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 December meeting

Dr. Major and his team will present their work on RNA engineering.
Dr. Major, principal investigator at IRIC, is a pioneer in bioinformatics in Montreal.
He has trained a few generations of bioinformaticians.
He is also one of the rare bioinformaticians to open his own wet-lab.

Here is a summary of his research.
We “want to understand and characterize human gene regulatory networks; link cell content to phenotypes; and, design and create artificial molecular components to peek and poke cell information and programmes. […] We are developing a suite of programs to analyze, model, predict, and determine RNA 2D and 3D structure.”
http://www.major.iric.ca/MajorLabEn/Home.html

As this is also the last meeting of 2015, and that the next meeting will not be before February, we are also going to go to Benelux after to celebrate the end of the year.

Agenda
16:00 – 16:05 Introduction and community announcements
16:05 – 16:45 “MiRBooking simulates the stoichiometric mode of action of microRNAs”, Dr. Major (IRIC)
16:45 – 17:05 Snacks and refreshments
17:05 – 17:35 “Structural Dynamics Control the MicroRNA Maturation Pathway”, Paul Dallaire, PhD (IRIC)
17:35 – 18:00 “Identification of dynamic motifs in RNA”, Mathieu Dupont (IRIC)

The meeting will take place Wednesday December the 2nd, from 16:00 to 18:00 in the Jacques-Genest auditorium at IRCM.
You can register at http://www.meetup.com/monbug. If you don’t want to use Meetup, you can register for the next meeting by sending an email to register@monbug.ca.






 November meeting

We hope to see you at our November meeting.

Our keynote speaker will be Dr. Barreiro, principal investigator at CHU Sainte-Justine, who will be presenting his research on the genomics of the immune system. For more information about his exciting research, have a look at his web site.

Ali Emami, who works in Dr. Rabasa-Lhoret at IRCM, will be presenting his research on an artificial pancreas, a project which could “have a great impact on the treatment of type 1 diabetes”.

After all our talks on genomics, we’re happy to have a talk on proteomics.
Bagci Halil, phD student in Dr. Côté’s laboratory, with be presenting his research on the the exploration of the signaling networks of Rho GTPases by BioID.

Agenda
16:00 – 16:05 Introduction and open floor to participants for community announcements (Alain Bateman)
16:05 – 16:45 “Genomics of the Immune System”, Luis Barreiro, phD (CHU Sainte-Justine)
16:45 – 17:05 Snacks and refreshments
17:05 – 17:35 “Glucagon Action Model in Type 1 Diabetes”, Ali Emami (IRCM)
17:35 – 18:00 “Exploring the signaling networks of Rho GTPases by BioID”, Bagci Halil (IRCM)

The meeting will take place Wednesday November the 4th, from 16:00 to 18:00 in the Jacques-Genest auditorium at IRCM.
You can register at http://www.meetup.com/monbug. If you don’t want to use Meetup, you can register for the next meeting by sending an email to register@monbug.ca.

 






 October meeting

We’re starting the autumn with three excellent presentations. We hope to see you at our October meeting, on Wednesday October the 7th, from 16:00 to 18:00 in the Jacques-Genest auditorium at IRCM.

Our keynote speaker will be Dr Savard, who will be presenting his research on human-computing games, illustrating how “computer games are not just fun, they also provide us amazing tools to harness the computational power of crowds on the web.”

Since he wasn’t able to present in September, Emmanuel Noutahi, phD candidate in Dr El-Mabrouk’s laboratory at the Université de Montréal, will be presenting at this meeting the ETE toolkit.

Assya Trofimov, MSc student in Dr Lemieux’s laboratory at IRIC, will be presenting the R library Shiny, a web application framework for R.Agenda

16:00 – 16:05 Introduction and open floor to participants for questions, comments or announcements (Alexis Blanchet-Cohen)
16:05 – 16:45 “Collaborative solving in a human computing game”, Olivier Tremblay Savard, PhD (McGill)
16:45 – 17:05 Snacks and beveragages
17:05 – 17:30 Phylogenetic tree exploration and visualization made easy with ETE, Emmanuel Noutahi, (Université de Montréal)
17:30 – 18:00 Shiny: A web application framework for R (Assya Trofimov)

You can register at http://www.meetup.com/monbug. If you don’t want to use Meetup, email us a register@monbug.ca.






 June meeting

We look forward to seeing you at our next meeting, on June the 3rd, at 16:00, in the main auditorium at IRCM.
Again, we have three very interesting talks. 🙂
You can register at http://www.meetup.com/monbug, or just by sending us an email at register@monbug.ca, if you prefer.

Brian Wilhelm, PhD, principal investigator at IRIC, will be presenting some of the bioinformatics challenges he faces in analyzing high-throughput genomic data, with the objective to better understand the basic mechanisms of transcription and the mutations in leukemia.
Nicole Uwimana will be talking about her project to bioinformatically identify cryptic genes.
Toby Hocking, PhD, “R programmer extraordinaire”, will be presenting a comparative study of the fastest way to find overlapping genomic regions.

Agenda

16:00 – 16:05 Introduction and open floor to participants for questions, comments or announcements (Alain Bateman or Alexis Blanchet-Cohen)
16:05 – 16:45 Using high-throughput technologies to understand the basic mechanisms of transcriptional regulation, and to study the mutations present in leukemia, Brian Wilhelm, PhD (IRIC)
16:45 – 17:05 Snacks and beverages
17:05 – 17:30 Identifying cryptic genes, Nicole Uwimana (IRCM)
17:30 – 18:00 What is the fastest way to find overlapping genomic regions?,  Toby Hocking, PhD (McGill)
https://github.com/tdhock/datatable-foverlaps






 Mike Zody

Download seminar posterPDF File
Talk Title :
Meat and Potatoes: Two Genomic Tales from Agriculture

Date / Time / Location:
Thursday, May 6th 2010 – 4:00 PM
McGill University
Room 232, Leacock Building.

Affiliation :
Broad Institute

URL
Mike Zody

Abstract :
Domestication of plants and animals marked a major turning point in human development, allowing sedentary societies to achieve tremendous growth through the maintenance of reliable sources of food. Growth of agricultural societies was accompanied by human-directed growth and evolution of domesticated species and, along with them, the pathogens that infected these species. I will present results from analysis of two very different genomic models: Phytophthora infestans, an oomycete plant pathogen that causes late blight of potatoes and tomatoes, and the domestic chicken, the largest source of animal protein for human consumption.

P. infestans was discovered in the 19th century and shown to be the cause of late blight, the disease responsible for the Great Irish Famine and other widespread potato crop failures throughout Europe. The pathogen spreads rapidly and is highly destructive on susceptible plant strains. Despite over a century of efforts at control through breeding resistant plants, late blight remains a major threat to world’s food supply, destroying over $6 billion of potatoes every year. Widespread outbreaks have occurred in both America and Europe in the past two years. Our analysis of the genome of P. infestans suggests that its ability to overcome control efforts may result from a highly dynamic genome that is undergoing rapid gene turnover, allowing it to diversify easily in the face of new selective pressures.

The chicken, Gallus gallus, was domesticated around 8,000 years ago in south Asia and has spread worldwide. Extensive selection by humans has led to domestic birds that show a wide range of color, growth, and reproductive variation compared to their wild ancestors, the red junglefowl. We have used SOLiD technology to resequence pools of birds selected from multiple domestic lines maintained for different production purposes and from red junglefowl populations. These data reveal multiple loci that appear to have been under strong selection during development of the domestic chicken, including one potential early domestication gene with a role in reproductive control. We also identified a number of sites of gene deletion that are fixed in one or more domestic chicken breeds, two of which have striking growth phenotypes.

These two diverse studies, drawing on the selective pressures at work in the farm environment, illustrate basic principles of how organisms evolve at a molecular level and adapt to both natural and human selective pressures. They further provide some guidance for agricultural improvements. Our P. infestans results suggest new methods for monitoring and may lead to better deployment of resistant strains. Our chicken findings identify multiple sites likely to have been selected for important production traits, providing targets for future breeding improvement as well as advancing our understanding of the chicken as a model organism.

 






 Sarah Jenna

Talk Title :
Download seminar posterPDF File

Searching for Signaling Balance through the Identification of Genetic Interactors of the Rab Guanine-nucleotide Dissociation Inhibitor gdi-1

Date / Time / Location:
Thursday April 8th, 2010 – 6:00 pm
Room S1-151 at IRIC

Affiliation :
UQAM

Personal Page
Sarah Jenna

Abstract :
Background
The symptoms of numerous diseases result from genetic mutations that disrupt the homeostasis maintained by the appropriate integration of signaling gene activities. The relationships between signaling genes suggest avenues through which homeostasis can be restored and disease symptoms subsequently reduced. Specifically, disease symptoms caused by loss-of-function mutations in a particular gene may be reduced by concomitant perturbations in genes with antagonistic activities.

Methodology/Principle Findings
Here we use network-neighborhood analyses to predict genetic interactions in Caenorhabditis elegans towards mapping antagonisms and synergisms between genes in an animal model. Most of the predicted interactions are novel, and the experimental validation establishes that our approach provides a gain in accuracy compared to previous efforts. In particular, we identified genetic interactors of gdi-1, the orthologue of GDI1, a gene associated with mental retardation in human. Interestingly, some gdi-1 interactors have human orthologues with known neurological functions, and upon validation of the interactions in mammalian systems, these orthologues would be potential therapeutic targets for GDI1-associated neurological disorders. We also observed the conservation of a gdi-1 interaction between different cellular systems in C. elegans, suggesting the involvement of GDI1 in human muscle degeneration.

Conclusions/Significance
We developed a novel predictor of genetic interactions that may have the ability to significantly streamline the identification of therapeutic targets for monogenic disorders involving genes conserved between human and C. elegans.

 






 Derek Ruths

Download seminar posterPDF File

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

Date / Time / Location:
Thursday March 11th, 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.

 






 Isidore Rigoutsos

Download seminar posterPDF File

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

Date / Time / Location:
Thursday February 11th, 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.

 






 Vanessa Dumeaux

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Talk Title :
Blood‐based transcriptomics in breast cancer epidemiology

Date / Time / Location:
Thursday January 14th, 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.

 






 Christian Landry

Download seminar posterPDF File

Talk Title :
How perfect can protein interactomes be?

Date / Time / Location:
Thursday, November 12th 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.