Samuel Marguerat, Thomas Skøt Jensen, Ulrik de Lichtenberg, Lars Juhl Jensen & Jürg Bähler
The more the merrier: comparative analysis of microarray studies on cell cycle-regulated genes in fission yeast. Yeast, 23(4), 261-277, 2006

Ulrik de Lichtenberg, Rasmus Wernersson, Thomas Skøt Jensen, Henrik Bjørn Nielsen, Anders Fausboll, Peer Schmidt, Flemming Bryde Hansen, Steen Knudsen, Søren Brunak. New weakly expressed cell cycle-regulated genes in yeast. Yeast, 22(15), 1191-2017, 2005

Ulrik de Lichtenberg, Lars Juhl Jensen, Anders Fausbøll, Thomas Skøt Jensen, Peer Bork & Søren Brunak. Comparison of computational methods for the identification of cell cycle regulated genes. Bioinformatics, 21(7), 1164-1171, 2005

Bähler J (2005). Cell-cycle control of gene expression in budding and fission yeast.
Annu. Rev. Genet. 39:69-94

Penkett CJ, Morris JA, Wood V, Bähler J (2006). YOGY: a web-based, integrated database to retrieve protein orthologs and associated Gene Ontology terms.
Nucleic Acids Res 34, W330-W334.

Varshavsky, R., Gottlieb, A., Linial, M. and Horn D. (2006) Novel Unsupervised Feature Filtering of Biological Data. Bioinformatics 22(14):e507-e513. doi:10.1093/bioinformatics/btl214

Sasson, O., Kaplan, N. and Linial, M (2006) Functional annotation prediction: All for one and one for all. Protein Science (2006), 15:1557-1562. 10.1110/ps.062185706

Schueler-Furman O, Glick E, Segovia J, Linial M. (2006) Is GAS1 a co-receptor for the GDNF family of ligands? Trends Pharmacol Sci. 27:72-77.

Fauré A, Naldi A, Chaouiya C, Thieffry D (2006). Dynamical analysis of a generic Boolean model for the control of the mammalian cell cycle. Bioinformatics 22: e124-31.

Gonzalez AG, Sánchez L, Thieffry D, Chaouiya C (2006). GINsim: a software suite for the qualitative modelling, simulation and analysis of regulatory networks. Biosystems 84: 91-100.

Remy E, Mendoza L, Thieffry D, Chaouiya C. (in press). From Logical Regulatory Graphs to Standard Petri Nets: Dynamic Roles and Functionality of Feedback Circuits. Transactions in Computational Systems Biology.

Chaouiya R, Remy E, Thieffry D (in press). Qualitative Petri Net modelling of genetic networks. Transactions in Computational Systems Biology.

de Jong H, Ropers D, Chaouiya C, Thieffry D (2005). Modélisation, analyse et simulation de réseaux de régulation génique. Biofutur 252: 36-40.

Remy E, Ruet P, Thieffry D (in press). Positive or negative regulatory circuit inference from multilevel dynamics. Proceedings of POSTA 2006.

Chaouiya C, de Jong H, Thieffry D (eds.) (2006). Dynamical Modelling of Biological Regulatory Networks. Special issue of BioSystem 84(2): 77-174.

Submitted:
Varshavsky, R, Horn D. and Linial M. (2006) BMC Bioinformatics (submitted)
Clustering Algorithms Optimizer - A Framework for Large Datasets.

Remy E, Ruet P, Thieffry D (submitted). Graphic requirements for multistability and attractive cycles in a Boolean dynamical framework. Advances in Applied Mathematics.