A5065093323- Epigenetics and DNA Methylation
- RNA modifications and cancer
- Molecular Biology Techniques and Applications
- Gene expression and cancer classification
- Identification and Quantification in Food
- Genomics and Phylogenetic Studies
- Environmental DNA in Biodiversity Studies
- Microbial Community Ecology and Physiology
- Genomics and Chromatin Dynamics
- Chronic Obstructive Pulmonary Disease (COPD) Research
- Amphibian and Reptile Biology
- interferon and immune responses
- Genetic Neurodegenerative Diseases
- Advanced biosensing and bioanalysis techniques
- Cell Image Analysis Techniques
- Asthma and respiratory diseases
- CRISPR and Genetic Engineering
- Metabolomics and Mass Spectrometry Studies
- Cancer-related molecular mechanisms research
- Single-cell and spatial transcriptomics
- Abdominal Trauma and Injuries
- Multiculturalism, Politics, Migration, Gender
- French Urban and Social Studies
- RNA and protein synthesis mechanisms
- Abdominal vascular conditions and treatments
McGill University
2022-2025
Queen's University
2018-2022
Ontario Genomics
2019
Abstract The functional effect of a gene edit by designer nucleases depends on the DNA repair outcome at targeted locus. While non-homologous end joining (NHEJ) results in various mutations, microhomology-mediated (MMEJ) creates precise deletions based alignment flanking microhomologies (µHs). Recently, sequence context surrounding nuclease-induced double strand breaks (DSBs) has been shown to predict outcomes, for which µH plays an important role. Here, we survey naturally occurring human...
Abstract Freshwater ecosystems are complex, diverse, and face multiple imminent threats that have led to changes in both structure function. It is urgent we develop standardize monitoring tools allow for rapid comprehensive assessment of freshwater communities understand their changing dynamics inform conservation. Environmental DNA surveys offer a means inventory monitor aquatic diversity, yet most studies focus on one or few taxonomic groups because technical challenges. In this study, (1)...
Variation in short tandem repeats (STRs) is implicated Mendelian disease and complex traits, but can be difficult to resolve with short-read genome sequencing. We present STRkit , a software package for genotyping STRs using long read sequencing (LRS) that uses nearby single-nucleotide variants improve accuracy without priori haplotype information. show has unique strengths versus other methods: it use data from both major LRS technologies (Pacific Biosciences HiFi [PB] Oxford Nanopore...
Abstract Repeatable experiments with accurate data collection and reproducible analyses are fundamental to the scientific method but may be difficult achieve in practice. Open‐source tools aid reproducibility of analysis, analogous generally lacking for sample other early stages inquiry. We introduce R package baRcodeR generating informative identifier (ID) codes digitally encoded linear or 2D barcodes. Codes can imported from an existing dataset (e.g. CSV file) generated rapidly , producing...
Summary Humans display remarkable inter-individual variation in immune response when exposed to identical challenges. Yet, our understanding of the genetic and epigenetic factors contributing such remains limited. Here we carried out in-depth genetic, epigenetic, transcriptional profiling on primary macrophages derived from a panel European African-ancestry individuals before after infection with influenza A virus (IAV). We show that baseline profiles are strongly predictive IAV across...
Large-scale sharing of genomic quantification data requires standardized access interfaces. In this Global Alliance for Genomics and Health project, we developed RNAget, an API secure to in matrix form. RNAget provides slicing matrices extract desired subsets is applicable all expression matrix-format data, including RNA sequencing microarrays. Further, it generalizes other sequence-based genomics such as ATAC-seq ChIP-seq.https://ga4gh-rnaseq.github.io/schema/docs/index.html.
Human epigenomic data has been generated by large consortia for thousands of cell types to be used as a reference map normal and disease chromatin states. Since epigenetic contains potentially identifiable information, similarly genetic data, most raw files these are stored in controlled-access databases. It is important protect but this should not hinder secure sharing valuable datasets.
Amphibians have unique genome characteristics including slow karyotypic evolution and cytogenetically undifferentiated sex chromosomes. Yet our understanding of amphibian genomes has not kept pace with that mammals birds, partially due to scarce genomic resources challenges associated large sizes high repetitiveness. We assembled annotated a chromosome-level for the western chorus frog ( Pseudacris triseriata ), species conservation concern importance in evolutionary research. Comparison new...
Abstract Repeatable experiments with accurate data collection and reproducible analyses are fundamental to the scientific method but may be difficult achieve in practice. Several flexible, open-source tools developed for R Python coding environments aid reproducibility of wrangling analysis research. In contrast, analogous generally lacking earlier stages, such as systematic labelling processing field samples hierarchical structure (e.g. time points individuals from multiple lines or...
Human epigenomic data has been generated by large consortia for thousands of cell types to be used as a reference map normal and disease chromatin states. Since epigenetic contains potentially identifiable information, similarly genetic data, most raw files these are stored in controlled-access databases. It is important protect but this should not hinder secure sharing valuable datasets.
ABSTRACT Freshwater ecosystems are complex, diverse and face a variety of imminent threats that have led to changes in both ecosystem structure function. It is urgent we develop standardize monitoring tools allowing for rapid comprehensive assessment freshwater communities understand their changing dynamics inform conservation. Environmental DNA surveys offer means inventory monitor aquatic diversity, yet most studies focus on one or few taxonomic groups only. In this study, sought 1)...