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The detection of communities is an important tool used to analyze the social graph of mobile phone users. Within each community, customers are susceptible of attracting new ones, retaining old ones and/or accepting new products or services…
Recent attacks of various viruses with having deep and extensive impact at a global scale has warranted that microbiome be studied extensively and in a robust analytic framework. Microbiome typically refers to the collective genomes of such…
Large graphs can be found in a wide array of scientific fields ranging from sociology and biology to scientometrics and computer science. Their analysis is by no means a trivial task due to their sheer size and complex structure. Such…
DNA rearrangement processes recombine gene segments that are organized on the chromosome in a variety of ways. The segments can overlap, interleave or one may be a subsegment of another. We use directed graphs to represent segment…
Machine learning methods can detect complex relationships between variables, but usually do not exploit domain knowledge. This is a limitation because in many scientific disciplines, such as systems biology, domain knowledge is available in…
Malware lineage studies the evolutionary relationships among malware and has important applications for malware analysis. A persistent limitation of prior malware lineage approaches is to consider every input sample a separate malware…
The phenotype of any organism on earth is, in large part, the consequence of interplay between numerous gene products encoded in the genome, and such interplay between gene products affects the evolutionary fate of the genome itself through…
Microbial networks, representing microbes as nodes and their interactions as edges, are crucial for understanding community dynamics in various environments. Analyzing microbiome networks is crucial for identifying keystone taxa that play…
The description of large temporal graphs requires effective methods giving an appropriate mesoscopic partition. Many approaches exist today to detect communities in static graphs. However, many networks are intrinsically dynamical, and need…
Ongoing advances in microbiome profiling have allowed unprecedented insights into the molecular activities of microbial communities. This has fueled a strong scientific interest in understanding the critical role the microbiome plays in…
Comorbidity carries significant implications for disease understanding and management. The genetic causes for comorbidity often trace back to mutations occurred either in the same gene associated with two diseases or in different genes…
The CRISPR (clustered regularly interspaced short palindromic repeats) mechanism allows bacteria to adaptively defend against phages by acquiring short genomic sequences (spacers) that target specific sequences in the viral genome. We…
Time series of graphs are increasingly prevalent in modern data and pose unique challenges to visual exploration and pattern extraction. This paper describes the development and application of matrix factorizations for exploration and…
A fundamental goal of microbial ecology is to understand what determines the diversity, stability, and structure of microbial ecosystems. The microbial context poses special conceptual challenges because of the strong mutual influences…
Stochastic phenotype switching has been suggested to play a beneficial role in microbial populations by leading to the division of labour among cells, or ensuring that at least some of the population survives an unexpected change in…
The intestinal microbiota plays important roles in digestion and resistance against entero-pathogens. As with other ecosystems, its species composition is resilient against small disturbances but strong perturbations such as antibiotics can…
Antibiotic resistance is a major threat to global health. It emerges in multispecies microbial communities under antibiotic exposure. This makes antibiotic spectrum -- a drug's distribution of effects across species -- a potential key…
Heterogeneous systems of active matter exhibit a range of complex emergent dynamical patterns. In particular, it is difficult to predict the properties of the mixed system based on its constituents. These considerations are particularly…
The rise of antimicrobial drug resistance is an imminent threat to global health that has warranted, and duly received, considerable attention within the medical, microbiological and modelling communities. Outbreaks of drug-resistant…
As more and more network-structured data sets are available, the statistical analysis of valued graphs has become common place. Looking for a latent structure is one of the many strategies used to better understand the behavior of a…