Professor of Ecology and Evolution
I am a theoretical ecologist interested in the temporal and spatio-temporal dynamics of ecological systems, from populations experiencing the spread of pathogens to large communities of interacting species in ecosystems. With an itinerant undergraduate and graduate trajectory that took me back and forth between biology and mathematics, I am deeply interested in the intersection of numbers and nature. I study ‘complex systems’ in Ecology and Epidemiology, to understand and predict patterns of variability and their connection to structure and scale. Biological systems in general with their diversity and interactions at different levels of organization represent this century’s challenge for quantitative approaches, including dynamical modeling, statistical inference and informatics. Ecological systems, including the Ecology and Evolution of infectious diseases, pose some of the most urgent and challenging problems today. See our Research page for specifics on our work.
Frederic is from France and he joined the lab as a Postdoctoral Scholar in the summer of 2020. He is a population geneticist fascinated by understanding how natural populations and species evolved and adapted to their environment. His research interest lies at the interface of computational biology, ecology, and evolutionary biology. During his career, he used combinations of various techniques for contributing to our understanding of how a broad variety of organisms, from plant pathogens to disease-vector mosquitoes and flies, responded and adapted to environmental and ecological changes. Frederic’s current research focuses on developing theories on falciparum malaria transmission from the perspective of the multigene family known as var, the analysis of the population structure of the parasite from molecular data, and computational models on these aspects. His work involves collaborations with our colleagues at the University of Melbourne and partner institutions in Ghana.
Armun is a PhD student in the Department of Ecology and Evolution. His research focuses on developing theory for the co-evolutionary dynamics and diversity structure of archaea and virus interactions mediated by CRISPR-Cas immunity. His research particularly applies to the acidothermophilic crenarchaea Sulfolobus islandicus, found in geothermal hot springs of Iceland, Russia, and North America. Armun completed his Bachelor’s degrees in Physics and Mathematics at the University of California, Santa Barbara. He later completed a Master’s degree in Particle Physics and Gravitation at Universitat de Barcelona. Armun is broadly interested in understanding the interplay of structure and dynamics at different levels of organization of high-dimensional communities, namely in the context of comparable time scales of ‘ecology’ and ‘evolution.’
I am a Ph.D. student in the Committee on Genetics, Genomics, and System Biology. My research focuses on the significance of population structure related to the diversity of var genes which encode the major surface antigen of malaria parasites, and the role of negative frequency-dependent selection through this structure on the epidemiology of malaria, especially the system’s response to intervention that reduces transmission intensity. My research also concerns the themes of trade-offs, optimization, and adaptation along a gradient of transmission intensity as evident in the host-pathogen interaction system of malaria. I am broadly interested in formulating theories for studying complex adaptive systems, in which the mapping between microscopic processes and macroscopic patterns is less intuitive and straightforward, due to reasons including the high dimensionality of the trait space, the effect of a partitioned higher-level organization, and so on.
Collaborators and previous lab members
Victoria Romero Aznar
Victoria is from Argentina and joined the lab as a postdoctoral scholar in 2016. While at UC she was also a fellow of the Mansueto Institute for Urban Studies. She received her Phd in Physics from the university of Buenos Aires, where she developed a non-linear stochastic model for the population dynamics of the mosquito Aedes aegypti, one of the main vectors of Dengue. She also conducted research in the Biology of Integrative Systems Lab at Leloir Institute Foundation, where she developed and analyzed prioritization methods for complex networks of biological origin. She is currently seeking to understand how spatial heterogeneity, population density, and socioeconomic disparity affect the transmission of vector-borne diseases in cities. She is developing stochastic transmission models that incorporate different assumptions on the effects of human and vector distributions and mobility. She is a physicist who is curious about complex systems, and their application to mathematical models to biology and social sciences. She enjoys exploring the outdoors and traveling.
She is back in Buenos Aires supported by CONICET and working at the University of Buenos Aires.
Rahul is a sixth-year PhD student in the Department of Ecology and Evolution. His research focuses on understanding the effects of climate, immunity, and movement on the emergence and re-emergence of viruses such as dengue and COVID-19 in human populations. He received a B.S.E. in Electrical Engineering from Princeton University in 2015. During his previous undergraduate work, he used mathematical models of disease transmission to compare how routine vaccination with candidate universal influenza vaccines might compare against conventional strain-matched vaccines in their effect on seasonal epidemic and pandemic sizes as well as antigenic evolution. More broadly, Rahul is interested in learning more about how human populations interact with rapidly evolving pathogens and the intersection between engineering, biology, and public policy.
Qixin joined the lab as a postdoctoral fellow in 2015 after completing her doctoral studies in Ecology and Evolutionary Biology from the University of Michigan (Ann Arbor). She is enthusiastic about build theoretical models and empirically apply them to understand the evolution and structuring of population diversities in time and space. She utilizes tools from population genetics, genomic evolution, and disease ecology. She is currently working on developing a modeling approach to capture signatures of frequency-dependent selection in the malaria system. Challenges involve reticulate evolution in the main antigen genes, the resulting immense diversity, and the consideration of transmission dynamics, all of which ask for non-conventional population genetics models. Previously (Ph.D dissertation), she developed a spatially explicit modeling framework for recovering population expansion histories. She also constructed a testing framework for local adaptation signatures in highly linked regions (such as chromosomal inversions). She applied this framework to Anopheles gambiae populations in which inversions were involved in maintaining local climatic adaptation.
Sergio A. Alcala-Corona
Sergio is from Mexico City and joined the lab as a postdoctoral scholar in 2018. He has an interdisciplinary background, he got his bachelor degree in Physics, made two masters, one in Computer Sciences and another in Nonlinear Dynamics, and he made his Ph.D. in Biomedical Sciences. His goal is to contribute to the understanding of complex diseases from a mathematical modeling perspective.
His research interests in general, involve the application of mathematical methods and network theory to biological complex systems, to understand both in dynamics and structure of them, specifically for modeling human diseases. During his PhD, his research was focused on structural aspects of Gene Regulation Networks, particularly, he used Systems Biology approaches to address the relationship between network structural modules and biological functions on Breast Cancer.
Currently, he is working on developing a mathematical theory based on ecological networks, that helps to understand the structural and dynamic aspects of the coevolutionary system composed of bacteriophages viruses, and bacteria/archaea that use the CRISPR immune system.
Sergio has been a lecturer at UNAM Mexico and worked as a software developer. He likes movies, documentaries, and series, and also he is enthusiastic about rock music.
James S. McDonnell Foundation postdoctoral scholar
Shai is from Israel and joined the lab as a postdoctoral scholar in 2015. His research interests involve the application of network theory to ecological systems, specifically in the field of disease ecology. In his early career, Shai was an avid field ecologist and worked in a variety of ecosystems including seasonal winter pools, tropical forests and desert habitats, and his PhD focused on the ecology and evolution of host-parasite interactions. Currently, Shai is working on extending the complexity of ecological networks using multilayer network theory. He applies this framework to study the temporal dynamics of the genetic structure of the malaria parasite, Plasmodium falciparum. He enjoys traveling and he is an enthusiastic jazz fan. He is currently a Senior Lecturer at Ben-Gurion University of the Negev.
Xiangjun is from China and join the lab as a postdoctoral scholar in 2014. He got his bachelor degree in Physics and PhD in Bioinformatics. Before joined the lab, he was a postdoctoral visiting fellow at NCBI/NLM/NIH, explored broadly in genome evolution and genome-wide transcriptional regulation. His research focus is quantitative study of human diseases from a network perspective. He used multidisciplinary skills to address practical questions in both human infectious diseases and human complex diseases. Currently, he is working on incorporating evolutionary information from sequences into theoretical epidemiology model to capture the realistic incidence dynamics and exploring the predictability of human influenza virus. He is a sports lover and enjoys traveling. He is currently a Professor of Public Health at Sun Yat-sen University.
Pamela is from Chile and joined the lab as a research assistant in 2011, to then start her PhD in 2012. She is interested in the interaction of ecological and evolutionary mechanisms driving diversity and its population structure. During her PhD she has been working on 1) the interface between the population dynamics of infectious diseases and environmental (climate) variability; 2) the relative importance of specific and generalized immunity in determining pathogen diversity patterns in urban and rural areas of developing countries; 3) how both fitness differences and the selection imposed by specific immunity (niche differences) influence strain diversity; and 4) the role of evolutionary processes on pathogen diversity.Pamela is currently an Assistant Professor of Microbiology and Statistics at the University of Illinois at Urbana-Champaign.
Mauricio Santos Vega
Mauricio is from Colombia and earned his Bachelor’s degree in biology from Pontificia Universiad Javeriana in Bogotá. After completeing his B.Sc. he worked as a data scientist for the Colombian government where he analyzed the economical effects of global warming. He obtained a M.Sc in Ecology and Evolutionary Biology from the University of Michigan under the supervision of Prof. Mercedes Pascual. He is broadly interested in understanding the dynamical consequences of the feedback between coupled human-natural systems that are under high environmental variability. Specifically, his research is on the interface between ecology of infectious diseases, urban ecology and public health. He combines statistical and mathematical models to study how economic and environmental factors at various spatio-temporal scales affect the dynamics of vector-borne diseases like malaria in urban landscapes.
Ruby is a graduate in Mathematics and Biology (Ecology & Evolution) at the University of Chicago. She spent part of her undergrad in Woods Hole, MA at the Marine Biological Laboratory modeling microbial bioreactors and bioremediation. She is interested in studying ecological systems at the intersection of human and environmental health, in particular infectious diseases and their response to climate change. Ruby is working on an age-structured malaria model, investigating how the reservoir of infection interacts with seasonal forcing. Ruby enjoys playing ultimate frisbee and exploring the outdoors.