Genome-scale metabolic model of the diatom Thalassiosira pseudonana highlights the importance of nitrogen and sulfur metabolism in redox balance

A Genome-Scale Metabolic Model of Thalassiosira pseudonana CCMP 1335 for a Systems-Level Understanding of Its Metabolism and Biotechnological Potential

(2020) Ahmad Ahmad et al.   Microorganisms

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

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

Preferential utilization of inorganic polyphosphate over other bioavailable phosphorus sources by the model diatoms Thalassiosira spp.

(2019) Julia M. Diaz et al.   ENVIRONMENTAL MICROBIOLOGY

The Macromolecular Basis of Phytoplankton C:N:P Under Nitrogen Starvation

(2019) Justin D. Liefer et al.   Frontiers in Microbiology

Organelle Studies and Proteome Analyses of Mitochondria and Plastids Fractions from the Diatom Thalassiosira pseudonana

(2019) Alexander F Schober et al.   PLANT AND CELL PHYSIOLOGY

Sulfonate-based networks between eukaryotic phytoplankton and heterotrophic bacteria in the surface ocean

(2019) Bryndan P. Durham et al.   Nature Microbiology

Defining and Evaluating Microbial Contributions to Metabolite Variation in Microbiome-Metabolome Association Studies

(2019) Cecilia Noecker et al.   mSystems

Nitrogen starvation induces distinct photosynthetic responses and recovery dynamics in diatoms and prasinophytes

(2018) Justin D. Liefer et al.   PLoS One

Ocean acidification conditions increase resilience of marine diatoms

(2018) Jacob J. Valenzuela et al.   Nature Communications

A mechanistic model of coral bleaching due to temperature-mediated light-driven reactive oxygen build-up in zooxanthellae

(2018) Mark E. Baird et al.   ECOLOGICAL MODELLING

Evolution of light-independent protochlorophyllide oxidoreductase

(2018) Pratishtha Vedalankar et al.   PROTOPLASMA

The potential for co-evolution of CO2-concentrating mechanisms and Rubisco in diatoms

(2017) Jodi N Young et al.   JOURNAL OF EXPERIMENTAL BOTANY

The role of Rubisco kinetics and pyrenoid morphology in shaping the CCM of haptophyte microalgae

(2017) Ana M C Heureux et al.   JOURNAL OF EXPERIMENTAL BOTANY

Clarification of Photorespiratory Processes and the Role of Malic Enzyme in Diatoms

(2017) Aubrey Davis et al.   PROTIST

Erroneous energy-generating cycles in published genome scale metabolic networks: Identification and removal

(2017) Claus Jonathan Fritzemeier et al.   PLoS Computational Biology

Large variation in the Rubisco kinetics of diatoms reveals diversity among their carbon-concentrating mechanisms

(2016) Jodi N. Young et al.   JOURNAL OF EXPERIMENTAL BOTANY

Changes in Relative Thylakoid Protein Abundance Induced by Fluctuating Light in the Diatom Thalassiosira pseudonana

(2016) Irina Grouneva et al.   JOURNAL OF PROTEOME RESEARCH

TransportDB 2.0: a database for exploring membrane transporters in sequenced genomes from all domains of life

(2016) Liam D. H. Elbourne et al.   NUCLEIC ACIDS RESEARCH

KEGG: new perspectives on genomes, pathways, diseases and drugs

(2016) Minoru Kanehisa et al.   NUCLEIC ACIDS RESEARCH

Mechanisms that increase the growth efficiency of diatoms in low light

(2016) Nerissa L. Fisher et al.   PHOTOSYNTHESIS RESEARCH

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

(2016) Jennifer Levering et al.   PLoS One

Two distinct pools of B12analogs reveal community interdependencies in the ocean

(2016) Katherine R. Heal et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Unique attributes of cyanobacterial metabolism revealed by improved genome-scale metabolic modeling and essential gene analysis

(2016) Jared T. Broddrick et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Improved Metabolic Models for E. coli and Mycoplasma genitalium from GlobalFit, an Algorithm That Simultaneously Matches Growth and Non-Growth Data Sets

(2016) Daniel Hartleb et al.   PLoS Computational Biology

Photosynthetic physiology and biomass partitioning in the model diatom Phaeodactylum tricornutum grown in a sinusoidal light regime

(2016) Denis Jallet et al.   Algal Research-Biomass Biofuels and Bioproducts

Dissolved organic matter produced by Thalassiosira pseudonana

(2015) Krista Longnecker et al.   MARINE CHEMISTRY

Energetic coupling between plastids and mitochondria drives CO2 assimilation in diatoms

(2015) Benjamin Bailleul et al.   NATURE

BiGG Models: A platform for integrating, standardizing and sharing genome-scale models

(2015) Zachary A. King et al.   NUCLEIC ACIDS RESEARCH

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

(2015) Ansgar Gruber et al.   PLANT JOURNAL

Phytoplankton–bacterial interactions mediate micronutrient colimitation at the coastal Antarctic sea ice edge

(2015) Erin M. Bertrand et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

InterProScan 5: genome-scale protein function classification

(2014) P. Jones et al.   BIOINFORMATICS

Localization of putative carbonic anhydrases in the marine diatom, Thalassiosira pseudonana

(2014) Mio Samukawa et al.   PHOTOSYNTHESIS RESEARCH

Mapping the diatom redox-sensitive proteome provides insight into response to nitrogen stress in the marine environment

(2014) S. Rosenwasser et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Cryptic carbon and sulfur cycling between surface ocean plankton

(2014) Bryndan P. Durham et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Emergent Biosynthetic Capacity in Simple Microbial Communities

(2014) Hsuan-Chao Chiu et al.   PLoS Computational Biology

29Si{1H} CP-MAS NMR comparison and ATR-FTIR spectroscopic analysis of the diatoms Chaetoceros muelleri and Thalassiosira pseudonana grown at different salinities

(2013) Sian M. La Vars et al.   ANALYTICAL AND BIOANALYTICAL CHEMISTRY

COBRApy: COnstraints-Based Reconstruction and Analysis for Python

(2013) Ali Ebrahim et al.   BMC Systems Biology

Processes and patterns of oceanic nutrient limitation

(2013) C. M. Moore et al.   Nature Geoscience

A common partitioning strategy for photosynthetic products in evolutionarily distinct phytoplankton species

(2013) Kimberly H. Halsey et al.   NEW PHYTOLOGIST

The MetaCyc database of metabolic pathways and enzymes and the BioCyc collection of Pathway/Genome Databases

(2013) Ron Caspi et al.   NUCLEIC ACIDS RESEARCH

Photosystem II protein clearance and FtsH function in the diatom Thalassiosira pseudonana

(2013) Douglas A. Campbell et al.   PHOTOSYNTHESIS RESEARCH

Rising CO2 Interacts with Growth Light and Growth Rate to Alter Photosystem II Photoinactivation of the Coastal Diatom Thalassiosira pseudonana

(2013) Gang Li et al.   PLoS One

Genome-wide diel growth state transitions in the diatom Thalassiosira pseudonana

(2013) J. Ashworth et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Future Retrievals of Water Column Bio-Optical Properties using the Hyperspectral Infrared Imager (HyspIRI)

(2013) Emmanuel Devred et al.   Remote Sensing

Use of phytoplankton-derived dissolved organic carbon by different types of bacterioplankton

(2012) Hugo Sarmento et al.   ENVIRONMENTAL MICROBIOLOGY

Elevated CO2concentrations affect the elemental stoichiometry and species composition of an experimental phytoplankton community

(2012) ANTONIE M. VERSCHOOR et al.   FRESHWATER BIOLOGY

ELEVATED CARBON DIOXIDE DIFFERENTIALLY ALTERS THE PHOTOPHYSIOLOGY OF THALASSIOSIRA PSEUDONANA (BACILLARIOPHYCEAE) AND EMILIANIA HUXLEYI (HAPTOPHYTA)1

(2012) Avery McCarthy et al.   JOURNAL OF PHYCOLOGY

Response of marine diatom communities to Late Quaternary abrupt climate changes

(2012) Pedro Cermeño et al.   JOURNAL OF PLANKTON RESEARCH

The Transcriptome and Proteome of the Diatom Thalassiosira pseudonana Reveal a Diverse Phosphorus Stress Response

(2012) Sonya T. Dyhrman et al.   PLoS One

Substrate-Controlled Succession of Marine Bacterioplankton Populations Induced by a Phytoplankton Bloom

(2012) H. Teeling et al.   SCIENCE

The Role of B Vitamins in Marine Biogeochemistry

(2011) Sergio A. Sañudo-Wilhelmy et al.   Annual Review of Marine Science

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

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

Insights into the Evolution of Vitamin B12 Auxotrophy from Sequenced Algal Genomes

(2011) K. E. Helliwell et al.   MOLECULAR BIOLOGY AND EVOLUTION

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

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

SignalP 4.0: discriminating signal peptides from transmembrane regions

(2011) Thomas Nordahl Petersen et al.   NATURE METHODS

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

A Single Peroxisomal Targeting Signal Mediates Matrix Protein Import in Diatoms

(2011) Nicola H. Gonzalez et al.   PLoS One

Genome characteristics of a generalist marine bacterial lineage

(2010) Ryan J Newton et al.   ISME Journal

Impact of chlororespiration on non-photochemical quenching of chlorophyll fluorescence and on the regulation of the diadinoxanthin cycle in the diatom Thalassiosira pseudonana

(2010) S. Cruz et al.   JOURNAL OF EXPERIMENTAL BOTANY

Acclimation to elevated carbon dioxide and ultraviolet radiation in the diatomThalassiosira pseudonana: Effects on growth, photosynthesis, and spectral sensitivity of photoinhibition

(2010) Cristina Sobrino et al.   LIMNOLOGY AND OCEANOGRAPHY

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

The Importance of Energy Balance in Improving Photosynthetic Productivity

(2010) D. M. Kramer et al.   PLANT PHYSIOLOGY

Chitin in Diatoms and Its Association with the Cell Wall

(2009) Colleen A. Durkin et al.   EUKARYOTIC CELL

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

The effect of pCO2 on carbon acquisition and intracellular assimilation in four marine diatoms

(2009) Scarlett Trimborn et al.   JOURNAL OF EXPERIMENTAL MARINE BIOLOGY AND ECOLOGY

A microbial source of phosphonates in oligotrophic marine systems

(2009) Sonya T. Dyhrman et al.   Nature Geoscience

HECTAR: A method to predict subcellular targeting in heterokonts

(2008) Bernhard Gschloessl et al.   BMC BIOINFORMATICS

Abundant and diverse bacteria involved in DMSP degradation in marine surface waters

(2008) Erinn C. Howard et al.   ENVIRONMENTAL MICROBIOLOGY

Nitrogen fixation-enhanced carbon sequestration in low nitrate, low chlorophyll seascapes

(2008) DM Karl et al.   MARINE ECOLOGY PROGRESS SERIES

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

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

Silicon Uptake in Diatoms Revisited: A Model for Saturable and Nonsaturable Uptake Kinetics and the Role of Silicon Transporters

(2007) K. Thamatrakoln et al.   PLANT PHYSIOLOGY