Summary

The final workshop is organized by Inria and will take place from December 9 to 11, 2024 in St. Malo, France at the Hotel Chateaubriand.

How to come?

  • There are direct trains from Paris. See the SNCF page.
  • The hotel is a 20-minute walk from the train station. See this map.
  • There are 21 return journeys a day from Rennes to Saint malo. The official seller is SNCF.
  • Come by car, boat, plane: see the Saint-Malo page.

Registration

Please contact pierre.peterlongo@inria.fr

Programme

Monday Morning

  • 09h20 – 09h30: Welcome introduction words, Alex
  • 09h30 – 10h30 WP4-5-6
    • 09h30 – 09h45: WP6: Alexander Schoenhuth
    • 09h45 – 10h00: WP4: Tomas Vinar
    • 10h00 – 10h15: WP5: Nadia Pisanti
    • 10h15 – 10h30: Discussions
  • 10h30 – 11h00  Coffee Break
  • 11h00 – 11h30: EstĂ©ban Gabory – Variable strings for pangenomes: Matching, Comparison, Indexing
  • 11h30 – 12h00: Khodor Hannoush – Pan-genome graph update strategies

Monday afternoon

  • 14h00 – 14h30: Nicola Rizzo – Exploiting uniqueness: seed-chain-extend alignment on elastic founder graphs
  • 14h30 – 15h00 (remote): Jorge Avila Cartes – Representations for the comparative and hierarchical analysis of pan-genomes
  • 15h00 – 15h30: Raghuram Dandinasivara Rangaram – Pan-genome representations for deep machine learning applications
  • 15h30 – 16h00: Coffee Break
  • WP1-2-3
    • 16h00 – 16h30: WP1: Veli Mäkinen
    • 16h30 – 17h00: WP2: Paola Bonizzoni
    • 17h00 – 17h30: WP3: Alexander Schoenhuth
    • 17h30 – 18h00: discussions. 

Tuesday Morning

  • 9h00 – 9h30: Alessia Petescia – Differential Analysis in the Context of Pan-Genome Graphs
  • 9h30 – 10h00 (remote): Konstantinn Bonnet – Interactive pan-genome graph visualization
  • 10h00 – 10h30 (remote): Pengfei Wang  – Counting overlapping pairs of strings
  • 10h30 – 11h00: Coffee Break + Walk

Tuesday Afternoon: 

  • 14h00 – 16h00: Discussion on the future impact of the project (Organized by Veli Mäkinen)
  • 16h00 – 16h30: Coffee break
  • 16h30 – 18h00: Richard Durbin and Gene Myers Talks

Wednesday Morning, career fair

  • 9h00 – 9h30: Planned industrial partners:
    • Tina Visnovska Bioinformatics Core Facility, Oslo University Hospital
  • 9h30 – 10h00:  PĂ­o Sierra – Insights into Transposable Elements from Pangenomes
  • 10h00 – 10h30: Coffee Break
  • 10h30 – 11:00: Francesco Andreace – Efficiently merging compacted de Bruijn graphs 
  • 11h00 – 12h00: Planned industrial partners:

12h00-14h00: lunch (possible take-away for early departures)

Participation is possible in person as well as online.

Final Workshop