Related papers: Graph Based Analysis for Gene Segment Organization…
Deciding whether a collection of unrooted trees is compatible is a fundamental problem in phylogenetics. Two different graph-theoretic characterizations of tree compatibility have recently been proposed. In one of these, tree compatibility…
We formulate conditions on a set of log-concave sequences, under which any linear combination of those sequences is log-concave, and further, of conditions under which linear combinations of log-concave sequences that have been transformed…
Shape graphs are complex geometrical structures commonly found in biological and anatomical systems. A shape graph is a collection of nodes, some connected by curvilinear edges with arbitrary shapes. Their high complexity stems from the…
Graph embedding algorithms are used to efficiently represent (encode) a graph in a low-dimensional continuous vector space that preserves the most important properties of the graph. One aspect that is often overlooked is whether the graph…
DNA based nanostructures built on a long single stranded DNA scaffold, known as DNA origamis, offer the possibility to organize various molecules at the nanometer scale in one pot experiments. The folding of the scaffold is guaranteed by…
Real data collected from different applications that have additional topological structures and connection information are amenable to be represented as a weighted graph. Considering the node labeling problem, Graph Neural Networks (GNNs)…
Linkage maps are used to identify the location of genes responsible for traits and diseases. New sequencing techniques have created opportunities to substantially increase the density of genetic markers. Such revolutionary advances in…
Structural changes in a network representation of a system (e.g.,different experimental conditions, time evolution), can provide insight on its organization, function and on how it responds to external perturbations. The deeper…
Background: Duplication of genes is important for evolution of molecular networks. Many authors have therefore considered gene duplication as a driving force in shaping the topology of molecular networks. In particular it has been noted…
We study DNA self-assembly and DNA computation using a coarse-grained DNA model within the directional dynamic bonding framework {[}C. Svaneborg, Comp. Phys. Comm. 183, 1793 (2012){]}. In our model, a single nucleotide or domain is…
The main statistical distributions applicable to the analysis of genome architecture and genome tracks are briefly discussed and critically assessed. Although the observed features in distributions of element lengths can be equally well…
We present an automated method of identifying communities of functionally related genes from the biomedical literature. These communities encapsulate human gene and protein interactions and identify groups of genes that are complementary in…
The 3D organisation of the genome in interphase cells is not a randomly folded polymer. Rather, experiments show that chromosomes arrange into a network of 3D compartments that correlate with biological processes, such as transcription,…
We develop new methods based on graph motifs for graph clustering, allowing more efficient detection of communities within networks. We focus on triangles within graphs, but our techniques extend to other clique motifs as well. Our…
Biological systems are driven by intricate interactions among the complex array of molecules that comprise the cell. Many methods have been developed to reconstruct network models of those interactions. These methods often draw on large…
The 3D folding of a mammalian gene can be studied by a polymer model, where the chromatin fibre is represented by a semiflexible polymer which interacts with multivalent proteins, representing complexes of DNA-binding transcription factors…
Graph signals are functions of the underlying graph. When the edge-weight between a pair of nodes is high, the corresponding signals generally have a higher correlation. As a result, the signals can be represented in terms of a graph-based…
Recently, Marcus et al. (Bioinformatics 2014) proposed to use a compressed de Bruijn graph to describe the relationship between the genomes of many individuals/strains of the same or closely related species. They devised an $O(n \log g)$…
Gene trees record the combination of gene level events, such as duplication, transfer and loss, and species level events, such as speciation and extinction. Gene tree-species tree reconciliation methods model these processes by drawing gene…
Most genes are part of larger families of evolutionary related genes. The history of gene families typically involves duplications and losses of genes as well as horizontal transfers into other organisms. The reconstruction of detailed gene…