CURRICULUM vitae

CURRICULUM vitae
Nicolas TURENNE
LISIS (UMR)
Université Paris-Est
Cité Descartes, 5, boulevard Descartes
Champs-sur-Marne
77454 Marne-la-Vallée Cedex 02
France
Position held
Phone: (33) 1-60-95-71-20
Cell: (33) 6-70-79-51-24
E-mail: [email protected]
http://www.cortext.net/
http://www.inra-ifris.org/
 LISIS (UMR) – Université Paris Est, Paris Area
Tenure Research scientist
Text & Knowledge Analytics group
January 2015
 INRA SenS unit – Université Paris Est, Paris Area
Tenure Research scientist
Text & Knowledge Analytics group
January 2011-December 2014
 INRA MIG unit, Paris Area
Tenure Research scientist
Text & Knowledge Analytics group
January 2004-December 2010
 INRA MIAJ unit, Paris Area
Assistant Research scientist
MegaDim group
April 2003-December 2003
Visting Fellow
 INRA Metarisk unit, Paris Area
Assistant Research scientist
Knowledge Analytics group
September 2001-March 2003
Education
 Institute of Cytology and Genetics (ITSIG SB-RAN), Novosibirsk Russia
Visiting research scientist
Structural Biology and Text Mining group
September 2010-December 2010
 University of Strasbourg, France
Ph.D. in Computational Linguistics and Statistical Learning.
Knowledge and Data Mining group, November 2000.
 University of Strasbourg, France
Diploma [M.Sc.] in Multivariate Analysis and Data Processing in Astrophysics, July
1994.
 Paul Sabatier University (Toulouse 3), France
Diploma [B.Sc.] in Physics, July 1991.
Research
Interests
Real-world social and information networks, their evolution. Organization, discovery and
usage of knowledge. My research problems are motivated by datasets in digital humanities,
and usage of computational linguistics and machine learning techniques.
Selected Honors
and Awards
 Best paper award, Text Mining Workshop at EMCSR, Vienna (Autria) 2002.
Publications
 submitted
TURENNE N. and PHAN T.T. x.ent: R Package for Entities and Relations Extraction
based on Unsupervised Learning and Document Structure, 25 pages, 2015.
TURENNE N., ANDRO M., CORBIERE R. and PHAN T.T. Open Data Platform for
Knowledge Access in Plant Health Domain : VESPA Mining, 5 pages, 2015
 Journals
TURENNE N Clustering and Relational Ambiguity: from Text Data to Natural Data
jdmdh:13 - Journal of Data Mining & Digital Humanities, June 24, 2014.
CETRO R., BARBIER M., BREUCKER Ph, EGGERMONT H., GAMBETTE Ph.,
KYRIACOPOULOU T., LE ROUX X., MARTINEAU C., TURENNE N. Approche
semi-automatique pour la définition de motifs d'argumentation d’un corpus de projets
scientifiques du domaine de la biodiversité », Revue des Nouvelles Technologies
de l'Information RNTI-SHS-2, "Fouilles de données et humanités numériques", p. 4780.
TURENNE N., TIYS E., IVANISENKO V., YUDIN N., IGNATIEVA E., VALOUR
D., DEGRELLE S.A., HUE I., “Finding Biomarkers in Non-Model Species :
Literature Mining of Transcription Factors involved in Bovine Embryo Development”,
Journal of Bio Data Mining , 2012, 5:12 .
HUE I, DEGRELLE SA, TURENNE N. Conceptus elongation in cattle : genes,
models and questions. Anim Reprod Sci. 2012 Sep ;134(1-2):19-28.
TURENNE N. Role of a web-based software platform for systems biology. J Comput
Sci Syst Biol. 2011 ;4:3.
TURENNE N., “Modeling Noun-Phrases Dynamics in Specialized Text Collections”,
Journal of Quantitative Linguistics, vol. 17, Issue 3, p. 212-228, 2010.
TURENNE, N., HUE, I., 2009. A combinatorics-based data-mining approach to timeseries microarray alignement. Vestnik VOGIS, 13 (1) : 109-113
TURENNE N (2009) Data Mining, a Tool for Systems Biology or a Systems Biology
Tool. J Comput Sci Syst Biol 2 : 216-218
TURENNE N, SCHWER S.R.. Temporal representation of gene interaction networks
from text databases - drosophila megalogaster and bacillus subtilis cases. International
Journal of data Mining and Bioinformatics (IJDMB), 2(1):36-53, 2008.
TURENNE N., "Apprentissage d'un ensemble pré-structuré de concepts d'un domaine:
l'outil GALEX", Mathématiques, Informatique et Sciences Humaines, Vol(148),41-71,
ISBN 09995-2314 1999, 30 pages.
 Refereed conference proceedings
TURENNE N., MESZAROS B. "KASKAD : a plat-form to extract temporal and
interaction relations for genes in texts", in the proceedings of International Workshop
on NanoBioTechnology (NanoBio'06), Saint-Petersburg, 2006.
TURENNE N. , BARBIER M.
"BELUGA : un outil pour l'analyse dynamique des
connaissances de la littérature scientifique d'un domaine. Première application au cas
des maladies à prions", In proceedings of Extraction et Gestion de Connaissances,
Hébrail G. and Lebart L. eds., Clermont-Ferrand, 2004, France.
TURENNE N. "Learning Semantic Classes for improving Mail Classification", dans
les actes de IJCAI Workshop TextMining and Link Analysis, Acapulco (Mexico),
2003, 6 pages.
TURENNE N. "Bayesian Discriminant Analysis for Lexical Semantic Tagging", à
paraître dans les actes du 16ième congrès European Meeting on Cybernetics and
Systems Research (EMCSR), Vienne (Autriche), 2002, 5 pages.
TURENNE N. "Nommage de classes de termes par consensus", à paraître dans les
actes du 6ième congrès Journées Internationales d'Analyse Statistique des Données
Textuelles (JADT), Saint-Malo (France), 2002 , Poster, 12 pages.
TURENNE N., "Term Clusters Evaluation by MonteCarlo Sampling", dans les actes
du 5ième congrès Journées Internationales d'Analyse Statistique des Données
Textuelles (JADT), Lausanne (Suisse), 2000, 12 pages.
TURENNE N., ROUSSELOT F., "A new Reformulation System: the SAROS Tool",
dans les actes du 11ième congrès Knowledge Acquisition Workshop (KAW), Banff
(Canada), 1998b , 15 pages.
TURENNE N., ROUSSELOT F., "Evaluation of 4 Clustering Methods used in TextMining", dans les actes du colloque TextMining, lors du 10ième congrès European
Conference on Machine Learning (ECML) , Chemnitz (Allemagne), 1998a , 15 pages.
Books and Book
chapters
 TURENNE Nicolas, Analyse de données textuelles sous R, 318 pages, ed. ISTE, Jan.
2016.
 TURENNE Nicolas, Knowledge Needs and Information Extraction , 269 pages, ed.
ISTE-Wiley, 2013.
 TURENNE Nicolas, Apprentissage statistique pour l'extraction de concepts à partir de
textes : application au filtrage d'informations textuelles. PhD thesis, Nov. 2000.
University of Strasbourg, France.
 TURENNE Nicolas, Dictionary of 20,000 terms in science and computing with
definitions (French, English, Russian), La Maison du Dictionnaire CD-ROM. LexPro
3.0 ISBN 2-85608-154-1 1998.
Major invited and
keynote talks
 invited talk about bioinformatics and textmining3rd Workshop on Algorithms in
bioinformatics , October 7-9, 2008, Laboratoire J.-V. Poncelet, Moscow, Russia.
 invited talk at the Computer Science Laboratory (LIGM) of Université Paris Est, about
the book release “information needs and information extraction” by ISTE-Wiley eds.,
25 January 2013,
Teaching
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Scientific
 Software, tools, data
Perl Language (2008 20h) University Paris 13 - Bachelor in Biology (Level 1)
SQL Language (2008, 10h) University Paris 13 - Bachelor in Biology (Level 2)
Data Mining (2008, 7h) University Paris 8 - Bachelor in Computer Science (Level 3)
Data Mining (2009, 20h) University Paris 9 - Master in Computer Science (Level 2)
Ontology (2009, 20h) University Paris 7 – Master in Comput. Linguistics (level 2)
Data Mining (2013-15, 30h) University Paris 5 –Bachelor in Data Mining (Level 3)
Corpus Processing with R (2013, 3h) TGIR Huma Num
community
activites
o
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o
o
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Vespa Platform for Health Plant 2014.
x.ent (R package) 2014.
Beluga software platform for dynamic knowledge analysis 2001-2006.
Kaskad software about gene network reconstruction (2006-2007).
SvcR – R package about clustering by a support vector clustering approach
(2008-2010).
Contribution to the Cortext platform working group (www.cortext.net) 20112013.
 Editor-in-Chief of Journal of Data Mining and Digital Humanities (JDMDH) (created
in may 2013 , published by www.episciences.org)
 Seminar organization of the Cortext group (www.cortext.net)
 Reviewer for:
Journal of Computer Science and Systems Biology (JCSSB) 2012 #JCSB-12-32
2011 #JCSB-11-32
2011 #JCSB-11-35
Cahiers de l’Agriculture
2015 #caa150005
Knowledge Based-Systems (KNOSYS)
2014 #KNOSYS-D-14-01017
2011 #KNOSYS-D-11-00360
BMC Bioinformatics
2014 #7638030351198303
Engineering Applications of Artificial Intelligence (EAAI) 2014 #14-729
2015 #15-282
2015 #15-344
PLOS ONE
2014 #PONE-D-13-46159R1
2015 #PONE-D-15-11198
Nucleic Acid Research (NAR)
2013 #03179
Journal of Management Information Systems (JMIS)
2014 #JMIS-7541
Sponsored
Projects
CFP “Corpus d’usage ISTEX » 2016-2017
Title : Full texts and Abstracts analysis
Sponsor: ISTEX national ,Sponsorship 50,000€
People: 3 staff researchers
CFP « Création d’archives numériques » (BSN5) 2015-2016
Title: Amélioration de l’océrisation d’une archive ouverte de bulletins de santé du végétal
Sponsor: Ministry of Education and Research, Sponsorship 30,000€
People: 4 staff researchers
CFP « Projets Exploratoires / Premier Soutien » (PEPS) EXIA 2015-2016
Title: Information Extraction and Applications
Sponsor: Univ. Paris Est and CNRS, Sponsorship 20,000€
People: 5 staff researchers
CFP “Pour et Sur le Plan Ecophyto” (PSPE) VESPA 2013-2016
Title : Platform Implementation for Information Access to an Open Newsletter Archive
Sponsor: Ministry of Agriculture and Ministry of Education ,Sponsorship 80,000€
People: 6 staff researchers
Industrial
Collaboration
 Systemis – PhD sponsoring project (CIFRE) about cybersecurity 2016-2019
 A.D.I.T (Technological Information Dissemination Agency) - Strasbourg 1997
 Neurosoft-Orthalis (Computing Society) - Strasbourg -1998