Genome-Scale Model Reveals Metabolic Basis of Biomass Partitioning in a Model Diatom

Modelling metabolism of the diatom Phaeodactylum tricornutum

(2015) D. Singh et al.   BIOCHEMICAL SOCIETY TRANSACTIONS

Potential of lipid metabolism in marine diatoms for biofuel production

(2015) Giuliana d’Ippolito et al.   Biotechnology for Biofuels

Engineering of oleaginous organisms for lipid production

(2015) Jennifer Levering et al.   CURRENT OPINION IN BIOTECHNOLOGY

Chloroplast-targeting protein expression in the oleaginous diatom Fistulifera solaris JPCC DA0580 toward metabolic engineering

(2015) Yoshihiko Sunaga et al.   JOURNAL OF BIOSCIENCE AND BIOENGINEERING

Energetic coupling between plastids and mitochondria drives CO2 assimilation in diatoms

(2015) Benjamin Bailleul et al.   NATURE

Designer diatom episomes delivered by bacterial conjugation

(2015) Bogumil J. Karas et al.   Nature Communications

Escher: A Web Application for Building, Sharing, and Embedding Data-Rich Visualizations of Biological Pathways

(2015) Zachary A. King et al.   PLoS Computational Biology

Complete enumeration of elementary flux modes through scalable demand-based subnetwork definition

(2014) Kristopher A. Hunt et al.   BIOINFORMATICS

UniProt: a hub for protein information

(2014)   NUCLEIC ACIDS RESEARCH

Inactivation of Phaeodactylum tricornutum urease gene using transcription activator-like effector nuclease-based targeted mutagenesis

(2014) Philip D. Weyman et al.   PLANT BIOTECHNOLOGY JOURNAL

Membrane Glycerolipid Remodeling Triggered by Nitrogen and Phosphorus Starvation inPhaeodactylum tricornutum

(2014) Heni Abida et al.   PLANT PHYSIOLOGY

Insights into the Regulation of DMSP Synthesis in the Diatom Thalassiosira pseudonana through APR Activity, Proteomics and Gene Expression Analyses on Cells Acclimating to Changes in Salinity, Light and Nitrogen

(2014) Nicola Louise Kettles et al.   PLoS One

Remodeling of intermediate metabolism in the diatomPhaeodactylum tricornutumunder nitrogen stress

(2014) Orly Levitan et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Genome engineering empowers the diatom Phaeodactylum tricornutum for biotechnology

(2014) Fayza Daboussi et al.   Nature Communications

Physiological and molecular analysis of carbon source supplementation and pH stress-induced lipid accumulation in the marine diatom Phaeodactylum tricornutum

(2013) Florence Mus et al.   APPLIED MICROBIOLOGY AND BIOTECHNOLOGY

Assimilating genome-scale metabolic reconstructions with modelBorgifier

(2013) John T. Sauls et al.   BIOINFORMATICS

Rapid determination of bulk microalgal biochemical composition by Fourier-Transform Infrared spectroscopy

(2013) Joshua J. Mayers et al.   BIORESOURCE TECHNOLOGY

Mapping condition-dependent regulation of metabolism in yeast through genome-scale modeling

(2013) Tobias Österlund et al.   BMC Systems Biology

A community-driven global reconstruction of human metabolism

(2013) Ines Thiele et al.   NATURE BIOTECHNOLOGY

The Transporter Classification Database

(2013) Milton H. Saier et al.   NUCLEIC ACIDS RESEARCH

Data, information, knowledge and principle: back to metabolism in KEGG

(2013) Minoru Kanehisa et al.   NUCLEIC ACIDS RESEARCH

Flux Balance Analysis of Cyanobacterial Metabolism: The Metabolic Network of Synechocystis sp. PCC 6803

(2013) Henning Knoop et al.   PLoS Computational Biology

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

(2013) Rasmus Agren et al.   PLoS Computational Biology

Assembly of eukaryotic algal chromosomes in yeast

(2013) Bogumil J Karas et al.   Journal of Biological Engineering

Separation and quantification of microalgal carbohydrates

(2012) David W. Templeton et al.   JOURNAL OF CHROMATOGRAPHY A

THE IMPACT OF NONPHOTOCHEMICAL QUENCHING OF FLUORESCENCE ON THE PHOTON BALANCE IN DIATOMS UNDER DYNAMIC LIGHT CONDITIONS1

(2012) Wanwen Su et al.   JOURNAL OF PHYCOLOGY

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

(2012) Michele Fabris et al.   PLANT JOURNAL

Gene Regulation of Carbon Fixation, Storage, and Utilization in the Diatom Phaeodactylum tricornutum Acclimated to Light/Dark Cycles

(2012) M. S. Chauton et al.   PLANT PHYSIOLOGY

Detailing the optimality of photosynthesis in cyanobacteria through systems biology analysis

(2012) J. Nogales et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

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

Recent advances in reconstruction and applications of genome-scale metabolic models

(2011) Tae Yong Kim et al.   CURRENT OPINION IN BIOTECHNOLOGY

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

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

Evolution and metabolic significance of the urea cycle in photosynthetic diatoms

(2011) Andrew E. Allen et al.   NATURE

SignalP 4.0: discriminating signal peptides from transmembrane regions

(2011) Thomas Nordahl Petersen et al.   NATURE METHODS

Quantitative prediction of cellular metabolism with constraint-based models: the COBRA Toolbox v2.0

(2011) Jan Schellenberger et al.   Nature Protocols

Localization of putative carbonic anhydrases in two marine diatoms, Phaeodactylum tricornutum and Thalassiosira pseudonana

(2011) Masaaki Tachibana et al.   PHOTOSYNTHESIS RESEARCH

The Response of Diatom Central Carbon Metabolism to Nitrogen Starvation Is Different from That of Green Algae and Higher Plants

(2011) N. L. Hockin et al.   PLANT PHYSIOLOGY

Zea mays iRS1563: A Comprehensive Genome-Scale Metabolic Reconstruction of Maize Metabolism

(2011) Rajib Saha et al.   PLoS One

Applications of diatoms and silica nanotechnology in biosensing, drug and gene delivery, and formation of complex metal nanostructures

(2011) Jafar Ezzati Nazhad Dolatabadi et al.   TRAC-TRENDS IN ANALYTICAL CHEMISTRY

BiGG: a Biochemical Genetic and Genomic knowledgebase of large scale metabolic reconstructions

(2010) Jan Schellenberger et al.   BMC BIOINFORMATICS

A detailed genome-wide reconstruction of mouse metabolism based on human Recon 1

(2010) Martin I Sigurdsson et al.   BMC Systems Biology

The biomass objective function

(2010) Adam M Feist et al.   CURRENT OPINION IN MICROBIOLOGY

Omic data from evolved E. coli are consistent with computed optimal growth from genome-scale models

(2010) Nathan E Lewis et al.   Molecular Systems Biology

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

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

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

Triacylglycerol accumulation and profiling in the model diatoms Thalassiosira pseudonana and Phaeodactylum tricornutum (Baccilariophyceae) during starvation

(2009) Eizadora T. Yu et al.   JOURNAL OF APPLIED PHYCOLOGY

Gene silencing in the marine diatom Phaeodactylum tricornutum

(2009) Valentina De Riso et al.   NUCLEIC ACIDS RESEARCH

Diatoms in biotechnology: modern tools and applications

(2008) Andrew Bozarth et al.   APPLIED MICROBIOLOGY AND BIOTECHNOLOGY

HECTAR: A method to predict subcellular targeting in heterokonts

(2008) Bernhard Gschloessl et al.   BMC BIOINFORMATICS

The Phaeodactylum genome reveals the evolutionary history of diatom genomes

(2008) Chris Bowler et al.   NATURE

A Model for Carbohydrate Metabolism in the Diatom Phaeodactylum tricornutum Deduced from Comparative Whole Genome Analysis

(2008) Peter G. Kroth et al.   PLoS One