases. While she is interested in infectious diseases generally, most of her experience is related to vector-borne diseases such as dengue, malaria, and Zika.  Isabel completed her medical training in Colombia. She joined the ID dynamics group in 2008 and completed a PhD in epidemiology and an MHS in Biostatistics at the Johns Hopkins Bloomberg School of Public Health in 2012.

Past Lab Members

Etienne Dean

Part II Student

Etienne is a Part II student in genetics. He wrote a literature review discussing the insights gained from phylogeographic analyses of SARS-CoV-2 and is currently working on a project to understand the factors influencing the number of SARS-CoV-2 mutations within communities.

Sohaib Ansari

Part II Student

Sohaib is a third-year medical student, studying Part II Genetics. Currently, he’s working on a project to model human mobility in Bangladesh and investigate any underlying patterns, ultimately to aid disease transmission predictions. He is interested in exploring how such modelling can be used in a public health context.