User profiles for D. Thieffry

Denis Thieffry

Professor of Systems Biology, Institut de Biologie de l'Ecole Normale Supérieure (IBENS) …
Verified email at ens.fr
Cited by 13380

SBML Level 3: an extensible format for the exchange and reuse of biological models

…, JC Schaff, LP Smith, MJ Swat, D Thieffry… - Molecular systems …, 2020 - embopress.org
Abstract Systems biology has experienced dramatic growth in the number, size, and
complexity of computational models. To reproduce simulation results and reuse models, …

From specific gene regulation to genomic networks: a global analysis of transcriptional regulation in Escherichia coli

D Thieffry, AM Huerta, E Pérez‐Rueda… - …, 1998 - Wiley Online Library
… Indeed, the network B constitutes a hierarchical regulatory tree, network C can be seen
as a set of small independent regulatory modules, whereas network D contains a set of …

[HTML][HTML] Logical modeling and dynamical analysis of cellular networks

…, J Saez-Rodriguez, T Helikar, D Thieffry… - Frontiers in …, 2016 - frontiersin.org
… (D) Hypergraph as an alternative definition of the Boolean model of (A–C) (merged arrows
denote AND operator). (E) Example motivating the introduction of a multi-valued variable; …

Dynamical analysis of a generic Boolean model for the control of the mammalian cell cycle

A Fauré, A Naldi, C Chaouiya, D Thieffry - Bioinformatics, 2006 - academic.oup.com
Motivation: To understand the behaviour of complex biological regulatory networks, a proper
integration of molecular data into a full-fledge formal dynamical model is ultimately required…

[HTML][HTML] GOToolBox: functional analysis of gene datasets based on Gene Ontology

D Martin, C Brun, E Remy, P Mouren, D Thieffry, B Jacq - Genome biology, 2004 - Springer
We have developed methods and tools based on the Gene Ontology (GO) resource allowing
the identification of statistically over- or under-represented terms in a gene dataset; the …

Dynamical behaviour of biological regulatory networks—I. Biological role of feedback loops and practical use of the concept of the loop-characteristic state

R Thomas, D Thieffry, M Kaufman - Bulletin of mathematical biology, 1995 - Springer
In the field of biological regulation, models dictated by expreimental work are usually
complex networks comprising intertwined feedback loops. In this paper the biological roles of …

RSAT 2015: regulatory sequence analysis tools

…, C Hernandez, D Thieffry… - Nucleic acids …, 2015 - academic.oup.com
RSAT (Regulatory Sequence Analysis Tools) is a modular software suite for the analysis of
cis-regulatory elements in genome sequences. Its main applications are (i) motif discovery, …

Genetic control of flower morphogenesis in Arabidopsis thaliana: a logical analysis.

L Mendoza, D Thieffry… - Bioinformatics (Oxford …, 1999 - academic.oup.com
MOTIVATION: A large number of molecular mechanisms at the basis of gene regulation
have been described during the last few decades. It is now becoming possible to address …

Dynamical behaviour of biological regulatory networks—II. Immunity control in bacteriophage lambda

D Thieffry, R Thomas - Bulletin of mathematical biology, 1995 - Springer
… (d) In the absence of CII and in the presence of CRO proteins, gene cI should be fully
repressed. It is proposed that K 1 = 0. (e) CII is fully expressed only when N is present and CI and …

RSAT 2011: regulatory sequence analysis tools

…, O Sand, C Herrmann, D Thieffry… - Nucleic acids …, 2011 - academic.oup.com
RSAT (Regulatory Sequence Analysis Tools) comprises a wide collection of modular tools
for the detection of cis -regulatory elements in genome sequences. Thirteen new programs …