Comparative in depth RNA sequencing of P. tricornutum’s morphotypes reveals specific features of the oval morphotype

[1]  P. Kersey,et al.  Integrative analysis of large scale transcriptome data draws a comprehensive landscape of Phaeodactylum tricornutum genome and evolutionary origin of diatoms , 2018, Scientific Reports.

[2]  Minoru Kanehisa,et al.  KEGG: new perspectives on genomes, pathways, diseases and drugs , 2016, Nucleic Acids Res..

[3]  Daniel J. Gaffney,et al.  A survey of best practices for RNA-seq data analysis , 2016, Genome Biology.

[4]  Minoru Kanehisa,et al.  KEGG as a reference resource for gene and protein annotation , 2015, Nucleic Acids Res..

[5]  W. Vyverman,et al.  Identification of the meiotic toolkit in diatoms and exploration of meiosis-specific SPO11 and RAD51 homologs in the sexual species Pseudo-nitzschia multistriata and Seminavis robusta , 2015, BMC Genomics.

[6]  P. Lerouge,et al.  Diatom-Specific Oligosaccharide and Polysaccharide Structures Help to Unravel Biosynthetic Capabilities in Diatoms , 2015, Marine drugs.

[7]  L. David,et al.  Cotranslational stabilization of Sec62/63 within the ER Sec61 translocon is controlled by distinct substrate-driven translocation events. , 2015, Molecular cell.

[8]  N. Davidovich,et al.  Reproductive properties of diatoms significant for their cultivation and biotechnology , 2015, Russian Journal of Plant Physiology.

[9]  D. Xia,et al.  Sec22 Regulates Endoplasmic Reticulum Morphology but Not Autophagy and Is Required for Eye Development in Drosophila , 2015, The Journal of Biological Chemistry.

[10]  W. Huber,et al.  Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2 , 2014, Genome Biology.

[11]  A. Nesvizhskii.  Proteogenomics: concepts, applications and computational strategies , 2014, Nature Methods.

[12]  A. Falciatore,et al.  The diversity of small non-coding RNAs in the diatom Phaeodactylum tricornutum , 2014, BMC Genomics.

[13]  Paul Theodor Pyl,et al.  HTSeq—a Python framework to work with high-throughput sequencing data , 2014, bioRxiv.

[14]  Liyan He,et al.  A Rare Phaeodactylum tricornutum Cruciform Morphotype: Culture Conditions, Transformation and Unique Fatty Acid Characteristics , 2014, PloS one.

[15]  C. Thermes,et al.  Library preparation methods for next-generation sequencing: tone down the bias. , 2014, Experimental cell research.

[16]  Guangce Wang,et al.  Silicon enhances the growth of Phaeodactylum tricornutum Bohlin under green light and low temperature , 2014, Scientific Reports.

[17]  A. Chiovitti,et al.  Characterization of the extracellular matrix of Phaeodactylum tricornutum (Bacillariophyceae): structure, composition, and adhesive characteristics , 2013, Journal of phycology.

[18]  Weijun Luo,et al.  Pathview: an R/Bioconductor package for pathway-based data integration and visualization , 2013, Bioinform..

[19]  Yuanfang Guan,et al.  Molecular and cellular mechanisms of neutral lipid accumulation in diatom following nitrogen deprivation , 2013, Biotechnology for Biofuels.

[20]  Baohua Zhu,et al.  Nuclear transition between the conjunction cells of Phaeodactylum tricornutum Bohlin (Bacillariophyta) , 2012, Journal of Ocean University of China.

[21]  R. Carlson,et al.  Potential role of multiple carbon fixation pathways during lipid accumulation in Phaeodactylum tricornutum , 2012, Biotechnology for Biofuels.

[22]  Steven L Salzberg,et al.  Fast gapped-read alignment with Bowtie 2 , 2012, Nature Methods.

[23]  C. Bowler,et al.  Chloroplast-mitochondria cross-talk in diatoms. , 2012, Journal of experimental botany.

[24]  Trina M. Norden-Krichmar,et al.  Characterization of the Small RNA Transcriptome of the Diatom, Thalassiosira pseudonana , 2011, PloS one.

[25]  C. Bowler,et al.  Physiological and molecular evidence that environmental changes elicit morphological interconversion in the model diatom Phaeodactylum tricornutum. , 2011, Protist.

[26]  Guangce Wang,et al.  Identification and characterization of microRNAs from Phaeodactylum tricornutum by high-throughput sequencing and bioinformatics analysis , 2011, BMC Genomics.

[27]  F. Brun,et al.  Monitoring the long-term stability of pelagic morphotypes in the model diatom Phaeodactylum tricornutum , 2011 .

[28]  Yan Li,et al.  Venom gland transcriptomes of two elapid snakes (Bungarus multicinctus and Naja atra) and evolution of toxin genes , 2011, BMC Genomics.

[29]  P. Lerouge,et al.  N-Glycans of Phaeodactylum tricornutum Diatom and Functional Characterization of Its N-Acetylglucosaminyltransferase I Enzyme* , 2010, The Journal of Biological Chemistry.

[30]  Mark C. Field,et al.  Cellular and Molecular Life Sciences REVIEW , 2022 .

[31]  C. Bowler,et al.  Oceanographic and biogeochemical insights from diatom genomes. , 2010, Annual review of marine science.

[32]  J. Weissenbach,et al.  Digital expression profiling of novel diatom transcripts provides insight into their biological functions , 2010, Genome Biology.

[33]  C. Bowler,et al.  Potential impact of stress activated retrotransposons on genome evolution in a marine diatom , 2009, BMC Genomics.

[34]  William Nicoll M.A. D.Sc..  I.—A contribution towards a knowledge of the Entozoa of British Marine Fishes.—Part II , 2009 .

[35]  Debashish Bhattacharya,et al.  Genomic Footprints of a Cryptic Plastid Endosymbiosis in Diatoms , 2009, Science.

[36]  E. Virginia Armbrust,et al.  The life of diatoms in the world's oceans , 2009, Nature.

[37]  V. Martin‐Jézéquel,et al.  Insights into the polymorphism of the diatom Phaeodactylum tricornutum Bohlin , 2009 .

[38]  Stéphane Douady,et al.  Plasticity and robustness of pattern formation in the model diatom Phaeodactylum tricornutum. , 2009, The New phytologist.

[39]  Lior Pachter,et al.  Sequence Analysis , 2020, Definitions.

[40]  Uma Maheswari,et al.  Update of the Diatom EST Database: a new tool for digital transcriptomics , 2008, Nucleic Acids Res..

[41]  Cole Trapnell,et al.  Ultrafast and memory-efficient alignment of short DNA sequences to the human genome , 2009, Genome Biology.

[42]  Jeffrey L. Brodsky,et al.  One step at a time: endoplasmic reticulum-associated degradation , 2008, Nature Reviews Molecular Cell Biology.

[43]  Leszek Rychlewski,et al.  The Phaeodactylum genome reveals the evolutionary history of diatom genomes , 2008, Nature.

[44]  J. Palmer,et al.  Horizontal gene transfer in eukaryotic evolution , 2008, Nature Reviews Genetics.

[45]  F. Ojeda,et al.  Phenotypic response of the diatom Phaeodactylum tricornutum Bohlin to experimental changes in the inorganic carbon system , 2008 .

[46]  C. Bowler,et al.  Genetic and phenotypic characterization of Phaeodactylum tricornutum (Bacillariophyceae) accessions 1 , 2007 .

[47]  G. Underwood,et al.  EXTRACELLULAR MATRIX ASSEMBLY IN DIATOMS (BACILLARIOPHYCEAE). V. ENVIRONMENTAL EFFECTS ON POLYSACCHARIDE SYNTHESIS IN THE MODEL DIATOM, PHAEODACTYLUM TRICORNUTUM 1 , 2006 .

[48]  A. Bacic,et al.  VARIATIONS IN THE SUBSTITUTED 3‐LINKED MANNANS CLOSELY ASSOCIATED WITH THE SILICIFIED WALLS OF DIATOMS 1 , 2005 .

[49]  Juan Miguel García-Gómez,et al.  BIOINFORMATICS APPLICATIONS NOTE Sequence analysis Manipulation of FASTQ data with Galaxy , 2005 .

[50]  C. Bowler,et al.  Comparative Genomics of the Pennate Diatom Phaeodactylum tricornutum1[w] , 2005, Plant Physiology.

[51]  Nicholas H. Putnam,et al.  The Genome of the Diatom Thalassiosira Pseudonana: Ecology, Evolution, and Metabolism , 2004, Science.

[52]  Claus Lindbjerg Andersen,et al.  Normalization of Real-Time Quantitative Reverse Transcription-PCR Data: A Model-Based Variance Estimation Approach to Identify Genes Suited for Normalization, Applied to Bladder and Colon Cancer Data Sets , 2004, Cancer Research.

[53]  R. Scheller,et al.  Syntaxin-6 SNARE involvement in secretory and endocytic pathways of cultured pancreatic beta-cells. , 2004, Molecular biology of the cell.

[54]  D. Mann,et al.  Experimental studies on sexual reproduction in diatoms. , 2004, International review of cytology.

[55]  H. Riezman,et al.  The ER v-SNAREs are required for GPI-anchored protein sorting from other secretory proteins upon exit from the ER , 2003, The Journal of cell biology.

[56]  Charles Barlowe,et al.  Analysis of Sec22p in endoplasmic reticulum/Golgi transport reveals cellular redundancy in SNARE protein function. , 2002, Molecular biology of the cell.

[57]  A. Ciechanover,et al.  The ubiquitin-proteasome proteolytic pathway: destruction for the sake of construction. , 2002, Physiological reviews.

[58]  Bor Luen Tang,et al.  Early/recycling endosomes-to-TGN transport involves two SNARE complexes and a Rab6 isoform , 2002, The Journal of cell biology.

[59]  F. Speleman,et al.  Accurate normalization of real-time quantitative RT-PCR data by geometric averaging of multiple internal control genes , 2002, Genome Biology.

[60]  Thomas D. Schmittgen,et al.  Analysis of relative gene expression data using real-time quantitative PCR and the 2(-Delta Delta C(T)) Method. , 2001, Methods.

[61]  F. Wendler,et al.  Syntaxin 6: The Promiscuous Behaviour of a SNARE Protein , 2001, Traffic.

[62]  D. Studer,et al.  A new approach for cryofixation by high‐pressure freezing , 2001, Journal of microscopy.

[63]  J. Rothman,et al.  Topological restriction of SNARE-dependent membrane fusion , 2000, Nature.

[64]  R. Kraft,et al.  Mammalian Sec61 Is Associated with Sec62 and Sec63* , 2000, The Journal of Biological Chemistry.

[65]  A. Ciechanover,et al.  Ubiquitin‐mediated proteolysis: biological regulation via destruction , 2000, BioEssays : news and reviews in molecular, cellular and developmental biology.

[66]  Susumu Goto,et al.  KEGG: Kyoto Encyclopedia of Genes and Genomes , 2000, Nucleic Acids Res..

[67]  R. Scheller,et al.  SNARE Membrane Trafficking Dynamics In Vivo , 1999, The Journal of cell biology.

[68]  J. Rayner,et al.  A novel SNARE complex implicated in vesicle fusion with the endoplasmic reticulum , 1997, The EMBO journal.

[69]  Y. Benjamini,et al.  Controlling the false discovery rate: a practical and powerful approach to multiple testing , 1995 .

[70]  A. Schmid,et al.  PROTEINACEOUS AND IMMUNOCHEMICAL DISTINCTIONS BETWEEN THE OVAL AND FUSIFORM MORPHOTYPES OF PHAEODACTYLUM TRICORNUTUM (BACILLARIOPHYCEAE) 1 , 1994 .

[71]  J. Johansen.  Morphological variability and cell wall composition of Phaeodactylum tricornutum (Bacillariophyceae) , 1991 .

[72]  David G. Mann,et al.  Diatoms: Biology and Morphology of the Genera , 1990 .

[73]  S. Rushforth,et al.  Occurrence of Phaedactylum tricornutum in the Great Salt Lake, Utah, USA , 1988 .

[74]  M. Borowitzka,et al.  THE POLYMORPHIC DIATOM PHAEODACTYLUM TRICORNUTUM: ULTRASTRUCTURE OF ITS MORPHOTYPES 1, 2 , 1978 .

[75]  R. Lewin,et al.  Observations on Phaeodactylum tricornutum. , 1958, Journal of general microbiology.

[76]  D. P. Wilson.  The Triradiate and other Forms of Nitzschia Closterium (Ehrenberg) Wm. Smith, Forma Minutissima of Allen and Nelson , 1946, Journal of the Marine Biological Association of the United Kingdom.

[77]  H. J. Carter.  I.—A descriptive account of four subspherous sponges, Arabian and British, with general observations , 1869 .

[78]  J. D. Macdonald.  I.—On the structure of the Diatomaceous frustule, and its genetic cycle , 1869 .

[79]  Thomas D. Schmittgen,et al.  Analysis of Relative Gene Expression Data Using Real-Time Quantitative PCR and the 2 2 DD C T Method , 2022 .