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Bioinformatics Biodiversity ACL Choke points Community ecology Benthic microbial communities Biogeochemistry Bloomier filter Coastal environments Protists COI Corallinales Mastophoroideae LSU rDNA Phylogeny Porolithon psbA SSU rDNA Genomics Indexing Abundance distribution Sequences comparison High-throughput sequencing Minimal Perfect Hash Functions Biogeography Brown algae Data structures
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Lucie Bittner CV

Associate Professor at Sorbonne Université
Environmental and Evolutionary Genomics

Co-head of the team Atelier de BioInformatique
Institut de Systématique, Evolution, Biodiversité
Muséum National d’Histoire Naturelle, Paris

 

Deciphering the diversity and evolution of non-model organisms has always attracted me. During my PhD, I studied molecular phylogeny and environmental diversity of macro-algae. During my post-docs, I moved to microbial ecology and studied taxonomical and functional environmental diversity using (meta)omics. I daily use bioinformatics, statistics, numerical ecology, and collaborate with modelers to integrate omics and oceanographic knowledge at the global ecosystem level.

Journal articles33 documents

  • Camille Marchet, Antoine Limasset, Lucie Bittner, Pierre Peterlongo. A resource-frugal probabilistic dictionary and applications in (meta)genomics. Discrete Applied Mathematics, Elsevier, 2020, 92-102 (Volume 274), ⟨10.1016/j.dam.2018.03.035⟩. ⟨hal-01322440⟩
  • Emile Faure, Fabrice Not, Anne-Sophie Benoiston, Karine Labadie, Lucie Bittner, et al.. Mixotrophic protists display contrasted biogeographies in the global ocean. ISME Journal, Nature Publishing Group, 2019, 13 (4), pp.1072-1083. ⟨10.1038/s41396-018-0340-5⟩. ⟨hal-02182433⟩
  • Luigi Caputi, Quentin Carradec, Damien Eveillard, Amos Kirilovsky, Eric Pelletier, et al.. Community‐Level Responses to Iron Availability in Open Ocean Plankton Ecosystems. Global Biogeochemical Cycles, American Geophysical Union, 2019, 3 (33), pp.391-419. ⟨10.1029/2018GB006022⟩. ⟨hal-02074931⟩
  • Eric Lewitus, Lucie Bittner, Shruti Malviya, Chris Bowler, Hélène Morlon. Clade-specific diversification dynamics of marine diatoms since the Jurassic. Nature Ecology & Evolution, Nature, 2018, 2 (11), pp.1715-1723. ⟨10.1038/s41559-018-0691-3⟩. ⟨hal-02408145⟩
  • Flora J. Vincent, Sébastien Colin, Sarah Romac, Eleonora Scalco, Lucie Bittner, et al.. The epibiotic life of the cosmopolitan diatom Fragilariopsis doliolus on heterotrophic ciliates in the open ocean. ISME Journal, Nature Publishing Group, 2018, 12 (4), pp.1094 - 1108. ⟨10.1038/s41396-017-0029-1⟩. ⟨hal-01762501⟩
  • Arnaud Meng, Erwan Corre, Ian Probert, Andres Gutierrez-Rodriguez, Raffaele Siano, et al.. Analysis of the genomic basis of functional diversity in dinoflagellates using a transcriptome-based sequence similarity network.. Molecular Ecology, Wiley, 2018, 27 (10), pp.2365-2380. ⟨10.1111/mec.14579⟩. ⟨hal-02879300⟩
  • Arnaud Meng, Camille Marchet, Erwan Corre, Pierre Peterlongo, Adriana Alberti, et al.. A de novo approach to disentangle partner identity and function in holobiont systems. Microbiome, BioMed Central, 2018, pp.1-35. ⟨10.1101/221424⟩. ⟨hal-01643153v2⟩
  • Paul Tréguer, Chris Bowler, Brivaëla Moriceau, Stephanie Dutkiewicz, Marion Gehlen, et al.. Influence of diatom diversity on the ocean biological carbon pump. Nature Geoscience, Nature Publishing Group, 2018, 11 (1), pp.27-37. ⟨10.1038/s41561-017-0028-x⟩. ⟨hal-01667978⟩
  • Camille Marchet, Lolita Lecompte, Antoine Limasset, Lucie Bittner, Pierre Peterlongo. A resource-frugal probabilistic dictionary and applications in bioinformatics. Discrete Applied Mathematics, Elsevier, 2018, pp.1-11. ⟨10.1016/j.dam.2018.03.035⟩. ⟨hal-01873312⟩
  • Anne-Sophie Benoiston, Federico Ibarbalz, Lucie Bittner, Lionel Guidi, Oliver Jahn, et al.. The evolution of diatoms and their biogeochemical functions. Philosophical Transactions of the Royal Society B: Biological Sciences, Royal Society, The, 2017, 372 (1728), pp.20160397. ⟨10.1098/rstb.2016.0397⟩. ⟨hal-02921882⟩
  • Guillem Chust, Meike Vogt, Fabio Benedetti, Teofil Nakov, Sébastien Villéger, et al.. Mare Incognitum: A Glimpse into Future Plankton Diversity and Ecology Research. Frontiers in Marine Science, Frontiers Media, 2017, 4, pp.68. ⟨10.3389/fmars.2017.00068⟩. ⟨hal-01545318⟩
  • Hugo Botebol, Gaëlle Lelandais, Christophe Six, Emmanuel Lesuisse, Arnaud Meng, et al.. Acclimation of a low iron adapted Ostreococcus strain to iron limitation through cell biomass lowering. Scientific Reports, Nature Publishing Group, 2017, 7 (1), pp.327. ⟨10.1038/s41598-017-00216-6⟩. ⟨hal-01502140⟩
  • Shruti Malviya, Eleonora Scalco, Stephane Audic, Flora Vincenta, Alaguraj Veluchamy, et al.. Insights into global diatom distribution and diversity in the world's ocean. Proceedings of the National Academy of Sciences of the United States of America , National Academy of Sciences, 2016, 113 (11), pp.E1516-E1525. ⟨10.1073/pnas.1509523113⟩. ⟨hal-01545320⟩
  • Lionel Guidi, Samuel Chaffron, Lucie Bittner, Damien Eveillard, Abdelhalim Larhlimi, et al.. Plankton networks driving carbon export in the oligotrophic ocean. Nature, Nature Publishing Group, 2016, 532, pp.465-470. ⟨10.1038/nature16942⟩. ⟨hal-01275276⟩
  • Dominik Forster, Micah Dunthorn, Fréderic Mahé, John R. Dolan, Stéphane Audic, et al.. Benthic protists: the under-charted majority. FEMS Microbiology Ecology, Wiley-Blackwell, 2016, 92 (8), pp.fiw120. ⟨10.1093/femsec/fiw120⟩. ⟨hal-01383722⟩
  • Dominik Forster, Lucie Bittner, Slim Karkar, Micah Dunthorn, Sarah Romac, et al.. Testing ecological theories with sequence similarity networks: marine ciliates exhibit similar geographic dispersal patterns as multicellular organisms. BMC Biology, BioMed Central, 2015, 13 (1), pp.16. ⟨10.1186/s12915-015-0125-5⟩. ⟨hal-01144173⟩
  • Elianne Sirnaes Egge, Torill Vik Johannessen, Tom Andersen, Wenche Eikrem, Lucie Bittner, et al.. Seasonal diversity and dynamics of haptophytes in the Skagerrak, Norway, explored by high-throughput sequencing. Molecular Ecology, Wiley, 2015, 24 (12), pp.3026-3042. ⟨10.1111/mec.13160⟩. ⟨hal-01545321⟩
  • Noan Le Bescot, Ian Probert, Margaux Carmichael, Julie Poulain, Sarah Romac, et al.. Eukaryotic plankton diversity in the sunlit ocean. Science, American Association for the Advancement of Science, 2015, 348 (6237), pp.1261605. ⟨10.1126/science.1261605⟩. ⟨hal-01253979⟩
  • Gipsi Lima-Mendez, Karoline Faust, Nicolas Henry, Johan Decelle, Sébastien Colin, et al.. Determinants of community structure in the global plankton interactome. Science, American Association for the Advancement of Science, 2015, 348 (6237), pp.1262073. ⟨10.1126/science.1262073⟩. ⟨hal-01234200⟩
  • Emilie Villar, Gregory F. Farrant, Michael Follows, Laurence Garczarek, Sabrina Speich, et al.. Environmental characteristics of Agulhas rings affect interocean plankton transport. Science, American Association for the Advancement of Science, 2015, 348 (6237), pp.1261447 - 1261447. ⟨10.1126/science.1261447⟩. ⟨hal-01893637⟩
  • Ramon Massana, Angélique Gobet, Stéphane Audic, David Bass, Lucie Bittner, et al.. Marine protist diversity in European coastal waters and sediments as revealed by high-throughput sequencing. Environmental Microbiology, Wiley-Blackwell, 2015, 17 (10), pp.4035-4049. ⟨10.1111/1462-2920.12955⟩. ⟨hal-01191731⟩
  • Ramiro Logares, Stéphane Audic, David Bass, Lucie Bittner, Christophe Boutte, et al.. Patterns of Rare and Abundant Marine Microbial Eukaryotes. Current Biology - CB, Elsevier, 2014, 24 (8), pp.813-821. ⟨10.1016/j.cub.2014.02.050⟩. ⟨hal-01149637⟩
  • Laure Guillou, Dipankar Bachar, Stéphane Audic, David Bass, Cédric Berney, et al.. The Protist Ribosomal Reference database (PR2): a catalog of unicellular eukaryote Small Sub-Unit rRNA sequences with curated taxonomy. Nucleic Acids Research, Oxford University Press, 2013, 41 (D1), pp.D597-D604. ⟨10.1093/nar/gks1160⟩. ⟨hal-01253994⟩
  • Lucie Bittner, Angélique Gobet, Stéphane Audic, Sarah Romac, Elianne S Egge, et al.. Diversity patterns of uncultured Haptophytes unravelled by pyrosequencing in Naples Bay.. Molecular Ecology, Wiley, 2013, 22 (1), pp.87-101. ⟨10.1111/mec.12108⟩. ⟨hal-00817857⟩
  • M. Sperling, J. Piontek, G. Gerdts, A. Wichels, H. Schunck, et al.. Effect of elevated CO2 on the dynamics of particle-attached and free-living bacterioplankton communities in an Arctic fjord. Biogeosciences, European Geosciences Union, 2013, 10 (1), pp.181-191. ⟨10.5194/bg-10-181-2013⟩. ⟨hal-01258225⟩
  • Elianne Egge, Lucie Bittner, Tom Andersen, Stéphane Audic, Colomban de Vargas, et al.. 454 Pyrosequencing to Describe Microbial Eukaryotic Community Composition, Diversity and Relative Abundance: A Test for Marine Haptophytes. PLoS ONE, Public Library of Science, 2013, 8 (9), pp.e74371. ⟨10.1371/journal.pone.0074371⟩. ⟨hal-01258226⟩
  • A. -S. Roy, S. M. Gibbons, H. Schunck, S. Owens, J. G. Caporaso, et al.. Ocean acidification shows negligible impacts on high-latitude bacterial community structure in coastal pelagic mesocosms. Biogeosciences, European Geosciences Union, 2013, 10 (1), pp.555-566. ⟨10.5194/bg-10-555-2013⟩. ⟨hal-01258227⟩
  • Thomas Silberfeld, Lucie Bittner, Cindy Fernandez-Garcia, Corinne Cruaud, Florence Rousseau, et al.. Species Diversity, Phylogeny and Large Scale Biogeographic Patterns of the Genus Padina (Phaeophyceae, Dictyotales). Journal of Phycology, Wiley, 2013, 49 (1), pp.130-142. ⟨10.1111/jpy.12027⟩. ⟨hal-01545323⟩
  • Johan Decelle, Ian Probert, Lucie Bittner, Yves Desdevises, Sébastien Colin, et al.. An original mode of symbiosis in open ocean plankton. Proceedings of the National Academy of Sciences of the United States of America , National Academy of Sciences, 2012, 109 (44), pp.18000-18005. ⟨10.1073/pnas.1212303109⟩. ⟨hal-01258241⟩
  • Lucie Bittner, Claude Payri, Gavin Maneveldt, Arnaud Couloux, Corinne Cruaud, et al.. Evolutionary history of the Corallinales (Corallinophycidae, Rhodophyta) inferred from nuclear, plastidial and mitochondrial genomes. Molecular Phylogenetics and Evolution, Elsevier, 2011, 61 (3), pp.697-713. ⟨10.1016/j.ympev.2011.07.019⟩. ⟨mnhn-02498527⟩
  • Lucie Bittner, Sébastien Halary, Claude Payri, Corinne Cruaud, Bruno de Reviers, et al.. Some considerations for analyzing biodiversity using integrative metagenomics and gene networks. Biology Direct, BioMed Central, 2010, 5 (5), pp.47. ⟨10.1186/1745-6150-5-47⟩. ⟨hal-02922363⟩
  • Line Le Gall, Claude Payri, Lucie Bittner, Gary Saunders. Multigene phylogenetic analyses support recognition of the Sporolithales ord. nov.. Molecular Phylogenetics and Evolution, Elsevier, 2010, 54 (1), pp.302-305. ⟨10.1016/j.ympev.2009.05.026⟩. ⟨mnhn-02498544⟩
  • Lucie Bittner, Claude Payri, A. Couloux, C. Cruaux, Bruno de Reviers, et al.. Molecular phylogeny of the Dictyotales and their position within the phaeophycean, based on nuclear, plastid and mitochondrial DNA sequence data.. Molecular Phylogenetics and Evolution, Elsevier, 2008, 46, pp.211-226. ⟨hal-00417514⟩

Conference papers4 documents

  • Arnaud Meng, Erwan Corre, Pierre Peterlongo, Camille Marchet, Adriana Alberti, et al.. A transcriptomic approach to study marine plankton holobionts . International Conference on Holobionts, Apr 2017, Paris, France. ⟨hal-01575069⟩
  • Camille Marchet, Antoine Limasset, Lucie Bittner, Pierre Peterlongo. A resource-frugal probabilistic dictionary and applications in (meta)genomics. Prageu Stringology Conference , Aug 2016, Prague, Czech Republic. ⟨hal-01386744⟩
  • Damien Eveillard, Lionel Guidi, Lucie Bittner, Samuel Chaffron, Jeroen Raes, et al.. Revealing and analyzing networks of marine microbial ecosystems. Conférence Jacques Monod - Marine Ecosystems Biology, 2015, Roscoff, France. ⟨hal-01176727⟩
  • Bruno de Reviers, Lucie Bittner, Thomas Silberfeld, Florence Rousseau. Advances in brown algal systematics.. 103° Congrès de la société botanique italienne, 17-19 sept, Sep 2008, Reggio Calabria, Italy. ⟨hal-00420179⟩

Poster communications1 document

  • Antoine Limasset, Camille Marchet, Pierre Peterlongo, Lucie Bittner. Minimal perfect hash functions in large scale bioinformatics Problem. JOBIM 2016, Jun 2016, Lyon, France. ⟨hal-01341718⟩

Book sections4 documents

  • Lucie Bittner. L’expédition Tara Océans, un rêve de marin, de science et de partage. Editions CNRS. Sciences. Bâtir de nouveaux mondes., 2019, 978-2-271-12626-9. ⟨hal-02922440⟩
  • Lucie Bittner, Lionel Guidi, Samuel Chaffron, Damien Eveillard. Les microbiomes de l'océan : une démarche à haut débit pour une compréhension globale et systémique. Laurent Palka. Microbiodiversité : un nouveau regard, 161 - 185, editions matériologiques, 2018. ⟨hal-01996304⟩
  • Chris Bowler, Lucie Bittner. Tara Océans et son flot de données : vers une compréhension multi-échelle de l'écosystème océan. Editions CNRS. Les Big Data à découvert, pp.238-239, 2017, 978-2-271-11464-8. ⟨hal-02922390⟩
  • Lucie Bittner, Chris Bowler. Tara Oceans : de l’odyssée à l’étude systémique de l’océan. Editions CNRS. L’Océan à découvert, pp.114- 115, 2017, 978-2-271-11652-9. ⟨hal-02922413⟩