Welcome on my website.
Here you can follow my scientific carrier as my interests. Some lessons and links are available to help you respectively for learning and make science.
News
- July 2020 PNDB Biodiversity research e-infrastructure products and services launch -> https://www.pndb.fr/
- Animation of 2 workshops (29-30 April & 27-28 May 2019) on data/metadata management for PNDB, Museum of Natural History, Paris
- Animation of 1 workshop/hackathon (20-21 december 2018) on data/metadata management and data analysis for OSU Ecce-Terra, Museum of Natural History, Paris
- EBVs workshop for "Journées Zones ateliers Sentinelles des Alpes" http://www.za-alpes.org/journees-zaa-sda/journees-zaa-sda-2018/.
- GEO BON All Hands Meeting https://geobon.org/about/events/geo-bon-all-hands-meeting-2018/ Beijing, July 9th-12th 2018.
- GCCBOSC2018, Portland, USA
- GCC2017, Montpellier
- GDR Ecostat meeting https://gdrecostat2017.sciencesconf.org/
- Trainer on RADseq data analysis on the 5th ITMO IFB national Bioinformatics school dedicated to NGS data analysis event
- Participation to the Oceanhackathon event
- Our Galaxy/Go-Docker project have been selected for Google Summer of Code through the Open Genome Informatics organization. Description of the project
- Gen2BIO Saint-Brieuc conference 2016: Animation of a slot dedicated to Citizen science (link towards my slides on CeSGO hub)
Research projects
- 2019-... GO-FAIR Implementation Network BiodiFAIRse
- 2018-... French national research e-infrastructure "Pôle National de Données de Biodiversité" (PNDB) project: A MNHN project with many partners (CNRS / AFB / INRA / IRD / IRSTEA / IFREMER / INERIS / CIRAD / BRGM / Université Montpellier and FRB)
- 2016-2020 PIA "65 Millions d'observateurs" project: A MNHN national project dedicated to create "tools" to facilitate and extend participation to citizen science projects related to Biodiversity study
- 2015-2020 CPER CeSGO project: A INRIA national project with the Brittany region to build the first French e-Science centre in Rennes
- 2012-2015 e-Biogenouest project: A first e-science approach dedicated to Life sciences labs from western France. Financial supports by Brittany and Pays de la Loire Regions through the Biogenouest core facilities network
- Participation to several projects :
- Since 2013 French Institute of Bioinformatics PIA national project, corresponding to the French Elixir node
- 2014-2016 UEB C@mpus innovative project dedicated to Virtual Research Environment concept transposition on several domains as mechanical or electronical research
- since 2013 National INCa project dedicated to the creation of a French Bioinformatics Network for NGS Cancer Diagnosis
Teaching
- 2016: Introduction to RADseq data analysis. presentation on CeSGO hub
- 2014-2016: Bioinformatics Tools, for Licence 2 Life sciences OBI Rennes1 University. presentation slides on CeSGO hub
- 2013-2016: Bioinformatics Introduction, for Master 2 Life sciences EFCE Rennes1 University
- 2012-2014: R Practical work, for Licence 3 Life sciences Rennes1 University
- 2012-2016: Member of the Galaxy Training Network through the Rennes GenOuest bioinformatics core facility and the GUGGO Western France Galaxy working Group
Animation task
- 2014-2016: Animation of the Virtual Research Environment IFB working group
- 2012-2016: Animation of the GUGGO Western France Galaxy working Group *Member of the MaDICSReproVirtuFlow working group
Publication
- R. David et al. (2020 FAIRness Literacy: the Achilles' Heel of applying FAIR Principles. Data Science Journal https://doi.org/10.5334/dsj-2020-032
- A.D. Rolland et al. (2019) RNA profiling of human testicular cells identifies syntenic lncRNAs associated with spermatogenesis. Hum Reprod. https://pubmed.ncbi.nlm.nih.gov/31247106/
- B. Batut et al. (2018) Community-driven data analysis training for biology. Cell Syst. https://www.ncbi.nlm.nih.gov/pubmed/29953864
- S. Cohen-Boulakia, K. Belhajjame, O. Collin, J. Chopard, C. Froidevaux, A. Gaignard, K. Hinsen, P. Larmande, Y. Le Bras, F. Lemoine, F. Mareuil, H. Ménager, C. Pradal, C. Blanchet (2017) Scientific workflows for computational reproducibility in the life sciences: Status, challenges and opportunities. Future Generation Computer Systems. Doi: http://dx.doi.org/10.1016/j.future.2017.01.012. Link
- Y. Le Bras, O. Collin, C. Monjeaud, V. Lacroix, E. Rivals, C. Lemaître, V. Miele, G. Sacomoto, C. Marchet, B. Cazaux, A. Zine El Aabidine, L. Salmela, S. Alves-Carvalho, A. Andrieux, R. Uricaru, P. Peterlongo (2016) Colib’read on galaxy: a tools suite dedicated to biological information extraction from raw NGS reads. Gigascience. doi: 10.1186/s13742-015-0105-2. Link
- F. Moreews, O. Sallou, H. Ménager, Y. Le Bras, C. Monjeaud, C. Blanchet, O. Collin (2015) BioShaDock: a community driven bioinformatics shared Docker-based tools registry. F1000Research 4 (1443). doi: 10.12688/f1000research.7536.1. Link
- F. Boyer, C. Mercier, A. Bonin, Y. Le Bras, P. Taberlet, E. Coissac (2015) OBITools: a Unix-inspired software package for DNA metabarcoding. Mol. Ecol. Resour. doi: 10.1111/1755-0998.12428. Link
- T. Darde, O. Sallou, E. Becker, B. Ecrard, C. Monjeaud, Y. Le Bras, B. Jégou, O. Collin, A. Rolland, F. Chalmel (2015) The ReproGenomics Viewer: an integrative cross-species toolbox for the reproductive science community. Nucleic Acids Res. doi: 10.1093/nar/gkv345. Link
- A. Bretaudeau, C. Monjeaud, Y. Le Bras, F. Legeai, O. Collin (2015) BioMAJ2Galaxy: automatic update of reference data in Galaxy using BioMAJ. GigaScience 4 (22). doi:10.1186/s13742-015-0063-8. Link
- L. Le Texier, J. Durand, A. Lavault, P. Hulin, O. Collin, Y. Le Bras, M C. Cuturi, E. Chiffoleau (2014) LIMLE, a New Molecule Over-Expressed following Activation, Is Involved in the Stimulatory Properties of Dendritic Cells. PLoS ONE 9(4): e93894. doi:10.1371/journal.pone.0093894. Link
- Y. Le Bras, A. Roult, C. Monjeaud, M. Bahin, O. Quénez, C. Heriveau, A. Bretaudeau, O. Sallou, O. Collin (2013) Towards a Life Sciences Virtual Research Environment : an e-Science initiative in Western France. JOBIM 2013. Link
- Y. Le Bras, N. Dechamp, F. Krieg, O. Filangi, R. Guyomard, M. Boussaha, H. Bovenhuis, T. G. Pottinger, P. Prunet, P. Le Roy, E. Quillet (2011) Detection of QTL with effects on osmoregulation capacities in the rainbow trout (Oncorhynchus mykiss). BMC Genetics 12: 46. Link
- A. Van Wormhoudt, B. Gaume, Y. Le Bras, V. Roussel, S. Huchette (2011) Two different and functional nuclear rDNA genes in the abalone Haliotis tuberculata: tissue differential expression. Genetica 139 (12) : 1-11. link
- Y. Le Bras, N. Dechamp, J. Montfort, A. Le Cam, F. Krieg, E. Quillet, P. Prunet, P. Le Roy (2010) Acclimation to seawater in rainbow trout: QTL/eQTL approach for plasmatic ions and gill tissue. Proc. 9th WCGALP. Link
- I. Leguen, N. Odjo, Y. Le Bras, B. Luthringer, D. Baron, G. Monod, P. Prunet (2010) Effect of seawater transfer on CYP1A gene expression in Rainbow Trout gills. Comp. Biochem. Physiol. Part A/ 156 : 211-217. link
- A. Van Wormhoudt, Y. Le Bras, S. Huchette (2009) Haliotis marmorata from Senegal ; a sister species of Haliotis tuberculata : Morphological and molecular evidence. Biochemical Systematics and Ecology 37 (6) : 747-755. link