Ontario Genomics-CANSSI Ontario Postdoctoral Fellowship in Genome Data Science

We are pleased to announce a new joint funding opportunity from Ontario Genomics and CANSSI Ontario, the Ontario regional centre of the Canadian Statistical Sciences Institute, establishing another joint .

This Fellowship, now in its third year, will support the work of an early-career investigator pursuing research in the areas of genomics and data science with an emphasis on genomic medicine, including, but not limited to, methodology, application, and translation of genomic prediction tools such as polygenic risk scores; human-computer interactions; or novel genomic computational approaches to therapeutic identification.

Proposed projects should be innovative, generalizable across applications, and not restricted to developing a predictive tool for a single application.

The Fellowship offers two-year salary support for up to $50,000 annually for postdoctoral fellows undertaking full-time research at a CANSSI Ontario partner university or their affiliated research institutes. Candidates are responsible for selecting, contacting, and securing the commitment of two faculty members to jointly supervise them in their project, one being a statistical geneticist, genetic epidemiologist, or environmental epidemiologist.

  • Funding Availability: Up to two years.
  • Maximum Fellowship Value: $50,000 annually for up to $100,000 over two years.

Contact

Ontario Genomics
Michael Dorrington, Manager, Strategic Partnerships
Telephone: 416.673.6562
Email: mdorrington@OntarioGenomics.ca

Erum Razvi, Advisor, Sector Innovation & Programs
Email: erazvi@OntarioGenomics.ca

CANSSI Ontario
Esther Berzunza, Program Manager
Telephone: 416-689-7271
Email: esther.berzunza@utoronto.ca


About

Ontario Genomics is a not-for-profit organization leading the application of genomics-based solutions to drive economic growth, improved quality of life and global leadership for Ontario. Ontario Genomics plays a vital role in advancing projects and programs by supporting the development of their proposals, helping them access diverse funding sources, and finding the right industry partners to take this research out of the lab to apply it to the world’s most pressing challenges. Since its inception in 2000, Ontario Genomics has raised more than $1.27 billion for genomics applied research in Ontario and directly supported more than 9,100 trainees and jobs. We have 110+ active projects, 500+ impactful partnerships and have secured $1.34 billion in follow-on investments.

CANSSI Ontario is the Ontario regional centre of CANSSI–a national institute offering the leadership and infrastructure necessary to increase and further develop statistical sciences research in Canada and promote the discipline. CANSSI Ontario seeks to support data-intensive, interdisciplinary research and strengthen the network of statistical and data scientists in Ontario and across Canada. www.canssiontario.utoronto.ca.

“Antenna-in-a-cell”: Forest Insect Pest Research and Management

Insects damage important crops and forests, and some insect species are responsible for the transmission of disease. If we better understand which compounds mediate the attraction of these insects, we could better control the damage. SPARK funding for this project will help Drs. Daniel Doucet and Jeremy Allison (Great Lakes Forestry Centre) develop the antenna-in-a-cell platform that aims to find physiologically active odorants and understand how they interact with the insects’ odorant receptors (OR). This research holds promise for the development of odorant molecules as operational insect lures.
The project focused the validation of the approach on two invasive insects of critical concern in forestry: the Emerald Ash Borer and the Brown Spruce Longhorned Beetle. The experiments have resulted in the identification of key ORs in both species which will, down the line, aid in the development of optimal odor blends to use against these two insect species.

All Awarded Projects

Drones for Breeding Better White Spruce

The field of tree genomics has seen unprecedented advances over the past decade. A suite of next generation genomic resources for improved tree breeding and selection will soon become available to breeders and forest managers, thanks to a project led by Drs. Ingo Ensminger (University of Toronto) and Nathalie Isabel (Forest and Environmental Genomics at Natural Resources Canada, Canadian Forest Service (CFS) – Quebec region) in partnership with PrecisionHawk.

An investment by Ontario Genomics through its Pre-Commercialization Business Development Fund (PBDF) will support rapid deployment of a software application to market. The software will allow users to determine the performance of individual trees and forest stands and to assess their phenology and water deficit at various time points in the season.

A team of scientists will use already established white spruce progeny trials in Quebec and Ontario and survey entire populations using a drone carrying optical sensors for leaf spectral measurements. Aerial sampling will be paralleled by leaf level sampling on subsets of seedlings on the ground (30-40 genotypes multiple times per site and year) looking at phenology, hydration level and spectral properties. The team will then develop algorithms for correlating plant phenology, leaf responses to hydration level and genotype information with drone-collected leaf spectral properties.

This survey data will be available to our partner company, PrecisionHawk, to create a software application that will be available to end users via the Algorithm Marketplace― the proprietary “app store” for drone data analysis.

These tools are expected to accelerate breeding cycles, through an innovative approach for large-scale phenotyping of tree responses to drought, monitor phenology, and assess differences between genotypes in large-scale field experiments.


All Awarded Projects

Delivery Strategies and Monitoring Tools for Bioremediation

BTEX compounds – benzene, toluene, ethylbenzene and xylenes – are natural components of crude oil and petroleum and are used in the synthesis of a wide range of useful materials and chemicals. They are also toxic, and benzene in particular is a known human carcinogen. In some mining sites, as a result of extraction, transportation and refining processes, as well as accidental spills and leaks, BTEX compounds frequently pollute groundwater in all industrialized regions of the globe.

In Canada and elsewhere, remediation of contaminated sites is difficult and costly. When possible, affected soils are dug up and treated or disposed of offsite. Dr. Elizabeth Edwards of the University of Toronto is working with SiREM, a Canadian leader in bioremediation, to scale up and commercialize anaerobic bioaugmentation cultures for in situ BTEX remediation. They were awarded $1M for this project led by Ontario Genomics.


All Awarded Projects

Isolating Uranium from Mine Discharge Water

Canada is the world’s second largest producer of uranium, and more uranium has been mined in Canada than in any other country (as of 2014). Although current treatment methods meet regulatory requirements for inactive sites, there are opportunities to develop new treatments that achieve consistent effluent quality in a cost-effective and sustainable manner, and which should allow for recovery of uranium and other metals from tailings sites.

One of the largest barriers to treating mine waste using bioremediation has been the challenge in maintaining treatment efficacy. Ontario Genomics is investing seed funding towards the first steps to develop genomics-enabled technology that will do just that.

Drs. Susan Glasauer (University of Guelph) and Nadia Mykytczuk (Laurentian University) are partnering with Denison Environmental and US-based company, Inotec, to develop a microbial electrode technology to sequester uranium from mine tailings and remediate water to discharge standards.

The use of microbial electrodes for the remediation of some elements of concern, such as selenium and arsenic, has already been successfully implemented by Inotec using their electro-biochemical reactor (EBR) technology. With seed funding, the research team will design a system to optimize uranium removal and recovery and perform bench scale testing of the technology using water from a former Uranium mine in Ontario. It is anticipated that this will lead to an improved understanding of the microbial pathways involved in free electron use, which may be applied by the mining industry to sequester uranium for long-term sustainable and cost-effective treatment of sites.


All Awarded Projects

Healthy Plant Growth with Enhanced Nutrition in Soil

Natural soil bacteria can play a critical role in plant health. Ontario Genomics is providing seed funding for an academic-industry partnership to identify soil containing these beneficial microorganisms with the goal of enhancing their benefits.

Boreal Agrominerals Inc. (Boreal) specializes in the mining and commercialization of Spanish River Carbonatite (SRC), an agro-mineral fertilizer which promotes soil balance and healthy plant growth. To identify the beneficial microorganisms that facilitate nutrient uptake by native plants and cash crops and to expand the economic potential of its product, Boreal is collaborating with researchers from Wilfrid Laurier University and Algoma University to characterize the distribution of microorganisms naturally found at various mining sites from the SRC deposit, located near Sudbury, Ontario.

The team will further investigate the effects of mining and site characteristics on soil microbial communities based primarily on nutrient solubilisation and plant nutrient availability. Once beneficial microorganisms are identified, Boreal aims to determine the specific functional mechanisms associated with nutrient solubilisation, acquisition, and transfer to plants.


All Awarded Projects

New Model System for Better Crops

To improve traits in monocot crops, such as wheat, corn and rice, we need a unique model for both prediction of candidate genes and the validation of effectiveness. Ontario Genomics is providing seed funding for an academic-industry partnership to do just that.

Frontier Agri-Science Inc., an Ontario Agri-Tech company, and Dr. Dario Bonetta (University of Ontario Institute of Technology) are developing and refining Brachypodium as a highly efficient and novel monocot model system for crop development for their industry partner BASF. This project could ultimately lead to the development of plant traits with herbicidal tolerance in key food crops, and a valuable service that Frontier can provide commercially.

This funding has created further opportunities for Frontier to acquire follow-on financing from Ontario Centres of Excellence (OCE).


All Awarded Projects

Diverse Chemical Libraries

Synthetic chemical libraries are a common source of drug discovery molecules. The challenge is that these libraries adhere to synthetic structures and biological activities. By contrast, naturally occurring chemicals have a vast diversity of structure, but their industrial or medical uses are limited due to the complexity and inaccessibility of these natural products.

Drs. Eiji Nambara, Peter McCourt (University of Toronto) and Dario Bonetta (University of Ontario Institute and Technology) plan to take these chemical libraries and expose them to a plethora of plant enzymes to exponentially increase the diversity of compounds with the hope of finding novel functions.

The team is using plant genomics resources to create libraries of various chemical compounds for industrial uses. In an effort to produce the advantages of these two systems, this project aims to set up an enhanced system to evaluate metabolic conversion of diverse chemical library by plant xenobiotic enzymes, which will be useful sources to identify chemicals with new functions.


All Awarded Projects

Biosensors for Healthy Plant Growth

Plant hormones determine plant growth, and breeding programs designed around hormone action have a big impact on crop yields.

Strigolactones (SL) are plant hormones that stimulate the growth of symbiotic mycorrhizal fungi that help promote plant growth and development. However, SL also triggers the germination of parasitic plant seeds that can compete with key crop plants, especially in the developing world. To better understand how these hormones interact with their receptors in plants, Dr. Peter McCourt (University of Toronto) and his team will use synthetic biology to develop a biosensor for SL activity. With SPARK and additional support from the DOE-Joint Genomics Institute, the team will synthesize over 250 SL receptor variants that will be screened for activity within the plants. This information will be used to develop a toolbox to promote the healthy growth of agriculturally important plants, instead of the noxious plants that compete with them.


All Awarded Projects

A Genetic Toolbox for Tomato Flavour Differentiation

Tomatoes, it is said, are the quintessence of summer in a bite. They are also responsible for more than half a billion dollars in annual farm gate sales and are Canada’s biggest fresh vegetable export. Canadian growers are facing competition due to lower production costs in other regions, leading to difficulties maintaining their market share. Canadian producers need to innovate in order to offer a differentiated product that will give them a competitive edge.

Generally, plant breeding programs focus on production traits such as yield or disease resistance. Drs. Charles Goulet (Université Laval) and David Liscombe (Vineland Research and Innovation Centre) are collaborating to ensure that new tomato varieties possess these traits, and something more important to the consumer – flavour. The team was awarded $1.8 million for this project, co-led by Genome Quebec and Ontario Genomics.


All Awarded Projects