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RNA design shows growing applications in synthetic biology and therapeutics, driven by the crucial role of RNA in various biological processes. A fundamental challenge is to find functional RNA sequences that satisfy given structural…
Longitudinal gene expression profiles of patients are collected in some clinical studies to monitor disease progression and understand disease etiology. The identification of gene sets that have coordinated changes with relevant clinical…
A basic problem in metagenomics is to assign a sequenced read to the correct species in the reference collection. In typical applications in genomic epidemiology and viral metagenomics the reference collection consists of set of species…
Evolution is a process that is influenced by various environmental factors, e.g. the interactions between different species, genes, and biogeographical properties. Hence, it is interesting to study the combined evolutionary history of…
The first step toward Seed Phenotyping i.e. the comprehensive assessment of complex seed traits such as growth, development, tolerance, resistance, ecology, yield, and the measurement of pa-rameters that form more complex traits is the…
We attempted to test biogeographic hypotheses proposed for the evolution of tropical faunas using mitochondrial DNA sequences of selected African mammalian taxa (Insectivora, Rodentia and Primates). 1/ we constructed a molecular phylogeny…
Horizontal gene transfer is an important contributor to evolution. According to Walter M.\ Fitch, two genes are xenologs if they are separated by at least one HGT. More formally, the directed Fitch graph has a set of genes is its vertices,…
Since the advent of modern bioinformatics, the challenging, multifaceted problem of reconstructing phylogenetic history from biological sequences has hatched perennial statistical and algorithmic innovation. Studies of the phylogenetic…
Gait recognition aims to identify a person at a distance, serving as a promising solution for long-distance and less-cooperation pedestrian recognition. Recently, significant advancements in gait recognition have achieved inspiring success…
Complex spatial and temporal patterns of gene expression underlie embryo differentiation, yet methods do not yet exist for the efficient genome-wide determination of spatial expression patterns during development. In situ imaging of…
Variations in complex traits are influenced by multiple genetic variants, environmental risk factors, and their interactions. Though substantial progress has been made in identifying single genetic variants associated with complex traits,…
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…
Phylogenetic networks extend phylogenetic trees to model non-vertical inheritance, by which a lineage inherits material from multiple parents. The computational complexity of estimating phylogenetic networks from genome-wide data with…
Deep generative models open new avenues for simulating realistic genomic data while preserving privacy and addressing data accessibility constraints. While previous studies have primarily focused on generating gene expression or haplotype…
Knowledge of the exact distribution of meiotic crossovers (COs) and gene conversions (GCs) is essential for understanding many aspects of population genetics and evolution, from haplotype structure and long-distance genetic linkage to the…
The haloarchaea are aerobic, heterotrophic, photophosphorylating prokaryotes, whose supposed closest relatives and ancestors, the methanogens, are CO2-reducing, anaerobic chemolithotrophs. Using two available haloarchaeal genomes we firstly…
We present a foundation modeling framework that leverages deep learning to uncover latent genetic signatures across the hematopoietic hierarchy. Our approach trains a fully connected autoencoder on multipotent progenitor cells, reducing…
Metagenomics provides a powerful new tool set for investigating evolutionary interactions with the environment. However, an absence of model-based statistical methods means that researchers are often not able to make full use of this…
Inferring the structure of gene regulatory networks (GRN) from gene expression data has many applications, from the elucidation of complex biological processes to the identification of potential drug targets. It is however a notoriously…
In recent years, cross-spectral iris recognition has emerged as a promising biometric approach to establish the identity of individuals. However, matching iris images acquired at different spectral bands (i.e., matching a visible (VIS) iris…