Institut de Mathématiques de Luminy


Files Type
  Berenguier Duncan, Tichit Laurent, Chaouiya Claudine, Naldi Aurélien, Graf Thomas, Thieffry Denis, Remy Elisabeth.
A compaction of discrete network dynamics emphasizing differentiation decisions.
Submitted, 2012.
2013 Berenguier Duncan, Chaouiya Claudine, Monteiro P. T., Naldi Aurélien, Remy Elisabeth et al.
Dynamical modeling and analysis of large cellular regulatory networks.
Chaos 23, 025114-1--025114-9, 2013.
  Chaouiya Claudine, Remy Elisabeth.
Logical modelling of regulatory networks, methods and applications [Editorial].
Bull. Math. Biol. 75, no. 6, 891--895, may 2013.
2012 Didier Gilles, Remy Elisabeth.
Relations between gene regulatory networks and cell dynamics in Boolean models.
Discrete Appl. Math. 160, no. 15, 2147--2157, 2012.
  Chaouiya C., Naldi A., Spinelli L, Monteiro P., Berenguier D., Grieco L., Mbodj A., Collombet S., Niarakis A., Tichit Laurent, Remy Elisabeth, Thieffry D.
Logical modelling of cellular decision processes with GINsim.
Conference JOBIM'12, 13th Open Days in Biology, Computer Science and Mathematics. Rennes, June 2012.
2011 Didier Gilles, Chaouiya Claudine, Remy Elisabeth.
Mapping multivalued onto Boolean dynamics.
J Theor Biol. 270(1):177-84, 2011.
  Chaouiya C., Naldi A., Remy Elisabeth, Thieffry D.
Petri net representation of multi-valued logical regulatory graphs.
Nat. Comput. 10, no. 2, 727--750, 2011.
  Naldi Aurélien, Remy Elisabeth, Thieffry Denis, Chaouiya Claudine. Dynamically consistent reduction of logical regulatory graphs.
Theoret. Comput. Sci. 412, no. 21, 2207--2218, 2011.
doi ACL
2009 Naldi Aurélien, Remy Elisabeth, Thieffry Denis, Chaouiya Claudine.
A reduction of logical regulatory graphs preserving essential dynamical properties.
Computational Methods in Systems Biology, CMSB’09, LNBI (Lect. Notes in Bioinformatics) 5688 :266-80, 2009.
2008 Lopez F., Textoris J., Bergon A., Didier Gilles, Remy Elisabeth, Granjeau S., Imbert J., Nguyen C., Puthier D.
TranscriptomeBrowser: a powerfull and flexible toolbox to explore productively the transcriptional landscape of the gene expression omnibus database.
PLoS ONE 3(12):e400, 2008.
doi ACL
  Remy Élisabeth, Ruet Paul.
From minimal signed circuits to the dynamics of Boolean regulatory networks.
Bioinformatics 24: i200-i226, 2008.
  Remy Élisabeth, Ruet Paul, Thieffry Denis.
Graphic requirements for multistability and attractive cycles in a Boolean dynamical framework.
Adv. in Appl. Math. 41, no. 3, 335--350, 2008.

Chaouiya Claudine, Remy Elisabeth, Thieffry Denis.
Petri net modelling of biological regulatory networks.
J. Discrete Algorithms 6, no. 2, 165--177, 2008.

doi ACL
2007 Textoris J., Lopez F., Didier Gilles, Remy Elisabeth, Granjeau S., Nguyen C., Puthier D.
DBF-MCL a new algorithm for rapidly and accurately axtracting cluster of co-regulated genes from microarray data.
JOBIM Marseille, 2007.
  Remy Élisabeth, Ruet Paul.
On differentiation and homeostatic behaviours of Boolean dynamical systems.
Transactions on Computational Systems Biology VIII, Springer LNCS 4780: 92-101, 2007.
Springer ACTI
Chaouiya Claudine, Remy Elisabeth, Thieffry Denis.
Qualitative Petri net modelling of genetic networks.
In C.Priami and G.Plotkin (Eds), Transactions on computational systems biology. VI, 95--112, Lecture Notes in Comput. Sci., 4220, Springer, Berlin, 2006.
doi ACTI
Chaouiya Claudine, Mendoza Luis, Remy Élisabeth, Ruet Paul, Thieffry Denis.
From logical regulatory graphs to standard Petri nets: dynamical roles and functionality of feedback circuits.
Transactions on Computational Systems Biology VII, Springer LNCS 4230: 56-72, 2006.
Springer ACTI

Remy Élisabeth, Ruet Paul, Thieffry Denis.
Positive or negative regulatory circuit inference from multilevel dynamics,
Positive Systems: Theory and Applications, Springer LNCIS 341: 263--270, 2006.

Simao E., Remy Elisabeth, Thieffry Denis, Chaouiya C.
Qualitative modelling of regulated metabolic pathway : application to the Tryptophan biosynthesis in E. Coli.
Bioinformatics 21, 190--196, 2005.

Chaouiya Claudine, Remy Élisabeth, Ruet Paul, Thieffry Denis.
Qualitative modelling of genetic networks: from logical regulatory graphs to standard Petri nets.
Application and Theory of Petri Nets, Lecture Notes in Computer Science 3099, pp. 137-156, Springer Verlag, 2004.

  Martin D., Brun C., Remy Elisabeth, Mouren P., Thieffry Denis, Jacq B.
GOToolBox: functional analysis of gene datasets based on Gene Ontology.
Genome Biology, vol.5,n. R101, 2004.

Mathieu Pierre, Remy Elisabeth.
Isoperimetry and heat kernel decay on percolation clusters.
Ann. Probab. 32, no. 1A, 100--128, 2004.

2003 Remy Elisabeth, Mossé Brigitte, Chaouiya Claudine, Thieffry Denis.
A description of dynamical graphs associated to elementary regulatory circuits.
Bioinformatics, vol. 1 n° 1, 1--7, 2003.
  Chaouiya Claudine, Remy Elisabeth, Mossé Brigitte, Thieffry Denis.
Qualitative analysis of regulatory graphs: a computational tool based on a discrete formal framework.
Positive systems (Rome, 2003), 119--126, Lecture Notes in Control and Inform. Sci., 294, Springer, Berlin, 2003.
2002 Didier Gilles, Brézellec P., Remy Elisabeth, Hénaut A.
GeneANOVA - gene expression analysis of variance.
Bioinformatics Applications Note vol. 18, pp.1-2, 2002.
2001 Mathieu Pierre, Remy Elisabeth.
Décroissance du noyau de la chaleur et isopérimétrie sur un amas de percolation [Heat kernel decay and isoperimetry on a percolation cluster].
C. R. Acad. Sci. Paris Sér. I Math. 332, no. 10, 927--931, 2001.
2001 Brezellec P., Didier G., Remy Elisabeth.
Classification de données d'expression : Voisinage local et dimension.
Soumis à JOBIM 2001.
Piatnitski A., Remy Elisabeth.
Homogenization of elliptic difference operators.
SIAM Journal of Mathematical Analysis, vol. 33, no. 1, 53--83, 2001.

1999 Homogénéisation d'opérateurs aux différences : approches analytique et probabiliste.
Thèse de doctorat, Université de Provence, octobre 1999.    abstract

Last update : january 20, 2014, EL.