Related papers: Robust and Scalable Models of Microbiome Dynamics
Rapidly assaying the diversity of a bacterial species present in a sample obtained from a hospital patient or an evironmental source has become possible after recent technological advances in DNA sequencing. For several applications it is…
The qualitative study of dynamical systems using bifurcation theory is key to understanding systems from biological clocks and neurons to physical phase transitions. Data generated from such systems can feature complex transients, an…
There has been a growing acknowledgement of the involvement of the gut microbiome - the collection of microbes that reside in our gut - in regulating our mood and behaviour. This phenomenon is referred to as the microbiome-gut-brain axis.…
Epidemic models are invaluable tools to understand and implement strategies to control the spread of infectious diseases, as well as to inform public health policies and resource allocation. However, current modeling approaches have…
In this paper we study a nonlinear reaction-diffusion system which models an infectious disease caused by bacteria such as those for cholera. One of the significant features in this model is that a certain portion of the recovered human…
New technologies for recording the activity of large neural populations during complex behavior provide exciting opportunities for investigating the neural computations that underlie perception, cognition, and decision-making. Nonlinear…
Bacterial resistance to antibiotic treatment is a huge concern: introduction of any new antibiotic is shortly followed by the emergence of resistant bacterial isolates in the clinic. This issue is compounded by a severe lack of new…
A plethora of networks is being collected in a growing number of fields, including disease transmission, international relations, social interactions, and others. As data streams continue to grow, the complexity associated with these highly…
Assessing the synergistic high-order behaviors (HOBs) that emerge from underlying structural mechanisms is crucial to characterize complex systems. This work leverages the combined use of predictability and information measures to detect…
Turing patterns play a fundamental role in morphogenesis and population dynamics, encoding key information about the underlying biological mechanisms. Yet, traditional inverse problems have largely relied on non-biological data such as…
Biological evolution of a population is governed by the fitness landscape, which is a map from genotype to fitness. However, a fitness landscape depends on the organisms environment, and evolution in changing environments is still poorly…
We present a mathematical model based on a system of partial differential equations (PDEs) with cross-diffusion and reaction terms to describe ecological interactions between multiple bacterial species and substrates within microaggregates,…
Dynamic prediction of causal effects under different treatment regimes conditional on an individual's characteristics and longitudinal history is an essential problem in precision medicine. This is challenging in practice because outcomes…
We develop Bayesian nonparametric models for spatially indexed data of mixed type. Our work is motivated by challenges that occur in environmental epidemiology, where the usual presence of several confounding variables that exhibit complex…
Accurate models of clinical actions and their impacts on disease progression are critical for estimating personalized optimal dynamic treatment regimes (DTRs) in medical/health research, especially in managing chronic conditions.…
A system-level framework of complex microbe-microbe and host-microbe chemical cross-talk would help elucidate the role of our gut microbiota in health and disease. Here we report a literature-curated interspecies network of the human gut…
Understanding how antibiotics inhibit bacteria can help to reduce antibiotic use and hence avoid antimicrobial resistance - yet few theoretical models exist for bacterial growth inhibition by a clinically relevant antibiotic treatment…
The intricate interplay between host organisms and their gut microbiota has catalyzed research into the microbiome's role in disease, shedding light on novel aspects of disease pathogenesis. However, the mechanisms through which the…
Scientific studies in the last two decades have established the central role of the microbiome in disease and health. Differential abundance analysis seeks to identify microbial taxa associated with sample groups defined by a factor such as…
We discuss three different aspects of the quantum dynamics of bio-molecular systems and more generally complex networks in the presence of strongly coupled environments. Firstly, we make a case for the systematic study of fundamental…