Computational Systems for Biology

School of Computer Science

McGill University

Algorithmics & Theoretical Bioinformatics

We design algorithms to study the properties of structural and mutational landscape of RNA and Proteins. Applications of these techniques range from evolutionary to synthetic biology studies.

Biophysical modeling

We develop computational tools to simulate folding dynamics and assembly of large biomolecular systems. Our research interests includes the analysis of Amyloid fibrils involved in diabetes and neurodegenerative disorders.

Human-Computing Games

Computer games are not just fun, they also provide us an amazing tools to harness the computational power of crowds on the web. We develop video games to solve hard problems in genomics, and analyze their theoretical performance.


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Error-correction of RNA sequencing data using secondary structure information.

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Design of RNA sequences folding into target secondary structures with nucleotide distribution.

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Prediction of local 3D motifs from RNA secondary structure predictions.

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A program to predict structured and unstructured regions in coding RNA sequences.

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Algorithms to explore RNA sequence-structure maps.

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A program to predict mutations altering native RNA secondary structures.

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A human-computing game for solving the multiple sequence alignment problem.

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An open crowd-computing platform to solve the multiple sequence alignment problem.

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Web servers and databases to study the stability of polymorphic amyloid fibrils.

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Structure prediction and alignment of transmembrane protein structures.

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Prediction of the energy landscape and folding pathways of β-sheet proteins.

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Articles in Refereed Journals

Articles in Refereed Conference Proceedings

Books or Book Chapters


Jérôme Waldispühl

Assistant professor in Computer Science. Group Leader.

Olivier Tremblay-Savard

Post-doctoral fellow. Crowdsourcing & Human-computing games.

Mohamed Smaoui

PhD Candidate. Proteomics & Structural Bioinformatics.

Vladimir Reinharz

PhD Student. Algorithms & RNA Bioinformatics.

Antoine Soulé

PhD student. RNA Bioinformatics.

David Becerra

PhD student. Protein folding.

Mohammed Shamrani

PhD student. Molecular computing & DNA nanotechnology.

Alexander Butyaev

PhD student. Crowdsourcing & Human-Computing games.

Carlos Gonzalez Oliver

M.Sc. student. Evolution of molecular systems.

Mohammad Kanj

Undergraduate student. Crowd-computing systems.

Nicolas Martin

Undergraduate student. Human-computing games.

Henry Lu

Undergraduate student. Human-computing games.

Chetan Pal Ashta

Undergraduate student. Protein folding.

Cody Mazza-Anthony

Undergraduate student. Protein folding.


We welcome applications at M.Sc. and PhD levels!

We are primarily looking for (i) candidates with a strong theoretical background in mathematics and computer science, or (ii) software engineers with expertise in the development of web and mobile applications, or (iii) biochemists with experience in computational simulation of molecular systems. We do not require a background in biology, but we expect from you curiosity, a strong desire to learn and a genuine interest in inter-disciplinary sciences.

Our research group is bilingual, multi-cultural, and has active collaborations with laboratories in Canada (McGill, University of Montréal, Institut de Recherches Cliniques de Montréal, University of Toronto) and France (École Polytechnique, Université Paris-Sud).

At the time of your application, we recommend you to contact the principal investigator. Please describe your background, strengths and area of interest. Explain also why you are a good fit for the position. Finally, indicate in your email if you have already applied to scholarships (E.g. NSERC or FRQNT) or if you are seeking funding.

When you will fill your McGill online application form, indicate ``Applications'' as a research area, wether you are interested in theoretical or applied research in our lab. This information is important to ensure a proper routing of your files.

Start your application now!


Our lab is located at the third floor of the Trottier Building:

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Contact Information

(Laboratory) 3630 University Street, Room 3106, Montreal QC
(Mailing address) 3480 University Street, Room 318, McConnell Engineering Bldg, Montreal QC H3A 0E9
(Phone) +1 514 398 5018

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