Jérôme Waldispühl group @ McGill
RNA Bioinformatics & Citizen Science

Research

RNA Bioinformatics

Computational methods to predict RNA 3D structures and molecules binding them

Citizen Science

Human-centered computing & Crowd-computing video games for genomic data analysis

Resources

Source code, databases, web servers

Project Description Resource Status
RNAmigos Prediction of small molecule binding RNA https://github.com/cgoliver/rnamigos2
RNAglib Python library for RNA structure analysis & prediction https://github.com/cgoliver/rnaglib
BayesPairing Prediction of RNA 3D modules https://jwgitlab.cs.mcgill.ca/sarrazin/rnabayespairing2
VeRNAl Fuzzy classification of RNA 3D motifs https://vernal.cs.mcgill.ca
RNA-MoIP Prediction of RNA 2.5D structures https://gitlab.info.uqam.ca/cbe/RNAMoIP
CaRNAval RNA 3D modules with long-range interactions https://carnaval.lisn.upsaclay.fr
Optimol Generative modeling of small molecule binding proteins https://github.com/jacquesboitreaud/OptiMol/
IncaRNAtion Design of RNA sequence with target 2D structure https://github.com/McGill-CSB/IncaRNAtion
aRNAhack Prediction of RNA functional sites https://jwgitlab.cs.mcgill.ca/vreinharz/arnhack
achARNement Reconstruction of ancestral RNA sequences https://jwgitlab.cs.mcgill.ca/vreinharz/acharnement
RNApyro Error correction of structured RNA sequences https://github.com/McGill-CSB/RNApyro
SPARCS Analysis of structural content of coding RNA http://csb.cs.mcgill.ca/sparcs/
MateRNAl Simulation of evolution of RNA under structural constraints https://jwgitlab.cs.mcgill.ca/cgoliver/maternal/
P3Fold Prediction of protein folding routes http://csb.cs.mcgill.ca/P3Fold/
Fibrilizer Analysis of Amyloid fibrils http://amyloid.cs.mcgill.ca/
RNAmutants Exploration of the RNA mutational landscape https://github.com/McGill-CSB/RNAmutants
CorRNA Prediction of RNA deleterious mutations https://github.com/McGill-CSB/corRna
PartiFold Prediction of transmembrane β-barrels
Borderlands Science Human microbiome sequence alignment http://dnapuzzles.org
Project Discovery 3 Flow cytometry gating http://dnapuzzles.org
Phylo DNA & RNA sequence alignment http://phylo.cs.mcgill.ca
ARGV Augmented reality 3D genome visualization http://argv.cs.mcgill.ca
Colony B Clustering of human microbiome data http://csb.cs.mcgill.ca/colonyb
Market Game Behavioral study in a market game http://dnapuzzles.org

Publications

Journal articles, conference papers, book chapters and preprints

Team

Jérôme Waldispühl

Group leader

Elena Nazarova

Research Associate

Alexander Butyaev

Research Associate

Roman Sarrazin-Gendron

PhD Student

Renata Mutalova

PhD student

Javona White Bear

PhD student

Parham Ghasemloo

PhD student

Visitors & Interns

Juan Carvajal (PhD Computer Systems Engineering, National University of Colombia)
Etienne Reboul (PhD Physico-Chemical Biology, University of Paris)

Alumni

Name Program Year Webpage
Cai, Eddie M.Sc. 2021-2023 https://www.linkedin.com/in/eddiecai
Henegar, Paul-André M.Sc. 2021-2023 https://www.linkedin.com/in/paul-andre-henegar
Chol, Arnaud M.Sc. 2021-2022 https://www.linkedin.com/in/arnaud-chol
Oliver, Carlos PhD 2017-2021 https://carlosoliver.co/
Yao, Hua-Ting PhD 2019-2021 https://htyao.gitlab.io/
Mounthanyvong, Julien M.Sc. 2019-2021 https://www.linkedin.com/in/julien-mounthanyvong
Patel, Yash M.Sc. 2018-2020 https://www.linkedin.com/in/yash-patel-52128b160
Boitreaud, Jacques M.Sc. 2019-2020 https://www.linkedin.com/in/jacques-boitreaud
Soulé, Antoine PhD 2012-2019 https://www.linkedin.com/in/antoine-soul%C3%A9-a3906351
Butyaev, Alexander PhD 2013-2019 https://www.linkedin.com/in/alexander-butyaev-b7a2005b
Mallet, Vincent M.Sc. 2018-2019 https://vincentx15.github.io/
Zhang, Eric M.Sc. 2016-2018 https://www.linkedin.com/in/eddiecai
Singh, Akash M.Sc. 2017-2018 https://akashzcoder.github.io/
Imtiyaz, Mansha M.Sc. 2017-2018 https://www.linkedin.com/in/manshaimtiyaz/
Kissel, Eric M.Sc. 2017-2018 https://www.linkedin.com/in/eric-kissel-944b71167
Atiia, Ali PhD 2012-2018 https://atiia.xyz
Becerra, David PhD 2012-2017 https://www.cs.mcgill.ca/~dbecer/
Mohajeri, Atefeh Postdoc 2012-2018 https://www.linkedin.com/in/atefehmohajeri/
Reinharz, Vladimir PhD & M.Sc. 2011-2016 https://cbe.uqam.ca/
Tremblay-Savard, Olivier Postdoc 2013-2015 https://home.cs.umanitoba.ca/~tremblao/
Rajagopal, Sriswetha M.Sc. 2013-2015 https://www.linkedin.com/in/sriswetha-rajagopal-43bb15107
Smaoui, Mohamed PhD & M.Sc. 2010-2014 https://www.cs.ku.edu.kw/resume/mohamed-smaoui/
Zhang, Yang M.Sc. 2012-2014 https://www.linkedin.com/in/olivia-zhang-27817982
Zheng, Dai B.Sc. 2015-2017 https://www.linkedin.com/in/zdaizhengdai/
Yao, Jason B.Sc. 2016-2017 https://www.linkedin.com/in/jason-yao
Kwak, Daniel B.Sc. 2010-2013 https://www.linkedin.com/in/daniel-kwak-ba6a5116/
Kam, Alfred B.Sc. 2010-2014 https://www.linkedin.com/in/kamalfred/
Lam, Rudolf B.Sc. 2010-2011 https://www.linkedin.com/in/rudolf-lam-308a74119/
Roumanis, Gary B.Sc. 2010-2011 https://garyroumanis.com/
Kawrykow, Alexander B.Sc. 2010-2011 https://www.linkedin.com/in/alexander-kawrykow-37992944/
Shenker, Salomon B.Sc. 2010-2011 https://www.linkedin.com/in/sol-shenker-840b7a112/

Open Positions

We welcome applications at all levels. 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

Our research is or was supported by: