Skip to Content »

MonBUG » author archive

 MonBUG is back!

Please RSVP for the first MonBUG meeting in 2015, on Wednesday March the 4th at 16:00.

We are establishing lists of potential speakers for future meetups. Please do not hesitate to contact us if you want to present on the project on which you are working, a bioinformatics tool you like, mathematics, … Given the diversity of fields covered by bioinformatics, we will try and organize each meeting around a common theme.

Stay tuned.

 PhD in bioinformatics @ U. Laval

At the Université Laval (Québec, Canada), we are seeking a PhD student with strong background and interest in Bioinformatics and Biostatistics to work on the regulation of
(and by) non-coding DNA using ultra high throughput sequencing data. The computational biology laboratory, headed by Professor Arnaud Droit, is developing new computational
biology tools for the next-generation sequencing data analysis. The candidate will be jointly supervised by Professors Arnaud Droit (computational biologist) and Lajmi
Lakhal-Chaieb (biostatician) and will work in collaboration with experimental biologists who will test hypotheses generated from the computational analyses back in the lab.
The position involves the development of R / Bioconductor packages for the analysis of high-throughput data, including computational algorithms development and
implementation of creative solutions for large volume data management and processing.

The successful candidate is expected to develop novel statistical algorithms relevant to the analysis of high throughput assays and to implement them into software programs
that are reusable, computationally efficient and effective.

The successful candidate will be awarded a competitive scholarship for a period of three years starting September 2012.


• A M.Sc. degree (or higher) in bioinformatics/statistics/computer science/applied mathematics or related field is required.
• Knowledge of R and C/C++ is a must.
• Must be organized and detail-oriented
• Good oral and written communication skills.

Interested graduate students must contact Arnaud Droit ( and Lajmi Lakhal-Chaieb ( as soon as possible.

 Scientists in Epigenomic Mapping by HTS

Institution / Department:
McGill University
Montréal, Qc

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.


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.


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.


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.


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


 Marie-Pierre Dubé

Talk Title :
Pharmacogenomics of warfarin: beyond dose prediction

Date / Time / Location:
Thursday April 12th, 2012 – 4:00 pm
Room S1-151 at IRIC

Affiliation :

Marie-Pierre Dubé

Abstract :
Warfarin is the most widely used medication to treat blood clots and to prevent new clots from forming. Unfortunately, it is also associated with serious bleeding that can lead to hospitalization and death. Despite recent advances in our ability to use genetics to predict a patient’s optimal warfarin therapeutic dose, a significant portion of patients still experience wide fluctuations in their monitoring results during long term therapy with warfarin. The present talk will present the strategies used by our group to find predictive genetic signatures of unstable warfarin test results associated with higher risk of bleeding.

 Ph.D/MSc Bioinformatics Student

Institution / Department:
Université Laval, Québec, Genomic Research Center
Québec, Qc

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 ( or
Dr. Arnaud Droit (

 Jackie Vogel

Talk Title :
Phosphorylation of γ-tubulin orchestrates polar microtubule formation during spindle assembly

Date / Time / Location:
Thursday March 8th, 2012 – 4:00 pm
Room S1-151 at IRIC

Affiliation :

Jackie Vogel

Abstract :
It is essential to accurately partition DNA during the division of biological cells. The mitotic spindle performs this function in eukaryotic cells. The spindle is a mechanically coupled and stereotyped biological machine with a well-defined parts list; microtubules, DNA (chromosomes), proteins that act as force-generators (molecular motors) or couple microtubules to chromosomes or each other, and signaling proteins (for example cyclin dependent kinase; Cdk1) which provide temporal and spatial control. Spindles in both budding yeast and human cells have two common design features; (1) microtubules that project from the spindle poles and attach to chromosomes, promoting the directed movement of chromosomes towards the spindle poles and (2) pairs of microtubules projecting from opposite poles which undergo anti-parallel sliding and drives spindle elongation. In the case of budding yeast, the system is very minimal- one microtubule attaches to each of the 16 duplicated chromosome (32), and 3-4 pairs of anti-parallel microtubules. All microtubules are assembled at nucleation sites containing γ-tubulin, an evolutionarily conserved microtubule nucleator, located at the spindle poles. Both sets of microtubules are critical for forming a functional bi-polar spindle. We use this simple system to characterize the roles of specific molecules in this process. Using a diverse set of quantitative tools, based in single cell and population measurements, we show that g-tubulin plays an unexpected role in orchestrating the formation of anti-parallel microtubules during the assembly of mitotic spindle. We propose a model where Cdk1-dependent phosphorylation of γ-tubulin allows each microtubule to behave independently of its neighbors during spindle assembly.

 Bioinformatics Engineer 1

Institution / Department:
Laboratory of Dr. Benjamin Haibe-Kains
Institut de recherches cliniques de Montréal (IRCM)

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.


  • 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 : or mail to:

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

 Post-Doc in Statistical genomics/Computational Biology

Institution / Department:
Laboratory of Dr. Raphael Gottardo
Fred Hutchinson Cancer Research Center

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.


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

 Simon Girard

Talk Title :
The personal genome ; A reality or a myth?

Date / Time / Location :
Thursday February 9th, 2012 – 4:00 pm
Room S1-151 at IRIC

Affiliation :
CHUM Research Centre

Simon Girard

Abstract :
The last decade has been revolutionary for the field of genetic / genomic. First, through mass genotyping studies, it has been possible to decipher the complexity of genomic variations. The recent breakthroughs in sequencing studies have allowed us to transpose our knowledge of genomic variations down to the level of a single individual. In the distance, we can see an era where an individual’s genome will be the key to a more personalized and efficient healthcare. However, before we get there, many challenges still have to be overcome. Possibly the biggest of those challenges is the lack of appropriate bioinformatic ressources to bring the personal sequencing to a population scale. Furthermore, our comprehension of many complex diseases is still too incomplete to be transfered to a single individual. The topic of this talk will be to discuss the bioinformatics challenges that stand in the way of the application of personal genome in everyday’s medicine.


 Cédric Chauve

Talk Title :
Looking for lost genomes

Date / Time / Location :
Wednesday December 14th, 2011 – 4:00 pm
Room 232, Leacock Building
McGill University
855 Sherbrooke Street West

This talk is sponsored by :

Affiliation :
Simon Fraser University

Cédric Chauve

Abstract :
Paleogenomics aims at reconstructing the genomes of extinct species, whose DNA can not be sequenced due to molecular decay. Hence the only possible approach is the study of current genomes (i.e. descendants of these extinct species) to detect conserved features that might indicate ancestral genomic characters and then to assemble these characters into ancestral genomes. In this talk I will describe recent (successfull?) efforts to reconstruct the architecture of ancient vertebrate genomes, from placental mammalians to amniotes.