How to infer gene networks from expression profiles, Molecular Systems Biology, vol.3, issue.1, p.78, 2007. ,
Inferring the conservative causal core of gene regulatory networks, BMC Systems Biology, vol.4, issue.1, p.132, 2010. ,
Wisdom of crowds for robust gene network inference, Nature Methods, vol.9, issue.8, pp.796-804, 2012. ,
Reverse Engineering: A Key Component of Systems Biology to Unravel Global Abiotic Stress Cross-Talk, Frontiers in Plant Science, vol.3, 2012. ,
Modeling cellular machinery through biological network comparison, Nature Biotechnology, vol.24, issue.4, pp.427-433, 2006. ,
Differential C3net reveals disease networks of direct physical interactions, BMC Bioinformatics, vol.12, issue.1, p.296, 2011. ,
Differential network biology, Molecular Systems Biology, vol.8, p.565, 2012. ,
Network Medicine: A Network-based Approach to Human Disease, Nature reviews. Genetics, vol.12, issue.1, pp.56-68, 2011. ,
Gene regulation by antisense transcription, Nature Reviews Genetics, vol.14, issue.12, pp.880-893, 2013. ,
A Cluster of Disease Resistance Genes in Arabidopsis Is Coordinately Regulated by Transcriptional Activation and RNA Silencing, The Plant Cell, vol.19, issue.9, pp.2929-2939, 2007. ,
Widespread anti-sense transcription in apple is correlated with siRNA production and indicates a large potential for transcriptional and/or post-transcriptional control, New Phytologist, vol.203, issue.1, pp.287-299, 2014. ,
URL : https://hal.archives-ouvertes.fr/hal-01209978
WGCNA: an R package for weighted correlation network analysis, BMC Bioinformatics, vol.9, issue.1, p.559, 2008. ,
ARACNE: An Algorithm for the Reconstruction of Gene Regulatory Networks in a Mammalian Cellular Context, BMC Bioinformatics, vol.7, issue.1, p.7, 2006. ,
NARROMI: a noise and redundancy reduction technique improves accuracy of gene regulatory network inference, Bioinformatics, vol.29, issue.1, pp.106-113, 2013. ,
Evaluation of statistical methods for normalization and differential expression in mRNA-Seq experiments, BMC Bioinformatics, vol.11, p.94, 2010. ,
The impact of quantile and rank normalization procedures on the testing power of gene differential expression analysis, BMC Bioinformatics, vol.14, p.124, 2013. ,
The mutual information: Detecting and evaluating dependencies between variables, Bioinformatics, vol.18, issue.2, pp.231-240, 2002. ,
A comprehensive comparison of association estimators for gene network inference algorithms, Bioinformatics, vol.30, issue.15, pp.2142-2149, 2014. ,
Network motifs in the transcriptional regulation network of Escherichia coli, Nature Genetics, vol.31, issue.1, pp.64-68, 2002. ,
An extended transcriptional regulatory network of Escherichia coli and analysis of its hierarchical structure and network motifs, Nucleic Acids Research, vol.32, issue.22, pp.6643-6649, 2004. ,
Topological and causal structure of the yeast transcriptional regulatory network, Nature Genetics, vol.31, issue.1, pp.60-63, 2002. ,
SynTReN: a generator of synthetic gene expression data for design and analysis of structure learning algorithms, BMC Bioinformatics, vol.7, issue.1, p.43, 2006. ,
Differential functional analysis and change motifs in gene networks to explore the role of anti-sense transcription, International Symposium on Bioinformatics Research and Applications, pp.117-126, 2016. ,
URL : https://hal.archives-ouvertes.fr/hal-01412515
Inference and differential analysis of extended core networks: A way to study anti-sense regulation, IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2016, pp.284-287, 2016. ,
URL : https://hal.archives-ouvertes.fr/hal-01467169
Cytoscape: A Software Environment for Integrated Models of Biomolecular Interaction Networks, Genome Research, vol.13, issue.11, pp.2498-2504, 2003. ,
Reducibility among Combinatorial Problems, Complexity of Computer Computations. The IBM Research Symposia Series, pp.85-103, 1972. ,
Steiner tree methods for optimal sub-network identification: an empirical study, BMC Bioinformatics, vol.14, p.144, 2013. ,