Lista de obras - Denis Thieffry - Dominio Público Uruguay

<i>Cis</i>-acting variation is common across regulatory layers but is often buffered during embryonic development

scientific article published on 11 December 2020

A Quantitative Multivariate Model of Human Dendritic Cell-T Helper Cell Communication

artículo científico publicado en 2019

A Reduction of Logical Regulatory Graphs Preserving Essential Dynamical Properties

article

A Transcription Factor Pulse Can Prime Chromatin for Heritable Transcriptional Memory

artículo científico publicado en 2016

A complete workflow for the analysis of full-size ChIP-seq (and similar) data sets using peak-motifs.

artículo científico publicado en 2012

A description of dynamical graphs associated to elementary regulatory circuits

artículo científico publicado en 2003

A logical analysis of the Drosophila gap-gene system

artículo científico publicado en 2001

Abstracts from the 3rd International Society for Computational Biology (ISCB) Student Council Symposium at the 15th Annual International Conference on Intelligent Systems for Molecular Biology (ISMB), Vienna, Austria, 21 July 2007

scholarly article by Adrien Fauré published in January 2007

Alternative epigenetic states understood in terms of specific regulatory structures.

artículo científico publicado en 2002

Automatic Inference of Regulatory and Dynamical Properties from Incomplete Gene Interaction and Expression Data

article

Bacterial molecular networks: bridging the gap between functional genomics and dynamical modelling

artículo científico

Bioinformatics in Siberia. First International Conference on Bioinformatics of Genome Regulation and Structure, Novosibirsk, Siberia, Russia, 24-27 August 1998.

artículo científico publicado en 1999

Biologie des systèmes : des réseaux d’interactions moléculaires à la médecine personnalisée

artículo científico publicado en 2009

C/EBPα Activates Pre-existing and De Novo Macrophage Enhancers during Induced Pre-B Cell Transdifferentiation and Myelopoiesis

artículo científico publicado en 2015

C/EBPα creates elite cells for iPSC reprogramming by upregulating Klf4 and increasing the levels of Lsd1 and Brd4.

artículo científico publicado en 2016

C/EBPα poises B cells for rapid reprogramming into induced pluripotent stem cells.

artículo científico publicado en 2013

CoCAS: a ChIP-on-chip analysis suite

artículo científico publicado en 2009

Computational Verification of Large Logical Models-Application to the Prediction of T Cell Response to Checkpoint Inhibitors

artículo científico publicado en 2020

Computational modeling of the main signaling pathways involved in mast cell activation

artículo científico

Contribution of ROS and metabolic status to neonatal and adult CD8+ T cell activation

scientific article published on 16 December 2019

Contributions of the 'Rouge-Cloître group' to the notion of 'messenger RNA'

artículo científico publicado el 1 de enero de 1997

Cooperation between T cell receptor and Toll-like receptor 5 signaling for CD4+ T cell activation

scientific article published on 16 April 2019

Cooperative development of logical modelling standards and tools with CoLoMoTo

artículo científico publicado en 2015

Cooperative development of logical modelling standards and tools with CoLoMoTo

article

Correction: Integrative Modelling of the Influence of MAPK Network on Cancer Cell Fate Decision.

artículo científico publicado en 2013

Course 10Modeling, analysis, and simulation of genetic regulatory networks: From differential equations to logical models

article

Deciphering and modelling the TGF-β signalling interplays specifying the dorsal-ventral axis of the sea urchin embryo

artículo científico publicado en 2020

Decision Diagrams for the Representation and Analysis of Logical Models of Genetic Networks

article

Definite-clause grammars for the analysis of cis-regulatory regions in E. coli.

artículo científico publicado en 1997

Derivation of Qualitative Dynamical Models from Biochemical Networks

Discovery of Drug Synergies in Gastric Cancer Cells Predicted by Logical Modeling

artículo científico publicado en 2015

Diversity and Plasticity of Th Cell Types Predicted from Regulatory Network Modelling ⬇️

artículo científico publicado el 2 de septiembre de 2010

Dynamical Boolean Modeling of Immunogenic Cell Death

artículo científico publicado en 2020

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

artículo científico

Dynamical analysis of the regulatory network defining the dorsal-ventral boundary of the Drosophila wing imaginal disc

artículo científico publicado en 2006

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

artículo científico publicado en 1995

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

artículo científico publicado en 1995

Dynamical modeling and analysis of large cellular regulatory networks.

artículo científico publicado en 2013

Dynamical modeling of biological regulatory networks

artículo científico publicado en 2005

Dynamical modeling of syncytial mitotic cycles in Drosophila embryos

artículo científico publicado en 2007

Dynamical modelling of pattern formation during embryonic development.

artículo científico publicado en 2003

Dynamical roles of biological regulatory circuits

artículo científico publicado en 2007

Dynamically consistent reduction of logical regulatory graphs

article

Epigenomics: Large scale analysis of chromatin modifications and transcription factors/genome interactions

scientific article published on 01 November 2005

Escherichia coli as a model system with which to study cell differentiation.

artículo científico publicado en 1996

Establishment of the dorso-ventral pattern during embryonic development of drosophila melanogasater: a logical analysis

artículo científico publicado en 1997

Formal derivation of qualitative dynamical models from biochemical networks.

artículo científico publicado en 2016

Forty years under the central dogma

artículo científico publicado en 1998

From experimental imaging techniques to virtual embryology.

artículo científico publicado en 2004

Functional organisation of Escherichia coli transcriptional regulatory network

artículo científico publicado en 2008

GINsim: a software suite for the qualitative modelling, simulation and analysis of regulatory networks

artículo científico publicado en 2006

GOToolBox: functional analysis of gene datasets based on Gene Ontology

artículo científico publicado en 2004

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

artículo científico publicado en 1999

Graphic requirements for multistability and attractive cycles in a Boolean dynamical framework

article published in 2008

Graphing genes, cells and embryos

article

Histone Chaperone SSRP1 is Essential for Wnt Signaling Pathway Activity During Osteoblast Differentiation

artículo científico publicado en 2016

IL-12 Signaling Contributes to the Reprogramming of Neonatal CD8+ T Cells

artículo científico publicado en 2020

Integrative modelling of the influence of MAPK network on cancer cell fate decision

artículo científico publicado en 2013

Interplay between SMAD2 and STAT5A is a critical determinant of IL-17A/IL-17F differential expression

artículo científico publicado en 2021

Introduction to 'picturing eggs, embryos and cells'.

artículo científico publicado en 2004

Introduction to the special issue. 'From embryology to developmental biology'.

artículo científico publicado en 2000

Jean Brachet's alternative scheme for protein synthesis

artículo científico publicado en 1996

Logical Modeling and Analysis of Cellular Regulatory Networks With GINsim 3.0.

artículo científico publicado en 2018

Logical Modeling and Dynamical Analysis of Cellular Networks

artículo científico publicado en 2016

Logical model specification aided by model-checking techniques: application to the mammalian cell cycle regulation

artículo científico publicado en 2016

Logical modeling of cell fate specification-Application to T cell commitment

artículo científico publicado en 2020

Logical modeling of lymphoid and myeloid cell specification and transdifferentiation.

artículo científico publicado en 2017

Logical modelling and analysis of cellular regulatory networks with GINsim 3.0

artículo científico publicado en 2018

Logical modelling of <i>in vitro</i> differentiation of human monocytes into dendritic cells unravels novel transcriptional regulatory interactions

artículo científico publicado en 2021

Logical modelling of Drosophila signalling pathways

artículo científico publicado en 2013

Logical modelling of cell cycle control in eukaryotes: a comparative study

artículo científico publicado en 2009

Logical modelling of gene regulatory networks with GINsim

artículo científico publicado en 2012

Logical modelling of regulatory networks with GINsim 2.3.

artículo científico publicado en 2009

Logical modelling of the role of the Hh pathway in the patterning of the Drosophila wing disc

artículo científico

Mathematical modelling of cell-fate decision in response to death receptor engagement

artículo científico publicado en 2010

Metagenome annotation using a distributed grid of undergraduate students

artículo científico publicado en 2008

MethMotif: an integrative cell specific database of transcription factor binding motifs coupled with DNA methylation profiles

artículo científico publicado en 2019

Model Checking Logical Regulatory Networks

article

Model checking to assess T-helper cell plasticity

artículo científico publicado en 2014

Modeling ERBB receptor-regulated G1/S transition to find novel targets for de novo trastuzumab resistance

artículo científico publicado en 2009

Modular logical modelling of the budding yeast cell cycle

artículo científico publicado en 2009

Modularity in development and evolution.

artículo científico publicado en 2000

On circuit functionality in Boolean networks

artículo científico publicado en 2013

Petri net modelling of biological regulatory networks

article published in 2008

Petri net representation of multi-valued logical regulatory graphs

article

Positive or negative regulatory circuit inference from multilevel dynamics

chapter; published in Lecture Notes in Control and Information Sciences 341

Prediction of Mutations to Control Pathways Enabling Tumor Cell Invasion with the CoLoMoTo Interactive Notebook (Tutorial)

artículo científico publicado en 2018

Prediction of Mutations to Control Pathways Enabling Tumour Cell Invasion with the CoLoMoTo Interactive Notebook (Tutorial)

Prediction of transcriptional regulatory sites in the complete genome sequence of Escherichia coli K-12.

artículo científico publicado en 1998

Prologue to the special issue of JTB dedicated to the memory of René Thomas (1928-2017): A journey through biological circuits, logical puzzles and complex dynamics

scientific article published on 24 April 2019

Proteomic Analysis of the SH2 Domain-containing Leukocyte Protein of 76 kDa (SLP76) Interactome in Resting and Activated Primary Mast Cells

artículo científico publicado en 2014

Proteomic analysis of the SH2 domain-containing leukocyte protein of 76 kDa (SLP76) interactome in resting and activated primary mast cells [corrected].

artículo científico publicado en 2013

Putting DNA on the map

artículo científico publicado en 2006

Qualitative Dynamical Modelling Can Formally Explain Mesoderm Specification and Predict Novel Developmental Phenotypes

artículo científico publicado en 2016

Qualitative analysis of gene networks.

artículo científico publicado en 1998

Qualitative modelling and simulation of developmental regulatory networks

article published in 2003

Qualitative modelling of regulated metabolic pathways: application to the tryptophan biosynthesis in E.coli

artículo científico publicado en 2005

RSAT 2011: regulatory sequence analysis tools.

artículo científico publicado en 2011

RSAT 2015: Regulatory Sequence Analysis Tools.

artículo científico publicado en 2015

RSAT 2018: regulatory sequence analysis tools 20th anniversary.

artículo científico publicado en 2018

RSAT matrix-clustering: dynamic exploration and redundancy reduction of transcription factor binding motif collections

RSAT matrix-clustering: dynamic exploration and redundancy reduction of transcription factor binding motif collections.

artículo científico publicado en 2017

RSAT peak-motifs: fast extraction of transcription factor binding motifs from full-size ChIP-seq datasets

RSAT peak-motifs: motif analysis in full-size ChIP-seq datasets

artículo científico publicado en 2011

RSAT variation-tools: An accessible and flexible framework to predict the impact of regulatory variants on transcription factor binding

artículo científico publicado en 2019

Rationalizing early embryogenesis in the 1930s: Albert Dalcq on gradients and fields

artículo científico publicado el 1 de enero de 2001

Reduction of logical models of regulatory networks yields insight into dynamical properties

article

RegulonDB: a database on transcriptional regulation in Escherichia coli ⬇️

artículo científico publicado el 1 de enero de 1998

René Thomas (1928-2017): From DNA denaturation to positive gene regulation, kinetic logic and complex dynamical systems

artículo científico publicado en 2017

SBML Level 3 package: Qualitative Models, Version 1, Release 1.

artículo científico publicado en 2015

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

artículo científico publicado en 2020

SBML qualitative models: a model representation format and infrastructure to foster interactions between qualitative modelling formalisms and tools

artículo científico publicado en 2013

Segmenting the fly embryo: a logical analysis of the pair-rule cross-regulatory module.

artículo científico publicado en 2003

Segmenting the fly embryo: logical analysis of the role of the segment polarity cross-regulatory module

artículo científico publicado en 2008

Selected bibliography on history of embryology and development.

artículo científico publicado en 2000

Setting the basis of best practices and standards for curation and annotation of logical models in biology-highlights of the [BC]2 2019 CoLoMoTo/SysMod Workshop

scientific article published on 21 April 2020

Syncytial apoptosis signaling network induced by the HIV-1 envelope glycoprotein complex: an overview.

artículo científico publicado en 2015

Syntactic recognition of regulatory regions in Escherichia coli.

artículo científico publicado en 1996

TFregulomeR reveals transcription factors' context-specific features and functions

artículo científico publicado en 2020

The CoLoMoTo Interactive Notebook: Accessible and Reproducible Computational Analyses for Qualitative Biological Networks

The CoLoMoTo Interactive Notebook: Accessible and Reproducible Computational Analyses for Qualitative Biological Networks.

artículo científico publicado en 2018

The Minimum Information about a Molecular Interaction Causal Statement (MI2CAST)

artículo científico publicado en 2020

The Systems Biology Markup Language (SBML) Level 3 Package: Qualitative Models, Version 1, Release 1.

artículo científico

The activation trajectory of plasmacytoid dendritic cells in vivo during a viral infection

artículo científico publicado en 2020

The genome in context: biologists and philosophers on epigenetics

artículo científico publicado en 2002

The modularity of biological regulatory networks

artículo científico publicado en 1999

The shortest path is not the one you know: application of biological network resources in precision oncology research

artículo científico publicado en 2015

Toxicity and neuroendocrine regulation of the immune response: a model analysis.

artículo científico publicado en 1996

Transcription Factors Drive Tet2-Mediated Enhancer Demethylation to Reprogram Cell Fate

artículo científico publicado en 2018

Transcription Factors Drive Tet2-Mediated Enhancer Demethylation to Reprogram Cell Fate

scientific article published on 13 September 2018

Transcriptional and epigenetic signatures of zygotic genome activation during early Drosophila embryogenesis

artículo científico publicado en 2013

UPMaBoSS: A Novel Framework for Dynamic Cell Population Modeling

publication published on 02 March 2022

[Prediction of transcription and genomic sequences]. ⬇️

artículo científico publicado en 2004

miR-9 controls the timing of neurogenesis through the direct inhibition of antagonistic factors

artículo científico publicado en 2012

Lista de obras de Denis Thieffry

<i>Cis</i>-acting variation is common across regulatory layers but is often buffered during embryonic development

A Quantitative Multivariate Model of Human Dendritic Cell-T Helper Cell Communication

A Reduction of Logical Regulatory Graphs Preserving Essential Dynamical Properties

A Transcription Factor Pulse Can Prime Chromatin for Heritable Transcriptional Memory

A complete workflow for the analysis of full-size ChIP-seq (and similar) data sets using peak-motifs.

A description of dynamical graphs associated to elementary regulatory circuits

A logical analysis of the Drosophila gap-gene system

Abstracts from the 3rd International Society for Computational Biology (ISCB) Student Council Symposium at the 15th Annual International Conference on Intelligent Systems for Molecular Biology (ISMB), Vienna, Austria, 21 July 2007

Alternative epigenetic states understood in terms of specific regulatory structures.

Automatic Inference of Regulatory and Dynamical Properties from Incomplete Gene Interaction and Expression Data

Bacterial molecular networks: bridging the gap between functional genomics and dynamical modelling

Bioinformatics in Siberia. First International Conference on Bioinformatics of Genome Regulation and Structure, Novosibirsk, Siberia, Russia, 24-27 August 1998.

Biologie des systèmes : des réseaux d’interactions moléculaires à la médecine personnalisée

C/EBPα Activates Pre-existing and De Novo Macrophage Enhancers during Induced Pre-B Cell Transdifferentiation and Myelopoiesis

C/EBPα creates elite cells for iPSC reprogramming by upregulating Klf4 and increasing the levels of Lsd1 and Brd4.

C/EBPα poises B cells for rapid reprogramming into induced pluripotent stem cells.

CoCAS: a ChIP-on-chip analysis suite

Computational Verification of Large Logical Models-Application to the Prediction of T Cell Response to Checkpoint Inhibitors

Computational modeling of the main signaling pathways involved in mast cell activation

Contribution of ROS and metabolic status to neonatal and adult CD8+ T cell activation

Contributions of the 'Rouge-Cloître group' to the notion of 'messenger RNA'

Cooperation between T cell receptor and Toll-like receptor 5 signaling for CD4+ T cell activation

Cooperative development of logical modelling standards and tools with CoLoMoTo

Cooperative development of logical modelling standards and tools with CoLoMoTo

Correction: Integrative Modelling of the Influence of MAPK Network on Cancer Cell Fate Decision.

Course 10Modeling, analysis, and simulation of genetic regulatory networks: From differential equations to logical models

Deciphering and modelling the TGF-β signalling interplays specifying the dorsal-ventral axis of the sea urchin embryo

Decision Diagrams for the Representation and Analysis of Logical Models of Genetic Networks

Definite-clause grammars for the analysis of cis-regulatory regions in E. coli.

Derivation of Qualitative Dynamical Models from Biochemical Networks

Discovery of Drug Synergies in Gastric Cancer Cells Predicted by Logical Modeling

Diversity and Plasticity of Th Cell Types Predicted from Regulatory Network Modelling ⬇️

Dynamical Boolean Modeling of Immunogenic Cell Death

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

Dynamical analysis of the regulatory network defining the dorsal-ventral boundary of the Drosophila wing imaginal disc

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

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

Dynamical modeling and analysis of large cellular regulatory networks.

Dynamical modeling of biological regulatory networks

Dynamical modeling of syncytial mitotic cycles in Drosophila embryos

Dynamical modelling of pattern formation during embryonic development.

Dynamical roles of biological regulatory circuits

Dynamically consistent reduction of logical regulatory graphs

Epigenomics: Large scale analysis of chromatin modifications and transcription factors/genome interactions

Escherichia coli as a model system with which to study cell differentiation.

Establishment of the dorso-ventral pattern during embryonic development of drosophila melanogasater: a logical analysis

Formal derivation of qualitative dynamical models from biochemical networks.

Forty years under the central dogma

From experimental imaging techniques to virtual embryology.

Functional organisation of Escherichia coli transcriptional regulatory network

GINsim: a software suite for the qualitative modelling, simulation and analysis of regulatory networks

GOToolBox: functional analysis of gene datasets based on Gene Ontology

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

Graphic requirements for multistability and attractive cycles in a Boolean dynamical framework

Graphing genes, cells and embryos

Histone Chaperone SSRP1 is Essential for Wnt Signaling Pathway Activity During Osteoblast Differentiation

IL-12 Signaling Contributes to the Reprogramming of Neonatal CD8+ T Cells

Integrative modelling of the influence of MAPK network on cancer cell fate decision

Interplay between SMAD2 and STAT5A is a critical determinant of IL-17A/IL-17F differential expression

Introduction to 'picturing eggs, embryos and cells'.

Introduction to the special issue. 'From embryology to developmental biology'.

Jean Brachet's alternative scheme for protein synthesis

Logical Modeling and Analysis of Cellular Regulatory Networks With GINsim 3.0.

Logical Modeling and Dynamical Analysis of Cellular Networks

Logical model specification aided by model-checking techniques: application to the mammalian cell cycle regulation

Logical modeling of cell fate specification-Application to T cell commitment

Logical modeling of lymphoid and myeloid cell specification and transdifferentiation.

Logical modelling and analysis of cellular regulatory networks with GINsim 3.0

Logical modelling of <i>in vitro</i> differentiation of human monocytes into dendritic cells unravels novel transcriptional regulatory interactions

Logical modelling of Drosophila signalling pathways

Logical modelling of cell cycle control in eukaryotes: a comparative study

Logical modelling of gene regulatory networks with GINsim

Logical modelling of regulatory networks with GINsim 2.3.

Logical modelling of the role of the Hh pathway in the patterning of the Drosophila wing disc

Mathematical modelling of cell-fate decision in response to death receptor engagement

Metagenome annotation using a distributed grid of undergraduate students

MethMotif: an integrative cell specific database of transcription factor binding motifs coupled with DNA methylation profiles

Model Checking Logical Regulatory Networks

Model checking to assess T-helper cell plasticity