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\n \n 2023\n \n \n (6)\n \n \n

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\n \n\n \n \n \n \n \n \n Pan-Arctic plankton community structure and its global connectivity.\n \n \n \n \n\n\n \n Ibarbalz, F.; Henry, N.; Mahé, F.; Ardyna, M.; Zingone, A.; Scalco, E.; Lovejoy, C.; Lombard, F.; Jaillon, O.; Iudicone, D.; Malviya, S.; Sullivan, M.; Chaffron, S.; Karsenti, E.; Babin, M.; Boss, E.; Wincker, P.; Zinger, L.; de Vargas, C.; Bowler, C.; and Karp-Boss, L.\n\n\n \n\n\n\n Elementa, 11(1). 2023.\n \n\n\n\n
\n\n\n\n \n \n $\"Pan-Arctic$ Paper\n \n \n\n \n \n doi\n \n \n\n \n link\n \n \n\n bibtex\n \n\n \n\n \n \n \n 3 downloads\n \n \n\n \n \n \n \n \n \n \n\n \n \n \n\n\n\n

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@article{ibarbalz_pan-arctic_2023,\n\ttitle = {Pan-{Arctic} plankton community structure and its global connectivity},\n\tvolume = {11},\n\turl = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-85153373692&doi=10.1525%2felementa.2022.00060&partnerID=40&md5=bb16ef3967b61a807bdc6efba1b69c97},\n\tdoi = {10.1525/elementa.2022.00060},\n\tnumber = {1},\n\tjournal = {Elementa},\n\tauthor = {Ibarbalz, F.M. and Henry, N. and Mahé, F. and Ardyna, M. and Zingone, A. and Scalco, E. and Lovejoy, C. and Lombard, F. and Jaillon, O. and Iudicone, D. and Malviya, S. and Sullivan, M.B. and Chaffron, S. and Karsenti, E. and Babin, M. and Boss, E. and Wincker, P. and Zinger, L. and de Vargas, C. and Bowler, C. and Karp-Boss, L.},\n\tyear = {2023},\n}\n\n

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\n \n\n \n \n \n \n \n \n Computing marine plankton connectivity under thermal constraints.\n \n \n \n \n\n\n \n Manral, D.; Iovino, D.; Jaillon, O.; Masina, S.; Sarmento, H.; Iudicone, D.; Amaral-Zettler, L.; and van Sebille, E.\n\n\n \n\n\n\n Frontiers in Marine Science, 10. 2023.\n \n\n\n\n
\n\n\n\n \n \n $\"Computing$ Paper\n \n \n\n \n \n doi\n \n \n\n \n link\n \n \n\n bibtex\n \n\n \n\n \n\n \n \n \n \n \n \n \n\n \n \n \n\n\n\n

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@article{manral_computing_2023,\n\ttitle = {Computing marine plankton connectivity under thermal constraints},\n\tvolume = {10},\n\turl = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-85148282111&doi=10.3389%2ffmars.2023.1066050&partnerID=40&md5=204b591624c3025d7dad34a7e775dc1e},\n\tdoi = {10.3389/fmars.2023.1066050},\n\tjournal = {Frontiers in Marine Science},\n\tauthor = {Manral, D. and Iovino, D. and Jaillon, O. and Masina, S. and Sarmento, H. and Iudicone, D. and Amaral-Zettler, L. and van Sebille, E.},\n\tyear = {2023},\n}\n\n

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\n \n\n \n \n \n \n \n \n Plankton biogeography in the 21st century and impacts of climate change: advances through genomics [Biogéographie du plancton au XXIe siècle et impacts du changement climatique: avancées par la génomique].\n \n \n \n \n\n\n \n Frémont, P.; Gehlen, M.; and Jaillon, O.\n\n\n \n\n\n\n Comptes Rendus - Biologies, 346: 13–24. 2023.\n \n\n\n\n
\n\n\n\n \n \n $\"Plankton$ Paper\n \n \n\n \n \n doi\n \n \n\n \n link\n \n \n\n bibtex\n \n\n \n\n \n\n \n \n \n \n \n \n \n\n \n \n \n\n\n\n

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@article{fremont_plankton_2023,\n\ttitle = {Plankton biogeography in the 21st century and impacts of climate change: advances through genomics [{Biogéographie} du plancton au {XXIe} siècle et impacts du changement climatique: avancées par la génomique]},\n\tvolume = {346},\n\turl = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-85158866976&doi=10.5802%2fcrbiol.107&partnerID=40&md5=ae6dee0a908cb5dc90761ac7039564ae},\n\tdoi = {10.5802/crbiol.107},\n\tjournal = {Comptes Rendus - Biologies},\n\tauthor = {Frémont, P. and Gehlen, M. and Jaillon, O.},\n\tyear = {2023},\n\tpages = {13--24},\n}\n\n

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\n \n\n \n \n \n \n \n \n Mirusviruses link herpesviruses to giant viruses.\n \n \n \n \n\n\n \n Gaïa, M.; Meng, L.; Pelletier, E.; Forterre, P.; Vanni, C.; Fernandez-Guerra, A.; Jaillon, O.; Wincker, P.; Ogata, H.; Krupovic, M.; and Delmont, T. O.\n\n\n \n\n\n\n Nature, 616(7958): 783–789. April 2023.\n Number: 7958 Publisher: Nature Publishing Group\n\n\n\n
\n\n\n\n \n \n $\"Mirusviruses$ Paper\n \n \n\n \n \n doi\n \n \n\n \n link\n \n \n\n bibtex\n \n\n \n \n \n abstract \n \n\n \n\n \n \n \n \n \n \n \n\n \n \n \n \n \n \n \n \n \n \n \n \n \n\n\n\n

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@article{gaia_mirusviruses_2023,\n\ttitle = {Mirusviruses link herpesviruses to giant viruses},\n\tvolume = {616},\n\tcopyright = {2023 The Author(s)},\n\tissn = {1476-4687},\n\turl = {https://www.nature.com/articles/s41586-023-05962-4},\n\tdoi = {10.1038/s41586-023-05962-4},\n\tabstract = {DNA viruses have a major influence on the ecology and evolution of cellular organisms1–4, but their overall diversity and evolutionary trajectories remain elusive5. Here we carried out a phylogeny-guided genome-resolved metagenomic survey of the sunlit oceans and discovered plankton-infecting relatives of herpesviruses that form a putative new phylum dubbed Mirusviricota. The virion morphogenesis module of this large monophyletic clade is typical of viruses from the realm Duplodnaviria6, with multiple components strongly indicating a common ancestry with animal-infecting Herpesvirales. Yet, a substantial fraction of mirusvirus genes, including hallmark transcription machinery genes missing in herpesviruses, are closely related homologues of giant eukaryotic DNA viruses from another viral realm, Varidnaviria. These remarkable chimaeric attributes connecting Mirusviricota to herpesviruses and giant eukaryotic viruses are supported by more than 100 environmental mirusvirus genomes, including a near-complete contiguous genome of 432 kilobases. Moreover, mirusviruses are among the most abundant and active eukaryotic viruses characterized in the sunlit oceans, encoding a diverse array of functions used during the infection of microbial eukaryotes from pole to pole. The prevalence, functional activity, diversification and atypical chimaeric attributes of mirusviruses point to a lasting role of Mirusviricota in the ecology of marine ecosystems and in the evolution of eukaryotic DNA viruses.},\n\tlanguage = {en},\n\tnumber = {7958},\n\turldate = {2023-06-05},\n\tjournal = {Nature},\n\tauthor = {Gaïa, Morgan and Meng, Lingjie and Pelletier, Eric and Forterre, Patrick and Vanni, Chiara and Fernandez-Guerra, Antonio and Jaillon, Olivier and Wincker, Patrick and Ogata, Hiroyuki and Krupovic, Mart and Delmont, Tom O.},\n\tmonth = apr,\n\tyear = {2023},\n\tnote = {Number: 7958\nPublisher: Nature Publishing Group},\n\tkeywords = {Phylogenetics, Evolutionary genetics, Marine biology, Metagenomics, Viral genetics},\n\tpages = {783--789},\n\tfile = {Full Text PDF:C\\:\\\\Users\\\\ojaillon\\\\Zotero\\\\storage\\\\I59LSIIQ\\\\Gaïa et al. - 2023 - Mirusviruses link herpesviruses to giant viruses.pdf:application/pdf},\n}\n\n

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\n \n\n \n \n \n \n \n \n Climate genomics—Geoscientists, ecologists, and geneticists must reinforce their collaborations to confront climate change.\n \n \n \n \n\n\n \n Caccavo, J. A.; Frémont, P.; Jaillon, O.; and Gehlen, M.\n\n\n \n\n\n\n Global Change Biology, n/a(n/a). 2023.\n _eprint: https://onlinelibrary.wiley.com/doi/pdf/10.1111/gcb.16924\n\n\n\n
\n\n\n\n \n \n $\"Climate$ Paper\n \n \n\n \n \n doi\n \n \n\n \n link\n \n \n\n bibtex\n \n\n \n \n \n abstract \n \n\n \n\n \n \n \n \n \n \n \n\n \n \n \n \n \n \n \n \n \n \n \n \n \n\n\n\n

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@article{caccavo_climate_2023,\n\ttitle = {Climate genomics—{Geoscientists}, ecologists, and geneticists must reinforce their collaborations to confront climate change},\n\tvolume = {n/a},\n\tcopyright = {© 2023 The Authors. Global Change Biology published by John Wiley \\& Sons Ltd.},\n\tissn = {1365-2486},\n\turl = {https://onlinelibrary.wiley.com/doi/abs/10.1111/gcb.16924},\n\tdoi = {10.1111/gcb.16924},\n\tabstract = {Geoscientists and ecologists alike must confront the impact of climate change on ecosystems and the services they provide. In the marine realm, major changes are projected in net primary and export production, with significant repercussions on food security, carbon storage, and climate system feedbacks. However, these projections do not include the potential for rapid linear evolution to facilitate adaptation to environmental change. Climate genomics confronts this challenge by assessing the vulnerability of ecosystem services to climate change. Because DNA is the primary biological repository of detectable environmentally selected mutations (showing evidence of change before impacts arise in morphological or metabolic patterns), genomics provides a window into selection in response to climate change, while also recording neutral processes deriving from stochastic mechanisms (Lowe et al., Trends in Ecology \\& Evolution, 2017; 32:141–152). Due to the revolution afforded by sequencing technology developments, genomics can now meet ecologists and climate scientists in a cross-disciplinary space fertile for collaborations. Collaboration between geoscientists, ecologists, and geneticists must be reinforced in order to combine modeling and genomics approaches at every scale to improve our understanding and the management of ecosystems under climate change. To this end, we present advances in climate genomics from plankton to larger vertebrates, stressing the interactions between modeling and genomics, and identifying future work needed to develop and expand the field of climate genomics.},\n\tlanguage = {en},\n\tnumber = {n/a},\n\tyear = {2023},\n\turldate = {2023-09-08},\n\tjournal = {Global Change Biology},\n\tauthor = {Caccavo, Jilda Alicia and Frémont, Paul and Jaillon, Olivier and Gehlen, Marion},\n\tyear = {2023},\n\tnote = {\\_eprint: https://onlinelibrary.wiley.com/doi/pdf/10.1111/gcb.16924},\n\tkeywords = {climate change, genetically-informed species distribution modelling, genomics, genotype-environment association, interdisciplinary collaboration},\n\tfile = {Full Text PDF:C\\:\\\\Users\\\\ojaillon\\\\Zotero\\\\storage\\\\BHSQNZJ2\\\\Caccavo et al. - Climate genomics—Geoscientists, ecologists, and ge.pdf:application/pdf;Snapshot:C\\:\\\\Users\\\\ojaillon\\\\Zotero\\\\storage\\\\JBMZAH9C\\\\gcb.html:text/html},\n}\n\n

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\n \n\n \n \n \n \n \n \n Ocean-wide comparisons of mesopelagic planktonic community structures.\n \n \n \n \n\n\n \n Rigonato, J.; Budinich, M.; Murillo, A. A.; Brandão, M. C.; Pierella Karlusich, J. J.; Soviadan, Y. D.; Gregory, A. C.; Endo, H.; Kokoszka, F.; Vik, D.; Henry, N.; Frémont, P.; Labadie, K.; Zayed, A. A.; Dimier, C.; Picheral, M.; Searson, S.; Poulain, J.; Kandels, S.; Pesant, S.; Karsenti, E.; Bork, P.; Bowler, C.; Cochrane, G.; de Vargas, C.; Eveillard, D.; Gehlen, M.; Iudicone, D.; Lombard, F.; Ogata, H.; Stemmann, L.; Sullivan, M. B.; Sunagawa, S.; Wincker, P.; Chaffron, S.; and Jaillon, O.\n\n\n \n\n\n\n ISME Communications, 3(1): 1–11. August 2023.\n Number: 1 Publisher: Nature Publishing Group\n\n\n\n
\n\n\n\n \n \n $\"Ocean-wide$ Paper\n \n \n\n \n \n doi\n \n \n\n \n link\n \n \n\n bibtex\n \n\n \n \n \n abstract \n \n\n \n\n \n \n \n \n \n \n \n\n \n \n \n \n \n \n \n\n\n\n

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@article{rigonato_ocean-wide_2023,\n\ttitle = {Ocean-wide comparisons of mesopelagic planktonic community structures},\n\tvolume = {3},\n\tcopyright = {2023 ISME Publications B.V},\n\tissn = {2730-6151},\n\turl = {https://www.nature.com/articles/s43705-023-00279-9},\n\tdoi = {10.1038/s43705-023-00279-9},\n\tabstract = {For decades, marine plankton have been investigated for their capacity to modulate biogeochemical cycles and provide fishery resources. Between the sunlit (epipelagic) layer and the deep dark waters, lies a vast and heterogeneous part of the ocean: the mesopelagic zone. How plankton composition is shaped by environment has been well-explored in the epipelagic but much less in the mesopelagic ocean. Here, we conducted comparative analyses of trans-kingdom community assemblages thriving in the mesopelagic oxygen minimum zone (OMZ), mesopelagic oxic, and their epipelagic counterparts. We identified nine distinct types of intermediate water masses that correlate with variation in mesopelagic community composition. Furthermore, oxygen, NO3− and particle flux together appeared as the main drivers governing these communities. Novel taxonomic signatures emerged from OMZ while a global co-occurrence network analysis showed that about 70\\% of the abundance of mesopelagic plankton groups is organized into three community modules. One module gathers prokaryotes, pico-eukaryotes and Nucleo-Cytoplasmic Large DNA Viruses (NCLDV) from oxic regions, and the two other modules are enriched in OMZ prokaryotes and OMZ pico-eukaryotes, respectively. We hypothesize that OMZ conditions led to a diversification of ecological niches, and thus communities, due to selective pressure from limited resources. Our study further clarifies the interplay between environmental factors in the mesopelagic oxic and OMZ, and the compositional features of communities.},\n\tlanguage = {en},\n\tnumber = {1},\n\turldate = {2023-09-08},\n\tjournal = {ISME Communications},\n\tauthor = {Rigonato, Janaina and Budinich, Marko and Murillo, Alejandro A. and Brandão, Manoela C. and Pierella Karlusich, Juan J. and Soviadan, Yawouvi Dodji and Gregory, Ann C. and Endo, Hisashi and Kokoszka, Florian and Vik, Dean and Henry, Nicolas and Frémont, Paul and Labadie, Karine and Zayed, Ahmed A. and Dimier, Céline and Picheral, Marc and Searson, Sarah and Poulain, Julie and Kandels, Stefanie and Pesant, Stéphane and Karsenti, Eric and Bork, Peer and Bowler, Chris and Cochrane, Guy and de Vargas, Colomban and Eveillard, Damien and Gehlen, Marion and Iudicone, Daniele and Lombard, Fabien and Ogata, Hiroyuki and Stemmann, Lars and Sullivan, Matthew B. and Sunagawa, Shinichi and Wincker, Patrick and Chaffron, Samuel and Jaillon, Olivier},\n\tmonth = aug,\n\tyear = {2023},\n\tnote = {Number: 1\nPublisher: Nature Publishing Group},\n\tkeywords = {Community ecology, Microbial ecology},\n\tpages = {1--11},\n\tfile = {Full Text PDF:C\\:\\\\Users\\\\ojaillon\\\\Zotero\\\\storage\\\\DEFDCACC\\\\Rigonato et al. - 2023 - Ocean-wide comparisons of mesopelagic planktonic c.pdf:application/pdf},\n}\n\n

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\n \n\n \n \n \n \n \n \n The Ocean Gene Atlas v2.0: online exploration of the biogeography and phylogeny of plankton genes.\n \n \n \n \n\n\n \n Vernette, C.; Lecubin, J.; Sánchez, P.; Acinas, S.; Babin, M.; Bork, P.; Boss, E.; Bowler, C.; Cochrane, G.; De Vargas, C.; Gorsky, G.; Guidi, L.; Grimsley, N.; Hingamp1, P.; Iudicone, D.; Jaillon, O.; Kandels-Lewis, S.; Karp-Boss, L.; Karsenti, E.; Not, F.; Ogata, H.; Poulton, N.; Pesant, S.; Sardet, C.; Speich, S.; Stemmann, L.; Sullivan, M.; Sunagawa, S.; Wincker, P.; Sunagawa, S.; Delmont, T.; Acinas, S.; Pelletier, E.; Hingamp, P.; and Lescot, M.\n\n\n \n\n\n\n Nucleic Acids Research, 50(W1): W516–W526. 2022.\n \n\n\n\n
\n\n\n\n \n \n $\"The$ Paper\n \n \n\n \n \n doi\n \n \n\n \n link\n \n \n\n bibtex\n \n\n \n\n \n\n \n \n \n \n \n \n \n\n \n \n \n\n\n\n

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@article{vernette_ocean_2022,\n\ttitle = {The {Ocean} {Gene} {Atlas} v2.0: online exploration of the biogeography and phylogeny of plankton genes},\n\tvolume = {50},\n\turl = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-85134369900&doi=10.1093%2fnar%2fgkac420&partnerID=40&md5=144777415fc9240c9c185479bccb43fb},\n\tdoi = {10.1093/nar/gkac420},\n\tnumber = {W1},\n\tjournal = {Nucleic Acids Research},\n\tauthor = {Vernette, C. and Lecubin, J. and Sánchez, P. and Acinas, S.G. and Babin, M. and Bork, P. and Boss, E. and Bowler, C. and Cochrane, G. and De Vargas, C. and Gorsky, G. and Guidi, L. and Grimsley, N. and Hingamp1, P. and Iudicone, D. and Jaillon, O. and Kandels-Lewis, S. and Karp-Boss, L. and Karsenti, E. and Not, F. and Ogata, H. and Poulton, N. and Pesant, S. and Sardet, C. and Speich, S. and Stemmann, L. and Sullivan, M.B. and Sunagawa, S. and Wincker, P. and Sunagawa, S. and Delmont, T.O. and Acinas, S.G. and Pelletier, E. and Hingamp, P. and Lescot, M.},\n\tyear = {2022},\n\tpages = {W516--W526},\n}\n\n

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\n \n\n \n \n \n \n \n \n Functional repertoire convergence of distantly related eukaryotic plankton lineages abundant in the sunlit ocean.\n \n \n \n \n\n\n \n Delmont, T.; Gaia, M.; Hinsinger, D.; Frémont, P.; Vanni, C.; Fernandez-Guerra, A.; Eren, A.; Kourlaiev, A.; d'Agata , L.; Clayssen, Q.; Villar, E.; Labadie, K.; Cruaud, C.; Poulain, J.; Da Silva, C.; Wessner, M.; Noel, B.; Aury, J.; Sunagawa, S.; Acinas, S.; Bork, P.; Karsenti, E.; Bowler, C.; Sardet, C.; Stemmann, L.; de Vargas, C.; Wincker, P.; Lescot, M.; Babin, M.; Gorsky, G.; Grimsley, N.; Guidi, L.; Hingamp, P.; Jaillon, O.; Kandels, S.; Iudicone, D.; Ogata, H.; Pesant, S.; Sullivan, M.; Not, F.; Lee, K.; Boss, E.; Cochrane, G.; Follows, M.; Poulton, N.; Raes, J.; Sieracki, M.; Speich, S.; Pelletier, E.; and Coordinators, T. O.\n\n\n \n\n\n\n Cell Genomics, 2(5). 2022.\n \n\n\n\n
\n\n\n\n \n \n $\"Functional$ Paper\n \n \n\n \n \n doi\n \n \n\n \n link\n \n \n\n bibtex\n \n\n \n\n \n\n \n \n \n \n \n \n \n\n \n \n \n\n\n\n

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@article{delmont_functional_2022,\n\ttitle = {Functional repertoire convergence of distantly related eukaryotic plankton lineages abundant in the sunlit ocean},\n\tvolume = {2},\n\turl = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-85131102051&doi=10.1016%2fj.xgen.2022.100123&partnerID=40&md5=b9aabdbaa6b03b5021caba0641a918a4},\n\tdoi = {10.1016/j.xgen.2022.100123},\n\tnumber = {5},\n\tjournal = {Cell Genomics},\n\tauthor = {Delmont, T.O. and Gaia, M. and Hinsinger, D.D. and Frémont, P. and Vanni, C. and Fernandez-Guerra, A. and Eren, A.M. and Kourlaiev, A. and d'Agata, L. and Clayssen, Q. and Villar, E. and Labadie, K. and Cruaud, C. and Poulain, J. and Da Silva, C. and Wessner, M. and Noel, B. and Aury, J.-M. and Sunagawa, S. and Acinas, S.G. and Bork, P. and Karsenti, E. and Bowler, C. and Sardet, C. and Stemmann, L. and de Vargas, C. and Wincker, P. and Lescot, M. and Babin, M. and Gorsky, G. and Grimsley, N. and Guidi, L. and Hingamp, P. and Jaillon, O. and Kandels, S. and Iudicone, D. and Ogata, H. and Pesant, S. and Sullivan, M.B. and Not, F. and Lee, K.-B. and Boss, E. and Cochrane, G. and Follows, M. and Poulton, N. and Raes, J. and Sieracki, M. and Speich, S. and Pelletier, E. and Coordinators, Tara Oceans},\n\tyear = {2022},\n}\n\n

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\n \n\n \n \n \n \n \n \n Giant Viruses Encode Actin-Related Proteins.\n \n \n \n \n\n\n \n Da Cunha, V.; Gaia, M.; Ogata, H.; Jaillon, O.; Delmont, T.; and Forterre, P.\n\n\n \n\n\n\n Molecular Biology and Evolution, 39(2). 2022.\n \n\n\n\n
\n\n\n\n \n \n $\"Giant$ Paper\n \n \n\n \n \n doi\n \n \n\n \n link\n \n \n\n bibtex\n \n\n \n\n \n \n \n 3 downloads\n \n \n\n \n \n \n \n \n \n \n\n \n \n \n\n\n\n

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@article{da_cunha_giant_2022,\n\ttitle = {Giant {Viruses} {Encode} {Actin}-{Related} {Proteins}},\n\tvolume = {39},\n\turl = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-85124793034&doi=10.1093%2fmolbev%2fmsac022&partnerID=40&md5=8072d886da74aa2b5e0a55a410f5ff48},\n\tdoi = {10.1093/molbev/msac022},\n\tnumber = {2},\n\tjournal = {Molecular Biology and Evolution},\n\tauthor = {Da Cunha, V. and Gaia, M. and Ogata, H. and Jaillon, O. and Delmont, T.O. and Forterre, P.},\n\tyear = {2022},\n}\n\n

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\n \n\n \n \n \n \n \n \n Genomic evidence for global ocean plankton biogeography shaped by large-scale current systems.\n \n \n \n \n\n\n \n Richter, D.; Watteaux, R.; Vannier, T.; Leconte, J.; Frémont, P.; Reygondeau, G.; Maillet, N.; Henry, N.; Benoit, G.; Da Silva, O.; Delmont, T.; Fernàndez-Guerra, A.; Suweis, S.; Narci, R.; Berney, C.; Eveillard, D.; Gavory, F.; Guidi, L.; Labadie, K.; Mahieu, E.; Poulain, J.; Romac, S.; Roux, S.; Dimier, C.; Kandels, S.; Picheral, M.; Searson, S.; Pesant, S.; Aury, J.; Brum, J.; Lemaitre, C.; Pelletier, E.; Bork, P.; Sunagawa, S.; Lombard, F.; Karp-Boss, L.; Bowler, C.; Sullivan, M.; Karsenti, E.; Mariadassou, M.; Probert, I.; Peterlongo, P.; Wincker, P.; de Vargas, C.; D'alcalà, M.; Iudicone, D.; and Jaillon, O.\n\n\n \n\n\n\n eLife, 11. 2022.\n \n\n\n\n
\n\n\n\n \n \n $\"Genomic$ Paper\n \n \n\n \n \n doi\n \n \n\n \n link\n \n \n\n bibtex\n \n\n \n\n \n \n \n 2 downloads\n \n \n\n \n \n \n \n \n \n \n\n \n \n \n\n\n\n

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@article{richter_genomic_2022,\n\ttitle = {Genomic evidence for global ocean plankton biogeography shaped by large-scale current systems},\n\tvolume = {11},\n\turl = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-85135499947&doi=10.7554%2feLife.78129&partnerID=40&md5=aace4d33deb2d66e8171477127904d1f},\n\tdoi = {10.7554/eLife.78129},\n\tjournal = {eLife},\n\tauthor = {Richter, D.J. and Watteaux, R. and Vannier, T. and Leconte, J. and Frémont, P. and Reygondeau, G. and Maillet, N. and Henry, N. and Benoit, G. and Da Silva, O. and Delmont, T.O. and Fernàndez-Guerra, A. and Suweis, S. and Narci, R. and Berney, C. and Eveillard, D. and Gavory, F. and Guidi, L. and Labadie, K. and Mahieu, E. and Poulain, J. and Romac, S. and Roux, S. and Dimier, C. and Kandels, S. and Picheral, M. and Searson, S. and Pesant, S. and Aury, J.-M. and Brum, J.R. and Lemaitre, C. and Pelletier, E. and Bork, P. and Sunagawa, S. and Lombard, F. and Karp-Boss, L. and Bowler, C. and Sullivan, M.B. and Karsenti, E. and Mariadassou, M. and Probert, I. and Peterlongo, P. and Wincker, P. and de Vargas, C. and D'alcalà, M.R. and Iudicone, D. and Jaillon, O.},\n\tyear = {2022},\n}\n\n

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\n \n\n \n \n \n \n \n \n Restructuring of plankton genomic biogeography in the surface ocean under climate change.\n \n \n \n \n\n\n \n Frémont, P.; Gehlen, M.; Vrac, M.; Leconte, J.; Delmont, T. O.; Wincker, P.; Iudicone, D.; and Jaillon, O.\n\n\n \n\n\n\n Nature Climate Change, 12(4): 393–401. April 2022.\n Number: 4 Publisher: Nature Publishing Group\n\n\n\n
\n\n\n\n \n \n $\"Restructuring$ Paper\n \n \n\n \n \n doi\n \n \n\n \n link\n \n \n\n bibtex\n \n\n \n \n \n abstract \n \n\n \n \n \n 1 download\n \n \n\n \n \n \n \n \n \n \n\n \n \n \n \n \n \n \n \n \n \n \n \n \n\n\n\n

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@article{fremont_restructuring_2022,\n\ttitle = {Restructuring of plankton genomic biogeography in the surface ocean under climate change},\n\tvolume = {12},\n\tcopyright = {2022 The Author(s), under exclusive licence to Springer Nature Limited},\n\tissn = {1758-6798},\n\turl = {https://www.nature.com/articles/s41558-022-01314-8},\n\tdoi = {10.1038/s41558-022-01314-8},\n\tabstract = {The impact of climate change on diversity, functioning and biogeography of marine plankton remains a major unresolved issue. Here environmental niches are evidenced for plankton communities at the genomic scale for six size fractions from viruses to meso-zooplankton. The spatial extrapolation of these niches portrays ocean partitionings south of 60° N into climato-genomic provinces characterized by signature genomes. By 2090, under the RCP8.5 future climate scenario, provinces are reorganized over half of the ocean area considered, and almost all provinces are displaced poleward. Particularly, tropical provinces expand at the expense of temperate ones. Sea surface temperature is identified as the main driver of changes (50\\%), followed by phosphate (11\\%) and salinity (10\\%). Compositional shifts among key planktonic groups suggest impacts on the nitrogen and carbon cycles. Provinces are linked to estimates of carbon export fluxes which are projected to decrease, on average, by 4\\% in response to biogeographical restructuring.},\n\tlanguage = {en},\n\tnumber = {4},\n\turldate = {2023-06-05},\n\tjournal = {Nature Climate Change},\n\tauthor = {Frémont, Paul and Gehlen, Marion and Vrac, Mathieu and Leconte, Jade and Delmont, Tom O. and Wincker, Patrick and Iudicone, Daniele and Jaillon, Olivier},\n\tmonth = apr,\n\tyear = {2022},\n\tnote = {Number: 4\nPublisher: Nature Publishing Group},\n\tkeywords = {Biogeochemistry, Marine biology, Biogeography, Climate-change ecology, Molecular ecology},\n\tpages = {393--401},\n\tfile = {Version soumise:C\\:\\\\Users\\\\ojaillon\\\\Zotero\\\\storage\\\\LI3BGR65\\\\Frémont et al. - 2022 - Restructuring of plankton genomic biogeography in .pdf:application/pdf},\n}\n\n

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\n \n\n \n \n \n \n \n \n Genomic adaptation of the picoeukaryote Pelagomonas calceolata to iron-poor oceans revealed by a chromosome-scale genome sequence.\n \n \n \n \n\n\n \n Guérin, N.; Ciccarella, M.; Flamant, E.; Frémont, P.; Mangenot, S.; Istace, B.; Noel, B.; Belser, C.; Bertrand, L.; Labadie, K.; Cruaud, C.; Romac, S.; Bachy, C.; Gachenot, M.; Pelletier, E.; Alberti, A.; Jaillon, O.; Wincker, P.; Aury, J.; and Carradec, Q.\n\n\n \n\n\n\n Communications Biology, 5(1): 1–14. September 2022.\n Number: 1 Publisher: Nature Publishing Group\n\n\n\n
\n\n\n\n \n \n $\"Genomic$ Paper\n \n \n\n \n \n doi\n \n \n\n \n link\n \n \n\n bibtex\n \n\n \n \n \n abstract \n \n\n \n \n \n 3 downloads\n \n \n\n \n \n \n \n \n \n \n\n \n \n \n \n \n \n \n \n \n \n \n\n\n\n

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@article{guerin_genomic_2022,\n\ttitle = {Genomic adaptation of the picoeukaryote {Pelagomonas} calceolata to iron-poor oceans revealed by a chromosome-scale genome sequence},\n\tvolume = {5},\n\tcopyright = {2022 The Author(s)},\n\tissn = {2399-3642},\n\turl = {https://www.nature.com/articles/s42003-022-03939-z},\n\tdoi = {10.1038/s42003-022-03939-z},\n\tabstract = {The smallest phytoplankton species are key actors in oceans biogeochemical cycling and their abundance and distribution are affected with global environmental changes. Among them, algae of the Pelagophyceae class encompass coastal species causative of harmful algal blooms while others are cosmopolitan and abundant. The lack of genomic reference in this lineage is a main limitation to study its ecological importance. Here, we analysed Pelagomonas calceolata relative abundance, ecological niche and potential for the adaptation in all oceans using a complete chromosome-scale assembled genome sequence. Our results show that P. calceolata is one of the most abundant eukaryotic species in the oceans with a relative abundance favoured by high temperature, low-light and iron-poor conditions. Climate change projections based on its relative abundance suggest an extension of the P. calceolata habitat toward the poles at the end of this century. Finally, we observed a specific gene repertoire and expression level variations potentially explaining its ecological success in low-iron and low-nitrate environments. Collectively, these findings reveal the ecological importance of P. calceolata and lay the foundation for a global scale analysis of the adaptation and acclimation strategies of this small phytoplankton in a changing environment.},\n\tlanguage = {en},\n\tnumber = {1},\n\turldate = {2023-06-05},\n\tjournal = {Communications Biology},\n\tauthor = {Guérin, Nina and Ciccarella, Marta and Flamant, Elisa and Frémont, Paul and Mangenot, Sophie and Istace, Benjamin and Noel, Benjamin and Belser, Caroline and Bertrand, Laurie and Labadie, Karine and Cruaud, Corinne and Romac, Sarah and Bachy, Charles and Gachenot, Martin and Pelletier, Eric and Alberti, Adriana and Jaillon, Olivier and Wincker, Patrick and Aury, Jean-Marc and Carradec, Quentin},\n\tmonth = sep,\n\tyear = {2022},\n\tnote = {Number: 1\nPublisher: Nature Publishing Group},\n\tkeywords = {Comparative genomics, Metagenomics, Biogeography, Water microbiology},\n\tpages = {1--14},\n\tfile = {Full Text PDF:C\\:\\\\Users\\\\ojaillon\\\\Zotero\\\\storage\\\\HNBPN4LK\\\\Guérin et al. - 2022 - Genomic adaptation of the picoeukaryote Pelagomona.pdf:application/pdf},\n}\n\n

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\n \n\n \n \n \n \n \n \n Compendium of 530 metagenome-assembled bacterial and archaeal genomes from the polar Arctic Ocean.\n \n \n \n \n\n\n \n Royo-Llonch, M.; Sánchez, P.; Ruiz-González, C.; Salazar, G.; Pedrós-Alió, C.; Sebastián, M.; Labadie, K.; Paoli, L.; M. Ibarbalz, F.; Zinger, L.; Churcheward, B.; Babin, M.; Bork, P.; Boss, E.; Cochrane, G.; de Vargas, C.; Gorsky, G.; Grimsley, N.; Guidi, L.; Hingamp, P.; Iudicone, D.; Jaillon, O.; Kandels, S.; Not, F.; Ogata, H.; Pesant, S.; Poulton, N.; Raes, J.; Sardet, C.; Speich, S.; Setmmann, L.; Sullivan, M.; Chaffron, S.; Eveillard, D.; Karsenti, E.; Sunagawa, S.; Wincker, P.; Karp-Boss, L.; Bowler, C.; Acinas, S.; and Coordinators, T. O.\n\n\n \n\n\n\n Nature Microbiology, 6(12): 1561–1574. 2021.\n \n\n\n\n
\n\n\n\n \n \n $\"Compendium$ Paper\n \n \n\n \n \n doi\n \n \n\n \n link\n \n \n\n bibtex\n \n\n \n\n \n\n \n \n \n \n \n \n \n\n \n \n \n\n\n\n

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@article{royo-llonch_compendium_2021,\n\ttitle = {Compendium of 530 metagenome-assembled bacterial and archaeal genomes from the polar {Arctic} {Ocean}},\n\tvolume = {6},\n\turl = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-85119623497&doi=10.1038%2fs41564-021-00979-9&partnerID=40&md5=126d376fb6cd0773e3e1a820c7f981c0},\n\tdoi = {10.1038/s41564-021-00979-9},\n\tnumber = {12},\n\tjournal = {Nature Microbiology},\n\tauthor = {Royo-Llonch, M. and Sánchez, P. and Ruiz-González, C. and Salazar, G. and Pedrós-Alió, C. and Sebastián, M. and Labadie, K. and Paoli, L. and M. Ibarbalz, F. and Zinger, L. and Churcheward, B. and Babin, M. and Bork, P. and Boss, E. and Cochrane, G. and de Vargas, C. and Gorsky, G. and Grimsley, N. and Guidi, L. and Hingamp, P. and Iudicone, D. and Jaillon, O. and Kandels, S. and Not, F. and Ogata, H. and Pesant, S. and Poulton, N. and Raes, J. and Sardet, C. and Speich, S. and Setmmann, L. and Sullivan, M.B. and Chaffron, S. and Eveillard, D. and Karsenti, E. and Sunagawa, S. and Wincker, P. and Karp-Boss, L. and Bowler, C. and Acinas, S.G. and Coordinators, Tara Oceans},\n\tyear = {2021},\n\tpages = {1561--1574},\n}\n\n

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\n \n\n \n \n \n \n \n \n Environmental vulnerability of the global ocean epipelagic plankton community interactome.\n \n \n \n \n\n\n \n Chaffron, S.; Delage, E.; Budinich, M.; Vintache, D.; Henry, N.; Nef, C.; Ardyna, M.; Zayed, A.; Junger, P.; Galand, P.; Lovejoy, C.; Murray, A.; Sarmento, H.; Acinas, S.; Babin, M.; Iudicone, D.; Jaillon, O.; Karsenti, E.; Wincker, P.; Karp-Boss, L.; Sullivan, M.; Bowler, C.; De Vargas, C.; and Eveillard, D.\n\n\n \n\n\n\n Science Advances, 7(35). 2021.\n \n\n\n\n
\n\n\n\n \n \n $\"Environmental$ Paper\n \n \n\n \n \n doi\n \n \n\n \n link\n \n \n\n bibtex\n \n\n \n\n \n \n \n 9 downloads\n \n \n\n \n \n \n \n \n \n \n\n \n \n \n\n\n\n

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@article{chaffron_environmental_2021,\n\ttitle = {Environmental vulnerability of the global ocean epipelagic plankton community interactome},\n\tvolume = {7},\n\turl = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-85113800852&doi=10.1126%2fsciadv.abg1921&partnerID=40&md5=370b58229c0827fa7af5b9a996f48a4b},\n\tdoi = {10.1126/sciadv.abg1921},\n\tnumber = {35},\n\tjournal = {Science Advances},\n\tauthor = {Chaffron, S. and Delage, E. and Budinich, M. and Vintache, D. and Henry, N. and Nef, C. and Ardyna, M. and Zayed, A.A. and Junger, P.C. and Galand, P.E. and Lovejoy, C. and Murray, A.E. and Sarmento, H. and Acinas, S.G. and Babin, M. and Iudicone, D. and Jaillon, O. and Karsenti, E. and Wincker, P. and Karp-Boss, L. and Sullivan, M.B. and Bowler, C. and De Vargas, C. and Eveillard, D.},\n\tyear = {2021},\n}\n\n

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\n \n\n \n \n \n \n \n \n Niche adaptation promoted the evolutionary diversification of tiny ocean predators.\n \n \n \n \n\n\n \n Latorre, F.; Deutschmann, I.; Labarre, A.; Obiol, A.; Krabberød, A.; Pelletier, E.; Sieracki, M.; Cruaud, C.; Jaillon, O.; Massana, R.; and Logares, R.\n\n\n \n\n\n\n Proceedings of the National Academy of Sciences of the United States of America, 118(25). 2021.\n \n\n\n\n
\n\n\n\n \n \n $\"Niche$ Paper\n \n \n\n \n \n doi\n \n \n\n \n link\n \n \n\n bibtex\n \n\n \n\n \n\n \n \n \n \n \n \n \n\n \n \n \n\n\n\n

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@article{latorre_niche_2021,\n\ttitle = {Niche adaptation promoted the evolutionary diversification of tiny ocean predators},\n\tvolume = {118},\n\turl = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-85108345425&doi=10.1073%2fpnas.2020955118&partnerID=40&md5=b77c73c54767a92634d3316a80cdf0b8},\n\tdoi = {10.1073/pnas.2020955118},\n\tnumber = {25},\n\tjournal = {Proceedings of the National Academy of Sciences of the United States of America},\n\tauthor = {Latorre, F. and Deutschmann, I.M. and Labarre, A. and Obiol, A. and Krabberød, A.K. and Pelletier, E. and Sieracki, M.E. and Cruaud, C. and Jaillon, O. and Massana, R. and Logares, R.},\n\tyear = {2021},\n}\n\n

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\n \n\n \n \n \n \n \n \n Comparative genomics reveals new functional insights in uncultured MAST species.\n \n \n \n \n\n\n \n Labarre, A.; López-Escardó, D.; Latorre, F.; Leonard, G.; Bucchini, F.; Obiol, A.; Cruaud, C.; Sieracki, M.; Jaillon, O.; Wincker, P.; Vandepoele, K.; Logares, R.; and Massana, R.\n\n\n \n\n\n\n ISME Journal, 15(6): 1767–1781. 2021.\n \n\n\n\n
\n\n\n\n \n \n $\"Comparative$ Paper\n \n \n\n \n \n doi\n \n \n\n \n link\n \n \n\n bibtex\n \n\n \n\n \n\n \n \n \n \n \n \n \n\n \n \n \n\n\n\n

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@article{labarre_comparative_2021,\n\ttitle = {Comparative genomics reveals new functional insights in uncultured {MAST} species},\n\tvolume = {15},\n\turl = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-85100024624&doi=10.1038%2fs41396-020-00885-8&partnerID=40&md5=d1d93b9f44e7f3e9de9c6e1db7b36786},\n\tdoi = {10.1038/s41396-020-00885-8},\n\tnumber = {6},\n\tjournal = {ISME Journal},\n\tauthor = {Labarre, A. and López-Escardó, D. and Latorre, F. and Leonard, G. and Bucchini, F. and Obiol, A. and Cruaud, C. and Sieracki, M.E. and Jaillon, O. and Wincker, P. and Vandepoele, K. and Logares, R. and Massana, R.},\n\tyear = {2021},\n\tpages = {1767--1781},\n}\n\n

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\n \n\n \n \n \n \n \n \n Eukaryotic virus composition can predict the efficiency of carbon export in the global ocean.\n \n \n \n \n\n\n \n Kaneko, H.; Blanc-Mathieu, R.; Endo, H.; Chaffron, S.; Delmont, T.; Gaia, M.; Henry, N.; Hernández-Velázquez, R.; Nguyen, C.; Mamitsuka, H.; Forterre, P.; Jaillon, O.; de Vargas, C.; Sullivan, M.; Suttle, C.; Guidi, L.; and Ogata, H.\n\n\n \n\n\n\n iScience, 24(1). 2021.\n \n\n\n\n
\n\n\n\n \n \n $\"Eukaryotic$ Paper\n \n \n\n \n \n doi\n \n \n\n \n link\n \n \n\n bibtex\n \n\n \n\n \n\n \n \n \n \n \n \n \n\n \n \n \n\n\n\n

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@article{kaneko_eukaryotic_2021,\n\ttitle = {Eukaryotic virus composition can predict the efficiency of carbon export in the global ocean},\n\tvolume = {24},\n\turl = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-85099230363&doi=10.1016%2fj.isci.2020.102002&partnerID=40&md5=84adb85690fb34f383be40a536dea9d0},\n\tdoi = {10.1016/j.isci.2020.102002},\n\tnumber = {1},\n\tjournal = {iScience},\n\tauthor = {Kaneko, H. and Blanc-Mathieu, R. and Endo, H. and Chaffron, S. and Delmont, T.O. and Gaia, M. and Henry, N. and Hernández-Velázquez, R. and Nguyen, C.H. and Mamitsuka, H. and Forterre, P. and Jaillon, O. and de Vargas, C. and Sullivan, M.B. and Suttle, C.A. and Guidi, L. and Ogata, H.},\n\tyear = {2021},\n}\n\n

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\n \n\n \n \n \n \n \n \n Complement activation promoted by the lectin pathway mediates C3aR-dependent sarcoma progression and immunosuppression.\n \n \n \n \n\n\n \n Magrini, E.; Di Marco, S.; Mapelli, S. N.; Perucchini, C.; Pasqualini, F.; Donato, A.; Guevara Lopez, M. d. l. L.; Carriero, R.; Ponzetta, A.; Colombo, P.; Cananzi, F.; Supino, D.; Reis, E. S.; Peano, C.; Inforzato, A.; Jaillon, S.; Doni, A.; Lambris, J. D.; Mantovani, A.; and Garlanda, C.\n\n\n \n\n\n\n Nature Cancer, 2(2): 218–232. February 2021.\n Number: 2 Publisher: Nature Publishing Group\n\n\n\n
\n\n\n\n \n \n $\"Complement$ Paper\n \n \n\n \n \n doi\n \n \n\n \n link\n \n \n\n bibtex\n \n\n \n \n \n abstract \n \n\n \n\n \n \n \n \n \n \n \n\n \n \n \n \n \n \n \n \n \n \n \n\n\n\n

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@article{magrini_complement_2021,\n\ttitle = {Complement activation promoted by the lectin pathway mediates {C3aR}-dependent sarcoma progression and immunosuppression},\n\tvolume = {2},\n\tcopyright = {2021 The Author(s), under exclusive licence to Springer Nature America, Inc. part of Springer Nature},\n\tissn = {2662-1347},\n\turl = {https://www.nature.com/articles/s43018-021-00173-0},\n\tdoi = {10.1038/s43018-021-00173-0},\n\tabstract = {Complement has emerged as a component of tumor-promoting inflammation. We conducted a systematic assessment of the role of complement activation and effector pathways in sarcomas. C3−/−, MBL1/2−/− and C4−/− mice showed reduced susceptibility to 3-methylcholanthrene sarcomagenesis and transplanted sarcomas, whereas C1q and factor B deficiency had marginal effects. Complement 3a receptor (C3aR), but not C5aR1 and C5aR2, deficiency mirrored the phenotype of C3−/− mice. C3 and C3aR deficiency were associated with reduced accumulation and functional skewing of tumor-associated macrophages, increased T-cell activation and response to anti-PD-1 therapy. Transcriptional profiling of sarcoma-infiltrating macrophages and monocytes revealed the enrichment of the major histocompatibility complex II–dependent antigen presentation pathway in C3-deficient cells. In patients, C3aR expression correlated with a macrophage population signature, and C3-deficiency-associated signatures predicted better clinical outcome. These results suggest that the lectin pathway and C3a–C3aR axis are key components of complement and macrophage-mediated sarcoma promotion and immunosuppression.},\n\tlanguage = {en},\n\tnumber = {2},\n\turldate = {2023-06-05},\n\tjournal = {Nature Cancer},\n\tauthor = {Magrini, Elena and Di Marco, Sabrina and Mapelli, Sarah N. and Perucchini, Chiara and Pasqualini, Fabio and Donato, Alessia and Guevara Lopez, Maria de la Luz and Carriero, Roberta and Ponzetta, Andrea and Colombo, Piergiuseppe and Cananzi, Ferdinando and Supino, Domenico and Reis, Edimara S. and Peano, Clelia and Inforzato, Antonio and Jaillon, Sebastien and Doni, Andrea and Lambris, John D. and Mantovani, Alberto and Garlanda, Cecilia},\n\tmonth = feb,\n\tyear = {2021},\n\tnote = {Number: 2\nPublisher: Nature Publishing Group},\n\tkeywords = {Cancer, Sarcoma, Cancer immunotherapy, Complement cascade},\n\tpages = {218--232},\n\tfile = {Version acceptée:C\\:\\\\Users\\\\ojaillon\\\\Zotero\\\\storage\\\\57EUNP8H\\\\Magrini et al. - 2021 - Complement activation promoted by the lectin pathw.pdf:application/pdf},\n}\n\n

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\n \n\n \n \n \n \n \n \n Macroscale patterns of oceanic zooplankton composition and size structure.\n \n \n \n \n\n\n \n Brandão, M. C.; Benedetti, F.; Martini, S.; Soviadan, Y. D.; Irisson, J.; Romagnan, J.; Elineau, A.; Desnos, C.; Jalabert, L.; Freire, A. S.; Picheral, M.; Guidi, L.; Gorsky, G.; Bowler, C.; Karp-Boss, L.; Henry, N.; de Vargas, C.; Sullivan, M. B.; Stemmann, L.; and Lombard, F.\n\n\n \n\n\n\n Scientific Reports, 11(1): 15714. August 2021.\n Number: 1 Publisher: Nature Publishing Group\n\n\n\n
\n\n\n\n \n \n $\"Macroscale$ Paper\n \n \n\n \n \n doi\n \n \n\n \n link\n \n \n\n bibtex\n \n\n \n \n \n abstract \n \n\n \n\n \n \n \n \n \n \n \n\n \n \n \n \n \n \n \n\n\n\n

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@article{brandao_macroscale_2021,\n\ttitle = {Macroscale patterns of oceanic zooplankton composition and size structure},\n\tvolume = {11},\n\tcopyright = {2021 The Author(s)},\n\tissn = {2045-2322},\n\turl = {https://www.nature.com/articles/s41598-021-94615-5},\n\tdoi = {10.1038/s41598-021-94615-5},\n\tabstract = {Ocean plankton comprise organisms from viruses to fish larvae that are fundamental to ecosystem functioning and the provision of marine services such as fisheries and CO2 sequestration. The latter services are partly governed by variations in plankton community composition and the expression of traits such as body size at community-level. While community assembly has been thoroughly studied for the smaller end of the plankton size spectrum, the larger end comprises ectotherms that are often studied at the species, or group-level, rather than as communities. The body size of marine ectotherms decreases with temperature, but controls on community-level traits remain elusive, hindering the predictability of marine services provision. Here, we leverage Tara Oceans datasets to determine how zooplankton community composition and size structure varies with latitude, temperature and productivity-related covariates in the global surface ocean. Zooplankton abundance and median size decreased towards warmer and less productive environments, as a result of changes in copepod composition. However, some clades displayed the opposite relationships, which may be ascribed to alternative feeding strategies. Given that climate models predict increasingly warmed and stratified oceans, our findings suggest that zooplankton communities will shift towards smaller organisms which might weaken their contribution to the biological carbon pump.},\n\tlanguage = {en},\n\tnumber = {1},\n\turldate = {2023-06-05},\n\tjournal = {Scientific Reports},\n\tauthor = {Brandão, Manoela C. and Benedetti, Fabio and Martini, Séverine and Soviadan, Yawouvi Dodji and Irisson, Jean-Olivier and Romagnan, Jean-Baptiste and Elineau, Amanda and Desnos, Corinne and Jalabert, Laëtitia and Freire, Andrea S. and Picheral, Marc and Guidi, Lionel and Gorsky, Gabriel and Bowler, Chris and Karp-Boss, Lee and Henry, Nicolas and de Vargas, Colomban and Sullivan, Matthew B. and Stemmann, Lars and Lombard, Fabien},\n\tmonth = aug,\n\tyear = {2021},\n\tnote = {Number: 1\nPublisher: Nature Publishing Group},\n\tkeywords = {Ecology, Ocean sciences},\n\tpages = {15714},\n\tfile = {Full Text PDF:C\\:\\\\Users\\\\ojaillon\\\\Zotero\\\\storage\\\\P2GY3X39\\\\Brandão et al. - 2021 - Macroscale patterns of oceanic zooplankton composi.pdf:application/pdf},\n}\n\n

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\n \n 2020\n \n \n (3)\n \n \n

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\n \n\n \n \n \n \n \n \n Tara Oceans: towards global ocean ecosystems biology.\n \n \n \n \n\n\n \n Sunagawa, S.; Acinas, S.; Bork, P.; Bowler, C.; Babin, M.; Boss, E.; Cochrane, G.; de Vargas, C.; Follows, M.; Gorsky, G.; Grimsley, N.; Guidi, L.; Hingamp, P.; Iudicone, D.; Jaillon, O.; Kandels, S.; Karp-Boss, L.; Karsenti, E.; Lescot, M.; Not, F.; Ogata, H.; Pesant, S.; Poulton, N.; Raes, J.; Sardet, C.; Sieracki, M.; Speich, S.; Stemmann, L.; Sullivan, M.; Wincker, P.; Eveillard, D.; Lombard, F.; and Coordinators, T. O.\n\n\n \n\n\n\n Nature Reviews Microbiology, 18(8): 428–445. 2020.\n \n\n\n\n
\n\n\n\n \n \n $\"Tara$ Paper\n \n \n\n \n \n doi\n \n \n\n \n link\n \n \n\n bibtex\n \n\n \n\n \n\n \n \n \n \n \n \n \n\n \n \n \n\n\n\n

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@article{sunagawa_tara_2020,\n\ttitle = {Tara {Oceans}: towards global ocean ecosystems biology},\n\tvolume = {18},\n\turl = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-85087944187&doi=10.1038%2fs41579-020-0364-5&partnerID=40&md5=5215145ef00f976626b87b8a36877fa1},\n\tdoi = {10.1038/s41579-020-0364-5},\n\tnumber = {8},\n\tjournal = {Nature Reviews Microbiology},\n\tauthor = {Sunagawa, S. and Acinas, S.G. and Bork, P. and Bowler, C. and Babin, M. and Boss, E. and Cochrane, G. and de Vargas, C. and Follows, M. and Gorsky, G. and Grimsley, N. and Guidi, L. and Hingamp, P. and Iudicone, D. and Jaillon, O. and Kandels, S. and Karp-Boss, L. and Karsenti, E. and Lescot, M. and Not, F. and Ogata, H. and Pesant, S. and Poulton, N. and Raes, J. and Sardet, C. and Sieracki, M. and Speich, S. and Stemmann, L. and Sullivan, M.B. and Wincker, P. and Eveillard, D. and Lombard, F. and Coordinators, Tara Oceans},\n\tyear = {2020},\n\tpages = {428--445},\n}\n\n

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\n \n\n \n \n \n \n \n \n Genome resolved biogeography of mamiellales.\n \n \n \n \n\n\n \n Leconte, J.; Benites, L.; Vannier, T.; Wincker, P.; Piganeau, G.; and Jaillon, O.\n\n\n \n\n\n\n Genes, 11(1). 2020.\n \n\n\n\n
\n\n\n\n \n \n $\"Genome$ Paper\n \n \n\n \n \n doi\n \n \n\n \n link\n \n \n\n bibtex\n \n\n \n\n \n \n \n 1 download\n \n \n\n \n \n \n \n \n \n \n\n \n \n \n\n\n\n

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@article{leconte_genome_2020,\n\ttitle = {Genome resolved biogeography of mamiellales},\n\tvolume = {11},\n\turl = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-85077855628&doi=10.3390%2fgenes11010066&partnerID=40&md5=bf8d79bccef689b0b657aa61a4e82568},\n\tdoi = {10.3390/genes11010066},\n\tnumber = {1},\n\tjournal = {Genes},\n\tauthor = {Leconte, J. and Benites, L.F. and Vannier, T. and Wincker, P. and Piganeau, G. and Jaillon, O.},\n\tyear = {2020},\n}\n\n

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\n \n\n \n \n \n \n \n \n Genome-enabled phylogenetic and functional reconstruction of an araphid pennate diatom Plagiostriata sp. CCMP470, previously assigned as a radial centric diatom, and its bacterial commensal.\n \n \n \n \n\n\n \n Sato, S.; Nanjappa, D.; Dorrell, R. G.; Vieira, F. R. J.; Kazamia, E.; Tirichine, L.; Veluchamy, A.; Heilig, R.; Aury, J.; Jaillon, O.; Wincker, P.; Fussy, Z.; Obornik, M.; Muñoz-Gómez, S. A.; Mann, D. G.; Bowler, C.; and Zingone, A.\n\n\n \n\n\n\n Scientific Reports, 10(1): 9449. June 2020.\n Number: 1 Publisher: Nature Publishing Group\n\n\n\n
\n\n\n\n \n \n $\"Genome-enabled$ Paper\n \n \n\n \n \n doi\n \n \n\n \n link\n \n \n\n bibtex\n \n\n \n \n \n abstract \n \n\n \n\n \n \n \n \n \n \n \n\n \n \n \n \n \n \n \n\n\n\n

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@article{sato_genome-enabled_2020,\n\ttitle = {Genome-enabled phylogenetic and functional reconstruction of an araphid pennate diatom {Plagiostriata} sp. {CCMP470}, previously assigned as a radial centric diatom, and its bacterial commensal},\n\tvolume = {10},\n\tcopyright = {2020 The Author(s)},\n\tissn = {2045-2322},\n\turl = {https://www.nature.com/articles/s41598-020-65941-x},\n\tdoi = {10.1038/s41598-020-65941-x},\n\tabstract = {Diatoms are an ecologically fundamental and highly diverse group of algae, dominating marine primary production in both open-water and coastal communities. The diatoms include both centric species, which may have radial or polar symmetry, and the pennates, which include raphid and araphid species and arose within the centric lineage. Here, we use combined microscopic and molecular information to reclassify a diatom strain CCMP470, previously annotated as a radial centric species related to Leptocylindrus danicus, as an araphid pennate species in the staurosiroid lineage, within the genus Plagiostriata. CCMP470 shares key ultrastructural features with Plagiostriata taxa, such as the presence of a sternum with parallel striae, and the presence of a highly reduced labiate process on its valve; and this evolutionary position is robustly supported by multigene phylogenetic analysis. We additionally present a draft genome of CCMP470, which is the first genome available for a staurosiroid lineage. 270 Pfams (19\\%) found in the CCMP470 genome are not known in other diatom genomes, which otherwise does not hold big novelties compared to genomes of non-staurosiroid diatoms. Notably, our DNA library contains the genome of a bacterium within the Rhodobacterales, an alpha-proteobacterial lineage known frequently to associate with algae. We demonstrate the presence of commensal alpha-proteobacterial sequences in other published algal genome and transcriptome datasets, which may indicate widespread and persistent co-occurrence.},\n\tlanguage = {en},\n\tnumber = {1},\n\turldate = {2023-06-05},\n\tjournal = {Scientific Reports},\n\tauthor = {Sato, Shinya and Nanjappa, Deepak and Dorrell, Richard G. and Vieira, Fabio Rocha Jimenez and Kazamia, Elena and Tirichine, Leila and Veluchamy, Alaguraj and Heilig, Roland and Aury, Jean-Marc and Jaillon, Olivier and Wincker, Patrick and Fussy, Zoltan and Obornik, Miroslav and Muñoz-Gómez, Sergio A. and Mann, David G. and Bowler, Chris and Zingone, Adriana},\n\tmonth = jun,\n\tyear = {2020},\n\tnote = {Number: 1\nPublisher: Nature Publishing Group},\n\tkeywords = {Ecology, Microbiology},\n\tpages = {9449},\n\tfile = {Full Text PDF:C\\:\\\\Users\\\\ojaillon\\\\Zotero\\\\storage\\\\JWDXWL29\\\\Sato et al. - 2020 - Genome-enabled phylogenetic and functional reconst.pdf:application/pdf},\n}\n\n

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\n \n 2019\n \n \n (7)\n \n \n

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\n \n\n \n \n \n \n \n \n Gene Expression Changes and Community Turnover Differentially Shape the Global Ocean Metatranscriptome.\n \n \n \n \n\n\n \n Salazar, G.; Paoli, L.; Alberti, A.; Huerta-Cepas, J.; Ruscheweyh, H.; Cuenca, M.; Field, C.; Coelho, L.; Cruaud, C.; Engelen, S.; Gregory, A.; Labadie, K.; Marec, C.; Pelletier, E.; Royo-Llonch, M.; Roux, S.; Sánchez, P.; Uehara, H.; Zayed, A.; Zeller, G.; Carmichael, M.; Dimier, C.; Ferland, J.; Kandels, S.; Picheral, M.; Pisarev, S.; Poulain, J.; Acinas, S.; Babin, M.; Bork, P.; Boss, E.; Bowler, C.; Cochrane, G.; de Vargas, C.; Follows, M.; Gorsky, G.; Grimsley, N.; Guidi, L.; Hingamp, P.; Iudicone, D.; Jaillon, O.; Kandels-Lewis, S.; Karp-Boss, L.; Karsenti, E.; Not, F.; Ogata, H.; Pesant, S.; Poulton, N.; Raes, J.; Sardet, C.; Speich, S.; Stemmann, L.; Sullivan, M.; Sunagawa, S.; Wincker, P.; and Coordinators, T. O.\n\n\n \n\n\n\n Cell, 179(5): 1068–1083.e21. 2019.\n \n\n\n\n
\n\n\n\n \n \n $\"Gene$ Paper\n \n \n\n \n \n doi\n \n \n\n \n link\n \n \n\n bibtex\n \n\n \n\n \n \n \n 9 downloads\n \n \n\n \n \n \n \n \n \n \n\n \n \n \n\n\n\n

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@article{salazar_gene_2019,\n\ttitle = {Gene {Expression} {Changes} and {Community} {Turnover} {Differentially} {Shape} the {Global} {Ocean} {Metatranscriptome}},\n\tvolume = {179},\n\turl = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-85074784610&doi=10.1016%2fj.cell.2019.10.014&partnerID=40&md5=dfe8b78f0819bd1767883d7dc041bfc4},\n\tdoi = {10.1016/j.cell.2019.10.014},\n\tnumber = {5},\n\tjournal = {Cell},\n\tauthor = {Salazar, G. and Paoli, L. and Alberti, A. and Huerta-Cepas, J. and Ruscheweyh, H.-J. and Cuenca, M. and Field, C.M. and Coelho, L.P. and Cruaud, C. and Engelen, S. and Gregory, A.C. and Labadie, K. and Marec, C. and Pelletier, E. and Royo-Llonch, M. and Roux, S. and Sánchez, P. and Uehara, H. and Zayed, A.A. and Zeller, G. and Carmichael, M. and Dimier, C. and Ferland, J. and Kandels, S. and Picheral, M. and Pisarev, S. and Poulain, J. and Acinas, S.G. and Babin, M. and Bork, P. and Boss, E. and Bowler, C. and Cochrane, G. and de Vargas, C. and Follows, M. and Gorsky, G. and Grimsley, N. and Guidi, L. and Hingamp, P. and Iudicone, D. and Jaillon, O. and Kandels-Lewis, S. and Karp-Boss, L. and Karsenti, E. and Not, F. and Ogata, H. and Pesant, S. and Poulton, N. and Raes, J. and Sardet, C. and Speich, S. and Stemmann, L. and Sullivan, M.B. and Sunagawa, S. and Wincker, P. and Coordinators, Tara Oceans},\n\tyear = {2019},\n\tpages = {1068--1083.e21},\n}\n\n

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\n \n\n \n \n \n \n \n \n Global Trends in Marine Plankton Diversity across Kingdoms of Life.\n \n \n \n \n\n\n \n Ibarbalz, F.; Henry, N.; Brandão, M.; Martini, S.; Busseni, G.; Byrne, H.; Coelho, L.; Endo, H.; Gasol, J.; Gregory, A.; Mahé, F.; Rigonato, J.; Royo-Llonch, M.; Salazar, G.; Sanz-Sáez, I.; Scalco, E.; Soviadan, D.; Zayed, A.; Zingone, A.; Labadie, K.; Ferland, J.; Marec, C.; Kandels, S.; Picheral, M.; Dimier, C.; Poulain, J.; Pisarev, S.; Carmichael, M.; Pesant, S.; Acinas, S.; Babin, M.; Bork, P.; Boss, E.; Bowler, C.; Cochrane, G.; de Vargas, C.; Follows, M.; Gorsky, G.; Grimsley, N.; Guidi, L.; Hingamp, P.; Iudicone, D.; Jaillon, O.; Karp-Boss, L.; Karsenti, E.; Not, F.; Ogata, H.; Poulton, N.; Raes, J.; Sardet, C.; Speich, S.; Stemmann, L.; Sullivan, M.; Sunagawa, S.; Wincker, P.; Pelletier, E.; Bopp, L.; Lombard, F.; Zinger, L.; and Coordinators, T. O.\n\n\n \n\n\n\n Cell, 179(5): 1084–1097.e21. 2019.\n \n\n\n\n
\n\n\n\n \n \n $\"Global$ Paper\n \n \n\n \n \n doi\n \n \n\n \n link\n \n \n\n bibtex\n \n\n \n\n \n\n \n \n \n \n \n \n \n\n \n \n \n\n\n\n

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@article{ibarbalz_global_2019,\n\ttitle = {Global {Trends} in {Marine} {Plankton} {Diversity} across {Kingdoms} of {Life}},\n\tvolume = {179},\n\turl = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-85074775816&doi=10.1016%2fj.cell.2019.10.008&partnerID=40&md5=3073940434738ada9f8c2412207b08d4},\n\tdoi = {10.1016/j.cell.2019.10.008},\n\tnumber = {5},\n\tjournal = {Cell},\n\tauthor = {Ibarbalz, F.M. and Henry, N. and Brandão, M.C. and Martini, S. and Busseni, G. and Byrne, H. and Coelho, L.P. and Endo, H. and Gasol, J.M. and Gregory, A.C. and Mahé, F. and Rigonato, J. and Royo-Llonch, M. and Salazar, G. and Sanz-Sáez, I. and Scalco, E. and Soviadan, D. and Zayed, A.A. and Zingone, A. and Labadie, K. and Ferland, J. and Marec, C. and Kandels, S. and Picheral, M. and Dimier, C. and Poulain, J. and Pisarev, S. and Carmichael, M. and Pesant, S. and Acinas, S.G. and Babin, M. and Bork, P. and Boss, E. and Bowler, C. and Cochrane, G. and de Vargas, C. and Follows, M. and Gorsky, G. and Grimsley, N. and Guidi, L. and Hingamp, P. and Iudicone, D. and Jaillon, O. and Karp-Boss, L. and Karsenti, E. and Not, F. and Ogata, H. and Poulton, N. and Raes, J. and Sardet, C. and Speich, S. and Stemmann, L. and Sullivan, M.B. and Sunagawa, S. and Wincker, P. and Pelletier, E. and Bopp, L. and Lombard, F. and Zinger, L. and Coordinators, Tara Oceans},\n\tyear = {2019},\n\tpages = {1084--1097.e21},\n}\n\n

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\n \n\n \n \n \n \n \n \n Elucidation of Codon Usage Signatures across the Domains of Life.\n \n \n \n \n\n\n \n Novoa, E.; Jungreis, I.; Jaillon, O.; Kellis, M.; and Leitner, T.\n\n\n \n\n\n\n Molecular Biology and Evolution, 36(10): 2328–2339. 2019.\n \n\n\n\n
\n\n\n\n \n \n $\"Elucidation$ Paper\n \n \n\n \n \n doi\n \n \n\n \n link\n \n \n\n bibtex\n \n\n \n\n \n\n \n \n \n \n \n \n \n\n \n \n \n\n\n\n

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@article{novoa_elucidation_2019,\n\ttitle = {Elucidation of {Codon} {Usage} {Signatures} across the {Domains} of {Life}},\n\tvolume = {36},\n\turl = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-85072628380&doi=10.1093%2fmolbev%2fmsz124&partnerID=40&md5=ce54617416a6f013e2e3bed1bef07c36},\n\tdoi = {10.1093/molbev/msz124},\n\tnumber = {10},\n\tjournal = {Molecular Biology and Evolution},\n\tauthor = {Novoa, E.M. and Jungreis, I. and Jaillon, O. and Kellis, M. and Leitner, T.},\n\tyear = {2019},\n\tpages = {2328--2339},\n}\n\n

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\n \n\n \n \n \n \n \n \n Assessing the viral content of uncultured picoeukaryotes in the global-ocean by single cell genomics.\n \n \n \n \n\n\n \n Castillo, Y.; Mangot, J.; Benites, L.; Logares, R.; Kuronishi, M.; Ogata, H.; Jaillon, O.; Massana, R.; Sebastián, M.; and Vaqué, D.\n\n\n \n\n\n\n Molecular Ecology, 28(18): 4272–4289. 2019.\n \n\n\n\n
\n\n\n\n \n \n $\"Assessing$ Paper\n \n \n\n \n \n doi\n \n \n\n \n link\n \n \n\n bibtex\n \n\n \n\n \n\n \n \n \n \n \n \n \n\n \n \n \n\n\n\n

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@article{castillo_assessing_2019,\n\ttitle = {Assessing the viral content of uncultured picoeukaryotes in the global-ocean by single cell genomics},\n\tvolume = {28},\n\turl = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-85073082744&doi=10.1111%2fmec.15210&partnerID=40&md5=3017a38a3da45f49bfd50dba165b6e7d},\n\tdoi = {10.1111/mec.15210},\n\tnumber = {18},\n\tjournal = {Molecular Ecology},\n\tauthor = {Castillo, Y.M. and Mangot, J.-F. and Benites, L.F. and Logares, R. and Kuronishi, M. and Ogata, H. and Jaillon, O. and Massana, R. and Sebastián, M. and Vaqué, D.},\n\tyear = {2019},\n\tpages = {4272--4289},\n}\n\n

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\n \n\n \n \n \n \n \n \n Marine DNA Viral Macro- and Microdiversity from Pole to Pole.\n \n \n \n \n\n\n \n Gregory, A.; Zayed, A.; Conceição-Neto, N.; Temperton, B.; Bolduc, B.; Alberti, A.; Ardyna, M.; Arkhipova, K.; Carmichael, M.; Cruaud, C.; Dimier, C.; Domínguez-Huerta, G.; Ferland, J.; Kandels, S.; Liu, Y.; Marec, C.; Pesant, S.; Picheral, M.; Pisarev, S.; Poulain, J.; Tremblay, J.; Vik, D.; Acinas, S.; Babin, M.; Bork, P.; Boss, E.; Bowler, C.; Cochrane, G.; de Vargas, C.; Follows, M.; Gorsky, G.; Grimsley, N.; Guidi, L.; Hingamp, P.; Iudicone, D.; Jaillon, O.; Kandels-Lewis, S.; Karp-Boss, L.; Karsenti, E.; Not, F.; Ogata, H.; Poulton, N.; Raes, J.; Sardet, C.; Speich, S.; Stemmann, L.; Sullivan, M.; Sunagawa, S.; Wincker, P.; Culley, A.; Dutilh, B.; Roux, S.; and Coordinators, T. O.\n\n\n \n\n\n\n Cell, 177(5): 1109–1123.e14. 2019.\n \n\n\n\n
\n\n\n\n \n \n $\"Marine$ Paper\n \n \n\n \n \n doi\n \n \n\n \n link\n \n \n\n bibtex\n \n\n \n\n \n\n \n \n \n \n \n \n \n\n \n \n \n\n\n\n

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@article{gregory_marine_2019,\n\ttitle = {Marine {DNA} {Viral} {Macro}- and {Microdiversity} from {Pole} to {Pole}},\n\tvolume = {177},\n\turl = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-85065207169&doi=10.1016%2fj.cell.2019.03.040&partnerID=40&md5=330cd5d709cce0eba01bab60553357e1},\n\tdoi = {10.1016/j.cell.2019.03.040},\n\tnumber = {5},\n\tjournal = {Cell},\n\tauthor = {Gregory, A.C. and Zayed, A.A. and Conceição-Neto, N. and Temperton, B. and Bolduc, B. and Alberti, A. and Ardyna, M. and Arkhipova, K. and Carmichael, M. and Cruaud, C. and Dimier, C. and Domínguez-Huerta, G. and Ferland, J. and Kandels, S. and Liu, Y. and Marec, C. and Pesant, S. and Picheral, M. and Pisarev, S. and Poulain, J. and Tremblay, J.-É. and Vik, D. and Acinas, S.G. and Babin, M. and Bork, P. and Boss, E. and Bowler, C. and Cochrane, G. and de Vargas, C. and Follows, M. and Gorsky, G. and Grimsley, N. and Guidi, L. and Hingamp, P. and Iudicone, D. and Jaillon, O. and Kandels-Lewis, S. and Karp-Boss, L. and Karsenti, E. and Not, F. and Ogata, H. and Poulton, N. and Raes, J. and Sardet, C. and Speich, S. and Stemmann, L. and Sullivan, M.B. and Sunagawa, S. and Wincker, P. and Culley, A.I. and Dutilh, B.E. and Roux, S. and Coordinators, Tara Oceans},\n\tyear = {2019},\n\tpages = {1109--1123.e14},\n}\n\n

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\n \n\n \n \n \n \n \n \n Discovering millions of plankton genomic markers from the Atlantic Ocean and the Mediterranean Sea.\n \n \n \n \n\n\n \n Arif, M.; Gauthier, J.; Sugier, K.; Iudicone, D.; Jaillon, O.; Wincker, P.; Peterlongo, P.; and Madoui, M.\n\n\n \n\n\n\n Molecular Ecology Resources, 19(2): 526–535. 2019.\n \n\n\n\n
\n\n\n\n \n \n $\"Discovering$ Paper\n \n \n\n \n \n doi\n \n \n\n \n link\n \n \n\n bibtex\n \n\n \n\n \n \n \n 2 downloads\n \n \n\n \n \n \n \n \n \n \n\n \n \n \n\n\n\n

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@article{arif_discovering_2019,\n\ttitle = {Discovering millions of plankton genomic markers from the {Atlantic} {Ocean} and the {Mediterranean} {Sea}},\n\tvolume = {19},\n\turl = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-85062061284&doi=10.1111%2f1755-0998.12985&partnerID=40&md5=2538b6c11562546e1cad03e2429b2f1a},\n\tdoi = {10.1111/1755-0998.12985},\n\tnumber = {2},\n\tjournal = {Molecular Ecology Resources},\n\tauthor = {Arif, M. and Gauthier, J. and Sugier, K. and Iudicone, D. and Jaillon, O. and Wincker, P. and Peterlongo, P. and Madoui, M.-A.},\n\tyear = {2019},\n\tpages = {526--535},\n}\n\n

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\n \n\n \n \n \n \n \n \n Single cell genomics yields a wide diversity of small planktonic protists across major ocean ecosystems.\n \n \n \n \n\n\n \n Sieracki, M. E.; Poulton, N. J.; Jaillon, O.; Wincker, P.; de Vargas, C.; Rubinat-Ripoll, L.; Stepanauskas, R.; Logares, R.; and Massana, R.\n\n\n \n\n\n\n Scientific Reports, 9(1): 6025. April 2019.\n Number: 1 Publisher: Nature Publishing Group\n\n\n\n
\n\n\n\n \n \n $\"Single$ Paper\n \n \n\n \n \n doi\n \n \n\n \n link\n \n \n\n bibtex\n \n\n \n \n \n abstract \n \n\n \n\n \n \n \n \n \n \n \n\n \n \n \n \n \n \n \n \n \n \n \n\n\n\n

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@article{sieracki_single_2019,\n\ttitle = {Single cell genomics yields a wide diversity of small planktonic protists across major ocean ecosystems},\n\tvolume = {9},\n\tcopyright = {2019 The Author(s)},\n\tissn = {2045-2322},\n\turl = {https://www.nature.com/articles/s41598-019-42487-1},\n\tdoi = {10.1038/s41598-019-42487-1},\n\tabstract = {Marine planktonic protists are critical components of ocean ecosystems and are highly diverse. Molecular sequencing methods are being used to describe this diversity and reveal new associations and metabolisms that are important to how these ecosystems function. We describe here the use of the single cell genomics approach to sample and interrogate the diversity of the smaller (pico- and nano-sized) protists from a range of oceanic samples. We created over 900 single amplified genomes (SAGs) from 8 Tara Ocean samples across the Indian Ocean and the Mediterranean Sea. We show that flow cytometric sorting of single cells effectively distinguishes plastidic and aplastidic cell types that agree with our understanding of protist phylogeny. Yields of genomic DNA with PCR-identifiable 18S rRNA gene sequence from single cells was low (15\\% of aplastidic cell sorts, and 7\\% of plastidic sorts) and tests with alternate primers and comparisons to metabarcoding did not reveal phylogenetic bias in the major protist groups. There was little evidence of significant bias against or in favor of any phylogenetic group expected or known to be present. The four open ocean stations in the Indian Ocean had similar communities, despite ranging from 14°N to 20°S latitude, and they differed from the Mediterranean station. Single cell genomics of protists suggests that the taxonomic diversity of the dominant taxa found in only several hundreds of microliters of surface seawater is similar to that found in molecular surveys where liters of sample are filtered.},\n\tlanguage = {en},\n\tnumber = {1},\n\turldate = {2023-06-05},\n\tjournal = {Scientific Reports},\n\tauthor = {Sieracki, M. E. and Poulton, N. J. and Jaillon, O. and Wincker, P. and de Vargas, C. and Rubinat-Ripoll, L. and Stepanauskas, R. and Logares, R. and Massana, R.},\n\tmonth = apr,\n\tyear = {2019},\n\tnote = {Number: 1\nPublisher: Nature Publishing Group},\n\tkeywords = {Microbial ecology, Marine biology, Microbial biooceanography, Microbiology techniques},\n\tpages = {6025},\n\tfile = {Full Text PDF:C\\:\\\\Users\\\\ojaillon\\\\Zotero\\\\storage\\\\2D4BNNVJ\\\\Sieracki et al. - 2019 - Single cell genomics yields a wide diversity of sm.pdf:application/pdf},\n}\n\n

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\n \n\n \n \n \n \n \n \n A global ocean atlas of eukaryotic genes.\n \n \n \n \n\n\n \n Carradec, Q.; Pelletier, E.; Da Silva, C.; Alberti, A.; Seeleuthner, Y.; Blanc-Mathieu, R.; Lima-Mendez, G.; Rocha, F.; Tirichine, L.; Labadie, K.; Kirilovsky, A.; Bertrand, A.; Engelen, S.; Madoui, M.; Méheust, R.; Poulain, J.; Romac, S.; Richter, D. J.; Yoshikawa, G.; Dimier, C.; Kandels-Lewis, S.; Picheral, M.; Searson, S.; Jaillon, O.; Aury, J.; Karsenti, E.; Sullivan, M. B.; Sunagawa, S.; Bork, P.; Not, F.; Hingamp, P.; Raes, J.; Guidi, L.; Ogata, H.; de Vargas, C.; Iudicone, D.; Bowler, C.; and Wincker, P.\n\n\n \n\n\n\n Nature Communications, 9(1): 373. January 2018.\n Number: 1 Publisher: Nature Publishing Group\n\n\n\n
\n\n\n\n \n \n $\"A$ Paper\n \n \n\n \n \n doi\n \n \n\n \n link\n \n \n\n bibtex\n \n\n \n \n \n abstract \n \n\n \n \n \n 4 downloads\n \n \n\n \n \n \n \n \n \n \n\n \n \n \n \n \n \n \n \n \n \n \n\n\n\n

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@article{carradec_global_2018,\n\ttitle = {A global ocean atlas of eukaryotic genes},\n\tvolume = {9},\n\tcopyright = {2018 The Author(s)},\n\tissn = {2041-1723},\n\turl = {https://www.nature.com/articles/s41467-017-02342-1},\n\tdoi = {10.1038/s41467-017-02342-1},\n\tabstract = {While our knowledge about the roles of microbes and viruses in the ocean has increased tremendously due to recent advances in genomics and metagenomics, research on marine microbial eukaryotes and zooplankton has benefited much less from these new technologies because of their larger genomes, their enormous diversity, and largely unexplored physiologies. Here, we use a metatranscriptomics approach to capture expressed genes in open ocean Tara Oceans stations across four organismal size fractions. The individual sequence reads cluster into 116 million unigenes representing the largest reference collection of eukaryotic transcripts from any single biome. The catalog is used to unveil functions expressed by eukaryotic marine plankton, and to assess their functional biogeography. Almost half of the sequences have no similarity with known proteins, and a great number belong to new gene families with a restricted distribution in the ocean. Overall, the resource provides the foundations for exploring the roles of marine eukaryotes in ocean ecology and biogeochemistry.},\n\tlanguage = {en},\n\tnumber = {1},\n\turldate = {2023-06-05},\n\tjournal = {Nature Communications},\n\tauthor = {Carradec, Quentin and Pelletier, Eric and Da Silva, Corinne and Alberti, Adriana and Seeleuthner, Yoann and Blanc-Mathieu, Romain and Lima-Mendez, Gipsi and Rocha, Fabio and Tirichine, Leila and Labadie, Karine and Kirilovsky, Amos and Bertrand, Alexis and Engelen, Stefan and Madoui, Mohammed-Amin and Méheust, Raphaël and Poulain, Julie and Romac, Sarah and Richter, Daniel J. and Yoshikawa, Genki and Dimier, Céline and Kandels-Lewis, Stefanie and Picheral, Marc and Searson, Sarah and Jaillon, Olivier and Aury, Jean-Marc and Karsenti, Eric and Sullivan, Matthew B. and Sunagawa, Shinichi and Bork, Peer and Not, Fabrice and Hingamp, Pascal and Raes, Jeroen and Guidi, Lionel and Ogata, Hiroyuki and de Vargas, Colomban and Iudicone, Daniele and Bowler, Chris and Wincker, Patrick},\n\tmonth = jan,\n\tyear = {2018},\n\tnote = {Number: 1\nPublisher: Nature Publishing Group},\n\tkeywords = {Genomics, Microbial ecology, Marine biology, Water microbiology},\n\tpages = {373},\n\tfile = {Full Text PDF:C\\:\\\\Users\\\\ojaillon\\\\Zotero\\\\storage\\\\JB88BNXB\\\\Carradec et al. - 2018 - A global ocean atlas of eukaryotic genes.pdf:application/pdf},\n}\n\n

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\n \n\n \n \n \n \n \n \n Single-cell genomics of multiple uncultured stramenopiles reveals underestimated functional diversity across oceans.\n \n \n \n \n\n\n \n Seeleuthner, Y.; Mondy, S.; Lombard, V.; Carradec, Q.; Pelletier, E.; Wessner, M.; Leconte, J.; Mangot, J.; Poulain, J.; Labadie, K.; Logares, R.; Sunagawa, S.; de Berardinis, V.; Salanoubat, M.; Dimier, C.; Kandels-Lewis, S.; Picheral, M.; Searson, S.; Pesant, S.; Poulton, N.; Stepanauskas, R.; Bork, P.; Bowler, C.; Hingamp, P.; Sullivan, M. B.; Iudicone, D.; Massana, R.; Aury, J.; Henrissat, B.; Karsenti, E.; Jaillon, O.; Sieracki, M.; de Vargas, C.; and Wincker, P.\n\n\n \n\n\n\n Nature Communications, 9(1): 310. January 2018.\n Number: 1 Publisher: Nature Publishing Group\n\n\n\n
\n\n\n\n \n \n $\"Single-cell$ Paper\n \n \n\n \n \n doi\n \n \n\n \n link\n \n \n\n bibtex\n \n\n \n \n \n abstract \n \n\n \n \n \n 1 download\n \n \n\n \n \n \n \n \n \n \n\n \n \n \n \n \n \n \n \n \n \n \n\n\n\n

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@article{seeleuthner_single-cell_2018,\n\ttitle = {Single-cell genomics of multiple uncultured stramenopiles reveals underestimated functional diversity across oceans},\n\tvolume = {9},\n\tcopyright = {2018 The Author(s)},\n\tissn = {2041-1723},\n\turl = {https://www.nature.com/articles/s41467-017-02235-3},\n\tdoi = {10.1038/s41467-017-02235-3},\n\tabstract = {Single-celled eukaryotes (protists) are critical players in global biogeochemical cycling of nutrients and energy in the oceans. While their roles as primary producers and grazers are well appreciated, other aspects of their life histories remain obscure due to challenges in culturing and sequencing their natural diversity. Here, we exploit single-cell genomics and metagenomics data from the circumglobal Tara Oceans expedition to analyze the genome content and apparent oceanic distribution of seven prevalent lineages of uncultured heterotrophic stramenopiles. Based on the available data, each sequenced genome or genotype appears to have a specific oceanic distribution, principally correlated with water temperature and depth. The genome content provides hypotheses for specialization in terms of cell motility, food spectra, and trophic stages, including the potential impact on their lifestyles of horizontal gene transfer from prokaryotes. Our results support the idea that prominent heterotrophic marine protists perform diverse functions in ocean ecology.},\n\tlanguage = {en},\n\tnumber = {1},\n\turldate = {2023-06-05},\n\tjournal = {Nature Communications},\n\tauthor = {Seeleuthner, Yoann and Mondy, Samuel and Lombard, Vincent and Carradec, Quentin and Pelletier, Eric and Wessner, Marc and Leconte, Jade and Mangot, Jean-François and Poulain, Julie and Labadie, Karine and Logares, Ramiro and Sunagawa, Shinichi and de Berardinis, Véronique and Salanoubat, Marcel and Dimier, Céline and Kandels-Lewis, Stefanie and Picheral, Marc and Searson, Sarah and Pesant, Stephane and Poulton, Nicole and Stepanauskas, Ramunas and Bork, Peer and Bowler, Chris and Hingamp, Pascal and Sullivan, Matthew B. and Iudicone, Daniele and Massana, Ramon and Aury, Jean-Marc and Henrissat, Bernard and Karsenti, Eric and Jaillon, Olivier and Sieracki, Mike and de Vargas, Colomban and Wincker, Patrick},\n\tmonth = jan,\n\tyear = {2018},\n\tnote = {Number: 1\nPublisher: Nature Publishing Group},\n\tkeywords = {Genomics, Microbial ecology, Marine biology, Water microbiology},\n\tpages = {310},\n\tfile = {Full Text PDF:C\\:\\\\Users\\\\ojaillon\\\\Zotero\\\\storage\\\\A3V3MFRC\\\\Seeleuthner et al. - 2018 - Single-cell genomics of multiple uncultured strame.pdf:application/pdf},\n}\n\n

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\n \n\n \n \n \n \n \n \n A new sequence data set of SSU rRNA gene for Scleractinia and its phylogenetic and ecological applications.\n \n \n \n \n\n\n \n Arrigoni, R.; Vacherie, B.; Benzoni, F.; Stefani, F.; Karsenti, E.; Jaillon, O.; Not, F.; Nunes, F.; Payri, C.; Wincker, P.; and Barbe, V.\n\n\n \n\n\n\n Molecular Ecology Resources, 17(5): 1054–1071. 2017.\n \n\n\n\n
\n\n\n\n \n \n $\"A$ Paper\n \n \n\n \n \n doi\n \n \n\n \n link\n \n \n\n bibtex\n \n\n \n\n \n\n \n \n \n \n \n \n \n\n \n \n \n\n\n\n

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@article{arrigoni_new_2017,\n\ttitle = {A new sequence data set of {SSU} {rRNA} gene for {Scleractinia} and its phylogenetic and ecological applications},\n\tvolume = {17},\n\turl = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-85031422214&doi=10.1111%2f1755-0998.12640&partnerID=40&md5=2476e57981c2161e8a22e10e7f41ccf9},\n\tdoi = {10.1111/1755-0998.12640},\n\tnumber = {5},\n\tjournal = {Molecular Ecology Resources},\n\tauthor = {Arrigoni, R. and Vacherie, B. and Benzoni, F. and Stefani, F. and Karsenti, E. and Jaillon, O. and Not, F. and Nunes, F. and Payri, C. and Wincker, P. and Barbe, V.},\n\tyear = {2017},\n\tpages = {1054--1071},\n}\n\n

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\n \n\n \n \n \n \n \n \n Viral to metazoan marine plankton nucleotide sequences from the Tara Oceans expedition.\n \n \n \n \n\n\n \n Alberti, A.; Poulain, J.; Engelen, S.; Labadie, K.; Romac, S.; Ferrera, I.; Albini, G.; Aury, J.; Belser, C.; Bertrand, A.; Cruaud, C.; Da Silva, C.; Dossat, C.; Gavory, F.; Gas, S.; Guy, J.; Haquelle, M.; Jacoby, E.; Jaillon, O.; Lemainque, A.; Pelletier, E.; Samson, G.; Wessner, M.; Acinas, S.; Royo-Llonch, M.; Cornejo-Castillo, F.; Logares, R.; Fernández-Gómez, B.; Bowler, C.; Cochrane, G.; Amid, C.; Hoopen, P.; De Vargas, C.; Grimsley, N.; Desgranges, E.; Kandels-Lewis, S.; Ogata, H.; Poulton, N.; Sieracki, M.; Stepanauskas, R.; Sullivan, M.; Brum, J.; Duhaime, M.; Poulos, B.; Hurwitz, B.; Pesant, S.; Karsenti, E.; Wincker, P.; Bazire, P.; Beluche, O.; Bertrand, L.; Besnard-Gonnet, M.; Bordelais, I.; Boutard, M.; Dubois, M.; Dumont, C.; Ettedgui, E.; Fernandez, P.; Garcia, E.; Aiach, N.; Guerin, T.; Hamon, C.; Brun, E.; Lebled, S.; Lenoble, P.; Louesse, C.; Mahieu, E.; Mairey, B.; Martins, N.; Megret, C.; Milani, C.; Muanga, J.; Orvain, C.; Payen, E.; Perroud, P.; Petit, E.; Robert, D.; Ronsin, M.; Vacherie, B.; Bork, P.; Boss, E.; Follows, M.; Gorsky, G.; Hingamp, P.; Iudicone, D.; Karp-Boss, L.; Not, F.; Raes, J.; Sardet, C.; Speich, S.; Stemmann, L.; Sunagawa, S.; Team, G. T.; and Coordinators, T. O. C.\n\n\n \n\n\n\n Scientific Data, 4. 2017.\n \n\n\n\n
\n\n\n\n \n \n $\"Viral$ Paper\n \n \n\n \n \n doi\n \n \n\n \n link\n \n \n\n bibtex\n \n\n \n\n \n \n \n 1 download\n \n \n\n \n \n \n \n \n \n \n\n \n \n \n\n\n\n

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@article{alberti_viral_2017,\n\ttitle = {Viral to metazoan marine plankton nucleotide sequences from the {Tara} {Oceans} expedition},\n\tvolume = {4},\n\turl = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-85026786061&doi=10.1038%2fsdata.2017.93&partnerID=40&md5=1521dd8e37432d63b45cd9c61387bf61},\n\tdoi = {10.1038/sdata.2017.93},\n\tjournal = {Scientific Data},\n\tauthor = {Alberti, A. and Poulain, J. and Engelen, S. and Labadie, K. and Romac, S. and Ferrera, I. and Albini, G. and Aury, J.-M. and Belser, C. and Bertrand, A. and Cruaud, C. and Da Silva, C. and Dossat, C. and Gavory, F. and Gas, S. and Guy, J. and Haquelle, M. and Jacoby, E. and Jaillon, O. and Lemainque, A. and Pelletier, E. and Samson, G. and Wessner, M. and Acinas, S.G. and Royo-Llonch, M. and Cornejo-Castillo, F.M. and Logares, R. and Fernández-Gómez, B. and Bowler, C. and Cochrane, G. and Amid, C. and Hoopen, P.T. and De Vargas, C. and Grimsley, N. and Desgranges, E. and Kandels-Lewis, S. and Ogata, H. and Poulton, N. and Sieracki, M.E. and Stepanauskas, R. and Sullivan, M.B. and Brum, J.R. and Duhaime, M.B. and Poulos, B.T. and Hurwitz, B.L. and Pesant, S. and Karsenti, E. and Wincker, P. and Bazire, P. and Beluche, O. and Bertrand, L. and Besnard-Gonnet, M. and Bordelais, I. and Boutard, M. and Dubois, M. and Dumont, C. and Ettedgui, E. and Fernandez, P. and Garcia, E. and Aiach, N.G. and Guerin, T. and Hamon, C. and Brun, E. and Lebled, S. and Lenoble, P. and Louesse, C. and Mahieu, E. and Mairey, B. and Martins, N. and Megret, C. and Milani, C. and Muanga, J. and Orvain, C. and Payen, E. and Perroud, P. and Petit, E. and Robert, D. and Ronsin, M. and Vacherie, B. and Bork, P. and Boss, E. and Follows, M. and Gorsky, G. and Hingamp, P. and Iudicone, D. and Karp-Boss, L. and Not, F. and Raes, J. and Sardet, C. and Speich, S. and Stemmann, L. and Sunagawa, S. and Team, Genoscope Technical and Coordinators, Tara Oceans Consortium},\n\tyear = {2017},\n}\n\n

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\n \n\n \n \n \n \n \n \n Shaping the evolutionary tree of green plants: evidence from the GST family.\n \n \n \n \n\n\n \n Monticolo, F.; Colantuono, C.; and Chiusano, M. L.\n\n\n \n\n\n\n Scientific Reports, 7(1): 14363. October 2017.\n Number: 1 Publisher: Nature Publishing Group\n\n\n\n
\n\n\n\n \n \n $\"Shaping$ Paper\n \n \n\n \n \n doi\n \n \n\n \n link\n \n \n\n bibtex\n \n\n \n \n \n abstract \n \n\n \n\n \n \n \n \n \n \n \n\n \n \n \n \n \n \n \n\n\n\n

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@article{monticolo_shaping_2017,\n\ttitle = {Shaping the evolutionary tree of green plants: evidence from the {GST} family},\n\tvolume = {7},\n\tcopyright = {2017 The Author(s)},\n\tissn = {2045-2322},\n\tshorttitle = {Shaping the evolutionary tree of green plants},\n\turl = {https://www.nature.com/articles/s41598-017-14316-w},\n\tdoi = {10.1038/s41598-017-14316-w},\n\tabstract = {Glutathione-S-transferases (GSTs) are encoded by genes belonging to a wide ubiquitous family in aerobic species and catalyze the conjugation of electrophilic substrates to glutathione (GSH). GSTs are divided in different classes, both in plants and animals. In plants, GSTs function in several pathways, including those related to secondary metabolites biosynthesis, hormone homeostasis, defense from pathogens and allow the prevention and detoxification of damage from heavy metals and herbicides. 1107 GST protein sequences from 20 different plant species with sequenced genomes were analyzed. Our analysis assigns 666 unclassified GSTs proteins to specific classes, remarking the wide heterogeneity of this gene family. Moreover, we highlighted the presence of further subclasses within each class. Regarding the class GST-Tau, one possible subclass appears to be present in all the Tau members of ancestor plant species. Moreover, the results highlight the presence of members of the Tau class in Marchantiophytes and confirm previous observations on the absence of GST-Tau in Bryophytes and green algae. These results support the hypothesis regarding the paraphyletic origin of Bryophytes, but also suggest that Marchantiophytes may be on the same branch leading to superior plants, depicting an alternative model for green plants evolution.},\n\tlanguage = {en},\n\tnumber = {1},\n\turldate = {2023-06-05},\n\tjournal = {Scientific Reports},\n\tauthor = {Monticolo, Francesco and Colantuono, Chiara and Chiusano, Maria Luisa},\n\tmonth = oct,\n\tyear = {2017},\n\tnote = {Number: 1\nPublisher: Nature Publishing Group},\n\tkeywords = {Plant evolution, Classification and taxonomy},\n\tpages = {14363},\n\tfile = {Full Text PDF:C\\:\\\\Users\\\\ojaillon\\\\Zotero\\\\storage\\\\YDAZV6HG\\\\Monticolo et al. - 2017 - Shaping the evolutionary tree of green plants evi.pdf:application/pdf},\n}\n\n

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\n \n\n \n \n \n \n \n \n IL-1R8 is a checkpoint in NK cells regulating anti-tumour and anti-viral activity.\n \n \n \n \n\n\n \n Molgora, M.; Bonavita, E.; Ponzetta, A.; Riva, F.; Barbagallo, M.; Jaillon, S.; Popović, B.; Bernardini, G.; Magrini, E.; Gianni, F.; Zelenay, S.; Jonjić, S.; Santoni, A.; Garlanda, C.; and Mantovani, A.\n\n\n \n\n\n\n Nature, 551(7678): 110–114. November 2017.\n Number: 7678 Publisher: Nature Publishing Group\n\n\n\n
\n\n\n\n \n \n $\"IL-1R8$ Paper\n \n \n\n \n \n doi\n \n \n\n \n link\n \n \n\n bibtex\n \n\n \n \n \n abstract \n \n\n \n\n \n \n \n \n \n \n \n\n \n \n \n \n \n \n \n\n\n\n

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@article{molgora_il-1r8_2017,\n\ttitle = {{IL}-{1R8} is a checkpoint in {NK} cells regulating anti-tumour and anti-viral activity},\n\tvolume = {551},\n\tcopyright = {2017 Macmillan Publishers Limited, part of Springer Nature. All rights reserved.},\n\tissn = {1476-4687},\n\turl = {https://www.nature.com/articles/nature24293},\n\tdoi = {10.1038/nature24293},\n\tabstract = {Interleukin-1 receptor 8 (IL-1R8), a negative regulator of the IL-1 family of cytokines, restrains the activity of natural killer (NK) cells, suggesting that IL-1R8 acts as a checkpoint regulator of NK cell activation and that its blockade may be of use in cancer therapy.},\n\tlanguage = {en},\n\tnumber = {7678},\n\turldate = {2023-06-05},\n\tjournal = {Nature},\n\tauthor = {Molgora, Martina and Bonavita, Eduardo and Ponzetta, Andrea and Riva, Federica and Barbagallo, Marialuisa and Jaillon, Sébastien and Popović, Branka and Bernardini, Giovanni and Magrini, Elena and Gianni, Francesca and Zelenay, Santiago and Jonjić, Stipan and Santoni, Angela and Garlanda, Cecilia and Mantovani, Alberto},\n\tmonth = nov,\n\tyear = {2017},\n\tnote = {Number: 7678\nPublisher: Nature Publishing Group},\n\tkeywords = {Immunosurveillance, NK cells},\n\tpages = {110--114},\n\tfile = {Full Text PDF:C\\:\\\\Users\\\\ojaillon\\\\Zotero\\\\storage\\\\4QEJSBHE\\\\Molgora et al. - 2017 - IL-1R8 is a checkpoint in NK cells regulating anti.pdf:application/pdf},\n}\n\n

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\n \n\n \n \n \n \n \n \n Accessing the genomic information of unculturable oceanic picoeukaryotes by combining multiple single cells.\n \n \n \n \n\n\n \n Mangot, J.; Logares, R.; Sánchez, P.; Latorre, F.; Seeleuthner, Y.; Mondy, S.; Sieracki, M. E.; Jaillon, O.; Wincker, P.; Vargas, C. d.; and Massana, R.\n\n\n \n\n\n\n Scientific Reports, 7(1): 41498. January 2017.\n Number: 1 Publisher: Nature Publishing Group\n\n\n\n
\n\n\n\n \n \n $\"Accessing$ Paper\n \n \n\n \n \n doi\n \n \n\n \n link\n \n \n\n bibtex\n \n\n \n \n \n abstract \n \n\n \n\n \n \n \n \n \n \n \n\n \n \n \n \n \n \n \n \n \n \n \n\n\n\n

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@article{mangot_accessing_2017,\n\ttitle = {Accessing the genomic information of unculturable oceanic picoeukaryotes by combining multiple single cells},\n\tvolume = {7},\n\tcopyright = {2017 The Author(s)},\n\tissn = {2045-2322},\n\turl = {https://www.nature.com/articles/srep41498},\n\tdoi = {10.1038/srep41498},\n\tabstract = {Pico-sized eukaryotes play key roles in the functioning of marine ecosystems, but we still have a limited knowledge on their ecology and evolution. The MAST-4 lineage is of particular interest, since it is widespread in surface oceans, presents ecotypic differentiation and has defied culturing efforts so far. Single cell genomics (SCG) are promising tools to retrieve genomic information from these uncultured organisms. However, SCG are based on whole genome amplification, which normally introduces amplification biases that limit the amount of genomic data retrieved from a single cell. Here, we increase the recovery of genomic information from two MAST-4 lineages by co-assembling short reads from multiple Single Amplified Genomes (SAGs) belonging to evolutionary closely related cells. We found that complementary genomic information is retrieved from different SAGs, generating co-assembly that features {\\textgreater}74\\% of genome recovery, against about 20\\% when assembled individually. Even though this approach is not aimed at generating high-quality draft genomes, it allows accessing to the genomic information of microbes that would otherwise remain unreachable. Since most of the picoeukaryotes still remain uncultured, our work serves as a proof-of-concept that can be applied to other taxa in order to extract genomic data and address new ecological and evolutionary questions.},\n\tlanguage = {en},\n\tnumber = {1},\n\turldate = {2023-06-05},\n\tjournal = {Scientific Reports},\n\tauthor = {Mangot, Jean-François and Logares, Ramiro and Sánchez, Pablo and Latorre, Fran and Seeleuthner, Yoann and Mondy, Samuel and Sieracki, Michael E. and Jaillon, Olivier and Wincker, Patrick and Vargas, Colomban de and Massana, Ramon},\n\tmonth = jan,\n\tyear = {2017},\n\tnote = {Number: 1\nPublisher: Nature Publishing Group},\n\tkeywords = {Microbial genetics, Bioinformatics, Ecological genetics, Genomic analysis},\n\tpages = {41498},\n\tfile = {Full Text PDF:C\\:\\\\Users\\\\ojaillon\\\\Zotero\\\\storage\\\\3PRPZMKK\\\\Mangot et al. - 2017 - Accessing the genomic information of unculturable .pdf:application/pdf},\n}\n\n

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\n \n 2016\n \n \n (4)\n \n \n

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\n \n\n \n \n \n \n \n \n Reverse transcriptase genes are highly abundant and transcriptionally active in marine plankton assemblages.\n \n \n \n \n\n\n \n Lescot, M.; Hingamp, P.; Kojima, K.; Villar, E.; Romac, S.; Veluchamy, A.; Boccara, M.; Jaillon, O.; Iudicone, D.; Bowler, C.; Wincker, P.; Claverie, J.; and Ogata, H.\n\n\n \n\n\n\n ISME Journal, 10(5): 1134–1146. 2016.\n \n\n\n\n
\n\n\n\n \n \n $\"Reverse$ Paper\n \n \n\n \n \n doi\n \n \n\n \n link\n \n \n\n bibtex\n \n\n \n\n \n\n \n \n \n \n \n \n \n\n \n \n \n\n\n\n

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@article{lescot_reverse_2016,\n\ttitle = {Reverse transcriptase genes are highly abundant and transcriptionally active in marine plankton assemblages},\n\tvolume = {10},\n\turl = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-84948397541&doi=10.1038%2fismej.2015.192&partnerID=40&md5=b0e20b6bd100a8044b460df4a827f402},\n\tdoi = {10.1038/ismej.2015.192},\n\tnumber = {5},\n\tjournal = {ISME Journal},\n\tauthor = {Lescot, M. and Hingamp, P. and Kojima, K.K. and Villar, E. and Romac, S. and Veluchamy, A. and Boccara, M. and Jaillon, O. and Iudicone, D. and Bowler, C. and Wincker, P. and Claverie, J.-M. and Ogata, H.},\n\tyear = {2016},\n\tpages = {1134--1146},\n}\n\n

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\n \n\n \n \n \n \n \n \n Transcriptome analyses of the Dof-like gene family in grapevine reveal its involvement in berry, flower and seed development.\n \n \n \n \n\n\n \n da Silva, D. C.; da Silveira Falavigna, V.; Fasoli, M.; Buffon, V.; Porto, D. D.; Pappas, G. J.; Pezzotti, M.; Pasquali, G.; and Revers, L. F.\n\n\n \n\n\n\n Horticulture Research, 3(1): 1–10. August 2016.\n Number: 1 Publisher: Nature Publishing Group\n\n\n\n
\n\n\n\n \n \n $\"Transcriptome$ Paper\n \n \n\n \n \n doi\n \n \n\n \n link\n \n \n\n bibtex\n \n\n \n \n \n abstract \n \n\n \n\n \n \n \n \n \n \n \n\n \n \n \n \n \n \n \n\n\n\n

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@article{da_silva_transcriptome_2016,\n\ttitle = {Transcriptome analyses of the {Dof}-like gene family in grapevine reveal its involvement in berry, flower and seed development},\n\tvolume = {3},\n\tcopyright = {2016 The Author(s)},\n\tissn = {2052-7276},\n\turl = {https://www.nature.com/articles/hortres201642},\n\tdoi = {10.1038/hortres.2016.42},\n\tabstract = {The Dof (DNA-binding with one finger) protein family spans a group of plant transcription factors involved in the regulation of several functions, such as plant responses to stress, hormones and light, phytochrome signaling and seed germination. Here we describe the Dof-like gene family in grapevine (Vitis vinifera L.), which consists of 25 genes coding for Dof. An extensive in silico characterization of the VviDofL gene family was performed. Additionally, the expression of the entire gene family was assessed in 54 grapevine tissues and organs using an integrated approach with microarray (cv Corvina) and real-time PCR (cv Pinot Noir) analyses. The phylogenetic analysis comparing grapevine sequences with those of Arabidopsis, tomato, poplar and already described Dof genes in other species allowed us to identify several duplicated genes. The diversification of grapevine DofL genes during evolution likely resulted in a broader range of biological roles. Furthermore, distinct expression patterns were identified between samples analyzed, corroborating such hypothesis. Our expression results indicate that several VviDofL genes perform their functional roles mainly during flower, berry and seed development, highlighting their importance for grapevine growth and production. The identification of similar expression profiles between both approaches strongly suggests that these genes have important regulatory roles that are evolutionally conserved between grapevine cvs Corvina and Pinot Noir.},\n\tlanguage = {en},\n\tnumber = {1},\n\turldate = {2023-06-05},\n\tjournal = {Horticulture Research},\n\tauthor = {da Silva, Danielle Costenaro and da Silveira Falavigna, Vítor and Fasoli, Marianna and Buffon, Vanessa and Porto, Diogo Denardi and Pappas, Georgios Joannis and Pezzotti, Mario and Pasquali, Giancarlo and Revers, Luís Fernando},\n\tmonth = aug,\n\tyear = {2016},\n\tnote = {Number: 1\nPublisher: Nature Publishing Group},\n\tkeywords = {Plant morphogenesis, Transcriptomics},\n\tpages = {1--10},\n\tfile = {Full Text PDF:C\\:\\\\Users\\\\ojaillon\\\\Zotero\\\\storage\\\\SKX7PC2I\\\\da Silva et al. - 2016 - Transcriptome analyses of the Dof-like gene family.pdf:application/pdf},\n}\n\n

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\n \n\n \n \n \n \n \n \n The nuclear genome of Rhazya stricta and the evolution of alkaloid diversity in a medically relevant clade of Apocynaceae.\n \n \n \n \n\n\n \n Sabir, J. S. M.; Jansen, R. K.; Arasappan, D.; Calderon, V.; Noutahi, E.; Zheng, C.; Park, S.; Sabir, M. J.; Baeshen, M. N.; Hajrah, N. H.; Khiyami, M. A.; Baeshen, N. A.; Obaid, A. Y.; Al-Malki, A. L.; Sankoff, D.; El-Mabrouk, N.; and Ruhlman, T. A.\n\n\n \n\n\n\n Scientific Reports, 6(1): 33782. September 2016.\n Number: 1 Publisher: Nature Publishing Group\n\n\n\n
\n\n\n\n \n \n $\"The$ Paper\n \n \n\n \n \n doi\n \n \n\n \n link\n \n \n\n bibtex\n \n\n \n \n \n abstract \n \n\n \n\n \n \n \n \n \n \n \n\n \n \n \n \n \n \n \n \n \n\n\n\n

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@article{sabir_nuclear_2016,\n\ttitle = {The nuclear genome of {Rhazya} stricta and the evolution of alkaloid diversity in a medically relevant clade of {Apocynaceae}},\n\tvolume = {6},\n\tcopyright = {2016 The Author(s)},\n\tissn = {2045-2322},\n\turl = {https://www.nature.com/articles/srep33782},\n\tdoi = {10.1038/srep33782},\n\tabstract = {Alkaloid accumulation in plants is activated in response to stress, is limited in distribution and specific alkaloid repertoires are variable across taxa. Rauvolfioideae (Apocynaceae, Gentianales) represents a major center of structural expansion in the monoterpenoid indole alkaloids (MIAs) yielding thousands of unique molecules including highly valuable chemotherapeutics. The paucity of genome-level data for Apocynaceae precludes a deeper understanding of MIA pathway evolution hindering the elucidation of remaining pathway enzymes and the improvement of MIA availability in planta or in vitro. We sequenced the nuclear genome of Rhazya stricta (Apocynaceae, Rauvolfioideae) and present this high quality assembly in comparison with that of coffee (Rubiaceae, Coffea canephora, Gentianales) and others to investigate the evolution of genome-scale features. The annotated Rhazya genome was used to develop the community resource, RhaCyc, a metabolic pathway database. Gene family trees were constructed to identify homologs of MIA pathway genes and to examine their evolutionary history. We found that, unlike Coffea, the Rhazya lineage has experienced many structural rearrangements. Gene tree analyses suggest recent, lineage-specific expansion and diversification among homologs encoding MIA pathway genes in Gentianales and provide candidate sequences with the potential to close gaps in characterized pathways and support prospecting for new MIA production avenues.},\n\tlanguage = {en},\n\tnumber = {1},\n\turldate = {2023-06-05},\n\tjournal = {Scientific Reports},\n\tauthor = {Sabir, Jamal S. M. and Jansen, Robert K. and Arasappan, Dhivya and Calderon, Virginie and Noutahi, Emmanuel and Zheng, Chunfang and Park, Seongjun and Sabir, Meshaal J. and Baeshen, Mohammed N. and Hajrah, Nahid H. and Khiyami, Mohammad A. and Baeshen, Nabih A. and Obaid, Abdullah Y. and Al-Malki, Abdulrahman L. and Sankoff, David and El-Mabrouk, Nadia and Ruhlman, Tracey A.},\n\tmonth = sep,\n\tyear = {2016},\n\tnote = {Number: 1\nPublisher: Nature Publishing Group},\n\tkeywords = {Genome informatics, Molecular evolution, Secondary metabolism},\n\tpages = {33782},\n\tfile = {Full Text PDF:C\\:\\\\Users\\\\ojaillon\\\\Zotero\\\\storage\\\\46QQINPI\\\\Sabir et al. - 2016 - The nuclear genome of Rhazya stricta and the evolu.pdf:application/pdf},\n}\n\n

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\n \n\n \n \n \n \n \n \n Survey of the green picoalga Bathycoccus genomes in the global ocean.\n \n \n \n \n\n\n \n Vannier, T.; Leconte, J.; Seeleuthner, Y.; Mondy, S.; Pelletier, E.; Aury, J.; de Vargas, C.; Sieracki, M.; Iudicone, D.; Vaulot, D.; Wincker, P.; and Jaillon, O.\n\n\n \n\n\n\n Scientific Reports, 6(1): 37900. November 2016.\n Number: 1 Publisher: Nature Publishing Group\n\n\n\n
\n\n\n\n \n \n $\"Survey$ Paper\n \n \n\n \n \n doi\n \n \n\n \n link\n \n \n\n bibtex\n \n\n \n \n \n abstract \n \n\n \n\n \n \n \n \n \n \n \n\n \n \n \n \n \n \n \n \n \n\n\n\n

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@article{vannier_survey_2016,\n\ttitle = {Survey of the green picoalga {Bathycoccus} genomes in the global ocean},\n\tvolume = {6},\n\tcopyright = {2016 The Author(s)},\n\tissn = {2045-2322},\n\turl = {https://www.nature.com/articles/srep37900},\n\tdoi = {10.1038/srep37900},\n\tabstract = {Bathycoccus is a cosmopolitan green micro-alga belonging to the Mamiellophyceae, a class of picophytoplankton that contains important contributors to oceanic primary production. A single species of Bathycoccus has been described while the existence of two ecotypes has been proposed based on metagenomic data. A genome is available for one strain corresponding to the described phenotype. We report a second genome assembly obtained by a single cell genomics approach corresponding to the second ecotype. The two Bathycoccus genomes are divergent enough to be unambiguously distinguishable in whole DNA metagenomic data although they possess identical sequence of the 18S rRNA gene including in the V9 region. Analysis of 122 global ocean whole DNA metagenome samples from the Tara-Oceans expedition reveals that populations of Bathycoccus that were previously identified by 18S rRNA V9 metabarcodes are only composed of these two genomes. Bathycoccus is relatively abundant and widely distributed in nutrient rich waters. The two genomes rarely co-occur and occupy distinct oceanic niches in particular with respect to depth. Metatranscriptomic data provide evidence for gain or loss of highly expressed genes in some samples, suggesting that the gene repertoire is modulated by environmental conditions.},\n\tlanguage = {en},\n\tnumber = {1},\n\turldate = {2023-06-05},\n\tjournal = {Scientific Reports},\n\tauthor = {Vannier, Thomas and Leconte, Jade and Seeleuthner, Yoann and Mondy, Samuel and Pelletier, Eric and Aury, Jean-Marc and de Vargas, Colomban and Sieracki, Michael and Iudicone, Daniele and Vaulot, Daniel and Wincker, Patrick and Jaillon, Olivier},\n\tmonth = nov,\n\tyear = {2016},\n\tnote = {Number: 1\nPublisher: Nature Publishing Group},\n\tkeywords = {Comparative genomics, Metagenomics, Biogeography},\n\tpages = {37900},\n\tfile = {Full Text PDF:C\\:\\\\Users\\\\ojaillon\\\\Zotero\\\\storage\\\\3GG2DFLR\\\\Vannier et al. - 2016 - Survey of the green picoalga Bathycoccus genomes i.pdf:application/pdf},\n}\n\n

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\n \n 2015\n \n \n (7)\n \n \n

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\n \n\n \n \n \n \n \n \n Marine protist diversity in European coastal waters and sediments as revealed by high-throughput sequencing.\n \n \n \n \n\n\n \n Massana, R.; Gobet, A.; Audic, S.; Bass, D.; Bittner, L.; Boutte, C.; Chambouvet, A.; Christen, R.; Claverie, J.; Decelle, J.; Dolan, J.; Dunthorn, M.; Edvardsen, B.; Forn, I.; Forster, D.; Guillou, L.; Jaillon, O.; Kooistra, W.; Logares, R.; Mahé, F.; Not, F.; Ogata, H.; Pawlowski, J.; Pernice, M.; Probert, I.; Romac, S.; Richards, T.; Santini, S.; Shalchian-Tabrizi, K.; Siano, R.; Simon, N.; Stoeck, T.; Vaulot, D.; Zingone, A.; and de Vargas, C.\n\n\n \n\n\n\n Environmental Microbiology, 17(10): 4035–4049. 2015.\n \n\n\n\n
\n\n\n\n \n \n $\"Marine$ Paper\n \n \n\n \n \n doi\n \n \n\n \n link\n \n \n\n bibtex\n \n\n \n\n \n\n \n \n \n \n \n \n \n\n \n \n \n\n\n\n

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@article{massana_marine_2015,\n\ttitle = {Marine protist diversity in {European} coastal waters and sediments as revealed by high-throughput sequencing},\n\tvolume = {17},\n\turl = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-85027923076&doi=10.1111%2f1462-2920.12955&partnerID=40&md5=3b0f853102fca1691ce22fe9466ed7ce},\n\tdoi = {10.1111/1462-2920.12955},\n\tnumber = {10},\n\tjournal = {Environmental Microbiology},\n\tauthor = {Massana, R. and Gobet, A. and Audic, S. and Bass, D. and Bittner, L. and Boutte, C. and Chambouvet, A. and Christen, R. and Claverie, J.-M. and Decelle, J. and Dolan, J.R. and Dunthorn, M. and Edvardsen, B. and Forn, I. and Forster, D. and Guillou, L. and Jaillon, O. and Kooistra, W.H.C.F. and Logares, R. and Mahé, F. and Not, F. and Ogata, H. and Pawlowski, J. and Pernice, M.C. and Probert, I. and Romac, S. and Richards, T. and Santini, S. and Shalchian-Tabrizi, K. and Siano, R. and Simon, N. and Stoeck, T. and Vaulot, D. and Zingone, A. and de Vargas, C.},\n\tyear = {2015},\n\tpages = {4035--4049},\n}\n\n

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\n \n\n \n \n \n \n \n \n Patterns and ecological drivers of ocean viral communities.\n \n \n \n \n\n\n \n Brum, J.; Cesar Ignacio-Espinoza, J.; Roux, S.; Doulcier, G.; Acinas, S.; Alberti, A.; Chaffron, S.; Cruaud, C.; De Vargas, C.; Gasol, J.; Gorsky, G.; Gregory, A.; Guidi, L.; Hingamp, P.; Iudicone, D.; Not, F.; Ogata, H.; Pesant, S.; Poulos, B.; Schwenck, S.; Speich, S.; Dimier, C.; Kandels-Lewis, S.; Picheral, M.; Searson, S.; Bork, P.; Bowler, C.; Sunagawa, S.; Wincker, P.; Karsenti, E.; Sullivan, M.; Boss, E.; Follows, M.; Grimsley, N.; Jaillon, O.; Karp-Boss, L.; Krzic, U.; Raes, J.; Reynaud, E.; Sardet, C.; Sieracki, M.; Stemmann, L.; Velayoudon, D.; and Weissenbach, J.\n\n\n \n\n\n\n Science, 348(6237). 2015.\n \n\n\n\n
\n\n\n\n \n \n $\"Patterns$ Paper\n \n \n\n \n \n doi\n \n \n\n \n link\n \n \n\n bibtex\n \n\n \n\n \n\n \n \n \n \n \n \n \n\n \n \n \n\n\n\n

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@article{brum_patterns_2015,\n\ttitle = {Patterns and ecological drivers of ocean viral communities},\n\tvolume = {348},\n\turl = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-84929998256&doi=10.1126%2fscience.1261498&partnerID=40&md5=51f403691b1fe82548ea4b42bb542a60},\n\tdoi = {10.1126/science.1261498},\n\tnumber = {6237},\n\tjournal = {Science},\n\tauthor = {Brum, J.R. and Cesar Ignacio-Espinoza, J. and Roux, S. and Doulcier, G. and Acinas, S.G. and Alberti, A. and Chaffron, S. and Cruaud, C. and De Vargas, C. and Gasol, J.M. and Gorsky, G. and Gregory, A.C. and Guidi, L. and Hingamp, P. and Iudicone, D. and Not, F. and Ogata, H. and Pesant, S. and Poulos, B.T. and Schwenck, S.M. and Speich, S. and Dimier, C. and Kandels-Lewis, S. and Picheral, M. and Searson, S. and Bork, P. and Bowler, C. and Sunagawa, S. and Wincker, P. and Karsenti, E. and Sullivan, M.B. and Boss, E. and Follows, M. and Grimsley, N. and Jaillon, O. and Karp-Boss, L. and Krzic, U. and Raes, J. and Reynaud, E.G. and Sardet, C. and Sieracki, M. and Stemmann, L. and Velayoudon, D. and Weissenbach, J.},\n\tyear = {2015},\n}\n\n

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\n \n\n \n \n \n \n \n \n Determinants of community structure in the global plankton interactome.\n \n \n \n \n\n\n \n Lima-Mendez, G.; Faust, K.; Henry, N.; Decelle, J.; Colin, S.; Carcillo, F.; Chaffron, S.; Ignacio-Espinosa, J.; Roux, S.; Vincent, F.; Bittner, L.; Darzi, Y.; Wang, J.; Audic, S.; Berline, L.; Bontempi, G.; Cabello, A.; Coppola, L.; Cornejo-Castillo, F.; D'Ovidio, F.; De Meester, L.; Ferrera, I.; Garet-Delmas, M.; Guidi, L.; Lara, E.; Pesant, S.; Royo-Llonch, M.; Salazar, G.; Sánchez, P.; Sebastian, M.; Souffreau, C.; Dimier, C.; Picheral, M.; Searson, S.; Kandels-Lewis, S.; Gorsky, G.; Not, F.; Ogata, H.; Speich, S.; Stemmann, L.; Weissenbach, J.; Wincker, P.; Acinas, S.; Sunagawa, S.; Bork, P.; Sullivan, M.; Karsenti, E.; Bowler, C.; De Vargas, C.; Raes, J.; Boss, E.; Follows, M.; Grimsley, N.; Hingamp, P.; Iudicone, D.; Jaillon, O.; Karp-Boss, L.; Krzic, U.; Reynaud, E.; Sardet, C.; Sieracki, M.; Velayoudon, D.; and coordinators , T. O.\n\n\n \n\n\n\n Science, 348(6237). 2015.\n \n\n\n\n
\n\n\n\n \n \n $\"Determinants$ Paper\n \n \n\n \n \n doi\n \n \n\n \n link\n \n \n\n bibtex\n \n\n \n\n \n \n \n 3 downloads\n \n \n\n \n \n \n \n \n \n \n\n \n \n \n\n\n\n

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@article{lima-mendez_determinants_2015,\n\ttitle = {Determinants of community structure in the global plankton interactome},\n\tvolume = {348},\n\turl = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-84929997716&doi=10.1126%2fscience.1262073&partnerID=40&md5=f4bf6d5cb76300279c0723fdee56b3a6},\n\tdoi = {10.1126/science.1262073},\n\tnumber = {6237},\n\tjournal = {Science},\n\tauthor = {Lima-Mendez, G. and Faust, K. and Henry, N. and Decelle, J. and Colin, S. and Carcillo, F. and Chaffron, S. and Ignacio-Espinosa, J.C. and Roux, S. and Vincent, F. and Bittner, L. and Darzi, Y. and Wang, J. and Audic, S. and Berline, L. and Bontempi, G. and Cabello, A.M. and Coppola, L. and Cornejo-Castillo, F.M. and D'Ovidio, F. and De Meester, L. and Ferrera, I. and Garet-Delmas, M.-J. and Guidi, L. and Lara, E. and Pesant, S. and Royo-Llonch, M. and Salazar, G. and Sánchez, P. and Sebastian, M. and Souffreau, C. and Dimier, C. and Picheral, M. and Searson, S. and Kandels-Lewis, S. and Gorsky, G. and Not, F. and Ogata, H. and Speich, S. and Stemmann, L. and Weissenbach, J. and Wincker, P. and Acinas, S.G. and Sunagawa, S. and Bork, P. and Sullivan, M.B. and Karsenti, E. and Bowler, C. and De Vargas, C. and Raes, J. and Boss, E. and Follows, M. and Grimsley, N. and Hingamp, P. and Iudicone, D. and Jaillon, O. and Karp-Boss, L. and Krzic, U. and Reynaud, E.G. and Sardet, C. and Sieracki, M. and Velayoudon, D. and coordinators, Tara Oceans},\n\tyear = {2015},\n}\n\n

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\n \n\n \n \n \n \n \n \n Eukaryotic plankton diversity in the sunlit ocean.\n \n \n \n \n\n\n \n De Vargas, C.; Audic, S.; Henry, N.; Decelle, J.; Mahé, F.; Logares, R.; Lara, E.; Berney, Ć.; Le Bescot, N.; Probert, I.; Carmichael, M.; Poulain, J.; Romac, S.; Colin, S.; Aury, J.; Bittner, L.; Chaffron, S.; Dunthorn, M.; Engelen, S.; Flegontova, O.; Guidi, L.; Horák, A.; Jaillon, O.; Lima-Mendez, G.; Lukeš, J.; Malviya, S.; Morard, R.; Mulot, M.; Scalco, E.; Siano, R.; Vincent, F.; Zingone, A.; Dimier, C.; Picheral, M.; Searson, S.; Kandels-Lewis, S.; Acinas, S.; Bork, P.; Bowler, C.; Gorsky, G.; Grimsley, N.; Hingamp, P.; Iudicone, D.; Not, F.; Ogata, H.; Pesant, S.; Raes, J.; Sieracki, M.; Speich, S.; Stemmann, L.; Sunagawa, S.; Weissenbach, J.; Wincker, P.; Karsenti, E.; Boss, E.; Follows, M.; Karp-Boss, L.; Krzic, U.; Reynaud, E.; Sardet, C.; Sullivan, M.; Velayoudon, D.; and Coordinators, T. O.\n\n\n \n\n\n\n Science, 348(6237). 2015.\n \n\n\n\n
\n\n\n\n \n \n $\"Eukaryotic$ Paper\n \n \n\n \n \n doi\n \n \n\n \n link\n \n \n\n bibtex\n \n\n \n\n \n\n \n \n \n \n \n \n \n\n \n \n \n\n\n\n

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@article{de_vargas_eukaryotic_2015,\n\ttitle = {Eukaryotic plankton diversity in the sunlit ocean},\n\tvolume = {348},\n\turl = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-84929996994&doi=10.1126%2fscience.1261605&partnerID=40&md5=0699d32e3ef22c0b67cb255d42c65a77},\n\tdoi = {10.1126/science.1261605},\n\tnumber = {6237},\n\tjournal = {Science},\n\tauthor = {De Vargas, C. and Audic, S. and Henry, N. and Decelle, J. and Mahé, F. and Logares, R. and Lara, E. and Berney, Ć. and Le Bescot, N. and Probert, I. and Carmichael, M. and Poulain, J. and Romac, S. and Colin, S. and Aury, J.-M. and Bittner, L. and Chaffron, S. and Dunthorn, M. and Engelen, S. and Flegontova, O. and Guidi, L. and Horák, A. and Jaillon, O. and Lima-Mendez, G. and Lukeš, J. and Malviya, S. and Morard, R. and Mulot, M. and Scalco, E. and Siano, R. and Vincent, F. and Zingone, A. and Dimier, C. and Picheral, M. and Searson, S. and Kandels-Lewis, S. and Acinas, S.G. and Bork, P. and Bowler, C. and Gorsky, G. and Grimsley, N. and Hingamp, P. and Iudicone, D. and Not, F. and Ogata, H. and Pesant, S. and Raes, J. and Sieracki, M.E. and Speich, S. and Stemmann, L. and Sunagawa, S. and Weissenbach, J. and Wincker, P. and Karsenti, E. and Boss, E. and Follows, M. and Karp-Boss, L. and Krzic, U. and Reynaud, E.G. and Sardet, C. and Sullivan, M.B. and Velayoudon, D. and Coordinators, Tara Oceans},\n\tyear = {2015},\n}\n\n

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\n \n\n \n \n \n \n \n \n Environmental characteristics of Agulhas rings affect interocean plankton transport.\n \n \n \n \n\n\n \n Villar, E.; Farrant, G.; Follows, M.; Garczarek, L.; Speich, S.; Audic, S.; Bittner, L.; Blanke, B.; Brum, J.; Brunet, C.; Casotti, R.; Chase, A.; Dolan, J.; D'Ortenzio, F.; Gattuso, J.; Grima, N.; Guidi, L.; Hill, C.; Jahn, O.; Jamet, J.; Goff, H.; Lepoivre, C.; Malviya, S.; Pelletier, E.; Romagnan, J.; Roux, S.; Santini, S.; Scalco, E.; Schwenck, S.; Tanaka, A.; Testor, P.; Vannier, T.; Vincent, F.; Zingone, A.; Dimier, C.; Picheral, M.; Searson, S.; Kandels-Lewis, S.; Bork, P.; Boss, E.; De Vargas, C.; Gorsky, G.; Ogata, H.; Pesant, S.; Sullivan, M.; Sunagawa, S.; Wincker, P.; Karsenti, E.; Bowler, C.; Not, F.; Hingamp, P.; Iudicone, D.; Acinas, S.; Grimsley, N.; Jaillon, O.; Karp-Boss, L.; Krzic, U.; Raes, J.; Reynaud, E.; Sardet, C.; Sieracki, M.; Stemmann, L.; Velayoudon, D.; and Weissenbach, J.\n\n\n \n\n\n\n Science, 348(6237). 2015.\n \n\n\n\n
\n\n\n\n \n \n $\"Environmental$ Paper\n \n \n\n \n \n doi\n \n \n\n \n link\n \n \n\n bibtex\n \n\n \n\n \n \n \n 4 downloads\n \n \n\n \n \n \n \n \n \n \n\n \n \n \n\n\n\n

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@article{villar_environmental_2015,\n\ttitle = {Environmental characteristics of {Agulhas} rings affect interocean plankton transport},\n\tvolume = {348},\n\turl = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-84929993120&doi=10.1126%2fscience.1261447&partnerID=40&md5=6fb6428024f3657767a7f3e02a4e97ad},\n\tdoi = {10.1126/science.1261447},\n\tnumber = {6237},\n\tjournal = {Science},\n\tauthor = {Villar, E. and Farrant, G.K. and Follows, M. and Garczarek, L. and Speich, S. and Audic, S. and Bittner, L. and Blanke, B. and Brum, J.R. and Brunet, C. and Casotti, R. and Chase, A. and Dolan, J.R. and D'Ortenzio, F. and Gattuso, J.-P. and Grima, N. and Guidi, L. and Hill, C.N. and Jahn, O. and Jamet, J.-L. and Goff, H.L. and Lepoivre, C. and Malviya, S. and Pelletier, E. and Romagnan, J.-B. and Roux, S. and Santini, S. and Scalco, E. and Schwenck, S.M. and Tanaka, A. and Testor, P. and Vannier, T. and Vincent, F. and Zingone, A. and Dimier, C. and Picheral, M. and Searson, S. and Kandels-Lewis, S. and Bork, P. and Boss, E. and De Vargas, C. and Gorsky, G. and Ogata, H. and Pesant, S. and Sullivan, M.B. and Sunagawa, S. and Wincker, P. and Karsenti, E. and Bowler, C. and Not, F. and Hingamp, P. and Iudicone, D. and Acinas, S.G. and Grimsley, N. and Jaillon, O. and Karp-Boss, L. and Krzic, U. and Raes, J. and Reynaud, E.G. and Sardet, C. and Sieracki, M. and Stemmann, L. and Velayoudon, D. and Weissenbach, J.},\n\tyear = {2015},\n}\n\n

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\n \n\n \n \n \n \n \n \n Structure and function of the global ocean microbiome.\n \n \n \n \n\n\n \n Sunagawa, S.; Coelho, L.; Chaffron, S.; Kultima, J.; Labadie, K.; Salazar, G.; Djahanschiri, B.; Zeller, G.; Mende, D.; Alberti, A.; Cornejo-Castillo, F.; Costea, P.; Cruaud, C.; D'Ovidio, F.; Engelen, S.; Ferrera, I.; Gasol, J.; Guidi, L.; Hildebrand, F.; Kokoszka, F.; Lepoivre, C.; Lima-Mendez, G.; Poulain, J.; Poulos, B.; Royo-Llonch, M.; Sarmento, H.; Vieira-Silva, S.; Dimier, C.; Picheral, M.; Searson, S.; Kandels-Lewis, S.; Boss, E.; Follows, M.; Karp-Boss, L.; Krzic, U.; Reynaud, E.; Sardet, C.; Sieracki, M.; Velayoudon, D.; Bowler, C.; De Vargas, C.; Gorsky, G.; Grimsley, N.; Hingamp, P.; Iudicone, D.; Jaillon, O.; Not, F.; Ogata, H.; Pesant, S.; Speich, S.; Stemmann, L.; Sullivan, M.; Weissenbach, J.; Wincker, P.; Karsenti, E.; Raes, J.; Acinas, S.; and Bork, P.\n\n\n \n\n\n\n Science, 348(6237). 2015.\n \n\n\n\n
\n\n\n\n \n \n $\"Structure$ Paper\n \n \n\n \n \n doi\n \n \n\n \n link\n \n \n\n bibtex\n \n\n \n\n \n \n \n 19 downloads\n \n \n\n \n \n \n \n \n \n \n\n \n \n \n\n\n\n

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@article{sunagawa_structure_2015,\n\ttitle = {Structure and function of the global ocean microbiome},\n\tvolume = {348},\n\turl = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-84929992013&doi=10.1126%2fscience.1261359&partnerID=40&md5=18c7238d49b2eb1d1595fdc5a1e78292},\n\tdoi = {10.1126/science.1261359},\n\tnumber = {6237},\n\tjournal = {Science},\n\tauthor = {Sunagawa, S. and Coelho, L.P. and Chaffron, S. and Kultima, J.R. and Labadie, K. and Salazar, G. and Djahanschiri, B. and Zeller, G. and Mende, D.R. and Alberti, A. and Cornejo-Castillo, F.M. and Costea, P.I. and Cruaud, C. and D'Ovidio, F. and Engelen, S. and Ferrera, I. and Gasol, J.M. and Guidi, L. and Hildebrand, F. and Kokoszka, F. and Lepoivre, C. and Lima-Mendez, G. and Poulain, J. and Poulos, B.T. and Royo-Llonch, M. and Sarmento, H. and Vieira-Silva, S. and Dimier, C. and Picheral, M. and Searson, S. and Kandels-Lewis, S. and Boss, E. and Follows, M. and Karp-Boss, L. and Krzic, U. and Reynaud, E.G. and Sardet, C. and Sieracki, M. and Velayoudon, D. and Bowler, C. and De Vargas, C. and Gorsky, G. and Grimsley, N. and Hingamp, P. and Iudicone, D. and Jaillon, O. and Not, F. and Ogata, H. and Pesant, S. and Speich, S. and Stemmann, L. and Sullivan, M.B. and Weissenbach, J. and Wincker, P. and Karsenti, E. and Raes, J. and Acinas, S.G. and Bork, P.},\n\tyear = {2015},\n}\n\n

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\n \n\n \n \n \n \n \n \n Open science resources for the discovery and analysis of Tara Oceans data.\n \n \n \n \n\n\n \n Pesant, S.; Not, F.; Picheral, M.; Kandels-Lewis, S.; Le Bescot, N.; Gorsky, G.; Iudicone, D.; Karsenti, E.; Speich, S.; Troublé, R.; Dimier, C.; and Searson, S.\n\n\n \n\n\n\n Scientific Data, 2(1): 150023. May 2015.\n Number: 1 Publisher: Nature Publishing Group\n\n\n\n
\n\n\n\n \n \n $\"Open$ Paper\n \n \n\n \n \n doi\n \n \n\n \n link\n \n \n\n bibtex\n \n\n \n \n \n abstract \n \n\n \n \n \n 3 downloads\n \n \n\n \n \n \n \n \n \n \n\n \n \n \n \n \n \n \n \n \n \n \n\n\n\n

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@article{pesant_open_2015,\n\ttitle = {Open science resources for the discovery and analysis of {Tara} {Oceans} data},\n\tvolume = {2},\n\tcopyright = {2015 The Author(s)},\n\tissn = {2052-4463},\n\turl = {https://www.nature.com/articles/sdata201523},\n\tdoi = {10.1038/sdata.2015.23},\n\tabstract = {The Tara Oceans expedition (2009–2013) sampled contrasting ecosystems of the world oceans, collecting environmental data and plankton, from viruses to metazoans, for later analysis using modern sequencing and state-of-the-art imaging technologies. It surveyed 210 ecosystems in 20 biogeographic provinces, collecting over 35,000 samples of seawater and plankton. The interpretation of such an extensive collection of samples in their ecological context requires means to explore, assess and access raw and validated data sets. To address this challenge, the Tara Oceans Consortium offers open science resources, including the use of open access archives for nucleotides (ENA) and for environmental, biogeochemical, taxonomic and morphological data (PANGAEA), and the development of on line discovery tools and collaborative annotation tools for sequences and images. Here, we present an overview of Tara Oceans Data, and we provide detailed registries (data sets) of all campaigns (from port-to-port), stations and sampling events.},\n\tlanguage = {en},\n\tnumber = {1},\n\turldate = {2023-06-05},\n\tjournal = {Scientific Data},\n\tauthor = {Pesant, Stéphane and Not, Fabrice and Picheral, Marc and Kandels-Lewis, Stefanie and Le Bescot, Noan and Gorsky, Gabriel and Iudicone, Daniele and Karsenti, Eric and Speich, Sabrina and Troublé, Romain and Dimier, Céline and Searson, Sarah},\n\tmonth = may,\n\tyear = {2015},\n\tnote = {Number: 1\nPublisher: Nature Publishing Group},\n\tkeywords = {Biodiversity, Ocean sciences, Ecological genetics, Biooceanography},\n\tpages = {150023},\n\tfile = {Full Text PDF:C\\:\\\\Users\\\\ojaillon\\\\Zotero\\\\storage\\\\99GGZC7Q\\\\Pesant et al. - 2015 - Open science resources for the discovery and analy.pdf:application/pdf},\n}\n\n

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\n \n\n \n \n \n \n \n \n Metagenomic 16S rDNA Illumina tags are a powerful alternative to amplicon sequencing to explore diversity and structure of microbial communities.\n \n \n \n \n\n\n \n Logares, R.; Sunagawa, S.; Salazar, G.; Cornejo-Castillo, F.; Ferrera, I.; Sarmento, H.; Hingamp, P.; Ogata, H.; de Vargas, C.; Lima-Mendez, G.; Raes, J.; Poulain, J.; Jaillon, O.; Wincker, P.; Kandels-Lewis, S.; Karsenti, E.; Bork, P.; and Acinas, S.\n\n\n \n\n\n\n Environmental Microbiology, 16(9): 2659–2671. 2014.\n \n\n\n\n
\n\n\n\n \n \n $\"Metagenomic$ Paper\n \n \n\n \n \n doi\n \n \n\n \n link\n \n \n\n bibtex\n \n\n \n\n \n \n \n 1 download\n \n \n\n \n \n \n \n \n \n \n\n \n \n \n\n\n\n

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@article{logares_metagenomic_2014,\n\ttitle = {Metagenomic {16S} {rDNA} {Illumina} tags are a powerful alternative to amplicon sequencing to explore diversity and structure of microbial communities},\n\tvolume = {16},\n\turl = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-84906944378&doi=10.1111%2f1462-2920.12250&partnerID=40&md5=060ce9cc4399243561b884b3534d35eb},\n\tdoi = {10.1111/1462-2920.12250},\n\tnumber = {9},\n\tjournal = {Environmental Microbiology},\n\tauthor = {Logares, R. and Sunagawa, S. and Salazar, G. and Cornejo-Castillo, F.M. and Ferrera, I. and Sarmento, H. and Hingamp, P. and Ogata, H. and de Vargas, C. and Lima-Mendez, G. and Raes, J. and Poulain, J. and Jaillon, O. and Wincker, P. and Kandels-Lewis, S. and Karsenti, E. and Bork, P. and Acinas, S.G.},\n\tyear = {2014},\n\tpages = {2659--2671},\n}\n\n

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\n \n\n \n \n \n \n \n \n The rainbow trout genome provides novel insights into evolution after whole-genome duplication in vertebrates.\n \n \n \n \n\n\n \n Berthelot, C.; Brunet, F.; Chalopin, D.; Juanchich, A.; Bernard, M.; Noël, B.; Bento, P.; Da Silva, C.; Labadie, K.; Alberti, A.; Aury, J.; Louis, A.; Dehais, P.; Bardou, P.; Montfort, J.; Klopp, C.; Cabau, C.; Gaspin, C.; Thorgaard, G. H.; Boussaha, M.; Quillet, E.; Guyomard, R.; Galiana, D.; Bobe, J.; Volff, J.; Genêt, C.; Wincker, P.; Jaillon, O.; Crollius, H. R.; and Guiguen, Y.\n\n\n \n\n\n\n Nature Communications, 5(1): 3657. April 2014.\n Number: 1 Publisher: Nature Publishing Group\n\n\n\n
\n\n\n\n \n \n $\"The$ Paper\n \n \n\n \n \n doi\n \n \n\n \n link\n \n \n\n bibtex\n \n\n \n \n \n abstract \n \n\n \n\n \n \n \n \n \n \n \n\n \n \n \n \n \n \n \n \n \n\n\n\n

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@article{berthelot_rainbow_2014,\n\ttitle = {The rainbow trout genome provides novel insights into evolution after whole-genome duplication in vertebrates},\n\tvolume = {5},\n\tcopyright = {2014 The Author(s)},\n\tissn = {2041-1723},\n\turl = {https://www.nature.com/articles/ncomms4657},\n\tdoi = {10.1038/ncomms4657},\n\tabstract = {Vertebrate evolution has been shaped by several rounds of whole-genome duplications (WGDs) that are often suggested to be associated with adaptive radiations and evolutionary innovations. Due to an additional round of WGD, the rainbow trout genome offers a unique opportunity to investigate the early evolutionary fate of a duplicated vertebrate genome. Here we show that after 100 million years of evolution the two ancestral subgenomes have remained extremely collinear, despite the loss of half of the duplicated protein-coding genes, mostly through pseudogenization. In striking contrast is the fate of miRNA genes that have almost all been retained as duplicated copies. The slow and stepwise rediploidization process characterized here challenges the current hypothesis that WGD is followed by massive and rapid genomic reorganizations and gene deletions.},\n\tlanguage = {en},\n\tnumber = {1},\n\turldate = {2023-06-05},\n\tjournal = {Nature Communications},\n\tauthor = {Berthelot, Camille and Brunet, Frédéric and Chalopin, Domitille and Juanchich, Amélie and Bernard, Maria and Noël, Benjamin and Bento, Pascal and Da Silva, Corinne and Labadie, Karine and Alberti, Adriana and Aury, Jean-Marc and Louis, Alexandra and Dehais, Patrice and Bardou, Philippe and Montfort, Jérôme and Klopp, Christophe and Cabau, Cédric and Gaspin, Christine and Thorgaard, Gary H. and Boussaha, Mekki and Quillet, Edwige and Guyomard, René and Galiana, Delphine and Bobe, Julien and Volff, Jean-Nicolas and Genêt, Carine and Wincker, Patrick and Jaillon, Olivier and Crollius, Hugues Roest and Guiguen, Yann},\n\tmonth = apr,\n\tyear = {2014},\n\tnote = {Number: 1\nPublisher: Nature Publishing Group},\n\tkeywords = {Gene duplication, Genome evolution, Molecular evolution},\n\tpages = {3657},\n\tfile = {Full Text PDF:C\\:\\\\Users\\\\ojaillon\\\\Zotero\\\\storage\\\\3VC8ID8P\\\\Berthelot et al. - 2014 - The rainbow trout genome provides novel insights i.pdf:application/pdf},\n}\n\n

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\n \n\n \n \n \n \n \n \n Sequencing of diverse mandarin, pummelo and orange genomes reveals complex history of admixture during citrus domestication.\n \n \n \n \n\n\n \n Wu, G. A.; Prochnik, S.; Jenkins, J.; Salse, J.; Hellsten, U.; Murat, F.; Perrier, X.; Ruiz, M.; Scalabrin, S.; Terol, J.; Takita, M. A.; Labadie, K.; Poulain, J.; Couloux, A.; Jabbari, K.; Cattonaro, F.; Del Fabbro, C.; Pinosio, S.; Zuccolo, A.; Chapman, J.; Grimwood, J.; Tadeo, F. R.; Estornell, L. H.; Muñoz-Sanz, J. V.; Ibanez, V.; Herrero-Ortega, A.; Aleza, P.; Pérez-Pérez, J.; Ramón, D.; Brunel, D.; Luro, F.; Chen, C.; Farmerie, W. G.; Desany, B.; Kodira, C.; Mohiuddin, M.; Harkins, T.; Fredrikson, K.; Burns, P.; Lomsadze, A.; Borodovsky, M.; Reforgiato, G.; Freitas-Astúa, J.; Quetier, F.; Navarro, L.; Roose, M.; Wincker, P.; Schmutz, J.; Morgante, M.; Machado, M. A.; Talon, M.; Jaillon, O.; Ollitrault, P.; Gmitter, F.; and Rokhsar, D.\n\n\n \n\n\n\n Nature Biotechnology, 32(7): 656–662. July 2014.\n Number: 7 Publisher: Nature Publishing Group\n\n\n\n
\n\n\n\n \n \n $\"Sequencing$ Paper\n \n \n\n \n \n doi\n \n \n\n \n link\n \n \n\n bibtex\n \n\n \n \n \n abstract \n \n\n \n\n \n \n \n \n \n \n \n\n \n \n \n \n \n \n \n \n \n \n \n\n\n\n

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@article{wu_sequencing_2014,\n\ttitle = {Sequencing of diverse mandarin, pummelo and orange genomes reveals complex history of admixture during citrus domestication},\n\tvolume = {32},\n\tcopyright = {2014 The Author(s)},\n\tissn = {1546-1696},\n\turl = {https://www.nature.com/articles/nbt.2906},\n\tdoi = {10.1038/nbt.2906},\n\tabstract = {Genome sequences of nine species of citrus, including oranges, pummelos and mandarins, reveal pathways of domestication and provide resources for breeding.},\n\tlanguage = {en},\n\tnumber = {7},\n\turldate = {2023-06-05},\n\tjournal = {Nature Biotechnology},\n\tauthor = {Wu, G. Albert and Prochnik, Simon and Jenkins, Jerry and Salse, Jerome and Hellsten, Uffe and Murat, Florent and Perrier, Xavier and Ruiz, Manuel and Scalabrin, Simone and Terol, Javier and Takita, Marco Aurélio and Labadie, Karine and Poulain, Julie and Couloux, Arnaud and Jabbari, Kamel and Cattonaro, Federica and Del Fabbro, Cristian and Pinosio, Sara and Zuccolo, Andrea and Chapman, Jarrod and Grimwood, Jane and Tadeo, Francisco R. and Estornell, Leandro H. and Muñoz-Sanz, Juan V. and Ibanez, Victoria and Herrero-Ortega, Amparo and Aleza, Pablo and Pérez-Pérez, Julián and Ramón, Daniel and Brunel, Dominique and Luro, François and Chen, Chunxian and Farmerie, William G. and Desany, Brian and Kodira, Chinnappa and Mohiuddin, Mohammed and Harkins, Tim and Fredrikson, Karin and Burns, Paul and Lomsadze, Alexandre and Borodovsky, Mark and Reforgiato, Giuseppe and Freitas-Astúa, Juliana and Quetier, Francis and Navarro, Luis and Roose, Mikeal and Wincker, Patrick and Schmutz, Jeremy and Morgante, Michele and Machado, Marcos Antonio and Talon, Manuel and Jaillon, Olivier and Ollitrault, Patrick and Gmitter, Frederick and Rokhsar, Daniel},\n\tmonth = jul,\n\tyear = {2014},\n\tnote = {Number: 7\nPublisher: Nature Publishing Group},\n\tkeywords = {Peptides, Biochemistry, Synthetic biology, Translation},\n\tpages = {656--662},\n\tfile = {Full Text PDF:C\\:\\\\Users\\\\ojaillon\\\\Zotero\\\\storage\\\\RECEGBLV\\\\Wu et al. - 2014 - Sequencing of diverse mandarin, pummelo and orange.pdf:application/pdf},\n}\n\n

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\n \n\n \n \n \n \n \n \n Genome and transcriptome analysis of the grapevine (Vitis vinifera L.) WRKY gene family.\n \n \n \n \n\n\n \n Wang, M.; Vannozzi, A.; Wang, G.; Liang, Y.; Tornielli, G. B.; Zenoni, S.; Cavallini, E.; Pezzotti, M.; and Cheng, Z. (.\n\n\n \n\n\n\n Horticulture Research, 1(1): 1–16. March 2014.\n Number: 1 Publisher: Nature Publishing Group\n\n\n\n
\n\n\n\n \n \n $\"Genome$ Paper\n \n \n\n \n \n doi\n \n \n\n \n link\n \n \n\n bibtex\n \n\n \n \n \n abstract \n \n\n \n\n \n \n \n \n \n \n \n\n \n \n \n \n \n \n \n \n \n\n\n\n

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@article{wang_genome_2014,\n\ttitle = {Genome and transcriptome analysis of the grapevine ({Vitis} vinifera {L}.) {WRKY} gene family},\n\tvolume = {1},\n\tcopyright = {2013 The Author(s)},\n\tissn = {2052-7276},\n\turl = {https://www.nature.com/articles/hortres201416},\n\tdoi = {10.1038/hortres.2014.16},\n\tabstract = {The plant WRKY gene family represents an ancient and complex class of zinc-finger transcription factors (TFs) that are involved in the regulation of various physiological processes, such as development and senescence, and in plant response to many biotic and abiotic stresses. Despite the growing number of studies on the genomic organisation of WRKY gene family in different species, little information is available about this family in grapevine (Vitis vinifera L.). In the present study, a total number of 59 putative grapevine WRKY transcription factors (VvWRKYs) were identified based on the analysis of various genomic and proteomic grapevine databases. According to their structural and phylogentic features, the identified grapevine WRKY transcription factors were classified into three main groups. In order to shed light into their regulatory roles in growth and development as well as in response to biotic and abiotic stress in grapevine, the VvWRKYs expression profiles were examined in publicly available microarray data. Bioinformatics analysis of these data revealed distinct temporal and spatial expression patterns of VvWRKYs in various tissues, organs and developmental stages, as well as in response to biotic and abiotic stresses. To also extend our analysis to situations not covered by the arrays and to validate our results, the expression profiles of selected VvWRKYs in response to drought stress, Erysiphe necator (powdery mildew) infection, and hormone treatments (salicilic acid and ethylene), were investigated by quantitative real-time reverse transcription PCR (qRT-PCR). The present study provides a foundation for further comparative genomics and functional studies of this important class of transcriptional regulators in grapevine.},\n\tlanguage = {en},\n\tnumber = {1},\n\turldate = {2023-06-05},\n\tjournal = {Horticulture Research},\n\tauthor = {Wang, Min and Vannozzi, Alessandro and Wang, Gang and Liang, Ying-Hai and Tornielli, Giovanni Battista and Zenoni, Sara and Cavallini, Erika and Pezzotti, Mario and Cheng, Zong-Ming (Max)},\n\tmonth = mar,\n\tyear = {2014},\n\tnote = {Number: 1\nPublisher: Nature Publishing Group},\n\tkeywords = {Genomics, Transcriptomics, Plant genetics},\n\tpages = {1--16},\n\tfile = {Full Text PDF:C\\:\\\\Users\\\\ojaillon\\\\Zotero\\\\storage\\\\5RLBMPZ7\\\\Wang et al. - 2014 - Genome and transcriptome analysis of the grapevine.pdf:application/pdf},\n}\n\n

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\n \n 2013\n \n \n (2)\n \n \n

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\n \n\n \n \n \n \n \n \n Genomic evidence for ameiotic evolution in the bdelloid rotifer Adineta vaga.\n \n \n \n \n\n\n \n Flot, J.; Hespeels, B.; Li, X.; Noel, B.; Arkhipova, I.; Danchin, E. G. J.; Hejnol, A.; Henrissat, B.; Koszul, R.; Aury, J.; Barbe, V.; Barthélémy, R.; Bast, J.; Bazykin, G. A.; Chabrol, O.; Couloux, A.; Da Rocha, M.; Da Silva, C.; Gladyshev, E.; Gouret, P.; Hallatschek, O.; Hecox-Lea, B.; Labadie, K.; Lejeune, B.; Piskurek, O.; Poulain, J.; Rodriguez, F.; Ryan, J. F.; Vakhrusheva, O. A.; Wajnberg, E.; Wirth, B.; Yushenova, I.; Kellis, M.; Kondrashov, A. S.; Mark Welch, D. B.; Pontarotti, P.; Weissenbach, J.; Wincker, P.; Jaillon, O.; and Van Doninck, K.\n\n\n \n\n\n\n Nature, 500(7463): 453–457. August 2013.\n Number: 7463 Publisher: Nature Publishing Group\n\n\n\n
\n\n\n\n \n \n $\"Genomic$ Paper\n \n \n\n \n \n doi\n \n \n\n \n link\n \n \n\n bibtex\n \n\n \n \n \n abstract \n \n\n \n\n \n \n \n \n \n \n \n\n \n \n \n \n \n \n \n \n \n\n\n\n

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@article{flot_genomic_2013,\n\ttitle = {Genomic evidence for ameiotic evolution in the bdelloid rotifer {Adineta} vaga},\n\tvolume = {500},\n\tcopyright = {2013 The Author(s)},\n\tissn = {1476-4687},\n\turl = {https://www.nature.com/articles/nature12326},\n\tdoi = {10.1038/nature12326},\n\tabstract = {The genome of the asexual rotifer Adineta vaga lacks homologous chromosomes; instead, its allelic regions are rearranged and sometimes found on the same chromosome in a palindromic fashion, a structure reminiscent of the primate Y chromosome and of other mitotic lineages such as cancer cells.},\n\tlanguage = {en},\n\tnumber = {7463},\n\turldate = {2023-06-05},\n\tjournal = {Nature},\n\tauthor = {Flot, Jean-François and Hespeels, Boris and Li, Xiang and Noel, Benjamin and Arkhipova, Irina and Danchin, Etienne G. J. and Hejnol, Andreas and Henrissat, Bernard and Koszul, Romain and Aury, Jean-Marc and Barbe, Valérie and Barthélémy, Roxane-Marie and Bast, Jens and Bazykin, Georgii A. and Chabrol, Olivier and Couloux, Arnaud and Da Rocha, Martine and Da Silva, Corinne and Gladyshev, Eugene and Gouret, Philippe and Hallatschek, Oskar and Hecox-Lea, Bette and Labadie, Karine and Lejeune, Benjamin and Piskurek, Oliver and Poulain, Julie and Rodriguez, Fernando and Ryan, Joseph F. and Vakhrusheva, Olga A. and Wajnberg, Eric and Wirth, Bénédicte and Yushenova, Irina and Kellis, Manolis and Kondrashov, Alexey S. and Mark Welch, David B. and Pontarotti, Pierre and Weissenbach, Jean and Wincker, Patrick and Jaillon, Olivier and Van Doninck, Karine},\n\tmonth = aug,\n\tyear = {2013},\n\tnote = {Number: 7463\nPublisher: Nature Publishing Group},\n\tkeywords = {Genome evolution, Evolutionary genetics, Evolutionary biology},\n\tpages = {453--457},\n\tfile = {Full Text PDF:C\\:\\\\Users\\\\ojaillon\\\\Zotero\\\\storage\\\\R6IR6XER\\\\Flot et al. - 2013 - Genomic evidence for ameiotic evolution in the bde.pdf:application/pdf},\n}\n\n

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\n \n\n \n \n \n \n \n \n Exploring nucleo-cytoplasmic large DNA viruses in Tara Oceans microbial metagenomes.\n \n \n \n \n\n\n \n Hingamp, P.; Grimsley, N.; Acinas, S. G.; Clerissi, C.; Subirana, L.; Poulain, J.; Ferrera, I.; Sarmento, H.; Villar, E.; Lima-Mendez, G.; Faust, K.; Sunagawa, S.; Claverie, J.; Moreau, H.; Desdevises, Y.; Bork, P.; Raes, J.; de Vargas, C.; Karsenti, E.; Kandels-Lewis, S.; Jaillon, O.; Not, F.; Pesant, S.; Wincker, P.; and Ogata, H.\n\n\n \n\n\n\n The ISME Journal, 7(9): 1678–1695. September 2013.\n Number: 9 Publisher: Nature Publishing Group\n\n\n\n
\n\n\n\n \n \n $\"Exploring$ Paper\n \n \n\n \n \n doi\n \n \n\n \n link\n \n \n\n bibtex\n \n\n \n \n \n abstract \n \n\n \n\n \n \n \n \n \n \n \n\n \n \n \n \n \n \n \n\n\n\n

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@article{hingamp_exploring_2013,\n\ttitle = {Exploring nucleo-cytoplasmic large {DNA} viruses in {Tara} {Oceans} microbial metagenomes},\n\tvolume = {7},\n\tcopyright = {2013 The Author(s)},\n\tissn = {1751-7370},\n\turl = {https://www.nature.com/articles/ismej201359},\n\tdoi = {10.1038/ismej.2013.59},\n\tabstract = {Nucleo-cytoplasmic large DNA viruses (NCLDVs) constitute a group of eukaryotic viruses that can have crucial ecological roles in the sea by accelerating the turnover of their unicellular hosts or by causing diseases in animals. To better characterize the diversity, abundance and biogeography of marine NCLDVs, we analyzed 17 metagenomes derived from microbial samples (0.2–1.6 μm size range) collected during the Tara Oceans Expedition. The sample set includes ecosystems under-represented in previous studies, such as the Arabian Sea oxygen minimum zone (OMZ) and Indian Ocean lagoons. By combining computationally derived relative abundance and direct prokaryote cell counts, the abundance of NCLDVs was found to be in the order of 104–105 genomes ml−1 for the samples from the photic zone and 102–103 genomes ml−1 for the OMZ. The Megaviridae and Phycodnaviridae dominated the NCLDV populations in the metagenomes, although most of the reads classified in these families showed large divergence from known viral genomes. Our taxon co-occurrence analysis revealed a potential association between viruses of the Megaviridae family and eukaryotes related to oomycetes. In support of this predicted association, we identified six cases of lateral gene transfer between Megaviridae and oomycetes. Our results suggest that marine NCLDVs probably outnumber eukaryotic organisms in the photic layer (per given water mass) and that metagenomic sequence analyses promise to shed new light on the biodiversity of marine viruses and their interactions with potential hosts.},\n\tlanguage = {en},\n\tnumber = {9},\n\turldate = {2023-06-05},\n\tjournal = {The ISME Journal},\n\tauthor = {Hingamp, Pascal and Grimsley, Nigel and Acinas, Silvia G. and Clerissi, Camille and Subirana, Lucie and Poulain, Julie and Ferrera, Isabel and Sarmento, Hugo and Villar, Emilie and Lima-Mendez, Gipsi and Faust, Karoline and Sunagawa, Shinichi and Claverie, Jean-Michel and Moreau, Hervé and Desdevises, Yves and Bork, Peer and Raes, Jeroen and de Vargas, Colomban and Karsenti, Eric and Kandels-Lewis, Stefanie and Jaillon, Olivier and Not, Fabrice and Pesant, Stéphane and Wincker, Patrick and Ogata, Hiroyuki},\n\tmonth = sep,\n\tyear = {2013},\n\tnote = {Number: 9\nPublisher: Nature Publishing Group},\n\tkeywords = {Metagenomics, Microbial biooceanography},\n\tpages = {1678--1695},\n\tfile = {Full Text PDF:C\\:\\\\Users\\\\ojaillon\\\\Zotero\\\\storage\\\\UF9AVZZE\\\\Hingamp et al. - 2013 - Exploring nucleo-cytoplasmic large DNA viruses in .pdf:application/pdf},\n}\n\n

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\n \n 2012\n \n \n (1)\n \n \n

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\n \n\n \n \n \n \n \n \n The banana (Musa acuminata) genome and the evolution of monocotyledonous plants.\n \n \n \n \n\n\n \n D’Hont, A.; Denoeud, F.; Aury, J.; Baurens, F.; Carreel, F.; Garsmeur, O.; Noel, B.; Bocs, S.; Droc, G.; Rouard, M.; Da Silva, C.; Jabbari, K.; Cardi, C.; Poulain, J.; Souquet, M.; Labadie, K.; Jourda, C.; Lengellé, J.; Rodier-Goud, M.; Alberti, A.; Bernard, M.; Correa, M.; Ayyampalayam, S.; Mckain, M. R.; Leebens-Mack, J.; Burgess, D.; Freeling, M.; Mbéguié-A-Mbéguié, D.; Chabannes, M.; Wicker, T.; Panaud, O.; Barbosa, J.; Hribova, E.; Heslop-Harrison, P.; Habas, R.; Rivallan, R.; Francois, P.; Poiron, C.; Kilian, A.; Burthia, D.; Jenny, C.; Bakry, F.; Brown, S.; Guignon, V.; Kema, G.; Dita, M.; Waalwijk, C.; Joseph, S.; Dievart, A.; Jaillon, O.; Leclercq, J.; Argout, X.; Lyons, E.; Almeida, A.; Jeridi, M.; Dolezel, J.; Roux, N.; Risterucci, A.; Weissenbach, J.; Ruiz, M.; Glaszmann, J.; Quétier, F.; Yahiaoui, N.; and Wincker, P.\n\n\n \n\n\n\n Nature, 488(7410): 213–217. August 2012.\n Number: 7410 Publisher: Nature Publishing Group\n\n\n\n
\n\n\n\n \n \n $\"The$ Paper\n \n \n\n \n \n doi\n \n \n\n \n link\n \n \n\n bibtex\n \n\n \n \n \n abstract \n \n\n \n\n \n \n \n \n \n \n \n\n \n \n \n \n \n \n \n \n \n\n\n\n

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@article{dhont_banana_2012,\n\ttitle = {The banana ({Musa} acuminata) genome and the evolution of monocotyledonous plants},\n\tvolume = {488},\n\tcopyright = {2012 The Author(s)},\n\tissn = {1476-4687},\n\turl = {https://www.nature.com/articles/nature11241},\n\tdoi = {10.1038/nature11241},\n\tabstract = {The sequencing and analysis of the banana genome is reported; these results inform plant phylogenetic relationships and genome evolution, and provide a resource for future genetic improvement of this important crop species.},\n\tlanguage = {en},\n\tnumber = {7410},\n\turldate = {2023-06-05},\n\tjournal = {Nature},\n\tauthor = {D’Hont, Angélique and Denoeud, France and Aury, Jean-Marc and Baurens, Franc-Christophe and Carreel, Françoise and Garsmeur, Olivier and Noel, Benjamin and Bocs, Stéphanie and Droc, Gaëtan and Rouard, Mathieu and Da Silva, Corinne and Jabbari, Kamel and Cardi, Céline and Poulain, Julie and Souquet, Marlène and Labadie, Karine and Jourda, Cyril and Lengellé, Juliette and Rodier-Goud, Marguerite and Alberti, Adriana and Bernard, Maria and Correa, Margot and Ayyampalayam, Saravanaraj and Mckain, Michael R. and Leebens-Mack, Jim and Burgess, Diane and Freeling, Mike and Mbéguié-A-Mbéguié, Didier and Chabannes, Matthieu and Wicker, Thomas and Panaud, Olivier and Barbosa, Jose and Hribova, Eva and Heslop-Harrison, Pat and Habas, Rémy and Rivallan, Ronan and Francois, Philippe and Poiron, Claire and Kilian, Andrzej and Burthia, Dheema and Jenny, Christophe and Bakry, Frédéric and Brown, Spencer and Guignon, Valentin and Kema, Gert and Dita, Miguel and Waalwijk, Cees and Joseph, Steeve and Dievart, Anne and Jaillon, Olivier and Leclercq, Julie and Argout, Xavier and Lyons, Eric and Almeida, Ana and Jeridi, Mouna and Dolezel, Jaroslav and Roux, Nicolas and Risterucci, Ange-Marie and Weissenbach, Jean and Ruiz, Manuel and Glaszmann, Jean-Christophe and Quétier, Francis and Yahiaoui, Nabila and Wincker, Patrick},\n\tmonth = aug,\n\tyear = {2012},\n\tnote = {Number: 7410\nPublisher: Nature Publishing Group},\n\tkeywords = {Humanities and Social Sciences, multidisciplinary, Science},\n\tpages = {213--217},\n\tfile = {Full Text PDF:C\\:\\\\Users\\\\ojaillon\\\\Zotero\\\\storage\\\\ZWUETDVB\\\\D’Hont et al. - 2012 - The banana (Musa acuminata) genome and the evoluti.pdf:application/pdf},\n}\n\n

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\n \n\n \n \n \n \n \n \n A holistic approach to marine Eco-systems biology.\n \n \n \n \n\n\n \n Karsenti, E.; Acinas, S.; Bork, P.; Bowler, C.; de Vargas, C.; Raes, J.; Sullivan, M.; Arendt, D.; Benzoni, F.; Claverie, J.; Follows, M.; Gorsky, G.; Hingamp, P.; Iudicone, D.; Jaillon, O.; Kandels-Lewis, S.; Krzic, U.; Not, F.; Ogata, H.; Pesant, S.; Reynaud, E.; Sardet, C.; Sieracki, M.; Speich, S.; Velayoudon, D.; Weissenbach, J.; Wincker, P.; Abergel, C.; Arslan, D.; Audic, S.; Aury, J.; Babic, N.; Beaufort, L.; Bittner, L.; Boss, E.; Boutte, C.; Brum, J.; Carmichael, M.; Casotti, R.; Chambouvet, A.; Chang, P.; Chica, C.; Clerissi, C.; Colin, S.; Cornejo-Castillo, F.; Da Silva, C.; De Monte, S.; Decelle, J.; Desdevises, Y.; Dimier, C.; Dolan, J.; Duhaime, M.; Durrieu de Madron, X.; d'Ortenzio , F.; d'Ovidio , F.; Ferrera, I.; Garczarek, L.; Garet-Delmas, M.; Gasmi, S.; Gasol, J.; Grimsley, N.; Heilig, R.; Ignacio-Espinoza, J.; Jamet, J.; Karp-Boss, L.; Katinka, M.; Khalili, H.; Kolber, Z.; Le Bescot, N.; Le Gofff, H.; Lima-Mendez, G.; Mahé, F.; Mazzocchi, M.; Montresor, M.; Morin, P.; Noel, B.; Pedrós-Alió, C.; Pelletier, E.; Perez, Y.; Picheral, M.; Piganeau, G.; Poirot, O.; Poulain, J.; Poulton, N.; Prejger, F.; Prihoda, J.; Probert, I.; Rampal, J.; Reverdin, G.; Romac, S.; Romagnan, J.; Roullier, F.; Rouviere, C.; Samson, G.; Santini, S.; Sarmento, H.; Sciandra, A.; Solonenko, S.; Stemmann, L.; Subirana, L.; Sunagawa, S.; Tanaka, A.; Testor, P.; Thompson, A.; Tichanné-Seltzer, V.; Tirichine, L.; Toulza, E.; Tozzi, S.; Veluchamy, A.; and Zingone, A.\n\n\n \n\n\n\n PLoS Biology, 9(10). 2011.\n \n\n\n\n
\n\n\n\n \n \n $\"A$ Paper\n \n \n\n \n \n doi\n \n \n\n \n link\n \n \n\n bibtex\n \n\n \n\n \n \n \n 22 downloads\n \n \n\n \n \n \n \n \n \n \n\n \n \n \n\n\n\n

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@article{karsenti_holistic_2011,\n\ttitle = {A holistic approach to marine {Eco}-systems biology},\n\tvolume = {9},\n\turl = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-80055082475&doi=10.1371%2fjournal.pbio.1001177&partnerID=40&md5=6fb10613919a4a0a032a95ffdc0a4fd8},\n\tdoi = {10.1371/journal.pbio.1001177},\n\tnumber = {10},\n\tjournal = {PLoS Biology},\n\tauthor = {Karsenti, E. and Acinas, S.G. and Bork, P. and Bowler, C. and de Vargas, C. and Raes, J. and Sullivan, M. and Arendt, D. and Benzoni, F. and Claverie, J.-M. and Follows, M. and Gorsky, G. and Hingamp, P. and Iudicone, D. and Jaillon, O. and Kandels-Lewis, S. and Krzic, U. and Not, F. and Ogata, H. and Pesant, S. and Reynaud, E.G. and Sardet, C. and Sieracki, M.E. and Speich, S. and Velayoudon, D. and Weissenbach, J. and Wincker, P. and Abergel, C. and Arslan, D. and Audic, S. and Aury, J.M. and Babic, N. and Beaufort, L. and Bittner, L. and Boss, E. and Boutte, C. and Brum, J. and Carmichael, M. and Casotti, R. and Chambouvet, A. and Chang, P. and Chica, C. and Clerissi, C. and Colin, S. and Cornejo-Castillo, F.M. and Da Silva, C. and De Monte, S. and Decelle, J. and Desdevises, Y. and Dimier, C. and Dolan, J. and Duhaime, M. and Durrieu de Madron, X. and d'Ortenzio, F. and d'Ovidio, F. and Ferrera, I. and Garczarek, L. and Garet-Delmas, M.J. and Gasmi, S. and Gasol, J.M. and Grimsley, N. and Heilig, R. and Ignacio-Espinoza, J. and Jamet, J.L. and Karp-Boss, L. and Katinka, M. and Khalili, H. and Kolber, Z. and Le Bescot, N. and Le Gofff, H. and Lima-Mendez, G. and Mahé, F. and Mazzocchi, M.G. and Montresor, M. and Morin, P. and Noel, B. and Pedrós-Alió, C. and Pelletier, E. and Perez, Y. and Picheral, M. and Piganeau, G. and Poirot, O. and Poulain, J. and Poulton, N. and Prejger, F. and Prihoda, J. and Probert, I. and Rampal, J. and Reverdin, G. and Romac, S. and Romagnan, J.B. and Roullier, F. and Rouviere, C. and Samson, G. and Santini, S. and Sarmento, H. and Sciandra, A. and Solonenko, S. and Stemmann, L. and Subirana, L. and Sunagawa, S. and Tanaka, A. and Testor, P. and Thompson, A. and Tichanné-Seltzer, V. and Tirichine, L. and Toulza, E. and Tozzi, S. and Veluchamy, A. and Zingone, A.},\n\tyear = {2011},\n}\n\n

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\n \n\n \n \n \n \n \n \n Genome sequence of the stramenopile Blastocystis, a human anaerobic parasite.\n \n \n \n \n\n\n \n Denoeud, F.; Roussel, M.; Noel, B.; Wawrzyniak, I.; Da Silva, C.; Diogon, M.; Viscogliosi, E.; Brochier-Armanet, C.; Couloux, A.; Poulain, J.; Segurens, B.; Anthouard, V.; Texier, C.; Blot, N.; Poirier, P.; Ng, G.; Tan, K.; Artiguenave, F.; Jaillon, O.; Aury, J.; Delbac, F.; Wincker, P.; Vivarès, C.; and El Alaoui, H.\n\n\n \n\n\n\n Genome Biology, 12(3). 2011.\n \n\n\n\n
\n\n\n\n \n \n $\"Genome$ Paper\n \n \n\n \n \n doi\n \n \n\n \n link\n \n \n\n bibtex\n \n\n \n\n \n\n \n \n \n \n \n \n \n\n \n \n \n\n\n\n

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@article{denoeud_genome_2011,\n\ttitle = {Genome sequence of the stramenopile {Blastocystis}, a human anaerobic parasite},\n\tvolume = {12},\n\turl = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-79953094250&doi=10.1186%2fgb-2011-12-3-r29&partnerID=40&md5=53c22d837d9a312fcf80e48cece4f954},\n\tdoi = {10.1186/gb-2011-12-3-r29},\n\tnumber = {3},\n\tjournal = {Genome Biology},\n\tauthor = {Denoeud, F. and Roussel, M. and Noel, B. and Wawrzyniak, I. and Da Silva, C. and Diogon, M. and Viscogliosi, E. and Brochier-Armanet, C. and Couloux, A. and Poulain, J. and Segurens, B. and Anthouard, V. and Texier, C. and Blot, N. and Poirier, P. and Ng, G.C. and Tan, K.S.W. and Artiguenave, F. and Jaillon, O. and Aury, J.-M. and Delbac, F. and Wincker, P. and Vivarès, C.P. and El Alaoui, H.},\n\tyear = {2011},\n}\n\n

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\n \n\n \n \n \n \n \n \n These invisible actors who control the aquatic environments [Ces acteurs invisibles qui contrôlent les milieux aquatiques].\n \n \n \n \n\n\n \n Not, F.; Debroas, D.; Jebbar, M.; and Jaillon, O.\n\n\n \n\n\n\n Biofutur, (319): 34–38. 2011.\n \n\n\n\n
\n\n\n\n \n \n $\"These$ Paper\n \n \n\n \n\n \n link\n \n \n\n bibtex\n \n\n \n\n \n\n \n \n \n \n \n \n \n\n \n \n \n\n\n\n

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@article{not_these_2011,\n\ttitle = {These invisible actors who control the aquatic environments [{Ces} acteurs invisibles qui contrôlent les milieux aquatiques]},\n\turl = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-79953153758&partnerID=40&md5=d783849ae0c58c1c7376c22ead547f71},\n\tnumber = {319},\n\tjournal = {Biofutur},\n\tauthor = {Not, F. and Debroas, D. and Jebbar, M. and Jaillon, O.},\n\tyear = {2011},\n\tpages = {34--38},\n}\n\n

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\n \n\n \n \n \n \n \n \n Plasticity of animal genome architecture unmasked by rapid evolution of a pelagic tunicate.\n \n \n \n \n\n\n \n Denoeud, F.; Henriet, S.; Mungpakdee, S.; Aury, J.; Da Silva, C.; Brinkmann, H.; Mikhaleva, J.; Olsen, L.; Jubin, C.; Cañestro, C.; Bouquet, J.; Danks, G.; Poulain, J.; Campsteijn, C.; Adamski, M.; Cross, I.; Yadetie, F.; Muffato, M.; Louis, A.; Butcher, S.; Tsagkogeorga, G.; Konrad, A.; Singh, S.; Jensen, M.; Cong, E.; Eikeseth-Otteraa, H.; Noel, B.; Anthouard, V.; Porcel, B.; Kachouri-Lafond, R.; Nishino, A.; Ugolini, M.; Chourrout, P.; Nishida, H.; Aasland, R.; Huzurbazar, S.; Westhof, E.; Delsuc, F.; Lehrach, H.; Reinhardt, R.; Weissenbach, J.; Roy, S.; Artiguenave, F.; Postlethwait, J.; Manak, J.; Thompson, E.; Jaillon, O.; Du Pasquier, L.; Boudinot, P.; Liberles, D.; Volff, J.; Philippe, H.; Lenhard, B.; Crollius, H.; Wincker, P.; and Chourrout, D.\n\n\n \n\n\n\n Science, 330(6009): 1381–1385. 2010.\n \n\n\n\n
\n\n\n\n \n \n $\"Plasticity$ Paper\n \n \n\n \n \n doi\n \n \n\n \n link\n \n \n\n bibtex\n \n\n \n\n \n\n \n \n \n \n \n \n \n\n \n \n \n\n\n\n

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@article{denoeud_plasticity_2010,\n\ttitle = {Plasticity of animal genome architecture unmasked by rapid evolution of a pelagic tunicate},\n\tvolume = {330},\n\turl = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-78649705889&doi=10.1126%2fscience.1194167&partnerID=40&md5=b9847f3db8d1967bcbc56d6306e4a8a2},\n\tdoi = {10.1126/science.1194167},\n\tnumber = {6009},\n\tjournal = {Science},\n\tauthor = {Denoeud, F. and Henriet, S. and Mungpakdee, S. and Aury, J.-M. and Da Silva, C. and Brinkmann, H. and Mikhaleva, J. and Olsen, L.C. and Jubin, C. and Cañestro, C. and Bouquet, J.-M. and Danks, G. and Poulain, J. and Campsteijn, C. and Adamski, M. and Cross, I. and Yadetie, F. and Muffato, M. and Louis, A. and Butcher, S. and Tsagkogeorga, G. and Konrad, A. and Singh, S. and Jensen, M.F. and Cong, E.H. and Eikeseth-Otteraa, H. and Noel, B. and Anthouard, V. and Porcel, B.M. and Kachouri-Lafond, R. and Nishino, A. and Ugolini, M. and Chourrout, P. and Nishida, H. and Aasland, R. and Huzurbazar, S. and Westhof, E. and Delsuc, F. and Lehrach, H. and Reinhardt, R. and Weissenbach, J. and Roy, S.W. and Artiguenave, F. and Postlethwait, J.H. and Manak, J.R. and Thompson, E.M. and Jaillon, O. and Du Pasquier, L. and Boudinot, P. and Liberles, D.A. and Volff, J.-N. and Philippe, H. and Lenhard, B. and Crollius, H.R. and Wincker, P. and Chourrout, D.},\n\tyear = {2010},\n\tpages = {1381--1385},\n}\n\n

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\n \n\n \n \n \n \n \n \n Périgord black truffle genome uncovers evolutionary origins and mechanisms of symbiosis.\n \n \n \n \n\n\n \n Martin, F.; Kohler, A.; Murat, C.; Balestrini, R.; Coutinho, P. M.; Jaillon, O.; Montanini, B.; Morin, E.; Noel, B.; Percudani, R.; Porcel, B.; Rubini, A.; Amicucci, A.; Amselem, J.; Anthouard, V.; Arcioni, S.; Artiguenave, F.; Aury, J.; Ballario, P.; Bolchi, A.; Brenna, A.; Brun, A.; Buée, M.; Cantarel, B.; Chevalier, G.; Couloux, A.; Da Silva, C.; Denoeud, F.; Duplessis, S.; Ghignone, S.; Hilselberger, B.; Iotti, M.; Marçais, B.; Mello, A.; Miranda, M.; Pacioni, G.; Quesneville, H.; Riccioni, C.; Ruotolo, R.; Splivallo, R.; Stocchi, V.; Tisserant, E.; Viscomi, A. R.; Zambonelli, A.; Zampieri, E.; Henrissat, B.; Lebrun, M.; Paolocci, F.; Bonfante, P.; Ottonello, S.; and Wincker, P.\n\n\n \n\n\n\n Nature, 464(7291): 1033–1038. April 2010.\n Number: 7291 Publisher: Nature Publishing Group\n\n\n\n
\n\n\n\n \n \n $\"Périgord$ Paper\n \n \n\n \n \n doi\n \n \n\n \n link\n \n \n\n bibtex\n \n\n \n \n \n abstract \n \n\n \n\n \n \n \n \n \n \n \n\n \n \n \n \n \n \n \n \n \n\n\n\n

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@article{martin_perigord_2010,\n\ttitle = {Périgord black truffle genome uncovers evolutionary origins and mechanisms of symbiosis},\n\tvolume = {464},\n\tcopyright = {2010 The Author(s)},\n\tissn = {1476-4687},\n\turl = {https://www.nature.com/articles/nature08867},\n\tdoi = {10.1038/nature08867},\n\tabstract = {The genome of the Périgord black truffle Tuber melanosporum Vittad., a gourmet delicacy that grows symbiotically on the roots of European oak, has been sequenced. This is the largest and most complex fungal genome so far sequenced. The genome is unusually gene-poor, but rich in the mobile genetic elements known as transposons. Comparison with the sequence of Laccaria bicolor, another ectomycorrhizal symbiotic fungus, reveals contrasting gene sets reflecting two different molecular toolkits that have evolved independently to fit the root symbiont lifestyle. Cultivation of the truffle is a complicated process, and most truffles are still harvested from the wild. So the analysis of genetic traits related to fruiting and symbiosis could help boost crop production and make black truffles more widely available.},\n\tlanguage = {en},\n\tnumber = {7291},\n\turldate = {2023-06-05},\n\tjournal = {Nature},\n\tauthor = {Martin, Francis and Kohler, Annegret and Murat, Claude and Balestrini, Raffaella and Coutinho, Pedro M. and Jaillon, Olivier and Montanini, Barbara and Morin, Emmanuelle and Noel, Benjamin and Percudani, Riccardo and Porcel, Bettina and Rubini, Andrea and Amicucci, Antonella and Amselem, Joelle and Anthouard, Véronique and Arcioni, Sergio and Artiguenave, François and Aury, Jean-Marc and Ballario, Paola and Bolchi, Angelo and Brenna, Andrea and Brun, Annick and Buée, Marc and Cantarel, Brandi and Chevalier, Gérard and Couloux, Arnaud and Da Silva, Corinne and Denoeud, France and Duplessis, Sébastien and Ghignone, Stefano and Hilselberger, Benoît and Iotti, Mirco and Marçais, Benoît and Mello, Antonietta and Miranda, Michele and Pacioni, Giovanni and Quesneville, Hadi and Riccioni, Claudia and Ruotolo, Roberta and Splivallo, Richard and Stocchi, Vilberto and Tisserant, Emilie and Viscomi, Arturo Roberto and Zambonelli, Alessandra and Zampieri, Elisa and Henrissat, Bernard and Lebrun, Marc-Henri and Paolocci, Francesco and Bonfante, Paola and Ottonello, Simone and Wincker, Patrick},\n\tmonth = apr,\n\tyear = {2010},\n\tnote = {Number: 7291\nPublisher: Nature Publishing Group},\n\tkeywords = {Fungi, Genome evolution, Symbiosis},\n\tpages = {1033--1038},\n\tfile = {Full Text PDF:C\\:\\\\Users\\\\ojaillon\\\\Zotero\\\\storage\\\\NCP88WA7\\\\Martin et al. - 2010 - Périgord black truffle genome uncovers evolutionar.pdf:application/pdf},\n}\n\n

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\n \n\n \n \n \n \n \n \n Molecular mechanisms of late apoptotic/necrotic cell clearance.\n \n \n \n \n\n\n \n Poon, I. K. H.; Hulett, M. D.; and Parish, C. R.\n\n\n \n\n\n\n Cell Death & Differentiation, 17(3): 381–397. March 2010.\n Number: 3 Publisher: Nature Publishing Group\n\n\n\n
\n\n\n\n \n \n $\"Molecular$ Paper\n \n \n\n \n \n doi\n \n \n\n \n link\n \n \n\n bibtex\n \n\n \n \n \n abstract \n \n\n \n\n \n \n \n \n \n \n \n\n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n\n\n\n

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@article{poon_molecular_2010,\n\ttitle = {Molecular mechanisms of late apoptotic/necrotic cell clearance},\n\tvolume = {17},\n\tcopyright = {2010 Macmillan Publishers Limited},\n\tissn = {1476-5403},\n\turl = {https://www.nature.com/articles/cdd2009195},\n\tdoi = {10.1038/cdd.2009.195},\n\tabstract = {Phagocytosis serves as one of the key processes involved in development, maintenance of tissue homeostasis, as well as in eliminating pathogens from an organism. Under normal physiological conditions, dying cells (e.g., apoptotic and necrotic cells) and pathogens (e.g., bacteria and fungi) are rapidly detected and removed by professional phagocytes such as macrophages and dendritic cells (DCs). In most cases, specific receptors and opsonins are used by phagocytes to recognize and bind their target cells, which can trigger the intracellular signalling events required for phagocytosis. Depending on the type of target cell, phagocytes may also release both immunomodulatory molecules and growth factors to orchestrate a subsequent immune response and wound healing process. In recent years, evidence is growing that opsonins and receptors involved in the removal of pathogens can also aid the disposal of dying cells at all stages of cell death, in particular plasma membrane-damaged cells such as late apoptotic and necrotic cells. This review provides an overview of the molecular mechanisms and the immunological outcomes of late apoptotic/necrotic cell removal and highlights the striking similarities between late apoptotic/necrotic cell and pathogen clearance.},\n\tlanguage = {en},\n\tnumber = {3},\n\turldate = {2023-06-05},\n\tjournal = {Cell Death \\& Differentiation},\n\tauthor = {Poon, I. K. H. and Hulett, M. D. and Parish, C. R.},\n\tmonth = mar,\n\tyear = {2010},\n\tnote = {Number: 3\nPublisher: Nature Publishing Group},\n\tkeywords = {Apoptosis, general, Life Sciences, Biochemistry, Cell Biology, Cell Cycle Analysis, Stem Cells},\n\tpages = {381--397},\n\tfile = {Full Text PDF:C\\:\\\\Users\\\\ojaillon\\\\Zotero\\\\storage\\\\QE6VNM5T\\\\Poon et al. - 2010 - Molecular mechanisms of late apoptoticnecrotic ce.pdf:application/pdf},\n}\n\n

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\n \n 2009\n \n \n (1)\n \n \n

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\n \n\n \n \n \n \n \n \n \"Changing by doubling\", the impact of Whole Genome Duplications in the evolution of eukaryotes.\n \n \n \n \n\n\n \n Jaillon, O.; Aury, J.; and Wincker, P.\n\n\n \n\n\n\n Comptes Rendus - Biologies, 332(2-3): 241–253. 2009.\n \n\n\n\n
\n\n\n\n \n \n $\""Changing$ Paper\n \n \n\n \n \n doi\n \n \n\n \n link\n \n \n\n bibtex\n \n\n \n\n \n\n \n \n \n \n \n \n \n\n \n \n \n\n\n\n

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@article{jaillon_changing_2009,\n\ttitle = {"{Changing} by doubling", the impact of {Whole} {Genome} {Duplications} in the evolution of eukaryotes},\n\tvolume = {332},\n\turl = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-61549103128&doi=10.1016%2fj.crvi.2008.07.007&partnerID=40&md5=09528ed7bf5c10ccf77d61f888cf9bd8},\n\tdoi = {10.1016/j.crvi.2008.07.007},\n\tnumber = {2-3},\n\tjournal = {Comptes Rendus - Biologies},\n\tauthor = {Jaillon, O. and Aury, J.-M. and Wincker, P.},\n\tyear = {2009},\n\tpages = {241--253},\n}\n\n

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\n \n 2008\n \n \n (5)\n \n \n

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\n \n\n \n \n \n \n \n \n Annotating genomes with massive-scale RNA sequencing.\n \n \n \n \n\n\n \n Denoeud, F.; Aury, J.; Da Silva, C.; Noel, B.; Rogier, O.; Delledonne, M.; Morgante, M.; Valle, G.; Wincker, P.; Scarpelli, C.; Jaillon, O.; and Artiguenave, F.\n\n\n \n\n\n\n Genome Biology, 9(12). 2008.\n \n\n\n\n
\n\n\n\n \n \n $\"Annotating$ Paper\n \n \n\n \n \n doi\n \n \n\n \n link\n \n \n\n bibtex\n \n\n \n\n \n\n \n \n \n \n \n \n \n\n \n \n \n\n\n\n

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@article{denoeud_annotating_2008,\n\ttitle = {Annotating genomes with massive-scale {RNA} sequencing},\n\tvolume = {9},\n\turl = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-58149513263&doi=10.1186%2fgb-2008-9-12-r175&partnerID=40&md5=af45f11c555a14ea9ced2cf5acf3f91b},\n\tdoi = {10.1186/gb-2008-9-12-r175},\n\tnumber = {12},\n\tjournal = {Genome Biology},\n\tauthor = {Denoeud, F. and Aury, J.-M. and Da Silva, C. and Noel, B. and Rogier, O. and Delledonne, M. and Morgante, M. and Valle, G. and Wincker, P. and Scarpelli, C. and Jaillon, O. and Artiguenave, F.},\n\tyear = {2008},\n}\n\n

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\n \n\n \n \n \n \n \n \n Translational control of intron splicing in eukaryotes.\n \n \n \n \n\n\n \n Jaillon, O.; Bouhouche, K.; Gout, J.; Aury, J.; Noel, B.; Saudemont, B.; Nowacki, M.; Serrano, V.; Porcel, B.; Ségurens, B.; Le Mouël, A.; Lepère, G.; Schächter, V.; Bétermier, M.; Cohen, J.; Wincker, P.; Sperling, L.; Duret, L.; and Meyer, E.\n\n\n \n\n\n\n Nature, 451(7176): 359–362. 2008.\n \n\n\n\n
\n\n\n\n \n \n $\"Translational$ Paper\n \n \n\n \n \n doi\n \n \n\n \n link\n \n \n\n bibtex\n \n\n \n\n \n\n \n \n \n \n \n \n \n\n \n \n \n\n\n\n

\n

@article{jaillon_translational_2008,\n\ttitle = {Translational control of intron splicing in eukaryotes},\n\tvolume = {451},\n\turl = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-38349125022&doi=10.1038%2fnature06495&partnerID=40&md5=c2b59515e757f00bdbcd679ec0c82f82},\n\tdoi = {10.1038/nature06495},\n\tnumber = {7176},\n\tjournal = {Nature},\n\tauthor = {Jaillon, O. and Bouhouche, K. and Gout, J.-F. and Aury, J.-M. and Noel, B. and Saudemont, B. and Nowacki, M. and Serrano, V. and Porcel, B.M. and Ségurens, B. and Le Mouël, A. and Lepère, G. and Schächter, V. and Bétermier, M. and Cohen, J. and Wincker, P. and Sperling, L. and Duret, L. and Meyer, E.},\n\tyear = {2008},\n\tpages = {359--362},\n}\n\n

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\n \n\n \n \n \n \n \n \n The genome sequence of the model ascomycete fungus Podospora anserina.\n \n \n \n \n\n\n \n Espagne, E.; Lespinet, O.; Malagnac, F.; Da Silva, C.; Jaillon, O.; Porcel, B.; Couloux, A.; Aury, J.; Ségurens, B.; Poulain, J.; Anthouard, V.; Grossetete, S.; Khalili, H.; Coppin, E.; Déquard-Chablat, M.; Picard, M.; Contamine, V.; Arnaise, S.; Bourdais, A.; Berteaux-Lecellier, V.; Gautheret, D.; de Vries, R.; Battaglia, E.; Coutinho, P.; Danchin, E.; Henrissat, B.; Khoury, R.; Sainsard-Chanet, A.; Boivin, A.; Pinan-Lucarré, B.; Sellem, C.; Debuchy, R.; Wincker, P.; Weissenbach, J.; and Silar, P.\n\n\n \n\n\n\n Genome biology, 9(5): R77. 2008.\n \n\n\n\n
\n\n\n\n \n \n $\"The$ Paper\n \n \n\n \n \n doi\n \n \n\n \n link\n \n \n\n bibtex\n \n\n \n\n \n\n \n \n \n \n \n \n \n\n \n \n \n\n\n\n

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@article{espagne_genome_2008,\n\ttitle = {The genome sequence of the model ascomycete fungus {Podospora} anserina.},\n\tvolume = {9},\n\turl = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-48949118871&doi=10.1186%2fgb-2008-9-5-r77&partnerID=40&md5=b3cd929b25983af5c981e9526f9a5276},\n\tdoi = {10.1186/gb-2008-9-5-r77},\n\tnumber = {5},\n\tjournal = {Genome biology},\n\tauthor = {Espagne, E. and Lespinet, O. and Malagnac, F. and Da Silva, C. and Jaillon, O. and Porcel, B.M. and Couloux, A. and Aury, J.M. and Ségurens, B. and Poulain, J. and Anthouard, V. and Grossetete, S. and Khalili, H. and Coppin, E. and Déquard-Chablat, M. and Picard, M. and Contamine, V. and Arnaise, S. and Bourdais, A. and Berteaux-Lecellier, V. and Gautheret, D. and de Vries, R.P. and Battaglia, E. and Coutinho, P.M. and Danchin, E.G. and Henrissat, B. and Khoury, R.E. and Sainsard-Chanet, A. and Boivin, A. and Pinan-Lucarré, B. and Sellem, C.H. and Debuchy, R. and Wincker, P. and Weissenbach, J. and Silar, P.},\n\tyear = {2008},\n\tpages = {R77},\n}\n\n

\n

\n\n\n\n

\n\n\n

\n \n\n \n \n \n \n \n \n Analysis of sequence variability in the macronuclear DNA of Paramecium tetraurelia: A somatic view of the germline.\n \n \n \n \n\n\n \n Duret, L.; Cohen, J.; Jubin, C.; Dessen, P.; Goût, J.; Mousset, S.; Aury, J.; Jaillon, O.; Noël, B.; Arnaiz, O.; Bétermier, M.; Wincker, P.; Meyer, E.; and Sperling, L.\n\n\n \n\n\n\n Genome Research, 18(4): 585–596. 2008.\n \n\n\n\n
\n\n\n\n \n \n $\"Analysis$ Paper\n \n \n\n \n \n doi\n \n \n\n \n link\n \n \n\n bibtex\n \n\n \n\n \n\n \n \n \n \n \n \n \n\n \n \n \n\n\n\n

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@article{duret_analysis_2008,\n\ttitle = {Analysis of sequence variability in the macronuclear {DNA} of {Paramecium} tetraurelia: {A} somatic view of the germline},\n\tvolume = {18},\n\turl = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-41649113803&doi=10.1101%2fgr.074534.107&partnerID=40&md5=20cab0091060048b30173f439e25c3b3},\n\tdoi = {10.1101/gr.074534.107},\n\tnumber = {4},\n\tjournal = {Genome Research},\n\tauthor = {Duret, L. and Cohen, J. and Jubin, C. and Dessen, P. and Goût, J.-F. and Mousset, S. and Aury, J.-M. and Jaillon, O. and Noël, B. and Arnaiz, O. and Bétermier, M. and Wincker, P. and Meyer, E. and Sperling, L.},\n\tyear = {2008},\n\tpages = {585--596},\n}\n\n

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\n \n\n \n \n \n \n \n \n Genome sequence of the metazoan plant-parasitic nematode Meloidogyne incognita.\n \n \n \n \n\n\n \n Abad, P.; Gouzy, J.; Aury, J.; Castagnone-Sereno, P.; Danchin, E. G. J.; Deleury, E.; Perfus-Barbeoch, L.; Anthouard, V.; Artiguenave, F.; Blok, V. C.; Caillaud, M.; Coutinho, P. M.; Dasilva, C.; De Luca, F.; Deau, F.; Esquibet, M.; Flutre, T.; Goldstone, J. V.; Hamamouch, N.; Hewezi, T.; Jaillon, O.; Jubin, C.; Leonetti, P.; Magliano, M.; Maier, T. R.; Markov, G. V.; McVeigh, P.; Pesole, G.; Poulain, J.; Robinson-Rechavi, M.; Sallet, E.; Ségurens, B.; Steinbach, D.; Tytgat, T.; Ugarte, E.; van Ghelder, C.; Veronico, P.; Baum, T. J.; Blaxter, M.; Bleve-Zacheo, T.; Davis, E. L.; Ewbank, J. J.; Favery, B.; Grenier, E.; Henrissat, B.; Jones, J. T.; Laudet, V.; Maule, A. G.; Quesneville, H.; Rosso, M.; Schiex, T.; Smant, G.; Weissenbach, J.; and Wincker, P.\n\n\n \n\n\n\n Nature Biotechnology, 26(8): 909–915. August 2008.\n Number: 8 Publisher: Nature Publishing Group\n\n\n\n
\n\n\n\n \n \n $\"Genome$ Paper\n \n \n\n \n \n doi\n \n \n\n \n link\n \n \n\n bibtex\n \n\n \n \n \n abstract \n \n\n \n\n \n \n \n \n \n \n \n\n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n\n\n\n

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@article{abad_genome_2008,\n\ttitle = {Genome sequence of the metazoan plant-parasitic nematode {Meloidogyne} incognita},\n\tvolume = {26},\n\tcopyright = {2008 The Author(s)},\n\tissn = {1546-1696},\n\turl = {https://www.nature.com/articles/nbt.1482},\n\tdoi = {10.1038/nbt.1482},\n\tabstract = {Biological control of the root-knot nematode Meloidogyne incognita, one of the world's most destructive crop pathogens, presents a major opportunity for safely improving global agricultural yields. Its 86-Mb genome—the first to be sequenced for a strictly parthenogenetic species—provides a blueprint to design new strategies for plant protection.},\n\tlanguage = {en},\n\tnumber = {8},\n\turldate = {2023-06-05},\n\tjournal = {Nature Biotechnology},\n\tauthor = {Abad, Pierre and Gouzy, Jérôme and Aury, Jean-Marc and Castagnone-Sereno, Philippe and Danchin, Etienne G. J. and Deleury, Emeline and Perfus-Barbeoch, Laetitia and Anthouard, Véronique and Artiguenave, François and Blok, Vivian C. and Caillaud, Marie-Cécile and Coutinho, Pedro M. and Dasilva, Corinne and De Luca, Francesca and Deau, Florence and Esquibet, Magali and Flutre, Timothé and Goldstone, Jared V. and Hamamouch, Noureddine and Hewezi, Tarek and Jaillon, Olivier and Jubin, Claire and Leonetti, Paola and Magliano, Marc and Maier, Tom R. and Markov, Gabriel V. and McVeigh, Paul and Pesole, Graziano and Poulain, Julie and Robinson-Rechavi, Marc and Sallet, Erika and Ségurens, Béatrice and Steinbach, Delphine and Tytgat, Tom and Ugarte, Edgardo and van Ghelder, Cyril and Veronico, Pasqua and Baum, Thomas J. and Blaxter, Mark and Bleve-Zacheo, Teresa and Davis, Eric L. and Ewbank, Jonathan J. and Favery, Bruno and Grenier, Eric and Henrissat, Bernard and Jones, John T. and Laudet, Vincent and Maule, Aaron G. and Quesneville, Hadi and Rosso, Marie-Noëlle and Schiex, Thomas and Smant, Geert and Weissenbach, Jean and Wincker, Patrick},\n\tmonth = aug,\n\tyear = {2008},\n\tnote = {Number: 8\nPublisher: Nature Publishing Group},\n\tkeywords = {Biotechnology, general, Life Sciences, Agriculture, Biomedicine, Bioinformatics, Biomedical Engineering/Biotechnology},\n\tpages = {909--915},\n\tfile = {Full Text PDF:C\\:\\\\Users\\\\ojaillon\\\\Zotero\\\\storage\\\\QAGIJM67\\\\Abad et al. - 2008 - Genome sequence of the metazoan plant-parasitic ne.pdf:application/pdf},\n}\n\n

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\n \n 2007\n \n \n (1)\n \n \n

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\n \n\n \n \n \n \n \n \n The grapevine genome sequence suggests ancestral hexaploidization in major angiosperm phyla.\n \n \n \n \n\n\n \n Jaillon, O.; Aury, J.; Noel, B.; Policriti, A.; Clepet, C.; Casagrande, A.; Choisne, N.; Aubourg, S.; Vitulo, N.; Jubin, C.; Vezzi, A.; Legeai, F.; Hugueney, P.; Dasilva, C.; Horner, D.; Mica, E.; Jublot, D.; Poulain, J.; Bruyère, C.; Billault, A.; Segurens, B.; Gouyvenoux, M.; Ugarte, E.; Cattonaro, F.; Anthouard, V.; Vico, V.; Del Fabbro, C.; Alaux, M.; Di Gaspero, G.; Dumas, V.; Felice, N.; Paillard, S.; Juman, I.; Moroldo, M.; Scalabrin, S.; Canaguier, A.; Le Clainche, I.; Malacrida, G.; Durand, E.; Pesole, G.; Laucou, V.; Chatelet, P.; Merdinoglu, D.; Delledonne, M.; Pezzotti, M.; Lecharny, A.; Scarpelli, C.; Artiguenave, F.; Pè, M. E.; Valle, G.; Morgante, M.; Caboche, M.; Adam-Blondon, A.; Weissenbach, J.; Quétier, F.; Wincker, P.; and The French–Italian Public Consortium for Grapevine Genome Characterization\n\n\n \n\n\n\n Nature, 449(7161): 463–467. September 2007.\n Number: 7161 Publisher: Nature Publishing Group\n\n\n\n
\n\n\n\n \n \n $\"The$ Paper\n \n \n\n \n \n doi\n \n \n\n \n link\n \n \n\n bibtex\n \n\n \n \n \n abstract \n \n\n \n\n \n \n \n \n \n \n \n\n \n \n \n \n \n \n \n \n \n\n\n\n

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@article{jaillon_grapevine_2007,\n\ttitle = {The grapevine genome sequence suggests ancestral hexaploidization in major angiosperm phyla},\n\tvolume = {449},\n\tcopyright = {2007 The Author(s)},\n\tissn = {1476-4687},\n\turl = {https://www.nature.com/articles/nature06148},\n\tdoi = {10.1038/nature06148},\n\tabstract = {The fourth genome sequence of a flowering plant, the second of a woody plant species and the first for a fruit crop. These important boxes are ticked by the genome sequence published in this issue. The new sequence is particularly revealing about the role of gene duplication in the evolution of the flowering plants. But the reason why non-geneticists will turn to it is more to do with its commercial application: the crop is the grapevine (Vitis vinifera) and the variety is Pinot Noir.},\n\tlanguage = {en},\n\tnumber = {7161},\n\turldate = {2023-06-05},\n\tjournal = {Nature},\n\tauthor = {Jaillon, Olivier and Aury, Jean-Marc and Noel, Benjamin and Policriti, Alberto and Clepet, Christian and Casagrande, Alberto and Choisne, Nathalie and Aubourg, Sébastien and Vitulo, Nicola and Jubin, Claire and Vezzi, Alessandro and Legeai, Fabrice and Hugueney, Philippe and Dasilva, Corinne and Horner, David and Mica, Erica and Jublot, Delphine and Poulain, Julie and Bruyère, Clémence and Billault, Alain and Segurens, Béatrice and Gouyvenoux, Michel and Ugarte, Edgardo and Cattonaro, Federica and Anthouard, Véronique and Vico, Virginie and Del Fabbro, Cristian and Alaux, Michaël and Di Gaspero, Gabriele and Dumas, Vincent and Felice, Nicoletta and Paillard, Sophie and Juman, Irena and Moroldo, Marco and Scalabrin, Simone and Canaguier, Aurélie and Le Clainche, Isabelle and Malacrida, Giorgio and Durand, Eléonore and Pesole, Graziano and Laucou, Valérie and Chatelet, Philippe and Merdinoglu, Didier and Delledonne, Massimo and Pezzotti, Mario and Lecharny, Alain and Scarpelli, Claude and Artiguenave, François and Pè, M. Enrico and Valle, Giorgio and Morgante, Michele and Caboche, Michel and Adam-Blondon, Anne-Françoise and Weissenbach, Jean and Quétier, Francis and Wincker, Patrick and {The French–Italian Public Consortium for Grapevine Genome Characterization}},\n\tmonth = sep,\n\tyear = {2007},\n\tnote = {Number: 7161\nPublisher: Nature Publishing Group},\n\tkeywords = {Humanities and Social Sciences, multidisciplinary, Science},\n\tpages = {463--467},\n\tfile = {Full Text PDF:C\\:\\\\Users\\\\ojaillon\\\\Zotero\\\\storage\\\\F874S46B\\\\Jaillon et al. - 2007 - The grapevine genome sequence suggests ancestral h.pdf:application/pdf},\n}\n\n

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\n \n 2006\n \n \n (2)\n \n \n

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\n \n\n \n \n \n \n \n \n Global trends of whole-genome duplications revealed by the ciliate Paramecium tetraurelia.\n \n \n \n \n\n\n \n Aury, J.; Jaillon, O.; Duret, L.; Noel, B.; Jubin, C.; Porcel, B.; Ségurens, B.; Daubin, V.; Anthouard, V.; Aiach, N.; Arnaiz, O.; Billaut, A.; Beisson, J.; Blanc, I.; Bouhouche, K.; Ĉmara, F.; Duharcourt, S.; Guigo, R.; Gogendeau, D.; Katinka, M.; Keller, A.; Kissmehl, R.; Klotz, C.; Koll, F.; Le Mouël, A.; Lepère, G.; Malinsky, S.; Nowacki, M.; Nowak, J.; Plattner, H.; Poulain, J.; Ruiz, F.; Serrano, V.; Zagulski, M.; Dessen, P.; Bétermier, M.; Weissenbach, J.; Scarpelli, C.; Schächter, V.; Sperling, L.; Meyer, E.; Cohen, J.; and Wincker, P.\n\n\n \n\n\n\n Nature, 444(7116): 171–178. 2006.\n \n\n\n\n
\n\n\n\n \n \n $\"Global$ Paper\n \n \n\n \n \n doi\n \n \n\n \n link\n \n \n\n bibtex\n \n\n \n\n \n\n \n \n \n \n \n \n \n\n \n \n \n\n\n\n

\n

@article{aury_global_2006,\n\ttitle = {Global trends of whole-genome duplications revealed by the ciliate {Paramecium} tetraurelia},\n\tvolume = {444},\n\turl = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-33750858684&doi=10.1038%2fnature05230&partnerID=40&md5=6990adec043fbe5e3fe8d55536723ee1},\n\tdoi = {10.1038/nature05230},\n\tnumber = {7116},\n\tjournal = {Nature},\n\tauthor = {Aury, J.-M. and Jaillon, O. and Duret, L. and Noel, B. and Jubin, C. and Porcel, B.M. and Ségurens, B. and Daubin, V. and Anthouard, V. and Aiach, N. and Arnaiz, O. and Billaut, A. and Beisson, J. and Blanc, I. and Bouhouche, K. and Ĉmara, F. and Duharcourt, S. and Guigo, R. and Gogendeau, D. and Katinka, M. and Keller, A.-M. and Kissmehl, R. and Klotz, C. and Koll, F. and Le Mouël, A. and Lepère, G. and Malinsky, S. and Nowacki, M. and Nowak, J.K. and Plattner, H. and Poulain, J. and Ruiz, F. and Serrano, V. and Zagulski, M. and Dessen, P. and Bétermier, M. and Weissenbach, J. and Scarpelli, C. and Schächter, V. and Sperling, L. and Meyer, E. and Cohen, J. and Wincker, P.},\n\tyear = {2006},\n\tpages = {171--178},\n}\n\n

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\n \n\n \n \n \n \n \n \n Gene loss and evolutionary rates following whole-genome duplication in teleost fishes.\n \n \n \n \n\n\n \n Brunet, F.; Crollius, H.; Paris, M.; Aury, J.; Gibert, P.; Jaillon, O.; Laudet, V.; and Robinson-Rechavi, M.\n\n\n \n\n\n\n Molecular Biology and Evolution, 23(9): 1808–1816. 2006.\n \n\n\n\n
\n\n\n\n \n \n $\"Gene$ Paper\n \n \n\n \n \n doi\n \n \n\n \n link\n \n \n\n bibtex\n \n\n \n\n \n\n \n \n \n \n \n \n \n\n \n \n \n\n\n\n

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@article{brunet_gene_2006,\n\ttitle = {Gene loss and evolutionary rates following whole-genome duplication in teleost fishes},\n\tvolume = {23},\n\turl = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-33748183184&doi=10.1093%2fmolbev%2fmsl049&partnerID=40&md5=ea15d537371ef669fcc12003bb99122a},\n\tdoi = {10.1093/molbev/msl049},\n\tnumber = {9},\n\tjournal = {Molecular Biology and Evolution},\n\tauthor = {Brunet, F.G. and Crollius, H.R. and Paris, M. and Aury, J.-M. and Gibert, P. and Jaillon, O. and Laudet, V. and Robinson-Rechavi, M.},\n\tyear = {2006},\n\tpages = {1808--1816},\n}\n\n

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\n \n 2005\n \n \n (3)\n \n \n

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\n \n\n \n \n \n \n \n \n The fish, model for research: Tetraodon, fish with model genome [Le poisson: Modèle de recherche. Tetraodon poisson au génome modèle].\n \n \n \n \n\n\n \n Esnault, Y.; Jaillon, O.; Aury, J.; Weissenbach, J.; and Crollius, H.\n\n\n \n\n\n\n Biofutur, (254): 24–28. 2005.\n \n\n\n\n
\n\n\n\n \n \n $\"The$ Paper\n \n \n\n \n\n \n link\n \n \n\n bibtex\n \n\n \n\n \n\n \n \n \n \n \n \n \n\n \n \n \n\n\n\n

\n

@article{esnault_fish_2005,\n\ttitle = {The fish, model for research: {Tetraodon}, fish with model genome [{Le} poisson: {Modèle} de recherche. {Tetraodon} poisson au génome modèle]},\n\turl = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-16344366725&partnerID=40&md5=d77cc3f1cf07edd82a100a26544aaff1},\n\tnumber = {254},\n\tjournal = {Biofutur},\n\tauthor = {Esnault, Y. and Jaillon, O. and Aury, J.-M. and Weissenbach, J. and Crollius, H.R.},\n\tyear = {2005},\n\tpages = {24--28},\n}\n\n

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\n \n\n \n \n \n \n \n \n Comparative analysis of BAC and whole genome shotgun sequences from an Anopheles gambiae region related to Plasmodium encapsulation.\n \n \n \n \n\n\n \n Eiglmeier, K.; Wincker, P.; Cattolico, L.; Anthouard, V.; Holm, I.; Eckenberg, R.; Quesneville, H.; Jaillon, O.; Collins, F.; Weissenbach, J.; Brey, P.; and Roth, C.\n\n\n \n\n\n\n Insect Biochemistry and Molecular Biology, 35(8): 799–814. 2005.\n \n\n\n\n
\n\n\n\n \n \n $\"Comparative$ Paper\n \n \n\n \n \n doi\n \n \n\n \n link\n \n \n\n bibtex\n \n\n \n\n \n\n \n \n \n \n \n \n \n\n \n \n \n\n\n\n

\n

@article{eiglmeier_comparative_2005,\n\ttitle = {Comparative analysis of {BAC} and whole genome shotgun sequences from an {Anopheles} gambiae region related to {Plasmodium} encapsulation},\n\tvolume = {35},\n\turl = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-23844455713&doi=10.1016%2fj.ibmb.2005.02.020&partnerID=40&md5=f402059b197c35f3440008be367ae8a2},\n\tdoi = {10.1016/j.ibmb.2005.02.020},\n\tnumber = {8},\n\tjournal = {Insect Biochemistry and Molecular Biology},\n\tauthor = {Eiglmeier, K. and Wincker, P. and Cattolico, L. and Anthouard, V. and Holm, I. and Eckenberg, R. and Quesneville, H. and Jaillon, O. and Collins, F.H. and Weissenbach, J. and Brey, P.T. and Roth, C.W.},\n\tyear = {2005},\n\tpages = {799--814},\n}\n\n

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\n \n\n \n \n \n \n \n \n Genome evolution and biodiversity in teleost fish.\n \n \n \n \n\n\n \n Volff, J.\n\n\n \n\n\n\n Heredity, 94(3): 280–294. March 2005.\n Number: 3 Publisher: Nature Publishing Group\n\n\n\n
\n\n\n\n \n \n $\"Genome$ Paper\n \n \n\n \n \n doi\n \n \n\n \n link\n \n \n\n bibtex\n \n\n \n \n \n abstract \n \n\n \n\n \n \n \n \n \n \n \n\n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n\n\n\n

\n

@article{volff_genome_2005,\n\ttitle = {Genome evolution and biodiversity in teleost fish},\n\tvolume = {94},\n\tcopyright = {2005 The Genetics Society},\n\tissn = {1365-2540},\n\turl = {https://www.nature.com/articles/6800635},\n\tdoi = {10.1038/sj.hdy.6800635},\n\tabstract = {Teleost fish, which roughly make up half of the extant vertebrate species, exhibit an amazing level of biodiversity affecting their morphology, ecology and behaviour as well as many other aspects of their biology. This huge variability makes fish extremely attractive for the study of many biological questions, particularly of those related to evolution. New insights gained from different teleost species and sequencing projects have recently revealed several peculiar features of fish genomes that might have played a role in fish evolution and speciation. There is now substantial evidence that a round of tetraploidization/rediploidization has taken place during the early evolution of the ray-finned fish lineage, and that hundreds of duplicate pairs generated by this event have been maintained over hundreds of millions of years of evolution. Differential loss or subfunction partitioning of such gene duplicates might have been involved in the generation of fish variability. In contrast to mammalian genomes, teleost genomes also contain multiple families of active transposable elements, which might have played a role in speciation by affecting hybrid sterility and viability. Finally, the amazing diversity of sex determination systems and the plasticity of sex chromosomes observed in teleost might have been involved in both pre- and postmating reproductive isolation. Comparison of data generated by current and future genome projects as well as complementary studies in other species will allow one to approach the molecular and evolutionary mechanisms underlying genome diversity in fish, and will certainly significantly contribute to our understanding of gene evolution and function in humans and other vertebrates.},\n\tlanguage = {en},\n\tnumber = {3},\n\turldate = {2023-06-05},\n\tjournal = {Heredity},\n\tauthor = {Volff, J.-N.},\n\tmonth = mar,\n\tyear = {2005},\n\tnote = {Number: 3\nPublisher: Nature Publishing Group},\n\tkeywords = {Ecology, general, Biomedicine, Human Genetics, Cytogenetics, Evolutionary Biology, Plant Genetics and Genomics},\n\tpages = {280--294},\n\tfile = {Full Text PDF:C\\:\\\\Users\\\\ojaillon\\\\Zotero\\\\storage\\\\RQG65GJK\\\\Volff - 2005 - Genome evolution and biodiversity in teleost fish.pdf:application/pdf},\n}\n\n

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\n \n 2004\n \n \n (1)\n \n \n

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\n \n\n \n \n \n \n \n \n Whole genome sequence comparisons and \"full-lenght\" cDNA sequence: A combined approach to evaluate and improve Arabidopsis genome annotation.\n \n \n \n \n\n\n \n Castelli, V.; Aury, J.; Jaillon, O.; Wincker, P.; Clepet, C.; Menard, M.; Cruaud, C.; Quétier, F.; Scarpelli, C.; Schächter, V.; Temple, G.; Caboche, M.; Weissenbach, J.; and Salanoubat, M.\n\n\n \n\n\n\n Genome Research, 14(3): 406–413. 2004.\n \n\n\n\n
\n\n\n\n \n \n $\"Whole$ Paper\n \n \n\n \n \n doi\n \n \n\n \n link\n \n \n\n bibtex\n \n\n \n\n \n\n \n \n \n \n \n \n \n\n \n \n \n\n\n\n

\n

@article{castelli_whole_2004,\n\ttitle = {Whole genome sequence comparisons and "full-lenght" {cDNA} sequence: {A} combined approach to evaluate and improve {Arabidopsis} genome annotation},\n\tvolume = {14},\n\turl = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-12144288780&doi=10.1101%2fgr.1515604&partnerID=40&md5=f2d744ac4a6fa1e93d7e030da7f3181c},\n\tdoi = {10.1101/gr.1515604},\n\tnumber = {3},\n\tjournal = {Genome Research},\n\tauthor = {Castelli, V. and Aury, J.-M. and Jaillon, O. and Wincker, P. and Clepet, C. and Menard, M. and Cruaud, C. and Quétier, F. and Scarpelli, C. and Schächter, V. and Temple, G. and Caboche, M. and Weissenbach, J. and Salanoubat, M.},\n\tyear = {2004},\n\tpages = {406--413},\n}\n\n

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\n \n 2003\n \n \n (4)\n \n \n

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\n \n\n \n \n \n \n \n \n Comparative genomic analysis reveals independent expansion of a lineage-specific gene family in vertebrates: The class II cytokine receptors and their ligands in mammals and fish.\n \n \n \n \n\n\n \n Lutfalla, G.; Crollius, H.; Stange-Thomann, N.; Jaillon, O.; Mogensen, K.; and Monneron, D.\n\n\n \n\n\n\n BMC Genomics, 4. 2003.\n \n\n\n\n
\n\n\n\n \n \n $\"Comparative$ Paper\n \n \n\n \n \n doi\n \n \n\n \n link\n \n \n\n bibtex\n \n\n \n\n \n\n \n \n \n \n \n \n \n\n \n \n \n\n\n\n

\n

@article{lutfalla_comparative_2003,\n\ttitle = {Comparative genomic analysis reveals independent expansion of a lineage-specific gene family in vertebrates: {The} class {II} cytokine receptors and their ligands in mammals and fish},\n\tvolume = {4},\n\turl = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-9144250427&doi=10.1186%2f1471-2164-4-29&partnerID=40&md5=0c986ebe330c654033a5840f5df68708},\n\tdoi = {10.1186/1471-2164-4-29},\n\tjournal = {BMC Genomics},\n\tauthor = {Lutfalla, G. and Crollius, H.R. and Stange-Thomann, N. and Jaillon, O. and Mogensen, K. and Monneron, D.},\n\tyear = {2003},\n}\n\n

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\n \n\n \n \n \n \n \n \n Assessing the Drosophila melanogaster and Anopheles gambiae genome annotations using genome-wide sequence comparisons.\n \n \n \n \n\n\n \n Jaillon, O.; Dossat, C.; Eckenberg, R.; Eiglmeier, K.; Segurens, B.; Aury, J.; Roth, C.; Scarpelli, C.; Brey, P.; Weissenbach, J.; and Wincker, P.\n\n\n \n\n\n\n Genome Research, 13(7): 1595–1599. 2003.\n \n\n\n\n
\n\n\n\n \n \n $\"Assessing$ Paper\n \n \n\n \n \n doi\n \n \n\n \n link\n \n \n\n bibtex\n \n\n \n\n \n\n \n \n \n \n \n \n \n\n \n \n \n\n\n\n

\n

@article{jaillon_assessing_2003,\n\ttitle = {Assessing the {Drosophila} melanogaster and {Anopheles} gambiae genome annotations using genome-wide sequence comparisons},\n\tvolume = {13},\n\turl = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-0038486910&doi=10.1101%2fgr.922503&partnerID=40&md5=f70f84f0565276ab015f7ccb555c2a2c},\n\tdoi = {10.1101/gr.922503},\n\tnumber = {7},\n\tjournal = {Genome Research},\n\tauthor = {Jaillon, O. and Dossat, C. and Eckenberg, R. and Eiglmeier, K. and Segurens, B. and Aury, J.M. and Roth, C.W. and Scarpelli, C. and Brey, P.T. and Weissenbach, J. and Wincker, P.},\n\tyear = {2003},\n\tpages = {1595--1599},\n}\n\n

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\n \n\n \n \n \n \n \n \n An active non-LTR retrotransposon with tandem structure in the compact genome of pufferfish Tetraodon nigroviridis.\n \n \n \n \n\n\n \n Bouneau, L.; Fischer, C.; Ozouf-Costaz, C.; Froschauer, A.; Jaillon, O.; Coutanceau, J.; Körting, C.; Weissenbach, J.; Bernot, A.; and Volff, J.\n\n\n \n\n\n\n Genome Research, 13(7): 1686–1695. 2003.\n \n\n\n\n
\n\n\n\n \n \n $\"An$ Paper\n \n \n\n \n \n doi\n \n \n\n \n link\n \n \n\n bibtex\n \n\n \n\n \n\n \n \n \n \n \n \n \n\n \n \n \n\n\n\n

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@article{bouneau_active_2003,\n\ttitle = {An active non-{LTR} retrotransposon with tandem structure in the compact genome of pufferfish {Tetraodon} nigroviridis},\n\tvolume = {13},\n\turl = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-0038148190&doi=10.1101%2fgr.726003&partnerID=40&md5=5a03f9e8e6d69d1350dd13e4a5ec4a29},\n\tdoi = {10.1101/gr.726003},\n\tnumber = {7},\n\tjournal = {Genome Research},\n\tauthor = {Bouneau, L. and Fischer, C. and Ozouf-Costaz, C. and Froschauer, A. and Jaillon, O. and Coutanceau, J.-P. and Körting, C. and Weissenbach, J. and Bernot, A. and Volff, J.-N.},\n\tyear = {2003},\n\tpages = {1686--1695},\n}\n\n

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\n \n\n \n \n \n \n \n \n Genome-wide analyses based on comparative genomics.\n \n \n \n \n\n\n \n Jaillon, O.; Aury, J.; Roest Crollius, H.; Salanoubat, M.; Wincker, P.; Dossat, C.; Castelli, V.; Boudet, N.; Samair, S.; Eckenberg, R.; Bonneval, S.; Saurin, W.; Scarpelli, C.; Schächter, V.; and Weissenbach, J.\n\n\n \n\n\n\n Cold Spring Harbor Symposia on Quantitative Biology, 68: 275–282. 2003.\n \n\n\n\n
\n\n\n\n \n \n $\"Genome-wide$ Paper\n \n \n\n \n \n doi\n \n \n\n \n link\n \n \n\n bibtex\n \n\n \n\n \n\n \n \n \n \n \n \n \n\n \n \n \n\n\n\n

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@article{jaillon_genome-wide_2003,\n\ttitle = {Genome-wide analyses based on comparative genomics},\n\tvolume = {68},\n\turl = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-3242700337&doi=10.1101%2fsqb.2003.68.275&partnerID=40&md5=17d6fb5529ac476838ea17fec3cfa291},\n\tdoi = {10.1101/sqb.2003.68.275},\n\tjournal = {Cold Spring Harbor Symposia on Quantitative Biology},\n\tauthor = {Jaillon, O. and Aury, J.-M. and Roest Crollius, H. and Salanoubat, M. and Wincker, P. and Dossat, C. and Castelli, V. and Boudet, N. and Samair, S. and Eckenberg, R. and Bonneval, S. and Saurin, W. and Scarpelli, C. and Schächter, V. and Weissenbach, J.},\n\tyear = {2003},\n\tpages = {275--282},\n}\n\n

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\n \n 2002\n \n \n (6)\n \n \n

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\n \n\n \n \n \n \n \n \n Exploring root symbiotic programs in the model legume Medicago truncatula using EST analysis.\n \n \n \n \n\n\n \n Journet, E.; van Tuinen, D.; Gouzy, J.; Crespeau, H.; Carreau, V.; Farmer, M.; Niebel, A.; Schiex, T.; Jaillon, O.; Chatagnier, O.; Godiard, L.; Micheli, F.; Kahn, D.; Gianinazzi-Pearson, V.; and Gamas, P.\n\n\n \n\n\n\n Nucleic Acids Research, 30(24): 5579–5592. 2002.\n \n\n\n\n
\n\n\n\n \n \n $\"Exploring$ Paper\n \n \n\n \n \n doi\n \n \n\n \n link\n \n \n\n bibtex\n \n\n \n\n \n\n \n \n \n \n \n \n \n\n \n \n \n\n\n\n

\n

@article{journet_exploring_2002,\n\ttitle = {Exploring root symbiotic programs in the model legume {Medicago} truncatula using {EST} analysis},\n\tvolume = {30},\n\turl = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-0037115831&doi=10.1093%2fnar%2fgkf685&partnerID=40&md5=511d207fce42d932f2e47dd4fb4d55b9},\n\tdoi = {10.1093/nar/gkf685},\n\tnumber = {24},\n\tjournal = {Nucleic Acids Research},\n\tauthor = {Journet, E.-P. and van Tuinen, D. and Gouzy, J. and Crespeau, H. and Carreau, V. and Farmer, M.-J. and Niebel, A. and Schiex, T. and Jaillon, O. and Chatagnier, O. and Godiard, L. and Micheli, F. and Kahn, D. and Gianinazzi-Pearson, V. and Gamas, P.},\n\tyear = {2002},\n\tpages = {5579--5592},\n}\n\n

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\n \n\n \n \n \n \n \n \n Remarkable compartmentalization of transposable elements and pseudogenes in the heterochromatin of the Tetraodon nigroviridis genome.\n \n \n \n \n\n\n \n Dasilva, C.; Hadji, H.; Ozouf-Costaz, C.; Nicaud, S.; Jaillon, O.; Weissenbach, J.; and Crollius, H.\n\n\n \n\n\n\n Proceedings of the National Academy of Sciences of the United States of America, 99(21): 13636–13641. 2002.\n \n\n\n\n
\n\n\n\n \n \n $\"Remarkable$ Paper\n \n \n\n \n \n doi\n \n \n\n \n link\n \n \n\n bibtex\n \n\n \n\n \n\n \n \n \n \n \n \n \n\n \n \n \n\n\n\n

\n

@article{dasilva_remarkable_2002,\n\ttitle = {Remarkable compartmentalization of transposable elements and pseudogenes in the heterochromatin of the {Tetraodon} nigroviridis genome},\n\tvolume = {99},\n\turl = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-0037108746&doi=10.1073%2fpnas.202284199&partnerID=40&md5=c97da99f9a72a6e4a44162e11b197699},\n\tdoi = {10.1073/pnas.202284199},\n\tnumber = {21},\n\tjournal = {Proceedings of the National Academy of Sciences of the United States of America},\n\tauthor = {Dasilva, C. and Hadji, H. and Ozouf-Costaz, C. and Nicaud, S. and Jaillon, O. and Weissenbach, J. and Crollius, H.R.},\n\tyear = {2002},\n\tpages = {13636--13641},\n}\n\n

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\n \n\n \n \n \n \n \n \n The genome sequence of the malaria mosquito Anopheles gambiae.\n \n \n \n \n\n\n \n Holt, R.; Mani Subramanian, G.; Halpern, A.; Sutton, G.; Charlab, R.; Nusskern, D.; Wincker, P.; Clark, A.; Ribeiro, J.; Wides, R.; Salzberg, S.; Loftus, B.; Yandell, M.; Majoros, W.; Rusch, D.; Lai, Z.; Kraft, C.; Abril, J.; Anthouard, V.; Arensburger, P.; Atkinson, P.; Baden, H.; de Berardinis, V.; Baldwin, D.; Benes, V.; Biedler, J.; Blass, C.; Bolanos, R.; Boscus, D.; Barnstead, M.; Cai, S.; Center, A.; Chatuverdi, K.; Christophides, G.; Chrystal, M.; Clamp, M.; Cravchik, A.; Curwen, V.; Dana, A.; Delcher, A.; Dew, I.; Evans, C.; Flanigan, M.; Grundschober-Freimoser, A.; Friedli, L.; Gu, Z.; Guan, P.; Guigo, R.; Hillenmeyer, M.; Hladun, S.; Hogan, J.; Hong, Y.; Hoover, J.; Jaillon, O.; Ke, Z.; Kodira, C.; Kokoza, E.; Koutsos, A.; Letunic, I.; Levitsky, A.; Liang, Y.; Lin, J.; Lobo, N.; Lopez, J.; Malek, J.; McIntosh, T.; Meister, S.; Miller, J.; Mobarry, C.; Mongin, E.; Murphy, S.; O'Brochta, D.; Pfannkoch, C.; Qi, R.; Regier, M.; Remington, K.; Shao, H.; Sharakhova, M.; Sitter, C.; Shetty, J.; Smith, T.; Strong, R.; Sun, J.; Thomasova, D.; Ton, L.; Topalis, P.; Tu, Z.; Unger, M.; Walenz, B.; Wang, A.; Wang, J.; Wang, M.; Wang, X.; Woodford, K.; Wortman, J.; Wu, M.; Yao, A.; Zdobnov, E.; Zhang, H.; Zhao, Q.; Zhao, S.; Zhu, S.; Zhimulev, I.; Coluzzi, M.; della Torre, A.; Roth, C.; Louis, C.; Kalush, F.; Mural, R.; Myers, E.; Adams, M.; Smith, H.; Broder, S.; Gardner, M.; Fraser, C.; Birney, E.; Bork, P.; Brey, P.; Craig Venter, J.; Weissenbach, J.; Kafatos, F.; Collins, F.; and Hoffman, S.\n\n\n \n\n\n\n Science, 298(5591): 129–149. 2002.\n \n\n\n\n
\n\n\n\n \n \n $\"The$ Paper\n \n \n\n \n \n doi\n \n \n\n \n link\n \n \n\n bibtex\n \n\n \n\n \n\n \n \n \n \n \n \n \n\n \n \n \n\n\n\n

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@article{holt_genome_2002,\n\ttitle = {The genome sequence of the malaria mosquito {Anopheles} gambiae},\n\tvolume = {298},\n\turl = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-0037020114&doi=10.1126%2fscience.1076181&partnerID=40&md5=5a33ee029adfecd2e6d7e16c2a6ccfbf},\n\tdoi = {10.1126/science.1076181},\n\tnumber = {5591},\n\tjournal = {Science},\n\tauthor = {Holt, R.A. and Mani Subramanian, G. and Halpern, A. and Sutton, G.G. and Charlab, R. and Nusskern, D.R. and Wincker, P. and Clark, A.G. and Ribeiro, J.M.C. and Wides, R. and Salzberg, S.L. and Loftus, B. and Yandell, M. and Majoros, W.H. and Rusch, D.B. and Lai, Z. and Kraft, C.L. and Abril, J.F. and Anthouard, V. and Arensburger, P. and Atkinson, P.W. and Baden, H. and de Berardinis, V. and Baldwin, D. and Benes, V. and Biedler, J. and Blass, C. and Bolanos, R. and Boscus, D. and Barnstead, M. and Cai, S. and Center, A. and Chatuverdi, K. and Christophides, G.K. and Chrystal, M.A. and Clamp, M. and Cravchik, A. and Curwen, V. and Dana, A. and Delcher, A. and Dew, I. and Evans, C.A. and Flanigan, M. and Grundschober-Freimoser, A. and Friedli, L. and Gu, Z. and Guan, P. and Guigo, R. and Hillenmeyer, M.E. and Hladun, S.L. and Hogan, J.R. and Hong, Y.S. and Hoover, J. and Jaillon, O. and Ke, Z. and Kodira, C. and Kokoza, E. and Koutsos, A. and Letunic, I. and Levitsky, A. and Liang, Y. and Lin, J.-J. and Lobo, N.F. and Lopez, J.R. and Malek, J.A. and McIntosh, T.C. and Meister, S. and Miller, J. and Mobarry, C. and Mongin, E. and Murphy, S.D. and O'Brochta, D.A. and Pfannkoch, C. and Qi, R. and Regier, M.A. and Remington, K. and Shao, H. and Sharakhova, M.V. and Sitter, C.D. and Shetty, J. and Smith, T.J. and Strong, R. and Sun, J. and Thomasova, D. and Ton, L.Q. and Topalis, P. and Tu, Z. and Unger, M.F. and Walenz, B. and Wang, A. and Wang, J. and Wang, M. and Wang, X. and Woodford, K.J. and Wortman, J.R. and Wu, M. and Yao, A. and Zdobnov, E.M. and Zhang, H. and Zhao, Q. and Zhao, S. and Zhu, S.C. and Zhimulev, I. and Coluzzi, M. and della Torre, A. and Roth, C.W. and Louis, C. and Kalush, F. and Mural, R.J. and Myers, E.W. and Adams, M.D. and Smith, H.O. and Broder, S. and Gardner, M.J. and Fraser, C.M. and Birney, E. and Bork, P. and Brey, P.T. and Craig Venter, J. and Weissenbach, J. and Kafatos, F.C. and Collins, F.H. and Hoffman, S.L.},\n\tyear = {2002},\n\tpages = {129--149},\n}\n\n

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\n \n\n \n \n \n \n \n \n Four-hundred million years of conserved synteny of human Xp and Xq genes on three Tetraodon chromosomes.\n \n \n \n \n\n\n \n Grützner, F.; Crollius, H.; Lütjens, G.; Jaillon, O.; Weissenbach, J.; Ropers, H.; and Haaf, T.\n\n\n \n\n\n\n Genome Research, 12(9): 1316–1322. 2002.\n \n\n\n\n
\n\n\n\n \n \n $\"Four-hundred$ Paper\n \n \n\n \n \n doi\n \n \n\n \n link\n \n \n\n bibtex\n \n\n \n\n \n\n \n \n \n \n \n \n \n\n \n \n \n\n\n\n

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@article{grutzner_four-hundred_2002,\n\ttitle = {Four-hundred million years of conserved synteny of human {Xp} and {Xq} genes on three {Tetraodon} chromosomes},\n\tvolume = {12},\n\turl = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-0036739053&doi=10.1101%2fgr.222402&partnerID=40&md5=6e4314a1931686a2e39ba83964033f7e},\n\tdoi = {10.1101/gr.222402},\n\tnumber = {9},\n\tjournal = {Genome Research},\n\tauthor = {Grützner, F. and Crollius, H.R. and Lütjens, G. and Jaillon, O. and Weissenbach, J. and Ropers, H.-H. and Haaf, T.},\n\tyear = {2002},\n\tpages = {1316--1322},\n}\n\n

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\n \n\n \n \n \n \n \n \n Variability of the nonstructural 5A protein of hepatitis C virus type 3a isolates and relation to interferon sensitivity.\n \n \n \n \n\n\n \n Castelain, S.; Khorsi, H.; Roussel, J.; Francçois, C.; Jaillon, O.; Capron, D.; Penin, F.; Wychowski, C.; Meurs, E.; Duverlie, G.; and Group, f. t. A. N. d. R. s. l. S. A.\n\n\n \n\n\n\n Journal of Infectious Diseases, 185(5): 573–583. 2002.\n \n\n\n\n
\n\n\n\n \n \n $\"Variability$ Paper\n \n \n\n \n \n doi\n \n \n\n \n link\n \n \n\n bibtex\n \n\n \n\n \n\n \n \n \n \n \n \n \n\n \n \n \n\n\n\n

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@article{castelain_variability_2002,\n\ttitle = {Variability of the nonstructural {5A} protein of hepatitis {C} virus type 3a isolates and relation to interferon sensitivity},\n\tvolume = {185},\n\turl = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-0036498746&doi=10.1086%2f339051&partnerID=40&md5=873a96a82326cf62b9f334d16bdd2661},\n\tdoi = {10.1086/339051},\n\tnumber = {5},\n\tjournal = {Journal of Infectious Diseases},\n\tauthor = {Castelain, S. and Khorsi, H. and Roussel, J. and Francçois, C. and Jaillon, O. and Capron, D. and Penin, F. and Wychowski, C. and Meurs, E. and Duverlie, G. and Group, for the Agence Nationale de Recherche sur le SIDA AC11},\n\tyear = {2002},\n\tpages = {573--583},\n}\n\n

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\n \n\n \n \n \n \n \n \n Genome-wide comparisons between human and tetraodon.\n \n \n \n \n\n\n \n Roest Crollius, H.; Jaillon, O.; Bernot, A.; Pelletier, E.; Dasilva, C.; Bouneau, L.; Burge, C.; Yeh, R.; Quetier, F.; Saurin, W.; and Weissenbach, J.\n\n\n \n\n\n\n Ernst Schering Research Foundation workshop, (36): 11–29. 2002.\n \n\n\n\n
\n\n\n\n \n \n $\"Genome-wide$ Paper\n \n \n\n \n\n \n link\n \n \n\n bibtex\n \n\n \n\n \n\n \n \n \n \n \n \n \n\n \n \n \n\n\n\n

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@article{roest_crollius_genome-wide_2002,\n\ttitle = {Genome-wide comparisons between human and tetraodon.},\n\turl = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-0036372216&partnerID=40&md5=a6e5fc9930e0ade73634bfaeb8bf8620},\n\tnumber = {36},\n\tjournal = {Ernst Schering Research Foundation workshop},\n\tauthor = {Roest Crollius, H. and Jaillon, O. and Bernot, A. and Pelletier, E. and Dasilva, C. and Bouneau, L. and Burge, C. and Yeh, R.F. and Quetier, F. and Saurin, W. and Weissenbach, J.},\n\tyear = {2002},\n\tpages = {11--29},\n}\n\n

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\n \n 2001\n \n \n (3)\n \n \n

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\n \n\n \n \n \n \n \n \n Human-ovine comparative sequencing of a 250-kb imprinted domain encompassing the callipyge (clpg) locus and identification of six imprinted transcripts: DLK1, DAT, GTL2, PEG11, antiPEG11, and MEG8.\n \n \n \n \n\n\n \n Charlier, C.; Segers, K.; Wagenaar, D.; Karim, L.; Berghmans, S.; Jaillon, O.; Shay, T.; Weissenbach, J.; Cockett, N.; Gyapay, G.; and Georges, M.\n\n\n \n\n\n\n Genome Research, 11(5): 850–862. 2001.\n \n\n\n\n
\n\n\n\n \n \n $\"Human-ovine$ Paper\n \n \n\n \n \n doi\n \n \n\n \n link\n \n \n\n bibtex\n \n\n \n\n \n\n \n \n \n \n \n \n \n\n \n \n \n\n\n\n

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@article{charlier_human-ovine_2001,\n\ttitle = {Human-ovine comparative sequencing of a 250-kb imprinted domain encompassing the callipyge (clpg) locus and identification of six imprinted transcripts: {DLK1}, {DAT}, {GTL2}, {PEG11}, {antiPEG11}, and {MEG8}},\n\tvolume = {11},\n\turl = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-17744365941&doi=10.1101%2fgr.172701&partnerID=40&md5=0c5b747208d260c6b6bd0922e3b57be4},\n\tdoi = {10.1101/gr.172701},\n\tnumber = {5},\n\tjournal = {Genome Research},\n\tauthor = {Charlier, C. and Segers, K. and Wagenaar, D. and Karim, L. and Berghmans, S. and Jaillon, O. and Shay, T. and Weissenbach, J. and Cockett, N. and Gyapay, G. and Georges, M.},\n\tyear = {2001},\n\tpages = {850--862},\n}\n\n

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\n \n\n \n \n \n \n \n \n The complete genome sequence of the lactic acid bacterium lactococcus lactis ssp. lactis IL1403.\n \n \n \n \n\n\n \n Bolotin, A.; Wincker, P.; Mauger, S.; Jaillon, O.; Malarme, K.; Weissenbach, J.; Ehrlich, S.; and Sorokin, A.\n\n\n \n\n\n\n Genome Research, 11(5): 731–753. 2001.\n \n\n\n\n
\n\n\n\n \n \n $\"The$ Paper\n \n \n\n \n \n doi\n \n \n\n \n link\n \n \n\n bibtex\n \n\n \n\n \n\n \n \n \n \n \n \n \n\n \n \n \n\n\n\n

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@article{bolotin_complete_2001,\n\ttitle = {The complete genome sequence of the lactic acid bacterium lactococcus lactis ssp. lactis {IL1403}},\n\tvolume = {11},\n\turl = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-0035021812&doi=10.1101%2fgr.GR-1697R&partnerID=40&md5=5be526471605602b8c963f57765d6153},\n\tdoi = {10.1101/gr.GR-1697R},\n\tnumber = {5},\n\tjournal = {Genome Research},\n\tauthor = {Bolotin, A. and Wincker, P. and Mauger, S. and Jaillon, O. and Malarme, K. and Weissenbach, J. and Ehrlich, S.D. and Sorokin, A.},\n\tyear = {2001},\n\tpages = {731--753},\n}\n\n

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\n \n\n \n \n \n \n \n \n The DNA sequence and comparative analysis of human chromosome 20.\n \n \n \n \n\n\n \n Deloukas, P.; Matthews, L. H.; Ashurst, J.; Burton, J.; Gilbert, J. G. R.; Jones, M.; Stavrides, G.; Almeida, J. P.; Babbage, A. K.; Bagguley, C. L.; Bailey, J.; Barlow, K. F.; Bates, K. N.; Beard, L. M.; Beare, D. M.; Beasley, O. P.; Bird, C. P.; Blakey, S. E.; Bridgeman, A. M.; Brown, A. J.; Buck, D.; Burrill, W.; Butler, A. P.; Carder, C.; Carter, N. P.; Chapman, J. C.; Clamp, M.; Clark, G.; Clark, L. N.; Clark, S. Y.; Clee, C. M.; Clegg, S.; Cobley, V. E.; Collier, R. E.; Connor, R.; Corby, N. R.; Coulson, A.; Coville, G. J.; Deadman, R.; Dhami, P.; Dunn, M.; Ellington, A. G.; Frankland, J. A.; Fraser, A.; French, L.; Garner, P.; Grafham, D. V.; Griffiths, C.; Griffiths, M. N. D.; Gwilliam, R.; Hall, R. E.; Hammond, S.; Harley, J. L.; Heath, P. D.; Ho, S.; Holden, J. L.; Howden, P. J.; Huckle, E.; Hunt, A. R.; Hunt, S. E.; Jekosch, K.; Johnson, C. M.; Johnson, D.; Kay, M. P.; Kimberley, A. M.; King, A.; Knights, A.; Laird, G. K.; Lawlor, S.; Lehvaslaiho, M. H.; Leversha, M.; Lloyd, C.; Lloyd, D. M.; Lovell, J. D.; Marsh, V. L.; Martin, S. L.; McConnachie, L. J.; McLay, K.; McMurray, A. A.; Milne, S.; Mistry, D.; Moore, M. J. F.; Mullikin, J. C.; Nickerson, T.; Oliver, K.; Parker, A.; Patel, R.; Pearce, T. A. V.; Peck, A. I.; Phillimore, B. J. C. T.; Prathalingam, S. R.; Plumb, R. W.; Ramsay, H.; Rice, C. M.; Ross, M. T.; Scott, C. E.; Sehra, H. K.; Shownkeen, R.; Sims, S.; Skuce, C. D.; Smith, M. L.; Soderlund, C.; Steward, C. A.; Sulston, J. E.; Swann, M.; Sycamore, N.; Taylor, R.; Tee, L.; Thomas, D. W.; Thorpe, A.; Tracey, A.; Tromans, A. C.; Vaudin, M.; Wall, M.; Wallis, J. M.; Whitehead, S. L.; Whittaker, P.; Willey, D. L.; Williams, L.; Williams, S. A.; Wilming, L.; Wray, P. W.; Hubbard, T.; Durbin, R. M.; Bentley, D. R.; Beck, S.; Rogers, J.; and The Wellcome Trust Sanger Institute\n\n\n \n\n\n\n Nature, 414(6866): 865–871. December 2001.\n Number: 6866 Publisher: Nature Publishing Group\n\n\n\n
\n\n\n\n \n \n $\"The$ Paper\n \n \n\n \n \n doi\n \n \n\n \n link\n \n \n\n bibtex\n \n\n \n \n \n abstract \n \n\n \n\n \n \n \n \n \n \n \n\n \n \n \n \n \n \n \n \n \n\n\n\n

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@article{deloukas_dna_2001,\n\ttitle = {The {DNA} sequence and comparative analysis of human chromosome 20},\n\tvolume = {414},\n\tcopyright = {2001 Macmillan Magazines Ltd.},\n\tissn = {1476-4687},\n\turl = {https://www.nature.com/articles/414865a},\n\tdoi = {10.1038/414865a},\n\tabstract = {The finished sequence of human chromosome 20 comprises 59,187,298 base pairs (bp) and represents 99.4\\% of the euchromatic DNA. A single contig of 26 megabases (Mb) spans the entire short arm, and five contigs separated by gaps totalling 320 kb span the long arm of this metacentric chromosome. An additional 234,339 bp of sequence has been determined within the pericentromeric region of the long arm. We annotated 727 genes and 168 pseudogenes in the sequence. About 64\\% of these genes have a 5′ and a 3′ untranslated region and a complete open reading frame. Comparative analysis of the sequence of chromosome 20 to whole-genome shotgun-sequence data of two other vertebrates, the mouse Mus musculus and the puffer fish Tetraodon nigroviridis, provides an independent measure of the efficiency of gene annotation, and indicates that this analysis may account for more than 95\\% of all coding exons and almost all genes.},\n\tlanguage = {en},\n\tnumber = {6866},\n\turldate = {2023-06-05},\n\tjournal = {Nature},\n\tauthor = {Deloukas, P. and Matthews, L. H. and Ashurst, J. and Burton, J. and Gilbert, J. G. R. and Jones, M. and Stavrides, G. and Almeida, J. P. and Babbage, A. K. and Bagguley, C. L. and Bailey, J. and Barlow, K. F. and Bates, K. N. and Beard, L. M. and Beare, D. M. and Beasley, O. P. and Bird, C. P. and Blakey, S. E. and Bridgeman, A. M. and Brown, A. J. and Buck, D. and Burrill, W. and Butler, A. P. and Carder, C. and Carter, N. P. and Chapman, J. C. and Clamp, M. and Clark, G. and Clark, L. N. and Clark, S. Y. and Clee, C. M. and Clegg, S. and Cobley, V. E. and Collier, R. E. and Connor, R. and Corby, N. R. and Coulson, A. and Coville, G. J. and Deadman, R. and Dhami, P. and Dunn, M. and Ellington, A. G. and Frankland, J. A. and Fraser, A. and French, L. and Garner, P. and Grafham, D. V. and Griffiths, C. and Griffiths, M. N. D. and Gwilliam, R. and Hall, R. E. and Hammond, S. and Harley, J. L. and Heath, P. D. and Ho, S. and Holden, J. L. and Howden, P. J. and Huckle, E. and Hunt, A. R. and Hunt, S. E. and Jekosch, K. and Johnson, C. M. and Johnson, D. and Kay, M. P. and Kimberley, A. M. and King, A. and Knights, A. and Laird, G. K. and Lawlor, S. and Lehvaslaiho, M. H. and Leversha, M. and Lloyd, C. and Lloyd, D. M. and Lovell, J. D. and Marsh, V. L. and Martin, S. L. and McConnachie, L. J. and McLay, K. and McMurray, A. A. and Milne, S. and Mistry, D. and Moore, M. J. F. and Mullikin, J. C. and Nickerson, T. and Oliver, K. and Parker, A. and Patel, R. and Pearce, T. A. V. and Peck, A. I. and Phillimore, B. J. C. T. and Prathalingam, S. R. and Plumb, R. W. and Ramsay, H. and Rice, C. M. and Ross, M. T. and Scott, C. E. and Sehra, H. K. and Shownkeen, R. and Sims, S. and Skuce, C. D. and Smith, M. L. and Soderlund, C. and Steward, C. A. and Sulston, J. E. and Swann, M. and Sycamore, N. and Taylor, R. and Tee, L. and Thomas, D. W. and Thorpe, A. and Tracey, A. and Tromans, A. C. and Vaudin, M. and Wall, M. and Wallis, J. M. and Whitehead, S. L. and Whittaker, P. and Willey, D. L. and Williams, L. and Williams, S. A. and Wilming, L. and Wray, P. W. and Hubbard, T. and Durbin, R. M. and Bentley, D. R. and Beck, S. and Rogers, J. and {The Wellcome Trust Sanger Institute}},\n\tmonth = dec,\n\tyear = {2001},\n\tnote = {Number: 6866\nPublisher: Nature Publishing Group},\n\tkeywords = {Humanities and Social Sciences, multidisciplinary, Science},\n\tpages = {865--871},\n\tfile = {Full Text PDF:C\\:\\\\Users\\\\ojaillon\\\\Zotero\\\\storage\\\\FXY33H6R\\\\Deloukas et al. - 2001 - The DNA sequence and comparative analysis of human.pdf:application/pdf},\n}\n\n

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\n \n 2000\n \n \n (5)\n \n \n

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\n \n\n \n \n \n \n \n \n Characterization and repeat analysis of the compact genome of the freshwater pufferfish Tetraodon nigroviridis.\n \n \n \n \n\n\n \n Crollius, H.; Jaillon, O.; Dasilva, C.; Ozouf-Costaz, C.; Fizames, C.; Fischer, C.; Bouneau, L.; Billault, A.; Quetier, F.; Saurin, W.; Bernot, A.; and Weissenbach, J.\n\n\n \n\n\n\n Genome Research, 10(7): 939–949. 2000.\n \n\n\n\n
\n\n\n\n \n \n $\"Characterization$ Paper\n \n \n\n \n \n doi\n \n \n\n \n link\n \n \n\n bibtex\n \n\n \n\n \n\n \n \n \n \n \n \n \n\n \n \n \n\n\n\n

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@article{crollius_characterization_2000,\n\ttitle = {Characterization and repeat analysis of the compact genome of the freshwater pufferfish {Tetraodon} nigroviridis},\n\tvolume = {10},\n\turl = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-0033860203&doi=10.1101%2fgr.10.7.939&partnerID=40&md5=e1e25dede8be4bb052b2973e4bb51e8d},\n\tdoi = {10.1101/gr.10.7.939},\n\tnumber = {7},\n\tjournal = {Genome Research},\n\tauthor = {Crollius, H.R. and Jaillon, O. and Dasilva, C. and Ozouf-Costaz, C. and Fizames, C. and Fischer, C. and Bouneau, L. and Billault, A. and Quetier, F. and Saurin, W. and Bernot, A. and Weissenbach, J.},\n\tyear = {2000},\n\tpages = {939--949},\n}\n\n

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\n \n\n \n \n \n \n \n \n Estimate of human gene number provided by genome-wide analysis using Tetraodon nigroviridis DNA sequence.\n \n \n \n \n\n\n \n Crollius, H.; Jaillon, O.; Bernot, A.; Dasilva, C.; Bouneau, L.; Fischer, C.; Fizames, C.; Wincker, P.; Brottier, P.; Quétier, F.; Saurin, W.; and Weissenbach, J.\n\n\n \n\n\n\n Nature Genetics, 25(2): 235–240. 2000.\n \n\n\n\n
\n\n\n\n \n \n $\"Estimate$ Paper\n \n \n\n \n \n doi\n \n \n\n \n link\n \n \n\n bibtex\n \n\n \n\n \n\n \n \n \n \n \n \n \n\n \n \n \n\n\n\n

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@article{crollius_estimate_2000,\n\ttitle = {Estimate of human gene number provided by genome-wide analysis using {Tetraodon} nigroviridis {DNA} sequence},\n\tvolume = {25},\n\turl = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-0000508290&doi=10.1038%2f76118&partnerID=40&md5=952d7066648aa2a3b7b04cb59d3ef91c},\n\tdoi = {10.1038/76118},\n\tnumber = {2},\n\tjournal = {Nature Genetics},\n\tauthor = {Crollius, H.R. and Jaillon, O. and Bernot, A. and Dasilva, C. and Bouneau, L. and Fischer, C. and Fizames, C. and Wincker, P. and Brottier, P. and Quétier, F. and Saurin, W. and Weissenbach, J.},\n\tyear = {2000},\n\tpages = {235--240},\n}\n\n

\n

\n\n\n\n

\n\n\n

\n \n\n \n \n \n \n \n \n Karyotype and chromosome location of characteristic tandem repeats in the pufferfish Tetraodon nigroviridis.\n \n \n \n \n\n\n \n Fischer, C.; Ozouf-Costaz, C.; Crollius, H.; Dasilva, C.; Jaillon, O.; Bouneau, L.; Bonillo, C.; Weissenbach, J.; and Bernot, A.\n\n\n \n\n\n\n Cytogenetics and Cell Genetics, 88(1-2): 50–55. 2000.\n \n\n\n\n
\n\n\n\n \n \n $\"Karyotype$ Paper\n \n \n\n \n\n \n link\n \n \n\n bibtex\n \n\n \n\n \n\n \n \n \n \n \n \n \n\n \n \n \n\n\n\n

\n

@article{fischer_karyotype_2000,\n\ttitle = {Karyotype and chromosome location of characteristic tandem repeats in the pufferfish {Tetraodon} nigroviridis},\n\tvolume = {88},\n\turl = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-0034066280&partnerID=40&md5=53b574c398713554f487eb9541246f8d},\n\tnumber = {1-2},\n\tjournal = {Cytogenetics and Cell Genetics},\n\tauthor = {Fischer, C. and Ozouf-Costaz, C. and Crollius, H.R. and Dasilva, C. and Jaillon, O. and Bouneau, L. and Bonillo, C. and Weissenbach, J. and Bernot, A.},\n\tyear = {2000},\n\tpages = {50--55},\n}\n\n

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\n \n\n \n \n \n \n \n \n The gene encoding the mouse homologue of the human osteoclast-specific 116-kDa V-ATPase subunit bears a deletion in osteosclerotic (oc/oc) mutants.\n \n \n \n \n\n\n \n Scimeca, J.; Franchi, A.; Trojani, C.; Parrinello, H.; Grosgeorge, J.; Robert, C.; Jaillon, O.; Poirier, C.; Gaudray, P.; and Carle, G.\n\n\n \n\n\n\n Bone, 26(3): 207–213. 2000.\n \n\n\n\n
\n\n\n\n \n \n $\"The$ Paper\n \n \n\n \n \n doi\n \n \n\n \n link\n \n \n\n bibtex\n \n\n \n\n \n\n \n \n \n \n \n \n \n\n \n \n \n\n\n\n

\n

@article{scimeca_gene_2000,\n\ttitle = {The gene encoding the mouse homologue of the human osteoclast-specific 116-{kDa} {V}-{ATPase} subunit bears a deletion in osteosclerotic (oc/oc) mutants},\n\tvolume = {26},\n\turl = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-18344407785&doi=10.1016%2fS8756-3282%2899%2900278-1&partnerID=40&md5=29fcc9dc91a7f10c2cb6328bd21dda6c},\n\tdoi = {10.1016/S8756-3282(99)00278-1},\n\tnumber = {3},\n\tjournal = {Bone},\n\tauthor = {Scimeca, J.-C. and Franchi, A. and Trojani, C. and Parrinello, H. and Grosgeorge, J. and Robert, C. and Jaillon, O. and Poirier, C. and Gaudray, P. and Carle, G.F.},\n\tyear = {2000},\n\tpages = {207--213},\n}\n\n

\n

\n\n\n\n

\n\n\n

\n \n\n \n \n \n \n \n \n How many genes in human gerome? [Le nombre de genes dans le genome humain: Les paris sont ouverts].\n \n \n \n \n\n\n \n Crollius, H.; and Jaillon, O.\n\n\n \n\n\n\n Medecine/Sciences, 16(8-9): 988–990. 2000.\n \n\n\n\n
\n\n\n\n \n \n $\"How$ Paper\n \n \n\n \n \n doi\n \n \n\n \n link\n \n \n\n bibtex\n \n\n \n\n \n\n \n \n \n \n \n \n \n\n \n \n \n\n\n\n

\n

@article{crollius_how_2000,\n\ttitle = {How many genes in human gerome? [{Le} nombre de genes dans le genome humain: {Les} paris sont ouverts]},\n\tvolume = {16},\n\turl = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-0033863643&doi=10.4267%2f10608%2f1772&partnerID=40&md5=953cf4584b5b0786652080294c88c02a},\n\tdoi = {10.4267/10608/1772},\n\tnumber = {8-9},\n\tjournal = {Medecine/Sciences},\n\tauthor = {Crollius, H.R. and Jaillon, O.},\n\tyear = {2000},\n\tpages = {988--990},\n}\n\n

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\n\n\n\n\n\n

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\n \n 1998\n \n \n (2)\n \n \n

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\n \n \n

\n \n\n \n \n \n \n \n \n Amplification and detection of the terminal 3' non-coding region of hepatitis C virus isolates.\n \n \n \n \n\n\n \n Khorsi, H.; Salabi, T.; Castelain, S.; Jaillon, O.; Zawadzki, P.; Capron, J.; Eb, F.; Wychowski, C.; and Duverlie, G.\n\n\n \n\n\n\n Research in Virology, 149(2): 115–121. 1998.\n \n\n\n\n
\n\n\n\n \n \n $\"Amplification$ Paper\n \n \n\n \n \n doi\n \n \n\n \n link\n \n \n\n bibtex\n \n\n \n\n \n\n \n \n \n \n \n \n \n\n \n \n \n\n\n\n

\n

@article{khorsi_amplification_1998,\n\ttitle = {Amplification and detection of the terminal 3' non-coding region of hepatitis {C} virus isolates},\n\tvolume = {149},\n\turl = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-0032033385&doi=10.1016%2fS0923-2516%2898%2980087-3&partnerID=40&md5=6037fc47c0bd4e9b44abb56fe6c9a355},\n\tdoi = {10.1016/S0923-2516(98)80087-3},\n\tnumber = {2},\n\tjournal = {Research in Virology},\n\tauthor = {Khorsi, H. and Salabi, T. and Castelain, S. and Jaillon, O. and Zawadzki, P. and Capron, J.P. and Eb, F. and Wychowski, C. and Duverlie, G.},\n\tyear = {1998},\n\tpages = {115--121},\n}\n\n

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\n\n\n\n

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\n \n\n \n \n \n \n \n \n Sequence analysis of the NS5A protein of European hepatitis C virus 1b isolates and relation to interferon sensitivity.\n \n \n \n \n\n\n \n Duverlie, G.; Khorsi, H.; Castelain, S.; Jaillon, O.; Izopet, J.; Lunel, F.; Eb, F.; Penin, F.; and Wychowski, C.\n\n\n \n\n\n\n Journal of General Virology, 79(6): 1373–1381. 1998.\n \n\n\n\n
\n\n\n\n \n \n $\"Sequence$ Paper\n \n \n\n \n \n doi\n \n \n\n \n link\n \n \n\n bibtex\n \n\n \n\n \n\n \n \n \n \n \n \n \n\n \n \n \n\n\n\n

\n

@article{duverlie_sequence_1998,\n\ttitle = {Sequence analysis of the {NS5A} protein of {European} hepatitis {C} virus 1b isolates and relation to interferon sensitivity},\n\tvolume = {79},\n\turl = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-0031836249&doi=10.1099%2f0022-1317-79-6-1373&partnerID=40&md5=c1a54a89b25a9cc82544c3c3be0400fa},\n\tdoi = {10.1099/0022-1317-79-6-1373},\n\tnumber = {6},\n\tjournal = {Journal of General Virology},\n\tauthor = {Duverlie, G. and Khorsi, H. and Castelain, S. and Jaillon, O. and Izopet, J. and Lunel, F. and Eb, F. and Penin, F. and Wychowski, C.},\n\tyear = {1998},\n\tpages = {1373--1381},\n}\n\n

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\n \n 1997\n \n \n (2)\n \n \n

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\n \n\n \n \n \n \n \n \n Effect of obesity and regional adiposity on the QTc interval in women.\n \n \n \n \n\n\n \n Park, J.; and Swan, P. D.\n\n\n \n\n\n\n International Journal of Obesity, 21(12): 1104–1110. December 1997.\n Number: 12 Publisher: Nature Publishing Group\n\n\n\n
\n\n\n\n \n \n $\"Effect$ Paper\n \n \n\n \n \n doi\n \n \n\n \n link\n \n \n\n bibtex\n \n\n \n \n \n abstract \n \n\n \n\n \n \n \n \n \n \n \n\n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n\n\n\n

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@article{park_effect_1997,\n\ttitle = {Effect of obesity and regional adiposity on the {QTc} interval in women},\n\tvolume = {21},\n\tcopyright = {1997 Macmillan Publishers Limited},\n\tissn = {1476-5497},\n\turl = {https://www.nature.com/articles/0800521},\n\tdoi = {10.1038/sj.ijo.0800521},\n\tabstract = {OBJECTIVES: To determine whether differences in body fat composition and body fat distribution patterns are associated with a prolongation of the corrected QT interval for heart rate (QTc) on the electrocardiogram (EKG) during rest and exercise.},\n\tlanguage = {en},\n\tnumber = {12},\n\turldate = {2023-06-05},\n\tjournal = {International Journal of Obesity},\n\tauthor = {Park, J.-J. and Swan, P. D.},\n\tmonth = dec,\n\tyear = {1997},\n\tnote = {Number: 12\nPublisher: Nature Publishing Group},\n\tkeywords = {general, Metabolic Diseases, Epidemiology, Health Promotion and Disease Prevention, Internal Medicine, Medicine/Public Health, Public Health},\n\tpages = {1104--1110},\n}\n\n

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\n \n\n \n \n \n \n \n \n Electrocardiographic QTc interval: short-term weight loss effects.\n \n \n \n \n\n\n \n Pietrobelli, A.; Rothacker, D.; Gallagher, D.; and Heymsfield, S. B.\n\n\n \n\n\n\n International Journal of Obesity, 21(2): 110–114. February 1997.\n Number: 2 Publisher: Nature Publishing Group\n\n\n\n
\n\n\n\n \n \n $\"Electrocardiographic$ Paper\n \n \n\n \n \n doi\n \n \n\n \n link\n \n \n\n bibtex\n \n\n \n \n \n abstract \n \n\n \n\n \n \n \n \n \n \n \n\n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n\n\n\n

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@article{pietrobelli_electrocardiographic_1997,\n\ttitle = {Electrocardiographic {QTc} interval: short-term weight loss effects},\n\tvolume = {21},\n\tcopyright = {1997 Macmillan Publishers Limited},\n\tissn = {1476-5497},\n\tshorttitle = {Electrocardiographic {QTc} interval},\n\turl = {https://www.nature.com/articles/0800374},\n\tdoi = {10.1038/sj.ijo.0800374},\n\tabstract = {OBJECTIVE: Prolongation of the QTc interval is a risk factor for ventricular arrhythmias and sudden death. There is a correlation between body mass index (BMI) and QTc, with longer intervals observed in obese subjects. Dieting and weight loss on selected diets are also associated with prolongation of the QTc interval, although the mechanisms and risk factors of this syndrome are not clearly established. The aim of the current investigation was to determine if short-term weight loss over seven days while living on a metabolic ward influences cardiac repolarization as indicated by QT interval duration. DESIGN AND SUBJECTS: The elctrocardiogram QT, RR, and QTc (QT/RR0.5) intervals were assessed in 30 healthy obese (BMI{\\textgreater}27 kg/m2) men and women ingesting a balanced 1120 kcal/d formula diet (23\\% kcal as fat and 52 g protein/d). RESULTS: Weight loss (3.9±1.7 kg) over seven days had no measurable effect on the RR interval and there was a significant (P=0.02) shortening of the QT interval (mean±s.d., 0.395±0.028–0.386±0.027 s) and borderline significant (P=0.11) shortening of the QTc (0.411±0.028–0.404±0.025 s) interval. The QTc interval normalized in three subjects with prolonged baseline QTc ({\\textgreater}0.44 s). A statistically significant (P=0.007) reduction in systolic blood pressure early in the course of weight loss (day 2) accompanied the electrocardiographic changes. CONCLUSION: These results fail to support the development of cardiac repolarization abnormalities in obese patients who ingest a nutritionally balanced low calorie diet over seven days. A significant reduction in QT interval duration and amelioration of abnormally prolonged baseline QTc intervals suggest improved cardiac repolarization with early weight loss.},\n\tlanguage = {en},\n\tnumber = {2},\n\turldate = {2023-06-05},\n\tjournal = {International Journal of Obesity},\n\tauthor = {Pietrobelli, A. and Rothacker, D. and Gallagher, D. and Heymsfield, S. B.},\n\tmonth = feb,\n\tyear = {1997},\n\tnote = {Number: 2\nPublisher: Nature Publishing Group},\n\tkeywords = {general, Metabolic Diseases, Epidemiology, Health Promotion and Disease Prevention, Internal Medicine, Medicine/Public Health, Public Health},\n\tpages = {110--114},\n}\n\n

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\n \n 1996\n \n \n (1)\n \n \n

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\n \n\n \n \n \n \n \n \n A model of measles virus–induced immunosuppression: Enhanced susceptibility of neonatal human PBLs.\n \n \n \n \n\n\n \n Tishon, A.; Manchester, M.; Scheiflinger, F.; and Oldstone, M. B. A.\n\n\n \n\n\n\n Nature Medicine, 2(11): 1250–1254. November 1996.\n Number: 11 Publisher: Nature Publishing Group\n\n\n\n
\n\n\n\n \n \n $\"A$ Paper\n \n \n\n \n \n doi\n \n \n\n \n link\n \n \n\n bibtex\n \n\n \n \n \n abstract \n \n\n \n\n \n \n \n \n \n \n \n\n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n\n\n\n

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@article{tishon_model_1996,\n\ttitle = {A model of measles virus–induced immunosuppression: {Enhanced} susceptibility of neonatal human {PBLs}},\n\tvolume = {2},\n\tcopyright = {1996 Springer Nature America, Inc.},\n\tissn = {1546-170X},\n\tshorttitle = {A model of measles virus–induced immunosuppression},\n\turl = {https://www.nature.com/articles/nm1196-1250},\n\tdoi = {10.1038/nm1196-1250},\n\tabstract = {Measles virus (MV) still incites one of the most contagious infections of humankind. Despite the development and use of an excellent live attenuated virus vaccine, over one million infants and children continue to die each year from measles1–3. The main cause of morbidity and mortality is virus–induced immunosuppression of lymphocyte function, which allows secondary infections. Here we report an in vivo model for the study of MV–induced immunosuppression. Human peripheral blood leukocytes (PBLs) grafted onto mice with severe combined immunodeficiency disease (SCID mice) to create hu–PBLS–SCID mice produce human IgG that is suppressed by MV infection, immunosuppression is dependent on the involvement of live virus and is dramatically more severe for PBLs obtained from newborns than PBLs from adults. Suppression of IgG synthesis by PBLs from newborns occurs as early as ten days after administration of MV to hu–PBLS–SCID mice compared with 44 days required for PBLs from adults. Further, MV infection of SCID mice reconstituted with PBLs from newborns reduces IgG production 26 ± 5–fold (mean ± 1 s.e.m.) as compared with only a 6 ± 0.5–fold reduction in adults. MV RNA could be detected in live human PBLs recovered from SCID mice as long as 110 days after MV infection began. The profound immunosuppression we observe in PBLs from infants probably contributes to the morbidity and mortality observed in infants vaccinated with measles virus. Further, this model should be useful for accessing the potential immunosuppressive abilities of newly isolated field (wild–type) virus isolates and newly designed vaccines containing attenuated MV or subunit vaccines, as well as in dissecting the role played by maternal antibodies to MV on the ability of the virus to enhance or abort the virus–induced immunosuppression.},\n\tlanguage = {en},\n\tnumber = {11},\n\turldate = {2023-06-05},\n\tjournal = {Nature Medicine},\n\tauthor = {Tishon, Antoinette and Manchester, Marianne and Scheiflinger, Friedrich and Oldstone, Michael B. A.},\n\tmonth = nov,\n\tyear = {1996},\n\tnote = {Number: 11\nPublisher: Nature Publishing Group},\n\tkeywords = {general, Biomedicine, Cancer Research, Infectious Diseases, Metabolic Diseases, Molecular Medicine, Neurosciences},\n\tpages = {1250--1254},\n\tfile = {Full Text PDF:C\\:\\\\Users\\\\ojaillon\\\\Zotero\\\\storage\\\\NFKNEZDP\\\\Tishon et al. - 1996 - A model of measles virus–induced immunosuppression.pdf:application/pdf},\n}\n\n

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\n \n undefined\n \n \n (1)\n \n \n

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\n \n\n \n \n \n \n \n \n Global Change Biology \\textbar Environmental Change Journal \\textbar Wiley Online Library.\n \n \n \n \n\n\n \n \n\n\n \n\n\n\n \n \n\n\n\n
\n\n\n\n \n \n $\"Global$ Paper\n \n \n\n \n\n \n link\n \n \n\n bibtex\n \n\n \n\n \n\n \n \n \n \n \n \n \n\n \n \n \n\n\n\n

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@misc{noauthor_global_nodate,\n\ttitle = {Global {Change} {Biology} {\\textbar} {Environmental} {Change} {Journal} {\\textbar} {Wiley} {Online} {Library}},\n\turl = {https://onlinelibrary-wiley-com.insb.bib.cnrs.fr/doi/10.1111/gcb.16924},\n\turldate = {2023-09-08},\n\tfile = {Global Change Biology | Environmental Change Journal | Wiley Online Library:C\\:\\\\Users\\\\ojaillon\\\\Zotero\\\\storage\\\\K27H8MWD\\\\gcb.html:text/html},\n}\n

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