A bioinformatics analyst position is available at the Département de biologie of the Université de Sherbrooke (Sherbrooke, Québec). The selected candidate will integrate a young, dynamic and multidisciplinary team of researchers in functional genomics/systems biology/synthetic biology, and will be in charge of analyzing data for genome assembly/annotation, transcriptomics (RNA-seq and derivatives), chromatin-immunoprecipitation (ChIP-seq), proteomics, etc. The work will primarily consist in the development of pipelines using of existing computational tools. The candidate will interact directly with principal investigators/postdocs/students, and will play a critical role in the success of innovative research projects. A state-of-the-art computing infrastructure as well as a variety of bioinformatics softwares will be at the disposal of the candidate.

Minimum qualifications
• Masters in bioinformatics or other relevant field, or B.Sc and >3 years of relevant work experience.
• Excellent programming (C, C++, or Java) and scripting (Perl or Python) skills under a UNIX/linux environment
• Solid analytical and statistical skills.
• Ability to multitask and keep track of several projects in parallel.
• Strong abilities for team work, both with other bioinformaticians and with biologists
Preferred qualifications
• Experience handling high-throughput DNA/RNA sequencing data
• Fluent in French and English

Application deadline: September 26th 2011

Funding is guaranteed for two years. This opportunity could lead to a permanent position at the Université de Sherbrooke. To apply formally, submit the following documents in PDF format:

1. A brief statement of research interests, qualifications and experience and why you feel you are a good candidate for this position.
2. Curriculum vitae.
3. The names and contact details of at least two references willing to provide a confidential letter of recommendation upon request.

Please send applications and inquiries to Sébastien Rodrigue (sebastien.rodrigue[at]usherbrooke.ca) or Nicolas Gévry (nicolas.gévry[at]usherbrooke.ca).

Institution / Department:
Laboratory of Dr. Daniel Sinnett
CHU Ste-Justine / Université de Montréal

Description:
We seek a bioinformatician to contribute to various analysis pipelines associated with ultrahigh-throughput DNA sequencing instruments including but not limited to ABI SOLiD, Illumina HiSeq200. Research applications utilizing these platforms include exome sequencing, whole-genome sequencing, whole-transcriptome sequencing (RNA-Seq) in a cancer genomics context. Responsibilities will include using in-house and third party software and algorithms to take sequence output and conduct specialized downstream bioinformatics analyses, and working closely with other members of the bioinformatics and sequencing teams to develop bioinformatics solutions for the analysis of complex large-scale datasets, particularly in the context of cancer.
Candidates should have a minimum of a MSc in Computer science, bioinformatics or a related area (or BSc with 3+ years of work experience). Applicants with computing skills and a strong interest in biological problems from a numerate discipline (engineering, physics, mathematics, biophysics) are also encouraged to apply. Candidates should have expertise in Unix/Linux operating systems, be skilled in the use of MySQL databases and have strong knowledge of programming and scripting languages like Perl, Python, Java, C++. Knowledge of statistical analysis languages such as R is a plus.

This promises to be an exciting and challenging role with the opportunity to work with the latest sequencing technology in an academic research environment.

Application deadline :
Applications will be reviewed immediately and continue until the job is filled

Contact :
Interested candidates may send a letter of interest and CV including names and addresses of referees to :
Dr. Jasmine Healy at jasmine.healy[at]umontreal.ca

Institution / Department / Company:
Caprion Proteomics
(Montreal, Canada Area)

Description:
Caprion is seeking a highly motivated individual with experience in bioinformatics and proteomics. The Bioinformatician will perform analysis of proteomic mass spectrometry data using commercial and proprietary software. The successful candidate will also be responsible for evaluating sources of protein annotations and mass spectrometry data, testing analysis software and automating processes to streamline the production pipeline. The Bioinformatician will also be responsible for documenting various steps of the research platform, implementing QC procedures and providing scientific recommendations to improve the quality of the results.

REQUIREMENTS:
- BSc in Bioinformatics, or equivalent (MS level degree preferred).
- Five years of work experience in genomics, proteomics or related field.
- Experience with a scripting language such as Perl, Python or Ruby.
- Experience with relational databases such as Oracle, SQL Server or MySQL.
- Ability to effectively use SQL to design queries for extraction of data from Oracle and MySQL databases.
- Solid understanding of molecular biology, proteomics and mass spectrometry.
- Strong oral and written communication skills.

Download official Job posting
Contact :
HR Department
careers[at]caprion.com

Institution / Department:
Beaulieu-Saucier Pharmacogenomics Center
U. Montreal (Montreal, Canada Area)

Description:
Summary
Responsible for all data manipulation and data management tasks for the center. This includes the design and maintenance of databases (Oracle, MySQL, SQL Server) to support internal software development; handling of very large data transformation tasks, often converting very large (100+ gB) flat files into a different format for analysis. Development of internal reporting solutions from several different data sources, using SQL and web-based programmatic solutions (Perl). Needs to be comfortable with data manipulation from a wide variety of data sources (flat files, Excel Spreadsheets, MySQL, Oracle, SQL Server and custom sources).

Needed skills
- At least two years of professional experience as a data achitect
- Strong data architecture skills
- Strong SQL/PLSQL
- Strong knowledge of Perl
- Strong knowledge of Linux
- Ability to write ETL code
- Knowledge of web-based programming
- Good knowledge of database administration tasks for Oracle, MySQL and SQL Server (backup, restore, cloning and performance tuning)
- Working knowledge of french and english, but spoken and written

Desired skill
- Knowledge of pharmacogenomics or genetics

Application deadline :
Friday, November 19th, 2010

Contact :
Christopher Beck
cbeck[at]pharmacogenomics.ca

Institution / Department:
Beaulieu-Saucier Pharmacogenomics Center
U. Montreal (Montreal, Canada Area)

Description:
Roles and Duties: This position will participate in the development of cutting-edge software applications and suites dedicated to solving the most pressing and complex challenges in translational biomedical science. A Junior-Level Bioinformatician will work closely with senior members of the PGx team and will contribute to all facets of programming and application building. Specific projects may include front-end web interface/web service development, back-end computational programming, algorithm/tool development, or process scripting. Additional responsibilities will consist of specification/documentation writing, broad-scope and unit-level quality assurance and testing, and diligent code and application maintenance. A junior-level bioinformatician will also be expected to manage project timelines and deadlines and organize team support over multiple project tasks.

REQUIREMENTS:
- A BA/BS in Computer Science, Information Science, or a related field is required for this position.
- Specific experience with Java/C# and Perl (or an equivalent scripting language) is required.
- Experience creating and managing relational databases and familiarity with UNIX environments is desired.
- Prior web development experience (PHP, HTML, Ruby on Rails) is required for this position.
- At least two years’ programming experience is desired.
- Candidate must show a demonstrated aptitude for learning and programming in new languages, possess excellent written and verbal communication skills.

Application deadline :
Friday, November 19th, 2010

Contact :
Christopher Beck
cbeck[at]pharmacogenomics.ca

Institution / Department:
LISA lab
U. Montreal campus, Pavillon Aisenstadt (Montreal, Canada Area)

Description:
The LISA machine learning lab looking for a full-time software developer with experience in large code bases constructed by a team of programmers, with at least a bachelor degree in computer science or software engineering or the equivalent. Preference is given to those with experience in python and C/C++ under linux and open-source code management tools. Prior knowledge in machine learning and statistics are a plus but not necessary to start the job (they will be acquired or refined over the first few months on the job). See the Theano library for an example of the code development taking place at the lab. An important quality of the person sought is leadership, to manage the development of applied machine learning projects or of such a library, with a team of a dozen or more graduate students. That person will be expected to present and explain his ideas and his work, verbally or in writing, and to interact with the lab’s industrial partners, who apply and port into their products the algorithms developed in the lab. Knowledge of French is a plus, as both French and English are used in the lab.

To abide by Canadian labor laws, preference must be given to Canadian citizens or residents.

Skills

Python programming, C++, open source software development, leadership/management skills, numerical computation, statistics, machine learning, French language, written/oral communication skills, agile programming

Application deadline :
Ongoing — until position is filled

Contact :
Yoshua Bengio, bengioy[at]iro.umontreal.ca

Company Description

The LISA is a very successful research lab, with a large number of publications every year, several industrial contracts, and two chairs with long-term funding. The candidate will participate in research projects and technology transfer, and be expected not only to contribute and lead software development efforts but also to interact with partners. The LISA machine learning lab is part of the computer science department of Université de Montréal.

Fondée en 1878, l’Université de Montréal forme aujourd’hui avec ses deux écoles affiliées, l’École Polytechnique et HEC Montréal, le premier complexe universitaire au Québec et le deuxième au Canada. Elle accueille plus de 55 000 étudiants, emploie 10 000 personnes et décerne près de 10 000 diplômes à tous les cycles d’études. Montréalaise par ses racines, internationale par vocation, l’Université de Montréal compte parmi les plus grandes universités de la francophonie.

Institution / Department:
College of Natural Sciences, Department of Information & Computer Sciences
U. of Hawaii Manoa

Description:
Participate as a Junior Bioinformatician in the project, entitled “Pacific Center for Emerging Infectious Diseases Research”. Design and develop bioinformatics and large-scale data analysis research tools and methods in support of research conducted by investigators of the Pacific Center for Emerging Infectious Diseases Research at the University of Hawaii at Manoa. Provide general and customized consulting and assistance. Develop and present bioinformatics training workshops. Maintain the Bioinformatics core computational infrastructure and install and update databases. Assist the Core Director in the planning and organization of the annual Bioinformatics Colloquium. Performs related work and other duties as assigned.

Application deadline :
Continuous – application review begins November 04, 2010

Contact :
Dr. Guylaine Poisson
808-956-3496
guylaine(at)hawaii.edu
Official Listing

Institution / Department:
Awadalla Lab
CHU Ste-Justine / Université de Montréal

Description:
The Awadalla Lab at the CHU Ste-Justine centre de recherche and Université de Montréal is looking for a full time bioinformatician. The work will concern processing genotype and next-generation sequencing data for SNP detection, genomics, and transcriptomics for studies in the genetics of cancer, malaria, immunodeficiency and metabolic health. The appropriate candidate will have strong programming skills and a basic knowledge of genomics. A bachelors or a masters degree in bioinformatics or closely related field is required.
Please send a CV, coverletter, and the names and emails of three references at the contact email below

Application deadline :
Applications will be reviewed immediately and continue until the job is filled

Contact :
philip.awadalla(at)umontreal.ca
Awadalla Lab

Institution / Department:
EmbryoGENE
Laval University

Description:
Le réseau EmbryoGENE (www.embryogene.ca) est à la recherche d’un bioinformaticien/professionnel de recherche pour le développement de nouveaux outils d’analyse de données. Les différentes activités du réseau couvrent :le séquençage à haut débit, la recherche de variants d’épissage, le développement de biopuces d’ADN, la sélection de gènes candidats, la recherche d’orthologues, l’identification de sentiers métabolique, l’étude comparative de résultats obtenus à l’échelle nationale (meta-analyse) et le développement de nouveaux outils d’analyse épigénétique (analyse comparative de la méthylation). (English version not available)

Application deadline :
N / A

Contact :
julie.nieminen(at)fsaa.ulaval.ca
EmbryoGENE