Open positions

PhD position in computational biology: Algorithm development for real-time classification of mass spectrometry data

Job description

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).

Requirements

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.

Applicants must send their application letter, CV and contact information to Arnaud Droit (arnaud.droit@crchuq.ulaval.ca) and Maxence Wisztorski (maxence.wisztorski@univ-lille1.fr).

Javascript Developer for ElasticSearch plugins

Job description

We are looking for an experienced javascript developer to fill a position in our computational biology laboratory. We are developing a bioinformatics analysis portal based on ElasticSearch and are in close contact with an anglophone partner in Ireland. The candidate will work closely with the bioinformaticians of the laboratory and our partner to conceptualize and create javascript visualization plugins compatible with ElasticSearch / kibana, which will solve life science challenges and allow analysis of massive data. The candidate will have to be operational very quickly.

Requirements

– DEC / BAC in computer science, software engineering or equivalent
– Bilingual (English is mandatory, functional French)
– At least 2 years experience in javascript and web development
– 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

Workplace

University Hospital Laval (CHUL), City of Québec.
Possibility of visiting our partner in Ireland for a few weeks.

Availability

As soon as possible

Duration of the contract

12 months and up

Most of our open positions are posted on www.bioinformatics.ca. Search for Université Laval institution.