Institution/Company:

The University of British Columbia

Location:

Vancouver

, British Columbia

 Canada

Job Type:

Postdoctoral

Degree Level Required:

PhD

46 days ago Apply now

Description:

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.

Responsibilities:

  • 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

Qualifications:

  • 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.

Additional Information:

Organizational Status

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.

How to Apply:

To be considered, postdoctoral applications must be sent to amrit.singh@hli.ubc.ca and reference PDF-Mitacs in the subject line. Please add the following to the email:

  1. Brief statement of research interest
  2. CV
  3. One reference letter from former supervisor

Due to the volume of candidates, only selected candidates will be invited for an interview.

Department

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.

Remuneration: $70,000/year

Duration: 2 years

 

Keywords:

bioinformatics

machine learning

omics

pytorch

python

Posted on: