M.Sc./Ph.D. Opportunities

Ph.D. student sought to study soil biodiversity using bioinformatics tools & state-of-the-art environmental DNA technology

Dr. Sarah (Sally) Adamowicz & Dr. Rob Hanner (Integrative Biology)

POSITION DESCRIPTION: We are seeking a strong and independent graduate student to study soil biodiversity and its response to varied restoration practices using state-of-the-art environmental DNA technology and bioinformatic tools for data analyses. The candidate will be involved in developing novel molecular approaches to study soil biodiversity across multiple taxonomic levels including both prokaryotes and eukaryotes. The research will include opportunities to study species interactions (e.g. plant root microbiome) and the efficacy of varied soil amendments that could help accelerate ecological succession across soil disturbance gradients. The research will take place in the boreal forest of Northern Ontario and relates to mining operations taking place there. The selected candidate will gain experience in bioinformatics, molecular biology, spatial ecology, environmental chemistry, and environmental restoration. The candidate will be part of a collaborative research team that seeks to study biodiversity moderation at the landscape scale. The applicants should hold a M.Sc. degree in one of the following fields: Bioinformatics, Biology, Biotechnology, Molecular Biology, Soil Science, or in any other program that is relevant to the proposed research activities. The principal laboratory is located at the University of Guelph’s Biodiversity Institute in Guelph (ON, Canada). The candidate will also interact with colleagues from Kirkland Lake Gold Corp, the University of Saskatchewan, and multiple faculty members from Guelph. The project will begin in September 2021.

PROGRAM CHOICE: This project includes both analytical and biological research components. Depending upon the applicants' background and primary research interests, the selected student could enroll through either the PhD program in Integrative Biology or the PhD program in Bioinformatics, University of Guelph.

HOW TO APPLY: All interested candidates need to send a letter of interest, a CV, a copy of University transcripts, a writing example (such as a publication, MSc thesis chapter, or other project), and the names and email addresses of three referees to: rhanner@uoguelph.ca & sadamowi@uoguelph.ca. If available, and particularly for applicants interested in the PhD in Bioinformatics program, we also encourage applicants to send a code example from your work or your GitHub link. Preference will be given to citizens and permanent residents of Canada. Review of applications will commence on May 10, 2021, and selected applicants will be invited for an interview via videoconferencing. After a discussion and mutual agreement about moving forward, the applicant will also need to apply formally to the appropriate PhD graduate program at the University of Guelph.

The University of Guelph is committed to equity in its policies, practices, and programs, supports diversity in its teaching, learning and work environments, and ensures that applications from members of underrepresented groups are seriously considered under its employment equity policy. All qualified individuals who would contribute to the further diversification of our University community are encouraged to apply.

FOR FURTHER INFORMATION: Please see the following links for further information about the University of Guelph, the relevant PhD programs, and stipend information.

https://www.uoguelph.ca/

https://www.uoguelph.ca/ib/graduate_home

https://www.uoguelph.ca/bioinformatics/programs

https://www.uoguelph.ca/cbs/cbs-research/student-stipend-information

 


Dr. Dan Tulpan (Animal Biosciences)

M.Sc. Position in Computational Biology (Dairy)

Please visit the Animal Biosciences website for more information on the project.

 


Dr. Andreas Heyland (Integrative Biology)

(Seeking M.Sc. Bioinformatics student)

Brief Outline of Proposed Research Project
The overall goal of this research project is to conduct a structural phylogenomic analysis of integrins to predict thyroid hormone binding capacity in invertebrates, and to test evolutionary hypotheses about thyroid hormone signaling and function. We will pull potential thyroid hormone-binding integrin sequences from NCBI protein databases, align sequences, and use homology modeling to predict structure. We will then evaluate these structures for thyroid hormone binding potential and conserved motifs at the putative binding site.


Job Description
The successful candidate will assemble a bioinformatics pipeline to automate the process of sequence alignment and homology modeling. The input proteins are heterodimeric, creating an interesting problem to solve. Given, for example, 4 alpha and 4 beta proteins, there are 16 possible protein assemblages. The pipeline must therefore iterate each possible alpha and beta protein pairing before pruning pairings with a low fit quality. The candidate must have basic programming knowledge and will ideally be familiar with Python, as well as with bioinformatics (BLAST, sequence alignment, protein modeling).

Please contact Dr. Heyland directly if you are an interested applicant.

 


Evaluating changes in the tonsil microbiome in Streptococcus suis disease in pigs

Dr. Nicole Ricker (Pathobiology)

There are two research opportunity focus possibilities:

1. Microbiology/AMR/Pathogenomics:

Through this work, students will develop important bioinformatics skills and techniques for analyzing genomic and metagenomic data from a diversity of next-generation sequencing technologies and relate these to the disease status of the animals and other research questions. Projects could include shotgun sequencing of microbiome samples and functional analysis of bacterial communities; mixed Enterobacteriaceae enrichment plasmid extractions and long-read sequencing assembly; bio-marker discovery and development of tools for monitoring AMR and pathogens in the food chain and the environment.

2. Predictive Modeling and Big Data Initiatives:

Students will utilize machine learning techniques to evaluate shotgun sequencing data for their ability to track bacterial pathogens and predict disease development.  Projects include comparative genomics of bacterial isolates for specific traits relating to disease development, as well as shotgun metagenomics of microbiome samples to reveal relevant functional categories that correlate with improved health outcomes.  Students will learn the importance of annotation and standardization in publicly available databases, and use data mining techniques to identify taxonomic or functional bio-markers that can be integrated into decision support tools for livestock production.

Please contact Dr. Ricker directly if you are an interested applicant.

 


Graduate Student Opportunity in ECOLOGY/BIOINFORMATICS

Dr. Karl Cottenie (Integrative Biology)

ABOUT THE PROJECT

A MSc/PhD graduate student position is available in the laboratory of Dr. Cottenie in the Department of Integrative Biology in the College of Biological Science (www.cottenielab.org). The main research theme in my lab (www.cottenielab.org) centers around metacommunity dynamics, and we study this in a wide variety of systems, from fish to small mammals to macroinvertebrates to transposable elements within the genome. I am currently expanding my research focus to microbiome studies, and the first system that I will study is the microbiome of Canada Jays in Algonquin Park. Some of the questions we are interested in are determining the effect of very local dispersal (vertical transmission from parents to offspring) and regional dispersal (dispersal of parents and offspring in the landscape) on the oral and gut microbiome of Canada Jay individuals.

REQUIREMENTS

I am looking for an enthusiastic graduate student who wants a research project that combines ecological field work with bioinformatics to study relevant questions in ecology through advanced statistical analyses in R. This position is open to Canadian citizens or permanent residents. Other strong candidates are also welcome to apply.

FUNDING

MSc students in the College of Biological Science are funded at a minimum of $21,259 per year, and the minimum guaranteed duration of support is 6 semesters. For more details regarding funding, see Student Stipend Information. Depending on eligibility, students may also apply for a wide range of internal and external scholarships. See the full list of available Scholarships and Awards for more information.

INTERESTED IN APPLYING?

To learn more about this project and the application process, contact me (cottenie@uoguelph.ca) with your CV and your research interests. Because of the interdisciplinary nature of this project, depending on your interests and future goals, you could either apply as an MSc student in Integrative Biology (www.uoguelph.ca/ib) or as an MSc student in Bioinformatics (https://www.uoguelph.ca/bioinformatics/). Since this might change the research focus, we can determine together the most relevant program for you. 2 I also encourage you to visit the websites above to determine what the University of Guelph can offer you during your graduate education, and I highly recommend that you contact my current graduate students to get a sense of what my advisor style is, and whether it would fit with your needs. My graduate students are Anna Solecki (asolecki@uoguelph.ca), Brent Saylor (bsaylor@uoguelph.ca), Carolyn Trombley (ctromble@uoguelph.ca), Jenny Gleason (jgleason@uoguelph.ca), Marie-Eugenie Maggia (mmaggia@uoguelph.ca), and Simon Denomme-Brown (denommes@uoguelph.ca).