Evolutionary Optimization of Convolutional Neural Networks for Cancer miRNA Biomarkers Classification
A. Lopez-Rincon, A. Tonda, M. Elati, O. Schwander, B. Piwowarski, P. Gallinari
Applied Soft Computing (2018): 65: 91-100

Latent network-based representations for large-scale gene expression data analysis
W. Dhifli, M. Elati
BMC Bioinformatics (2018): to appear.

Evolutionary Mining of Skyline Clusters of Attributed Graph Data
W. Dhifli, N. Karabadji, M. Elati
Information Sciences (2018): to appear.

CoRegCAD : a framework from regulatory network to metabolic engineering
P. Trébulle, J-M Nicaud, M. Elati
10th International Workshop on Bio-Design Automation (2018): to appear.

Automating Systems Biology
AdaLab consortium
(2018): In preparation.


Inference and interrogation of a coregulatory network in the context of lipid accumulation in Yarrowia lipolytica
P. Trébulle, J-M Nicaud, Ch. Leplat , M. Elati*
Nature npj Systems Biology and Applications (2017): Aug 11;3:21. eCollection 2017.
PMID: 28955503 | doi: 10.1038/s41540-017-0024-1

An Evolutionary Schema for Mining Skyline Clusters of Attributed Graph Data
W. Dhifli, N. O. Da Costa, M. Elati*
IEEE Congress on Evolutionary Computation (2017): pp. 2102-2109

Integrating transcriptional activity in genome-scale models of metabolism
D. Trejo Banos, P. Trébulle, M. Elati*
BMC Systems Biology (2017): 11(Suppl 7):134
PMID:29322933 | doi:10.1186/s12918-017-0507-0

Discovery of Functional Motifs from the Interface Region of Oligomeric Proteins using Frequent Subgraph Mining
T. K. Saha, A. Katebi, W. Dhifli, M. Al Hassan
IEEE/ACM Transactions on Computational Biology and Bioinformatics (2017): In Press
PMID:28961123 | doi:10.1109/TCBB.2017.2756879

MR-SimLab: Scalable Subgraph Selection with Label Similarity for Big Data.
W. Dhifli, S. Aridhi, E. M. Nguifo.
Information Systems (Elsevier) (2017): 69: 155–163


GREAT: a web portal for Genome Regulatory Architecture Tools
Bouyioukos C, Bucchini F, Elati M*, Képès F
Nucleic acids research (2016): gkw384.
PMID:27151196 | doi: 10.1093/nar/gkw384

A Bayesian approach to construct context-specific gene ontology
Njah H, Jamoussi S, Mahdi W and Elati M
Computational Intelligence in Bioinformatics and Computational Biology (CIBCB), IEEE, pp. 1-6, 2016
PMID:  | doi: 10.1109/CIBCB.2016.7758127

Analysis tools for the interplay between genome layout and regulation
Bouyioukos C, Elati M, Képès F.
BMC Bioinformatics (2016): (Suppl 5):191
PMID:27294345 | doi: 10.1186/s12859-016-1047-0

Toward an Efficient Multi-class Classification in an Open Universe
W. Dhifli, A. B. Diallo.
12th International Conference on Machine Learning and Data Mining (MLDM), New York City, NY, USA 2016

Networks interrogation for genotype-phenotype study of the yeast diauxic shift
Trejo D, Khan S, Trebulle P, Elati M.
17th International conference on systems biology (ICSB), Barcelona, 2016

ProtNN: Fast and Accurate Protein 3D-Structure Classification in Structural and Topological Space.
W. Dhifli, A. B. Diallo.
BMC BioData Mining 9 (1): 1-17, 2016


CoRegNet: reconstruction and integrated analysis of co-regulatory networks
R. Nicolle, F. Radvanyi, and M. Elati*
Bioinformatics (2015): btv305
PMID:225979476 | doi: 10.1093/bioinformatics/btv305

A model for gene deregulation detection using expression data
T. Picchetti, J. Chiquet, M. Elati, P. Neuvial, R. Nicolle, E. Birmelé
BMC Systems Biology (2015): 9(Suppl 6):S6
PMID:26679516 | doi: 10.1186/1752-0509-9-S6-S6

A systems biology approach towards the prediction of ciliopathy mechanisms
Koutroumpas, K., Dam, J. V., Toedt, G., Lu, Q., Reeuwijk, J. V., Boldt, K., … Elati, M., Képès, F.
Cilia (2015): 4(Suppl 1)
 doi: 10.1186/2046-2530-4-S1-P88

Protocols for probing genome architecture of regulatory networks in hydrocarbon and lipid microorganisms
Bouyioukos C, Elati M, Képès F.
In “Protocols for Hydrocarbon Microbiology, Higher structure genomic organization” (2015): vol 8, K. Timmis, T. McGenity (Eds), Springer Protocols Series
doi: 10.1007/8623_2015_92


Differences in gene transcriptomic pattern of Plasmodium falciparum in children with cerebral malaria and asymptomatic carriers.
Almelli T, Nuel G, Bischoff E, Aubouy A, Elati M, Wang CW, Dillies MA, Copée JY, Nko Ayissi G, Basco LK, Rogier C, Tuikue Ndam N , Deloron P , Tahar R
PLoS One, 9: e114401, 2014
PMID: 25479608 | doi: 10.1371/journal.pone.0114401

PEPPER: Cytoscape app for Protein complex Expansion using Protein-Protein intERaction networks
Ch. Winterhalter, R. Nicolle, A. Louis, C. To, F. Radvanyi, and M. Elati*.
Bioinformatics, doi: 10.1093/btu517, 2014
PMID: 25138169 | doi: 10.1093/bioinformatics/btu517

Hybrid method inference for the construction of cooperative regulatory network in human
I. Chebil, R. Nicolle, G. Santini, C. Rouveirol and M. Elati*.
IEEE transactions on nanobioscience, 13: 97-103, 2014
PMID: 24771593 | doi: 10.1109/TNB.2014.2316920

Genome Regulatory Architecture Tools
Bouyioukos C, Elati M, Képès F
Proceedings of the Evry Spring School on advances in Systems and Synthetic Biology. (Eds. Amar P, Képès F, Norris V.), EDP Sciences,  (2014): p39-48.


PreCisIon: PREdiction of CIS-regulatory elements improved by gene’s positION
Mohamed Elati*, Rémy Nicolle, Ivan Junier, David Fernandez, Rim Fekih, Julio Font and François Képès
Nucleic Acids Research, 41(3):1406-1415, 2013
PMID: 23241390 | doi: 10.1093/nar/gks1286

Hybrid method inference for the construction of cooperative regulatory network in human.
Inès Chebil, Remy Nicolle, Guillaume Santini, Céline Rouveirol and Mohamed Elati
Bioinformatics and Biomedicine (BIBM’13), IEEE, Shanghai, 2013
PMID: 24771593 | doi: 10.1109/TNB.2014.2316920

A parallel genetic programming for single class classification
Cuong To and Mohamed Elati
Genetic and evolutionary computation (GECCO), ACM Companion, 1579-1586, Amesterdam, 2013
No PMID | doi: 10.1145/2464576.2466811

SETNET: Ensemble Method techniques for Learning Regulatory Networks
Inès Chebil, Mohamed Elati, Guillaume Santini and Céline Rouveirol.
Machine Learning and Applications (ICMLA’13), IEEE, USA, 2013
PMID:  | doi: 10.1109/ICMLA.2013.14

Multi-objective optimization for relevant sub-graph extraction
Mohamed Elati, Cuong To and Rémy Nicolle
Learning and Intelligent OptimizatioN (LION’7), LNCS, Italy, 2013
PMID:  | doi: 10.1007/978-3-642-44973-4_12

2012-2007 (selection)

Network transformation of gene expression for feature extraction
Rémy Nicolle, Mohamed Elati and François Radvanyi
Machine Learning and Applications (ICMLA’11), IEEE 1:108-113, USA, 2012

Boosting binding sites prediction using gene’s positions
Mohamed Elati, Rim Fekih, Remy Nicolle, Ivan Junier, Joan Herisson, François Képès
Algorithms in Bioinformatics (WABI’11), LNCS – 6833: 92-103, 2011

Unsupervised Learning for Gene Regulation Network Inference from Expression Data: A Review
Mohamed Elati, Céline Rouveirol
In book “Algorithms in Computational Molecular Biology: Techniques, Approaches and Applications”, M. Elloumi and A. Y. Zomaya (Eds), Wiley, 2011

Prediction of catalytic efficiency to discover new enzymatic activities
Chloé Sarnowski, Pablo Carbonell, Mohamed Elati and Jean-Loup Faulon
Machine Learning in Systems Biology (MLSB’10), pp. 153-56, Edinburgh, 2010

Identification of functional modules based on transcriptional regulation structure
Etienne Birmelé, Mohamed Elati*, Céline Rouveirol, Christophe Ambroise
BMC Proceedings, S4:1753-6561, 2008

LICORN: learning co-operative regulation networks from expression data
Mohamed Elati*, Pierre Neuvial, Monique Bolotin-Fukuhara, Emmanuel Barillot, François Radvanyi and Céline Rouveirol
Bioinformatics, 23:2407-2414, 2007

Fouille de données pour l’extraction de grands réseaux de régulation génétique
Mohamed Elati*, Céline Rouveirol, François Radvanyi
Modélisation et simulation pour la post-génomique, Technique et science informatiques RSTI série TSI vol 26: 173-196, 2007