Fouzia Moussouni-Marzolf

Contact Information

INSERM UMR U991 "Foie, Métabolismes et Cancer"
Tel :  +33 2 99 54 74 07
Fax : +33 2 99 54 01 37
Email: fouzia.moussouni_at_univ-rennes1.fr
Web https://perso.univ-rennes1.fr/fouzia.moussouni/ (French only)


Education

1993-1997
        PhD, Université Paris XIII, France
        Thesis title: “Design and specification of parallel string searching algorithms”
        Reviewers :
        Pr. Maxime Crochemore, Université Marne-La-vallée
        Pr Jean-Frédéric Myoupo, Université D’Amiens.
1991-1992
        Research Master thesis, Université Montpellier II.
        Subject: Interoperability in multi-database systems: Modeling via petri-nets.
1985-1990
        Engineer Diploma in Informatics,
        University of Sciences and Technologies, Algiers.


Professional Experience in Research

Oct/1999 - present
                 Associate professor in Bioinformatics at Université de Rennes1 (Maître de
                 Conférences). Member of INSERM U991 - Group "Iron and Liver : physiological and pathologoical aspects"        

09/2003 – 02/2004 and 09/2004 – 12/2004 and 11/2011
                 Visiting research position in Berlin, Humboldt University,
                 funded by the European Science Foundation (ESF)
               
02/1998- 10/1999
                Post-doctoral researcher (Research Associate)
                Information Management Group, Computer Science Department,
                Manchester University, UK.

1994-1996
               Research & Teaching assistant (ATER) at LIPN.
               Université Paris XIII, Paris, France.  

03/2004 birth of son Kateb Marzolf
08/2009 birth of son Yannis Marzolf

Research Interests


METHODOLOGIES:  
  • Database management systems
  • Formal modeling of knowledge devoted to molecular biology, (inc. relational, object-oriented, ontology-based and description logic).
  • Systematic integration issues for building scientific data warehouse systems
  • Data quality awareness during the process of data integration from multiple bio-web resources
  • Design of formal bio-ontologies: classifying, querying, and reasoning using formal specifications.
  • Extraction of patterns of biological entities over time using text mining techniques.  

APPLICATION AREAS:

  • Transcriptome analysis, specific to a genome, organ or a pathology: design of GEDAW and GIMS [3,4,11,17,19].
  • Medical informatics and bio-medical Knowledge interoperability to better assist the analysis of pathology specific DNA-chips [7,9,12] : design of BioMeke, a joint work with EA-3888, currently Inserm U936
  • Database profiling tools for data quality evaluation [1,2,5]  (design of QDex)
  • Modeling, specification and exploration of iron metabolism and relative diseases.
  • Extracting and building an integrated rich Lexics on iron metabolism from literature, using text mining techniques.


Teaching Activities

Postgradutes courses – Master

  • Data and Knowledge bases in a Biomedical context.
  • UML modeling for medical informatics master.
  • Scientific Datawarehousing.
  • Algorithmics for Bioinformatics Master.

Graduate Courses

  • Concepts and techniques for databases design.
  • Parallel string searching algorithms – practical training.

Undergraduate courses

  • Programming courses using python, C++ and Java.

Research Activities

Supervision


Boris Michenski, Pierre Le Marre, Bertrand Ameline-de-Cadeville, Mario Albrecht (in Manchester), Emilie Guérin (PhD Inserm U522), Nicolas Cauvet, Gwenaelle Marquet , Blandine Lainé, Anne Arcade, Nicolas Cauvet, Olivier Pareige, Karine Thiéry, Laurent Hennion, Gwenegan Rozé, Nicolas Lebreton, Hoel Saout, Nicolas Schnel

Membership

Past member of the ISIBio working group (Information System Integration in Biology). ISIBIO is an ACI IMPbio (jan 2004 - dec 2008).  In the context of ISIBio, several events were organised, including DILS 2008 (Data Integration in Life Science) in Paris-Evry (DILS 2007 took place in Pennsylvania and DILS 2006 in Cambridge)

Member of the national bioinformatics network “GDR Bioinformatique Moléculaire CNRS 3003”.

Génopole-Grand-Ouest : early member of Bioinformatics and Transcriptome platforms

IFR140 : Member of REGIvivis : Réseaux d’expression génétique, in vivo, in vitro et in silico.


In-House Commitees

Hiring committee   univ Rennes1

Postgraduate School  VAS


Conference Program Commitees

PC poster session,  ECCB - 2014 in Strasbourg.

NETTAB-2012 Supplement

Co-organisation de EIC-2012 "European Iron Club",  in Rennes.

Co-organisation Journée MOQA, joint to JOBIM 2010 – Méta Données et Ontologies pour la Qualité des Annotations

DILS 2008 (Data Integration in the Life Sciences)

WISE 2007 workshop - Approaches and Architectures for Web Data Integration and Mining in Life Sciences.

ICIQ 2006 (Int. Conf. On Information Quality), organised yearly by the MIT.


Publications

More recent papers / communications :

Moussouni F, Berti-Equille L, (2013) "Cleaning, Integrating and Warehousing Genomic Data from Biomedical Resources", in Biological Knowledge Discovery Handbook, Wiley Series on Bioinformatics, IEEE Computer Society.

Moussouni F, AMELINE-DE-CADEVILLE B, LESER U and LOREAL O, (2012) "Retrospective Analysis of a Gene by Mining Texts: The Hepcidin gene use-case”, in JOBIM 2012

Amedline-De-Cadeville B., Loréal O and Moussouni-Marzolf F, (2012) "Time-based Retrospective Analysis of Hepcidin Gene by Mining Texts", Poster presented at the European Iron Club, EIC-2012, Rennes.

[1] Moussouni F, Berti-Equille L, Rozé G, Loréal O and Guérin E (2007) Q-DEX: A database profiler for generic bio-data exploration and quality aware integration. Int. Conf. on Web Information Systems Engineering WISE 2007 Workshops. Paru dans Lecture Notes in Computer Sciences 4832: 5-16.

[2] Rozé G., Moussouni F. and  Berti-Equille L. (2007), QDEX : a Quality Based Biomedical Data Profiling and Exploration, ISMB/ECCB 2007 Vienna. Poster Abstract.

[3] Guérin E, Marquet G, Chabalier J, Troadec MB, Guguen-Guillouzo C, Loréal O, Burgun A, Moussouni F. Combining biomedical knowledge and transcriptomic data to extract new knowledge on genes, online Journal of Integrative Bioinformatics, 3(2) 2006.

[4] Guérin E, Marquet G., Burgun, A, Loréal, O, Berti-Equille, L, Leser U, Moussouni, F. Integrating and warehousing liver gene expression data and related biomedical resources in GEDAW. DILS 2005, San Diego, paru dans Lecture Notes in Bioinformatics, 2005, 3615, 158-174.

[5] Berti-Equille L, Moussouni F, Quality-Aware Integration and Warehousing of Genomic Data. Proc. of the 10th Intl. Conference on Information Quality (IQ’05), Massachusetts Institute of Technology, Cambridge, U.S.A. (2005)

[6] Guérin E, Marquet G, Burgun A, Loréal O,  Moussouni F, GEDAW : un environnement intégré pour l’analyse du transcriptome, In  « Ontologie, Grille et intégration Sémantique pour la Biologie », Journée satellite de JOBIM 2005

[7] Marquet G, Burgun A, Moussouni F, Guérin E, Le Duff F, Loréal O. BioMeKe: an ontology-based biomedical knowledge extraction system devoted to transcriptome analysis. Journal of Studies in Health Technology and Informatics (2003); 95:80-5.

[8] Guérin E, Moussouni F, Courselaud B, Loréal O, Modélisation d’un entrepôt de données dédié à l’analyse du transcriptome hépatique, Actes de JOBIM 2002 - Journée Ouverte Biologie Informatique et Mathématiques – Saint-Malo.

[9] Burgun A, Bodenreider O, Le Duff F, Moussouni F, Loréal O, Representation of roles in biomedical ontologies : a case study in functional genomics, American Medical Informatics Association conference, AMIA 2002.

[10] Paton, N.W., Khan, S.A., Hayes, A., Moussouni, F., Brass, A., Eilbeck, K., Goble, C.A., Hubbard, S. and Oliver, S.G., Conceptual Modelling of Genomic Information, Reparution au Yearbook of Medical Informatics, R. Haux and C. Kulikowski (eds), 610-619, Schattauer, 2002.

[11] Berti-Equille L, Moussouni F, Arcade A, (2002), Integration of biological data on transcriptome. Revue Ingénierie des Systèmes d’Information (ISI). Aux Editions Hermès.

[12] Moussouni F, Burgun A, Le Duff F, Guérin E, Loréal O, (2002), Respective contributions of MGED, GeneOntology and UMLS for transcriptome analysis. « from Genotype to Phenotype: Linking Bioinformatics and Medical Informatics Ontologies » workshop. Meeting Review in Comparative and Functional Genomics J (2002); 3: 447–450.

[13] Marquet G, Burgun A, Moussouni F, Guérin E, Loréal O, An integrative approach of biomedical knowledge via ontologies for liver transcriptome analysis -  Poster on Abstract, Workshop on Ontology for biology, Heidelberg, Nov 7-8 2002

[14] Guérin E, Moussouni F, (2001), Transcriptome hépatique : modélisation par une approche UML, aux cahiers du numérique, N° Spécial : L’information médicale numérique. Vol 2 – N°2-2001. Aux éditions Hermès.

[15] Guérin E, Moussouni F, Berti-Equille L, (2001), Intégration de données sur le transcriptome. Actes de la journée de travail bi-thématique du GDR-PRC I3. Dec 2001.

[16] Moussouni F, Berti-Equille L, (2001), Ontologies and mapping rules for merging data from public databanks and gene expression experiments, Communication on Abstract submission,  Colloque "Ontologie et Biologie Moléculaire", INRIA-Alpes, Grenoble.

[17] N.W. Paton, S. Khan, A. Hayes, F. Moussouni , A. Brass, K. Eilbeck, C.A. Goble, S. Hubbard, S.G. Oliver. (2000) Conceptual Modelling on Genomic Information. Bioinformatics journal, Vol 16, No 6, 548-558.

[18] Norman W. Paton, Shakeel A. Khan, Andy Hayes, F. Moussouni, Michael J. Cornell, Karen Eilbeck, Andy Brass, Carole A. Goble, Stephen H. Oliver, (2000); GIMS - Genome Information Management System. In Intelligent System in Molecular Biology, Poster abstract ISMB 2000.

[19] F. Moussouni, N. W.Paton, A. Hayes, S. Oliver, C. Goble, A. Brass. (1999) Database Challenges for Genome Information in the Post Sequencing Phase. In proc. of the 10th international conference on databases and expert systems applications DEXA’99, Lecture Notes in Computer Science, Vol 1677 pp 540-549.

[20] F. Moussouni, C. Lavault. (1998) Optimal Pattern Matching on d-Dimensional Meshes : Generalize, In proc. of the International Conference on Principals of Distributed Systems (OPODIS). Aux éditions Hermès.

[21] F. Moussouni, C. Lavault. (1996) Distributed string matching algorithm on the N-cube, In proc. of the International-European Conference on Parallelism, EUROPAR’96, Lyon France, appeared in Lecture Notes in Computer Science, vol-1123, pp 832-835.

[22] F. Moussouni. Reconnaissance parallèle de motifs sur l’hypercube, (1995) Dans la revue "Parallélisme Réseaux et Répartition" de la série "Protocoles et programmation dans les réseaux", pp 121-140, Aux éditions HERMES. (version parus aussi en rapport interne)

[23] C.Lavault, F. Moussouni. (1995) N-cube string matching algorithm with long texts, In proc. of the 8th Combinatorics and Computer Science Conference, CCS’95 Brest-France 1995, appeared in Lecture Notes in Computer Science, vol-1120, pp 328-340.

[24] F. Moussouni. (1994) Reconnaissance de motifs sur machines à mémoires distribuées, Dans les actes des 6èmes Rencontres Francophones en Parallélisme RENPAR’94, pp 328