Matthieu VIGNES

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Matthieu-titou-munro.jpg

Newanima.gif As from July 2014, I will be a senior lecturer in statistical genetics at Massey university IFS !

Research fellow (in detached position from July 2014) in the Math dpt of the INRA (The French institute for agronomy, food and environment) in Toulouse (MIA-T Unit).

Research interests

  • Probabilistic graphical models: Bayesian networks, Markov random fields, mean-field like approximations, EM procedures, MCMC...
  • Applications to system biology: relevant integration of different sources of molecular data in a probabilistic framework. In particular: genetical genomics (incl. network reconstruction).
  • Some extensions: handling missing data, overlapping clustering, modelling of a complex system with missing components, causal interpretation.
  • Modelling root front dynamics of plants.

Reviewer for AISTATS, Bioinformatics, BMC Systems Biology, IEEE/ACM TCBB, the Journal of Mathematical Modelling and Algorithms, the J-SFdS, MARAMI 2010, Neurocomputing, Math. Model. Nat. Phenom. and PLoS ONE.

Member of the AIGM (formerly MSTGA) and the NETBIO workgroups. Involved in FRAGENOMICS and SUNYFUEL ANR research projects. Co-organizer of the AIGM workshop series: 'Graphical models for reasoning on biological systems: computational challenges' (ECCS'10 satellite meeting), AIGM'12 (ECAI workshop), AIGM'13 and AIGM'14 (with N. Peyrard, S. Robin, R. Sabbadin and T. Schiex).

Software development : SpaCEM3.

Selected publications

  • Newanima.gif Magali Champion, Sébastien Gadat, Christine Cierco-Ayrolles and Matthieu Vignes. Sparse multivariate regression with L2-Boosting algorithm. J. Statist. Plann. Inference, accepted (2014). [article (pdf)]
  • Gwenaëlle Marchand, Vân-Anh Huynh-Thu, Nolan Kane, Sandrine Arribat, Didier Varès, David Rengel, Sandrine Balzergue, Loren Rieseberg Patrick Vincourt, Pierre Geurts, Matthieu Vignes* and Nicolas B. Langlade*. Bridging physiological and evolutionary time scales in a gene regulatory network. New Phytologist, 203(2):685-696 (2014). [article (pdf) and link to Suppl. Info.]
  • Nathalie Villa-Vialaneix, Magali SanCristobal, Matthieu Vignes, Laurence Liaubet. Joint network inference with the consensual LASSO. QTQM, 11(1):39-60 (2014). [article (pdf)].
  • David Allouche*, Christine Cierco-Ayrolles*, Simon de Givry*, Gérald Guillermin*, Brigitte Mangin*, Thomas Schiex*, Jimmy Vandel* and Matthieu Vignes*. A Panel of Learning Methods for the Reconstruction of Gene Regulatory Networks in a Systems Genetics (2013). In Gene Network Inference, Verification of Methods for Systems Genetics Data, Alberto de la Fuente (Ed.). [chapter (pdf)] and [book (Springer website)].
  • Lionel Dupuy and Matthieu Vignes. An algorithm for the simulation of the growth of root systems on deformable domains. J. Theor. Biol., 310:164-174 (2012). [article (pdf)].
  • Jimmy Vandel, Brigitte Mangin, Matthieu Vignes, Damien Leroux, Olivier Loudet, Marie-Laure Martin-Magniette, Simon de Givry. Inférence de réseaux de régulation de gènes au travers de scores étendus dans les réseaux bayésiens. RIA, 26(6):679-708 (2012). [article].
  • Matthieu Vignes, Jimmy Vandel, David Allouche, Nidal Ramadan-Alban, Christine Cierco-Ayrolles, Thomas Schiex, Brigitte Mangin and Simon de Givry. Gene regulatory network reconstruction using Bayesian networks, the Dantzig selector, the Lasso and their meta-analysis. (after SaAB team won the DREAM5 Challenge 3A on the reconstruction of GRN in the context of Systems Genetics data) PLoS ONE, 6(12):e29165 (2011). [article].
  • Matthieu Vignes, Juliette Blanchet, Damien Leroux and Florence Forbes. SpaCEM3, a software for biological module detection when data is incomplete, high dimensional and dependent. Bioinformatics, 27(6):881-882 (2011). [article (pdf), software website].
  • Lionel Dupuy, Matthieu Vignes, Blair McKenzie and Philip White. The dynamics of root meristem distribution in the soil. Plant Cell Environ., 33(3):358-369 (2010). [article (pdf)].
  • Juliette Blanchet* and Matthieu Vignes*. A model-based approach to gene clustering with missing observations reconstruction in a Markov random field framework. J. Comput. Biol., 16(3): 475-486 (2009). [article (pdf)].
  • Matthieu Vignes and Florence Forbes. Gene clustering via integrated Markov models combining individual and pairwise features. IEEE/ACM Trans. Comput. Biol. Bioinform., 6(2): 260-270 (2009). [article (pdf)].
  • Matthieu Vignes. Modèles markoviens graphiques pour la fusion de données individuelles et d'interactions : application à la classification de gènes. PhD thesis [in French]. Dir: Florence Forbes and Gilles Celeux. Université Joseph Fourier Grenoble 1, France (2007).

Collaborations

Florence Forbes (INRIA Rhône-Alpes, France), Juliette Blanchet (LTHE, France), Lionel Dupuy (JHI, Scotland), Nicolas Langlade, Gwénaëlle Marchand, Lucas Marmiesse, David Rengel, Susana Rivas, Magali San Cristobal, Patrick Vincourt (INRA Toulouse, France), Marie-Laure Martin Magniette (INRA AgroParisTech, France), Olivier Loudet, Francisco Cubillos (VAST lab, IJPB, France), A. de la Fuente (Bioinformatics @ Leibniz Institute for Farm Animal Research, Germany), Béatrice Denoyes-Rothan (INRA Bordeaux, France), Amparo Monfort (IRTA, Spain), Willy Schwab (TUM, Germany), Sophie Lamarre, Sébastien Déjean, Sophie Lamarre (INSA Toulouse), and members of the MIA-T unit in Toulouse.

Students: Amit Kumar (MSc 2008, univ. Abertay, Scot), Nidal Ramadan (M2R / ENSAI 2010, univ Rennes, Fr), Magali Champion (M2R 2011, PhD 2011-2014, univ. Toulouse 3, France), Laëtitia Bonneval (M1P 2011, univ. Toulouse 1, Fr), Damien Dufourcq (INSA Toulouse 2012, Fr), Gérald Guillermin (M1P 2012, univ. Toulouse 3, Fr), Soda Thiam (INSA Toulouse 2012, Fr), Maxime Godeau and Thibault Suarez (ISAE SupAero 2013, Fr) Steve van Ginkel (M1P 2014, univ. Toulouse 3, Fr).

Qualifications

  • PhD in Statistics: University Joseph Fourier - Grenoble 1 (2007).
  • ENS Lyon Alumni'02.
  • B.Sc & M.Sc in Mathematics: University Claude Bernard - Lyon 1 (2001 & 2002).
  • Agregation de Mathematiques (2002).

Teaching

  • "Statistics and learning" to 5th year students of SupAero, with Emmanuel Rachelson and Probability, with Jérémie Bigot.
  • Statistics: basics to advanced subjects to undergraduates in Biology or Economics, to PhD students and scientists from research institutes.
  • General mathematics: algebra and analysis and Statistics to undergraduates in Mathematics and Physics.
  • General science courses to high-school pupils.

Employment history

  • 2014-present: senior lecturer at Massey university (New-Zealand).
  • 2009-present [detached position from 2014]: research fellow at the INRA (France).
  • 2006-2009: statistician with BioSS (Aberdeen and Dundee, Scotland).
  • 2002-2006: research and teaching assistant at Joseph Fourier University (Grenoble, France) and with team Mistis, INRIA Rhône-Alpes (France).

Violons d'Ingres

  • Mountaineering and/or running: climbing, skiing, hiking, hill running (over 2/3rd of a Munroist, 88 to go, spatially speaking here), an enthusiastic former Dundee Hawk and a Manikou in my heart  :-), orienteering course, biking,...
  • Music (clarinet).
  • Travels.

Contact informations

Links

Génotoul BioInfo
Équipe RECORD
IMABS
Outils personnels