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

Description:
Gérer les demandes des clients utilisateurs de l’application web Nanuq, s’assurer de leur compréhension et de leur satisfaction face à l’application. (English version not available)

For more information, visit the Genome Quebec Website

Application deadline :
N / A

Contact :
Genome Quebec Website

Description:
To lead the Bioinformatics development at the Genome Quebec and McGill University Innovation Center, Genome Quebec is seeking a Director, for its Bioinformatics platform.

For more information, visit the Genome Quebec Website

Application deadline :
N / A

Contact :
Genome Quebec Website

Description:
La personne développe et implémente par la méthode Agile (scrum) de grandes bases de données, des interfaces et des logiciels scientifiques d’analyses bioinformatiques dans l’application web Nanuq, création de l’équipe de bioinformatique pour déservir les services de génotypage, de génomique fonctionelle, de protéomique et de séquençage du Centre d’innovation Génome Québec et Université McGill. (English version not available)

For more information, visit the Genome Quebec Website

Application deadline :
March 31st, 2010

Contact :
Genome Quebec Website

Additional information :
This is a temporary position for the replacement of a maternity leave

Description:
We are looking for a research technician within the labs of Dr Hallett and Thomas at McGill University. The applicant should have prior experience with bioinformatics, biostatistics and systems biology approaches. In particular, strong applicants would have prior experience in the analysis of gene expression data.

Application deadline :
April 1st, 2010

Contact :
Dr. Mike Hallett: hallett[at]mcb.mcgill.ca

Download seminar poster

Talk Title :
Deriving Executable Models of Biochemical Network Dynamics from
Qualitative and Semi-Quantitative Data.

Date / Time / Location:
Thursday March 11^th, 2010 - 6:00 pm
Room S1-151 at IRIC

Affiliation :
McGill’s MCB

Personal Page
Ruths Research

Abstract :
Progress in advancing our understanding of biological systems is limited by their sheer complexity, the cost of laboratory materials and equipment, and limitations of current laboratory technology. Computational and mathematical modeling provides ways to address these limitations through hypothesis generation and testing without experimentation - allowing researchers to analyze system structure and dynamics in silico and, then, design lab experiments that yield desired information about phenomena of interest.
These models, however, are only as accurate and complete as the data used to build them. Currently most models are constructed from quantitative experimental data. However, since accurate quantitative measurements are hard to obtain and difficult to adapt from literature and online databases, new sources of data for building models need to be explored. In my research, I design methods for building and executing computational models of cellular networks based on qualitative experimental data, which is more abundant, easier to obtain, and reliably reproducible. Such executable models allow for in silico perturbation, simulation, and exploration of biological systems.
In this talk, I will present two general strategies for building and executing Petri net-based models of biochemical networks. Both have been successfully used to model and predict the dynamics of signaling networks in normal and cancer cell lines, rivaling the accuracy of existing methods trained on quantitative data.

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Talk Title :
Short RNAs and Organism-specific Aspects of Process Regulation

Date / Time / Location:
Thursday February 11^th, 2010 - 6:00 pm
Room S1-151 at IRIC

Affiliation :
IBM Research

Personal Page
Isidore Rigoutsos

Abstract :
In this talk, I will discuss the possibility that a potentially significant portion of cellular process regulation may be mediated by genomic sequences that need not be conserved across organisms. Evidence in support of this viewpoint comes from computational analyses as well as experimental work by us and by others. The ramifications of such findings for the onset and progression of disease will also be examined.

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Talk Title :
Blood‐based transcriptomics in breast cancer epidemiology

Date / Time / Location:
Thursday January 14^th, 2010 - 6:00 pm
Room S1-151 at IRIC

Affiliation :
University of Tromsø

URL
Vanessa Dumeaux

Abstract :
Given the number of factors that influence expression regulation, it is not surprising that often more than one strong signal is present in any given high-dimensional dataset. Peripheral blood is an ideal surrogate tissue as it has the potential to reflect responses to changes in the immediate and distant environments by alterations of gene expression levels. Thus, there is growing evidence that use of peripheral blood cells for transcriptome analysis is valuable to assess environmental- or disease- associated gene signatures.
During this talk, I will focus on altered gene expression in blood by inter-individual or lifestyle factors, breast cancer diagnosis and late-side effects related to breast cancer treatment (e.g. chronic fatigue). Significant results are obtained by examining the biological implications grouped into gene sets, rather than specific single genes tested for differential expression. Perturbed pathways were more or less numerous and distinct across variables with also some similarities emerging, perhaps unsurprisingly, in terms of immune response. Refined analysis identifying key genes specific to blood cell subtypes can also provide exciting functional information.
It is within the prospective cohort design that the most successful examples of biomarkers and disease outcome are found - this will be where the novel design of the Norwegian Women and Cancer (NOWAC) postgenome study can prove valuable.

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Talk Title :
The role of evolutionarily conserved ligand-interacting binding-site residues

Date / Time / Location:
Thursday,December 10^th 2009 - 6:00 pm
McGill University
Room 232, Leacock Building
855 Sherbrooke Street West

Affiliation :
Université Sherbrooke

URL
Rafael Najmanovich

Abstract :
Evolutionarily conserved ligand-interacting binding-site residues are thought to be important to satisfy physico-chemical binding constraints. Recently we demonstrated that non-homologous proteins that evolved to bind similar ligands contain highly dissimilar patterns of conserved ligand-interacting binding-site residues. While the importance of conserved residues is unquestionable, these results suggest that conserved residues may play extra roles. We suggest that conserved residues may play the additional role of preventing the promiscuous binding of similar molecules present in the cellular milieu. Different patterns of conservation would reflect distinct cellular contexts. In support of this hypothesis, we created a dataset (and associated web-interface) of proteins with known structures containing binding site mutations in which both the wild type and mutant were crystallized with the ligand (as well as sometimes in the Apo form) demonstrating that the mutation does not prevent ligand binding. The dataset includes over 5000 entries containing between one and four mutations on residues with varying degrees of conservation in contact with ligands with varying levels of cognate similarity. Due to the experimental bias towards mutations on highly conserved residues, there are numerous cases of often-drastic changes on highly conserved residues bound to cognate ligands. If such drastic mutations do not prevent binding, the conserved residues in question must have a different essential function, including that of preventing promiscuity among other possibilities.

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Talk Title :
How perfect can protein interactomes be?

Date / Time / Location:
Thursday, November 12^th 2009 - 6:00 pm
McGill University
Room 232, Leacock Building
855 Sherbrooke Street West

Affiliation :
Université Laval

URL
Christian Landry

Abstract :
Evolutionary theory tells us that biological systems need not be optimized and may very well accumulate nonfunctional elements. Mutational and demographic processes contribute to the cluttering of eukaryotic genomes and transcriptional networks with “junk” DNA and spurious DNA binding sites. Here, I question whether such a notion should be applied to protein interactomes- that is, whether these protein interactomes are expected to contain a fraction of nonselected, nonfunctional protein-protein interactions. I discuss evidence for the existence of these non-functional interactions in kinase-substrate networks from the analysis of the evolution of phosphoproteomes of mammals and fungi.