Jean Fred Fontaine

I am a scientist in the Computational Biology and Data Mining group at the Johannes Gutenberg University of Mainz, Germany. I am also the Editor-in-chief of Genomics and Computational Biology, a peer-reviewed and open-access biomedical journal. I am interested in Computational Biology and Integrative Bioinformatics. My work involves the analysis of high throughput biological data, analysis of biological sequences, databases and text mining.

Genomics and Computational Biology, Vol 1, No 1 (2015)

Research Articles

Processed Small RNAs in Archaea and BHB Elements
Sarah Juliane Berkemer, Christian Höner zu Siederdissen, Fabian Amman, Axel Wintsche, Sebastian Will, Ivo Hofacker, Sonja Prohaska, Peter Stadler
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Visual Characterization of Misclassified Class C GPCRs through Manifold-based Machine Learning Methods
Martha Ivon Cardenas, Alfredo Vellido, Caroline König, René Alquezar, Jesús Giraldo
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The Expanded p53 Interactome as a Predictive Model for Cancer Therapy
Michelle Hussain, Kun Tian, Luciano Mutti, Marija Krstic-Demonacos, Jean-Marc Schwartz
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Reviews

Current and Emerging Themes in the Structural Analysis of Viral RNA Genomes: Applications for the Development of Novel Therapeutic Drugs
Cristina Romero-López, Alfredo Berzal-Herranz
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Resources

Protein Function Easily Investigated by Genomics Data Mining Using the ProteINSIDE Online Tool
Nicolas Kaspric, Matthieu Reichstadt, Brigitte Picard, Jérémy Tournayre, Muriel Bonnet
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Analytical Workflows

Principles of ChIP-seq Data Analysis Illustrated with Examples
Giovanna Ambrosini, René Dreos, Philipp Bucher
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Development of Biocomputing resources

  • Gene set to diseases: disease enrichment analysis on gene sets using literature data.
  • Alkemio: rank thousands of chemicals for any topics using document categorization.
  • Génie: rank all genes for any topic in their literature using orthology information.
  • Medline Ranker: Search PubMed biomedical abstracts using statistical approach.
  • CellFinder: Study annotations, bibliography, gene and protein expression in stem cells and derivatives.
  • HIPPIE: Study and filter the network of human protein-protein interaction data.
  • QiSampler: R script to evaluate alternative scoring schemes for list of items (e.g. genes) based on a very small set of positives.
  • PESCADOR: Extract and analyse a network of gene and protein interactions from a set of PubMed abstracts.
  • ERPIN Easy RNA Profile IdentificatioN is an RNA motif search program.

Publications in peer-reviewed journals

    2016

  • de Oliveira KA, Kaergel E, Heinig M, Fontaine JF, Patone G, Muro EM, Mathas S, Hummel M, Andrade-Navarro MA, Hübner N, Scheidereit C. A roadmap of constitutive NF-κB activity in Hodgkin lymphoma: Dominant roles of p50 and p52 revealed by genome-wide analyses. Genome Med. 2016 Mar 17;8(1):28. doi:10.1186/s13073-016-0280-5. 26988706
  • 2015

  • Fontaine JF, Priller J, Spruth E, Perez-Iratxeta C, Andrade-Navarro MA. Assessment of curated phenotype mining in neuropsychiatric disorder literature. Methods. 2015 Mar;74:90-6. doi: 10.1016/j.ymeth.2014.11.022. Epub 2014 Dec 5. 25484337.
  • 2014

  • Gijón-Correas JA, Andrade-Navarro MA, Fontaine JF. Alkemio: association of chemicals with biomedical topics by text and data mining. Nucleic Acids Res. 2014 Jul;42(Web Server issue):W422-9. doi:10.1093/nar/gku432 . Epub 2014 May 16. 24838570.
  • Stachelscheid H, Seltmann S, Lekschas F, Fontaine JF, Mah N, Neves M, Andrade-Navarro MA, Leser U, Kurtz A. CellFinder: a cell data repository. Nucleic Acids Res. 2014 Jan;42(Database issue):D950-8. doi:10.1093/nar/gkt1264 . Epub 2013 Dec 3. 24304896 .
  • 2013

  • Rodríguez-Seguel E, Mah N, Naumann H, Pongrac MI, Cerdá-Esteban N, Fontaine JF, Wang Y, Chen W, Andrade-Navarro MA, Spagnoli MF. Mutually exclusive signaling signatures define the hepatic and pancreatic progenitor cell lineages divergence. Genes Dev. 2013 Sep 1;27(17):1932-46. 24013505 . doi:10.1101/gad.220244.113 .
  • Seltmann S, Stachelscheid H, Damaschun A, Jansen L, Lekschas F, Fontaine JF, Nguyen-Dobinsky TN, Leser U, Kurtz A. CELDA - an ontology for the comprehensive representation of cells in complex systems. BMC Bioinformatics. 2013 Jul 17;14:228. 23865855. doi:10.1186/1471-2105-14-228 .
  • Neves M, Damaschun A, Mah N, Lekschas F, Seltmann S, Stachelscheid H, Fontaine JF, Kurtz A, Leser U. Preliminary evaluation of the CellFinder literature curation pipeline for gene expression in kidney cells and anatomical parts. Database (Oxford). 2013 Apr 18;2013(0):bat020. Print 2013. 23599415.
  • Jacques C, Guillotin D, Fontaine JF, Franc B, Mirebeau-Prunier D, Fleury A, Malthiery Y, Savagner F. DNA Microarray and miRNA Analyses Reinforce the Classification of Follicular Thyroid Tumors. J Clin Endocrinol Metab. 2013 May;98(5):E981-9. 23569218. doi:10.1210/jc.2012-4006
  • Ortuño FM, Rojas I, Andrade-Navarro MA, Fontaine JF. Using cited references to improve the retrieval of related biomedical documents. BMC Bioinformatics. 2013 Mar 27;14(1):113. 23537461. doi:10.1186/1471-2105-14-113 . (Highly accessed, featured in the Effective Health Care Program's weekly article alert (see it in SRCMethodsLibrary)).
  • Mirebeau-Prunier D, Le Pennec S, Jacques C, Fontaine JF, Gueguen N, Boutet-Bouzamondo N, Donnart A, Malthièry Y, Savagner F. Estrogen-Related Receptor Alpha Modulates Lactate Dehydrogenase Activity in Thyroid Tumors. PLoS ONE. 2013; 8(3):e58683. 23516535. doi:10.1371/journal.pone.0058683
  • Rousselle A, Qadri F, Leukel L, Yilmaz R, Fontaine JF, Sihn G, Bader M, Ahluwalia A, Duchene J. CXCL5 limits macrophage foam cell formation in atherosclerosis. J Clin Invest. 2013 Mar 1;123(3):1343-7. 23376791. doi:10.1172/JCI66580
  • Schaefer MH, Lopes TJ, Mah N, Shoemaker JE, Matsuoka Y, Fontaine JF, Louis-Jeune C, Eisfeld AJ, Neumann G, Perez-Iratxeta C, Kawaoka Y, Kitano H, Andrade-Navarro MA. Adding protein context to the human protein-protein interaction network to reveal meaningful interactions. PLoS Comput Biol. 2013 Jan;9(1):e1002860. doi:10.1371/journal.pcbi.1002860 . Epub 2013 Jan 3. 23143269.
  • Suter B, Fontaine JF, Yildirimman R, Raskó T, Schaefer MH, Rasche A, Porras P, Vázquez-Álvarez BM, Russ J, Rau K, Foulle R, Zenkner M, Saar K, Herwig R, Andrade-Navarro MA, Wanker EE. Development and application of a DNA microarray-based yeast two-hybrid system. Nucleic Acids Res. 2013 Feb 1;41(3):1496-507. doi: 10.1093/nar/gks1329. Epub 2012 Dec 28. 23275563 . (NAR Feature Article)
  • 2012

  • Schaefer MH, Fontaine JF, Vinayagam A, Porras P, Wanker EE, Andrade-Navarro MA. HIPPIE: Integrating Protein Interaction Networks with Experiment Based Quality Scores. PLoS One. 2012;7(2):e31826. Epub 2012 Feb 14. 22348130
  • 2011

  • Barbosa-Silva A, Fontaine JF, Donnard ER, Stussi F, Ortega JM, Andrade-Navarro MA. PESCADOR, a web-based tool to assist text-mining of biointeractions extracted from PubMed queries. BMC Bioinformatics. 2011 Nov 9;12(1):435. 22070195. (Highly accessed)
  • Lopes TJ, Schaefer M, Shoemaker J, Matsuoka Y, Fontaine JF, Neumann G, Andrade-Navarro MA, Kawaoka Y, Kitano H. Tissue-specific subnetworks and characteristics of publicly available human protein interaction databases. Bioinformatics. 2011 Sep 1;27(17):2414-2421. 21798963.
  • Frahm S, Slimak MA, Ferrarese L, Santos-Torres J, Antolin-Fontes B, Auer S, Filkin S, Pons S, Fontaine JF, Tsetlin V, Maskos U, Ibañez-Tallon I. Aversion to Nicotine Is Regulated by the Balanced Activity of β4 and α5 Nicotinic Receptor Subunits in the Medial Habenula. Neuron. 2011 May 12;70(3):522-35. 21555077.
  • Krallinger M, Vazquez M, Leitner F, Salgado D, Chatr-Aryamontri A, Winter A, Perfetto L, Briganti L, Licata L, Iannuccelli M, Castagnoli L, Cesareni G, Tyers M, Schneider G, Rinaldi F, Leaman R, Gonzalez G, Matos S, Kim S, Wilbur WJ, Rocha L, Shatkay H, Tendulkar AV, Agarwal S, Liu F, Wang X, Rak R, Noto K, Elkan C, Lu Z, Dogan RI, Fontaine JF, Andrade-Navarro MA, Valencia A. The Protein-Protein Interaction tasks of BioCreative III: classification/ranking of articles and linking bio-ontology concepts to full text. BMC Bioinformatics. 2011 Oct 3;12 Suppl 8:S3 (22151929. doi:10.1186/1471-2105-12-S8-S3).
  • Fontaine JF, Priller F, Barbosa-Silva A, Andrade-Navarro MA. Génie: literature-based gene prioritization at multi genomic scale. Nucleic Acids Res. 2011 Jul;39(Web Server issue):W455-61. doi:10.1093/nar/gkr246 . Epub 2011 May 23. 21609954.
  • Fontaine JF, Suter B and Andrade-Navarro MA. QiSampler: evaluation of scoring schemes for high-throughput datasets using a repetitive sampling strategy on gold standards. BMC Research Notes 2011, 4:57. 21388526 . doi:10.1186/1756-0500-4-57 .
  • 2010

  • Barbosa-Silva, A., Soldatos TG, Magalhães, ILF, Pavlopoulos, GA, Fontaine, J.F., Andrade-Navarro, M.A., Schneider R., Ortega, JM. LAITOR: Literature assistant for identification of terms co-occurrences and relationships. BMC Bioinformatics. 2010 Feb 1;11(1):70. 20122157 . doi:10.1186/1471-2105-11-70 . (Highly accessed)
  • 2009

  • Raharijaona M, Le Pennec S, Poirier J, Mirebeau-Prunier D, Rouxel C, Jacques C, Fontaine JF, Malthiery Y, Houlgatte R, Savagner F. PGC-1-Related Coactivator Modulates Mitochondrial-Nuclear Crosstalk through Endogenous Nitric Oxide in a Cellular Model of Oncocytic Thyroid Tumours. PLoS ONE. 2009; 4(11): e7964. 19956726 . doi:10.1371/journal.pone.0007964 .
  • Fontaine JF, Mirebeau-Prunier D, Raharijaona M, Franc B, Triau S, Rodien P, Goëau-Brissonniére O, Karayan-Tapon L, Mello M, Houlgatte R, Malthièry Y and Savagner F. Increasing the number of thyroid lesions classes in microarray analysis improves the relevance of diagnostic markers. PLoS ONE. 2009 Oct 29;4(10):e7632. 19893615 . doi:10.1371/journal.pone.0007632 .
  • Fontaine JF, Barbosa-Silva A, Schaefer M, Huska MR, Muro EM and Andrade-Navarro MA. MedlineRanker: Flexible Ranking of Biomedical Literature. Nucleic Acids Research 2009, 37: W141-W146. 19429696 . doi:10.1093/nar/gkp353 .
  • Jacques, C.*, Fontaine, J.-F.*, Franc, B., Mirebeau, D., Triau, S., Savagner, F., Malthiery, Y.: Death-associated protein 3 is overexpressed in human thyroid oncocytic tumors. British Journal of Cancer. 2009 Jul 7; 101(1): 132-8. 19536094 . doi:10.1038/sj.bjc.6605111 .
  • Before 2009

  • Fontaine JF, Mirebeau-Prunier D, Franc B, Triau S, Rodien P, Houlgatte R, Malthièry Y, Savagner F. Microarray analysis refines classification of non-medullary thyroid tumours of uncertain malignancy. Oncogene. 2008 Apr 3;27(15):2228-36. Epub 2007 Oct 29. 17968324 . doi:10.1038/sj.onc.1210853 .
  • Lambert A, Legendre M, Fontaine JF, Gautheret D. Computing expectation values for RNA motifs using discrete convolutions. BMC Bioinformatics. 2005 May 13;6:118. 15892887 . doi:10.1186/1471-2105-6-118 .
  • Lambert A, Fontaine JF, Legendre M, Leclerc F, Permal E, Major F, Putzer H, Delfour O, Michot B, Gautheret D. The ERPIN server: an interface to profile-based RNA motif identification. Nucleic Acids Res. 2004 Jul 1;32(Web Server issue):W160-5. 15215371 . doi:10.1093/nar/gkh418 .

* Authors have contributed equally.

Publications in meeting proceedings

  • Jan Aerts, Jean-Fred Fontaine, Michael Lappe, Raghu Machiraju, Cydney Nielsen, Andrea Schafferhans, Svenja Simon, Matt Ward, and Jarke J. van Wijk. Sequence Data Visualization. Biological Data Visualization (Dagstuhl Seminar 12372), Dagstuhl Reports 2013 Feb 20; 2(9):143-147 (doi:10.4230/DagRep.2.9.131)
  • Miriah Meyer, Jan Aerts, Dan Evanko, Jean-Fred Fontaine, Martin Krzywinski, Raghu Machiraju, Kay Nieselt, Jos Roerdink, and Bang Wong. A Framework for Effective Visualization Design. Biological Data Visualization (Dagstuhl Seminar 12372). Dagstuhl Reports 2013 Feb 20; 2(9):152-153 (doi:10.4230/DagRep.2.9.131)
  • Fontaine, J.F., Andrade-Navarro, M.A. Fast classification of scientific abstracts related to protein-protein interaction using a naïve Bayesian linear classifier. The proceedings for the BioCreative III Workshop, 2010, Bethesda, Maryland, USA. (ISBN: 978-1-4507-3685-5). Pages 67-72.

Other publications

  • Fontaine JF, Malthièry Y and Savagner F. Microarrays et tumeurs thyroïdiennes de potentiel de malignité incertain. Médecine Clinique endocrinologie & diabète, n°58, Mai-Juin 2012

Patent

  • Houlgatte R, Franc B, Fontaine JF, Malthiery Y and Savagner F (2009): Methods for the prognosis or for the diagnosis of a thyroid disease. European Patent Office, EP2132329.

Professional activities

  • Editor-in-chief: Genomics and Computational Biology, a peer reviewed and open-access biomedical journal.
  • Associate editor: BMC Research Notes.
  • Program Committee and chairman: International Work-Conference on Bioinformatics and Biomedical Engineering (IWBBIO 2013 to 2016).
  • Referee for Scientific Journals: Bioinformatics, BMC Medical Informatics and Decision Making, BMC Research Notes, BMC Bioinformatics, Nucleic Acids Research.

Talks

To be updated.

  • Fontaine, J.-F. (2013): Text and Data Mining for Biomedical Research. The Perfect Swell: Text and Data Mining for Data Driven Innovation. British Library, London, United Kingdom. Sept 27.
  • Fontaine, J.-F. (2011): Genie: literature-based gene prioritization at multi genomic scale. Fouille de texte pour la biologie. Amphithéatre IRI-IRCICA, Campus CNRS de la Haute-Borne, University of Lille 1, Villeneuve d'Ascq, France. Sept 22. Links: event, abstract and slides.
  • Fontaine, J.-F. and Andrade-Navarro, MA. (2010): Orthology-based phenotypic inference from disease models to human applications. Third Annual Meeting of the German National Genome Research Network (NGFN) NGFN-Plus and NGFN-Transfer in the Program of Medical Genome Research. Henri Ford building, Berlin, Germany. Nov 25-27
  • Fontaine, J.-F. and Andrade-Navarro, MA. (2010): Manual annotations from biological databases improve text-mining-based prioritization of human genes. Workshop on Advances in Bio Text Mining. VIB life sciences research institute, Ghent University, Ghent, Belgium. May 10-11
  • Spruth, E.J., Fontaine, J.-F., Priller, J., Neumann, B. and Andrade, MA. (2009): Phenotype descriptions for neurodegenerative diseases. Neuronet fourth project meeting, German National Genome Research Network (NGFN). DKFZ communications center, Heidelberg, Germany, December 4-5
  • Fontaine, J.-F., Barbosa-Silva, A., Muro, EM. & Andrade-Navarro, MA. (2009): Connecting genes to diseases by text mining and data integration. Status Seminar of the Helmholtz Alliance on Systems Biology. Heidelberg, Germany, October 26-27
  • Fontaine, J.-F., Barbosa-Silva, A. & Andrade-Navarro, MA. (2009): Data integration & generation of phenotype-protein-drug networks of neurodegenerative diseases. Neuronet third project meeting, German National Genome Research Network (NGFN). Lindow, Germany, June 5-6
  • Fontaine, J.-F., Savagner, F., Mirebeau, D., Raharijaona, M. , Houlgatte, R., Franc, B. & Malthièry, Y. (2007): How molecular exploration of 11 classes of follicular thyroid lesions improves the classification of tumour of uncertain malignant potential. 32th Annual Meeting of the European Thyroid Association. Leipzig, Germany. September 1-5 (Horm Res 2007;68(Suppl.3):36) (doi:10.1159/000107669)

Posters

To be updated.

  • Fontaine JF and Andrade-Navarro MA. Mining the biomedical literature to predict associations of chemicals and drugs with cancer. Systems Medicine in Cancer Meeting 2013, June 14-15, Berlin, Germany. 2013
  • Mah N, Fontaine JF, Andrade-Navarro MA. Uncovering markers of cell identity change from transcriptome profiles. RNA 2013, The 18th Annual Meeting of the RNA Society, Congress Center Davos, June 11-16, Davos, Switzerland. 2013
  • Mah N, Fontaine JF, Andrade-Navarro MA. Uncovering markers of cell identity change from transcriptome profiles. Cancer Day 2012, Max Delbrück Center for Molecular Medicine, Nov-14, Berlin, Germany. 2012
  • Schaefer M., Lopes T., Mah N., Shoemaker J., Matsuoka Y., Fontaine J., Louis-Jeune C., Eisfeld A., Neumann G., Perez-Iratxeta C., Kawaoka Y., Kitano H., Andrade-Navarro M. Adding protein context to the human protein-protein interaction network to reveal meaningful interactions. ECCB'12 - European Conference on Computational Biology 2012, September 9-12, Basel, Switzerland, 2012.
  • de Oliveira KAP , Kaergel E , Patone G , Heinig M , Fontaine JF , Hummel M , Andrade M , Huebner N and Scheidereit. NF‐κB‐subunit specific gene networks in Hodgkin’s lymphoma. Meeting: NF-kappaB Signaling and Biology: From Bench to Bedside (X1), March 18-23 Whistler Conference Centre, Whistler, British Columbia Canada, 2012.
  • Martin Schaefer, Jean-Fred Fontaine, Arunachalam Vinayagam, Pablo Porras, Erich E. Wanker, Miguel A. Andrade-Navarro. Integrating protein interaction networks with experiment based quality scores. RECOMB::DREAM. Barcelona, Spain. Oct 14 - 19, 2011.
  • A Barbosa-Silva1, J-F Fontaine, ER Donnard, F Stussi, JM Ortega, MA Andrade-Navarro. Efficient network curation using the text-mining web tool Pescador. X-meeting 2011 (AB3C / SoIBio). Florianopolis SC, Brazil. October 12-15, 2011.
  • Mirebeau-Prunier D, Le Pennec S, Jacques C, Fontaine JF, Gueguen N, Donnart A, Bouzamondo N, Malthièry Y, Savagner F. Estrogen-related receptor alpha modulates a key enzyme of glycolysis : the lactate dehydrogenase. Auditorium Maximum of the Jagiellonian University Krupnicza Str 33 31-126 Kraków Poland, September 10-14, 2011.
  • Schaefer M, Lopes TJS, Russ J, Fontaine JF, Vinayagam A, Porras-Milan P, Kitano H, Wanker EE and Andrade-Navarro MA. HIPPIE: a web tool for querying the human interactome and evaluating experimental PPI screens. ISMB/ECCB. Vienna, Austria, July 17 - 19, 2011.
  • Spruth, E.*, Fontaine, J.F.*, Andrade-Navarro, M.A., Priller, J. Phenome descriptions of neurodegenerative diseases. Congress of the German Society for Psychiatry and Psychotherapy (DGPPN). International Congress Center Berlin (ICC Berlin), Berlin, Germany, Nov 24-27, 2010.
  • Muro, E.M., Fontaine, J.F. and Andrade-Navarro, M.A. Alternative splicing as a marker of disease. 9th European Conference on Computational Biology. Ghent, Belgium, September 26-29, 2010.
  • Fontaine, J.F., A. Barbosa-Silva, E. Spruth, J. Priller, M.A. Andrade-Navarro. Hypothesis generation for neurodegenerative diseases pathogenesis by text mining. Mid-term review. Helmholtz Alliance on Systems Biology. DKFZ communications center, Heidelberg, Germany, January 13-14, 2010.
  • Muro, E.M., Fontaine, J.F. and Andrade-Navarro, M.A. Alternative splicing and disease. Mid-term review. Helmholtz Alliance on Systems Biology. DKFZ communications center, Heidelberg, Germany, January 13-14, 2010.
  • Kärgel, E., Patone G., Saar K., Fontaine J.-F. , Muro E., Hübner N., Andrade M., Scheidereit C. Study of the non-canonical activation pathway of NF-kB at a genome-wide level. Mid-term review. Helmholtz Alliance on Systems Biology. DKFZ communications center, Heidelberg, Germany, January 13-14, 2010.
  • Ramminger, E., A. Barbosa, J.F. Fontaine, K. Scharf, J. Russ, A. Vinayagam, R. Kalis, C. Hänig, M.A. Andrade-Navarro, E.E. Wanker. Connecting human proteins to APP by systematic interaction mapping. Mid-term review. Helmholtz Alliance on Systems Biology. DKFZ communications center, Heidelberg, Germany, January 13-14, 2010.
  • Fontaine, J.-F., Barbosa-Silva, A., Spruth E., Priller J. & Andrade-Navarro, MA. (2009): Hypothesis generation for neurodegenerative diseases pathogenesis by text mining. 2nd Annual Meeting of NGFN-Plus and NGFN-Transfer in the Program of Medical Genome Research and 8th annual meeting of the German National Genome Research Network (NGFN). Henry-Ford building (Free University). Berlin, Germany, November 28-30, 2009.
  • Muro, EM., Fontaine, J.-F. & Andrade-Navarro, MA. (2009): Analysis of non-coding RNA function and evolution. 2nd Annual Meeting of NGFN-Plus and NGFN-Transfer in the Program of Medical Genome Research and 8th annual meeting of the German National Genome Research Network (NGFN). Henry-Ford building (Free University). Berlin, Germany, November 28-30, 2009.
  • Porras-Millán, P., A. Haug, R. Kalis, T. Rasko, K. Rau, M. Zenkner, J.F. Fontaine, M. Andrade, E. Wanker. An interaction network links proteins from the ubiquitin proteasome system to neurodegenerative disease processes. 2nd Annual Meeting of NGFN-Plus and NGFN-Transfer in the Program of Medical Genome Research and 8th annual meeting of the German National Genome Research Network (NGFN). Henry-Ford building (Free University). Berlin, Germany, November 28-30, 2009.
  • Fontaine, J.-F., Barbosa-Silva, A. & Andrade-Navarro, MA. (2009): Prioritization of scientific abstracts for biomedical research, Open Days in Biology, Computer Science and Mathematics, Nantes, France, June 9-11
  • Fontaine, J.-F., Barbosa-Silva, A. & Andrade-Navarro, MA. (2008): Ranking the biomedical literature for optimised experimental designs, First Annual Meeting NGFN-Plus and NGFN-Transfer in the Program of Medical Genome Research, Munich, Germany, December 12-13
  • Fontaine, J.-F., Savagner, F., Mirebeau, D., Raharijaona, M., Franc, B., Houlgatte, R. & Malthièry, Y. (2007): Gene-expression based functional analysis and classification of thyroid tumours, 34th Young Researcher Forum, Ile des Embiez, France, October 15-19
  • Fontaine, J.-F., Savagner, F., Mirebeau, D., Raharijaona, M., Franc, B., Houlgatte, R. & Malthièry, Y. (2007): Molecular classification of the follicular thyroid lesions by microarray data, 32nd FEBS Congress, Vienna, Austria, July 5-7
  • Fontaine, J.-F., Savagner, F., Melo, M., Ballester, B. , Houlgatte, R., & Malthièry, Y. (2006): Transcriptomic analysis of the oncocytic signal in vesicular thyroid tumours, European Congress of Endocrinology, Glasgow, UK, April 1-5 (Endocrine Abstracts (2006) 11 P888)
  • Fontaine, J.-F., Savagner, F., Melo, M., Ballester, B., Houlgatte, R. & Malthièry, Y. (2005): Transcriptional analysis of the oncocytic signal in vesicular thyroid tumours, Annual congress of the French society of biochemistry and molecular biology, Nantes, France, October 24-26
  • Fontaine, J.-F., Savagner, F., & Malthièry, Y. (2005): High-throughput functional analysis of thyroid tumors, Angers University Forum, Angers, France, June 16
  • Legendre, M., Lambert, A., Fontaine, J.-F., & Gautheret, D. (2004): Profile-based RNA motif identification using the ERPIN Web Server. Fifth Open Days in Biology, Computer Science and Mathematics, Montréal, Canada, June 28-30.
  • Offmann, B., Fontaine, J.-F., & Cadet, F. (2002): BISAR, a java tool for the Fourier analysis of biological sequences. Third Open Days in Biology, Computer Science and Mathematics, Saint-Malo, France, June 10-12

* Authors have contributed equally to this work.

Ph.D thesis in French

  • Fontaine JF (2007): Caractérisation et classification moléculaire des pathologies thyroïdiennes par approche transcriptomique. Université d'Angers. Manuscript on the HAL server.

Teaching

  • 2003-2007 (assistant professor): Computer science and Bioinformatics, University of Angers, France
  • 3 days R/Bioconductor course for biologists, Max Delbrück Center, Berlin.
    • Introduction to R
    • Introduction to Bioconductor

Student supervisions

  • Master project (3 months, 2015-2016): analysis of ChIP-seq data.
  • Master internship (3 months, 2015): integration of NGS data.
  • Master student (4 weeks, 2015): analysis of NGS data.
  • Master internship (3 months, 2013): benchmarks for drug prediction methods.
  • Master internship (3 months, 2013): sequence analysis for phosphorylation sites.
  • Ph.D. internship (3 months, 2011): text mining on full text articles.
  • Bachelor internship (6 weeks, 2011): web services for text mining.
  • Master internship (3 months, 2011): automatic cutoff computations for QiSampler.
  • Many short undergraduate students projects (2003-2007): computer Science.