Mathieu Blanchette's

Computational Genomics Lab


OUR RESEARCH


We develop cutting-edge computational approaches to key questions in genomics and evolution. We design algorithmic, machine learning, and statistical approaches to solve real-world questions from biology, and work in tight collaboration with biologists, biochemists, and geneticists to put our tools to use to make biological discoveries. We are particularly interested in: (i) How do genomes evolve, and what does that tell us about their functions? (ii) How is gene expression regulated, and what role does 3D chromosome organization play?

Ancestral genomics. In early work, we showed that the complete genomes of certain ancient mammls living more than 70 million years ago can be inferred computational with remarkable accuracy. We continue our work to improve ancestral genome reconstruction and push back the limits of reconstructability. We are now designing approaches to use these computationally reconstructed mammalian genomes to improve the detection of transcription factor binding sites, micro-RNA target sets and remnants of ancient transposable elements and pseudogenes.
Key collaborator: Abdoulaye Banire Diallo (Computer Science, McGill).

Transposable element annotation. We are developing PIATEA, a system to integrate multiple types of evidence for the prediction of transposable elements. PIATEA uses a multivariate Hidden Markov Model to integrate both computational and experimental evidence.
Key collaborator: Thomas Bureau (Biology, McGill).

3D genomics Chromosomes are folded in each cell's nucleus in a highly complex yet organized and dynamic manner. Experimental approaches (e.g. 5C, Hi-C) have emerged to indirectly measure chromosome conformation. We develop computational approaches to interpret this noisy data, including statistical normalization, high-resolution intra and inter-chromosomal contact frequency estimation, to 3D modeling and identification of conformational biomarkers of cancer.
Key collaborator: Josee Dostie (Biochemistry, McGill).

Plant genome assembly and evolution Plant genomes have complex histories of polyploidization which makes many of them difficult to assemble yet powerful models of evolution. We are developing algorithms to assemble and compare genomes to identify key regulatory regions and study their evolution.
Key collaborator: Stephen Wright (Ecology and Evolutionary Biology, U. of Toronto).

Epigenetic and gene regulation Changes in DNA methylation is associated to changes in gene expression, cell types, and disease state. We are developing statistical approaches to maximize the interpretability of epigenetic data derived from complex samples. We are also working on machine learning approaches to better understand cell-type specificity in gene regulation.
Key collaborators: Tomi Pastinen (Human Genetics, McGill).
Elin Grundberg (Human Genetics, McGill).
Doina Precup (Computer Science, McGill).
Rob Sladek (Medicine, McGill).
Celia Greewood (Biostatistics and Epidemiology, McGill).

Plant genome assembly and evolution Plant genomes have complex histories of polyploidization which makes many of them difficult to assemble yet powerful models of evolution. We are developing algorithms to assemble and compare genomes to identify key regulatory regions and study their evolution.
Key collaborator: Stephen Wright (Ecology and Evolutionary Biology, U. of Toronto).

mRNA localization How do cells identify mRNAs that need to be localized to specific subcellular localization, and how to they bring it there? With our collaborators, we take an experimental/computational approach to the problem.
Key collaborators: Eric Lecuyer (Institut de Recherche Clinique).
Jerome Waldispuhl (Computer Science, McGill).

A multidisciplinary team


The lab's students come from all over the world and bring a wide variety expertise.


MEET THE TEAM




Prof. Mathieu Blanchette (Lab. Head)

Curriculum Vitae
Email

After completing his Ph.D. (U. of Washington, 2002) and postdoc (UC Santa Cruz, 2003), Mathieu joined the School of Computer Science at McGill and founded the Computational Genomics Lab. The research made by his awesome team has been published in more than 70 publications. Recently elected member of the College of Scholar of the Canadian Royal Society, he was a Sloan Fellow (2009), and received the Outstanding Young Computer Scientist Researcher Prize from the Canadian Association for Computer Science (2012), and the Chris Overton prize (2006). He loves teaching and supervising students, and received the Leo Yaffe prize for teaching (2008).



Douglas Hoen (Postdoc)

Doug works on multiple aspects of transposable element identification, studies their domestication, and leads our TE benchmarking effort.


Glenn Hickey (Postdoc)

Glenn leads PIATEA, our project to annotate transposable elements using a multivariate Hidden Markov Model.


Adrian Platts (Bioinformatician)

Adrian works on a multitude of projects related to plant genome assembly, annotation, and comparisons.


Christopher Cameron (Ph.D. student)

Chris is a machine learning expert working on the analysis of 5C and Hi-C data, aiming to maximize the resolution and accuracy that can be obtained from these data. Co-supervised by Josee Dostie.


Pablo Cingolani (Ph.D. student)

Pablo develops computational approaches to facilitate genome-wide association studies and maximize its power in the presence of epistasis. Co-supervised by Rob Sladek.


Rola Dali (Ph.D student)

Rola is a molecular biologist by training who recently completed a transition toward bioinformatics. She studies gene expression in brain cancer, as well as chromosomal organization within the nucleus from Hi-C data.


Mickael Leclercq (Ph.D. student)

Mickael is our micro-RNA expert. He develops machine learning approaches to identify them and their targets, and studies their expression and evolution. Co-supervised by Aboudlaye Banire Diallo.


Airin Ahia-Tabibi (Ph.D. student)

Airin digs through ancient genomes to find traces of extinct transposable elements and


Faizy Ahsan (M.Sc. student)

Faizy develops cutting-edge machine learning approaches to predict and understand enhancer cell-type specificity. Co-supervised by Doina Precup.


Maia Kaplan (M.Sc. student)

Maia combines her computational and wet lab skills to study the function of domesticated transposable elements. Co-supervised by Thomas Bureau.


Willie Chang (Ugrad student)

Willy develops an approach to infer chromatin contacts from ChIP-seq data.


Marc-Antoine Dumais (Ugrad student)

Marc-Antoine deals with allele-specific chromosome conformation.

LAB ALUMNI (to be completed)


  1. Krister Swenson (postdoc, 2014), now an assistant professor at Universite Montpellier 2 (France)
  2. James Wagner (PhD, 2014), Analyst, Epic (USA)
  3. Mathieu Lavallee-Adam (PhD, 2013), now a postdoc at the Scripps Institute (Yates Lab)
  4. Abdoulaye Banire-Diallo (PhD, 2009), now an associate professor at UQAM (Computer Science)
  5. Javad Sadri (postdoc, 2011), now a lecturer at Concordia University (Computer Science)
  6. Pierre-Etienne Jacques (postdoc, 2006), now a assistant professor at Universite de Sherbrooke (Biology)

WE ARE HIRING!

We are always on the lookout for new talents.
Undergrad or graduate student, postdoc or programmer, contact us if you want to join the lab!



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Contact Information

Trottier Bldg, room 3107, located at 3630 University.
Mailing address:
McConnell Engineering Bldg. Room 318
3480 University,
Montreal, Qc, Canada, H3A 0E9
(514) 398-5209
blanchem@cs.mcgill.ca