Bio2M team & Plateform

KmerToulouse Mini-symposium

Programme du mini-symposium “K-mer days 2025– Applications in oncology”

Séminaire k-mer days

Les 26 et 27 juin 2025 au Amphithéâtre IUCT, 1 avenue Irène Joliot-Curie, 31100 Toulouse

  • Organisateurs:
    • Stéphane Pyronnet
    • Thérèse Commes
    • Camille Marchet

Program

Thursday 26: Session 1: From large scale high-throughput sequencing to k-mer indexes

  • 14:30–15:00 State of Logan. Rayan Chikhi. Institut Pasteur, Paris
  • 15:00–15:30 Vizitig: Interactive exploration and biologically-rich queries simultaneously to assembled and raw RNA-Seq data. Bastien Degardins, Charles Paperman, Camille Marchet. CRIStAL, CNRS - Université de Lille.
  • 15:30–16:00 Fixing SRA metadata for cancer research. Fiona Hak, Daniel Gautheret. I2BC, Université de Paris Saclay Coffee break
  • 16:30–17:00 REINDEER2: Dynamically index 10,000+ RNA-seq samples and their abundances. Yohan Hernandez-Courbevoie, Camille Marchet, Mikaël Salson, Antoine Limasset. CRIStAL, CNRS - Université de Lille.
  • 17:00–17:30 Kaminari: a resource-frugal index for approximate colored k-mer queries. Victor Levallois. INRIA, Rennes
  • 17:30–18:00 ELLIPSIS-FL : Full length transcript reconstruction and quantification in single cell Smart-seq3 data. Marie Van Hecke. Ghent University, Belgium.
  • 18:00–20:00 Free Time
  • 20:00–23:00 Diner – Au Gascon – 9 rue des Jacobins

Friday 27: Session 2: Applications, focus in oncology

  • 09:00–09:30 K-mer design and applications. Benoit Guibert, Chloé Bessière, Camelia Sennaoui. IRMB, INSERM – Université de Montpellier.
  • 09:30–10:00 K-mer/AML/splicing. Raïssa Silva, Jérôme Reboul. IRMB, INSERM – Université de Montpellier.
  • 10:00–10:30 K-mer/AML/diagnostic. Florence Rufflé, Thèrèse Commes. IRMB, INSERM – Université de Montpellier.
  • 10:30–11:00 Coffee break
  • 11:00–11:30 ScanR’n: Autonomous pipelines for detection, localization and quantification of tumor RNA variants. Sandra Dailhau, Chloé Bessière, Stéphane Pyronnet. CRCT, INSERM – Université de Toulouse.
  • 11:30–12:00 Automatic linkage between clinical metadata and transcription variants detected and quantified by k-mers. Thomas Louvet, Sandra Dailhau, Chloé Bessière, Stéphane Pyronnet. CRCT, INSERM – Université de Toulouse.
  • 12:00–12:30 K-mer central: towards a database of k-mer signatures for oncogenic events. Daniel Gautheret. I2BC, Université de Paris Saclay.
  • 12:30–14:00 Lunch
  • 14:00–16:00
    • Working group #1: next-generation k-mer indexes
    • Working group #2: next-generation k-mer-based pipelines

Documents

Equipes

Paris-Saclay - I2BC

  • Daniel Gautheret
  • Mélina Gallopin
  • Fiona Hak
  • Safa Maddouré

Lille - CRIStAL

  • Mikael Salson
  • Camille Marchet
  • Antoine Limasset
  • Bastien Degardins
  • Yohan Hernandez-Courbevoie
  • Florian Ingels

Pasteur

  • Rayan Chikhi
  • Francesco Andreace
  • Charles Paperman

Montpellier - Bio2M

  • Thérèse Commes
  • Nicolas Gilbert
  • Jerome Reboul
  • Benoit Guibert
  • Anthony Boureux
  • Florence Rufllé
  • Raïssa Silva
  • Cédric Riedel
  • Camelia Sennaoui
  • Matéo Traissac
  • Mickael Coquerelle

Toulouse - CRCT

  • Stéphane Pyronnet
  • Chloé Bessière
  • Sandra Dailhau
  • Gael Jalowicki
  • Christophe Klopp

Rennes - Inria/GenScale

  • Victor Levallois

Brest - IMT atlantique

  • Bastien Pasdeloup

Montpellier - IRD

  • Julie Orjuela

Ghent - Dept. of Information Technology, IDLab, Ghent University

  • Marie van Hecke

Dijon - Senior Data Scientist chez Oncodesign Precision Medicine

  • Nathalie Jeanray