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 et d'informatique mathématique (LaCIM) - Anne Bergeron

• From 2014 to 2017

• The aim of this Associated Team is the development of comparative genomics models and methods for the analysis of eukaryote genes structure evolution. Our goal 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 meeting took place in 2016. S. Blanquart and J.-S. Varré met A. Bergeron and K. Swenson in Montpellier, from 13th to 15th of April. J.-S. Varré and K. Swenson met A. Bergeron in Montréal, from 8th to 19th of November.

Inria International Partners

Informal International Partners

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

• Childhood Leukaemia Investigation Prague (CLIP), Department of Pediatric Hematology/Oncology, 2nd Faculty of Medicine, Charles University, Prague, Czech Republic: Collaboration with Michaela Kotrová and Eva Fronkova on leukemia diagnosis and follow-up.

• 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.

• Département des Sciences de la Vie, Faculté des Sciences de Liège: Collaboration with Denis Beaurain on nonribosomal peptides.

• 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.

• Institute of Biosciences and Bioresources, Bari: Collaboration with Nunzia Scotti on the assembly of plant mitochondrial genomes.

• 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 on nonribosomal peptides.

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

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

Participation in Other International Programs

• Participation in the EuroClonality-NGS consortium. This consortium aims at standardizing the study of immune repertoire, clonality and minimal residual disease in leukemia at the european level. We are part of the bioinformatics workgroup led by Nikos Darzentas (CEITEC, Brno, Czech Republic).