A refined genome-scale reconstruction ofChlamydomonasmetabolism provides a platform for systems-level analyses

The geographical distribution of fossil fuels unused when limiting global warming to 2 °C

(2015) Christophe McGlade et al.   NATURE

Integration of transcriptomics and metabolomics data specifies the metabolic response of Chlamydomonas to rapamycin treatment

(2015) Sabrina Kleessen et al.   PLANT JOURNAL

The response of Chlamydomonas reinhardtii to nitrogen deprivation: a systems biology analysis

(2015) Jeong-Jin Park et al.   PLANT JOURNAL

Metabolite Profiling and Integrative Modeling Reveal Metabolic Constraints for Carbon Partitioning under Nitrogen Starvation in the Green AlgaeHaematococcus pluvialis

(2014) Lee Recht et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Enhancement of extraplastidic oil synthesis inChlamydomonas reinhardtiiusing a type-2 diacylglycerol acyltransferase with a phosphorus starvation-inducible promoter

(2014) Masako Iwai et al.   PLANT BIOTECHNOLOGY JOURNAL

Systems Analysis of the Response of Photosynthesis, Metabolism, and Growth to an Increase in Irradiance in the Photosynthetic Model Organism Chlamydomonas reinhardtii

(2014) T. Mettler et al.   PLANT CELL

Transforming RNA-Seq Data to Improve the Performance of Prognostic Gene Signatures

(2014) Isabella Zwiener et al.   PLoS One

Defining functional DNA elements in the human genome

(2014) M. Kellis et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Green genes: bioinformatics and systems-biology innovations drive algal biotechnology

(2014) Maarten J.M.F. Reijnders et al.   TRENDS IN BIOTECHNOLOGY

The Chlamydomonas genome project: a decade on

(2014) Ian K. Blaby et al.   TRENDS IN PLANT SCIENCE

Remodeling of Membrane Lipids in Iron-starvedChlamydomonas

(2013) Eugen I. Urzica et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Nitric oxide controls nitrate and ammonium assimilation in Chlamydomonas reinhardtii

(2013) Emanuel Sanz-Luque et al.   JOURNAL OF EXPERIMENTAL BOTANY

Basic and applied uses of genome-scale metabolic network reconstructions of Escherichia coli

(2013) D. McCloskey et al.   Molecular Systems Biology

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

(2013) Minoru Kanehisa et al.   NUCLEIC ACIDS RESEARCH

Systems-Level Analysis of Nitrogen Starvation-Induced Modifications of Carbon Metabolism in a Chlamydomonas reinhardtii Starchless Mutant

(2013) I. K. Blaby et al.   PLANT CELL

Metabolic acclimation to excess light intensity inChlamydomonas reinhardtii

(2013) MARIA C. DAVIS et al.   PLANT CELL AND ENVIRONMENT

Large Scale Comparison of Gene Expression Levels by Microarrays and RNAseq Using TCGA Data

(2013) Yan Guo et al.   PLoS One

Hypoxic survival requires a 2-on-2 hemoglobin in a process involving nitric oxide

(2013) A. Hemschemeier et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Retrograde bilin signaling enablesChlamydomonasgreening and phototrophic survival

(2013) Deqiang Duanmu et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Analysis ofChlamydomonasthiamin metabolism in vivo reveals riboswitch plasticity

(2013) Michael Moulin et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Carotenoid deficiency triggers autophagy in the model green algaChlamydomonas reinhardtii

(2012) María Esther Pérez-Pérez et al.   Autophagy

Flux balance analysis of primary metabolism in Chlamydomonas reinhardtii

(2012) Nanette R Boyle et al.   BMC Systems Biology

Characterization of an internal type-II NADH dehydrogenase from Chlamydomonas reinhardtii mitochondria

(2012) Renaud Lecler et al.   CURRENT GENETICS

Three Acyltransferases and Nitrogen-responsive Regulator Are Implicated in Nitrogen Starvation-induced Triacylglycerol Accumulation inChlamydomonas

(2012) Nanette R. Boyle et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Impact of Oxidative Stress on Ascorbate Biosynthesis inChlamydomonasvia Regulation of theVTC2Gene Encoding a GDP-l-galactose Phosphorylase

(2012) Eugen I. Urzica et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Drought, salt, and temperature stress-induced metabolic rearrangements and regulatory networks

(2012) J. Krasensky et al.   JOURNAL OF EXPERIMENTAL BOTANY

Metabolic and gene expression changes triggered by nitrogen deprivation in the photoautotrophically grown microalgae Chlamydomonas reinhardtii and Coccomyxa sp. C-169

(2012) Joseph Msanne et al.   PHYTOCHEMISTRY

Systems andTrans-System Level Analysis Identifies Conserved Iron Deficiency Responses in the Plant Lineage

(2012) Eugen I. Urzica et al.   PLANT CELL

The Geological Record of Ocean Acidification

(2012) B. Honisch et al.   SCIENCE

Shrinking the Metabolic Solution Space Using Experimental Datasets

(2012) Jennifer L. Reed   PLoS Computational Biology

RELATCH: relative optimality in metabolic networks explains robust metabolic and regulatory responses to perturbations

(2012) Joonhoon Kim et al.   GENOME BIOLOGY

The chloroplast proteome: a survey from the Chlamydomonas reinhardtii perspective with a focus on distinctive features

(2011) Mia Terashima et al.   CURRENT GENETICS

A chloroplast pathway for the de novo biosynthesis of triacylglycerol inChlamydomonas reinhardtii

(2011) Jilian Fan et al.   FEBS LETTERS

Metabolic modeling of Chlamydomonas reinhardtii: energy requirements for photoautotrophic growth and maintenance

(2011) Anna M. J. Kliphuis et al.   JOURNAL OF APPLIED PHYCOLOGY

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

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

Systems Biology Approach inChlamydomonasReveals Connections between Copper Nutrition and Multiple Metabolic Steps

(2011) Madeli Castruita et al.   PLANT CELL

Survival of starving yeast is correlated with oxidative stress response and nonrespiratory mitochondrial function

(2011) A. A. Petti et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

From RNA-seq reads to differential expression results

(2011) Alicia Oshlack et al.   GENOME BIOLOGY

iMAT: an integrative metabolic analysis tool

(2010) Hadas Zur et al.   BIOINFORMATICS

Microalgae: The Potential for Carbon Capture

(2010) Richard Sayre   BIOSCIENCE

Biodiesel from algae: challenges and prospects

(2010) Stuart A Scott et al.   CURRENT OPINION IN BIOTECHNOLOGY

Characterizing the Anaerobic Response ofChlamydomonas reinhardtiiby Quantitative Proteomics

(2010) Mia Terashima et al.   MOLECULAR & CELLULAR PROTEOMICS

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

(2010) Ines Thiele et al.   Nature Protocols

Changes in Transcript Abundance in Chlamydomonas reinhardtii following Nitrogen Deprivation Predict Diversion of Metabolism

(2010) R. Miller et al.   PLANT PHYSIOLOGY

An Outlook on Microalgal Biofuels

(2010) R. H. Wijffels et al.   SCIENCE

Synthesizing and Salvaging NAD+: Lessons Learned from Chlamydomonas reinhardtii

(2010) Huawen Lin et al.   PLoS Genetics

Accomplishments in genome-scale in silico modeling for industrial and medical biotechnology

(2009) Caroline B. Milne et al.   Biotechnology Journal

A Proteomic Survey of Chlamydomonas reinhardtii Mitochondria Sheds New Light on the Metabolic Plasticity of the Organelle and on the Nature of the  -Proteobacterial Mitochondrial Ancestor

(2009) A. Atteia et al.   MOLECULAR BIOLOGY AND EVOLUTION

Applications of genome-scale metabolic reconstructions

(2009) Matthew A Oberhardt et al.   Molecular Systems Biology

Interpreting Expression Data with Metabolic Flux Models: Predicting Mycobacterium tuberculosis Mycolic Acid Production

(2009) Caroline Colijn et al.   PLoS Computational Biology

iBsu1103: a new genome-scale metabolic model of Bacillus subtilis based on SEED annotations

(2009) Christopher S Henry et al.   GENOME BIOLOGY

Network-based prediction of human tissue-specific metabolism

(2008) Tomer Shlomi et al.   NATURE BIOTECHNOLOGY

Selective mRNA translation coordinates energetic and metabolic adjustments to cellular oxygen deprivation and reoxygenation inArabidopsis thaliana

(2008) Cristina Branco-Price et al.   PLANT JOURNAL