Omics and Beyond

This page contains publications and resources relevant to the various omics research done with Phaeodactylum tricornutum and Thalassiosira pseudonana. This includes genomics, transcriptomics, proteomics, metabolomics, and the specialized omics (acetylomics, methylomics, lipdomics etc).

Genomics

A genomics approach reveals the global genetic polymorphism, structure, and functional diversity of ten accessions of the marine model diatom Phaeodactylum tricornutum. (2020) https://doi.org/10.1038/s41396-019-0528-3

  • Genomics approach analyzing P. tricornutum to study populations and clades, asexual reproduction, different selection pressures and metabolic pressures in nature

Flux balance analysis of primary metabolism in the diatom Phaeodactylum tricornutum. (2016) https://doi.org/10.1111/tpj.13081

  • A metabolic network constructed for P. tricornutum incorporating the genome, biochemical literature, and online bioinformatic databases, could explore in silico different knockout conditions

Transcription factors in microalgae: genome-wide prediction and comparative analysis. (2016) https://doi.org/10.1186/s12864-016-2610-9

  • Pipeline combining BLAST, HMMER and InterProScan software to identify and classify transcription factors in algae including P. tricornutum

The diversity of small non-coding RNAs in the diatom Phaeodactylum tricornutum. (2014) https://doi.org/10.1186/1471-2164-15-698

  • The first comprehensive characterization of all small non-coding RNAs in P. tricornutum

Identification and bioinformatics analysis of pseudogenes from whole genome sequence of Phaeodactylum tricornutum. (2013) https://doi.org/10.1007/s11434-012-5174-3

  • Pipeline for identification of pseudogenes in P. tricornutum

Identification and Characterization of an Extracellular Alkaline Phosphatase in the Marine Diatom Phaeodactylum tricornutum. (2013) https://doi.org/10.1007/s10126-013-9494-3

  • Method for identifying and characterizing an extracellular protein in P. tricornutum (nucleic acid and amino acid sequence analysis, proteomic analysis, comparative genomics, quantitative PCR, gel filtration chromatography, assays, phylogenetic analysis)

Identification of G protein-coupled receptor signaling pathway proteins in marine diatoms using comparative genomics. (2013) https://doi.org/10.1186/1471-2164-14-503

  • Comparative genomics approach to find GPCR signalling pathways in T. pseudonana and P. tricornutum

Biosynthesis of fucoxanthin and diadinoxanthin and function of initial pathway genes in Phaeodactylum tricornutum. (2012) https://doi.org/10.1093/jxb/ers211

  • Combined approach to elucidate biosynthetic pathways in P. tricornutum, putative genes selected from a genomic database, function identified by genetic pathway complementation in E. coli, intermediate carotenoid products confirmed by TLC from P. tricornutum and final products measured

The Phaeodactylum genome reveals the evolutionary history of diatom genomes. (2008) https://doi.org/10.1038/nature07410

  • Reports the first complete genome sequence of P. tricornutum and compares it to T. pseudonana

Comparative genomics of the pennate diatom Phaeodactylum tricornutum. (2005) https://doi.org/10.1104/pp.104.052829

  • EST analysis between P. tricornutum and other algae based on the GenBank nonredundant protein database, the COG profile database, the Pfam protein domains database, and the newly created diatom EST database

 

Transcriptomics

Large scale maximum average power multiple inference on time-course count data with application to RNA-seq analysis. (2020) https://doi.org/10.1111/biom.13144

  • Better model for analysis of RNA-seq data in P. tricornutum

Downregulation of mitochondrial alternative oxidase affects chloroplast function, redox status and stress response in a marine diatom. (2019) https://doi.org/10.1111/nph.15479

  • AOX knockdown lines in P. tricornutum analyzed with transcriptome and metabolome profiles as well as photosynthetic rates

Comparative in depth RNA sequencing of P. tricornutum's morphotypes reveals specific features of the oval morphotype. (2018) https://doi.org/10.1038/s41598-018-32519-7

  • Analyzes morphogenesis using high-throughput RNA-sequencing and transcriptome analysis, compared to biological process and molecular functions, first transcriptome wide characterization of three morphotypes of the same P. tricornutum strain

Integrative analysis of large scale transcriptome data draws a comprehensive landscape of Phaeodactylum tricornutum genome and evolutionary origin of diatoms. (2018) https://doi.org/10.1038/s41598-018-23106-x

  • Combination of 90 RNA-seq datasets under different growth conditions to explore the P. tricornutum genome

Molecular adaptations to phosphorus deprivation and comparison with nitrogen deprivation responses in the diatom Phaeodactylum tricornutum. (2018) https://doi.org/10.1371/journal.pone.0193335

  • Combinatorial approach of transcriptomics, metabolomics, physiological and biochemical experiments to analyze the response to phosphorus deprivation in P. tricornutum

Orchestration of transcriptome, proteome and metabolome in the diatom Phaeodactylum tricornutum during nitrogen limitation. (2018) https://doi.org/10.1016/j.algal.2018.08.012

  • Integrative approach with transcriptome, physiology, proteome and metabolome (Omics based approach) to analyze P. tricornutum during various nitrogen and light conditions

Screening for Biologically Annotated Drugs That Trigger Triacylglycerol Accumulation in the Diatom Phaeodactylum. (2018) https://doi.org/10.1104/pp.17.01804

  • Created a phenotypic assay for oil droplet accumulation (aka high TAG yield) for P. tricornutum to screen a library of 1200 drugs, analyzed the transcriptomic response as well, found that diatoms are also sensitive to endocrine disruoptors

Transcriptome, Biochemical and Growth Responses of the Marine Phytoplankter Phaeodactylum Tricornutum Bohlin (Bacillariophyta) to Copepod Grazer Presence. (2018) https://doi.org/10.1159/000488839

  • Combinatorial approach including transcriptome, biochemical and growth responses in P. tricornutum due to the presence of a grazer

A comparison of the effects of copper nanoparticles and copper sulfate on Phaeodactylum tricornutum physiology and transcription. (2017) https://doi.org/10.1016/j.etap.2017.08.029

  • Physiological and transcriptome analysis of P. tricornutum effected by copper nanoparticles and copper sulfate

Dynamic responses to silicon in Thalasiossira pseudonana - Identification, characterisation and classification of signature genes and their corresponding protein motifs. (2017) https://doi.org/10.1038/s41598-017-04921-0

  • Metabolomic and transcriptomic (using T. pseudonana whole genome 60mer oligonucleotide microarray) analysis of T. pseudonana due to silicon exposure

Investigating mixotrophic metabolism in the model diatom Phaeodactylum tricornutum. (2017) https://doi.org/10.1098/rstb.2016.0404

  • Incorporates transcriptomics, metabolomics, metabolic modelling and physiological data to study the effects of glycerol on P. tricornutum

Ocean acidification modulates expression of genes and physiological performance of a marine diatom. (2017) https://doi.org/10.1371/journal.pone.0170970

  • qRT-PCR expression analysis of targeted genes in response to certain environmental conditions in P. tricornutum

The Combination of RNA and Protein Profiling Reveals the Response to Nitrogen Depletion in Thalassiosira pseudonana. (2017) https://doi.org/10.1038/s41598-017-09546-x 

  • Incorporation of physiological data with RNA and protein profiling data to elucidate changes during N depletion in T. pseudonana

The Influence of a Cryptochrome on the Gene Expression Profile in the Diatom Phaeodactylum tricornutum under Blue Light and in Darkness. (2017) https://doi.org/10.1093/pcp/pcx127

  • Examined role of CryP in regulating transcription in P. tricornutum using comparative RNA-seq of WT and mutant CryP knockdown strains, strains knocked down in previous publication

Pan-transcriptomic analysis identifies coordinated and orthologous functional modules in the diatoms Thalassiosira pseudonana and Phaeodactylum tricornutum. (2016) https://doi.org/10.1016/j.margen.2015.10.011

  • Integrated analysis including expression patterns, gene functions, cis-regulatory DNA sequence motifs, shows coordination of transcriptional responses in diatoms over changing environmental conditions, resource available at http://networks.systemsbiologymet/diatom-portal

Noncoding and coding transcriptome responses of a marine diatom to phosphate fluctuations. (2016) https://doi.org/10.1111/nph.13787

  • Global transcriptome analysis using strand-specific RNA sequencing, identified long intergenic nonprotein coding RNAs in response to phosphate conditions in P. tricornutum

Profiling of the Early Nitrogen Stress Response in the Diatom Phaeodactylum tricornutum Reveals a Novel Family of RING-Domain Transcription Factors. (2016) https://doi.org/10.1104/pp.15.01300

  • Transcriptome modelling of P. tricornutum identifies novel family of transcription factors

Proteomic analyses bring new insights into the effect of a dark stress on lipid biosynthesis in Phaeodactylum tricornutum. (2016) https://doi.org/10.1038/srep25494

  • Proteomic analysis using iTRAQ (LC-MS/MS based) approach, combined with KEGG analysis in P. tricornutum due to nitrogen depletion

Transcript level coordination of carbon pathways during silicon starvation-induced lipid accumulation in the diatom Thalassiosira pseudonana. (2016) https://doi.org/10.1111/nph.13843

  • Transcriptome analysis in T. pseudonana due to silicon starvation conditions, also characterized growth, cell cycle progression, chloroplast replication, fatty acid composition, pigmentation and photosynthetic parameters as well as lipid accumulation

Transcriptional Orchestration of the Global Cellular Response of a Model Pennate Diatom to Diel Light Cycling under Iron Limitation. (2016) https://doi.org/10.1371/journal.pgen.1006490

  • Physiological, metabolite composition, transcriptomic analysis of P. tricornutum during different levels of iron and light

Analysis of the Proteome of the Marine Diatom Phaeodactylum tricornutum Exposed to Aluminum Providing Insights into Aluminum Toxicity Mechanisms. (2015) https://doi.org/10.1021/acs.est.5b03272

  • Array of proteomic, transcriptomic, biochemical techniques to describe the cellular response of P. tricornutum to brief, sublethal aluminum concentrations

Whole-cell response to nitrogen deprivation in the diatom Phaeodactylum tricornutum. (2015) https://doi.org/10.1093/jxb/erv340

  • Integrated physiological, transcriptional, and metabolite data to understand the response of P. tricornutum to nitrogen deprivation

Systems-level analysis of the metabolic responses of the diatom Phaeodactylum tricornutum to phosphorus stress. (2014) https://doi.org/10.1111/1462-2920.12411

  • Transcriptome profiling in combination with biochemical investigations in P. tricornutum identified the genes upregulated and downregulated with phosphorous stress

Genome-wide diel growth state transitions in the diatom Thalassiosira pseudonana. (2013) https://doi.org/10.1073/pnas.1300962110

  • Genome-wide physiological and transcriptomic survey to see change in transcriptional changes in culture for T. pseudonana

Using transcriptomic profiles in the diatom Phaeodactylum tricornutum to identify and prioritize stressors. (2013) https://doi.org/10.1016/j.aquatox.2013.04.002

  • Developed toxicity identification evaluation-like gene expression assay, combines flow cytometry, gene expression microarray analysis for transcriptomic profiles, confirmed using qPCR for P. tricornutum

Influence of cobalamin scarcity on diatom molecular physiology and identification of a cobalamin acquisition protein. (2012) https://doi.org/10.1073/pnas.1201731109

  • Proteomic profiling and RNA-sequencing transcriptomic analysis pipeline for P. tricornutum and T. pseudonana

Whole-genome expression analysis reveals a role for death-related genes in stress acclimation of the diatom Thalassiosira pseudonana. (2012) https://doi.org/10.1111/j.1462-2920.2011.02468.x

  • A whole-genome expression analysis pipeline based on EST libraries for T. pseudonana

Genome-Wide Profiling of Responses to Cadmium in the Diatom Phaeodactylum tricornutum. (2011) https://doi.org/10.1021/es2002259

  • Explains how to use the P. tricornutum whole-genome 60-mer oligonucleotide microarrays from Agilent  as well as statistical analysis of the microarray data for expression along with qRT-PCR

Digital expression profiling of novel diatom transcripts provides insight into their biological functions. (2010) https://doi.org/10.1186/gb-2010-11-8-r85

  • Method for systematic analysis of ESTs from P. tricornutum grown in different conditions to analyze transcripts that are similarly and differentially expressed, along with functional annotation to find patterns in the expression of genes as well as novel transcrips and functions

Genome-Wide Transcriptome Analyses of Silicon Metabolism in Phaeodactylum tricornutum Reveal the Multilevel Regulation of Silicic Acid Transporters. (2009) https://doi.org/10.1371/journal.pone.0007458

  • Uses whole genome expression analysis in P. tricornutum to find differentially expressed genes (transcriptional response) to environmental stimuli

Whole-genome expression profiling of the marine diatom Thalassiosira pseudonana identifies genes involved in silicon bioprocesses. (2008) https://doi.org/10.1073/pnas.0707946105

  • Uses tiled arrays to identify putative new genes not typically detected on microarrays in T. pseudonana 

The Diatom EST database. (2005) https://doi.org/10.1093/nar/gki121

  • Database containing 30000 ESTs from P. tricornutum and T. pseudonana (PtDB and TpDB), EST data can be retrieved on Pfam domains, Cluster of Orthologous Groups (COG) and Gene Ontologies (GO)

 

Proteomics

Structural and functional analyses of photosystem II in the marine diatom Phaeodactylum tricornutum. (2019) https://doi.org/10.1073/pnas.1906726116

  • Combination of cryoelectron tomography, proteomics, and biophysical analyses to study photosystem II in P. tricornutum

Genome Annotation of a Model Diatom Phaeodactylum tricornutum Using an Integrated Proteogenomic Pipeline. (2018) https://doi.org/10.1016/j.molp.2018.08.005

  • Developed an integrated proteogenomic pipeline and applied it toward improved annotation of the P. tricornutum genome using mass spectrometry based proteomics data, pipeline developed is available to be used for any sequenced eukaryote

Orchestration of transcriptome, proteome and metabolome in the diatom Phaeodactylum tricornutum during nitrogen limitation. (2018) https://doi.org/10.1016/j.algal.2018.08.012

  • Integrative approach with transcriptome, physiology, proteome and metabolome (Omics based approach) to analyze P. tricornutum during various nitrogen and light conditions

Quantitative Proteomics Reveals Common and Specific Responses of a Marine Diatom Thalassiosira pseudonana to Different Macronutrient Deficiencies. (2018) https://doi.org/10.3389/fmicb.2018.02761

  • A combined physiological and quantitative proteomics approach toward studying the response of T. pseudonana to deficiencies in nitrogen, phosphorus and silicon

Toxicological effects of CdSe nanocrystals on the marine diatom Phaeodactylum tricornutum: The first mass spectrometry-based proteomic approach. (2018) https://doi.org/10.1016/j.ecoenv.2018.01.043

  • Mass spectrometry-based proteomic approach to analyze the effects of CdSe nanocrystals on P. tricornutum

The Combination of RNA and Protein Profiling Reveals the Response to Nitrogen Depletion in Thalassiosira pseudonana. (2017) https://doi.org/10.1038/s41598-017-09546-x 

  • Incorporation of physiological data with RNA and protein profiling data to elucidate changes during N depletion in T. pseudonana

High light stress triggers distinct proteomic responses in the marine diatom Thalassiosira pseudonana. (2016) https://doi.org/10.1186/s12864-016-3335-5

  • Proteomic analysis combined with biochemical analyses for T. pseudonana during high light

Proteome response of Phaeodactylum tricornutum, during lipid accumulation induced by nitrogen depletion. (2016) https://doi.org/10.1016/j.algal.2016.06.015

  • Proteomic analysis using iTRAQ (LC-MS/MS based) approach, combined with KEGG analysis in P. tricornutum due to nitrogen depletion

Proteomic analyses bring new insights into the effect of a dark stress on lipid biosynthesis in Phaeodactylum tricornutum. (2016) https://doi.org/10.1038/srep25494

  • Combinatorial approach of physiological, proteomic (iTRAQ) and genomic (qRT-PCR) approaches to study the expression of proteins during dark stress in P. tricornutum

Plastid proteome prediction for diatoms and other algae with secondary plastids of the red lineage. (2015) https://doi.org/10.1111/tpj.12734

  • Created ASAFind, a customized prediction tool to identify nuclear-encoded plastid proteins in algae with secondary plastids of the red lineage based on the output of SignalP and identification of the conserved ASAFP’ motifs and transit peptides, tested and subcellular localization was verified, works for T. pseudonana and P. tricornutum

Analysis of the Proteome of the Marine Diatom Phaeodactylum tricornutum Exposed to Aluminum Providing Insights into Aluminum Toxicity Mechanisms. (2015) https://doi.org/10.1021/acs.est.5b03272

  • Array of proteomic, transcriptomic, biochemical techniques to describe the cellular response of P. tricornutum to brief, sublethal aluminum concentrations

Examination of metabolic responses to phosphorus limitation via proteomic analyses in the marine diatom Phaeodactylum tricornutum. (2015) https://doi.org/10.1038/srep10373

  • Proteomic profiling in P. tricornutum measured phosphorus limitation metabolic response

Methylcrotonyl-CoA Carboxylase Regulates Triacylglycerol Accumulation in the Model Diatom Phaeodactylum tricornutum. (2014) https://doi.org/10.1105/tpc.114.124982

  • Uses RNAi to knockdown the gene MCC2 after the label-free quantitative protemics approach identified it was significantly upregulated (confirmed by quantitative RT PCR and protein gel blot analysis)

Phosphoproteomic Analysis Provides Novel Insights into Stress Responses in Phaeodactylum tricornutum, a Model Diatom. (2014) https://doi.org/10.1021/pr401290u

 

  • Protein phosphorylation (phosphoproteomic analysis) was measured for the first time to identify protein phosphorylation on serine, threonine, tyrosine sites on peptides and proteins, further validated using Western blotting

Proteomics to reveal metabolic network shifts towards lipid accumulation following nitrogen deprivation in the diatom Phaeodactylum tricornutum. (2014) https://doi.org/10.1007/s10811-013-0050-3

  • Method for proteomics analysis for P. tricornutum

Influence of cobalamin scarcity on diatom molecular physiology and identification of a cobalamin acquisition protein. (2012) https://doi.org/10.1073/pnas.1201731109

  • Proteomic profiling and RNA-sequencing transcriptomic analysis pipeline for P. tricornutum and T. pseudonana

The Thylakoid Membrane Proteome of Two Marine Diatoms Outlines Both Diatom-Specific and Species-Specific Features of the Photosynthetic Machinery. (2011) https://doi.org/10.1021/pr200600f

  • Proteomics approach (BN/SDS-PGAE coupled with mass spectrometry analysis) serves as a tool to confirm and improve genome-derived protein models in P. tricornutum and T. pseudonana

Deciphering diatom biochemical pathways via whole-cell proteomics. (2009) https://doi.org/10.3354/ame01284

  • Method for whole cell high-throughput shotgun proteomics to identify proteins expressed by T. pseudonana

 

Metabolomics

Downregulation of mitochondrial alternative oxidase affects chloroplast function, redox status and stress response in a marine diatom. (2019) https://doi.org/10.1111/nph.15479

  • AOX knockdown lines in P. tricornutum analyzed with transcriptome and metabolome profiles as well as photosynthetic rates

Chemical Mutagenesis and Fluorescence-Based High-Throughput Screening for Enhanced Accumulation of Carotenoids in a Model Marine Diatom Phaeodactylum tricornutum. (2018) https://doi.org/10.3390/md16080272

  • Used chemical mutagenesis to generate mutants for P. tricornutum and studied common metabolic pathways in a genome scale metabolic model to analyze fucoxanthin, pigmentation, and lipid metabolism, screened in a high throughput manner using fluorescence and integrated LC-MS data (High throughput screen for industrial applications)

Molecular adaptations to phosphorus deprivation and comparison with nitrogen deprivation responses in the diatom Phaeodactylum tricornutum. (2018) https://doi.org/10.1371/journal.pone.0193335

  • Combinatorial approach of transcriptomics, metabolomics, physiological and biochemical experiments to analyze the response to phosphorus deprivation in P. tricornutum

Orchestration of transcriptome, proteome and metabolome in the diatom Phaeodactylum tricornutum during nitrogen limitation. (2018) https://doi.org/10.1016/j.algal.2018.08.012

  • Integrative approach with transcriptome, physiology, proteome and metabolome (Omics based approach) to analyze P. tricornutum during various nitrogen and light conditions

Dynamic responses to silicon in Thalasiossira pseudonana - Identification, characterisation and classification of signature genes and their corresponding protein motifs. (2017) https://doi.org/10.1038/s41598-017-04921-0

  • Metabolomic and transcriptomic (using T. pseudonana whole genome 60mer oligonucleotide microarray) analysis of T. pseudonana due to silicon exposure

Investigating mixotrophic metabolism in the model diatom Phaeodactylum tricornutum. (2017) https://doi.org/10.1098/rstb.2016.0404

  • Incorporates transcriptomics, metabolomics, metabolic modelling and physiological data to study the effects of glycerol on P. tricornutum

Flux balance analysis of primary metabolism in the diatom Phaeodactylum tricornutum. (2016) https://doi.org/10.1111/tpj.13081

  • A metabolic network constructed for P. tricornutum incorporating the genome, biochemical literature, and online bioinformatic databases, could explore in silico different knockout conditions

Genome-Scale Model Reveals Metabolic Basis of Biomass Partitioning in a Model Diatom. (2016) https://doi.org/10.1371/journal.pone.0155038

Metabolome Analysis Reveals Betaine Lipids as Major Source for Triglyceride Formation, and the Accumulation of Sedoheptulose during Nitrogen-Starvation of Phaeodactylum tricornutum. (2016) https://doi.org/10.1371/journal.pone.0164673

  • General metabolome analysis in P. tricornutum during nitrogen depletion

Transcriptional Orchestration of the Global Cellular Response of a Model Pennate Diatom to Diel Light Cycling under Iron Limitation. (2016) https://doi.org/10.1371/journal.pgen.1006490

  • Physiological, metabolite composition, transcriptomic analysis of P. tricornutum during different levels of iron and light

Remodeling of intermediate metabolism in the diatom Phaeodactylum tricornutum under nitrogen stress. (2015) https://doi.org/10.1073/pnas.1419818112 

  • Metabolic modelling in P. tricornutum, includes a model that incorporates biochemical, physiological, bioinformatics, and reverse genetics approaches

Whole-cell response to nitrogen deprivation in the diatom Phaeodactylum tricornutum. (2015) https://doi.org/10.1093/jxb/erv340

  • Integrated physiological, transcriptional, and metabolite data to understand the response of P. tricornutum to nitrogen deprivation

Tracking the sterol biosynthesis pathway of the diatom Phaeodactylum tricornutum. (2014) https://doi.org/10.1111/nph.12917

  • Using DiatomCyc, reconstructed mevalonate and sterol biosynthetic pathways for P. tricornutum in silico and experimentally verified the pathways using enzyme inhibitors, gene silencing and heterologous gene expression approaches

Metabolic Analysis of Adaptation to Short-Term Changes in Culture Conditions of the Marine Diatom Thalassiosira pseudonana. (2013) https://doi.org/10.1371/journal.pone.0067340

  • Method for metabolic and lipodomic profiling in T. pseudonana

 

Other Omics

Acetylome Profiling Reveals Extensive Lysine Acetylation of the Fatty Acid Metabolism Pathway in the Diatom Phaeodactylum tricornutum. (2018) https://doi.org/10.1074/mcp.RA117.000339

  • Acetylome profiling of P. tricronutum

An integrative analysis of post-translational histone modifications in the marine diatom Phaeodactylum tricornutum. (2015) https://doi.org/10.1186/s13059-015-0671-8

  • High resolution mass spectrometry to identify the full repertoire of post-translational modifications on histones in P. tricornutum, combinatorial analysis of histone marks and DNA methylation highlights the presence of an epigenetic code, profiles three specific histone marks, shows code is dynamic, first genome-wide characterization of the histone code in stramenophiles and marine phytoplankton

Membrane Glycerolipid Remodeling Triggered by Nitrogen and Phosphorus Starvation in Phaeodactylum tricornutum. (2015) https://doi.org/10.1104/pp.114.252395

  • First defined reference for the glycerolipidome of P. tricornutum under a variety of conditions

Phosphoproteomic Analysis Provides Novel Insights into Stress Responses in Phaeodactylum tricornutum, a Model Diatom. (2014) https://doi.org/10.1021/pr401290u

  • Protein phosphorylation (phosphoproteomic analysis) was measured for the first time to identify protein phosphorylation on serine, threonine, tyrosine sites on peptides and proteins, further validated using Western blotting

Insights into the role of DNA methylation in diatoms by genome-wide profiling in Phaeodactylum tricornutum. (2013) https://doi.org/10.1038/ncomms3091

  • Provides the first whole-genome methylome for P. tricornutum (DNA cytosine methylation)

Metabolic Analysis of Adaptation to Short-Term Changes in Culture Conditions of the Marine Diatom Thalassiosira pseudonana. (2013) https://doi.org/10.1371/journal.pone.0067340

  • Method for metabolic and lipodomic profiling in T. pseudonana

Protocol: Chromatin immunoprecipitation (ChIP) methodology to investigate histone modifications in two model diatom species. (2012) https://doi.org/10.1186/1746-4811-8-48

  • ChIP protocol for P. tricornutum and T. pseudonana to extract chromatin in a reproducible way, can do the ChIP assay with quantitative PCR, optimized procedure goes over growth conditions, cross linking, sonication, validation of the protocol gives control genes and transposable elements, easily adopted for other diatoms and eukaryotic phytoplankton