Emmanuelle Becker

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Lecturer in Bioinformatics, University of Rennes


Dyliss team, Irisa / Inria Rennes-Bretagne Atlantique,
Campus de Beaulieu, 35042 Rennes Cedex, France.
Tel: +33 (0) 2 99 84 25 67
Fax: +33 (0) 2 99 84 71 71
Email: prenom.nom@univ-rennes1.fr
Email: prenom.nom@irisa.fr



 

Research interests


 

Thématique de recherche autour des graphes biologiques :

Je m’intéresse à l’étude des réseaux d’interactions protéine-protéine modélisés comme de grands graphes biologiques. J’y étudie nottament les relations entre topologie du graphe et fonction cellulaire, afin de faire de l’inférence fonctionnelle.
  • Sujet de stage de M2 disponible [ici]
  • Pour les stages de M1, me contacter.


Thématique de recherche autour de l’analyse de données –omiques :

J’ai participé à l’analyse de données génomique, protéomique, épigénétique, etc dans de nombreux projets de recherche. Aujourd’hui, je m’interesse au développement des méthodes d’intégration et de méta-analyse de données -omiques hétérogènes.
 

 

Teaching stuff


 

Applied statitics for computer science Bachelor Students 

Object Oriented Programming for Master's student

  • Basic Exercices : Just a little bit of Java syntax [PDF]+[PDF], Encapsulation and information hiding [PDF]
  • Bioinformatics Exercices : GC content of sequences (one-dimensional tables) [PDF]+[sequence], Motif finding with PSSM matrices [PDF]+[classes], Fire spreading, Epidemy spreading (bi-dimensional tables) [PDF], Preys vs. Predators (Collections) [PDF], Hierarchical clustering (Collections, Recursivity) [PDF]

Erasmus+ Lessons for Statistics in Salerno

 

Method, 2019

 

Advanced R for data analysis for Master's students (see ENT)

Systems Biology for Master's students (see ENT)

Introduction to computational ecology for Master's students (see ENT)

Python for Biologists for Bachelor Students (see ENT)

Atelier de Biostatistiques for Biology Bachelor's students (see ENT)

 

Publications


 

[26] Xie B, Becker E, Stuparevic I, Wery M , Descrimes M, Morillon A, and Primig M. The anti-cancer drug 5-fluorouracil affects cell cycle regulators and long non-coding RNAs with regulatory potential in yeast. RNA Biology, 2019

[25] Darde T, Gaudriault P, Beranger R, Lancien C, Caillarec-Joly A, Sallou O, Bonvallot N, Costet N, Chevrier C, Mazaud-Guittot S, Jégou B,  Collin O, Becker E, Rolland A-D and Chalmel F. TOXsIgN : A public repository for toxicological signatures at the IRSET. Bioinformatics, 2018.

[24] Leverrier-Penna S, Mitchell RT, Becker E, Lecante L, Ben Maamar M, Lavoué V, ristensen DM, Jégou B, Dejucq-Rainsford N, Mazaud-Gittot S. Ibuprofen is deleterious for the development of first trimester human fetal ovary ex vivo. Human Reprod, 2018.

[23]  Houzet L , Pérez-Losada M, Matusali G, Deleage C, Dereuddre-Bosquet N, Satie AP, Aubry F, Becker E, Jégou B, Le Grand R, Keele BF, Crandall KA and Dejucq-Rainsford N. Seminal SIV in cynomolgus macaques is dominated by virus originating from multiple genital organs. Journal of Virology, 2018.

[22] Dugay F, Llamas-Gutierrez F, Gournay M, Medane S, Mazet F, Christian-Chiforeanu D, Becker E, Lamy R, Léna H, Rioux-Leclercq N, Belaud-Rotureau MA and Cabilic F. Clinicopathological characteristics of ROS1- and RET-rearranged NSCLC in caucasian patients. Data from a cohort of 713 non-squamous NSCLC lacking KRAS/EGFR/HER2/BRAF/PIK3CA/ALK alterations. Oncotarget, 2017.

[21] Becker E, Com E, Lavigne R, Guilleux M-H, Evard B, Pineau C and Primig M. The protein expression landscape of mitosis and meiosis in diploid budding yeast. J. Proteomics, 2017.

[20] Hao* C, Gely-Pernot* A, Kervarrec C, Boudjema M, Becker E, Khil P, Tevosian S, Jégou B and  Smagulova F. Exposure to the widely used herbicide atrazine results in deregulation of global tissue-specific RNA transcription in the third generation and is associated with a global decrease of histone trimethylation in mice. Nucleic Acids Research, 2016.

[19] Xie B, Horecka J, Chu A, Davis RW, Becker E and Primig M. Ndt80 activates the meiotic ORC1 transcript isoform and SMA2 via a bi-directional middle sporulation element in Saccharomyces cerevisiae. RNA Biology, 2016.

[18] Chapple C E, Robisson  B, Spinelli  L, Guien  C, Becker E, Brun C. Extreme multifunctional proteins identified from a human protein interaction network. Nature Communications, 2015.

[17] Darde T, Sallou O, Becker E, Evrard B, Monjeau C, Le Bras Y, Jégou B, Collin O, Rolland A and Chalmel F. The ReproGenomics Viewer: an integrative cross-species toolbox for the reproductive science community. Nucleic Acids Research, Web-Server issue, 2015.

[16] Liu* Y, Stuparevic* I, Xie B, Becker E, Law M and Primig M. The conserved histone deacetylase Rpd3 and the DNA binding regulator Ume6 repress BOI1’s meiotic transcript isoform during vegetative growth in Saccharomyces cerevisiae. Mol. Microbiology, 2015.

Corrected in Mol. Microbiology, 2015, Volume 99, Issue 1, 217.

  [15] Gely-Pernot* A, Hao* C, Becker E, Stuparevic I, Kervarrec C, Chalmel F, Primig M, Jégou B and  Smagulova F. Worldwide used herbicide atrazine affects meiosis in male mice. BMC Genomics, 2015.

[14] Becker E, Liu Y, Lardenois A, Walther T, Horecka J, Stuparevic I, Law M, Lavigne R, Evrard E, Demougin P, Riffle M, Strich R, Davis R W, Pineau C and Primig M. Integrated RNA- and protein profiling of fermentation and respiration in diploid budding yeast provides insight into nutrient control of cell growth and development. J. of Proteomics, 2015.

[13] Petit* F G, Kervarrec* C, Jamin* S P, Smagulova F, Hao C, Becker E, Jégou  B, Chalmel F and   Primig M. Combining RNA- and Protein Profiling Data With Network Interactions Yields Clues About Gene Function in Mouse and Human Spermatogenesis. Biol. of Reproduction, 2015.

[12] Stuparevic I, Becker E, Law M and Primig M. The histone deacetylase Rpd3/Sin3/Ume6 complex represses an acetate inducible isoform of VTH2 in fermenting budding yeast cells. FEBS Letters, 2015

[11] Lardenois* A, Becker* E, Walther* T, Law M, Demougin P, Strich R and Primig M. Global alterations of the transcriptional landscape during budding yeast growth and development in the absence of Ume6-dependant chromatin modification. Mol. Genet. Genomics, 2015.

[10] Lardenois A*, Stuparevic I*, Liu Y*, Law M J, Becker E, Smagulova F, Waern K, Guilleux M-H, Horecka J, Chu A, Kervarrec C, Strich R, Snyder M, Davis R W, Steinmetz L M, and Primig M. The conserved histone deacetylase Rpd3 and its DNA binding subunit Ume6 control dynamic transcript architecture during mitotic growth and meiotic development. Nucleic Acids Research, 2014.

[9] Lavigne R, Becker E, Liu Y, Evrard B, Lardenois A, Primig M and Pineau C. Direct iterative protein profiling (DIPP) - an innovative method for large-scale protein detection applied to budding yeast mitosis. Mol Cell Proteomics, 2012.

[8] Becker E*, Robisson B*, Chapple CE, Guénoche A and Brun C. Multifunctional proteins revealed by overlapping clustering in protein interaction network. Bioinformatics, 2012.

[7] Souiai O*, Becker E*, Prieto C, Benkahla A, De las Rivas J and Brun C. Functional integrative levels in the human interactome recapitulate organ organization. PLoS One, 2011.

[6] Aucher W*, Becker E*, Ma E, Miron S, Martel A, Ochsenbein F, Marsolier-Kergoat M-C and Guerois R. A strategy for interaction site prediction between phospho-binding modules and their partners identified from proteomic data. Mol Cell Proteomics, 2010.

[5] Becker E., Guénoche A. and Brun C. (2009). Systèmes de classes chevauchantes pour la recherche de protéines multifonctionnelles. Actes JOBIM 2009, p.49-54, Nantes, 9-11 juin 2009.

[4] Becker E, Cotillard A, Meyer V, Madaoui H, Guerois R. HmmKalign : a tool for generating sub-optimal HMM alignments. Bioinformatics, 2007.

[3] Becker E*, Meyer V*, Madaoui H, Guerois R. Detection of a tandem BRCT in Xrs2 and Nbs1 with functional implications in the DNA damage response. Bioinformatics, 2006.

[2] Madaoui H, Becker E, Guérois R. Sequence search methods and scoring functions for the design of protein structures. Methods in Molecular Biology, 2006.

[1] Mousson F, Lautrette A, Thuret JY, Agez M, Courbeyrette R, Amigues B, Becker E, Neumann JM, Guerois R, Mann C, Ochsenbein F. Structural basis for the interaction of Asf1 with histone H3 and its functional implications. Proc Natl Acad Sci U S A, 2005.