January 23-24 2014, UPMC, Paris, France

SMPGD 2014

This workshop aims at gathering statisticians, computer scientists, and biologists to discuss new statistical methodologies for the analysis of high throughput biological data and the challenge arising herein.

This year we will celebrate the tenth edition of SMPGD in the heart of Paris, at University Pierre et Marie Curie. The workshop is organized by the Laboratoire de Génomique des Microorganismes and will feature 4 keynote speeches and 3 invited sesssions. The themes of the session are Metabolism, Evolution, and Statistical genomics. We also welcome submission of abstracts for contributions.

The conference will take place at the UPMC campus, Durand auditorium - Esclangon building (map)

Previous editions were in Amsterdam (2013) and Lyon (2012).

Visit smpgd.fr to get more general information about the SMPGD series of workshops.

Inscription to smpgd2014 is free but mandatory.

Book of abstracts

Detailled program


Deadline for submission of abstracts: 15th of December, 2013

Deadline for registration: 15th of December, 2013





Preliminary Program

Invited Speakers (abstracts)


  • Protein structure: David T. Jones (Computer Science, University College London)
  • Evolution: Frédéric Austerlitz (Eco-anthropologie et Ethnologie, Museum National d'Histoire Naturelle)
  • Big Data: Arnak Dalalyan (ENSAE / CREST, Université Paris-Est)
  • Phylogeny: Cécile Ané (Department of Statistics and Botanics, University of Wisconsin-Madison)


Contributed Sessions


  • Thursday 11:30 - Statistical Genomics (organizer: Bertrand Servin, abstracts)
    • Simon Boitard (Origine, Structure et Evolution de la Biodiversité, Museum National d'Histoire Naturelle) :
      Inferring the past dynamics of effective population size using genome wide molecular data
    • Anne-Louise Leutenegger (Genetic Variation and Human Diseases Lab, INSERM & Univ. Paris Diderot):
      Mapping genes in consanguineous and isolated populations in the era of high throughput sequencing
    • Christèle Robert-Granié (Station d’Amélioration Génétique des Animaux, INRA Toulouse) :
             Integration of genomic information into genetic evaluation model : Is it a good statistical model?

  • Thursday 15:55 - Phylogeny (organizer: Nicolas Lartillot, abstracts)
    • Alessandra Carbone (CQB, Université Pierre et Marie Curie - CNRS)
              Coding of evolutionary pathways in proteins: from sequence to function
    • Gergely J. Szöllősi (ELTE-MTA Biophysics Research Group - Eötvös University)
              Efficient Exploration of the Space of Reconciled Gene Trees
  • Friday 11:15 - Metabolism (organizer: Daniel Kahn, abstracts)
    • David Vallenet (Laboratory of Bioinformatics for Genomics and Metabolism, Génoscope)
      Enzyme survey and how to find new ones
    • Christoph Kaleta (Theoretical Systems Biology Friedrich-Schiller-Universität Jena)
             Tuned for speed – Elucidation of strategies for rapid metabolic adaptations in prokaryotes
    • Frank J. Bruggeman (Systems Bioinformatics, VU University, Amsterdam)
      Constraints, adaptability and optimality of metabolic networks



Selected Presentations

A fast homotopy algorithm for a large class of weighted classification problems and application to phylogeny (pdf)
Rigaill Guillem, Gutierrez Pierre, Chiquet Julien

Multi-trait genomic selection via multivariate regression with structured regularization (pdf)
Chiquet Julien, Robin Stéphane, Mary-Huard Tristan

Identifying Differentially Expressed Proteins by a Binary Threshold Model (pdf)
Gibb Sebastian, Strimmer Korbinian

Testing for Associations between Loci and Environmental Gradients Using Latent Factor Mixed Models (pdf)
Frichot Eric, Schoville Sean, Bouchard Guillaume, François Olivier

Evolution of Codon Usage Bias in E. coli (pdf)
Pouyet Fanny, Bailly-Bechet Marc, Guéguen Laurent

A New Gene-Based test of Association Using Extended Rasch Models (pdf)
Wang Wenjia

A Regularisation Path-Following Approach for Discovering Interactions in High-Dimensional Survival Data (pdf)
Dave Duverle, Takeuchi Ichiro, Tsuda Koji

The Causal Mediation Analysis in Genomic Data (pdf)
Malaguti Giulia, Affeldt Séverine, Isambert Hervé

On the robustness of the Generalized Fused Lasso to prior specifications (pdf)
Sophie Lambert-Lacroix, Hölger Hoefling, and Franck Picard

Testing 2 x 2 Association with Uncertain Classification (pdf)
Dijkstra Louis, Schönhuth Alexander

An RNA-Seq read count emission model for transcriptional landscape reconstruction with state-space models (pdf)
Mirauta Bogdan, Nicolas Pierre, Richard Hugues

The leave-p-out estimator of the prediction error as a U-statistic and its asymptotic tests (pdf)
Fuchs Mathias

Of cis, trans, and feedback regulation: Dissecting local regulation in yeast (pdf)
Gagneur Julien, Bader Daniel

Efficient statistical computations on genome-scale data using reduced representations (pdf)
Schliep Alexander, Md Pavel Mamhud.

Call for communications

Deadline for submission of communications : 15th of December 2013, before midnight in the timezone of your choice.


We accept submission of abstract of maximum 2 pages. The submitted abstract will have to follow the LNCS template (see here for more details) and first uploaded as pdf files. The best submissions will be selected for oral communications (15 minutes presentations) and not selected abstracts will be given the opportunity to present a poster during the poster session.

Please use the submit form on the left to submit an abstract (contact smpgd2014@sciencesconf.org in case of problem)




Visit smpgd.fr for more information about the SMPGD series of workshops.

We benefitted from the support and sponsor of:

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