To conduct data harmonization across multiple data-types including electronic health records, digital pathology, clinical notes and omics measurements (bulk and spatial) for patients undergoing heart transplantation. This position is strongly focused on method and software development related to 1) learning representations from multimodal data and 2) developing predictive models of rejection trajectories using multimodal data. Major responsibilities: 1) benchmarking existing methodologies for time-series data imputation, clustering and classification, 2) developing methods and software for the analysis of partially observed, multimodal time-series data, and 3) writing research proposals, reports and publications.
The Computational Biology Lab (https://cbl-hli.med.ubc.ca), led by Dr. Amrit Singh is located within the Centre for Heart Lung Innovation, Vancouver, Canada. The lab’s research is focused on understanding the molecular mechanisms of heart and lung disease, with a special interest on biomarker discovery and developing methods and tools for multiomics data integration and visualization.
The PROOF (Prevention of Organ Failure) Centre (www.proofcentre.ca) is a not-for-profit data analytics and biomarker development organization, founded in 2008 and co-hosted by the University of British Columbia (www.ubc.ca) and Providence Health Care (https://www.providencehealthcare.org/). The PROOF Centre harnesses the power of clinical, molecular and computational science, to develop new knowledge and biomarker-based tests to better predict, diagnose, manage and treat patients. Major biomarker programs focus on organ transplant, heart failure, chronic lung diseases, COVID-19, and several vaccine studies.
- Performs data cleaning and analyses of time-series multimodal data such as clinical notes, laboratory values, imaging data and omics data often found in electronic health records (e.g. https://physionet.org/content/mimiciv/0.4/)
- Research and select appropriate analytical methods and software
- Develop analysis plans as needed
- Develop Python scripts for data cleaning, analysis, benchmarking and visualization
- Develops Python libraries leveraging existing libraries for the analysis of multimodal data (e.g. spacy, napari, squidpy, genism, torch, torch_geometric_temporal)
- Works on a team with other researchers, statisticians, and computational biologists in the identification and completion of assigned research projects
- Collaborates with other researchers, clinicians and statisticians to share knowledge and strategies for data analysis
- Provide computational expertise and advice as needed
- Contributes to the development of study design plans
- Develops, implements, tests and documents scripts and procedures to perform analyses
- Assists in preparation of conference presentations, academic manuscripts, grant applications, and technical reports, as required
- Contributes to training and supervision of undergraduate and graduate students
- PhD degree (received within the last 5 years) with proven interest in research
- Proficient in Python and implementation of different deep learning architectures (e.g. ANNs, CNNs, RNNs, GNNs) in PyTorch
- Effective oral and written communication and interpersonal skills
- Able to work independently within a team environment, work on multiple projects concurrently and work effectively under pressure to meet deadlines
- Prior experience with partially observed time-series data is an asset but not a must.
- Prior experience with high performance computing is an asset but not a must.
- Prior experience with omics data is an asset but not a must.
How to Apply:
To be considered, postdoctoral applications must be sent to firstname.lastname@example.org and reference PDF-Mitacs in the subject line. Please add the following to the email:
- Brief statement of research interest
- One reference letter from former supervisor
Due to the volume of candidates, only selected candidates will be invited for an interview.
Anesthesiology, Pharmacology and Therapeutics; PROOF Centre of Excellence
Posting End Date
January 31, 2023
Expected Start Date
February 28, 2023
Note: Applications will be accepted until 11:59 PM on the day prior to the Posting End Date above. However, applications will be reviewed on an ongoing basis such that the position may be filled sooner.
Position: Joint position between the Computational Biology Lab and the PROOF Centre of Excellence.
Duration: 2 years
This posting is for the UBC Vancouver campus in British Columbia, Canada.
Please refer to reference number NC-56827 during correspondence about this position. Please visit the researcher profile of the supervisor for this position to learn more about their research.
Equity and diversity are essential to academic excellence. An open and diverse community fosters the inclusion of voices that have been underrepresented or discouraged. We encourage applications from members of groups that have been marginalized on any grounds enumerated under the B.C. Human Rights Code, including sex, sexual orientation, gender identity or expression, racialization, disability, political belief, religion, marital or family status, age, and/or status as a First Nation, Metis, Inuit, or Indigenous person.
The University of British Columbia is a global centre for research and teaching, consistently ranked among the top 20 public universities in the world. Since 1915, UBC’s entrepreneurial spirit has embraced innovation and challenged the status quo. UBC encourages its students, staff and faculty to challenge convention, lead discovery and explore new ways of learning. At UBC, bold thinking is given a place to develop into ideas that can change the world.
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