Related papers: CHERRY: a Computational metHod for accuratE pRedic…
HIV is a retrovirus that attacks the human immune system and can lead to death without proper treatment. In collaboration with the WHO and Wits University, we study how to improve the efficiency of HIV testing with the goal of eventual…
With the advent of high-throughput sequencing (HTS) in molecular biology and medicine, the need for scalable statistical solutions for modeling complex biological systems has become of critical importance. The increasing number of platforms…
Responsible for many complex human diseases including cancers, disrupted or abnormal gene interactions can be identified through their expression changes correlating with the progression of a disease. However, the examination of all…
We present a method that compares the protein interaction networks of two species to detect functionally similar (conserved) protein modules between them. The method is based on an algorithm we developed to identify matching subgraphs…
Physical contact remains difficult to trace in large metropolitan networks, though it is a key vehicle for the transmission of contagious outbreaks. Co-presence encounters during daily transit use provide us with a city-scale time-resolved…
Predicting non-covalent host-guest recognition remains challenging due to the complex interplay of electrostatics, dispersion, and steric effects, and the limited transferability of existing docking approaches to synthetic supramolecular…
Human to human transmissible infectious diseases spread in a population using human interactions as its transmission vector. The early stages of such an outbreak can be modeled by a graph whose edges encode these interactions between…
When designing control strategies for an infectious disease it is critical to identify the key pathways of transmission. Data on infected hosts - when they were born, where they lived and with whom they interacted - can help infer sources…
Accurate insect pest recognition is significant to protect the crop or take the early treatment on the infected yield, and it helps reduce the loss for the agriculture economy. Design an automatic pest recognition system is necessary…
Capturing the structured mixing within a population is key to the reliable projection of infectious disease dynamics and hence informed control. Both heterogeneity in the number of contacts and age-structured mixing have been repeatedly…
The ability to interpret and intervene model decisions is important for the adoption of computer-aided diagnosis methods in clinical workflows. Recent concept-based methods link the model predictions with interpretable concepts and modify…
Microbiome data analyses require statistical tools that can simultaneously decode microbes' reactions to the environment and interactions among microbes. We introduce CARlasso, the first user-friendly open-source and publicly available R…
At most 1-2% of the global virome has been sampled to date. Recent work has shown that predicting which host-virus interactions are possible but undiscovered or unrealized is, fundamentally, a network science problem. Here, we develop a…
A fundamental challenge in microbial ecology is determining whether bacteria compete or cooperate in different environmental conditions. With recent advances in genome-scale metabolic models, we are now capable of simulating interactions…
Cross-protection, which refers to a process whereby artificially inoculating a plant with a mild strain provides protection against a more aggressive isolate of the virus, is known to be an effective tool of disease control in plants. In…
Identifying the infection sources in a network, including the index cases that introduce a contagious disease into a population network, the servers that inject a computer virus into a computer network, or the individuals who started a…
A hub-based colony consists of multiple agents who share a common nest site called the hub. Agents perform tasks away from the hub like foraging for food or gathering information about future nest sites. Modeling hub-based colonies is…
While most studies emphasize on certain aspects of Pathogen-Host Interactions (PHI), such as the preferential attachment of bacteria or virus to its human receptor homolog, studies have attempted to methodically classify interactions among…
Clinical trials are crucial for drug development but are time consuming, expensive, and often burdensome on patients. More importantly, clinical trials face uncertain outcomes due to issues with efficacy, safety, or problems with patient…
While confirming the long held view that viruses do not closely imitate the use of their host's codon catalogue, Esposito and coworkers nevertheless consider it surprising that, despite having the ability to infect the same host, many…