M.Sc./Ph.D. Opportunities

MSc position to study the relationship between host genetics and pig gut microbiome  

Dr. Brandon Lillie (Pathobiology), Dr. Khurram Nadeem (Mathematics and Statistics), Dr. Vahab Farzan (Pathobiology and Population Medicine) 

PROJECT DESCRIPTION: The microbial colonization of the neonatal and adult gut plays a key role in function of immunological and metabolic pathways that influence disease resistance, health, and performance of pigs. Indeed, the mechanism-of-action of many commercially available intervention strategies and products designed to promote health and performance in pigs and replace antibiotics, is associated with their demonstrated ability to modify the composition of the gut microbiome. The application of molecular and bioinformatics methods has demonstrated that the gut microbiome is abundant, complex, and highly dynamic, partly influenced by host genetics.  The overall goal of this MSc project is to investigate the relationship between host genetics and the swine gut microbiome. The project is specifically aiming to identify the single nucleotide variants with known roles in innate immunity and host resistance to microbes, as well as SNPs spaced across the entire genome, using a genome wide association study (GWAS) approach.   

JOB DESCRIPTION: The successful candidate will develop and utilize bioinformatics pipelines to model various outcomes related to microbiome (Ex. alpha and beta diversity, microbiome composition) against single nucleotide variants through statistical modeling and genome wide association study.  

Selection of the successful candidate is based on a combination of academic criteria, relevant experience, and referees’ evaluations. Previous experience in programming (e.g., R or Python) and knowledge of statistical methods such as regression analysis will be considered an asset. Review of applications will begin immediately and continue until the position is filled. The interested candidates should send a CV, a copy of undergraduate transcripts, a code example, a writing sample, names of three references, and a cover letter stating interest in the above-mentioned research topic to Dr. Vahab Farzan at afarzan@uoguelph.ca.   

The University of Guelph is committed to an Employment Equity Program that includes special measures to achieve diversity among its faculty and staff. We therefore particularly encourage applications from members of underrepresented groups.  

 


Gaze Tracking: MSc/Ph.D. student(s) projects related to eye tracking analytics and computational modelling

Dr. Maz Fallah (Human Health & Nutritional Sciences)

POSITION DESCRIPTION: They say the eyes are a window to our souls. We continue to show how the eyes intrinsically reflect other brain functions. To this end, we are seeking a strong and independent graduate student to study how eye movements reflect underlying cognitive and perceptual processing, in health and disease. The candidate will investigate how gaze reflects feature- and object-based visual processing, decision-making, target selection, and cognitive strategies. The research involves designing experiments using infrared eye trackers, analyzing gaze metrics (e.g. saccadic reaction times, trajectories, end-point deviations, etc), advancing computational models, and potentially developing neural network models. The successful candidate will have a relevant background (e.g. neuroscience, informatics, psychology, cognitive science, etc) and programming skills (preference for Matlab).

Relevant recent papers in this area include: Oculomotor target selection is mediated by complex objects Gaze patterns during presentation of fixed and random phase radial frequency patterns Perceptual color space representations in the oculomotor system are modulated by surround suppression and biased selection

HOW TO APPLY: All interested MSc candidates need to send a letter of interest, a CV, a copy of university transcripts, a code example, and the name/email address of a referee to: mfallah@uoguelph.ca. All interested PhD candidates need to send a letter of interest, a CV, a copy of university transcripts, a code example, a writing sample (such as a publication, MSc thesis chapter, or other project), and the names and email addresses of two referees to: mfallah@uoguelph.ca. Due to funding constraints, preference will be given to citizens and permanent residents of Canada.

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.

 


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 either May 2022 or September 2022.

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. 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. 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.

 


Browse previous M.Sc./Ph.D. opportunities that have been filled.