List of works - Anne Siegel

A Logic for Checking the Probabilistic Steady-State Properties of Reaction Networks

scientific article published on 07 July 2017

A modeling approach to evaluate the balance between bioactivation and detoxification of MeIQx in human hepatocytes.

scientific article published on September 2017

A transcriptome multi-tissue analysis identifies biological pathways and genes associated with variations in feed efficiency of growing pigs

scientific article

Addressing <i>barriers in comprehensiveness, accessibility, reusability, interoperability and reproducibility of computational models in systems biology</i>

Analysis of Piscirickettsia salmonis Metabolism Using Genome-Scale Reconstruction, Modeling, and Testing.

scientific article published on 11 December 2017

BioQuali Cytoscape plugin: analysing the global consistency of regulatory networks

scientific article

Boolean network identification from perturbation time series data combining dynamics abstraction and logic programming.

scientific article

Combining graph and flux-based structures to decipher phenotypic essential metabolites within metabolic networks

scientific article published on 12 October 2017

Computational discovery of dynamic cell line specific Boolean Networks from multiplex time-course data

scientific article published on 29 October 2018

Deciphering transcriptional regulations coordinating the response to environmental changes

scientific article published on 16 January 2016

Designing Experiments to Discriminate Families of Logic Models

scientific article

Designing logical rules to model the response of biomolecular networks with complex interactions: an application to cancer modeling

scientific article

Discrete modeling for integration and analysis of large-scale signaling networks

scientific article published on 13 June 2022

Exhaustively characterizing feasible logic models of a signaling network using Answer Set Programming

scientific article

Exploring metabolism flexibility in complex organisms through quantitative study of precursor sets for system outputs.

scientific article published on 23 January 2014

Extended notions of sign consistency to relate experimental data to signaling and regulatory network topologies.

scientific article

Extending the Metabolic Network of Ectocarpus Siliculosus Using Answer Set Programming

article published in 2013

Formalizing and enriching phenotype signatures using Boolean networks

scientific article published on 06 February 2019

Fractal tiles associated with shift radix systems.

scientific article published on January 2011

Genome-Scale Metabolic Networks Shed Light on the Carotenoid Biosynthesis Pathway in the Brown Algae Saccharina japonica and Cladosiphon okamuranus

scientific article published on 16 November 2019

Genome-scale metabolic models of Microbacterium species isolated from a high altitude desert environment

scientific article published on 27 March 2020

Hybrid Metabolic Network Completion

In silico prediction of Heterocyclic Aromatic Amines metabolism susceptible to form DNA adducts in humans

scientific article published on 10 October 2018

Inferring Biochemical Reactions and Metabolite Structures to Understand Metabolic Pathway Drift

scientific article published on 17 January 2020

Inferring the role of transcription factors in regulatory networks

scientific article

Integrating quantitative knowledge into a qualitative gene regulatory network

scientific article

Integration of Biological Networks for Acidithiobacillus thiooxidans Describes a Modular Gene Regulatory Organization of Bioleaching Pathways

scientific article published on 01 January 2019

Learning Boolean logic models of signaling networks with ASP

Localizing potentially active post-transcriptional regulations in the Ewing's sarcoma gene regulatory network

scientific article published on 2 November 2010

Meneco, a Topology-Based Gap-Filling Tool Applicable to Degraded Genome-Wide Metabolic Networks

scientific article

MiR-202 controls female fecundity by regulating medaka oogenesis

scholarly article by Stéphanie Gay published in September 2018

Model of cap-dependent translation initiation in sea urchin: a step towards the eukaryotic translation regulation network.

scientific article published in March 2010

Model of the delayed translation of cyclin B maternal mRNA after sea urchin fertilization

scientific article published on 4 October 2016

Modelization of the regulation of protein synthesis following fertilization in sea urchin shows requirement of two processes: a destabilization of eIF4E:4E-BP complex and a great stimulation of the 4E-BP-degradation mechanism, both rapamycin-sensiti

scientific article

Molecular alterations induced by a high-fat high-fiber diet in porcine adipose tissues: variations according to the anatomical fat location

scientific article published on 18 February 2016

Putative bacterial interactions from metagenomic knowledge with an integrative systems ecology approach

scientific article published on 17 December 2015

Revisiting the Training of Logic Models of Protein Signaling Networks with ASP

Scalable and exhaustive screening of metabolic functions carried out by microbial consortia

scholarly article by Clémence Frioux published in September 2018

The genome of Ectocarpus subulatus - A highly stress-tolerant brown alga

scientific article published on 11 January 2020

The genome of Ectocarpus subulatus highlights unique mechanisms for stress tolerance in brown algae

The genome-scale metabolic network of Ectocarpus siliculosus (EctoGEM): a resource to study brown algal physiology and beyond

scientific article published on 27 August 2014

Topology and static response of interaction networks in molecular biology

scientific article

Toward systems biology in brown algae to explore acclimation and adaptation to the shore environment

scientific article published on 02 December 2011

Traceability, reproducibility and wiki-exploration for "à-la-carte" reconstructions of genome-scale metabolic models.

scientific article published on 23 May 2018

Using a large-scale knowledge database on reactions and regulations to propose key upstream regulators of various sets of molecules participating in cell metabolism

scientific article

caspo: a toolbox for automated reasoning on the response of logical signaling networks families

scientific article

List of works by Anne Siegel

A Logic for Checking the Probabilistic Steady-State Properties of Reaction Networks

A modeling approach to evaluate the balance between bioactivation and detoxification of MeIQx in human hepatocytes.

A transcriptome multi-tissue analysis identifies biological pathways and genes associated with variations in feed efficiency of growing pigs

Addressing <i>barriers in comprehensiveness, accessibility, reusability, interoperability and reproducibility of computational models in systems biology</i>

Analysis of Piscirickettsia salmonis Metabolism Using Genome-Scale Reconstruction, Modeling, and Testing.

BioQuali Cytoscape plugin: analysing the global consistency of regulatory networks

Boolean network identification from perturbation time series data combining dynamics abstraction and logic programming.

Combining graph and flux-based structures to decipher phenotypic essential metabolites within metabolic networks

Computational discovery of dynamic cell line specific Boolean Networks from multiplex time-course data

Deciphering transcriptional regulations coordinating the response to environmental changes

Designing Experiments to Discriminate Families of Logic Models

Designing logical rules to model the response of biomolecular networks with complex interactions: an application to cancer modeling

Discrete modeling for integration and analysis of large-scale signaling networks

Exhaustively characterizing feasible logic models of a signaling network using Answer Set Programming

Exploring metabolism flexibility in complex organisms through quantitative study of precursor sets for system outputs.

Extended notions of sign consistency to relate experimental data to signaling and regulatory network topologies.

Extending the Metabolic Network of Ectocarpus Siliculosus Using Answer Set Programming

Formalizing and enriching phenotype signatures using Boolean networks

Fractal tiles associated with shift radix systems.

Genome-Scale Metabolic Networks Shed Light on the Carotenoid Biosynthesis Pathway in the Brown Algae Saccharina japonica and Cladosiphon okamuranus

Genome-scale metabolic models of Microbacterium species isolated from a high altitude desert environment

Hybrid Metabolic Network Completion

In silico prediction of Heterocyclic Aromatic Amines metabolism susceptible to form DNA adducts in humans

Inferring Biochemical Reactions and Metabolite Structures to Understand Metabolic Pathway Drift

Inferring the role of transcription factors in regulatory networks

Integrating quantitative knowledge into a qualitative gene regulatory network

Integration of Biological Networks for Acidithiobacillus thiooxidans Describes a Modular Gene Regulatory Organization of Bioleaching Pathways

Learning Boolean logic models of signaling networks with ASP

Localizing potentially active post-transcriptional regulations in the Ewing's sarcoma gene regulatory network

Meneco, a Topology-Based Gap-Filling Tool Applicable to Degraded Genome-Wide Metabolic Networks

MiR-202 controls female fecundity by regulating medaka oogenesis

Model of cap-dependent translation initiation in sea urchin: a step towards the eukaryotic translation regulation network.

Model of the delayed translation of cyclin B maternal mRNA after sea urchin fertilization

Modelization of the regulation of protein synthesis following fertilization in sea urchin shows requirement of two processes: a destabilization of eIF4E:4E-BP complex and a great stimulation of the 4E-BP-degradation mechanism, both rapamycin-sensiti

Molecular alterations induced by a high-fat high-fiber diet in porcine adipose tissues: variations according to the anatomical fat location

Putative bacterial interactions from metagenomic knowledge with an integrative systems ecology approach

Revisiting the Training of Logic Models of Protein Signaling Networks with ASP

Scalable and exhaustive screening of metabolic functions carried out by microbial consortia

The genome of Ectocarpus subulatus - A highly stress-tolerant brown alga

The genome of Ectocarpus subulatus highlights unique mechanisms for stress tolerance in brown algae

The genome-scale metabolic network of Ectocarpus siliculosus (EctoGEM): a resource to study brown algal physiology and beyond

Topology and static response of interaction networks in molecular biology

Toward systems biology in brown algae to explore acclimation and adaptation to the shore environment

Traceability, reproducibility and wiki-exploration for "à-la-carte" reconstructions of genome-scale metabolic models.

Using a large-scale knowledge database on reactions and regulations to propose key upstream regulators of various sets of molecules participating in cell metabolism

caspo: a toolbox for automated reasoning on the response of logical signaling networks families