PhD position in computational biology: Algorithm development for real-time classification of mass spectrometry data
A PhD position in bioinformatics/computational biology is available at Laval University in the CHU de Quebec Research Center under the supervision of Dr Arnaud Droit and Dr Maxence Wisztorski from Université de Lille.
The so-called ‘omics’ technologies (genomics, transcriptomics, protemics, metabolomics, etc.) are powerful assets to understand biological mechanisms. However, these technologies generate a huge amount of heterogeneous data (Big Data). A new generation of bioinformatics tools is thus necessary to make optimal use of experimental data in multi-omic contexts.
The candidate will work on the computational biology problems involving real-time classification (both supervised and unsupervised) of mass spectrometry analytes. Mass spectrometry is used in several fields, such as biological and medical research, forensic sciences or food quality control, to finely characterize a sample or to classify samples. Recent technological developments in mass spectrometry have opened the possibility of real-time analysis in clinical and industrial context. For example, a hand-held instrument attached to a mass-spectrometer could provide instant feedback to an operating surgeon about the molecular characterization of a tumour.
The candidate will develop various multivariate analytic strategies and test their efficiency in classifying biological analytes based on mass-spectrometry data obtained from a prototype instrument. The candidate will also work on the implementation and optimisation of the best analytic strategies with the goal of providing a real-time solution.
The successful candidate will work with a dynamic team of 12 bioinformaticians at the CHU de Québec Research Center in a lively multidisciplinary context. He works also with researcher from Université de Lille. The candidate will have access to Compute Canada high performance computing (HPC) facilities. The bioinformatics group work in close collaboration with Compute Canada to port software tools to HPC infrastructure. The group also work in close collaboration with the various core facilities of the research center that offer data analysis services (including the proteomics facility that just acquired Orbitrap Fusion, Sciex 6500, 5600 and Synapt G2 Si).
A degree in bioinformatics, statistics, computer sciences or in a related discipline and a demonstrated knowledge of biochemistry are required. Experience programming with the R language is an asset.
– DEC / BAC in computer science, software engineering or equivalent
– Bilingual (English is mandatory, functional French)
– Be familiar with the D3, Angular, Node.js libraries
– Be familiar with NoSQL and ElasticSearch / kibana
– Be familiar with linux / freebsd environment
– Being familiar with python
University Hospital Laval (CHUL), City of Québec.
Possibility of visiting our partner in Ireland for a few weeks.
As soon as possible
Duration of the contract
12 months and up