Related papers: Extending the Overlap Graph for Gene Assembly in C…
Cellular phenotypes are determined by the dynamical activity of networks of co-regulated genes. Elucidating such networks is crucial for the understanding of normal cell physiology as well as for the dissection of complex pathologic…
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…
Motivated by DNA storage in living organisms, and by known biological mutation processes, we study the reverse-complement string-duplication system. We fully classify the conditions under which the system has full expressiveness, for all…
Gene tree/species tree reconciliation is a recent decisive progress in phylo-genetic methods, accounting for the possible differences between gene histories and species histories. Reconciliation consists in explaining these differences by…
Large scale databases are available that contain homologous gene families constructed from hundreds of complete genome sequences from across the three domains of Life. Here we discuss approches of increasing complexity aimed at extracting…
Gene set analysis, a popular approach for analysing high-throughput gene expression data, aims to identify sets of genes that show enriched expression patterns between two conditions. In addition to the multitude of methods available for…
Maximal clique enumeration (MCE) is a fundamental problem in graph theory and is used in many applications, such as social network analysis, bioinformatics, intelligent agent systems, cyber security, etc. Most existing MCE algorithms focus…
The supertree problem asking for a tree displaying a set of consistent input trees has been largely considered for the reconstruction of species trees. Here, we rather explore this framework for the sake of reconstructing a gene tree from a…
For two strings u, v over some alphabet A, we investigate the problem of embedding u into w as a subsequence under the presence of generalised gap constraints. A generalised gap constraint is a triple (i, j, C_{i, j}), where 1 <= i < j <=…
We study the challenges of applying deep learning to gene expression data. We find experimentally that there exists non-linear signal in the data, however is it not discovered automatically given the noise and low numbers of samples used in…
Gene interaction graphs aim to capture various relationships between genes and represent decades of biology research. When trying to make predictions from genomic data, those graphs could be used to overcome the curse of dimensionality by…
String diagrams provide an intuitive language for expressing networks of interacting processes graphically. A discrete representation of string diagrams, called string graphs, allows for mechanised equational reasoning by double-pushout…
Galled trees are widely studied as a recombination model in population genetics. This class of phylogenetic networks is generalized into galled networks by relaxing a structural condition. In this work, a linear recurrence formula is given…
Verifying safety and liveness over array systems is a highly challenging problem. Array systems naturally capture parameterized systems such as distributed protocols with an unbounded number of processes. Such distributed protocols often…
A statistical network model with overlapping communities can be generated as a superposition of mutually independent random graphs of varying size. The model is parameterized by the number of nodes, the number of communities, and the joint…
Many compilers, synthesizers, and theorem provers rely on rewrite rules to simplify expressions or prove equivalences. Developing rewrite rules can be difficult: rules may be subtly incorrect, profitable rules are easy to miss, and rulesets…
We introduce a notion of genus range as a set of values of genera over all surfaces into which a graph is embedded cellularly, and we study the genus ranges of a special family of four-regular graphs with rigid vertices that has been used…
The majority of the human genome consists of repeated sequences. An important type of repeated sequences common in the human genome are tandem repeats, where identical copies appear next to each other. For example, in the sequence…
Graph Neural Networks are powerful models for learning from graph-structured data, yet their effectiveness is often limited by two critical challenges: over-squashing, where information from distant nodes is excessively compressed, and…
Graph Neural Networks are powerful models for learning from graph-structured data, yet their effectiveness is often limited by two critical challenges: over-squashing, where information from distant nodes is excessively compressed, and…