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

Transcriptomic and metabolomic analysis of copper stress acclimation in Ectocarpus siliculosus highlights signaling and tolerance mechanisms in brown algae

(2014) Andrés Ritter et al.   BMC PLANT BIOLOGY

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

(2014) Simon M. Dittami et al.   MOLECULAR ECOLOGY

Opportunities and challenges for seaweed in the biobased economy

(2014) Jaap W. van Hal et al.   TRENDS IN BIOTECHNOLOGY

COBRApy: COnstraints-Based Reconstruction and Analysis for Python

(2013) Ali Ebrahim et al.   BMC Systems Biology

The challenge of constructing, classifying, and representing metabolic pathways

(2013) Ron Caspi et al.   FEMS MICROBIOLOGY LETTERS

Mannitol metabolism in brown algae involves a new phosphatase family

(2013) Agnès Groisillier et al.   JOURNAL OF EXPERIMENTAL BOTANY

Efficient ethanol production from brown macroalgae sugars by a synthetic yeast platform

(2013) Maria Enquist-Newman et al.   NATURE

Computational prediction and experimental validation of microRNAs in the brown alga Ectocarpus siliculosus

(2013) Bernard Billoud et al.   NUCLEIC ACIDS RESEARCH

Structure/Function Analysis of a Type III Polyketide Synthase in the Brown Alga Ectocarpus siliculosus Reveals a Biochemical Pathway in Phlorotannin Monomer Biosynthesis

(2013) L. Meslet-Cladiere et al.   PLANT CELL

An alternative pathway contributes to phenylalanine biosynthesis in plants via a cytosolic tyrosine:phenylpyruvate aminotransferase

(2013) Heejin Yoo et al.   Nature Communications

The RAVEN Toolbox and Its Use for Generating a Genome-scale Metabolic Model for Penicillium chrysogenum

(2013) Rasmus Agren et al.   PLoS Computational Biology

A genome-scale metabolic model of the lipid-accumulating yeast Yarrowia lipolytica

(2012) Nicolas Loira et al.   BMC Systems Biology

Plant genome-scale metabolic reconstruction and modelling

(2012) Cristiana Gomes de Oliveira Dal’Molin et al.   CURRENT OPINION IN BIOTECHNOLOGY

ORCAE: online resource for community annotation of eukaryotes

(2012) Lieven Sterck et al.   NATURE METHODS

The metabolic blueprint of Phaeodactylum tricornutum reveals a eukaryotic Entner-Doudoroff glycolytic pathway

(2012) Michele Fabris et al.   PLANT JOURNAL

Are we ready for genome-scale modeling in plants?

(2012) Eva Collakova et al.   PLANT SCIENCE

An Engineered Microbial Platform for Direct Biofuel Production from Brown Macroalgae

(2012) A. J. Wargacki et al.   SCIENCE

Marine macroalgae: an untapped resource for producing fuels and chemicals

(2012) Na Wei et al.   TRENDS IN BIOTECHNOLOGY

AlgaGEM – a genome-scale metabolic reconstruction of algae based on the Chlamydomonas reinhardtii genome

(2011) Cristiana Gomes de Oliveira Dal’Molin et al.   BMC GENOMICS

Microarray estimation of genomic inter-strain variability in the genus Ectocarpus (Phaeophyceae)

(2011) Simon M Dittami et al.   BMC MOLECULAR BIOLOGY

Brown algae

(2011) J. Mark Cock et al.   CURRENT BIOLOGY

Characterization of GDP-mannose Dehydrogenase from the Brown AlgaEctocarpus siliculosusProviding the Precursor for the Alginate Polymer

(2011) Raimund Tenhaken et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Genome-wide metabolic network reconstruction of the picoalga Ostreococcus

(2011) Elias W. Krumholz et al.   JOURNAL OF EXPERIMENTAL BOTANY

Metabolic network reconstruction of Chlamydomonas offers insight into light-driven algal metabolism

(2011) R. L. Chang et al.   Molecular Systems Biology

Primary amines protect against retinal degeneration in mouse models of retinopathies

(2011) Akiko Maeda et al.   Nature Chemical Biology

The MetaCyc database of metabolic pathways and enzymes and the BioCyc collection of pathway/genome databases

(2011) R. Caspi et al.   NUCLEIC ACIDS RESEARCH

Toward Systems Biology in Brown Algae to Explore Acclimation and Adaptation to the Shore Environment

(2011) Thierry Tonon et al.   OMICS-A JOURNAL OF INTEGRATIVE BIOLOGY

ETOILERegulates Developmental Patterning in the Filamentous Brown AlgaEctocarpus siliculosus

(2011) Aude Le Bail et al.   PLANT CELL

Integrative analysis of metabolite and transcript abundance during the short-term response to saline and oxidative stress in the brown alga Ectocarpus siliculosus

(2011) SIMON M. DITTAMI et al.   PLANT CELL AND ENVIRONMENT

OUROBOROS is a master regulator of the gametophyte to sporophyte life cycle transition in the brown alga Ectocarpus

(2011) S. M. Coelho et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Algae and humans share a molybdate transporter

(2011) M. Tejada-Jimenez et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Identification of a plant gene encoding glutamate/aspartate-prephenate aminotransferase: The last homeless enzyme of aromatic amino acids biosynthesis

(2010) Matthieu Graindorge et al.   FEBS LETTERS

The Ectocarpus genome and the independent evolution of multicellularity in brown algae

(2010) J. Mark Cock et al.   NATURE

High-throughput generation, optimization and analysis of genome-scale metabolic models

(2010) Christopher S Henry et al.   NATURE BIOTECHNOLOGY

What is flux balance analysis?

(2010) Jeffrey D Orth et al.   NATURE BIOTECHNOLOGY

A protocol for generating a high-quality genome-scale metabolic reconstruction

(2010) Ines Thiele et al.   Nature Protocols

A sequence-tagged genetic map for the brown alga Ectocarpus siliculosus provides large-scale assembly of the genome sequence

(2010) Svenja Heesch et al.   NEW PHYTOLOGIST

Diurnal oscillations of metabolite abundances and gene analysis provide new insights into central metabolic processes of the brown alga Ectocarpus siliculosus

(2010) Antoine Gravot et al.   NEW PHYTOLOGIST

The cell wall polysaccharide metabolism of the brown alga Ectocarpus siliculosus. Insights into the evolution of extracellular matrix polysaccharides in Eukaryotes

(2010) Gurvan Michel et al.   NEW PHYTOLOGIST

Central and storage carbon metabolism of the brown alga Ectocarpus siliculosus: insights into the origin and evolution of storage carbohydrates in Eukaryotes

(2010) Gurvan Michel et al.   NEW PHYTOLOGIST

Reinstatement of Ectocarpus crouaniorum Thuret in Le Jolis as a third common species of Ectocarpus (Ectocarpales, Phaeophyceae) in Western Europe, and its phenology at Roscoff, Brittany

(2010) Akira F. Peters et al.   PHYCOLOGICAL RESEARCH

AraGEM, a Genome-Scale Reconstruction of the Primary Metabolic Network in Arabidopsis

(2010) C. G. de Oliveira Dal'Molin et al.   PLANT PHYSIOLOGY

Mannitol-1-phosphate dehydrogenase activity in Ectocarpus siliculosus, a key role for mannitol synthesis in brown algae

(2010) Sylvie Rousvoal et al.   PLANTA

An integrative approach towards completing genome-scale metabolic networks

(2009) Nils Christian et al.   Molecular BioSystems

InParanoid 7: new algorithms and tools for eukaryotic orthology analysis

(2009) G. Ostlund et al.   NUCLEIC ACIDS RESEARCH

A Genome-Scale Metabolic Model of Arabidopsis and Some of Its Properties

(2009) M. G. Poolman et al.   PLANT PHYSIOLOGY

Tyrosine and Phenylalanine Are Synthesized within the Plastids in Arabidopsis

(2009) P. Rippert et al.   PLANT PHYSIOLOGY

Global expression analysis of the brown alga Ectocarpus siliculosus (Phaeophyceae) reveals large-scale reprogramming of the transcriptome in response to abiotic stress

(2009) Simon M Dittami et al.   GENOME BIOLOGY

Phylogeny.fr: robust phylogenetic analysis for the non-specialist

(2008) A. Dereeper et al.   NUCLEIC ACIDS RESEARCH