Vita Last changes : 2019/08/30 05:17
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I am a versatile scientist trained in biotechnology, computational science and data analysis, i.e. a computational biologist and bioinformatician. Although I spend most of my time in front of a computer, I am occasionally found in the field or working at the bench. My multidisciplinarity leads me to interact with all sorts of scholars: molecular biologists, mathematicians, geneticists, computer scientists, ecologists, ... ! Contact Information Born in France in 1980 Address: Bern, Switzerland Email address: florent dot angly at gmail dot com ---- ! Professional interests Bioinformatic and statistical methods for the analysis of big data Environmental genomics and novel computational approaches to mine metagenomic data Phage biogeography and biodiversity Microbial ecology and how concepts of ecology for macroorganisms might be applied to microbes Coral reef ecosystems and how coral reef health relates to human activities and changes in microbial communities Integration of omics data: metagenomics, metatranscriptomics, metaproteomics ---- ! Work experience ''2016-2019'' Electronic Lab Systems, [CSL Behring\|http://www.cslbehring.ch/], Bern, Switzerland. Lab automation scientist. ''2015'' * [Laboratory of Prof. Beatson\|http://beatsonlab.com/], The University of Queensland, Brisbane, Australia. Data analyst. ''2012-2014'' * [Australian Centre for Ecogenomics\|http://ecogenomic.org/], The University of Queensland, Brisbane, Australia. Discovery Early Career Researcher ([DECRA\|http://www.arc.gov.au/ncgp/decra.htm]). ''2011'' * [Australian Centre for Ecogenomics\|http://ecogenomic.org/], The University of Queensland, Brisbane, Australia. Postdoctoral research fellow. ''2010'' * [Laboratory of Dr. Tyson\|http://www.awmc.uq.edu.au/index.html?page=108642], Advanced Water Management Centre, The University of Queensland, Brisbane, Australia. Postdoctoral research fellow. ''2005-2009'' * [Laboratory of Prof. Rohwer\|http://phage.sdsu.edu], San Diego State University (SDSU), USA. PhD thesis research. ''2004'' * [Laboratory of Prof. Rohwer\|http://phage.sdsu.edu], San Diego State University (SDSU), USA. Internship. ''2003'' * Laboratory of Dr. du Manoir, Institute of Genetics and Cellular and Molecular Biology (IGBMC), Strasbourg, France. 4-week project directed by Prof. Stanislas du Manoir about the "High throughput bioinformatic analysis of the clones used in the production of CGH DNA chip". Mapping and characterization of the 250 clones by use of Perl programming and statistical analysis of repeated sequences with RepeatMasker. ''2002'' * Biology Informatics Statistics and Sociolinguistics Workshop (ABISS), Rouen University, France. 6-week internship directed by Laurent Mouchard (senior lecturer) for the "Installation of a full Blast pairwise sequences comparison system", including proteic and nucleic biological databases use, UNIX programming and installation of the BLAST package and its HTML interface. ''2001'' * Molecular Histology and Embryology Laboratory , Laennec Medicine Faculty, Lyon, France. 2-week internship directed by professor Jacqueline Trouillas for an "Initiation to research laboratory work". Study of hypophysary adenomas: publications reading, histological cuts realisation, coloration, and observation under optical and transmission electronic microscope, and following of the studied rat stem. ---- ! Education ''2013'' * [The University of Queensland\|http://www.uq.edu.au/], QLD, Australia. [Certificate of University Teaching Practice\|http://www.tedi.uq.edu.au/cutp-news] ''2005-2009'' * [San Diego State University (SDSU)\|http://www.sdsu.edu] / [Claremont Graduate University (CGU)\|http://www.cgu.edu], CA, USA. [PhD in Computational Science\|http://www.csrc.sdsu.edu]: [''A computational workflow for the estimation of environmental viral diversity in metagenomes''\|data/Angly_thesis_2009.pdf][img/pdfreaders-22px.png] ''2001-2004'' * [Strasbourg School of Biotechnology (ESBS)\|http://www-esbs.u-strasbg.fr/esbs/?lang=en], Strasbourg, France / Freiburg, Germany / Basel, Switzerland. Trinational degree Diplôme d'Ingénieur en Biotechnologie / Diplom Biotechnologe (~ M.Sc., 5th year of study). ''2000-2001'' * [Claude Bernard University, Lyon 1 (UCBL)\|http://www.univ-lyon1.fr], France. "Licence" of Cell Biology and Physiology, Genetics section (3rd year of study) ''1998-2000'' * [Claude Bernard University, Lyon 1 (UCBL)\|http://www.univ-lyon1.fr], France. "DEUG" of Sciences and Technologies, Life Sciences section, Biomathematics option (2nd year of study) ''1995-1998'' * [Notre-Dame de Bellegarde Secondary School\|http://ndbellegarde.fr], Neuville-sur-Saône, France. General scientific "Baccalauréat", Life and Earth Sciences section (~ A-level) ---- ! Publications ''2016'' * [img/peerj.gif] [Angly et al. (2016), ''Diuron tolerance and potential degradation by pelagic microbiomes in the Great Barrier Reef lagoon'', PeerJ 4:e1758\|https://doi.org/10.7717/peerj.1758] * [img/peerj.gif] [Angly et al. (2016), ''Marine microbial communities of the Great Barrier Reef lagoon are influenced by riverine floodwaters and seasonal weather events'', PeerJ 4:e1511\|https://doi.org/10.7717/peerj.1511] ''2014'' * [img/bmc.png] [de Cárcer et al. (2014), ''Evaluation of viral genome assembly and diversity estimation in deep metagenomes'', BMC Genomics 15:989\|http://dx.doi.org/10.1186/1471-2164-15-989] * [img/bmc.png] [Angly et al. (2014), ''CopyRighter: a rapid tool for improving the accuracy of microbial community profiles through lineage-specific gene copy number correction'', Microbiome 2:11\|http://dx.doi.org/10.1186/2049-2618-2-11] * [img/oxford.png] [Angly et al. (2014), ''The Bio-Community Perl toolkit for microbial ecology'', Bioinformatics 30(13): 1926-1927\|http://dx.doi.org/10.1093/bioinformatics/btu130] ''2013'' * [img/pnas.png] [Dove et al. (2013), ''Future reef decalcification under a business-as-usual carbon dioxide emission scenario'', PNAS 110(38):15342-15347\|http://dx.doi.org/10.1073/pnas.1302701110] ''2012'' * [img/wiley.png] [Cassman et al. (2012), ''Oxygen minimum zones harbour novel viral communities with low diversity'', Environmental Microbiology, 14(11):3043–3065\|http://dx.doi.org/10.1111/j.1462-2920.2012.02891.x] * [img/oxford.png] [Angly et al. (2012), ''Grinder: a versatile amplicon and shotgun sequence simulator'', Nucleic Acids Research 40(12):e94\|http://dx.doi.org/10.1093/nar/gks251] * [img/wiley.png] [Tamaki et al. (2012), ''Metagenomic analysis of DNA viruses in a wastewater treatment plant in tropical climate'', Environmental Microbiology 14(2):441-452\|http://dx.doi.org/10.1111/j.1462-2920.2011.02630.x] * [img/wiley.png] [Miller el al. (2012), ''Phage–bacteria relationships and CRISPR elements revealed by a metagenomic survey of the rumen microbiome'', Environmental Microbiology 14(1):207–227\|http://dx.doi.org/10.1111/j.1462-2920.2011.02593.x] ''2011'' * [img/elsevier.png] [Yang et al. (2011), ''Wastewater treatment systems harbor specific and diverse yeast communities'', Biochemical Engineering Journal 56-59:168-176\|http://dx.doi.org/10.1016/j.bej.2011.09.012] * [img/plos.png] [Skennerton et al. (2011), ''Phage encoded H-NS: a potential Achilles heel in the bacterial defence system'', PLoS ONE 6(5): e20095\|http://dx.doi.org/10.1371/journal.pone.0020095] * [img/medecine_sciences.png] [Angly and Tyson (2011), ''Des communautés de phages divergentes contrôlent-elles la microflore intestinale? (Are divergent viral communities controlling individual gut microbiota?)'', Médecine/Sciences, 27(3):229-231\|http://dx.doi.org/10.1051/medsci/2011273229] * [img/current_protocols.png] [Treangen et al. (2011), ''Next generation sequence assembly with AMOS'', Current Protocols in Bioinformatics, 33:11.8.1-11.8.18\|http://dx.doi.org/10.1002/0471250953.bi1108s33] * [img/pnas.png] [Willner et al. (2011), ''Metagenomic detection of phage-encoded platelet-binding factors in the human oral cavity'', PNAS, 108:4547-4553\|http://dx.doi.org/10.1073/pnas.1000089107] ''2010'' * [img/nature.png] [Reyes et al. (2010), ''Viruses in the fecal microbiota of monozygotic twins and their mothers'', Nature, 466:334–338\|http://dx.doi.org/10.1038/nature09199] [img/f1000.png] [Faculty of 1000\|http://f1000.com/4417956] [img/UQ.png] [UQ EAIT Impact Award\|http://www.eait.uq.edu.au/index.html?page=131802&pid=115415] * [img/nature.png] [Rodriguez-Brito et al. (2010), ''Viral and microbial community dynamics in four aquatic environments'', The ISME Journal, 4:739–751\|http://dx.doi.org/10.1038/ismej.2010.1] ''2009'' * [img/plos.png] [Angly et al. (2009), ''The GAAS metagenomic tool and its estimations of viral and microbial average genome size in four major biomes'', PLoS Computational Biology, 5(12):e1000593\|http://dx.doi.org/10.1371/journal.pcbi.1000593] * [img/plos.png] [Willner et al. (2009), ''Metagenomic analysis of respiratory tract DNA viral communities in cystic fibrosis and non-cystic fibrosis individuals'', PLoS ONE, 4(10):e7370\|http://dx.doi.org/10.1371/journal.pone.0007370] [img/f1000.png] [Faculty of 1000\|http://f1000.com/1280994] * [img/wiley.png] [Angly et al. (2009), ''Genomic analysis of multiple Roseophage SIO1 strains'', Environmental Microbiology, 11(11):2863-2873\|http://dx.doi.org/10.1111/j.1462-2920.2009.02021.x] * [img/wiley.png] [Vega Thurber et al. (2009), ''Metagenomic analysis of stressed coral holobionts'', Environmental Microbiology, 11(8):2148-2163\|http://dx.doi.org/10.1111/j.1462-2920.2009.01935.x] ''2008'' * [img/pnas.png] [Vega Thurber et al. (2008), ''Metagenomic analysis indicates that stressors induce production of herpes-like viruses in the coral Porites compressa'', PNAS, 105(47):18413-18418\|http://dx.doi.org/10.1073/pnas.0808985105] * [img/plos.png] [Qu A et al. (2008), ''Comparative metagenomics reveals host-specific metavirulomes and horizontal gene transfer elements in the chicken cecum microbiome'', PLoS One, 3(8):e2945\|http://dx.doi.org/10.1371/journal.pone.0002945] * [img/science_direct.png] [Breitbart M et al. (2008), ''Viral diversity and dynamics in an infant gut'', Research in Microbiology, 159(5):367-373\|http://dx.doi.org/10.1016/j.resmic.2008.04.006] * [img/nature.png] [Dinsdale EA et al. (2008), ''Functional metagenomic profiling of nine biomes'', Nature, 452:629-632\|http://dx.doi.org/10.1038/nature06810] * [img/nature.png] [Desnues C et al. (2008), ''Biodiversity and biogeography of phages stromatolites in modern stromatolites and thrombolites'', Nature, 452:340-343\|http://dx.doi.org/10.1038/nature06735] * [img/plos.png] [Dinsdale EA et al. (2008), ''Microbial ecology of four coral atolls in the Northern Line Islands'', PLoS ONE, 3(2):e1584\|http://dx.doi.org/10.1371/journal.pone.0001584] [img/f1000.png] [Faculty of 1000\|http://f1000.com/1102259] ''2007'' * [img/fems.png] [Hoffmann et al. (2007), ''Power law rank-abundance models for marine phage communities'', FEMS Microbiological Letters, 273(2):224–228\|http://dx.doi.org/10.1111/j.1574-6968.2007.00790.x] ''2006'' * [img/plos.png] [Angly FE et al. (2006), ''The marine viromes of four oceanic regions'', PLoS Biology, 4(11):e368\|http://dx.doi.org/10.1371/journal.pbio.0040368] [img/f1000.png] [Faculty of 1000\|http://f1000.com/1049323] ''2005'' * [img/bmc.png] [Angly FE et al. (2005), ''PHACCS, an online tool for estimating the structure and diversity of uncultured viral communities using metagenomic information'', BMC Bioinformatics, 6:41\|http://dx.doi.org/10.1186/1471-2105-6-41] ---- ! Conferences, symposia and courses * [Hacking Health Camp 2016\|http://hackinghealth.ca/fr/event/hacking-health-camp-fr/], France * [2nd Thünen Symposium on Soil Metagenomics\|http://www.soil-metagenomics.org], 2013, Germany (poster) * [14th International Symposium on Microbial Ecology\|http://www.isme-microbes.org/isme14], 2012, Denmark (posters) * [12th International Coral Reef Symposium\|http://www.icrs2012.com], 2012, Australia (speaker) * [Australian Society for Microbiology Annual Meeting\|http://www.asm2012.org], 2012, Australia (speaker) * [Federation of European Microbiological Societies 4th congress\|http://www2.kenes.com/fems2011/Pages/Home.aspx], 2011, Switzerland (speaker) * [NESCent workshop on High-throughput Biodiversity Research using Eukaryotic Metagenetics\|http://www.nescent.org/wg_eukmetagen/Main_Page], 2011, USA * [110th General Meeting of the American Society for Microbiology\|http://gm.asm.org/index.php/general-info/future-meeting-dates-a-locations], 2010, USA (poster) * [Cold Spring Harbor Laboratory course on Advanced Sequencing Technologies & Applications\|http://meetings.cshl.edu/courses/c-seqtech09.shtml], 2009, USA (lecturer) * [Telluride Science Research Center 2009 workshop on Cystic Fibrosis\|http://tellu003.secure.omnis.com/workshop_details.php?wid=67], 2009, USA * [17th Annual Conference on Intelligent Systems for Molecular Biology & 8th European Conference on Computational Biology\|http://www.iscb.org/ismbeccb2009/], 2009, Sweden (poster) * [6th Annual Rocky Mountain Bioinformatic Conference\|http://www.iscb.org/cms_addon/conferences/rocky08/], 2008, USA (speaker) * [Metagenomics 2008\|http://metagenomics.calit2.net/], USA (poster) * [12th International Symposium on Microbial Ecology\|http://www.kenes.com/isme12/], 2008, Australia (speaker) * [11th International Coral Reef Symposium\|http://www.nova.edu/ncri/11icrs/], 2008, USA (speaker) * [Genomes, Medicine and the Environment\|http://www.jcvi.org/cms/meetings/gme/], 2007, USA * [Computational Science Curriculum Development Forum and ACSESS for Industry\|http://www.csrc.sdsu.edu/csrc/acsess/annual2007.php], 2007, USA (poster) * [American Society of Limnology and Oceanography 2007 Meeting\|http://aslo.org/santafe2007/], USA (speaker) * [11th International Symposium on Microbial Ecology\|http://www.kenes.com/isme/], 2006, Austria (poster) * [Metagenomics 2006\|http://www.calit2.net/metagenomics2006/program.php], USA (poster) * [American Society of Limnology and Oceanography 2006 Meeting\|http://www.agu.org/meetings/os06/], USA * [Computational Science Curriculum Development Forum and ACSESS for Industry\|http://www.csrc.sdsu.edu/csrc/acsess/annual.php], 2005, USA (poster) * [San Diego Microbiology Group 2004 Annual Meeting\|http://biology.fullerton.edu/orgs/sdmg/], USA (poster) ---- ! Miscellaneous * University of Queensland strategic Postdoctoral Research Fellowship recipient * Member of the editorial board of the [Microbiome\|http://www.microbiomejournal.com] journal * Peer reviewer for [Australian Research Council\|http://www.arc.gov.au/], [Bioinformatics\|http://bioinformatics.oxfordjournals.org], [BMC Microbiology\|http://www.biomedcentral.com/bmcmicrobiol/], [Environmental Microbiology\|http://www3.interscience.wiley.com/journal/118491005/home], [FEMS Microbial Ecology\|http://onlinelibrary.wiley.com/journal/10.1111/%28ISSN%291574-6941], [Future Microbiology\|http://www.futuremedicine.com/loi/fmb/], [Microbiome\|http://www.microbiomejournal.com], [Molecular Biology and Evolution\|http://mbe.oxfordjournals.org/], [Molecular Ecology Resources\|http://onlinelibrary.wiley.com/journal/10.1111/%28ISSN%291755-0998], the [National Science Foundation\|http://www.nsf.gov/] (USA), [Nucleic Acids Research\|http://nar.oxfordjournals.org/], [PLoS ONE\|http://www.plosone.org] and [Scientific Reports\|http://www.nature.com/srep/index.html] * Member of the [Free Software Foundation\|http://www.fsf.org/] * [UQ Expert\|http://www.uq.edu.au/uqexperts/profile.php?staff_id=18141] * Computer skills Computer administration Distributed computing * Cluster environment * Parallel programming * Grid cyberinfrastructure * Web services Computer hardware Relational databases and SQL Programming languages Perl ([BioPerl\|http://www.bioperl.org/wiki/Main_Page] developer, [CPAN\|http://www.cpan.org/] developer) Python Octave/Matlab ([Octave Forge\|http://octave.sourceforge.net/] developer) C HTML PHP JavaScript *CGI Biology skills Biotechnology Microbiology Molecular biology Cell biology * Field skills ** Scientific SCUBA diving (Nitrox certified) * Known languages: French (native) English (fluent) German (fluent) Swedish (basic) TOC password :
	Wiki utilisant WiKiss 0.3 2025/07/20 23:24 -- 216.73.216.25	Edit (Help) / History

Vita

Last changes : 2019/08/30 05:17

Edit (Help) / History

I am a versatile scientist trained in biotechnology, computational science and data analysis, i.e. a computational biologist and bioinformatician. Although I spend most of my time in front of a computer, I am occasionally found in the field or working at the bench. My multidisciplinarity leads me to interact with all sorts of scholars: molecular biologists, mathematicians, geneticists, computer scientists, ecologists, ...

! Contact Information

Born in France in 1980

Address: Bern, Switzerland
Email address: florent dot angly at gmail dot com

----

! Professional interests

*Bioinformatic and statistical methods for the analysis of big data
*Environmental genomics and novel computational approaches to mine metagenomic data
*Phage biogeography and biodiversity
*Microbial ecology and how concepts of ecology for macroorganisms might be applied to microbes
*Coral reef ecosystems and how coral reef health relates to human activities and changes in microbial communities
*Integration of *omics data: metagenomics, metatranscriptomics, metaproteomics

----

! Work experience

''2016-2019''
* Electronic Lab Systems, [CSL Behring|http://www.cslbehring.ch/], Bern, Switzerland. Lab automation scientist.

''2015''
* [Laboratory of Prof. Beatson|http://beatsonlab.com/], The University of Queensland, Brisbane, Australia. Data analyst.

''2012-2014''
* [Australian Centre for Ecogenomics|http://ecogenomic.org/], The University of Queensland, Brisbane, Australia. Discovery Early Career Researcher ([DECRA|http://www.arc.gov.au/ncgp/decra.htm]).

''2011''
* [Australian Centre for Ecogenomics|http://ecogenomic.org/], The University of Queensland, Brisbane, Australia. Postdoctoral research fellow.

''2010''
* [Laboratory of Dr. Tyson|http://www.awmc.uq.edu.au/index.html?page=108642], Advanced Water Management Centre, The University of Queensland, Brisbane, Australia. Postdoctoral research fellow.

''2005-2009''
* [Laboratory of Prof. Rohwer|http://phage.sdsu.edu], San Diego State University (SDSU), USA. PhD thesis research.

''2004''
* [Laboratory of Prof. Rohwer|http://phage.sdsu.edu], San Diego State University (SDSU), USA. Internship.

''2003''
* Laboratory of Dr. du Manoir, Institute of Genetics and Cellular and Molecular Biology (IGBMC), Strasbourg, France. 4-week project directed by Prof. Stanislas du Manoir about the "High throughput bioinformatic analysis of the clones used in the production of CGH DNA chip". Mapping and characterization of the 250 clones by use of Perl programming and statistical analysis of repeated sequences with RepeatMasker.

''2002''
* Biology Informatics Statistics and Sociolinguistics Workshop (ABISS), Rouen University, France. 6-week internship directed by Laurent Mouchard (senior lecturer) for the "Installation of a full Blast pairwise sequences comparison system", including proteic and nucleic biological databases use, UNIX programming and installation of the BLAST package and its HTML interface.

''2001''
* Molecular Histology and Embryology Laboratory , Laennec Medicine Faculty, Lyon, France. 2-week internship directed by professor Jacqueline Trouillas for an "Initiation to research laboratory work". Study of hypophysary adenomas: publications reading, histological cuts realisation, coloration, and observation under optical and transmission electronic microscope, and following of the studied rat stem.

----

! Education

''2013''
* [The University of Queensland|http://www.uq.edu.au/], QLD, Australia. [Certificate of University Teaching Practice|http://www.tedi.uq.edu.au/cutp-news]

''2005-2009''
* [San Diego State University (SDSU)|http://www.sdsu.edu] / [Claremont Graduate University (CGU)|http://www.cgu.edu], CA, USA. [PhD in Computational Science|http://www.csrc.sdsu.edu]: [''A computational workflow for the estimation of environmental viral diversity in metagenomes''|data/Angly_thesis_2009.pdf][img/pdfreaders-22px.png]

''2001-2004''
* [Strasbourg School of Biotechnology (ESBS)|http://www-esbs.u-strasbg.fr/esbs/?lang=en], Strasbourg, France / Freiburg, Germany / Basel, Switzerland. Trinational degree Diplôme d'Ingénieur en Biotechnologie / Diplom Biotechnologe (~ M.Sc., 5th year of study).

''2000-2001''
* [Claude Bernard University, Lyon 1 (UCBL)|http://www.univ-lyon1.fr], France. "Licence" of Cell Biology and Physiology, Genetics section (3rd year of study)

''1998-2000''
* [Claude Bernard University, Lyon 1 (UCBL)|http://www.univ-lyon1.fr], France. "DEUG" of Sciences and Technologies, Life Sciences section, Biomathematics option (2nd year of study)

''1995-1998''
* [Notre-Dame de Bellegarde Secondary School|http://ndbellegarde.fr], Neuville-sur-Saône, France. General scientific "Baccalauréat", Life and Earth Sciences section (~ A-level)

----

! Publications

''2016''
* [img/peerj.gif] [Angly et al. (2016), ''Diuron tolerance and potential degradation by pelagic microbiomes in the Great Barrier Reef lagoon'', PeerJ 4:e1758|https://doi.org/10.7717/peerj.1758]
* [img/peerj.gif] [Angly et al. (2016), ''Marine microbial communities of the Great Barrier Reef lagoon are influenced by riverine floodwaters and seasonal weather events'', PeerJ 4:e1511|https://doi.org/10.7717/peerj.1511]

''2014''
* [img/bmc.png] [de Cárcer et al. (2014), ''Evaluation of viral genome assembly and diversity estimation in deep metagenomes'', BMC Genomics 15:989|http://dx.doi.org/10.1186/1471-2164-15-989]
* [img/bmc.png] [Angly et al. (2014), ''CopyRighter: a rapid tool for improving the accuracy of microbial community profiles through lineage-specific gene copy number correction'', Microbiome 2:11|http://dx.doi.org/10.1186/2049-2618-2-11]
* [img/oxford.png] [Angly et al. (2014), ''The Bio-Community Perl toolkit for microbial ecology'', Bioinformatics 30(13): 1926-1927|http://dx.doi.org/10.1093/bioinformatics/btu130]

''2013''
* [img/pnas.png] [Dove et al. (2013), ''Future reef decalcification under a business-as-usual carbon dioxide emission scenario'', PNAS 110(38):15342-15347|http://dx.doi.org/10.1073/pnas.1302701110]

''2012''
* [img/wiley.png] [Cassman et al. (2012), ''Oxygen minimum zones harbour novel viral communities with low diversity'', Environmental Microbiology, 14(11):3043–3065|http://dx.doi.org/10.1111/j.1462-2920.2012.02891.x]
* [img/oxford.png] [Angly et al. (2012), ''Grinder: a versatile amplicon and shotgun sequence simulator'', Nucleic Acids Research 40(12):e94|http://dx.doi.org/10.1093/nar/gks251]
* [img/wiley.png] [Tamaki et al. (2012), ''Metagenomic analysis of DNA viruses in a wastewater treatment plant in tropical climate'', Environmental Microbiology 14(2):441-452|http://dx.doi.org/10.1111/j.1462-2920.2011.02630.x]
* [img/wiley.png] [Miller el al. (2012), ''Phage–bacteria relationships and CRISPR elements revealed by a metagenomic survey of the rumen microbiome'', Environmental Microbiology 14(1):207–227|http://dx.doi.org/10.1111/j.1462-2920.2011.02593.x]

''2011''
* [img/elsevier.png] [Yang et al. (2011), ''Wastewater treatment systems harbor specific and diverse yeast communities'', Biochemical Engineering Journal 56-59:168-176|http://dx.doi.org/10.1016/j.bej.2011.09.012]

* [img/plos.png] [Skennerton et  al. (2011), ''Phage encoded H-NS: a potential Achilles heel in the bacterial defence system'', PLoS ONE 6(5): e20095|http://dx.doi.org/10.1371/journal.pone.0020095]
* [img/medecine_sciences.png] [Angly and Tyson (2011), ''Des communautés de phages divergentes contrôlent-elles la microflore intestinale? (Are divergent viral communities controlling individual gut microbiota?)'', Médecine/Sciences, 27(3):229-231|http://dx.doi.org/10.1051/medsci/2011273229]
* [img/current_protocols.png] [Treangen et al. (2011), ''Next generation sequence assembly with AMOS'', Current Protocols in Bioinformatics, 33:11.8.1-11.8.18|http://dx.doi.org/10.1002/0471250953.bi1108s33]
* [img/pnas.png] [Willner et al. (2011), ''Metagenomic detection of phage-encoded platelet-binding factors in the human oral cavity'', PNAS, 108:4547-4553|http://dx.doi.org/10.1073/pnas.1000089107]

''2010''
* [img/nature.png] [Reyes et al. (2010), ''Viruses in the fecal microbiota of monozygotic twins and their mothers'', Nature, 466:334–338|http://dx.doi.org/10.1038/nature09199] [img/f1000.png] [Faculty of 1000|http://f1000.com/4417956] [img/UQ.png] [UQ EAIT Impact Award|http://www.eait.uq.edu.au/index.html?page=131802&pid=115415]
* [img/nature.png] [Rodriguez-Brito et al. (2010), ''Viral and microbial community dynamics in four aquatic environments'', The ISME Journal, 4:739–751|http://dx.doi.org/10.1038/ismej.2010.1]

''2009''
* [img/plos.png] [Angly et al. (2009), ''The GAAS metagenomic tool and its estimations of viral and microbial average genome size in four major biomes'', PLoS Computational Biology, 5(12):e1000593|http://dx.doi.org/10.1371/journal.pcbi.1000593]
* [img/plos.png] [Willner et al. (2009), ''Metagenomic analysis of respiratory tract DNA viral communities in cystic fibrosis and non-cystic fibrosis individuals'', PLoS ONE, 4(10):e7370|http://dx.doi.org/10.1371/journal.pone.0007370]  [img/f1000.png] [Faculty of 1000|http://f1000.com/1280994]
* [img/wiley.png] [Angly et al. (2009), ''Genomic analysis of multiple Roseophage SIO1 strains'', Environmental Microbiology, 11(11):2863-2873|http://dx.doi.org/10.1111/j.1462-2920.2009.02021.x]
* [img/wiley.png] [Vega Thurber et al. (2009), ''Metagenomic analysis of stressed coral holobionts'', Environmental Microbiology, 11(8):2148-2163|http://dx.doi.org/10.1111/j.1462-2920.2009.01935.x]

''2008''
* [img/pnas.png] [Vega Thurber et al. (2008), ''Metagenomic analysis indicates that stressors induce production of herpes-like viruses in the coral Porites compressa'', PNAS, 105(47):18413-18418|http://dx.doi.org/10.1073/pnas.0808985105]
* [img/plos.png] [Qu A et al. (2008), ''Comparative metagenomics reveals host-specific metavirulomes and horizontal gene transfer elements in the chicken cecum microbiome'', PLoS One, 3(8):e2945|http://dx.doi.org/10.1371/journal.pone.0002945]
* [img/science_direct.png] [Breitbart M et al. (2008), ''Viral diversity and dynamics in an infant gut'', Research in Microbiology, 159(5):367-373|http://dx.doi.org/10.1016/j.resmic.2008.04.006]
* [img/nature.png] [Dinsdale EA et al. (2008), ''Functional metagenomic profiling of nine biomes'', Nature, 452:629-632|http://dx.doi.org/10.1038/nature06810]
* [img/nature.png] [Desnues C et al. (2008), ''Biodiversity and biogeography of phages stromatolites in modern stromatolites and thrombolites'', Nature, 452:340-343|http://dx.doi.org/10.1038/nature06735]
* [img/plos.png] [Dinsdale EA et al. (2008), ''Microbial ecology of four coral atolls in the Northern Line Islands'', PLoS ONE, 3(2):e1584|http://dx.doi.org/10.1371/journal.pone.0001584]  [img/f1000.png] [Faculty of 1000|http://f1000.com/1102259]

''2007''
* [img/fems.png] [Hoffmann et al. (2007), ''Power law rank-abundance models for marine phage communities'', FEMS Microbiological Letters, 273(2):224–228|http://dx.doi.org/10.1111/j.1574-6968.2007.00790.x]

''2006''
* [img/plos.png] [Angly FE et al. (2006), ''The marine viromes of four oceanic regions'', PLoS Biology, 4(11):e368|http://dx.doi.org/10.1371/journal.pbio.0040368]  [img/f1000.png] [Faculty of 1000|http://f1000.com/1049323]

''2005''
* [img/bmc.png] [Angly FE et al. (2005), ''PHACCS, an online tool for estimating the structure and diversity of uncultured viral communities using metagenomic information'', BMC Bioinformatics, 6:41|http://dx.doi.org/10.1186/1471-2105-6-41]

----

! Conferences, symposia and courses
* [Hacking Health Camp 2016|http://hackinghealth.ca/fr/event/hacking-health-camp-fr/], France 
* [2nd Thünen Symposium on Soil Metagenomics|http://www.soil-metagenomics.org], 2013, Germany (poster)
* [14th International Symposium on Microbial Ecology|http://www.isme-microbes.org/isme14], 2012, Denmark (posters)
* [12th International Coral Reef Symposium|http://www.icrs2012.com], 2012, Australia (speaker)
* [Australian Society for Microbiology Annual Meeting|http://www.asm2012.org], 2012, Australia (speaker)
* [Federation of European Microbiological Societies 4th congress|http://www2.kenes.com/fems2011/Pages/Home.aspx], 2011, Switzerland (speaker)
* [NESCent workshop on High-throughput Biodiversity Research using Eukaryotic Metagenetics|http://www.nescent.org/wg_eukmetagen/Main_Page], 2011, USA
* [110th General Meeting of the American Society for Microbiology|http://gm.asm.org/index.php/general-info/future-meeting-dates-a-locations], 2010, USA (poster)
* [Cold Spring Harbor Laboratory course on Advanced Sequencing Technologies & Applications|http://meetings.cshl.edu/courses/c-seqtech09.shtml], 2009, USA (lecturer)
* [Telluride Science Research Center 2009 workshop on Cystic Fibrosis|http://tellu003.secure.omnis.com/workshop_details.php?wid=67], 2009, USA
* [17th Annual Conference on Intelligent Systems for Molecular Biology & 8th European Conference on Computational Biology|http://www.iscb.org/ismbeccb2009/], 2009, Sweden (poster)
* [6th Annual Rocky Mountain Bioinformatic Conference|http://www.iscb.org/cms_addon/conferences/rocky08/], 2008, USA (speaker)
* [Metagenomics 2008|http://metagenomics.calit2.net/], USA (poster)
* [12th International Symposium on Microbial Ecology|http://www.kenes.com/isme12/], 2008, Australia (speaker)
* [11th International Coral Reef Symposium|http://www.nova.edu/ncri/11icrs/], 2008, USA (speaker) 
* [Genomes, Medicine and the Environment|http://www.jcvi.org/cms/meetings/gme/], 2007, USA
* [Computational Science Curriculum Development Forum and ACSESS for Industry|http://www.csrc.sdsu.edu/csrc/acsess/annual2007.php], 2007, USA (poster)
* [American Society of Limnology and Oceanography 2007 Meeting|http://aslo.org/santafe2007/], USA (speaker)
* [11th International Symposium on Microbial Ecology|http://www.kenes.com/isme/], 2006, Austria (poster)
* [Metagenomics 2006|http://www.calit2.net/metagenomics2006/program.php], USA (poster)
* [American Society of Limnology and Oceanography 2006 Meeting|http://www.agu.org/meetings/os06/], USA
* [Computational Science Curriculum Development Forum and ACSESS for Industry|http://www.csrc.sdsu.edu/csrc/acsess/annual.php], 2005, USA (poster)
* [San Diego Microbiology Group 2004 Annual Meeting|http://biology.fullerton.edu/orgs/sdmg/], USA (poster)

----

! Miscellaneous

* University of Queensland strategic Postdoctoral Research Fellowship recipient
* Member of the editorial board of the [Microbiome|http://www.microbiomejournal.com] journal
* Peer reviewer for [Australian Research Council|http://www.arc.gov.au/], [Bioinformatics|http://bioinformatics.oxfordjournals.org], [BMC Microbiology|http://www.biomedcentral.com/bmcmicrobiol/], [Environmental Microbiology|http://www3.interscience.wiley.com/journal/118491005/home], [FEMS Microbial Ecology|http://onlinelibrary.wiley.com/journal/10.1111/%28ISSN%291574-6941], [Future Microbiology|http://www.futuremedicine.com/loi/fmb/], [Microbiome|http://www.microbiomejournal.com], [Molecular Biology and Evolution|http://mbe.oxfordjournals.org/], [Molecular Ecology Resources|http://onlinelibrary.wiley.com/journal/10.1111/%28ISSN%291755-0998], the [National Science Foundation|http://www.nsf.gov/] (USA), [Nucleic Acids Research|http://nar.oxfordjournals.org/], [PLoS ONE|http://www.plosone.org] and [Scientific Reports|http://www.nature.com/srep/index.html]
* Member of the [Free Software Foundation|http://www.fsf.org/]
* [UQ Expert|http://www.uq.edu.au/uqexperts/profile.php?staff_id=18141]
* Computer skills
** Computer administration
** Distributed computing
*** Cluster environment
*** Parallel programming
*** Grid cyberinfrastructure
*** Web services
** Computer hardware
** Relational databases and SQL
** Programming languages
***Perl ([BioPerl|http://www.bioperl.org/wiki/Main_Page] developer, [CPAN|http://www.cpan.org/] developer)
***Python
***Octave/Matlab ([Octave Forge|http://octave.sourceforge.net/] developer)
***C
***HTML
***PHP
***JavaScript
***CGI

* Biology skills
** Biotechnology
** Microbiology
** Molecular biology
** Cell biology

* Field skills
** Scientific SCUBA diving (Nitrox certified)

* Known languages:
**French (native)
**English (fluent)
**German (fluent)
**Swedish (basic)

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