A5063076646- Malaria Research and Control
- Evolution and Genetic Dynamics
- COVID-19 epidemiological studies
- Influenza Virus Research Studies
- Mosquito-borne diseases and control
- Species Distribution and Climate Change
- Statistical Methods in Clinical Trials
- Scientific Computing and Data Management
- Assisted Reproductive Technology and Twin Pregnancy
- Biomedical Text Mining and Ontologies
- Cervical Cancer and HPV Research
- Bayesian Methods and Mixture Models
- Statistical Methods and Bayesian Inference
- COVID-19 Pandemic Impacts
- Health Systems, Economic Evaluations, Quality of Life
- Sensory Analysis and Statistical Methods
- Data-Driven Disease Surveillance
- Advanced Causal Inference Techniques
- Pneumonia and Respiratory Infections
- Hepatitis B Virus Studies
- vaccines and immunoinformatics approaches
- stochastic dynamics and bifurcation
- Gene Regulatory Network Analysis
- T-cell and B-cell Immunology
- Animal Ecology and Behavior Studies
University of Chicago
2015-2020
Icahn School of Medicine at Mount Sinai
2018-2019
University of Michigan
2011-2014
Michigan United
2011
Estimation of the effective reproductive number Rt is important for detecting changes in disease transmission over time. During Coronavirus Disease 2019 (COVID-19) pandemic, policy makers and public health officials are using to assess effectiveness interventions inform policy. However, estimation from available data presents several challenges, with critical implications interpretation course pandemic. The purpose this document summarize these illustrate them examples synthetic data, and,...
Abstract Estimation of the effective reproductive number, R t , is important for detecting changes in disease transmission over time. During COVID-19 pandemic, policymakers and public health officials are using to assess effectiveness interventions inform policy. However, estimation from available data presents several challenges, with critical implications interpretation course pandemic. The purpose this document summarize these illustrate them examples synthetic data, and, where possible,...
Food webs, networks of feeding relationships in an ecosystem, provide fundamental insights into mechanisms that determine ecosystem stability and persistence. A standard approach food-web analysis, network analysis general, has been to identify compartments, or modules, defined by many links within compartments few between them. This can large habitat boundaries the but may fail other important structures. Empirical analyses food webs have further limited low-resolution data for primary...
Significance Human papillomavirus (HPV) is the most common sexually transmitted infection. Understanding factors underlying prevalence and diversity of over 200 HPV types necessary to predict effects multivalent vaccines. We investigate transmission dynamics by fitting mechanistic models data from unvaccinated men. find that infection risk in a susceptible population is, on average, low concentrated high-risk individuals that, rather than inducing protective immunity, strongly increases...
Infectious diseases are notorious for their complex dynamics, which make it difficult to fit models test hypotheses. Methods based on state-space reconstruction have been proposed infer causal interactions in noisy, nonlinear dynamical systems. These "model-free" methods collectively known as convergent cross-mapping (CCM). Although CCM has theoretical support, natural systems routinely violate its assumptions. To identify the practical limits of inference under CCM, we simulated dynamics...
Pathogens compete for hosts through patterns of cross-protection conferred by immune responses to antigens. In Plasmodium falciparum malaria, the var multigene family encoding major blood-stage antigen PfEMP1 has evolved enormous genetic diversity ectopic recombination and mutation. With 50-60 genes per genome, it is unclear whether selection can act as a dominant force in structuring repertoires local populations. The combinatorial complexity system remains beyond reach existing strain...
Pathogens vary in their antigenic complexity. While some pathogens such as measles present a few relatively invariant targets to the immune system, others malaria display considerable diversity. How response copes presence of multiple antigens, and whether trade-off exists between breadth efficacy antibody (Ab)-mediated responses, are unsolved problems. We theoretical model affinity maturation B-cell receptors (BCRs) during primary infection examine how variation number accessible sites...
It is a truism that antimicrobial drugs select for resistance, but explaining pathogen- and population-specific variation in patterns of resistance remains an open problem. Like other common commensals, Streptococcus pneumoniae has demonstrated persistent coexistence drug-sensitive drug-resistant strains. Theoretically, this outcome unlikely. We modelled the dynamics competing strains S. to investigate impact transmission treatment-induced selective pressures on probability stable...
Recent advances in molecular biology, sensors, and digital medicine have led to an explosion of products services for high-resolution monitoring individual health. The N-of-1 study has emerged as important methodological tool harnessing these new data sources, enabling researchers compare the effectiveness health interventions at level a single individual.N-of-1 studies are susceptible several design flaws. We developed model that generates realistic enable optimize designs advance.Our...
Significance It is recognized that the risk of malaria in dry areas increased proximity irrigation infrastructure. Although historical evidence shows eventually risks subside on road to greater prosperity and food security, how this comes about remains poorly understood. We studied changes land use a large project semidesert region northwest India. The transition phase we describe, characterized by elevated despite raised control efforts, has already lasted for over decade. protracted nature...
The primary target of the human immune response to malaria parasite Plasmodium falciparum, P. falciparum erythrocyte membrane protein 1 (PfEMP1), is encoded by members hyper-diverse var gene family. exhibits antigenic variation via mutually exclusive expression (switching) ~60 genes within its genome. It thought that different variants exhibit host endothelial binding preferences in turn result manifestations disease. Var sequences comprise ancient sequence fragments, termed homology blocks...
Background: Influenza A/H3N2 has been circulating in humans since 1968, causing considerable morbidity and mortality. Although H3N2 incidence is highly seasonal, how such seasonality contributes to global phylogeographic migration dynamics not yet established. Results: Incorporating seasonally varying rates improves the modeling of migration. In our model, windows increased immigration map seasonal timing epidemic spread, while emigration decline. Seasonal patterns also correlate with...
Scholarly publishing has embraced electronic distribution in many respects, but the tools available through Internet and other advancing technologies have profound implications for scholarly communication beyond dissemination. We argue that to best serve science, process of must embrace these advances evolve. Here, we consider current state Ecology Evolutionary Biology (EEB) propose directions this evolution potential change. identify four pillars future scientific communication: (1) an...
With the rise of electronic publishing and inherent paradigm shifts for so many other scientific endeavours, it is time to consider a change in practices scholarly publication Ecology Evolutionary Biology. To facilitate speed quality science, future communication will rest on four pillars - an ecosystem products, immediate open access, peer review, full recognition participating process. These enable us build better tools discovery new relevant work individual scientists, one greatest...
A challenge in studying diverse multi-copy gene families is deciphering distinct functional types within immense sequence variation. Functional changes can some cases be tracked through the evolutionary history of a family; however phylogenetic approaches are not possible where diversify primarily by recombination. We take network theoretical approach to functionally classify highly recombining var antigenic family malaria parasite Plasmodium falciparum. sample DBLα from local population...
Abstract The high prevalence of human papillomavirus (HPV), the most common sexually transmitted infection, arises from coexistence over 200 genetically distinct types. Accurately predicting impact vaccines that target multiple types requires understanding factors determine HPV diversity. diversity many pathogens is driven by type-specific or “homologous” immunity, which promotes spread variants to hosts have little immunity. To test for homologous immunity and identify mechanisms...
With the rise of electronic publishing and inherent paradigm shifts for so many other scientific endeavours, it is time to consider a change in practices scholarly publication Ecology Evolutionary Biology. To facilitate speed quality science, future communication will rest on four pillars - an ecosystem products, immediate open access, peer review, full recognition participating process. These enable us build better tools discovery new relevant work individual scientists, one greatest...
We describe an approach for identifying groups of dynamically similar locations in spatial time-series data based on a simple Markov transition model. give maximum-likelihood, empirical Bayes, and fully Bayesian formulations the model, exhaustive, greedy, MCMC-based inference methods. The has been employed successfully several studies to reveal meaningful relationships between environmental patterns disease dynamics.
Abstract It is a truism that antimicrobial drugs select for resistance, but explaining pathogen- and population-specific variation in patterns of resistance remains an open problem. Like other common commensals, Streptococcus pneumoniae has demonstrated persistent coexistence drug-sensitive drug-resistant strains. Theoretically, this outcome unlikely. We modeled the dynamics competing strains S. to investigate impact transmission treatment-induced selective pressures on probability stable...
Abstract Pathogens compete for hosts through patterns of cross-protection conferred by immune responses to antigens. In Plasmodium falciparum malaria, the var multigene family encoding major blood-stage antigen Pf EMP1 has evolved enormous genetic diversity ectopic recombination and mutation. With 50-60 genes per genome, it is unclear whether selection can act as a dominant force in structuring repertoires local populations. The combinatorial complexity system remains beyond reach existing...