Alvin Qiu
Doctor of Medicine and Doctor of Philosophy (MDPhD)
Research Topic
Epigenomic Dysregulation in Synovial Sarcoma
Martin Hirst
Associate Professor
Research Classification
Carcinogenesis
Leukemia
Cellular Differentiation
Bioinformatics
Genomics
Molecular Genetics
Research Interests
Epigenomics
Relevant Degree Programs
Research Methodology
molecular biology
Computational Biology
DNA Sequencing
Recruitment
Complete these steps before you reach out to a faculty member!
Check requirements
- Familiarize yourself with program requirements. You want to learn as much as possible from the information available to you before you reach out to a faculty member. Be sure to visit the graduate degree program listing and program-specific websites.
- Check whether the program requires you to seek commitment from a supervisor prior to submitting an application. For some programs this is an essential step while others match successful applicants with faculty members within the first year of study. This is either indicated in the program profile under "Requirements" or on the program website.
Focus your search
- Identify specific faculty members who are conducting research in your specific area of interest.
- Establish that your research interests align with the faculty member’s research interests.
- Read up on the faculty members in the program and the research being conducted in the department.
- Familiarize yourself with their work, read their recent publications and past theses/dissertations that they supervised. Be certain that their research is indeed what you are hoping to study.
Make a good impression
- Compose an error-free and grammatically correct email addressed to your specifically targeted faculty member, and remember to use their correct titles.
- Do not send non-specific, mass emails to everyone in the department hoping for a match.
- Address the faculty members by name. Your contact should be genuine rather than generic.
- Include a brief outline of your academic background, why you are interested in working with the faculty member, and what experience you could bring to the department. The supervision enquiry form guides you with targeted questions. Ensure to craft compelling answers to these questions.
- Highlight your achievements and why you are a top student. Faculty members receive dozens of requests from prospective students and you may have less than 30 seconds to pique someone’s interest.
- Demonstrate that you are familiar with their research:
- Convey the specific ways you are a good fit for the program.
- Convey the specific ways the program/lab/faculty member is a good fit for the research you are interested in/already conducting.
- Be enthusiastic, but don’t overdo it.
Attend an information session
G+PS regularly provides virtual sessions that focus on admission requirements and procedures and tips how to improve your application.
Master's students
Doctoral students
Postdoctoral Fellows
Any time / year round
Supervision Enquiry
If you have reviewed some of this faculty member's publications, understand their research interests and have reviewed the admission requirements, you may submit a contact request to this supervisor.
Great Supervisor Week Mentions
Each year graduate students are encouraged to give kudos to their supervisors through social media and our website as part of #GreatSupervisorWeek. Below are students who mentioned this supervisor since the initiative was started in 2017.
I’m extremely grateful to have such a brilliant, caring, and enthusiastic supervisor. He has been supportive and motivating at every step of the PhD process. He is not only a role model as a scientist but also as a leader. He motivates his students and directs them on a path to better themselves.
Graduate Student Supervision
Master's Student Supervision (2010 - 2018)
Epigenetic heterogeneity revealed through single-cell DNA methylation sequencing (2018)
Increasing evidence of functional and transcriptional heterogeneity in phenotypically similar single-cells has prompted interest in protocols for obtaining parallel methylome data. Despite appreciable advancements in experimental protocols for single-cell DNA methylation measurements, methods for analyzing the resulting data are still immature. To address the challenge of stochastic data loss associated with single cell measurements, current strategies average methylation in windows or region sets. However previous studies have demonstrated that single CpGs are functional and our analysis of single cell methylation measurements revealed a rapid decay in concordance neighbouring CpG states beyond 1kb. To leverage the information content of individual CpGs in the context of single cell methylation measurements we developed an analytical strategy for deriving single-cell DNA methylation states using individual CpGs, which we term PDclust. We validated PDclust on existing datasets and on data we generated from single index-sorted murine and human hematopoietic stem cells (HSCs) that are highly enriched in functionally defined stem cells. Using PDClust, we identified epigenetically distinct subpopulations within these HSC populations. Strikingly, human cord blood derived HSC populations were separable by donor specific methylation states whereas more differentiated hematopoietic cells separated solely by cell type. Interestingly, removal of methylation sites near genetic variants did not impact this separation, suggesting that these epigenetic states may be a consequence of environmental differences. Finally, through protocol optimization and deep sequencing we generated one of the most comprehensive sets of single cell methylome profiles (20% of CpGs on average) and from these were able to generate genomewide profiles from as little as 6 epigenetically related HSCs to derive subtype-specific regulatory states.
View record
Publications
- MEF2B mutations in non-Hodgkin lymphoma dysregulate cell migration by decreasing MEF2B target gene activation (2015)
Nature Communications, 6 (1) - Epigenomics: Sequencing the Methylome (2013)
Array Comparative Genomic Hybridization, , 39--54 - Next Generation Sequencing Based Approaches to Epigenomics (2013)
Epigenetics and Pathology, 9 (5-6), 317--337 - Applications of New Sequencing Technologies for Transcriptome Analysis (2009)
Annu. Rev. Genom. Human Genet., 10 (1), 135--151 - Epigenetics and human disease (2009)
The International Journal of Biochemistry & Cell Biology, 41 (1), 136--146 - Massively parallel sequencing of the polyadenylated transcriptome of C. elegans (2009)
Genome Research, 19 (4), 657--666 - Genome-wide analysis of Nkx2.2 binding sites using ChIP-tag sequencing (ChIP-TS) (2007)
Developmental Biology, 306 (1), 354
Current Students & Alumni
This is a small sample of students and/or alumni that have been supervised by this researcher. It is not meant as a comprehensive list.
If this is your researcher profile you can log in to the Faculty & Staff portal to update your details and provide recruitment preferences.