|
|
2014-2015 : CNRS delegation GFPC,
Team, URGV Lab, |
||||||
|
|
-->
|||||||
|
|
Mail: tahi at ibisc.univ-evry.fr |
My main research interest is Bioinformatics and Computational Biology, notably:
In silico genome analysis
Non-coding RNA secondary structure prediction
Prediction at large scale of microRNAs in genomes
Data integration, ontology mapping
I have been involved in several projects:
I have been the coordinator for the partner of university of Evry in 3 projects of the Pôle de compétitivité System@tic.
The SAPHIR project of ANR Bio-Sys (2006-2009): "Systems for Approach for PHysiological Integration of Renal, cardiac, and respiratory functions for hypertension".
The VPH noE project ("Virtual Physiological Human") (2008-2011).
The STEP european project (2005-2007): "Strategy Towards the EuroPhysiome"
I have also been the coordinator for the partner of university of Evry in the 3 following national projects
The ACI MEDIAGRID project (2002-2004)
The AS (Scientific Action) Integration of Genomic Data Sources project (2003-2004)
The AS Modelling and Algorithmic of RNA structures (2002-2003)
All the algorithms we developed in our research projects on non-coding RNA prediction have been implemented and enhanced by software made available to the scientific community via the Web server EvryRNA (http://EvryRNA.ibisc.univ-evry.fr)
One can find:
P-DCFold: software for predicting RNA secondary structures including pseudoknots (Tahi et al. 2005)
SSCA: software selection of homologous sequences for predicting secondary structure by the comparative approach (Engelen and Tahi 2007)
Tfold: software for predicting RNA secondary structures combining SSCA and P- DCFold (Engelen and Tahi 2010)
miRNAFold: search software microRNA precursors (pre-miRNAs ) in the genomes (Tempel and Tahi 2012)
ncRNAclassifier: software for identifying microRNAs derived from transposable elements (Tempel et al. 2012)
BoostSVM: software for classifying pre- miRNA candidates true or false pre- miRNAs using a boosting SVM approach (Tran et al. 2012)
piRPred: software for classifying piRNA candidates into true or false piRNAs using a MKL approach (Brayet et al. 2014)
I teach mainly at the Computer Science department and the Biology Department of University of Evry.
At the Computer Science department :
Master MIAGE (M2, apprentissage et initial): course of Data Warehouse
Licence of Computer Sciences (L2): course of Introduction to data bases
At the Biology department, I teach in the Bioinformatics training GBI (Genie Biologie et Informatique) : :
Master (M2) GBI : course of data integration
Master (M1) GBI : course of Sequence algorithmics and course of Advances data bases.
I give two courses (of 3 houres each) of Bioinformatics and XML at the Graduate schools (Ecole doctorale) of Evry
I give regurarly since several years a course (of 3 houres) of Bioinformatics for the Second and third level at Telecom SudParis.
I'm (since 2003) the responsible of the computer science part of the training GBI
Currently, I am co-leader of the new proposal of a Master of Bioinformatics at the Universtity of Paris Saclay and the new proposal of a double license of informatics and biology at the University of Evry for the next Five Year.
S. Tempel, N. Pollet, Tahi F. ncRNAclassifier: a tool for detection and classification of transposable element sequences in RNA hairpins. BMC Bioinformatics 13(246), 2012. Here
S. Tempel, Tahi F. A fast ab-initio method for predicting miRNA precursors in genomes. Nucleic Acids Res. 40(11): e80, 2012. Here
S. Engelen, F. Tahi. Tfold: efficient in silico prediction of non-coding RNA secondary structures. Nucleic Acids Res. 38(1): 2453-66, 2010. Here
Tempel S, Rousseau C, Tahi F and Nicolas J. ModuleOrganizer: detecting modules in families of transposable elements. BMC Bioinformatics. 11(22), 2010. Here
Gilles Bernot, Fariza Tahi. Behaviour Preservation of a Biological Regulatory Network when Embedded into a Larger Network. Fundamenta Informaticae 91(3-4): 463-485, 2009. Here
Thomas SR, Baconnier P, Fontecave J, Françoise JP, Guillaud F, Hannaert P, Hernçndez A, Le Rolle V, Maziére P, Tahi F, White RJ. SAPHIR: a physiome core model of body fluid homeostasis and blood pressure regulation. Philos. Transact. A Math Phys Eng Sci. 13; 366(1878): 3175-97, 2008. Here
S. Engelen, F. Tahi. Predicting RNA secondary structure by the comparative approach : how to select the homologogous sequences. BMC Bioinformatics, vol. 8, no 1, 2007. Here
F. Tahi, S. Engelen, M. Regnier. P-DCFold or how to predict all kinds of pseudoknots in RNA secondary structures. International Journal on Artificial Intelligence Tools, vol. 14, no 5, p 703-716, 2005. Here
F. Tahi, M. Gouy, M. Regnier. Automatic RNA secondary structure prediction with a comparative approach. Computers and Chemistry, vol. 26, no 5, 2002. Here
F. Tahi, B. Achddou, C. Decraene, O. Alibert, H. Guiot, C. Auffray, G. Piétu. Automatic quantitation of hybridization signals on cDNA arrays. Biotechniques, 32:1386-1397, June 2002. Here
C. Decraene, B. Brugg, M. Ruberg, E. Eveno, C. Matingou, F. Tahi, C. Mariani, C. Auffray, G. Piétu. Identification of genes involved in ceramide-dependent neuronal apoptosis using cDNA arrays. Genome Biology, vol. 3, no 8, 2002. Here
G. Piétu, R. Mariage-Samson, N-A. Fayein, C. Matingou, E. Eveno, R. Houlgatte, C. Decraene, Y. Vandenbrouck, F. Tahi, M-D. Devignes, U. Wirkner, W. Ansorge, D. Cox, T. Nagase, N. Nomura, C. Auffray. The Genexpress IMAGE Knowledge Base of the Human Brain Transcriptome : A Prototype Integrated Resource for Functional and Computational Genomics. Genome Research, vol. 9, p 195-209, 1999. Here
S. Grumbach, F. Tahi. New Challenge for Compression Algorithms : Genetic Sequences. Journal of Information Processing and Management, (Invited paper), vol. 30, no 6, p 875-886, 1994. Here
S. Troncale, F. Tahi, D. Campard, J.P Vannier. Modélisation et simulation de la régulation de l’hématopoïèse précoce grâce aux réseaux de Petri hybrides fonctionnels. Techniques et Sciences Informatiques, numéro spécial “modélisation et simulation pour la post-génomique”. 26, p 99-124, 2007. Here
S. Grumbach, F. Tahi. Compression et compréhension des séquences de nucléotides. Techniques et Sciences Informatiques, numéro spécial Informatique et Génomes, vol. 14, no 2, p217-233, 1995.
Tahi, V. D. Tran, S. Tempel and E. Mahé. Bioinformatics of non-coding RNAs and GPUs. A case study: prediction at large scale of microRNAs in genomes. 33 pages. Dans livre intitulé Patterns for parallel programming on GPU's. Edité par F. Magoulès, Saxe Coburg Publications, 2013.
Amel Bouzeghoub, Abdeltif Elbyed, Fariza Tahi OMIE : Ontology Mapping within an Interactive and Extensible Environment. DILS (International Worshop on Data Integration in Life Sciences), 161-168, 2008. Here
R. Thomas, E. Abdulhay, P. Baconnier, J. Fontecave, J.P. Francoise, F. Guillaud, P. Hannaert, A. Hernandez, V. Le Rolle, P. Maziere, F. Tahi, F. Zehraoui. SAPHIR - a multi-scale, multi-resolution modeling environment targeting blood pressure regulation and fluid homeostasis. International Conference on the IEEE Engineering in Medecine and Biology Society, vol. 1, p 6648-52, 2007. Here
B. Benziane, A. Soukane, F. Tahi, S. R. Thomas. Resources for the renal physiome. ASN conference(39th Annual Renal Week Meeting), San Diego, Novembre 2006.
S.R. Thomas, F. Tahi, P. Harris, A. Lonie. The renal physiome project. 3rd IEEE International Symposium on Biomedical Imaging, Special session : Towards vertical integration of biomedical data. Washington, USA, pages 820-823, avril 2006. Here
S. Troncale, F. Tahi, D. Campard, J.P. Vannier, J. Guespin. Modelling and simulation with hybrid functional Petri nets the human early hematopoiesis. International Pacific Symposium on Biocomputing (PSB), Maui, Hawaii, USA, pages 427-438, Janvier 2006. Here
D. Campard, J. Guespin, F. Tahi, S. Troncale, J.P. Vannier. Modelisation of early hematopoiesis with hybrid functional Petri nets. In Proceedings of the Montpellier Spring School on Modelling Complex Biological Systems in the Context of Genomics, pages 167-172, Montpellier, France, avril 2005.
S. Troncale, D. Campard, F. Tahi, A. Hachami, J. Guespin, J.P. Vannier. Towards the Modelling and simulation with hybrid functional Petri nets the human early hematopoiesis. European Conference on Complex Systems (ECCS), Paris, France, septembre 2005.
S. Engelen, F. Tahi. An Open Problem in RNA Secondary Structure Prediction by the Comparative Approach. International Conference on Mathematics and Engineering Techniques in Medicine and Biological Sciences (METMBS), Las Vegas, Nevada, USA, pages 293-299, Juin 2004. Here
Collet, C. and Belha jjame, K. and Bernot, G. and Bobineau, C. and Bruno, G. and Finance, B. and Jouanot, F. and Kedad, Z. and Laurent, D. and Tahi, F. and Vargas-Solar, G. and Vu, T.T. and Xue, X. Towards a mediation system framework for transparent access to largely distributed sources. Int. Conf. on Semantics of a Networked World (ICSNW), pages 65-78, Paris 2004. Here
C. Collet, K. Belha jjame, G. Bernot, G. Bruno, B. Finance, Z. Kedad, D.Laurent, F. Tahi, G. Vargas-Solar, T.T. Vu, and X. Xue. Mediagrid : a mediation framework for a transparent access to biological data sources. Entity Relationship Conference (22nd International Conference on Conceptual Modeling), Chicago, Illinois, USA, October 2003. Publié dans CGI-EMISA Forum Proceedings, num 1, 2004.
F. Tahi, S. Engelen, M. Régnier. A fast algorithm for RNA secondary structure prediction including pseudoknots. BIBE 2003, 3rd IEEE Symposium on Bioinformatics and Bioengineering. Dans IEEE Computer Society proceedings, pages 11-17. Bethesda, Maryland, mars 2003.
F. Tahi, S. Engelen, M. Régnier. P-DCFold, an algorithm for RNA secondary structure prediction including all kinds of pseudoknots. ECCB 2003, European Conference on Computational Biology, Paris France. Dans ECCB Proceedings, pages 491-492, septembre 2003.
C. Auberger, F. Tahi, G. Bernot. Biological Regulatory Networks Embedment. ECCB 2003, European Conference on Computational Biology. Dans ECCB Proceedings, pages 561-563, Paris, septembre 2003.
C. Collet, K. Belha jjame, G. Bernot, G. Bruno, B. Finance, Z. Kedad, D.Laurent,F. Tahi, G. Vargas-Solar, T.T. Vu, and X. Xue. A mediation framework for a transparent access to biological data sources ECCB 2003, European Conference on Computational Biology, Paris France. In ECCB Proceedings, pages 69-70, septembre 2003.
F. Tahi, S. Engelen, M. Régnier. P-DCFold, an algorithm for RNA secondary structure prediction including all kinds of pseudoknots. RECOMB 2003, International Conference on Computational Biolology, Berlin, Allemagne. Dans Currents in Computational Molecular Biology, p 363-364. Avril 2003.
F. Tahi, Gilles Bernot, Christophe Auberger. Embedding properties of Biological Regulatory Networks. NIH Symposium on Biocomputation and Bioinformation. Digital Biology : The emerging paradigm, Bethesda, Maryland, USA. Poster avec Résumé dans NIH proceedings, novembre 2003.
C. Collet, K. Belhajjame, G. Bernot, G. Bruno, B. Finance, Z. Kedad, D.Laurent, F. Tahi, G. Vargas-Solar, T.T. Vu, and X. Xue. A mediation framework for a transparent access to biological data sources. NIH Symposium on Biocomputation and Bioinformation. Digital Biology : The emerging paradigm, Bethesda, Maryland, USA. Poster avec résumé Dans NIH proceedings, novembre 2003.
F. Tahi, Gilles Bernot, Christophe Auberger. Embedding properties of Biological Regulatory Networks. NIH Symposium on Biocomputation and Bioinformation. Digital Biology : The emerging paradigm 2003, novembre 2003, Bethesda, Maryland, USA. Dans NIH proceedings.
F. Tahi, S. Engelen, M. Régnier. P-DCFold, an algorithm for RNA secondary structure prediction including all kinds of pseudoknots. RECOMB 2003, International Conference on Computational Biolology, avril 2003, Berlin, Allemagne. Résumé dans Currents in Computational Molecular Biology.
F. Tahi, S. Engelen, M. Régnier. A fast algorithm for RNA secondary structure prediction including pseudoknots. WABI 2002, 2nd Workshop on Algorithms in BioInformatics, septembre 2002, Rome, Italie.
F. Tahi, B. Achddou, C. Decraene, C. Auffray, G. Piétu. XDotsReader, a software for automatic analysis of cDNA array images. RECOMB’02, avr 2002, Wachington. Dans Currents in Computational Molecular Biology.
F. Tahi, M. Régnier, M. Gouy. Automatic RNA secondary structure prediction with the comparative approach. RECOMB 2001, april 2001, Montréal. Résumé dans Currents in Computational Molecular Biology.
F. Tahi, B. Achddou, C. Decraene, C. Auffray, G. Piétu. XDotsReader, a software for automatic analysis of cDNA array images. RECOMB (Annual International Conference on Computational Biology), 18-21 avril 2002, Wachington, Etats-Unis. Résumé poster publié dans Currents in Computational Molecular Biology 2002, pages 174-175.
F. Tahi, M. Régnier, M. Gouy. Automatic RNA secondary structure prediction with the comparative approach. RECOMB, 18-21 april 2001, Montréal, Canada. Résumé poster publié dans Currents in Computational Molecular Biology 2001, pages 187-188. B. Achddou, F. Tahi, O. Alibert, C. Auffray, G. Piétu. XDotsReader, a software for automatic quantitation of high density arrays. Genome mapping and sequencing meeting, Cold Spring Harbor, 19-23 Mai 1999. Poster.
C. Decraene, R. Mariage-Samson, E. Eveno, N-A. Fayein, C. Matingou, F. Tahi, C. Auffray, G. Piétu. The Genexpress IMAGE Knowledge Base : A Prototype Integrated Resource for Characterization of Gene Transcripts involved on Muscle or Brain Functions. Genome mapping and sequencing meeting, Cold Spring Harbor, 19-23 Mai 1999. Demonstration.
G. Pietu, C. Decraene, I. Arnould, N.A. Fayein, C. Matingou, F. Tahi, R. Mariage-Sansom, C. Auffray. Characterization of novel genes involved in muscle or brain functions and neurodegeratives diseases by quantitative hybridization of high density cDNA arrays. Genome mapping and sequencing, 13-17 Mai 1998, Cold Spring Harbor, Etats-Unis. Communication Orale.
G. Pietu, C. Decraene, I. Arnould, N.A. Fayein, C. Matingou, F. Tahi, R. Mariage-Sansom, C. Auffray. Characterization of novel genes involved in brain functions by quantitative hybridization of high density cDNA arrays. Colloque “Nouvelles Stratégies d’étude du système nerveux central” , 30 avril 1998, Paris. Oral Communication.
G. Pietu, C. Decraene, I. Arnould, N.A. Fayein, C. Matingou, F. Tahi, R. Mariage-Sansom, C. Auffray. Characterization of novel genes involved in muscle or brain functions and neurodegeratives diseases by quantitative hybridization of high density cDNA arrays. Human Genome Europe 98, 4-6 mai 1998, Cannes, France. Oral Communication.
C. Decraene, M. Ruberg, B. Brugg, F. Tahi, R. Mariage-Sansom, C. Auffray, G. Piétu. Differential gene expression during the apoptosis of Neuronally-differentiated PC12 cells treated with C2-ceramide. Human Genome Europe 98, 4-6 mai 1998, Cannes, France. Oral Communication.
F. Tahi, M. Régnier. Enumeration and Asymptotics in Computational Biology. Workshop “Mathematical Analysis of Biological Sequences” , 4-6 Aout 1996, Trondheim, Norvège. Oral Communication.
S. Grumbach, F. Tahi. Compression of DNA sequences. Proc. IEEE Symp. on Data Compression, pages 340-350, 1993. Here
Tran, VD, Zerath B, Tempel S, Zehraoui F, Tahi, F. BoostSVM: A miRNA classifier with high accuracy using boosting SVM. JOBIM (Journées Ouvertes en Biologie, Informatique et Mathématiques), p 259-266, 2012.
Tempel S and Tahi, F. miRNAFold: A fast ab-initio method for searching for miRNA precursors in whole genomes. JOBIM, p 39-46, 2012.
F. Tahi, M. Besnard, G. Chandesris, S. Tempel and M. Trellet. EvryRNA: bioinformatics platform for non-coding RNA. JOBIM, p 327-328, 2012.
B. Zerath, S. Tempel, F. Tahi. Feature selection for microRNA prediction. JOBIM, p 493-494, 2012.
Tempel S and Tahi F. An automatic method for identifying TE-derived miRNAs. JOBIM, p 245-252, 2011.
Abchiche N and Tahi F. A multi-agent approach for biological models cooperation. Thematic Research School on Modeling Complex Biological Systems in the context of Genomics, La Colle Sur Loup. Oral communication, 2009.
Bouzeghoub A, Elbyed A, Tahi F. ROMIE: a Resource-based Ontology Mapping. IBISC-RR-2011-01.
S. Tempel, F. Tahi. An automatic method for identifying TE-derived miRNAs. IBISC-RR-2011-02.
S. Tempel, F Tahi. A fast ab initio method for predicting miRNA precursors in genomes. IBISC-RR-2011-03.
F. Tahi, S. Engelen. Tfold, a complete and interactive system for predicting non coding RNA secondary structures. IBISC-RR-2008-06.
F. Tahi, B. Benziane, A. Bouzeghoub, D. Courtaud, A. Elbyed, A. Soukane, SR. Thomas, F. Zehraoui. Vers un entrepôt de données XML pour le Physiome rénal. IBISC-RR-2008-04.
G. Bernot, F. Tahi. Behaviour Preservation of a Biological Regulatory Network when Embedded into a Larger Network. IBISC-RR-2008-01
