program

RECOMB-CG 2019 (Program)


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Program at a Glance

The program will be spread over three days.
Please note that the 1st is a travel day. There will be an informal welcome reception at a public place in the evening.
To get to the welcome reception and the conference venue, see the instructions on the “Attending” page.

The 4th will be a FULL day.
We hope that attendees will use the weekend to travel.

Morning Lunch Afternoon Evening
Oct 1 — — — Informal Welcome
Oct 2 Keynote and Proceedings Talks on-site Keynote, Proceedings, and Flash Poster Talks Free
Oct 3 Keynote and Proceedings Talks on-site Poster Session, Proceedings Talks and Group Activity Dinner at the Domaine de la Grande Sieste
Oct 4 Keynote and Proceedings Talks Free Keynote and Proceedings Talks —

Program

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— Find papers for the talks here. —    
— Find poster abstracts here. —

Morning Lunch Afternoon Evening
Oct 1 — — — 18:00 Informal Welcome at Les Terrasses de la Babote
Oct 2 08:00 Welcome – Registration
08:45 Information

Session 1 (chair: Krister Swenson)

09:00 Keynote: P. Lopez Garcia Unraveling microbial evolution through metagenomics and single cell genomics
10:00 Read-SpaM: assembly-free and alignment-free comparison of bacterial genomes with low sequencing coverage. A.-K. Lau, C.-A. Leimeister, S. Dörrer, C. Bleidorn and B. Morgenstern
10:30 Coffee break

Session 2 (chair: Manuel Lafond)

11:00 An Efficient Exact Algorithm for Computing All Pairwise Distances between Reconciliations in the Duplication-Transfer-Loss Model. S. Santichaivekin, R. Mawhorter and R. Libeskind-Hadas

11:30 Inferring Pareto-Optimal Reconciliations across Multiple Event Costs under the Duplication-Loss-Coalescence Model. R. Mawhorter, N. Liu, R. Libeskind-Hadas and Y.-C. Wu

 12:00 – 14:00
on-site 		Session 3 (chair: Jens Lagergren)

14:00 Keynote: R. da Fonseca Comparative genomics provides insight into the evolution of hemostasis in vertebrates

15:00 Operon-based approach for the inference of rRNA and tRNA evolutionary histories in bacteria. T. Pawliszak, M. Chua, C. K. Leung and O. Tremblay-Savard

15:30 SimSpliceEvol: Alternative splicing-aware simulation of biological sequence evolution. E. Kuitche Kamela, S. Jammali and A. Ouangraoua

16:00 Coffee break

Session 4 (chair: Aida Ouangraoua)

16:30 Fast and Highly Accurate Species Trees through Divide-and-Conquer using GTM. V. Smirnov and T. Warnow

17:00 Generating Normal Networks via Leaf Insertion and Nearest Neighbor Interchange. L. Zhang

17:30 Flash talks — to advertise your poster (2 minutes each)

18:00 End

 Free
Oct 3 08:30 Welcome – Registration

Session 5 (chair: Siavash Mirarab)

09:00 Keynote: A. Carbone Many probabilistic models to functionally classify genomic and metagenomic sequences

10:00 Epigenetic PaceMaker: Closed Form Algebraic Solutions. S. Snir

10:30 Coffee break

Session 6 (chair: Louxin Zhang)

11:00 Recovering rearranged cancer chromosomes from karyotype graphs. S. Aganezov, I. Zban, V. Aksenov, N. Alexeev and M. Schatz

11h30 SharpTNI: Counting and Sampling Parsimonious Transmission Networks under a Weak Bottleneck. P. Sashittal and M. El-Kebir

 12:00 – 13:00
on-site 		13:00 Poster session

Session 7 (chair: Fabio Pardi)

14:00 Forcing external constraints on tree inference using ASTRAL. M. Rabiee and S. Mirarab

14:30 Comparing Copy-Number Profiles Under Multi-Copy Amplifications and Deletions. G. Cordonnier and M. Lafond

15:00 Group Activity

Dinner at the Domaine de la Grande Sieste
Oct 4 09:00 Welcome – Registration

Session 8 (chair: Eric Rivals)

09:30 Keynote: R. Koszul InstaGRAAL and metaTOR: two (meta)genomes assembly
programs exploiting in vivo chromosomal contacts

10:30 Deconvoluting the Diversity of Within-host Pathogen Strains in a Multi-Locus Sequence Typing Framework. G. Liang Gan, E. Willie, C. Chauve and L. Chindelevitch

11:00 Coffee break

Session 9 (chair: Cedric Chauve)

11:30 Distinguishing successive ancient polyploidy levels based on genome-internal syntenic alignments. Y. Zhang, C. Zheng and D. Sankoff

12:00 Analysis of local genome rearrangement improves resolution of ancestral genomic maps in plants. D. P. Rubert, F. Henrique Viduani Martinez, J. Stoye and D. Doerr

 12:30 – 14:30
Free 		Session 10 (chair: Anne Bergeron)

14:30 Keynote: B. Nabholz Phylogeny, GC-Biased gene conversion and population size effect : what have we learn from birds evolutionary genomics in the last 10 years?

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Session 11 (chair: Sophia Yancopoulos)

15:30 Getting insight into the pan-genome structure with Pangtree. P. Dziadkiewicz and N. Dojer

16:00 End of conference

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Keynote Speakers

Alessandra Carbone (CNRS РSorbonne Universit̩)
Rute A. R. da Fonseca (University of Copenhagen)
Purificación López García (CNRS – University Paris-Sud/Paris-Saclay)
Romain Koszul (Insitut Pasteur)
Benoît Nabholz (Université de Montpellier)

Accepted Papers

  • Santi Santichaivekin, Ross Mawhorter and Ran Libeskind-Hadas.
    An Efficient Exact Algorithm for Computing All Pairwise Distances between Reconciliations in the Duplication-Transfer-Loss Model
  • Guo Liang Gan, Elijah Willie, Cedric Chauve and Leonid Chindelevitch.
    Deconvoluting the Diversity of Within-host Pathogen Strains in a Multi-Locus Sequence Typing Framework
  • Yue Zhang, Chunfang Zheng and David Sankoff.
    Distinguishing successive ancient polyploidy levels based on genome-internal syntenic alignments
  • Maryam Rabiee and Siavash Mirarab.
    Forcing external constraints on tree inference using ASTRAL
  • Louxin Zhang.
    Generating Normal Networks via Leaf Insertion and Nearest Neighbor Interchange
  • Sergey Aganezov, Ilya Zban, Vitaly Aksenov, Nikita Alexeev and Michael Schatz.
    Recovering rearranged cancer chromosomes from karyotype graphs
  • Palash Sashittal and Mohammed El-Kebir.
    SharpTNI: Counting and Sampling Parsimonious Transmission Networks under a Weak Bottleneck
  • Esaie Kuitche Kamela, Safa Jammali and Aida Ouangraoua.
    SimSpliceEvol: Alternative splicing-aware simulation of biological sequence evolution
  • Ross Mawhorter, Nuo Liu, Ran Libeskind-Hadas and Yi-Chieh Wu.
    Inferring Pareto-Optimal Reconciliations across Multiple Event Costs under the Duplication-Loss-Coalescence Model
  • Hunter Tidwell and Luay Nakhleh.
    Integrated likelihood for phylogenomics under a no-common-mechanism model
  • Garance Cordonnier and Manuel Lafond.
    Comparing Copy-Number Profiles Under Multi-Copy Amplifications and Deletions
  • Vladimir Smirnov and Tandy Warnow.
    Fast and Highly Accurate Species Trees through Divide-and-Conquer using GTM
  • Paulina Dziadkiewicz and Norbert Dojer.
    Getting insight into the pan-genome structure with Pangtree
  • Anna-Katharina Lau, Chris-Andre Leimeister, Svenja Dörrer, Christoph Bleidorn and Burkhard Morgenstern.
    Read-SpaM: assembly-free and alignment-free comparison of bacterial genomes with low sequencing coverage
  • Diego P. Rubert, Fábio Henrique Viduani Martinez, Jens Stoye and Daniel Doerr.
    Analysis of local genome rearrangement improves resolution of ancestral genomic maps in plants
  • Sagi Snir.
    Epigenetic PaceMaker: Closed Form Algebraic Solutions
  • Tomasz Pawliszak, Meghan Chua, Carson K. Leung and Olivier Tremblay-Savard.
    Operon-based approach for the inference of rRNA and tRNA evolutionary histories in bacteria

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