List of works - Damien Eveillard

A community perspective on the concept of marine holobionts: current status, challenges, and future directions

scientific article published on 25 February 2021

A community perspective on the concept of marine holobionts: state-of-the-art, challenges, and future directions

preprint

A community perspective on the concept of marine holobionts: state-of-the-art, challenges, and future directions

A metabolic approach to study algal-bacterial interactions in changing environments

scientific article published on 13 March 2014

A multi-objective constraint-based approach for modeling genome-scale microbial ecosystems

scientific article

A multi-scale constraint programming model of alternative splicing regulation

A shift in the archaeal nitrifier community in response to natural and anthropogenic disturbances in the northern Gulf of Mexico

scientific article

Ammonia-oxidizing bacterial community composition in estuarine and oceanic environments assessed using a functional gene microarray

scientific article

Antagonistic interactions between heterotrophic bacteria as a potential regulator of community structure of hypersaline microbial mats

scientific article

Author Correction: Roadmap for naming uncultivated Archaea and Bacteria

scientific article published on 12 November 2020

Beyond the Black Queen Hypothesis

scientific article published on 8 March 2016

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

scientific article published on 12 October 2017

Community‐Level Responses to Iron Availability in Open Ocean Plankton Ecosystems

article

Comparing Bacterial Genomes by Searching Their Common Intervals

Contribution of genome scale metabolic modeling to niche theory

scientific article published on 22 July 2021

Contribution of genome‐scale metabolic modelling to niche theory

scientific article published on 06 April 2022

Datascape: exploring heterogeneous dataspace

scientific article published on 5 April 2024

Deciphering transcriptional regulations coordinating the response to environmental changes

scientific article published on 16 January 2016

Decline in plankton diversity and carbon flux with reduced sea ice extent along the Western Antarctic Peninsula

scientific article published on 16 August 2021

Differential global distribution of marine picocyanobacteria gene clusters reveals distinct niche-related adaptive strategies

scientific article published in 2023

Environmental factors determining ammonia-oxidizing organism distribution and diversity in marine environments

scientific article

Extending the Metabolic Network of Ectocarpus Siliculosus Using Answer Set Programming

article published in 2013

Gene Expression Analysis of Zobellia galactanivorans during the Degradation of Algal Polysaccharides Reveals both Substrate-Specific and Shared Transcriptome-Wide Responses

scientific article published on 21 September 2017

Homogeneous decomposition of protein interaction networks: refining the description of intra-modular interactions

scientific article

Hybrid modeling of biological networks: mixing temporal and qualitative biological properties

scientific article

Impact of the species compartment definition on quantitative modeling of microbial communities

Including Ordinary Differential Equations Based Constraints in the Standard CP Framework

article by Alexandre Goldsztejn et al published 2010 in Lecture Notes in Computer Science

Integrated analysis of the gene neighbouring impact on bacterial metabolic networks.

scientific article

Integrating quantitative knowledge into a qualitative gene regulatory network

scientific article

Marine systems biology

scientific article published on 13 May 2015

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

scientific article

Modelling the complexity of plankton communities exploiting omics potential: From present challenges to an integrative pipeline

Multiscale Modeling of Alternative Splicing Regulation

OPINION PAPER Evolutionary Constraint-Based Formulation Requires New Bi-level Solving Techniques

article

Observational Needs Supporting Marine Ecosystems Modeling and Forecasting: From the Global Ocean to Regional and Coastal Systems

scientific article

On the Power of Uncertainties in Microbial System Modeling: No Need To Hide Them Anymore.

scientific article published in November 2017

Plankton networks driving carbon export in the oligotrophic ocean

scientific article

Probabilistic Approaches for Investigating Biological Networks

Probabilistic Modeling of Microbial Metabolic Networks for Integrating Partial Quantitative Knowledge Within the Nitrogen Cycle

scientific article published on 01 January 2018

Probabilistic modeling to estimate jellyfish ecophysiological properties and size distributions

scientific article published on 08 April 2020

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

scientific article published on 17 December 2015

REVIEW: Predictive ecology in a changing world

article

Roadmap for naming uncultivated Archaea and Bacteria

scientific article published on 08 June 2020

SIPPER: A flexible method to integrate heterogeneous data into a metabolic network

Seasonal and annual reoccurrence in betaproteobacterial ammonia-oxidizing bacterial population structure

scientific article

Structure and co-occurrence patterns in microbial communities under acute environmental stress reveal ecological factors fostering resilience.

scientific article

Tara Oceans: towards global ocean ecosystems biology

scientific article published on 12 May 2020

Targeting human Rad51 by specific DNA aptamers induces inhibition of homologous recombination

scientific article

Temporal constraints of a gene regulatory network: Refining a qualitative simulation

scientific article published on 13 May 2009

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

Time course gene expression in the one-carbon metabolism network using HepG2 cell line grown in folate-deficient medium

scientific article

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

scientific article published on 02 December 2011

Using hybrid automata modelling to study phenotypic plasticity and allocation strategies in the plant mycorrhizal mutualism

article

Using logic programming for modeling the one-carbon metabolism network to study the impact of folate deficiency on methylation processes

scientific article published on 7 June 2011

List of works by Damien Eveillard

A community perspective on the concept of marine holobionts: current status, challenges, and future directions

A community perspective on the concept of marine holobionts: state-of-the-art, challenges, and future directions

A community perspective on the concept of marine holobionts: state-of-the-art, challenges, and future directions

A metabolic approach to study algal-bacterial interactions in changing environments

A multi-objective constraint-based approach for modeling genome-scale microbial ecosystems

A multi-scale constraint programming model of alternative splicing regulation

A shift in the archaeal nitrifier community in response to natural and anthropogenic disturbances in the northern Gulf of Mexico

Ammonia-oxidizing bacterial community composition in estuarine and oceanic environments assessed using a functional gene microarray

Antagonistic interactions between heterotrophic bacteria as a potential regulator of community structure of hypersaline microbial mats

Author Correction: Roadmap for naming uncultivated Archaea and Bacteria

Beyond the Black Queen Hypothesis

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

Community‐Level Responses to Iron Availability in Open Ocean Plankton Ecosystems

Comparing Bacterial Genomes by Searching Their Common Intervals

Contribution of genome scale metabolic modeling to niche theory

Contribution of genome‐scale metabolic modelling to niche theory

Datascape: exploring heterogeneous dataspace

Deciphering transcriptional regulations coordinating the response to environmental changes

Decline in plankton diversity and carbon flux with reduced sea ice extent along the Western Antarctic Peninsula

Differential global distribution of marine picocyanobacteria gene clusters reveals distinct niche-related adaptive strategies

Environmental factors determining ammonia-oxidizing organism distribution and diversity in marine environments

Extending the Metabolic Network of Ectocarpus Siliculosus Using Answer Set Programming

Gene Expression Analysis of Zobellia galactanivorans during the Degradation of Algal Polysaccharides Reveals both Substrate-Specific and Shared Transcriptome-Wide Responses

Homogeneous decomposition of protein interaction networks: refining the description of intra-modular interactions

Hybrid modeling of biological networks: mixing temporal and qualitative biological properties

Impact of the species compartment definition on quantitative modeling of microbial communities

Including Ordinary Differential Equations Based Constraints in the Standard CP Framework

Integrated analysis of the gene neighbouring impact on bacterial metabolic networks.

Integrating quantitative knowledge into a qualitative gene regulatory network

Marine systems biology

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

Modelling the complexity of plankton communities exploiting omics potential: From present challenges to an integrative pipeline

Multiscale Modeling of Alternative Splicing Regulation

OPINION PAPER Evolutionary Constraint-Based Formulation Requires New Bi-level Solving Techniques

Observational Needs Supporting Marine Ecosystems Modeling and Forecasting: From the Global Ocean to Regional and Coastal Systems

On the Power of Uncertainties in Microbial System Modeling: No Need To Hide Them Anymore.

Plankton networks driving carbon export in the oligotrophic ocean

Probabilistic Approaches for Investigating Biological Networks

Probabilistic Modeling of Microbial Metabolic Networks for Integrating Partial Quantitative Knowledge Within the Nitrogen Cycle

Probabilistic modeling to estimate jellyfish ecophysiological properties and size distributions

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

REVIEW: Predictive ecology in a changing world

Roadmap for naming uncultivated Archaea and Bacteria

SIPPER: A flexible method to integrate heterogeneous data into a metabolic network

Seasonal and annual reoccurrence in betaproteobacterial ammonia-oxidizing bacterial population structure

Structure and co-occurrence patterns in microbial communities under acute environmental stress reveal ecological factors fostering resilience.

Tara Oceans: towards global ocean ecosystems biology

Targeting human Rad51 by specific DNA aptamers induces inhibition of homologous recombination

Temporal constraints of a gene regulatory network: Refining a qualitative simulation

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

Time course gene expression in the one-carbon metabolism network using HepG2 cell line grown in folate-deficient medium

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

Using hybrid automata modelling to study phenotypic plasticity and allocation strategies in the plant mycorrhizal mutualism

Using logic programming for modeling the one-carbon metabolism network to study the impact of folate deficiency on methylation processes