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Remote sensing is the process of detecting and monitoring the physical characteristics of an area by measuring its reflected and emitted radiation at a distance. It is being broadly used to monitor ecosystems, mainly for their preservation.…
Phylogenetic networks are generalizations of phylogenetic trees that allow the representation of reticulation events such as horizontal gene transfer or hybridization, and can also represent uncertainty in inference. A subclass of these,…
Phylogenetic inference, grounded in molecular evolution models, is essential for understanding the evolutionary relationships in biological data. Accounting for the uncertainty of phylogenetic tree variables, which include tree topologies…
When estimating a phylogeny from a multiple sequence alignment, researchers often assume the absence of recombination. However, if recombination is present, then tree estimation and all downstream analyses will be impacted, because…
Italian ryegrass is a grass weed commonly found in winter wheat fields that are competitive with winter wheat for moisture and nutrients. Ryegrass can cause substantial reductions in yield and grain quality if not properly controlled with…
The phenotype of any organism on earth is, in large part, the consequence of interplay between numerous gene products encoded in the genome, and such interplay between gene products affects the evolutionary fate of the genome itself through…
A holobiont is made up of a host organism together with its microbiota. In the context of animal breeding, the holobiont can be viewed as the single unit upon which selection operates. Therefore, integrating microbiota data into genomic…
Genomic Selection (GS) uses whole-genome information to predict crop phenotypes and accelerate breeding. Traditional GS methods, however, struggle with prediction accuracy for complex traits and large datasets. We propose DPCformer, a deep…
Genotype-to-Phenotype (G2P) prediction plays a pivotal role in crop breeding, enabling the identification of superior genotypes based on genomic data. Rice (Oryza sativa), one of the most important staple crops, faces challenges in…
Bayesian phylogenetics is vital for understanding evolutionary dynamics, and requires accurate and efficient approximation of posterior distributions over trees. In this work, we develop a variational Bayesian approach for ultrametric…
Adaptation of bacteria occurs predominantly via horizontal gene transfer (HGT). While it is widely recognized that horizontal acquisitions frequently encompass multiple genes, it is unclear what the size distribution of successfully…
Genome rearrangement distances are an established method in genome comparison. Works in this area may include various rearrangement operations representing large-scale mutations, gene orientation information, the number of nucleotides in…
Nowadays it is very important to maintain a high level security to ensure safe and trusted communication of information between various organizations. But secured data communication over internet and any other network is always under threat…
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…
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…
Detecting the interactions of genetic compounds like genes, SNPs, proteins, metabolites, etc. can potentially unravel the mechanisms behind complex traits and common genetic disorders. Several methods have been taken into consideration for…
Development of either drought-resistant or drought-tolerant varieties in rice (Oryza sativa L.), especially for high yield in the context of climate change, is a crucial task across the world. The need for high yielding rice varieties is a…
Unraveling the co-expression of genes across studies enhances the understanding of cellular processes. Inferring gene co-expression networks from transcriptome data presents many challenges, including spurious gene correlations, sample…
Populations of widely distributed species often encounter and adapt to specific environmental conditions. However, comprehensive characterization of the genetic basis of adaptation is demanding, requiring genome-wide genotype data, multiple…
Gait recognition with radio frequency (RF) signals enables many potential applications requiring accurate identification. However, current systems require individuals to be within a line-of-sight (LOS) environment and struggle with low…