Related papers: Alignment- and reference-free phylogenomics with c…
Genome assembly tools based on the de Bruijn graph framework rely on a parameter k, which represents a trade-off between several competing effects that are difficult to quantify. There is currently a lack of tools that would automatically…
Recent work has proven the existence of extreme inbreeding in a European ancestry sample taken from the contemporary UK population \cite{nature_01}. This result brings our attention again to a math problem related to inbreeding family trees…
Phylogenetic tree reconstruction is traditionally based on multiple sequence alignments (MSAs) and heavily depends on the validity of this information bottleneck. With increasing sequence divergence, the quality of MSAs decays quickly.…
Sequence comparison is a prerequisite to virtually all comparative genomic analyses. It is often realised by sequence alignment techniques, which are computationally expensive. This has led to increased research into alignment-free…
Diffusion models are state-of-the-art generative models, yet their samples often fail to satisfy application objectives such as safety constraints or domain-specific validity. Existing techniques for alignment require gradients, internal…
It has recently been discovered that many biological systems, when represented as graphs, exhibit a scale-free topology. One such system is the set of structural relationships among protein domains. The scale-free nature of this and other…
Each gene has its own evolutionary history which can substantially differ from the evolutionary histories of other genes. For example, some individual genes or operons can be affected by specific horizontal gene transfer and recombination…
We study a character-based phylogeny reconstruction problem when an incomplete set of data is given. More specifically, we consider the situation under the directed perfect phylogeny assumption with binary characters in which for some…
The main challenge in de novo assembly of NGS data is certainly to deal with repeats that are longer than the reads. This is particularly true for RNA- seq data, since coverage information cannot be used to flag repeated sequences, of which…
Binary relations derived from labeled rooted trees play an import role in mathematical biology as formal models of evolutionary relationships. The (symmetrized) Fitch relation formalizes xenology as the pairs of genes separated by at least…
We compute explicitly the automorphism and outer automorphism group of all large-type free-of-infinity Artin groups. Our strategy involves reconstructing the associated Deligne complexes in a purely algebraic manner, i.e. in a way that is…
Enormous volumes of short reads data from next-generation sequencing (NGS) technologies have posed new challenges to the area of genomic sequence comparison. The multiple sequence alignment approach is hardly applicable to NGS data due to…
Horizontal gene transfer inference approaches are usually based on gene sequences: parametric methods search for patterns that deviate from a particular genomic signature, while phylogenetic methods use sequences to reconstruct the gene and…
Disentangled representations can be useful in many downstream tasks, help to make deep learning models more interpretable, and allow for control over features of synthetically generated images that can be useful in training other models…
In this paper, we propose a depth-first search (DFS) algorithm for searching maximum matchings in general graphs. Unlike blossom shrinking algorithms, which store all possible alternative alternating paths in the super-vertices shrunk from…
Despite the success of deep learning for text and image data, tree-based ensemble models are still state-of-the-art for machine learning with heterogeneous tabular data. However, there is a significant need for tabular-specific…
Complex interactions between genes or proteins contribute a substantial part to phenotypic evolution. Here we develop an evolutionarily grounded method for the cross-species analysis of interaction networks by {\em alignment}, which maps…
Motivation: Working with a large number of genomes simultaneously is of great interest in genetic population and comparative genomics research. Bubbles discovery in multi-genomes coloured de bruijn graph for de novo genome assembly is a…
Genetic sequence data of pathogens are increasingly used to investigate transmission dynamics in both endemic diseases and disease outbreaks; such research can aid in development of appropriate interventions and in design of studies to…
In phylogenetics, a central problem is to infer the evolutionary relationships between a set of species $X$; these relationships are often depicted via a phylogenetic tree -- a tree having its leaves univocally labeled by elements of $X$…