Related papers: A phylogenetic approach disentangles interlocus ge…
GC-biased gene conversion (gBGC) is a recombination-associated process that favors the fixation of G/C alleles over A/T alleles. In mammals, gBGC is hypothesized to contribute to variation in GC content, rapidly evolving sequences, and the…
Statistical inference about the speciation process has often been based on the isolation-with-migration (IM) model, especially when the research aim is to learn about the presence or absence of gene flow during divergence. The generalised…
Somatic hypermutations of immunoglobulin (Ig) genes occuring during affinity maturation drive B-cell receptors' ability to evolve strong binding to their antigenic targets. The landscape of these mutations is highly heterogeneous, with…
Differences in the regional substitution patterns in the human genome created patterns of large-scale variation of base composition known as genomic isochores. To gain insight into the origin of the genomic isochores we develop a maximum…
Mutation rate variation across loci is well known to cause difficulties, notably identifiability issues, in the reconstruction of evolutionary trees from molecular sequences. Here we introduce a new approach for estimating general…
Phylogenetics uses alignments of molecular sequence data to learn about evolutionary trees relating species. Along branches, sequence evolution is modelled using a continuous-time Markov process characterised by an instantaneous rate…
Local and global inference methods have been developed to infer structural contacts from multiple sequence alignments of homologous proteins. They rely on correlations in amino-acid usage at contacting sites. Because homologous proteins…
Predicting protein-protein interactions from sequences is an important goal of computational biology. Various sources of information can be used to this end. Starting from the sequences of two interacting protein families, one can use…
Phylogenomics heavily relies on well-curated sequence data sets that consist, for each gene, exclusively of 1:1-orthologous. Paralogs are treated as a dangerous nuisance that has to be detected and removed. We show here that this severe…
In this paper, to unveil interpretable development-specific gene signatures in human PFC, we propose a novel gene selection method, named Interpretable Causality Gene Selection (ICGS), which adopts a Bayesian Network (BN) to represent…
Identity-by-descent (IBD) is a fundamental concept in genetics with many applications. In a common definition, two haplotypes are said to contain an IBD segment if they share a segment that is inherited from a recent shared common ancestor…
Galvanic coupled-intra-body communication (GC-IBC) is an innovative research area contributing to transform personalized medicine by enabling seamless connectivity and communication among implanted devices. To establish a reliable…
Reconstructing evolutionary histories and estimating the rate of evolution from molecular sequence data is of central importance in evolutionary biology and infectious disease research. We introduce a flexible Bayesian phylogenetic…
Repetitive motion tasks are common in robotics, but performance can degrade over time due to environmental changes and robot wear and tear. Iterative learning control (ILC) improves performance by using information from previous iterations…
Lateral gene transfer (LGT) is a common mechanism of non-vertical evolution where genetic material is transferred between two more or less distantly related organisms. It is particularly common in bacteria where it contributes to adaptive…
Obtaining multiple meaningfully diverse, high quality samples from Large Language Models for a fixed prompt remains an open challenge. Current methods for increasing diversity often only operate at the token-level, paraphrasing the same…
A number of studies have suggested using comparisons between DNA sequences of closely related bacterial isolates to estimate the relative rate of recombination to mutation for that bacterial species. We consider such an approach which uses…
In phylogenetic studies, the evolution of molecular sequences is assumed to have taken place along the phylogeny traced by the ancestors of extant species. In the presence of lateral gene transfer (LGT), however, this may not be the case,…
Understanding patterns of selectively neutral genetic variation is essential in order to model deviations from neutrality, caused for example by different forms of selection. Best understood is neutral genetic variation at a single locus,…
Using a weak migration and weak mutation approximation, I study the average waiting time to and the average duration of parapatric speciation. The description of reproductive isolation used is based on the classical Dobzhansky model and its…