Simon Dittami

Documents

Publications

	The Rhodoexplorer Platform for Red Algal Genomics and Whole-Genome Assemblies for Several Gracilaria Species Agnieszka P Lipinska , Stacy A Krueger-Hadfield , Olivier Godfroy , Simon M Dittami , Lígia Ayres-Ostrock Genome Biology and Evolution, 2023, 15 (7), pp.evad124. ⟨10.1093/gbe/evad124⟩ Journal articles hal-04190579v1
	The Saccharina latissima microbiome: Effects of region, season, and physiology Bertille Burgunter-Delamare , Sylvie Rousvoal , Erwan Legeay , Gwenn Tanguy , Stein Fredriksen Frontiers in Microbiology, 2023, 13, ⟨10.3389/fmicb.2022.1050939⟩ Journal articles hal-03951625v1
	Maintaining beneficial alga-associated bacterial communities under heat stress: Insights from controlled co-culture experiments using antibiotic-resistant bacterial strains Elham Karimi , Simon Dittami FEMS Microbiology Ecology, 2023, 99 (12), pp.fiad130. ⟨10.1093/femsec/fiad130⟩ Journal articles hal-04254487v1
	Insights into the potential for mutualistic and harmful host‐microbe interactions affecting brown alga freshwater acclimation Hetty Kleinjan , Clémence Frioux , Gianmaria Califano , Méziane Aite , Enora Fremy Molecular Ecology, In press, 32 (3), pp.703-723. ⟨10.1111/mec.16766⟩ Journal articles hal-03868898v1
	Inferring and comparing metabolism across heterogeneous sets of annotated genomes using AuCoMe Arnaud Belcour , Jeanne Got , Méziane Aite , Ludovic Delage , Jonas Collén Genome Research, 2023, 33, pp.972 - 987. ⟨10.1101/gr.277056.122⟩ Journal articles hal-04192851v3
	Effects of sampling and storage procedures on 16S rDNA amplicon sequencing results of kelp microbiomes Bertille Burgunter-Delamare , Gwenn Tanguy , Erwan Legeay , Catherine Boyen , Simon M. Dittami Marine Genomics, 2022, 63, pp.100944. ⟨10.1016/j.margen.2022.100944⟩ Journal articles hal-03618853v1
	Sharing Vitamin B12 between Bacteria and Microalgae Does Not Systematically Occur: Case Study of the Haptophyte Tisochrysis lutea Charlotte Nef , Simon M. Dittami , Raymond Kaas , Enora Briand , Cyril Noël Microorganisms, 2022, 10, ⟨10.3390/microorganisms10071337⟩ Journal articles hal-03845772v1
	Effect of essential oil-and iodine treatments on the bacterial microbiota of the brown alga Ectocarpus siliculosus Bertille Burgunter-Delamare , Catherine Boyen , Simon M Dittami Journal of Applied Phycology, 2021, 33, pp.459-470. ⟨10.1007/s10811-020-02286-y⟩ Journal articles hal-03030933v1
	Semi-Quantitative Targeted Gas Chromatography-Mass Spectrometry Profiling Supports a Late Side-Chain Reductase Cycloartenol-to-Cholesterol Biosynthesis Pathway in Brown Algae Jean Girard , Goulven Lanneau , Ludovic Delage , Cédric Leroux , Arnaud Belcour Frontiers in Plant Science, 2021, 12, pp.1-10. ⟨10.3389/fpls.2021.648426⟩ Journal articles hal-03222505v1
	Determination of the efficiency of filtration of cultures from microalgae and bacteria using hollow fiber filters J. Robla , J. García-Hierrro , F. J Alguacil , Simon M. Dittami , D. Marie Environmental Science : Water Research and Technology, 2021, 7 (7), pp.1230-1239. ⟨10.1039/D0EW00927J⟩ Journal articles hal-03428933v1
	A community perspective on the concept of marine holobionts: current status, challenges, and future directions Simon M. Dittami , Enrique Arboleda , J.-C. Auguet , Arite Bigalke , Enora Briand PeerJ, 2021, 9, pp.e10911. ⟨10.7717/peerj.10911⟩ Journal articles hal-03166872v2
	Robustness analysis of metabolic predictions in algal microbial communities based on different annotation pipelines Elham Karimi , Enora Geslain , Arnaud Belcour , Clémence Frioux , Méziane Aite PeerJ, 2021, 9, pp.1-24. ⟨10.7717/peerj.11344⟩ Journal articles hal-03223662v1
	The genome of Ectocarpus subulatus – A highly stress-tolerant brown alga Simon M. Dittami , Erwan Corre , Loraine Brillet-Guéguen , Agnieszka Lipinska , Noé Pontoizeau Marine Genomics, 2020, 52, pp.100740. ⟨10.1016/j.margen.2020.100740⟩ Journal articles hal-02866117v1
	Using automated reasoning to explore the metabolism of unconventional organisms: a first step to explore host–microbial interactions Clémence Frioux , Simon Dittami , Anne Siegel Biochemical Society Transactions, 2020, 48 (3), pp.901-913. ⟨10.1042/BST20190667⟩ Journal articles hal-02569935v1
	Metabolic Complementarity Between a Brown Alga and Associated Cultivable Bacteria Provide Indications of Beneficial Interactions Bertille Burgunter-Delamare , Hetty Kleinjan , Clémence Frioux , Enora Fremy , Margot Wagner Frontiers in Marine Science, 2020, 7, pp.1-11. ⟨10.3389/fmars.2020.00085⟩ Journal articles hal-02866101v2
	Revisiting Australian Ectocarpus subulatus (Phaeophyceae) from the Hopkins River: distribution, abiotic environment, and associated microbiota Simon M. Dittami , Akira F Peters , Bezhin Rosko , John West , Thierry Cariou Journal of Phycology, 2020, 56 (3), pp.719-729 Journal articles hal-02340942v2
	Genome Sequences of 72 Bacterial Strains Isolated from Ectocarpus subulatus: A Resource for Algal Microbiology Elham Karimi , Enora Geslain , Hetty Kleinjan , Gwenn Tanguy , Erwan Legeay Genome Biology and Evolution, 2020, 12 (1), pp.3647-3655. ⟨10.1093/gbe/evz278⟩ Journal articles hal-02553731v1
	Inferring Biochemical Reactions and Metabolite Structures to Understand Metabolic Pathway Drift Arnaud Belcour , Jean Girard , Méziane Aite , Ludovic Delage , Camille Trottier iScience, 2020, 23 (2), pp.100849. ⟨10.1016/j.isci.2020.100849⟩ Journal articles hal-01943880v2
	Evaluation of a new primer combination to minimize plastid contamination in 16S rDNA metabarcoding analyses of alga‐associated bacterial communities François Thomas , Simon Dittami , Maéva Brunet , Nolwen Le Duff , Gwenn Tanguy Environmental Microbiology Reports, 2019, 12 (1), pp.30-37. ⟨10.1111/1758-2229.12806⟩ Journal articles hal-02404303v1
	Genome–Scale Metabolic Networks Shed Light on the Carotenoid Biosynthesis Pathway in the Brown Algae Saccharina japonica and Cladosiphon okamuranus Delphine Nègre , Méziane Aite , Arnaud Belcour , Clémence Frioux , Loraine Brillet-Guéguen Antioxidants , 2019, 8 (11), pp.564. ⟨10.3390/antiox8110564⟩ Journal articles hal-02395080v1
	Seasonal and algal diet-driven patterns of the digestive microbiota of the European abalone Haliotis tuberculata, a generalist marine herbivore Angélique Gobet , Laëtitia Mest , Morgan Perennou , Simon M. Dittami , Claire Caralp Microbiome, 2018, 6, pp.60. ⟨10.1186/s40168-018-0430-7⟩ Journal articles hal-01774836v1
	Evolution and Expansion of the Prokaryote-Like Lipoxygenase Family in the Brown Alga Saccharina japonica Linhong Teng , Wentao Han , Xiao Fan , Dong Xu , Xiaowen Zhang Frontiers in Plant Science, 2017, 8, pp.2018. ⟨10.3389/fpls.2017.02018⟩ Journal articles hal-03940964v1
	Insights into the red algae and eukaryotic evolution from the genome of Porphyra umbilicalis (Bangiophyceae, Rhodophyta) Susan Brawley , Nicolas Blouin , Elizabeth Ficko-Blean , Glen Wheeler , Martin Lohr Proceedings of the National Academy of Sciences of the United States of America, 2017, 114 (31), pp.E6361-E6370. ⟨10.1073/pnas.1703088114⟩ Journal articles hal-02950557v1
	Detection of bacterial contaminants and hybrid sequences in the genome of the kelp Saccharina japonica using Taxoblast Simon Dittami , Erwan Corre PeerJ, 2017, 5, pp.e4073. ⟨10.7717/peerj.4073⟩ Journal articles hal-01654700v1
	Exploring the Cultivable Ectocarpus Microbiome Hetty Kleinjan , Christian Jeanthon , Catherine Boyen , Simon M. Dittami Frontiers in Microbiology, 2017, 8, pp.2456. ⟨10.3389/fmicb.2017.02456⟩ Journal articles hal-03940941v1
	Transitions between marine and freshwater environments provide new clues about the origins of multicellular plants and algae Simon M Dittami , Svenja Heesch , Jeanine L. Olsen , Jonas Collén Journal of Phycology, 2017, ⟨10.1111/jpy.12547⟩ Journal articles hal-01528781v1
	Meneco, a Topology-Based Gap-Filling Tool Applicable to Degraded Genome-Wide Metabolic Networks Sylvain Prigent , Clémence Frioux , Simon M Dittami , Sven Thiele , Abdelhalim Larhlimi PLoS Computational Biology, 2017, 13 (1), pp.32. ⟨10.1371/journal.pcbi.1005276⟩ Journal articles hal-01449100v1
	The genome of the seagrass Zostera marina reveals angiosperm adaptation to the sea Jeanine L. Olsen , Pierre Rouzé , Bram Verhelst , Yao-Cheng Y.-C. Lin , Till Bayer Nature, 2016, 530 (7590), pp.331-335. ⟨10.1038/nature16548⟩ Journal articles hal-01289099v1
	A Haploid System of Sex Determination in the Brown Alga Ectocarpus sp. Sophia S. Ahmed , J. Mark Cock , Eugenie Pessia , Remy Luthringer , Alexandre Cormier Current Biology - CB, 2014, 24 (17), pp.1945-1957. ⟨10.1016/j.cub.2014.07.042⟩ Journal articles hal-01132642v1
	The genome-scale metabolic network of Ectocarpus siliculosus (EctoGEM): a resource to study brown algal physiology and beyond. Sylvain Prigent , Guillaume Collet , Simon M Dittami , Ludovic Delage , Floriane Ethis de Corny The Plant Journal, 2014, 80 (2), pp.367-381. ⟨10.1111/tpj.12627⟩ Journal articles hal-01057153v1
	Transcriptomic and metabolomic analysis of copper stress acclimation in Ectocarpus siliculosus highlights signaling and tolerance mechanisms in brown algae Andrés Ritter , Simon M Dittami , Sophie Goulitquer , Juan A Correa , Catherine Boyen BMC Plant Biology, 2014, 14, pp.116. ⟨10.1186/1471-2229-14-116⟩ Journal articles hal-01311060v1
	Genome and metabolic network of "Candidatus Phaeomarinobacter ectocarpi" Ec32, a new candidate genus of Alphaproteobacteria frequently associated with brown algae Simon M Dittami , Tristan Barbeyron , Catherine Boyen , Jeanne Cambefort , Guillaume Collet Frontiers in Genetics, 2014, 5, pp.241. ⟨10.3389/fgene.2014.00241⟩ Journal articles hal-01079739v1
	A metabolic approach to study algal-bacterial interactions in changing environments. Simon M. Dittami , Damien Eveillard , Thierry Tonon Molecular Ecology, 2014, 23 (7), pp.1656-60. ⟨10.1111/mec.12670⟩ Journal articles hal-00936195v1
	Transcriptomic and metabolomic analysis of copper stress acclimation in Ectocarpus siliculosus highlights signaling and tolerance mechanisms in brown algae. Andrés Ritter , Simon M Dittami , Sophie Goulitquer , Juan A Correa , Catherine Boyen BMC Plant Biology, 2013, 14, pp.116 Journal articles hal-01113858v1
	Genome structure and metabolic features in the red seaweed Chondrus crispus shed light on evolution of the Archaeplastida. Jonas Collén , Betina Porcel , Wilfrid Carré , Steven G Ball , Cristian Chaparro Proceedings of the National Academy of Sciences of the United States of America, 2013, 110 (13), pp.5247-52. ⟨10.1073/pnas.1221259110⟩ Journal articles hal-01073830v1
	Genomes of extremophile crucifers: new platforms for comparative genomics and beyond. Simon M Dittami , Thierry Tonon Genome Biology, 2012, 13 (8), pp.166. ⟨10.1186/gb-2012-13-8-166⟩ Journal articles hal-00925419v1
	Towards deciphering dynamic changes and evolutionary mechanisms involved in the adaptation to low salinities in Ectocarpus (brown algae) Simon M. Dittami , Antoine Gravot , Sophie Goulitquer , Sylvie Rousvoal , Akira F. Peters The Plant Journal, 2012, 71 (3), pp.366 - 377. ⟨10.1111/j.1365-313X.2012.04982.x⟩ Journal articles hal-01208656v1
	The Ectocarpus Genome and Brown Algal Genomics The Ectocarpus Genome Consortium J. Mark Cock , Lieven Sterck , Sophia Ahmed , Andrew E. Allen , Grigoris Amoutzias Advances in Botanical Research, 2012, 64, pp.141 - 184. ⟨10.1016/B978-0-12-391499-6.00005-0⟩ Journal articles hal-02649287v1
	Integrative analysis of metabolite and transcript abundance during the short-term response to saline and oxidative stress in the brown alga Ectocarpus siliculosus. Simon M. Dittami , Antoine Gravot , David Renault , Sophie Goulitquer , Anja Eggert Plant, Cell and Environment, 2011, 34 (4), pp.629-642. ⟨10.1111/j.1365-3040.2010.02268.x⟩ Journal articles hal-00597335v1
	Microarray estimation of genomic inter-strain variability in the genus Ectocarpus (Phaeophyceae) Simon M Dittami , Caroline Proux , Sylvie Rousvoal , Akira F Peters , J Mark Cock BMC Molecular Biology, 2011, 12, pp.2. ⟨10.1186/1471-2199-12-2⟩ Journal articles hal-00925432v1
	Diurnal oscillations of metabolite abundances and gene analysis provide new insights into central metabolic processes of the brown alga Ectocarpus siliculosus Antoine Gravot , Simon Dittami , Sylvie Rousvoal , Raphaël Lugan , Anja Eggert New Phytologist, 2010, 188 (4), pp.98-110. ⟨10.1111/j.1469-8137.2010.03400.x⟩ Journal articles hal-02661518v1
	The $Ectocarpus$ genome and the independent evolution of multicellularity in brown algae J. Mark Cock , Lieven Sterck , Pierre Rouzé , Delphine Scornet , Andrew E. Allen Nature, 2010, 465 (7298), pp.617-621. ⟨10.1038/nature09016⟩ Journal articles cea-00906990v1
	Global expression analysis of the brown alga Ectocarpus siliculosus (Phaeophyceae) reveals large-scale reprogramming of the transcriptome in response to abiotic stress Simon M Dittami , Delphine Scornet , Jean-Louis Petit , Béatrice Segurens , Corinne da Silva Genome Biology, 2009, 10, pp.R66. ⟨10.1186/gb-2009-10-6-r66⟩ Journal articles hal-01806423v1
	Normalisation genes for expression analyses in the brown alga model Ectocarpus siliculosus Aude Le Bail , Simon Dittami , Pierre-Olivier de Franco , Sylvie Rousvoal , J. Mark Cock BMC Molecular Biology, 2008, 9, pp.75. ⟨10.1186/1471-2199-9-75⟩ Journal articles hal-01806432v1

	Toward the study of metabolic functions in algal holobionts Claire Lippold , Camille Trottier , Clémence Frioux , Marie Chevallier , Simon M Dittami 4ème Colloque de Génomique Environnementale, Sep 2017, Marseille, France Conference papers hal-01576484v1

	The Saccharina latissima microbiome: algal tissue matters more than region, season, and physiology Bertille Burgunter-Delamare , Sylvie Rousvoal , Erwan Legeay , Gwenn Tanguy , Stein Fredriksen 2022 Preprints, Working Papers, ... hal-03705545v1
	Changing microbial activities during low salinity acclimation in the brown alga Ectocarpus subulatus Hetty Kleinjan , Gianmaria Caliafano , Méziane Aite , Enora Fremy , Clémence Frioux 2021 Preprints, Working Papers, ... hal-03429533v1
	The genome of Ectocarpus subulatus -a highly stress-tolerant brown alga Simon M. Dittami , Erwan Corre , Loraine Brillet-Guéguen , Agnieszka Lipinska , Méziane Aite 2019 Preprints, Working Papers, ... hal-02333021v1

	Abiotic stress response in Ectocarpus siliculosis : a global approach Simon M. Dittami Genomics [q-bio.GN]. Rennes 1, 2009. English. ⟨NNT : ⟩ Theses tel-01110364v1

	Metabolic interactions between algae and bacteria in changing conditions Simon M. Dittami Biodiversity and Ecology. Sorbonne Université, 2022 Habilitation à diriger des recherches tel-04093436v1

Simon Dittami

Publications

The Rhodoexplorer Platform for Red Algal Genomics and Whole-Genome Assemblies for Several Gracilaria Species

The Saccharina latissima microbiome: Effects of region, season, and physiology

Maintaining beneficial alga-associated bacterial communities under heat stress: Insights from controlled co-culture experiments using antibiotic-resistant bacterial strains

Insights into the potential for mutualistic and harmful host‐microbe interactions affecting brown alga freshwater acclimation

Inferring and comparing metabolism across heterogeneous sets of annotated genomes using AuCoMe

Effects of sampling and storage procedures on 16S rDNA amplicon sequencing results of kelp microbiomes

Sharing Vitamin B12 between Bacteria and Microalgae Does Not Systematically Occur: Case Study of the Haptophyte Tisochrysis lutea

Effect of essential oil-and iodine treatments on the bacterial microbiota of the brown alga Ectocarpus siliculosus

Semi-Quantitative Targeted Gas Chromatography-Mass Spectrometry Profiling Supports a Late Side-Chain Reductase Cycloartenol-to-Cholesterol Biosynthesis Pathway in Brown Algae

Determination of the efficiency of filtration of cultures from microalgae and bacteria using hollow fiber filters

A community perspective on the concept of marine holobionts: current status, challenges, and future directions

Robustness analysis of metabolic predictions in algal microbial communities based on different annotation pipelines

The genome of Ectocarpus subulatus – A highly stress-tolerant brown alga

Using automated reasoning to explore the metabolism of unconventional organisms: a first step to explore host–microbial interactions

Metabolic Complementarity Between a Brown Alga and Associated Cultivable Bacteria Provide Indications of Beneficial Interactions

Revisiting Australian Ectocarpus subulatus (Phaeophyceae) from the Hopkins River: distribution, abiotic environment, and associated microbiota

Genome Sequences of 72 Bacterial Strains Isolated from Ectocarpus subulatus: A Resource for Algal Microbiology

Inferring Biochemical Reactions and Metabolite Structures to Understand Metabolic Pathway Drift

Evaluation of a new primer combination to minimize plastid contamination in 16S rDNA metabarcoding analyses of alga‐associated bacterial communities

Genome–Scale Metabolic Networks Shed Light on the Carotenoid Biosynthesis Pathway in the Brown Algae Saccharina japonica and Cladosiphon okamuranus

Seasonal and algal diet-driven patterns of the digestive microbiota of the European abalone Haliotis tuberculata, a generalist marine herbivore

Evolution and Expansion of the Prokaryote-Like Lipoxygenase Family in the Brown Alga Saccharina japonica

Insights into the red algae and eukaryotic evolution from the genome of Porphyra umbilicalis (Bangiophyceae, Rhodophyta)

Detection of bacterial contaminants and hybrid sequences in the genome of the kelp Saccharina japonica using Taxoblast

Exploring the Cultivable Ectocarpus Microbiome

Transitions between marine and freshwater environments provide new clues about the origins of multicellular plants and algae

Meneco, a Topology-Based Gap-Filling Tool Applicable to Degraded Genome-Wide Metabolic Networks

The genome of the seagrass Zostera marina reveals angiosperm adaptation to the sea

A Haploid System of Sex Determination in the Brown Alga Ectocarpus sp.

The genome-scale metabolic network of Ectocarpus siliculosus (EctoGEM): a resource to study brown algal physiology and beyond.

Transcriptomic and metabolomic analysis of copper stress acclimation in Ectocarpus siliculosus highlights signaling and tolerance mechanisms in brown algae

Genome and metabolic network of "Candidatus Phaeomarinobacter ectocarpi" Ec32, a new candidate genus of Alphaproteobacteria frequently associated with brown algae

A metabolic approach to study algal-bacterial interactions in changing environments.

Transcriptomic and metabolomic analysis of copper stress acclimation in Ectocarpus siliculosus highlights signaling and tolerance mechanisms in brown algae.

Genome structure and metabolic features in the red seaweed Chondrus crispus shed light on evolution of the Archaeplastida.

Genomes of extremophile crucifers: new platforms for comparative genomics and beyond.

Towards deciphering dynamic changes and evolutionary mechanisms involved in the adaptation to low salinities in Ectocarpus (brown algae)

The Ectocarpus Genome and Brown Algal Genomics The Ectocarpus Genome Consortium

Integrative analysis of metabolite and transcript abundance during the short-term response to saline and oxidative stress in the brown alga Ectocarpus siliculosus.

Microarray estimation of genomic inter-strain variability in the genus Ectocarpus (Phaeophyceae)

Diurnal oscillations of metabolite abundances and gene analysis provide new insights into central metabolic processes of the brown alga Ectocarpus siliculosus

The $Ectocarpus$ genome and the independent evolution of multicellularity in brown algae

Global expression analysis of the brown alga Ectocarpus siliculosus (Phaeophyceae) reveals large-scale reprogramming of the transcriptome in response to abiotic stress

Normalisation genes for expression analyses in the brown alga model Ectocarpus siliculosus

Toward the study of metabolic functions in algal holobionts

The Saccharina latissima microbiome: algal tissue matters more than region, season, and physiology

Changing microbial activities during low salinity acclimation in the brown alga Ectocarpus subulatus

The genome of Ectocarpus subulatus -a highly stress-tolerant brown alga

Abiotic stress response in Ectocarpus siliculosis : a global approach

Metabolic interactions between algae and bacteria in changing conditions