Related papers: A network approach to analyzing highly recombinant…
The problem of community detection in networks is usually formulated as finding a single partition of the network into some "correct" number of communities. We argue that it is more interpretable and in some regimes more accurate to…
Background: Elucidating gene regulatory networks is crucial for understanding normal cell physiology and complex pathologic phenotypes. Existing computational methods for the genome-wide ``reverse engineering'' of such networks have been…
For a phylogenetic tree, the phylogenetic diversity of a set A of taxa is the total weight of edges on paths to A. Finding small sets of maximal diversity is crucial for conservation planning, as it indicates where limited resources can be…
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 latest WHO report showed that the number of malaria cases climbed to 219 million last year, two million higher than last year. The global efforts to fight malaria have hit a plateau and the most significant underlying reason is…
Human associated microbial communities exert tremendous influence over human health and disease. With modern metagenomic sequencing methods it is possible to follow the relative abundance of microbes in a community over time. These…
Integrative network modeling of data arising from multiple genomic platforms provides insight into the holistic picture of the interactive system, as well as the flow of information across many disease domains including cancer. The basic…
In microbiome studies, it is often of great interest to identify clusters or partitions of microbiome profiles within a study population and to characterize the distinctive attributes of each resulting microbial community. While raw counts…
The Influenza virus can be considered as one of the most severe viruses that can infect multiple species with often fatal consequences to the hosts. The Hemagglutinin (HA) gene of the virus can be a target for antiviral drug development…
Network Phylogenetic Diversity (Network-PD) is a measure for the diversity of a set of species based on a rooted phylogenetic network (with branch lengths and inheritance probabilities on the reticulation edges) describing the evolution of…
Feedforward multilayer networks trained by supervised learning have recently demonstrated state of the art performance on image labeling problems such as boundary prediction and scene parsing. As even very low error rates can limit…
CoVariance Neural Networks (VNNs) perform graph convolutions on the empirical covariance matrix of signals defined over finite-dimensional Hilbert spaces, motivated by robustness and transferability properties. Yet, little is known about…
Inferring parameters related to the aggregation pattern of parasites and to their dispersal propensity is important for predicting their ecological consequences and evolutionary potential. Nonetheless, it is notoriously difficult to infer…
Many models of within-host malaria infection dynamics have been formulated since the pioneering work of Anderson et al. in 1989. Biologically, the goal of these models is to understand what governs the severity of infections, the patterns…
Characterization of host responses associated with severe malaria through an integrative approach is necessary to understand the dynamics of a \textit{Plasmodium cynomolgi} infection. In this study, we conducted temporal immune profiling,…
Lightweight deep learning approaches for malaria detection have gained attention for their potential to enhance diagnostics in resource constrained environments. For our study, we selected SqueezeNet1.1 as it is one of the most popular…
Phylogenetic networks provide a means of describing the evolutionary history of sets of species believed to have undergone hybridization or gene flow during their evolution. The mutation process for a set of such species can be modeled as a…
Motivation: Gene regulatory interactions are of fundamental importance to various biological functions and processes. However, only a few previous computational studies have claimed success in revealing genome-wide regulatory landscapes…
Malaria is a deadly disease which claims the lives of hundreds of thousands of people every year. Computational methods have been proven to be useful in the medical industry by providing effective means of classification of diagnostic…
Pedigrees are directed acyclic graphs that represent ancestral relationships between individuals in a population. Based on a schematic recombination process, we describe two simple Markov models for sequences evolving on pedigrees - Model R…