Section: Partnerships and Cooperations

International Initiatives

Inria Associate Teams not involved in an Inria International Labs

CG-ALCODE

• Title: Comparative Genomics for the analysis of gene structure evolution: ALternative CODing in Eukaryote genes through alternative splicing, transcription, and translation.

• International Partner (Institution - Laboratory - Researcher):

  • Université du Québec À Montréal (Canada) - Laboratoire de combinatoire, informatique et mathématique (LaCIM) - Anne Bergeron

• Start year: 2014

• See also: http://thales.math.uqam.ca/~cgalcode/

• The aim of this Associated Team is the development of comparative genomics models and methods for the analysis of eukaryotes gene structure evolution. The goal of the project is to answer very important questions arising from recent discoveries on the major role played by alternative transcription, splicing, and translation, in the functional diversification of eukaryote genes.

• Two working meetings of CG-ALCODE researchers took place in 2015. First, Samuel Blanquart, Anne Bergeron and Krister Swenson met each other in Montpellier, from 27th to 30th of April. Second, Samuel Blanquart, Jean Stéphane Varré spent two weeks in Montréal, from 1st to 11th November, to work with Anne Bergeron.

Informal International Partners

• Astrid Lindgrens Hospital, Stockholm University: Collaboration with Anna Nilsson and Shanie Saghafian-Hedengren on RNA sequencing of stromal cells.

• CWI Amsterdam: Collaboration with Alexander Schoenhuth and Jasmijn Baaijens on succinct data structures and algorithms for the assembly of viral quasispecies.

• Department of Statitics, North Carolina State University: Collaboration with Donald E. K. Martin on spaced seeds coverage.

• Gembloux Agro-Bio Tech, Université de Liège: Collaboration with Philippe Jacques on nonribosomal peptides.

• Institut für Biophysik und physikalische Biochemie, University of Regensburg: Collaboration with Rainer Merkl on ancestral sequence inference and synthesis.

• Makova lab, The Pennsylvania State University: Collaboration with Kateryna Makova and Samarth Rangavittal on the assembly of the gorilla Y chromosome, and visualisation of assembly graphs.

• Medvedev lab, The Pennsylvania State University: Collaboration with Paul Medvedev on algorithms for constructing de Bruijn graphs.

• Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark: Collaboration with Tilmann Weber on nonribosomal peptides.

• Proteome Informatics Group, Swiss Institute of Bioinformatics: Collaboration with Frédérique Lisacek and Markus Mueller on nonribosomal peptides.

• School of Social and Community Medicine, University of Bristol: Collaboration with John Moppett on leukemia follow-up.

• Science for Life Laboratory, Stockholm University: Collaboration with Lars Arvestad and Kristoffer Sahlin on genome scaffolding of contaminated libraries.

• Theoretical Biochemistry Group, Universität Wien: Collaboration with Andrea Tanzer and Ronny Lorenz on RNA folding and RNA kinetics.