The next frontier in human genomics explores its tissue specific function and the impact of the environment on the genome. The Canadian Epigenetics, Environment and Health Research Consortium (CEEHRC) has awarded McGill University five year funding (2012-2017) to establish one of two National Epigenomic Mapping Centres (EMCs) as well as an Epigenomic Data Coordination Centre (EDCC), which will operate under the principles of the International Human Epigenome Consortium (IHEC). These Epigenomic Centres are housed in the McGill University and Génome Québec Innovation Centre (Montreal, Canada), a world-class research facility for genomics and bioinformatics located on McGill University’s main campus. The facility holds a number of high-throughput sequencing technology platforms, automated laboratory processes, and large-scale computing supporting an array of genome-wide epigenome mapping techniques (including MethylC-seq, ChIP-seq, RNA-seq).

We are seeking a number of highly motivated and team-oriented individuals with good organizational, interpersonal, and communication skills to join the EMC and EDCC teams to tackle challenges in next-generation epigenomics within a dynamic multi-disciplinary environment.

Start-date: immediate.

Duration: up to 5 years.

BIOINFORMATICS SPECIALISTS
Support and develop various analysis pipelines associated with Next-Generation Sequencing (NGS)-based epigenomics experiments. The relevant techniques include but are not limited to: 1) whole-genome bisulphite sequencing (MethylC-seq.), 2) transcriptomic analysis (RNA-seq and smRNA-seq), and 3) chromatin-immunoprecipitation sequencing (ChIP-seq). The work will involve developing and utilizing sequence analysis pipelines using in-house and 3rd party tools or algorithms, and incorporating these into specialized analysis workflows. The successful candidate will work closely with other members of the Epigenomic Centers and with the wider informatics team and collaborating scientists at the Innovation Centre and beyond.
Duties/Responsibilities: To develop ad-hoc bioinformatics solutions for the analysis of complex genomic datasets, to analyze epigenome data using existing and extended software tools for collaborating scientists.
Qualifications: MSc (or BSc with 3+ years of work experience) in computational biology, mathematics, computer sciences, statistics or molecular biology. Demonstrated computer skills (e.g. programming in Perl, Python, C++, Java, mySQL) are required. Previous experience in processing and analyzing NGS data, genome annotation or in developing sequence analysis pipelines is necessary. Familiarity with databases and statistical computing programs, R and Matlab, would be useful.

BIOINFORMATICS SOFTWARE DEVELOPERS
Create web-interfaces and software for a portal that will be developed as part of the EDCC. Data and meta-data from the CEEHRC initiative will flow into this portal, which will provide summary reports and tools for data visualization, distribution and advanced analysis. This portal will be build from two existing software resources, NANUQ and CBRAIN, which will be adapted for the CEEHRC initiative to facilitate access to epigenomics resources produced by the consortium.
Duties/Responsibilities: Assisting in the design of repository software, protocols and web interfaces for the Epigenomics portal, working independently to implement and maintain bioinformatics software and repository, liaising with developers involved in other aspects of the project (LIMS, pipeline software) to achieve interoperability between modules.
Qualifications: BA or higher degree in computer science, software engineering or bioinformatics. Proficiency in Perl and Java. Demonstrated experience in web architecture and open source frameworks (Wicket Spring, WEB Services, Tomcat, Maven, Struts). Experience with relational database programming, including SQL, Hibernate, Ibatis, MySql). Familiarity with bioinformatics software tools is necessary.

POST-DOCTORAL FELLOWS IN COMPUTATIONAL EPIGENOMICS
A bioinformatics postdoctoral fellow will join a multidisciplinary team of biologists, genomicists, and bioinformaticians within the EMC. The project aims at mapping epigenetic marks (methylation, histone marks, gene expression) in healthy and patient-derived human tissue samples, and linking epigenetic variation to environmental, genetic and phenotypic variation.
Duties/Responsibilities: Primary and higher order analysis of epigenomics data, deconvolve mixed signals due to imperfect sample collection, and integrate them in order to reveal the mechanisms at play and their phenotypic consequences. He/she will face a number of algorithmic and statistical challenges whose solutions will have the potential of being published as methods papers, while specific data analyses will be published in collaboration with the team.
Qualifications: The successful candidate will hold a Ph.D. in bioinformatics or closely related area and will have experience in regulatory genomics or epigenomics. Ability to manage and analyze large biological data sets coming from next generation sequencing is a must, as is working knowledge of algorithms and statistics, and the ability to interact and communicate with biologists.

HOW TO APPLY

Applicants should submit a cover letter explaining their qualifications and their interest in this position, a curriculum vita and the names and contact information for three individuals who could provide letters of recommendation. Applications and all inquiries should be sent to emc.mcgill@gmail.com

Description:
Automated quantitative analysis of rodent behavior will be of vital importance in detection and quantification of complex phenotypes, for comprehensive analysis of human disease models, and for assessing the efficacy of various therapeutic strategies and their unexpected side effects.
This innovative project should enable a scientific community to perform behavioural research faster, more consistently and more efficiently than that which is possible with human observation or other technologies.

We are looking for a Ph.D/MSc Student who will work on new tools for the analysis of the behavioral responses in rodents. The project will provide training in computer vision technology, the design of automated assays and in behavioural analysis and screening techniques in mouse. The successful candidate will develop and validate an automated home-cage system for behavioural phenotyping in rodent. State of the art vision algorithms will be used to detect and identifies the behavioral profiles of the mouse. The motion and postural aspects of the rodent’s behavior are captured by the automated-system and fed into a pattern recognition algorithm where the signal is compared to a reference list of behavioral patterns and classified.
The candidate will be responsible for software development, system evaluation and validation and will have the opportunity to contribute to all aspects of the project.

Our needs:

We ask a Ph.D/MSc degree in statistics/biostatistics, computer science, physics, computational biology or other fields with strong quantitative training. Strong programming skills in C/C++, R, and similar languages are required. Previous experience with genomics or biological data analyses is a plus. You should have interest in phenotyping of laboratory rodent behavior. You should be proficient in English and have excellent scientific writing and presenting skills. You are an enthusiastic team player who is able to work independently, and who has good organizational and communicational skills.

The main tasks are:

1- Development of algorithms for integrated behavior classifications, and for typical behaviors.
2- Development of new analysis tools.
3- Analyzing and statistical testing of data of animal behavior.
4- Development of strategies to analyze complex data and resulting in a graphic representation.
5- Contributing to scientific publications on these topics.

Applications should be sent by email to:
Dr. Mohammed Filali (Mohammed.Filali@crchul.ulaval.ca) or
Dr. Arnaud Droit (arnaud.droit@crchuq.ulaval.ca)

Summary of Responsibilities

The candidate will take a lead role in establishing and managing the Bioinformatics core facility, developing automated analysis pipelines for processing high-throughput genomic data, and implementing in-house bioinformatics tools. Working collaboratively with the other members of the Bioinformatics and Computational laboratory, as well as IRCM researchers and external collaborators, the candidate will gather user and technical requirements, define functional specifications, design report formats, and routinely evaluate and monitor pipeline functioning and efficiency. In addition to the pipeline responsibilities, the candidate will work directly with users in the collection, management, interpretation, and analysis of biological/clinical data, with a focus on high-throughput sequencing data. The candidate will devote his time to the core facility and the Bioinformatics and Computational laboratory which houses the core facility headed by Professor Benjamin Haibe-Kains, to implement novel bioinformatics tools.

Requirements:

• PhD or M.Sc. in bioinformatics, computer science, and/or the life sciences, or a related field and a minimum of 3-5 years experience, more specifically:
• Expertise with a wide range of biological databases and resources, including, but not limited to GenBank, EnsEMBL, the UCSC genome browser, Reactome, and other similar resources.
• Knowledge and proficiency with genomic technologies and their applications, including high-throughput sequencing.
• Proficiency in programming using Perl/Python/Java/C++, statistical programming using R or related tools, web-development, and database query through SQL and ability to prototype software solutions for data analysis.
• Knowledge of standard concepts, practices, and procedures of software development
• Skills in both Unix/Windows environments
• Ability to work in fast paced, agile development environment and to take on a leadership role.
• Excellent problem-solving, organizational, communication and people skills.
• Excellent interpersonal and communication skills as well as the ability to work both independently and collaboratively in a deadline driven environment.
• Proficiency in English, basic knowledge of French is considered an asset.

Working conditions
Full time position with an initial two (2) year contract (renewable).The IRCM offers a competitive range of benefits.

Please submit your resume and cover letter no later than February 26, 2012 stating: Bioinformatics Engineer 1 contest at : benjamin.haibe.kains@ircm.qc.ca or mail to:

Dr. Benjamin Haibe-Kains
Institut de recherches cliniques de Montréal (IRCM)
110, Pine Avenue West
Montreal (Québec) H2W 1R7

A Postdoctoral Research Fellow position is available immediately in the Vaccine and
Infectious Disease Division (VIDD) of the Fred Hutchinson Cancer Research Center
(FHCRC), Seattle, W A. The successful applicant will work with Dr. Raphael Gottardo to develop statistical and computational methods for analyzing and integrating high throughput data from immunological assays such as flow cytometry, antigen microarrays, next generation sequencing, etc. He/She will also work with scientists from VIDD to apply the tools in the field of computational immunology and vaccine development. The successful applicant will interact with both scientists in VIDD and in the program in Computational Biology. The FHCRC provides a highly interactive and supportive environment for junior investigators to grow and develop their future career; it consistently ranks in the top 20 best places to work for postdocs, as surveyed by The Scientist.

Qualifications

Suitable applicants should have a PhD degree in statistics/biostatistics, computer science, applied mathematics, electrical/biomedical engineering, physics, computational biology or other fields with strong quantitative training. Strong programming skills in C/C++, R or similar languages are required. Previous experience with genomics or biological data analyses is a plus.

Pay,Benefits, & Work Schedule

Full time position, salary based on the NIH scale + excellent benefits

How To Apply
Visit this link

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).

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

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

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

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

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.