A5011459941- Bioinformatics and Genomic Networks
- Gene expression and cancer classification
- Folate and B Vitamins Research
- Genetic Mapping and Diversity in Plants and Animals
- Metabolomics and Mass Spectrometry Studies
- Nutrition, Genetics, and Disease
- Biotin and Related Studies
- Nutritional Studies and Diet
- Epigenetics and DNA Methylation
- Genetic and phenotypic traits in livestock
- Microbial Metabolic Engineering and Bioproduction
- Diet and metabolism studies
- Computational Drug Discovery Methods
- Adipose Tissue and Metabolism
- Ubiquitin and proteasome pathways
- Genetics and Neurodevelopmental Disorders
- Metabolism and Genetic Disorders
- Genomic variations and chromosomal abnormalities
- Molecular Biology Techniques and Applications
- Genetic Associations and Epidemiology
- Birth, Development, and Health
- Endoplasmic Reticulum Stress and Disease
- Metabolism, Diabetes, and Cancer
- Digestive system and related health
- Diet, Metabolism, and Disease
Université Laval
2017-2025
Centre hospitalier universitaire de Québec
2017-2024
Centre hospitalier de l'Université Laval
2017-2020
The Microsoft Research - University of Trento Centre for Computational and Systems Biology
2015-2018
Wilfrid Laurier University
2018
University of Trento
2015-2018
Montreal Clinical Research Institute
2012-2017
Université de Montréal
2012-2016
With the recent developments in field of multi-omics integration, interest factors such as data preprocessing, choice integration method and number different omics considered had increased. In this work, impact these is explored when solving problem sample classification, by comparing performances five unsupervised algorithms: Multiple Canonical Correlation Analysis, Co-Inertia Factor Joint Individual Variation Explained Similarity Network Fusion. These methods were applied to three real...
Drug repositioning offers numerous advantages, such as faster development timelines, reduced costs, and lower failure rates in drug development. Supervised machine learning is commonly used to score candidates but hindered by the lack of reliable negative data—drugs that fail due inefficacy or toxicity— which difficult access, lowering their prediction accuracy generalization. Positive-Unlabeled (PU) has been overcome this issue either randomly sampling unlabeled drugs identifying probable...
Polyphenol-rich foods are part of many nutritional interventions aimed at improving health and preventing cardiometabolic diseases (CMDs). Polyphenols have oxidative, inflammatory, and/or metabolic effects. Research into the chemistry biology polyphenol bioactives is prolific but knowledge their molecular interactions with proteins limited. We mined public data to (i) identify that interact or metabolize polyphenols, (ii) mapped these pathways networks, (iii) annotated functions enriched...
Multi-omics integration is key to fully understand complex biological processes in an holistic manner. Furthermore, multi-omics combined with new longitudinal experimental design can unreveal dynamic relationships between omics layers and identify players or interactions system development phenotypes. However, methods have address various designs do not guarantee interpretable results. The challenge of solve interpretation unlock the hidden knowledge within data. In this paper, we go beyond...
A critical step in preserving protein homeostasis is the recognition, binding, unfolding, and translocation of substrates by six AAA-ATPase proteasome subunits (ATPase-associated with various cellular activities) termed PSMC1-6, which are required for degradation proteins 26 S proteasomes. Here, we identified 15 de novo missense variants PSMC3 gene encoding subunit PSMC3/Rpt5 23 unrelated heterozygous patients an autosomal dominant form neurodevelopmental delay intellectual disability....
Network-based analysis of gene expression through co-expression networks can be used to investigate modular relationships occurring between genes performing different biological functions. An extended description each the network modules is therefore a critical step understand underlying processes contributing disease or phenotype. Biological integration, topology study and conditions comparison (e.g. wild vs mutant) are main methods do so, but date no tool combines them all into single...
The domesticated dog, Canis lupus familiaris, has been selectively bred to produce extreme diversity in phenotype and genotype. Dogs have an immense weight height. Specific differences metabolism not characterized small dogs as compared larger dogs.This study aims identify metabolic, clinical, microbiota between dogs.Gas chromatography/mass spectrometry, liquid chromatography/tandem mass clinical chemistry analysis, dual-energy X-ray absorptiometry, 16S pyrosequencing were used characterize...
Micronutrients are in small amounts foods, act concert, and require variable of time to see changes health risk for disease. These first principles incorporated into an intervention study designed develop new experimental strategies setting target recommendations food bioactives populations individuals.
Abstract Neurodevelopmental proteasomopathies represent a distinctive category of neurodevelopmental disorders (NDD) characterized by genetic variations within the 26S proteasome, protein complex governing eukaryotic cellular homeostasis. In our comprehensive study, we identified 23 unique variants in PSMC5 , which encodes AAA-ATPase proteasome subunit PSMC5/Rpt6, causing syndromic NDD 38 unrelated individuals. Overexpression altered human hippocampal neuron morphology, while knockdown led...
The involvement of vitamins and other micronutrients in intermediary metabolism was elucidated the mid 1900's at level individual biochemical reactions. Biochemical pathways remain foundational knowledgebase for understanding how micronutrient adequacy modulates health all life stages. Current daily recommended intakes were usually established on basis association a single nutrient to single, most sensitive adverse effect thus neglect interdependent pleiotropic effects biological systems....
Abstract Background Myocyte enhancer factor 2 transcription factors regulate essential transcriptional programs in various cell types. The activity of myocyte is modulated through interactions with cofactors, chromatin remodelers, and other regulatory proteins, which are dependent on context physiological state. In steroidogenic Leydig cells, MEF2A, MEF2C, MEF2D key regulators genes involved steroid hormone synthesis, reproductive function, oxidative stress defense. However, the specific...
Abstract Motivation Multi-omics data integration enables the global analysis of biological systems and discovery new insights. experimental designs have been further extended with a longitudinal dimension to study dynamic relationships between molecules. However, methods that integrate multi-omics are still in their infancy. Results We introduce R package timeOmics, generic analytical framework for data. The includes pre-processing, modeling clustering identify molecular features strongly...
DNA methylation (DNAme) erasure and reacquisition occur during prenatal male germ cell development; some further remodeling takes place after birth spermatogenesis. Environmental insults germline epigenetic reprogramming may affect DNAme, presenting a potential mechanism for transmission of environmental exposures across multiple generations.We investigated how DNAme is impacted by lifetime to diets containing either low or high, clinically relevant, levels the methyl donor folic acid...
Recently, expression quantitative loci (eQTL) mapping studies, where levels of thousands genes are viewed as traits, have been used to provide greater insight into the biology gene regulation. Originally, eQTLs were detected by applying standard QTL detection tools (using a "one at-a-time" approach), but this method ignores many possible interactions between genes. Several other methods proposed overcome these limitations, each them has some specific disadvantages. In paper, we present an...
Although the genetic basis of Duchenne muscular dystrophy has been known for almost thirty years, cellular and molecular mechanisms characterizing disease are not completely understood an efficacious treatment remains to be developed. In this study we analyzed proteomics data obtained with SomaLogic technology from blood serum a cohort patients matched healthy subjects. We developed workflow based on biomarker identification network-based pathway analysis that allowed us describe different...
Despite indications that hearts from the C57BL/6N and C57BL/6J mouse substrains differ in terms of their contractility responses to stress-induced overload, no information is available about underlying molecular cellular mechanisms. We tested whether subacute (48 hours) chronic (14 days) administration angiotensin II (500 ng/kg per day) had different effects on left ventricles male mice. higher blood pressure mice, induced fibrosis increased ventricular weight/body weight ratio cardiac...
The DNA damage inducible SOS response in bacteria serves to increase survival of the species at cost mutagenesis. first initiates error-free repair followed by error-prone repair. Here, we have employed a multi-omics approach elucidate temporal coordination response. Escherichia coli was grown batch cultivation bioreactors ensure highly controlled conditions, and low dose antibiotic ciprofloxacin used activate while avoiding extensive cell death. Our results show that expression genes...
Human infection with the coronavirus disease 2019 (COVID-19) is mediated by binding of spike protein severe acute respiratory syndrome 2 (SARS-CoV-2) to human angiotensin-converting enzyme (ACE2). The frequent mutations in receptor-binding domain (RBD) induced emergence variants increased contagion and can hinder vaccine efficiency. Hence, it crucial better understand mechanisms variant RBDs ACE2 develop efficient methods characterize this interaction. In work, we present an approach that...
Due to the grasshopper effect, Arctic food chain in Canada is contaminated with persistent organic pollutants (POPs) of industrial origin, including polychlorinated biphenyls and organochlorine pesticides. Exposure POPs may be a contributor greater incidence poor fetal growth, placental abnormalities, stillbirths, congenital defects shortened lifespan Inuit population compared non-Aboriginal Canadians. Although maternal exposure well established harm pregnancy outcomes, paternal transmission...
Validated protein biomarkers are needed for assessing health trajectories, predicting and subclassifying disease, optimizing diagnostic therapeutic clinical decision-making. The sensitivity, specificity, accuracy, precision of single or combinations may be altered by differences in physiological states limiting the ability to translate research results clinically useful tests. Aptamer based affinity assays were used test whether low abundant serum proteins differed on age, sex, fat mass a...
Background and Scope Weight loss success is dependent on the ability to refrain from regaining lost weight in time. This feature was shown be largely variable among individuals, these differences, with their underlying molecular processes, are diverse not completely elucidated. Altered plasma metabolites concentration could partly explain maintenance mechanisms. In present work, a systems biology approach has been applied investigate potential mechanisms involved within Diogenes weight-loss...