Related papers: Graph-based variant discovery reveals novel dynami…
Graph-based machine learning methods are useful tools in the identification and prediction of variation in genetic data. In particular, the comprehension of phenotypic effects at the cellular level is an accelerating research area in…
Feature models are widely used to capture the configuration space of software systems. Although automated reasoning has been studied for detecting problematic features and supporting configuration tasks, significantly less attention has…
The study of time-varying (dynamic) networks (graphs) is of fundamental importance for computer network analytics. Several methods have been proposed to detect the effect of significant structural changes in a time series of graphs. The…
Microbiome-based stratification of healthy individuals into compositional categories, referred to as "community types", holds promise for drastically improving personalized medicine. Despite this potential, the existence of community types…
The human microbiome is a complex ecological system, and describing its structure and function under different environmental conditions is important from both basic scientific and medical perspectives. Viewed through a biostatistical lens,…
We consider multivariate two-sample tests of means, where the location shift between the two populations is expected to be related to a known graph structure. An important application of such tests is the detection of differentially…
Methods that generate networks sharing a given degree distribution and global clustering can induce changes in structural properties other than that controlled for. Diversity in structural properties, in turn, can affect the outcomes of…
In biological experiments researchers often have information in the form of a graph that supplements observed numerical data. Incorporating the knowledge contained in these graphs into an analysis of the numerical data is an important and…
There is a growing awareness of the important roles that microbial communities play in complex biological processes. Modern investigation of these often uses next generation sequencing of metagenomic samples to determine community…
The fractal nature of graphs has traditionally been investigated by using the nodes of networks as the basic units. Here, instead, we propose to concentrate on the graph edges, and introduce a practical and computationally not demanding…
Two species with similar resource requirements respond in a characteristic way to variations in their habitat -- their abundances rise and fall in concert. We use this idea to learn how bacterial populations in the microbiota respond to…
Motivation: The gene content regulates the biology of an organism. It varies between species and between individuals of the same species. Although tools have been developed to identify gene content changes in bacterial genomes, none is…
Microbes are everywhere, including in and on our bodies, and have been shown to play key roles in a variety of prevalent human diseases. Consequently, there has been intense interest in the design of bacteriotherapies or "bugs as drugs,"…
The increasing prevalence of graph-structured data across various domains has intensified greater interest in graph classification tasks. While numerous sophisticated graph learning methods have emerged, their complexity often hinders…
In the past decade, cities have experienced rapid growth, expansion, and changes in their community structure. Many aspects of critical urban infrastructure are closely coupled with the human communities that they serve. Urban communities…
Structural variants compose the majority of human genetic variation, but are difficult to assess using current genomic sequencing technologies. Optical mapping technologies, which measure the size of chromosomal fragments between labeled…
Pangenome variation graphs (PVGs) allow for the representation of genetic diversity in a more nuanced way than traditional reference-based approaches. Here we focus on how PVGs are a powerful tool for studying genetic variation in viruses,…
Graphs are widely used in various fields of computer science. They have also found application in unrelated areas, leading to a diverse range of problems. These problems can be modeled as relationships between entities in various contexts,…
Microbial communities play important roles in the function and maintenance of various biosystems, ranging from human body to the environment. Current methods for analysis of microbial communities are typically based on taxonomic…
An important task in microbiome studies is to test the existence of and give characterization to differences in the microbiome composition across groups of samples. Important challenges of this problem include the large within-group…