Benjamin Good
Job Title
Assistant Professor
Employer
The Scripps Research Institute
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Overview
The Doctor of Philosophy in Bioinformatics (PhD)is an interdisciplinary program that combines the application of computer technology to the management and analysis of biological data. The result is that computers are being used to organize data generated from experiments into databases, develop new algorithms and software, and use this software for the interpretation and analysis of the data into meaningful biological information. For the past ten years, our PhD program has been training students to organize, visualize, analyze and interpret biological data. Students have access to world renowned bioinformaticians at the University of British Columbia, Simon Fraser University and the BC Cancer Agency, and have exposure to the latest technologies to develop their skills.
Strategic Program Objectives:
- To build on British Columbia's reputation and excellence in bioinformatics.
- To integrate bioinformatics into basic biology to further current research excellence in other life science sectors of the province.
- To foster collaborations locally, nationally and internationally.
What makes the program unique?
The Bioinformatics PhD program integrates academic centres in computer science, statistics, molecular biology and biotechnology, with translational groups at hospitals and at the clinical interface. The innovative partnership among the University of British Columbia, Simon Fraser University and the BC Cancer Agency allows students' access to experts in the field of bioinformatics, and exposure to original research and opportunities to complete significant practical work on real bioinformatics problems. Internships allow student mobility between Canadian and international universities, institutions and industries to further enhance collaborations among Canadian high-technology research groups in both the private and public sectors.
Program Structure
The major requirement for the Ph.D. is completion of a research dissertation meeting the Faculty of Graduate and Postdoctoral Studies requirements. There are no specific course requirements for the Ph.D. degree program apart from the dissertation. However, the student's Ph.D. dissertation committee has the prerogative to impose course requirements where course deficiencies are perceived.
All doctoral students are required to successfully complete a comprehensive examination, which consists of an oral and written component within the first 36 months of study. All students are required to present a Bioinformatics graduate program seminar upon completion of their program, and before their dissertation defense.
A student's committee for the doctorate will consist of the dissertation supervisor and three others. The supervisor and at least one other member must be members of the Bioinformatics graduate program.
Quick Facts
Program Enquiries
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Admission Information & Requirements
Program Instructions
Students must secure a supervisor before they can be admitted into the program. As well, they must meet the minimum admission requirements set out by Graduate and Post-doctoral Studies at UBC.
1) Check Eligibility
Minimum Academic Requirements
The Faculty of Graduate and Postdoctoral Studies establishes the minimum admission requirements common to all applicants, usually a minimum overall average in the B+ range (76% at UBC). The graduate program that you are applying to may have additional requirements. Please review the specific requirements for applicants with credentials from institutions in:
Each program may set higher academic minimum requirements. Please review the program website carefully to understand the program requirements. Meeting the minimum requirements does not guarantee admission as it is a competitive process.
English Language Test
Applicants from a university outside Canada in which English is not the primary language of instruction must provide results of an English language proficiency examination as part of their application. Tests must have been taken within the last 24 months at the time of submission of your application.
Minimum requirements for the two most common English language proficiency tests to apply to this program are listed below:
TOEFL: Test of English as a Foreign Language - internet-based
Overall score requirement: 100
Reading
22
Writing
21
Speaking
21
Listening
22
IELTS: International English Language Testing System
Overall score requirement: 7.0
Reading
6.0
Writing
6.0
Speaking
6.0
Listening
6.0
Other Test Scores
Some programs require additional test scores such as the Graduate Record Examination (GRE) or the Graduate Management Test (GMAT). The requirements for this program are:
The GRE is not required.
Prior degree, course and other requirements
Prior Degree Requirements
Students admitted to the Ph.D. degree program normally possess an M.Sc. degree in Bioinformatics or a related area, with clear evidence of research ability or potential.
Document Requirements
CV, Official transcripts, three letters of reference, Official English exam scores (if required)
2) Meet Deadlines
September 2025 Intake
Application Open Date
01 April 2024Canadian Applicants
Application Deadline: 15 January 2025
Transcript Deadline: 15 January 2025
Referee Deadline: 30 January 2025
International Applicants
Application Deadline: 15 January 2025
Transcript Deadline: 15 January 2025
Referee Deadline: 30 January 2025
3) Prepare Application
Transcripts
All applicants have to submit transcripts from all past post-secondary study. Document submission requirements depend on whether your institution of study is within Canada or outside of Canada.
Letters of Reference
A minimum of three references are required for application to graduate programs at UBC. References should be requested from individuals who are prepared to provide a report on your academic ability and qualifications.
Statement of Interest
Many programs require a statement of interest, sometimes called a "statement of intent", "description of research interests" or something similar.
Supervision
Students in research-based programs usually require a faculty member to function as their thesis supervisor. Please follow the instructions provided by each program whether applicants should contact faculty members.
Instructions regarding thesis supervisor contact for Doctor of Philosophy in Bioinformatics (PhD)
All applicants need firm commitment from a supervisor prior to applying.
Citizenship Verification
Permanent Residents of Canada must provide a clear photocopy of both sides of the Permanent Resident card.
4) Apply Online
All applicants must complete an online application form and pay the application fee to be considered for admission to UBC.
Research Information
Program Components
Students who secure an NSERC-CREATE scholarship will undertake a 3-4 month internship that may be local, within Canada or at an international University or Institution.
Research Facilities
Bioinformatics faculty are spread throughout the UBC campus, as well as off-campus at the BC Cancer Research Centre or hospital research labs and Institutions.
Tuition & Financial Support
Tuition
| Fees | Canadian Citizen / Permanent Resident / Refugee / Diplomat | International |
|---|---|---|
| Application Fee | $116.25 | $168.25 |
| Tuition * | ||
| Installments per year | 3 | 3 |
| Tuition per installment | $1,838.57 | $3,230.06 |
| Tuition per year (plus annual increase, usually 2%-5%) | $5,515.71 | $9,690.18 |
| Int. Tuition Award (ITA) per year (if eligible) | $3,200.00 (-) | |
| Other Fees and Costs | ||
| Student Fees (yearly) | $1,116.60 (approx.) | |
| Costs of living | Estimate your costs of living with our interactive tool in order to start developing a financial plan for your graduate studies. | |
* Regular, full-time tuition. For on-leave, extension, continuing or part time (if applicable) fees see UBC Calendar.
All fees for the year are subject to adjustment and UBC reserves the right to change any fees without notice at any time, including tuition and student fees. Tuition fees are reviewed annually by the UBC Board of Governors. In recent years, tuition increases have been 2% for continuing domestic students and between 2% and 5% for continuing international students. New students may see higher increases in tuition. Admitted students who defer their admission are subject to the potentially higher tuition fees for incoming students effective at the later program start date. In case of a discrepancy between this webpage and the UBC Calendar, the UBC Calendar entry will be held to be correct.
All fees for the year are subject to adjustment and UBC reserves the right to change any fees without notice at any time, including tuition and student fees. Tuition fees are reviewed annually by the UBC Board of Governors. In recent years, tuition increases have been 2% for continuing domestic students and between 2% and 5% for continuing international students. New students may see higher increases in tuition. Admitted students who defer their admission are subject to the potentially higher tuition fees for incoming students effective at the later program start date. In case of a discrepancy between this webpage and the UBC Calendar, the UBC Calendar entry will be held to be correct.
Financial Support
Applicants to UBC have access to a variety of funding options, including merit-based (i.e. based on your academic performance) and need-based (i.e. based on your financial situation) opportunities.
Program Funding Packages
All students accepted by a faculty member and enrolled in the program will be paid a minimum stipend of $24,300/year.
Average Funding
Based on the criteria outlined below, 30 students within this program were included in this study because they received funding through UBC in the form of teaching, research, academic assistantships or internal or external awards averaging $32,229.
- 9 students received Teaching Assistantships. Average TA funding based on 9 students was $10,203.
- 20 students received Research Assistantships. Average RA funding based on 20 students was $24,220.
- 2 students received Academic Assistantships. Average AA funding based on 2 students was $3,698.
- 30 students received internal awards. Average internal award funding based on 30 students was $9,330.
- 5 students received external awards. Average external award funding based on 5 students was $20,667.
Study Period: Sep 2022 to Aug 2023 - average funding for full-time PhD students enrolled in three terms per academic year in this program across years 1-4, the period covered by UBC's Minimum Funding Guarantee. Averages might mask variability in sources and amounts of funding received by individual students. Beyond year 4, funding packages become even more individualized.
Review methodology
Review methodology
Scholarships & awards (merit-based funding)
All applicants are encouraged to review the awards listing to identify potential opportunities to fund their graduate education. The database lists merit-based scholarships and awards and allows for filtering by various criteria, such as domestic vs. international or degree level.
Graduate Research Assistantships (GRA)
Many professors are able to provide Research Assistantships (GRA) from their research grants to support full-time graduate students studying under their supervision. The duties constitute part of the student's graduate degree requirements. A Graduate Research Assistantship is considered a form of fellowship for a period of graduate study and is therefore not covered by a collective agreement. Stipends vary widely, and are dependent on the field of study and the type of research grant from which the assistantship is being funded.
Graduate Teaching Assistantships (GTA)
Graduate programs may have Teaching Assistantships available for registered full-time graduate students. Full teaching assistantships involve 12 hours work per week in preparation, lecturing, or laboratory instruction although many graduate programs offer partial TA appointments at less than 12 hours per week. Teaching assistantship rates are set by collective bargaining between the University and the Teaching Assistants' Union.
Graduate Academic Assistantships (GAA)
Academic Assistantships are employment opportunities to perform work that is relevant to the university or to an individual faculty member, but not to support the student’s graduate research and thesis. Wages are considered regular earnings and when paid monthly, include vacation pay.
Financial aid (need-based funding)
Canadian and US applicants may qualify for governmental loans to finance their studies. Please review eligibility and types of loans.
All students may be able to access private sector or bank loans.
Foreign government scholarships
Many foreign governments provide support to their citizens in pursuing education abroad. International applicants should check the various governmental resources in their home country, such as the Department of Education, for available scholarships.
Working while studying
The possibility to pursue work to supplement income may depend on the demands the program has on students. It should be carefully weighed if work leads to prolonged program durations or whether work placements can be meaningfully embedded into a program.
International students enrolled as full-time students with a valid study permit can work on campus for unlimited hours and work off-campus for no more than 20 hours a week.
A good starting point to explore student jobs is the UBC Work Learn program or a Co-Op placement.
Tax credits and RRSP withdrawals
Students with taxable income in Canada may be able to claim federal or provincial tax credits.
Canadian residents with RRSP accounts may be able to use the Lifelong Learning Plan (LLP) which allows students to withdraw amounts from their registered retirement savings plan (RRSPs) to finance full-time training or education for themselves or their partner.
Please review Filing taxes in Canada on the student services website for more information.
Cost Estimator
Applicants have access to the cost estimator to develop a financial plan that takes into account various income sources and expenses.
Career Outcomes
12 students graduated between 2005 and 2013. Of these, career information was obtained for 12 alumni (based on research conducted between Feb-May 2016):
RI (Research-Intensive) Faculty: typically tenure-track faculty positions (equivalent of the North American Assistant Professor, Associate Professor, and Professor positions) in PhD-granting institutions
TI (Teaching-Intensive) Faculty: typically full-time faculty positions in colleges or in institutions not granting PhDs, and teaching faculty at PhD-granting institutions
Term Faculty: faculty in term appointments (e.g. sessional lecturers, visiting assistant professors, etc.)
Sample Employers in Higher Education
McGill UniversityStanford university
University of California - Santa Cruz
Harvard University
Simon Fraser University
University of California - Los Angeles
Sample Employers Outside Higher Education
Princess Margaret Cancer CentreVancouver Prostate Centre
Centre for Addiction and Mental Health
Dana Farber Cancer Institute
Omicia
Scripps Research Institute
Sample Job Titles Outside Higher Education
Postdoctoral Fellow (3)Independent Scientist
Senior Director of Bioinformatics
Assistant Professor
PhD Career Outcome Survey
You may view the full report on career outcomes of UBC PhD graduates on outcomes.grad.ubc.ca.Disclaimer
These data represent historical employment information and do not guarantee future employment prospects for graduates of this program. They are for informational purposes only. Data were collected through either alumni surveys or internet research.Alumni on Success
Enrolment, Duration & Other Stats
These statistics show data for the Doctor of Philosophy in Bioinformatics (PhD). Data are separated for each degree program combination. You may view data for other degree options in the respective program profile.
ENROLMENT DATA
| 2023 | 2022 | 2021 | 2020 | 2019 | |
|---|---|---|---|---|---|
| Applications | 24 | 22 | 36 | 33 | 27 |
| Offers | 5 | 9 | 10 | 9 | 4 |
| New Registrations | 2 | 6 | 7 | 8 | 4 |
| Total Enrolment | 52 | 49 | 47 | 44 | 42 |
Completion Rates & Times
This program has a graduation rate of 91% based on 25 students admitted between 2011 - 2014. Based on 16 graduations between 2020 - 2023 the minimum time to completion is 4.1 years and the maximum time is 8.88 years with an average of 6.1 years of study. All calculations exclude leave times.
Disclaimer
Admissions data refer to all UBC Vancouver applications, offers, new registrants for each registration year, May to April, e.g. data for 2022 refers to programs starting in 2022 Summer and 2022 Winter session, i.e. May 1, 2022 to April 30, 2023. Data on total enrolment reflects enrolment in Winter Session Term 1 and are based on snapshots taken on November 1 of each registration year. Program completion data are only provided for datasets comprised of more than 4 individuals. Graduation rates exclude students who transfer out of their programs. Rates and times of completion depend on a number of variables (e.g. curriculum requirements, student funding), some of which may have changed in recent years for some programs.
Upcoming Doctoral Exams
Friday, 6 December 2024 - 10:00am - 351, Biomedical Research Centre, 2222 Health Sciences Mall
Ishika Luthra
Guiding Future Genomics Research through Machine Learning: Functional DNA Analysis and Benchmarking
Research Supervisors
Supervision
Students in research-based programs usually require a faculty member to function as their thesis supervisor. Please follow the instructions provided by each program whether applicants should contact faculty members.
Instructions regarding thesis supervisor contact for Doctor of Philosophy in Bioinformatics (PhD)
All applicants need firm commitment from a supervisor prior to applying.
Advice and insights from UBC Faculty on reaching out to supervisors
These videos contain some general advice from faculty across UBC on finding and reaching out to a supervisor. They are not program specific.
This list shows faculty members with full supervisory privileges who are affiliated with this program. It is not a comprehensive list of all potential supervisors as faculty from other programs or faculty members without full supervisory privileges can request approvals to supervise graduate students in this program.
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Munzner, Tamara (Human-centered computing; visualization; information visualization; visual analytics; data science)
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Murphy, Michael (Bacteriology; Enzymes (including kinetics and mechanisms, and biocatalyst); Alternatives to antibiotics; Bacterial pathogenesis; Biological and Biochemical Mechanisms; Functional and Structural Proteomics; Microbial metal metabolism)
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Ng, Raymond Tak-yan (Data mining and analysis, health informatics, text summarization, text mining)
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Otto, Sarah (evolution, mathematical modeling, population genetics, genomic evolution, evolution of sex, yeast experimental evolution, Population genetics and evolutionary biology, yeast)
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Overall, Christopher Mark (Blood research, antiviral immunity)
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Park, Yongjin (Other basic medicine and life sciences; High dimensional data analysis; Biostatistical methods; Bioinformatics; single-cell genomics; Computational Biology; Causal inference; Bayesian machine learning)
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Pavlidis, Paul (Neurosciences, medical and physiological and health aspects; Engineering and technology; genomics; Bioinformatics; cellular and molecular neuroscience; Genetics; disorders of the nervous system; single-cell genomics; Computational Biology; Gene regulation)
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Plotkin, Steven (Biophysics theory and computation )
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Rieseberg, Loren (Bioinformatics; Genomics; Plant biology; adaptation; crops; invasive plants; plant evolutionary biology; speciation; weeds)
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Roth, Andrew (Bioinformatics; Cancer Evolution; Cancer omics data; computational statistics; Computational Biology; computational methods for studying clonal population structures and tumour evolution; Evolutionary cancer biology; genomics; Machine Learning; Methodological work in computational statistics; Molecular Oncology)
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Singh, Amritpal (Other basic medicine and life sciences; single cell multiomics; single cell spatial multiomics; data integration; Machine Learning; Biomarkers; heart and lung disease; High dimensional data analysis; Bioinformatics)
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Steidl, Christian (Hematological tumours; Cancer; Cancer biology; Pathology; lymphoma; tumor microenvironment; Precision Medicine; genomics)
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Steif, Adi (Bioinformatics; Algorithms and computational genomics; Genomics; Cancer genetics; Mechanisms of carcinogenesis; Cancer progression and metastasis; Statistical methods for high throughput data; High dimensional data analysis; Computational Biology; Machine Learning; Cancer Genomics; Single cell sequencing; Tumour evolution; Genomic technology development)
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Suttle, Curtis (Bioinformatics; Fisheries sciences; Immunology; Microbiology; Oceanography; Plant biology; Biological Oceanography; Environmental Virology; Marine Environment; Marine Microbiology; Microbial Diversity; Phage; Viral Discovery; Viruses)
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Swindale, Nicholas Vaughan (Bioinformatics; Neurosciences, biological and chemical aspects; Neurosciences, medical and physiological and health aspects; Eye and Visual System Diseases; Neuronal Modeling; Neuronal Systems; Visual System)
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Takei, Fumio (Molecular immunology, cancer, cell-cell interactions)
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Talhouk, Aline (Human reproduction and development sciences; Computer Science and Statistics; Epidemiology; Bioinformatics; Cancer of the Reproductive System; diagnostic models; Digital health; Machine Learning; personalized medicine; prevention; Privacy)
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Tam, Roger (Machine learning; Biomedical signal processing; Biomedical Design and Innovation; Biomedical Technologies; Computer Science and Statistics; Data Analytics; Medical Imaging; Machine Learning; Neurodegenerative diseases; Precision Medicine; Radiology)
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Tokuyama, Maria (Virology; Endogenous retroviruses (ERVs); Chronic interaction between viruses and the immune system)
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Tremlett, Helen (Epidemiology (except nutritional and veterinary epidemiology); multiple sclerosis; Neuroepidemiology; Pharmacoepidemiology; prodrome,; Drug safety and effectiveness; Pharmacogenomics; comorbidities; health administrative data; Gut microbiome; prodromes)
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Tropini, Carolina (Microbiology; Medical and biomedical engineering; Physical sciences; Bacteria; Bacteriophages; Bioengineering; Bioinformatics; Biological and Biochemical Mechanisms; Biophysics; Gut microbiota; Inflammatory bowel disease)
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Vallance, Bruce (Enteric bacterial pathogens, innate immunity, instestinal inflammation, host defense, inflammatory bowel disease, immunity in health and disease)
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Velenosi, Thomas (Pharmacology and pharmaceutical sciences, n.e.c.; Cancer drug development and therapeutics; Cancer molecular targets; Metabolomics; Lipid biology (including lipidomics); Pharmacometabolomics; Pharmacology; Lipidomics; mass spectrometry; Cancer; Stable isotope tracing; Bioinformatics)
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Wang, Zhen (Signal processing theory and applications, bioinformatics)
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Wasserman, Wyeth (Medical, health and life sciences; Medical and biomedical engineering; Creation of computational methods for the analysis of genome sequences (bioinformatics); Study of cis-regulatory elements controlling gene transcription; Applied analyses of genome sequences (genomics); Indigenous genomics)
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Doctoral Citations
A doctoral citation summarizes the nature of the independent research, provides a high-level overview of the study, states the significance of the work and says who will benefit from the findings in clear, non-specialized language, so that members of a lay audience will understand it.
| Year | Citation |
|---|---|
| 2020 | Dr. Chu improved the process of using computers to extract meaningful information from biological sequences such as DNA. He designed computer programs to store data in probabilistic data structures, which purposely store data as approximate signatures in order to surpass the computational memory and speed limits of representing the data perfectly. |
| 2020 | Dr. Gatev developed a new method for analyzing epigenetic data to characterize genomic regions of concordant DNA methylation, which is an important part of the epigenome. His approach was used to characterize sex differences in DNA methylation of blood tissue. This work will improve statistical discovery and validation in future applications. |
| 2019 | Dr. Lever developed methods to extract biomedical knowledge from published academic papers. Working at BC Cancer's Genome Sciences Centre, he used machine learning approaches to find genetic information useful to clinicians treating cancer patients in a personalized way. His results are accessed daily by cancer researchers around the world. |
| 2019 | DNA sequencing machines read the A, C, G, and T nucleotides that compose chromosomes, but they read only short snippets of DNA and make errors. Dr. Jackman developed tools to reconstruct the true genome sequence from imperfect DNA sequencing reads. He used these tools to assemble the western red cedar genome, which is four times larger than the human genome. |
| 2018 | Dr. Shrestha developed computational algorithms to identify and prioritize cancer driver genes. He identified a novel molecular subtype of malignant peritoneal mesothelioma, potentially vulnerable to immunotherapy. His work helps clinicians contextualize genomic information in clinical decision making, thus enabling precision oncology. |
| 2017 | Dr. Shi created computer methods that identify which DNA sequence alterations impact the on/off switches for gene activity. This research will help us understand how each person's DNA increases or decreases the risk for health problems. |
| 2017 | Dr. Mohamadi designed and developed a collection of novel algorithms and software tools for the analysis of massive bioinformatics data. Theses algorithms and software tools are publicly available for free to facilitate research at health and life sciences laboratories and other organizations worldwide. |
| 2017 | Dr. Chan studied how tumours from lymphoma patients evolved over time under treatment. He identified markers of treatment resistance that can be used towards the design of future diagnostic tests. His work exemplifies the application of genomics in precision medicine. |
| 2016 | Human genome sequencing is now being used to discover the cause of genetic diseases. Dr. Shyr's research improves the way doctors interpret a patient's DNA, and presents a novel computational algorithm to analyze DNA data. Collaborating with the BC Children's Hospital, his research provides patients with access to personalized treatments. |
| 2016 | Dr. Chen studied Bioinformatics to examine gene regulation as it applies to biological hypotheses. Her work contributes to a better understanding of the hierarchical regulation of genes and the differential expression between the sexes. This work will further our understanding of diseases and phenotypes. |
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Sample Thesis Submissions
Further Information
Specialization
Bioinformatics combines computational and biological disciplines.
Program Website
Faculty Overview
Academic Unit
Program Identifier
VGDPHD-CS
Classification
September 2025 Intake
Application Open Date
01 April 2024 Canadian Applicant Deadline
15 January 2025 International Applicant Deadline
15 January 2025 Program Enquiries
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Contact the program
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