A5050507388- Genomics and Phylogenetic Studies
- Genomics and Chromatin Dynamics
- Genetic Mapping and Diversity in Plants and Animals
- Bioinformatics and Genomic Networks
- Gene expression and cancer classification
- RNA and protein synthesis mechanisms
- Chromosomal and Genetic Variations
- Graph Theory and Algorithms
- PI3K/AKT/mTOR signaling in cancer
- Data Visualization and Analytics
- Genomics and Rare Diseases
- Genetic and phenotypic traits in livestock
- Genome Rearrangement Algorithms
- RNA modifications and cancer
- Lipid metabolism and biosynthesis
- Wnt/β-catenin signaling in development and cancer
- Cancer therapeutics and mechanisms
- Microbial Natural Products and Biosynthesis
- Scientific Computing and Data Management
- Autism Spectrum Disorder Research
- Infectious Diseases and Mycology
- Nitrogen and Sulfur Effects on Brassica
University of Saskatchewan
2015-2020
Agriculture and Agri-Food Canada
2014
The advent of high-resolution chromosome conformation capture assays (such as 5C, Hi-C and Pore-C) has allowed for unprecedented sequence-level investigations into the structure-function relationship genome. In order to comprehensively understand this relationship, computational tools are required that utilize data generated from these predict 3D genome organization (the reconstruction problem). Many have been developed answer need, but a comprehensive comparison their underlying algorithmic...
Rapamycin is a well-known inhibitor of the Target (TOR) signaling cascade; however, impact this drug on global genome function and organization in normal primary cells poorly understood. To explore impact, we treated human foreskin fibroblasts with rapamycin observed decrease cell proliferation without causing death. Upon treatment chromosomes 18 10 were repositioned to location similar that induced into quiescence by serum reduction. Although changes positioning occurred, comparative...
Development of yellow mustard (Sinapis alba L.) with superior quality traits (low erucic and linolenic acid contents, low glucosinolate content) can make this species as a potential oilseed crop. We have recently isolated three inbred lines Y1127, Y514 Y1035 (3.8%), medium (12.3%) high (20.8%) (C18∶3) content, respectively, in species. Inheritance studies detected two fatty desaturase 3 (FAD3) gene loci controlling the variation C18∶3 content. QTL mapping revealed that FAD3 responsible for...
Hi-C is a proximity-based ligation reaction used to detect regions of the genome that are close in 3D space (or "interacting"). Typically, results from experiments (contact maps) visualized as heatmaps or Circos plots. While informative, these visualizations do not directly represent genomic structure and folding, making interpretation underlying organization obscured. Our objective was generate graph-based contact map representation leads more intuitive structural visualization. Normalized...
Background: Many computational methods have been developed that leverage the results from biological experiments (such as Hi-C) to infer 3D organization of genome. Formally, this is referred genome reconstruction problem (3D-GRP). Hi-C data now being generated at increasingly high resolutions. As resolution increases, it has become computationally infeasible predict a with majority existing methods. None solution utilized non-procedural programming approach integer programming) despite...
ABSTRACT In order to comprehensively understand the structure-function relationship of genome, 3D genome structures must first be predicted from biological data (like Hi-C) using computational tools. Many these existing tools rely partially or completely on multi-dimensional scaling (MDS) embed in space. MDS is known have inherent problems when applied high-dimensional datasets like Hi-C. Alternatively, t-Distributed Stochastic Neighbor Embedding (t-SNE) able overcome but has not been...
Abstract Background Hi-C is a proximity-based ligation reaction used to detect regions of the genome that are close in 3D space (or “interacting”). Typically, results from experiments (whole-genome contact maps) visualized as heatmaps or Circos plots. While informative, these visualizations do not intuitively represent complex organization and folding space, making interpretation underlying genomic difficult. Our objective was utilize existing tools generate graph-based representation...
1 Abstract Background Many computational methods have been developed that leverage the results from biological experiments (such as Hi-C) to infer 3D organization of genome. Formally, this is referred genome reconstruction problem (3D-GRP). None existing for solving 3D-GRP utilized a non-procedural programming approach constraint or integer programming) despite established advantages and successful applications such approaches predicting structure other biomolecules. Our objective was...