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136 days ago


McGill University -

Professor Yue Li is hiring one Postdoc for the machine learning and AI research in healthcare. The position will be held at the School of Computer Science.

The broad adoption of electronic health records (EHR) systems has created rich digital healthcare data and opportunities for conducting transformative health informatics research. However, irregular patient visits, heterogeneous data modalities, restricted EHR data access, and data distribution shifts among hospitals hinder their full utility. Rapidly advancing machine learning (ML) research offer great promise including transformer-based deep generative models and federated learning framework.

In Li lab, we develop explainable AI (xAI) methods that adapt the state-of-the-art AI methods for real-world life science applications pertinent to human health. In a funded project, we proposed 3 aims:

Aim 1: Predicting patient health trajectories using AI. Through our collaboration with the co-PIs at the McGill University Health Centre (MUHC), we have access to irregular longitudinal patient records for over one million patients from Montreal metropolitan area. We will develop a foundational “HealthGPT” model with a focus on predicting future health trajectories of patients by learning the hidden clinical semantics from pretraining on the massive EHR data. We will adapt the recently developed time-series transformer architectures to effectively account for the unequally spaced time-series time in our EHR data.

Aim 2: Robust federated learning in healthcare sectors. Training large neural networks to learn clinical semantics requires big data. Through our extended network, we can gain secure access to patient data on-site beyond MUHC. By using federated learning (FL) framework, we can aggregate model parameters in a central server without sharing the patient data from each hospital. To build a robust FL model, we will tackle data distribution shifts or out-of-distribution (OOD) challenges among hospitals. We will use deep density estimators to model the distributions within health centres and train OOD-aware AI models that are tailored to each hospital in their prediction tasks while harnessing the information across hospitals.

Aim 3: building real-world deployable software healthcare system for federated learning. While many FL algorithms in healthcare were developed, very few have been deployed in the real-world healthcare systems. This aim addresses the software engineering problem in building secure, robust, and efficient network communications between hospitals to deploy state-of-the-art AI methods in the health systems using/adapting existing FL frameworks such as Flower (https://flower.dev/).

Name of the immediate Supervisor:           Yue Li

Work schedule:         Five working days (Monday through Friday)

Working hours:         40 hours per week, 9 a.m. to 5 p.m.

Work location:           Trottier building at McGill Downtown campus

Salary information:   50,000 / year + benefits

 Planned start and end dates of appointment (if applicable):

The position can start on September 1, 2023, and ends on September 1, 2024. The position can be extended by 1 year.

To apply:  Send your CV and cover letter to : yueli@cs.mcgill.ca

157 days ago


University Health Network -

JOB TITLE: Post-Doctoral Fellow in Computational Cancer Biology

Job Posting #: 924521

Site: Princess Margaret Research Institute

Department: Princess Margaret Cancer Center Living Biobank (PMLB)

Reports to: Principal Investigator

Hours: 37.5

Salary: $60,000 – 75,000: To commensurate with experience and consistent with UHN compensation policy

Status: Temporary Full-time (1 Year; with possible extension)

Posted Date: September 16,2023

Closing Date: December 1, 2023

The University Health Network, where “above all else the needs of patients come first”, encompasses Toronto General Hospital, Toronto Western Hospital, Princess Margaret Cancer Centre, Toronto Rehabilitation Institute and the Michener Institute of Education. The breadth of research, the complexity of the cases treated, and the magnitude of its educational enterprise has made UHN a national and international resource for patient care, research and education. With a long tradition of ground breaking firsts and a purpose of “Transforming lives and communities through excellence in care, discovery and learning”, the University Health Network (UHN), Canada’s largest research teaching hospital, brings together over 16,000 employees, more than 1,200 physicians, 8,000+ students, and many volunteers. UHN is a caring, creative place where amazing people are amazing the world.

Position Summary

The PM Living Biobank is headed by Dr. Ming-Sound Tsao, who has over 30 years of experience in cancer pathology. He is the (co-)author of more than 600 peer-reviewed articles in top epigenomic, biology and clinical journals. For an exhaustive list of publications, go to Dr. Tsao’s Google Scholar Profile. Dr. Haibe-Kains has over 15 years of experience in computational analysis of genomic and transcriptomic data, in the context of translational research. He is the (co-)author of more than 200 peer-reviewed articles in top bioinformatics and clinical journals. For an exhaustive list of publications, go to Dr. Haibe-Kains’ Google Scholar Profile. Dr. Lupien has over 20 years of experience in computational analysis of genomic and transcriptomic data, in the context of translational research. He is the (co-)author of more than 130 peer-reviewed articles in top epigenomic, biology and clinical journals. For an exhaustive list of publications, go to Dr. Lupien’s Google Scholar Profile.

The candidate will work in a large multidisciplinary team of 8 laboratories from the Princess Margaret Cancer Centre as part of as part of Terry Fox New Frontiers Research Project:

160 days ago


Centre for Molecular Medicine Norway (NCMM), University of Oslo -

The Computational Biology & Gene Regulation group led by Anthony Mathelier at the NCMM, a part of the Nordic EMBL Partnership for Molecular Medicine, is seeking an ambitious and highly motivated Postdoctoral Fellow or Researcher for a two-year position, starting as soon as possible in 2024. The selected candidate will play a pivotal role in a collaborative project spanning internationally renowned groups, namely those of Drs. Anshul Kundaje at Stanford University, USA, Wyeth Wasserman at the University of British Columbia, Canada, and Anthony Mathelier, NCMM, Norway. The position will be based in Norway. More information about the group can be found at https://mathelierlab.com/.

Join us to not only advance your career but also contribute to meaningful scientific discoveries and resources in the world of computational biology and gene regulation.

Position Description

The selected candidate will contribute to a cutting-edge project aimed at enhancing and expanding computational resources to decipher transcription factor (TF) – DNA interactions. The focus will be on the enhancement of the JASPAR (https://jaspar.elixir.no) and UniBind (https://unibind.uio.no)  databases, which are officially recognized by ELIXIR Norway as Norwegian bioinformatics services. Specifically, the candidate will utilize advanced deep learning techniques to provide refined models and data crucial for the analysis of disease mutations affecting gene expression.

The candidate can refer to the following publications: https://doi.org/10.1093/nar/gkac1143https://doi.org/10.1186/s12864-021-07760-6https://doi.org/10.1038/s41588-021-00782-6https://doi.org/10.1101/2022.12.20.520743https://doi.org/10.48550/arXiv.1704.02685https://doi.org/10.48550/arXiv.1811.00416.

160 days ago


Washington University in St Louis, MO, USA -

Liquid biopsy technology development for early and non-invasive diagnosis of brain tumors

A postdoctoral position with a bioinformatics focus is available in the Molecular Oncology Laboratory of Dr. Dimitrios Mathios, MD, at The Brain Tumor Center of Washington University School of Medicine. Our laboratory aims to harness the expansive knowledge in brain cancer genomics, cancer epigenomics and immunogenomics to design liquid biopsy assays that will help us diagnose patients with brain tumors without the need for invasive surgeries. The goal of the lab is to take the liquid biopsy technologies developed in the lab and translate them to tests that can be used to guide patient care.

Working Conditions

This position works in a laboratory environment with potential exposure to biological and chemical hazards. The individual must be physically able to wear protective equipment and to provide standard care to research animals.

Salary Range

Base pay is commensurate with experience.

Applicant Special Instructions

Interested candidates should send a cover letter, their C.V. and a list of two or three references to mathios@wustl.edu.

162 days ago


University of Alberta -

Are you passionate about unraveling the secrets of RNA and deciphering their functional structures? Do you have a strong background in bioinformatics and a burning curiosity to explore the dynamic world of RNA molecules? If so, we invite you to embark on an exciting research journey with us!

🔬 About Us:

At the Computational Biology Research and Analytics (COBRA) Lab at the University of Alberta, we are at the forefront of cutting-edge RNA research. In collaboration with Dr. Lara Mahal (Professor of Chemistry and Canada Excellence Research Chair in Glycomics) we are seeking a highly motivated and talented postdoctoral researcher to join our team of passionate scientists. Our mission is to advance our understanding of RNA biology and its implications in various biological processes.

🧬 Position Overview:

– **Position**: Postdoctoral Researcher in RNA Bioinformatics

– **Location**: Edmonton, Alberta

– **Duration**: One year with possibility of extension

– **Start Date**: As soon as possible


Why Join Us?

– Work in a dynamic and collaborative research environment.

– Access cutting-edge technology and resources for your research.

– Opportunities for career development and networking.

– Competitive salary and benefits package ($70,000 per annum).

Join us in unraveling the mysteries of RNA and making a significant impact in the field of molecular biology. Apply today and become an integral part of our innovative research team!