Publications (not up to date)

This folder holds the following references to publications, sorted by year and author.

There are 107 references in this bibliography folder.

Cai, W, Rambaud, J, Teboul, M, Masse, I, Benoit, G, Gustafsson, J, Delaunay, F, Laudet, V, and Pongratz, I (2008).
Expression levels of estrogen receptor beta are modulated by components of the molecular clock.
Mol Cell Biol, 28(2):784-93.

Coulon, A, Beslon, G, and Gandrillon, O (2008).
Large multiprotein structures modeling and simulation: the need for mesoscopic models.
Methods Mol Biol, 484:537-58.

Crauste, F, Pujo-Menjouet, L, Genieys, S, Molina, C, and Gandrillon, O (2008).
Adding self-renewal in committed erythroid progenitors improves the biological relevance of a mathematical model of erythropoiesis.
J Theor Biol, 250(2):322-38.

Gonin-Giraud, S, Bresson-Mazet, C, and Gandrillon, O (2008).
Involvement of the TGF-beta and mTOR/p70S6Kinase pathways in the transformation process induced by v-ErbA.
Leuk Res, 32(12):1878-88.

Hanriot, L, Keime, C, Gay, N, Faure, C, Dossat, C, Wincker, P, Scote-Blachon, C, Peyron, C, and Gandrillon, O (2008).
A combination of LongSAGE with Solexa sequencing is well suited to explore the depth and the complexity of transcriptome.
BMC Genomics, 9:418.

Klemal, J, Blachon, S, Soulet, A, Cremilleux, B, and Gandrillon, O (2008).
Constraint-based knowledge discovery from SAGE data.
In Silico Biol, 8(2):157-75.

Leyritz, J, Schicklin, S, Blachon, S, Keime, C, Robardet, C, Boulicaut, J, Besson, J, Pensa, RG, and Gandrillon, O (2008).
SQUAT: A web tool to mine human, murine and avian SAGE data.
BMC Bioinformatics, 9:378.

Pantalacci, S, Chaumot, A, Benoit, G, Sadier, A, Delsuc, F, Douzery, EJP, and Laudet, V (2008).
Conserved features and evolutionary shifts of the EDA signaling pathway involved in vertebrate skin appendage development.
Mol Biol Evol, 25(5):912-28.

Schubert, M, Brunet, F, Paris, M, Bertrand, S, Benoit, G, and Laudet, V (2008).
Nuclear hormone receptor signaling in amphioxus.
Dev Genes Evol, 218(11-12):651-65.

Blachon, S, Pensa, RG, Besson, J, Robardet, C, Boulicaut, J, and Gandrillon, O (2007).
Clustering formal concepts to discover biologically relevant knowledge from gene expression data.
In Silico Biol, 7(4-5):467-83.

Bresson, C, Keime, C, Faure, C, Letrillard, Y, Barbado, M, Sanfilippo, S, Benhra, N, Gandrillon, O, and Gonin-Giraud, S (2007).
Large-scale analysis by SAGE reveals new mechanisms of v-erbA oncogene action.
BMC Genomics, 8:390.

Keime, C, Semon, M, Mouchiroud, D, Duret, L, and Gandrillon, O (2007).
Unexpected observations after mapping LongSAGE tags to the human genome.
BMC Bioinformatics, 8:154.

Rosinski-Chupin, I, Briolay, J, Brouilly, P, Perrot, S, Gomez, SM, Chertemps, T, Roth, CW, Keime, C, Gandrillon, O, Couble, P, and Brey, PT (2007).
SAGE analysis of mosquito salivary gland transcriptomes during Plasmodium invasion.
Cell Microbiol, 9(3):708-24.

Benoit, G, Cooney, A, Giguere, V, Ingraham, H, Lazar, M, Muscat, G, Perlmann, T, Renaud, J, Schwabe, J, Sladek, F, Tsai, M, and Laudet, V (2006).
International Union of Pharmacology. LXVI. Orphan nuclear receptors.
Pharmacol Rev, 58(4):798-836.

Dazy, S, Gandrillon, O, Hyrien, O, and Prioleau, M (2006).
Broadening of DNA replication origin usage during metazoan cell differentiation.
EMBO Rep, 7(8):806-11.

Volakakis, N, Malewicz, M, Kadkhodai, B, Perlmann, T, and Benoit, G (2006).
Characterization of the Nurr1 ligand-binding domain co-activator interaction surface.
J Mol Endocrinol, 37(2):317-26.

Huang, J, Miao, X, Jin, W, Couble, P, Mita, K, Zhang, Y, Liu, W, Zhuang, L, Shen, Y, Keime, C, Gandrillon, O, Brouilly, P, Briolay, J, Zhao, G, and Huang, Y (2005).
Serial analysis of gene expression in the silkworm, Bombyx mori.
Genomics, 86(2):233-41.

Soula, H, Robardet, C, Perrin, F, Gripon, S, Beslon, G, and Gandrillon, O (2005).
Modeling the emergence of multi-protein dynamic structures by principles of self-organization through the use of 3DSpi, a multi-agent-based software.
BMC Bioinformatics, 6:228.

Benoit, G, Malewicz, M, and Perlmann, T (2004).
Digging deep into the pockets of orphan nuclear receptors: insights from structural studies.
Trends Cell Biol, 14(7):369-76.

Codina, A, Benoit, G, Gooch, JT, Neuhaus, D, Perlmann, T, and Schwabe, JWR (2004).
Identification of a novel co-regulator interaction surface on the ligand binding domain of Nurr1 using NMR footprinting.
J Biol Chem, 279(51):53338-45.

Damiola, F, Keime, C, Gonin-Giraud, S, Dazy, S, and Gandrillon, O (2004).
Global transcription analysis of immature avian erythrocytic progenitors: from self-renewal to differentiation.
Oncogene, 23(46):7628-43.

Keime, C, Damiola, F, Mouchiroud, D, Duret, L, and Gandrillon, O (2004).
Identitag, a relational database for SAGE tag identification and interspecies comparison of SAGE libraries.
BMC Bioinformatics, 5:143.

Nordzell, M, Aarnisalo, P, Benoit, G, Castro, DS, and Perlmann, T (2004).
Defining an N-terminal activation domain of the orphan nuclear receptor Nurr1.
Biochem Biophys Res Commun, 313(1):205-11.

Chelbi-alix, MK, Bobe, P, Benoit, G, Canova, A, and Pine, R (2003).
Arsenic enhances the activation of Stat1 by interferon gamma leading to synergistic expression of IRF-1.
Oncogene, 22(57):9121-30.

Dazy, S, Damiola, F, Parisey, N, Beug, H, and Gandrillon, O (2003).
The MEK-1/ERKs signalling pathway is differentially involved in the self-renewal of early and late avian erythroid progenitor cells.
Oncogene, 22(58):9205-16.