Evolution and regulation of nitrogen flux through compartmentalized metabolic networks in a marine diatom

Cross-compartment metabolic coupling enables flexible photoprotective mechanisms in the diatom Phaeodactylum tricornutum

(2019) Jared T. Broddrick et al.   NEW PHYTOLOGIST

An NMRA-Like Protein Regulates Gene Expression in Phytophthora capsici to Drive the Infection Cycle on Tomato

(2018) Jasmine Pham et al.   MOLECULAR PLANT-MICROBE INTERACTIONS

Orchestration of transcriptome, proteome and metabolome in the diatom Phaeodactylum tricornutum during nitrogen limitation

(2018) Ilse M. Remmers et al.   Algal Research-Biomass Biofuels and Bioproducts

The PRIDE database and related tools and resources in 2019: improving support for quantification data

(2018) Yasset Perez-Riverol et al.   NUCLEIC ACIDS RESEARCH

ModelFinder: fast model selection for accurate phylogenetic estimates

(2017) Subha Kalyaanamoorthy et al.   NATURE METHODS

JASPAR 2018: update of the open-access database of transcription factor binding profiles and its web framework

(2017) Aziz Khan et al.   NUCLEIC ACIDS RESEARCH

Nitrate Reductase Knockout Uncouples Nitrate Transport from Nitrate Assimilation and Drives Repartitioning of Carbon Flux in a Model Pennate Diatom

(2017) James K. McCarthy et al.   PLANT CELL

Elucidating dynamic metabolic physiology through network integration of quantitative time-course metabolomics

(2017) Aarash Bordbar et al.   Scientific Reports

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

(2016) Jennifer Levering et al.   PLoS One

Transcriptional Orchestration of the Global Cellular Response of a Model Pennate Diatom to Diel Light Cycling under Iron Limitation

(2016) Sarah R. Smith et al.   PLoS Genetics

Plant nitrogen assimilation and its regulation: a complex puzzle with missing pieces

(2015) Anne Krapp   CURRENT OPINION IN PLANT BIOLOGY

Whole-cell response to nitrogen deprivation in the diatomPhaeodactylum tricornutum

(2015) Leila Alipanah et al.   JOURNAL OF EXPERIMENTAL BOTANY

MitoFates: Improved Prediction of Mitochondrial Targeting Sequences and Their Cleavage Sites

(2015) Yoshinori Fukasawa et al.   MOLECULAR & CELLULAR PROTEOMICS

Energetic coupling between plastids and mitochondria drives CO2 assimilation in diatoms

(2015) Benjamin Bailleul et al.   NATURE

Plastid proteome prediction for diatoms and other algae with secondary plastids of the red lineage

(2015) Ansgar Gruber et al.   PLANT JOURNAL

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

(2015) Sabrina Kleessen et al.   PLANT JOURNAL

THB1, a truncated hemoglobin, modulates nitric oxide levels and nitrate reductase activity

(2015) Emanuel Sanz-Luque et al.   PLANT JOURNAL

Profiling of the Early Nitrogen Stress Response in the Diatom Phaeodactylum tricornutum Reveals a Novel Family of RING-Domain Transcription Factors

(2015) Michiel Matthijs et al.   PLANT PHYSIOLOGY

Understanding nitrate assimilation and its regulation in microalgae

(2015) Emanuel Sanz-Luque et al.   Frontiers in Plant Science

IQ-TREE: A Fast and Effective Stochastic Algorithm for Estimating Maximum-Likelihood Phylogenies

(2014) Lam-Tung Nguyen et al.   MOLECULAR BIOLOGY AND EVOLUTION

Flux profiling of photosynthetic carbon metabolism in intact plants

(2014) Robert Heise et al.   Nature Protocols

Chlamydomonas NZF1, a tandem-repeated zinc finger factor involved in nitrate signalling by controlling the regulatory geneNIT2

(2014) JOSE JAVIER HIGUERA et al.   PLANT CELL AND ENVIRONMENT

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

The Marine Microbial Eukaryote Transcriptome Sequencing Project (MMETSP): Illuminating the Functional Diversity of Eukaryotic Life in the Oceans through Transcriptome Sequencing

(2014) Patrick J. Keeling et al.   PLOS BIOLOGY

A novel protein, Pho92, has a conserved YTH domain and regulates phosphate metabolism by decreasing the mRNA stability ofPHO4inSaccharomyces cerevisiae

(2013) Hyun-Jun Kang et al.   BIOCHEMICAL JOURNAL

COBRApy: COnstraints-Based Reconstruction and Analysis for Python

(2013) Ali Ebrahim et al.   BMC Systems Biology

Proteomics to reveal metabolic network shifts towards lipid accumulation following nitrogen deprivation in the diatom Phaeodactylum tricornutum

(2013) Zhi-Kai Yang et al.   JOURNAL OF APPLIED PHYCOLOGY

MAFFT Multiple Sequence Alignment Software Version 7: Improvements in Performance and Usability

(2013) K. Katoh et al.   MOLECULAR BIOLOGY AND EVOLUTION

Transcription factor evolution in eukaryotes and the assembly of the regulatory toolkit in multicellular lineages

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

Nuclear retention of the transcription factor NLP7 orchestrates the early response to nitrate in plants

(2013) Chloé Marchive et al.   Nature Communications

Chloroplast-mitochondria cross-talk in diatoms

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

The place of diatoms in the biofuels industry

(2012) Mark Hildebrand et al.   Biofuels-UK

Phytoplankton succession and nitrogen utilization during the development of an upwelling bloom

(2011) SE Fawcett et al.   MARINE ECOLOGY PROGRESS SERIES

Evolution and metabolic significance of the urea cycle in photosynthetic diatoms

(2011) Andrew E. Allen et al.   NATURE

Recommendations for Reporting Metabolite Data

(2011) A. R. Fernie et al.   PLANT CELL

Analysis of raphidophyte assimilatory nitrate reductase reveals unique domain architecture incorporating a 2/2 hemoglobin

(2011) Jennifer J. Stewart et al.   PLANT MOLECULAR BIOLOGY

Reversed-phase chromatography with multiple fraction concatenation strategy for proteome profiling of human MCF10A cells

(2011) Yuexi Wang et al.   PROTEOMICS

The Generating Function of CID, ETD, and CID/ETD Pairs of Tandem Mass Spectra: Applications to Database Search

(2010) Sangtae Kim et al.   MOLECULAR & CELLULAR PROTEOMICS

The Mixed Lineage Nature of Nitrogen Transport and Assimilation in Marine Eukaryotic Phytoplankton: A Case Study of Micromonas

(2010) Sarah M. McDonald et al.   MOLECULAR BIOLOGY AND EVOLUTION

Transcription factor families inferred from genome sequences of photosynthetic stramenopiles

(2010) Edda Rayko et al.   NEW PHYTOLOGIST

trimAl: a tool for automated alignment trimming in large-scale phylogenetic analyses

(2009) S. Capella-Gutierrez et al.   BIOINFORMATICS

edgeR: a Bioconductor package for differential expression analysis of digital gene expression data

(2009) M. D. Robinson et al.   BIOINFORMATICS

BLAST+: architecture and applications

(2009) Christiam Camacho et al.   BMC BIOINFORMATICS

R2R3-type MYB transcription factor, CmMYB1, is a central nitrogen assimilation regulator in Cyanidioschyzon merolae

(2009) S. Imamura et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

PII in higher plants: a modern role for an ancient protein

(2009) R. Glen Uhrig et al.   TRENDS IN PLANT SCIENCE

HECTAR: A method to predict subcellular targeting in heterokonts

(2008) Bernhard Gschloessl et al.   BMC BIOINFORMATICS

MASIC: A software program for fast quantitation and flexible visualization of chromatographic profiles from detected LC–MS(/MS) features

(2008) Matthew E. Monroe et al.   COMPUTATIONAL BIOLOGY AND CHEMISTRY

A Diatom Gene Regulating Nitric-Oxide Signaling and Susceptibility to Diatom-Derived Aldehydes

(2008) Assaf Vardi et al.   CURRENT BIOLOGY

AtNOS/AtNOA1 Is a FunctionalArabidopsis thalianacGTPase and Not a Nitric-oxide Synthase

(2008) Magali Moreau et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

The Phaeodactylum genome reveals the evolutionary history of diatom genomes

(2008) Chris Bowler et al.   NATURE

Whole-cell response of the pennate diatom Phaeodactylum tricornutum to iron starvation

(2008) A. E. Allen et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA