相关论文: Combinatorial Topological Models for Phylogenetic …

Phylogenetic networks are notoriously difficult to reconstruct. Here we suggest that it can be useful to view unknown genetic distance along edges in phylogenetic networks as analogous to unknown resistance in electric circuits. This…

Disease-gene prediction (DGP) refers to the computational challenge of predicting associations between genes and diseases. Effective solutions to the DGP problem have the potential to accelerate the therapeutic development pipeline at early…

Parameter-efficient fine-tuning techniques such as low-rank adaptation (LoRA) enable large language models (LLMs) to adapt to downstream tasks efficiently. Federated learning (FL) further facilitates this process by enabling collaborative…

Tanglegrams are special graphs that consist of a pair of rooted binary trees with the same number of leaves, and a perfect matching between the two leaf-sets. These objects are of use in phylogenetics and are represented with straightline…

Dendrograms are a way to represent evolutionary relationships between organisms. Nowadays, these are inferred based on the comparison of genes or protein sequences by taking into account their differences and similarities. The genetic…

Research shows that gene duplication followed by either repurposing or removal of duplicated genes is an important contributor to evolution of gene and protein interaction networks. We aim to identify which characteristics of a network can…

A \emph{binary tanglegram} is a drawing of a pair of rooted binary trees whose leaf sets are in one-to-one correspondence; matching leaves are connected by inter-tree edges. For applications, for example, in phylogenetics, it is essential…

Binets and trinets are phylogenetic networks with two and three leaves, respectively. Here we consider the problem of deciding if there exists a binary level-1 phylogenetic network displaying a given set $\mathcal{T}$ of binary binets or…

In evolutionary biology, the speciation history of living organisms is represented graphically by a phylogeny, that is, a rooted tree whose leaves correspond to current species and branchings indicate past speciation events. Phylogenies are…

Here we show that deciding whether two rooted binary phylogenetic trees on the same set of taxa permit a cherry-picking sequence, a special type of elimination order on the taxa, is NP-complete. This improves on an earlier result which…

Normal networks are an important class of phylogenetic networks that have compelling mathematical properties which align with intuition about inference from genetic data. While tools enabling widespread use of phylogenetic networks in the…

Near-duplicate images are often generated when applying repeated photometric and geometric transformations that produce imperceptible variants of the original image. Consequently, a deluge of near-duplicates can be circulated online posing…

Multiplex networks are collections of networks with identical nodes but distinct layers of edges. They are genuine representations for a large variety of real systems whose elements interact in multiple fashions or flavors. However,…

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…

We introduce a biologically natural, mathematically tractable model of random phylogenetic network to describe evolution in the presence of hybridization. One of the features of this model is that the hybridization rate of the lineages…

Combining a set of phylogenetic trees into a single phylogenetic network that explains all of them is a fundamental challenge in evolutionary studies. Existing methods are computationally expensive and can either handle only small numbers…

Collapse Lineage Tree (CLTree) is a software tool that annotates, roots, and evaluates phylogenetic trees by using lineages. A recursive algorithm was designed to annotate the branches by the common taxonomic lineage of its descendants in a…

The inference of new information on the relatedness of species by phylogenetic trees based on DNA data is one of the main challenges of modern biology. But despite all technological advances, DNA sequencing is still a time-consuming and…

Phylogenetic networks are necessary to represent the tree of life expanded by edges to represent events such as horizontal gene transfers, hybridizations or gene flow. Not all species follow the paradigm of vertical inheritance of their…

The recent advances in sequencing technologies enables the assembly of individual genomes to the reference quality. How to integrate multiple genomes from the same species and to make the integrated representation accessible to biologists…