@article{chemidlin2021microbial,
  title={Microbial transfers from permanent grassland ecosystems to milk in dairy farms in the Comt{\'e} cheese area},
  author={Chemidlin Pr{\'e}vost-Bour{\'e}, N and Karimi, B and Sadet-Bourgeteau, S and Djemiel, C and Brie, M and Dumont, J and Campedelli, M and Nowak, V and Guyot, P and Letourneur, C and others},
  journal={Scientific reports},
  volume={11},
  number={1},
  pages={1--15},
  year={2021},
  publisher={Nature Publishing Group}
}

@article{djemiel2020biocom,
  title={BIOCOM-PIPE: a new user-friendly metabarcoding pipeline for the characterization of microbial diversity from 16S, 18S and 23S rRNA gene amplicons},
  author={Djemiel, Christophe and Dequiedt, Samuel and Karimi, Battle and Cottin, Aur{\'e}lien and Girier, Thibault and El Djoudi, Yassin and Wincker, Patrick and Leli{\`e}vre, M{\'e}lanie and Mondy, Samuel and Pr{\'e}vost-Bour{\'e}, Nicolas Chemidlin and others},
  journal={BMC bioinformatics},
  volume={21},
  number={1},
  pages={1--21},
  year={2020},
  publisher={Springer}
}

@article{chabbert2020multimodal,
  title={Multimodal assessment of flax dew retting and its functional impact on fibers and natural fiber composites},
  author={Chabbert, Brigitte and Padovani, Justine and Djemiel, Christophe and Ossemond, Jordane and Lema{\^\i}tre, Alain and Yoshinaga, Arata and Hawkins, Simon and Grec, Sebastien and Beaugrand, Johnny and Kurek, Bernard},
  journal={Industrial Crops and Products},
  volume={148},
  pages={112255},
  year={2020},
  publisher={Elsevier}
}

@article{djemiel2020mugreen,
  title={$\mu$green-db: a reference database for the 23S rRNA gene of eukaryotic plastids and cyanobacteria},
  author={Djemiel, Christophe and Plassard, Damien and Terrat, S{\'e}bastien and Crouzet, Olivier and Sauze, Joana and Mondy, Samuel and Nowak, Virginie and Wingate, Lisa and Og{\'e}e, J{\'e}r{\^o}me and Maron, Pierre-Alain},
  journal={Scientific reports},
  volume={10},
  number={1},
  pages={1--11},
  year={2020},
  publisher={Nature Publishing Group}
}

@article{djemiel2020targeted,
  title={Targeted metagenomics of retting in flax: the beginning of the quest to harness the secret powers of the microbiota},
  author={Djemiel, Christophe and Goulas, Estelle and Badalato, Nelly and Chabbert, Brigitte and Hawkins, Simon and Grec, S{\'e}bastien},
  journal={Frontiers in Genetics},
  volume={11},
  year={2020},
  publisher={Frontiers Media SA}
}

@article{karimi2020biogeography,
  title={Biogeography of soil microbial habitats across France},
  author={Karimi, Battle and Villerd, Jean and Dequiedt, Samuel and Terrat, S{\'e}bastien and Chemidlin-Pr{\'e}vost Bour{\'e}, Nicolas and Djemiel, Christophe and Leli{\`e}vre, M{\'e}lanie and Tripied, Julie and Nowak, Virginie and Saby, Nicolas PA and others},
  journal={Global Ecology and Biogeography},
  volume={29},
  number={8},
  pages={1399--1411},
  year={2020},
  publisher={Wiley Online Library}
}

@article{terrat2019,
  title={ReClustOR, a Re-Clustering tool using an Open-Reference method that improves OTU definition},
  author={Terrat, S{\'e}bastien and Djemiel, Christophe and Journay, Corentin and Karimi, Battle and Dequiedt, Samuel and Horrigue, Walid and Maron, Pierre-Alain and Pr{\'e}vost-Bour{\'e}, Nicolas Chemidlin   and Ranjard, Lionel},
  journal={Methods in Ecology and Evolution},
  volume={Accepted},
  number={},
  pages={},
  year={2019},
  publisher={Wiley Online Library}
}

@article{cenci2018nuclear,
  title={Nuclear genome sequence of the plastid-lacking cryptomonad Goniomonas avonlea provides insights into the evolution of secondary plastids},
  author={Cenci, Ugo and Sibbald, Shannon J and Curtis, Bruce A and Kamikawa, Ryoma and Eme, Laura and Moog, Daniel and Henrissat, Bernard and Mar{\'e}chal, Eric and Chabi, Malika and Djemiel, Christophe and others},
  journal={BMC biology},
  volume={16},
  number={1},
  pages={137},
  year={2018},
  publisher={BioMed Central}
}

@article{Djemiel2017,
author = {Djemiel, Christophe and Grec, S{\'{e}}bastien and Hawkins, Simon},
doi = {10.3389/fmicb.2017.02052},
file = {:Users/cdjemiel/Library/Mobile Documents/com{\~{}}apple{\~{}}CloudDocs/Documents/professionnel/Mendeley{\_}Desktop/Djemiel, Grec, Hawkins - 2017 - Characterization of Bacterial and Fungal Community Dynamics by High-Throughput Sequencing (HTS) Metabarc.pdf:pdf},
isbn = {0000000256},
issn = {1664-302X},
journal = {Frontiers in Microbiology},
month = {oct},
title = {{Characterization of Bacterial and Fungal Community Dynamics by High-Throughput Sequencing (HTS) Metabarcoding during Flax Dew-Retting}},
url = {http://journal.frontiersin.org/article/10.3389/fmicb.2017.02052/full},
volume = {8},
year = {2017}
}

@article{Bardou2014,
abstract = {BACKGROUND: Venn diagrams are commonly used to display list comparison. In biology, they are widely used to show the differences between gene lists originating from different differential analyses, for instance. They thus allow the comparison between different experimental conditions or between different methods. However, when the number of input lists exceeds four, the diagram becomes difficult to read. Alternative layouts and dynamic display features can improve its use and its readability.

RESULTS: jvenn is a new JavaScript library. It processes lists and produces Venn diagrams. It handles up to six input lists and presents results using classical or Edwards-Venn layouts. User interactions can be controlled and customized. Finally, jvenn can easily be embeded in a web page, allowing to have dynamic Venn diagrams.

CONCLUSIONS: jvenn is an open source component for web environments helping scientists to analyze their data. The library package, which comes with full documentation and an example, is freely available at http://bioinfo.genotoul.fr/jvenn.},
author = {Bardou, Philippe and Mariette, J{\'{e}}r{\^{o}}me and Escudi{\'{e}}, Fr{\'{e}}d{\'{e}}ric and Djemiel, Christophe and Klopp, Christophe},
doi = {10.1186/1471-2105-15-293},
file = {:Users/cdjemiel/Library/Mobile Documents/com{\~{}}apple{\~{}}CloudDocs/Documents/professionnel/Mendeley{\_}Desktop/Bardou et al. - 2014 - jvenn an interactive Venn diagram viewer.pdf:pdf},
issn = {1471-2105},
journal = {BMC bioinformatics},
keywords = {edward-venn,javascript,jquery,venn,vizualisation},
month = {jan},
pages = {293},
pmid = {25176396},
title = {{jvenn: an interactive Venn diagram viewer.}},
url = {http://www.ncbi.nlm.nih.gov/pubmed/25176396},
volume = {15},
year = {2014}
}

BACKGROUND: Venn diagrams are commonly used to display list comparison. In biology, they are widely used to show the differences between gene lists originating from different differential analyses, for instance. They thus allow the comparison between different experimental conditions or between different methods. However, when the number of input lists exceeds four, the diagram becomes difficult to read. Alternative layouts and dynamic display features can improve its use and its readability. RESULTS: jvenn is a new JavaScript library. It processes lists and produces Venn diagrams. It handles up to six input lists and presents results using classical or Edwards-Venn layouts. User interactions can be controlled and customized. Finally, jvenn can easily be embeded in a web page, allowing to have dynamic Venn diagrams. CONCLUSIONS: jvenn is an open source component for web environments helping scientists to analyze their data. The library package, which comes with full documentation and an example, is freely available at http://bioinfo.genotoul.fr/jvenn.