A5013030971- Genomics and Phylogenetic Studies
- Machine Learning in Bioinformatics
- Plant Molecular Biology Research
- Hepatitis B Virus Studies
- Plant Stress Responses and Tolerance
- MicroRNA in disease regulation
- Influenza Virus Research Studies
- Chromosomal and Genetic Variations
- Bacteriophages and microbial interactions
- Evolution and Paleontology Studies
- Hepatitis C virus research
- RNA modifications and cancer
- Bayesian Methods and Mixture Models
- Wheat and Barley Genetics and Pathology
- Genome Rearrangement Algorithms
- Plant-Microbe Interactions and Immunity
- Genetic diversity and population structure
- Plant Disease Resistance and Genetics
- Crop Yield and Soil Fertility
- Genetics, Bioinformatics, and Biomedical Research
- Algorithms and Data Compression
- Plant Genetic and Mutation Studies
- Plant nutrient uptake and metabolism
- Plant Reproductive Biology
- Cancer-related molecular mechanisms research
Université du Québec à Montréal
2015-2023
Advances in cloning and sequencing technology are yielding a massive number of viral genomes. The classification annotation these genomes constitute important assets the discovery genomic variability, taxonomic characteristics disease mechanisms. Existing methods often designed for specific well-studied family viruses. Thus, comparative studies could benefit from more generic, fast accurate tools classifying typing newly sequenced strains diverse virus families.Here, we introduce platform,...
Wheat is a major staple crop with broad adaptability to wide range of environmental conditions. This involves several stress and developmentally responsive genes, in which microRNAs (miRNAs) have emerged as important regulatory factors. However, the currently used approaches identify miRNAs this polyploid complex system focus on conserved highly expressed avoiding regularly those that are often lineage-specific, condition-specific, or appeared recently evolution. In addition, many biological...
The classification of pathogens in emerging and re-emerging viruses represents major interests taxonomic studies, functional genomics, host–pathogen interplay, prevention, disease treatments. It consists assigning a given sequence to its related group known sequences sharing similar characteristics traits. challenges such could be associated with several virus properties including recombination, mutation rate, multiplicity motifs, diversity. In domains as pathogen monitoring surveillance, it...
MicroRNAs (miRNAs) are emerging as important post-transcriptional regulators that may regulate key genes responsible for agronomic traits such grain yield and stress tolerance. Several studies identified species clades specific miRNA families associated with plant regulated genes. Here, we propose a novel resource provides data related to the expression of abiotic responsive miRNAs in wheat, one most staple food crops. This database allows query small RNA libraries, including silico...
Viral sequence classification is an important task in pathogen detection, epidemiological surveys and evolutionary studies. Statistical learning methods are widely used to classify identify viral sequences samples from environments. These face several challenges associated with the nature properties of genomes such as recombination, mutation rate diversity. Also, new generations sequencing technologies rise other difficulties by generating massive amounts fragmented sequences. While linear...
Abstract MicroRNAs (miRNAs) are emerging as important post tran-scriptional regulators that may regulate key plant genes responsible for agronomic traits such grain yield and stress tolerance. Several studies identified species clades specific miRNA families associated with regulated genes. Here, we propose a novel resource provides data related to the expression of abiotic responsive miRNAs in wheat, one most staple food crops. This database allows query small RNA libraries, including...
Abstract Motivation Advances in cloning and sequencing technology yielded a massive number of genome virus strains. The classification annotation these genomes constitute important assets the discovery genomic variability, taxonomic characteristics disease mechanisms. Existing methods are often designed for well-studied virus. Thus, viral comparative studies could benefit from more generic, fast accurate tools classifying typing newly sequenced strains diverse families. Results Here, we...
Abstract Genome rearrangement is one of the major forces driving processes evolution and disease development. The chromosomal position affected by these rearrangements are called breakpoints. breakpoints occurring during species known to be non randomly distributed. Detecting their landscape mapping them genomic features constitute an important in both comparative functional genomics. Several studies have attempted provide such based on pairwise comparison genes as conservation anchors. With...
The emergence of the Next Generation Sequencing increases drastically volume transcriptomic data. Although many standalone algorithms and workflows for novel microRNA (miRNA) prediction have been proposed, few are designed processing large sequence data from genomes, even fewer further annotate functional miRNAs by analyzing multiple libraries. We propose an improved pipeline a high facility implementing mirLibSpark based on Apache Spark framework. This is fastest actual method, provides...
The advances in variational inference are providing promising paths Bayesian estimation problems. These make phylogenetic an alternative approach to Markov Chain Monte Carlo methods for approximating the posterior. However, one of main drawbacks such approaches is modelling prior through fixed distributions, which could bias posterior approximation if they distant from current data distribution. In this paper, we propose and implementation framework relax rigidity densities by learning their...
Most evolutionary-oriented deep generative models do not explicitly consider the underlying evolutionary dynamics of biological sequences as it is performed within Bayesian phylogenetic inference framework. In this study, we propose a method for variational model (EvoVGM) that jointly approximates true posterior local parameters and generates sequence alignments. Moreover, instantiated tuned continuous-time Markov chain substitution such JC69, K80 GTR. We train via low-variance stochastic...