A5032926721- Atherosclerosis and Cardiovascular Diseases
- Angiogenesis and VEGF in Cancer
- Nuclear Receptors and Signaling
- Genomics and Phylogenetic Studies
- Genetics and Neurodevelopmental Disorders
- Chronic Lymphocytic Leukemia Research
- Congenital heart defects research
- Galectins and Cancer Biology
- Genomics and Chromatin Dynamics
- FOXO transcription factor regulation
- Evolution and Genetic Dynamics
- Bioinformatics and Genomic Networks
- Retinal Development and Disorders
- Neuroscience of respiration and sleep
- Lymphoma Diagnosis and Treatment
- Gene expression and cancer classification
- Plant and animal studies
- Protein Degradation and Inhibitors
- Cellular transport and secretion
- Scientific Computing and Data Management
- Glioma Diagnosis and Treatment
- Nerve injury and regeneration
- Neurogenesis and neuroplasticity mechanisms
- Adversarial Robustness in Machine Learning
- Steroid Chemistry and Biochemistry
McGill University
2012-2023
McGill Genome Centre
2023
Montreal Neurological Institute and Hospital
2012-2021
McGill University and Génome Québec Innovation Centre
2018-2020
Ontario Genomics
2018-2019
University of Ottawa
2010-2014
With the decreasing cost of sequencing and rapid developments in genomics technologies protocols, need for validated bioinformatics software that enables efficient large-scale data processing is growing.Here we present GenPipes, a flexible Python-based framework facilitates development deployment multi-step workflows optimized high-performance computing clusters cloud. GenPipes already implements 12 scalable pipelines various applications, including RNA sequencing, chromatin...
Topologically associating domains (TADs) have been proposed to be the basic unit of chromosome folding and shown play key roles in genome organization gene regulation. Several different tools are available for TAD prediction, but their properties never thoroughly assessed. In this manuscript, we compare output seven prediction on two published Hi-C data sets. predictions varied greatly between number, size distribution other biological properties. Assessed against a manual annotation TADs,...
Genome-wide association studies (GWAS) have identified hundreds of loci associated with coronary artery disease (CAD) and blood pressure (BP) or hypertension. Many these are not linked to traditional risk factors, nor do they include obvious candidate genes, complicating their functional characterization. We hypothesize that many GWAS vascular diseases modulate endothelial functions. Endothelial cells play critical roles in regulating homeostasis, such as forming a selective barrier,...
Significance Cyclin D2 is a cell cycle regulator with spatially restricted expression. Loss and gain of function in animal models also revealed role differentiation, but the mechanisms underlying this are incompletely understood. The cardiogenic transcription factor GATA4 an upstream cyclin D2. We show that cyclinD2 part forward reinforcing loop which feeds back to enhance activity through direct interaction. Mutations abrogate interactions associated human congenital heart disease. results...
Glioblastoma (GBM) is the most common and deadly malignant brain cancer of glial cell origin, with a median patient survival less than 20 months. Transcription factors FOXG1 TLE1 promote GBM propagation by supporting maintenance tumour-initiating cells (BTICs) stem-like properties. Here, we characterize target genes in patient-derived BTICs using ChIP-Seq RNA-Seq approaches. These studies identify 150 direct targets, several which are also involved proliferation, differentiation, survival,...
Glioblastoma is the most common and deadly malignant brain cancer. We now demonstrate that loss of function endosomal GTPase Rab35 in human tumor initiating cells (BTICs) increases glioblastoma growth decreases animal survival following BTIC implantation mouse brains. Mechanistically, we identify Arf5 interacts with guanine nucleotide exchange factor (GEF) for Rab35, DENND1/connecdenn, allosterically enhances its GEF activity toward Rab35. Knockdown either or cell migration, invasiveness,...
Bacteria excrete costly toxins to defend their ecological niche. The evolution of such antagonistic interactions between individuals is expected depend on both the social environment and strength resource competition. Antagonism be weak among highly similar genotypes because most are immune agents dissimilar these unlikely competing for same resources antagonism should not yield much benefit. therefore peak at intermediate genetic distance. We studied ability laboratory strains Pseudomonas...
The potential for evolutionary change is limited by the availability of genetic variation. Mutations are ultimate source new alleles, yet there have been few experimental investigations role novel mutations in multivariate phenotypic evolution. Here, we evaluated degree divergence observed a long-term evolution experiment whereby replicate lineages filamentous fungus Aspergillus nidulans were derived from single genotype and allowed to fix (beneficial) while maintained at two different...
Abstract Motivation Topologically Associating Domains (TADs) are chromatin structures that can be identified by analysis of Hi-C data. Tools currently available for TAD identification sensitive to experimental conditions such as coverage, resolution and noise level. Results Here, we present RobusTAD, a tool score boundaries in manner is robust these parameters. In doing so, RobusTAD eases comparative across multiple heterogeneous samples. Availability implemented R released under GPL...
ABSTRACT With the decreasing cost of sequencing and rapid developments in genomics technologies protocols, need for validated bioinformatics software that enables efficient large-scale data processing is growing. Here we present GenPipes, a flexible Python-based framework facilitates development deployment multi-step workflows optimized High Performance Computing clusters cloud. GenPipes already implements 12 scalable pipelines various applications, including RNA-Seq, ChIP-Seq, DNA-Seq,...
SHP1 EXPRESSION IS EPIGENETICALLY REGULATED AND INFLUENCES THE SENSITIVITY TO CHEMOTHERAPEUTIC AGENTS IN GLIOBLASTOMA CELLS
Polycomb Repressive Complex 2 (PRC2)-mediated histone H3K27 tri-methylation (H3K27me3) recruits canonical PRC1 (cPRC1) to maintain heterochromatin. In early development, polycomb-regulated genes are connected through long-range 3D interactions which resolve upon differentiation. Here, we report that polycomb looping is controlled by H3K27me3 spreading and regulates target gene silencing cell fate specification. Using glioma-derived H3 Lys-27-Met (H3K27M) mutations as tools restrict...
ABSTRACT Spinal cord motor neuron diversity and the ensuing variety of circuits allow for processing elaborate muscular behaviours such as body posture breathing. Little is known, however, about molecular mechanisms behind specification axial hypaxial neurons controlling postural respiratory functions respectively. Here we show that Groucho/TLE (TLE) transcriptional corepressor a multi-step regulator diversification in developing spinal cord. TLE first promotes at expense identity by...
Imitation learning seeks to learn an expert policy from sampled demonstrations. However, in the real world, it is often difficult find a perfect and avoiding dangerous behaviors becomes relevant for safety reasons. We present idea of \textit{learning avoid}, objective opposite imitation some sense, where agent learns avoid demonstrator given environment. define avoidance as process optimizing agent's reward while by demonstrator. In this work we develop framework defining suitable function...