Jérôme Waldispühl group @ McGill
Structural Bioinformatics & Citizen Science

Research

RNA Bioinformatics

We develop algorithms to predict RNA 3D structures and molecules binding them

Citizen Science

We develop crowd-computing games to analyze genomic data (See also dnapuzzles.org)

Resources

Web servers, databases, and source code

Structural bioinformatics (RNA & Proteins)


RNAmigos

Prediction of RNA-small molecule binding

VeRNAl

Catalog of RNA 3D motifs

BayesPairing

Prediction of RNA 3D modules

RNA-MoIP

Prediction of RNA 2.5D structures

aRNhAck

Prediction of RNA binding interfaces

IncaRNAtion

Sampling RNA sequences with target structure

CaRNAval

Catalog of RNA Recurrent Interaction Networks

ArchARNement

Reconstruction of ancestral RNA sequences

RNAmutants

Exploration of RNA sequence-structure maps

RNApyro

Error-correction of RNA sequencing data

SPARCS

Analysis of structural content of coding RNA

IncaRNAfbinv

Fragment-based design of RNA sequences

MateRNAl

Simulation of evolution of RNA populations

Optimol

Optimization of Protein-small molecule binding affinities

P3Fold

Prediction of protein folding routes

Fibrilizer

Analysis of polymorphic Amyloid fibrils

PartiFold

Prediction of transmembrane β-barrels

Human-Computing & Citizen science games


DNA Puzzles

Citizen science games in AAA games

Phylo

Citizen science puzzle game for genomics

Colony B

Citizen science mobile app for microbiome

Market

A collaborative crowd-computing game

3DGB

Immersive exploration of 3D genomes

Publications

Journal articles, conference papers, book chapters and preprints

Team

Jérôme Waldispühl

Group leader

Elena Nazarova

Research Associate

Alexander Butyaev

Research Associate

Chris Drogaris

Programmer

Carlos Gonzalez Oliver

PhD student

Roman Sarrazin-Gendron

PhD Student

Hua-Ting Yao

PhD student

Renata Mutalova

PhD student

Javona White Bear

PhD student

Parham Ghasemloo

PhD student

Tim Keding

M.Sc. student

Eddie Cai

M.Sc. student

Julien Mounthanyvong

M.Sc. student


Visitors & Interns

Juan Carvajal (PhD Computer Systems Engineering, National University of Colombia)
Xingyu Chen (B.Sc. Computer Science & Biology, McGill)
Yun Kai Peng (B.Sc. Computer Science, McGill)
Yixiong Sun (B.Sc. Computer Science & Biology, McGill)
Jonathan Broadbent (B.Sc. Computer Science & Biology, McGill)
Anssam Ghezala (B.Sc. Software Engineering, McGill)
Elsa Emilien (B.Sc. Software Engineering, McGill)
Taylor Lynn Curtis (B.Sc. Software Engineering, McGill)
Lara Kollokian (B.Sc. Software Engineering, McGill)
Ajay Patel (B.Sc. Software Engineering, McGill)
Jay Abi-Saad (B.Sc. Software Engineering, McGill)
Rayan Osseiran (B.Sc. Software Engineering, McGill)
Kyle Myers (B.Sc. Software Engineering, McGill)
Christiana Chen (B.Sc. Software Engineering, McGill)
Yousuf Badawi (B.Sc. Software Engineering, McGill)

Alumni

Yash Patel, M.Sc. (2018-2020)
Jacques Boitreaud, M.Sc. (2019-2020)
Antoine Soulé, PhD (2012-2019)
Alexander Butyaev, PhD (2013-2019)
Vincent Mallet, M.Sc. (2018-2019)
Eric Zhang, M.Sc. (2016-2018)
Akash Singh, M.Sc. (2017-2018)
Mansha Imtiyaz, M.Sc. (2017-2018)
Eric Kissel, M.Sc. (2017-2018)
Ali Atiia, PhD (2012-2018)
David Becerra, PhD (2012-2017)
Atefeh Mohajeri, Postdoc (2015-2017)
Vladimir Reinharz, M.Sc. (2011-2012), PhD (2012-2016)
Olivier Tremblay-Savard, Postdoc (2013-2015)
Sriswetha Rajagopal, M.Sc. (2013-2015)
Mohamed Smaoui, M.Sc. (2010-2011), PhD (2011-2014)
Yang (Olivia) Zhang, M.Sc. (2012-2014)
Zheng Dai, B.Sc. (2015-2017)
Jason Yao, B.Sc. (2016-2017)
Daniel Kwak, B.Sc. (2010-2013)
Alfred Kam, B.Sc. (2010-2014)
Rudolf Lam, B.Sc. (2010-2011)
Gary Roumanis, B.Sc. (2010-2011)
Alexander Kawrykow, B.Sc. (2010-2011)
Solomon Shenker, B.Sc. (2010-2011)

Open Positions

We welcome applications at all levels. We are primarily looking for candidates with a strong theoretical background in computer science and software engineers. We may also consider biologists or biochemists with a solid experience in programming.

Before submitting your online application, we recommend you to contact the group leader. Describe your background and motivation to pursue graduate studies, and include your CV and transcripts in your e-mail.

Importantly, when you will fill your McGill online application form, provide the name of Jérôme Waldispühl in the list of preferred supervisors. This information is important to ensure a proper routing of your files.

Start your application now!

Contact

Write us or stop by to say hello!

Mail Us

3480 University Street, Room 318
McConnell Engineering Bldg
Montréal QC H3A 0E9

Mail Us

(E-mail) jerome.waldispuhl@mcgill.ca
(Phone) +1 514 398 5018

Visit Us

3630 University Street, Room 3106
Trottier Bldg
Montréal QC H3A 2B3

Sponsors & Partners