Kimberly Mackay

Global Institue for Food Security · Data Management & Analytics

Development of yellow mustard (Sinapis alba L.) with superior quality traits (low erucic and linolenic acid contents, and low glucosinolate content) can make this species as a potential oilseed crop. We have recently isolated three inbred lines Y1127, Y514 and Y1035 with low (3.8%), medium (12.3%) and high (20.8%) linolenic acid (C18∶3) content, re...

Objectives: 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 Hi-C experiments (contact maps) are visualized as heatmaps or Circos plots. While informative, these visualizations do not directly represent genomic structure and folding, making the in...

In order to comprehensively understand the structure-function relationship of the genome, 3D genome structures must first be predicted from biological data (like Hi-C) using computational tools. Many of these existing tools rely partially or completely on multi-dimensional scaling (MDS) to embed predicted structures in 3D space. MDS is known to hav...

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 of the genome. In order to comprehensively understand this relationship, computational tools are required that utilize data generated from these assay...

Background Many computational methods have been developed that leverage the results from biological experiments (such as Hi-C) to infer the 3D organization of the genome. Formally, this is referred to as the 3D genome reconstruction problem (3D-GRP). None of the existing methods for solving the 3D-GRP have utilized a non-procedural programming appr...

A major goal of biological experiments is to identify the underlying biological mechanisms that drive phenotypic changes and disease states. Transcription factors are often inherent to this process due to their involvement in regulating gene expression. Transcription factors are proteins that bind distinct genomic sub-sequences called motifs. The i...

Background: Autism is a group of heterogeneous disorders defined by deficits in social interaction and communication. Typically, diagnosis depends on the results of a behavioural examination called the Autism Diagnostic Observation Schedule (ADOS). Unfortunately, administration of the ADOS exam is time consuming and requires a significant amount of...

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 Hi-C experiments (whole-genome contact maps) are visualized as heatmaps or Circos plots. While informative, these visualizations do not intuitively represent the complex organization and...

Background: In order for a cell’s genetic information to fit inside its nucleus, the chromosomes must undergo extensive folding and organization. It is possible that different genomic organizations (or architectures) may relate to distinct nuclear functions. Until recently it was difficult to investigate this relationship due to the lack of high-th...

Background: Hi-C is a proximity-based ligation reaction that detects regions of the genome that are close in 3D space (or "interacting"). Typically, results from Hi-C experiments (whole-genome contact maps) are visualized as heatmaps or Circos plots. While informative, these visualizations do not intuitively represent the complex organization and f...

Background: Chromosome Conformation Capture (3C) is a biological technique that can determine if two genomic regions are in close spatial proximity. This proximity is often referred to as an ”interaction”. Known interactions, also called interaction-controls, are needed to validate 3C results. Unfortunately, there are no identified interaction-cont...

Background: Rapamycin is well-known inhibitor of the Target of Rapamycin signalling cascade and is currently used clinically as an immunosuppressant. The effects of rapamycin have been extensively studied in various model organisms, but the global effects it has on gene expression in normal human primary cells remains unclear. Objective: Identify t...

Rapamycin is a well-known inhibitor of the Target of Rapamycin (TOR) signalling cascade; however, the impact of this drug on global genome function and organization in normal primary cells is poorly understood. To explore this impact, we treated primary human foreskin fibroblasts with rapamycin and observed a decrease in cell proliferation without...

Background: Rapamycin is an immunosurpressant drug that is currently used to prevent transplant rejection after organ donation. Additionally, it has been shown to prolong lifespan in various model organisms and has potential therapeutic uses in the treatment of certain cancers and Hutchinson-Gilford Progeria Syndrome. Within the cell, rapamycin act...

Background: Rapamycin is an immunosurpressant drug that is currently used to prevent transplant rejection after organ donation. Additionally, it has been shown to prolong lifespan in various model organisms and has potential therapeutic uses in the treatment of certain cancers and Hutchinson-Gilford Progeria Syndrome. Within the cell, rapamycin act...

Background: Rapamycin is an immunosuppressant drug that is currently used to prevent transplant rejection after organ donation. Additionally, it has been shown to prolong lifespan in various model organisms and has potential therapeutic uses in the treatment of certain cancers and Hutchinson-Gilford Progeria Syndrome. Within the cell, rapamycin act...