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Bibliographie thèse informatique documentaire et génétique

Achard F, Barillot E. Virgil : a database of rich links between GDB and GenBank. Nucleic. Acids Res., 1998, vol. 26, n°1, p. 100-101       

Andrade M, Valencia A, Automatic extraction of keywords from scientific text : application to the knowledge domain of protein families. Bioinformatics. 1998, vol. 14, n°7, p. 600-607       

Andrade MA, Bork P. Automated extraction of information in molecular biology. FEBS Letters. 2000, n° 476, p. 12-17           

Andrade MA, Valencia A. Automatic annotation for biological sequences by extraction of keywords from MEDLINE abstracts. Development of a prototype system. Proceedings of the Fifth International Conference on Intelligent Systems for Molecular Biology (ISMB 97), 1997, p. 25-32      

Andrade MA. Tools for automated protein annotation. Casadio R, Masotti L. Protein Sequence Analysis in the Genomic Era. Bologna (Italia) : CLUEB, 2001. [On line] <http://www.embl-heidelberg.de/~andrade/papers/boss99/chapter.html>

Andrade Miguel A, Sander C. Bioinformatics : from genome data to biological knowledge. Current Opinion in Biotechnology. 1997, vol. 8, n° 6, p. 675-683        

Attwood Teresa K. Genomics : The Babel of bioinformatics. Science, 2000, vol. 290, n°5491, p. 471-473           

Bairoch Amos, Apweiler Rolf. The SWISS-PROT protein sequence database and its supplement TrEMBL in 2000. Nucleic Acids Res. 2000, vol. 28, n° 1, p. 45-48    

Bikel Daniel M, Miller Scott, Schwartz Richard, Weische-del Ralph. Nymble : a high-performance learning name-finder. Proceeding of the 5th Conference on Applied Natural Language Processing (ANLP’97), Washington. 1997. p. 194-201. ACL. Accessible en ligne <URL : http://xxx.lanl.gov/abs/cmp-lg/9803003> 

Blaschke C, Andrade MA, Ouzounis C, Valencia A. Automatic extraction of biological information from Scientific text : protein-protein interactions. Proceedings of the seventh international conference on Intelligent Systems for Molecular Biology (ISMB 99), 1999, n°7, p. 60-67  

Catalano D, Licciulli F, D'Elia D, Attimonelli M. Update of KEYnet : a gene and protein names database for biosequences functional organisation. Nucleic Acids Research, 2000, Vol. 28, N° 1, p. 372-373    

Chee M, Yang R, Hubbell E. Accessing genetic information with high-density DNA arrays. Science. 1996, vol. 274, n° 5287, p. 610-614         

Collier N, Park HS, Ogata N, Tateishi UY, Nobata C, Ohta T, Sekimizu T, Imai H, Ibushi K, Tsujuii J. The GENIA project : corpus-based knowledge acquisition and information extraction from genome research papers, Proceedings of the European Association for Computational Linguistics (EACL) conference, 1999    

Davidson Duncan, Apweiler Rolf. Meeting the challenge of building gene function databases. Compte rendu de l'atelier HUGO/EU Workshop, Hinxton, Cambridge, UK, Mai 1999. [On Line] sans lieu : éditeur inconnu, sans date. URL : http://www.hgu.mrc.ac.uk/Research/Reports/Genefunc/report.htm        

Dickerson JA, Berleant D, Cox Z, Qi W, Ashlock D, Wurtele E. Creating metabolic network models using text mining and expert knowledge. Atlantic Symposium on Computational Biology. Genome Information Systems & Technology, 2001.          

Discala C, Benigni X, Barillot E, Vaysseix G. DBcat : a catalog of 500 biological databases. Nucleic Acids Research. 2000, vol. 28, p. 8-9  

Enright AJ, Iliopoulos I, Kyrpides NC, Ouzounis CA. Protein interaction maps for complete genomes based on gene fusion events. Nature. 1999, vol. 402, n° 6757, p. 86-90 

Faloutsos C, Oard DW. A Survey of Information Retrieval and Filtering Methods. Technical Report CS-TR-3514, Department of Computer Science, University of Maryland, College Park, 1995.     

Fields S ,Song OK. A novel genetic method to detect protein-protein interactions. Nature. 1989, n° 340, p. 245-246    

Fitch WM. Distinguishing homologous from analogous proteins. Systematic Zoology. 1970, vol. 19, n° 2, p. 99-113          

Fujibuchi W, Goto S, Migimatsu H, Uchiyama I, Ogiwara A, Akiyama Y, Kanehisa M. DBGET/LinkDB : an integrated database retrieval system. Pacific Symp. Biocomputing. 1998. p. 683-694           

Fukuda K, Tsunoda T, Tamura A, Takagi T. Toward information extraction : Identifying protein names from biological papers. Proceedings of the Pacific Symposium on Biocomputing, 1998, p. 707-718.  

Gerstein M., Jansen R. The current excitement in bioinformatics-analysis of whole-genome expression data : How does it relate to protein structure and function ? Current Opinion in Structural Biology. 2000, vol. 10, n° 5, p. 574-584

Goujon Bénédicte. Utilisation de l'exploration contextuelle pour l'aide à la veille technologique : Réalisation du système informatique VIGITEXT. Thèse science (traitement automatique du langage naturel) : Université Paris-Sorbonne, avril 2000. 550 p.

Hieter P, Boguski M. Functional genomics : it's all you read it. Science. 1997, n°278, p. 601-602    

Hishigaki Haretsugu, Ono Toshihide, Tanigami Akira, Takagi Toshihisa. Interaction-based Analysis of Protein Function and Network. Procedings of Genome Informatics conference (GIW’99) n°10, 1999, p. 257-258    

Humphreys B L, Lindberg DAB, Schoolman HM, Barnett GO. The Unified Medical language System : An informatics research collaboration. Journal of the American Medical Informatics Association, 1998, vol. 5, n° 1, p. 1-13   

Hunter Lawrence. Molecular Biology for Computer Scientists. In Hunter Lawrence. Artificial Intelligence and Molecular Biology. Cambrigde : AAAI Press, 1993, 500 p. ISBN 0-262-58115-9 (épuisé). En ligne : http://www.aaai.org//Library/Books/Hunter/hunter.html  

Jacquemin Christian, Zweigenbaum Pierre. Traitement automatique des langues pour l'accès au contenu des documents. In : Le document en sciences du traitement de l'information, Jacques Le Maitre, Jean Charlet et Catherine Garbay (Réd.), chapitre quatrième, p. 71-109. Toulouse : Cépadues, septembre 2000.     

Jenssen TK, Öberg LMJ, Andersson ML, Komorowski J. Methods for large-scale mining of networks of human genes. Proceedings of the SIAM Conference on Data Mining (SDM 2001). Chicago, IL, USA, 2001   

Kanehisa Minoru. Post-genome Informatics. Oxford, UK : Oxford University Press, 2000. 158 p. ISBN 0-19-850326   

Karp PD. Database links are a foundation for interoperability. Trends Biotechnol. 1996, vol 14, n°8, p. 273-279    

Kling R, Turner WA, Gherbi R. Hybridation des Savoirs. Réunion de l’ADEST sur le thème Social Informatics : Outiller les Pratiques Collectives Distribuées, Paris, 5 juin 2000. On line http://www.upmf-grenoble.fr/adest/seminaires/       

Licciulli F, Catalano D, D'Elia D, Lorusso V, Attimonelli M. KEYnet : a keywords database for biosequences functional organization. Nucleic Acids Research, 1999, Vol. 27, N° 1, p. 365-367           

Marcotte Edward M, Xenarios Ioannis, Eisenberg David. Mining literature for protein–protein interactions. Bioinformatics. 2001, vol. 17, n° 4, p. 359-363   

Masys Daniel R, Welsh John B, Fink J. Lynn , Gribskov Michael , Klacansky Igor, Corbeil Jacques. Use of keyword hierarchies to interpret gene expression patterns. Bioinformatics. 2001, vol. 17, n° 4, p. 319-326           

Mendoza L, Thieffry D, Alvarez-Buylla ER. Genetic control of flower morphogenesis in Arabidopsis thaliana : a logical analysis. Bioinformatics, 1999, vol. 15, p. 593-606           

MUC-6 : Proceedings of the Sixth Message Understanding Conference. Columbia, Mary-land : Morgan Kaufmann, 1996      

Nakao Mitsuteru, Bono H, Kawashima S, Kamiya T, Sato K, Goto S, Kanehisa M. Genome-scale Gene Expression Analysis and Pathway Reconstruction in KEGG. Genome Informatics, 1999, vol. 10, p. 94-103    

Ng SK, Wong M. Toward routine automatic pathway discovery from on-line scientific text abstracts. Genome Informatics 1999. Edited by Asai K, Miyano S, Takagi T. Tokyo : Universal Academy Press, 1999. p. 104-112    

Ohta Y, Yamamoto Y, Okazaki T, Uchiyama I, Takagi T. Automatic Construction of Knowledge Base from Biological Papers, Proceedings of the Fifth International Conference on Intelligent Systems for Molecular Biology (ISMB'97), 1997, p. 218-225          

Oliveros Juan Carlos, Blaschke Christian, Herrero Javier, Dopazo Joaquin, Valencia Alfonso. Expression Profiles and Biological Function. Proceedings of the Eleventh Workshop on Genome Informatics (GIW2000), Tokyo, 2000.     

Ono Toshihide, Hishigaki Haretsugu, Tanigami Akira, Takagi Toshihisa. Automated extraction of information on protein–protein interactions from the biological literature. Bioinformatics, 2001, vol. 17, p. 155-161    

Ono Toshihide, Hishigaki Haretsugu, Tanigami Akira, Takagi Toshihisa. Automatic Extraction of Information on Protein-Protein Interaction from Scientific Literature. Genome Informatics, 1999, n° 10, p. 296-297        

Pillet V, Roudani B, Quoniam L, Jacq B. Extraction automatique et représentation graphique de données biologiques : les interactions génétiques et moléculaires. Actes du colloque VSST’98, 1998, p. 215-226.       

Pillet Violaine. Méthodologie d’extraction automatique d’information à partir de la littérature scientifique en vue d’alimenter un nouveau système d’information. Application à la génétique moléculaire pour l’extraction d’information sur les interactions. Thèse sci. : Science de l’information et de la communication, 2000, 128 p., 00AIX30002 

Proux Denys. Muninn : une stratégie d’extraction d’informations dans des corpus spécialisés par application de méthodes d’analyse linguistique de surface et de représentation conceptuelle des structures sémantiques. Thèse informatique : faculté des sciences et techniques, université de Bourgogne, 2001, 211 p.        

Qi W, Berleant D. PathBinder : a system for mining Medline for protein interactions. Joint Bioinformatics Workshop, 3-4 Nov. 2000, Iowa City.      

Rebhan M, Chalifa-Caspi V, Prilusky J, Lancet D. GeneCards : A novel functional genomics compendium with automated data mining and query reformulation support. Bioinformatics, 1998, vol. 14, p. 656-664        

Rindflesch TC, Hunter L, Aronson AR. Mining molecular binding terminology from biomedical text. Proc AMIA Symp. 1999; p. 127-131.      

Rindflesch TC, Hunter L, Aronson AR. Mining molecular binding terminology from biomedical text. Proceedings of the AMIA Symp., 1999, p. 127-131    

Rindflesch TC, Tanabe L, Weinstein JN, Hunter L. EDGAR : extraction of drugs, genes and relations from the biomedical literature. Proceedings of the Pac Symp of Biocomput, 2000, p. 517-528           

Rocha Eduardo PC. Analyse exploratoire des génomes bactériens. Thèse de génétique cellulaire et moléculaire : Université de Versailles Saint-Quentin-en-Yvelines, 2000. 144 p.       

Salton G, McGill MJ. Introduction to Modern Information Retrieval. New York :  McGraw Hill Book Company, 1983. 448 p.     

Salton Gerard. Automatic Text Processing : The Transformation, Analysis, and Retrieval of Information by Computer. Massachusetts, USA : Addison-Wesley Publishing Company, 1989. 688p.     

Sekimizu T, Park H, Tsujii J. Identifying the interaction between genes and gene products based on frequently seen verbs in medline abstracts. Proccedings of the ninth Workshop on Genome Informatics (GIW’98). Universal Academy Press, ISBN 4-946443-52-5, 1998, p. 62-71 

Shatkay Hagit, Edwards Stephen, Wilbur W. John, Boguski Mark. Genes, Themes and Microarrays - Using Information Retrieval for Large-Scale Gene Analysis. International Conference on Intelligent Systems for Molecular Biology (ISMB 2000), 2000.   

Stapley BJ, Benoit G. Biobibliometrics : Information retrieval and visualization from co-occurrences of gene names in medline asbtracts. Proceedings of Pacific Symposium on Biocomputing, 2000, p. 529-540           

Stephens M, Palakal M, Mukhopadhyay S, Raje R, Mostafa J. Detecting Gene Relations from MEDLINE Abstracts. Pacific Symposium on Biocomputing n°6, 2001, p. 483-496          

Stoesser G, Baker W, van den Broek A, Camon E, Garcia-Pastor M, Kanz C, Kulikova T, Lombard V, Lopez R, Parkinson H, Redaschi N, Sterk P, Stoehr P, Tuli MA. The EMBL Nucleotide Sequence Database. Nucleic Acids Res, 2001, vol. 29, n°1, p. 17-21

Tanabe L, Scherf U, Smith LH, Lee JK, Hunter L, Weinstein JN. MedMiner : an Internet text-mining tool for biomedical information, with application to gene expression profiling. BioTechniques, 1999, vol. 27, p. 1210-1217           

The chipping forecast. Nature Genetics. 1999, supplement, vol. 21, n°1, p. 1-60    

The genome sequencing consortium. Initial sequencing and analysis of the human genome. Nature. 2001, n°409, p. 860-921   

Thomas J, Milward D, Ouzounis C, Pulman S, Carroll M. Automatic extraction of protein interactions from scientific abstracts. Proceedings of Pacific Symposium on Biocomputing 2000, p. 541-52           

Thomas J, Milward D, Ouzounis C, Pulman S, Carroll M. Automatic extraction of protein interactions from scientific abstracts. Proceedings of the Pac Symp Biocomput, 2000. p. 541-552      

Usuzaka S, Sim KL, Tanaka M. A machine learning approach to reducint the work of experts in article selection from database: a case study for regulatory relations of S. cerevisiae genes in MEDLINE. Proceedings of the Ninth Workshop on Genome Informatics, 1998, p. 91-101     

Van-Rijsbergen CJ. Information Retrieval. 2nd édition. London, UK : Butterworths, 1979. http://www.dcs.gla.ac.uk/Keith/Preface.html       

Wain HM, Blake JA, Bruford EA, Maltais LJ, Povey S. Report of ASHG-NW Gene Nomenclature Workshop. ASHG-NW Gene Nomenclature Workshop. Philadelphie, Octobre 2000. Accessible en ligne <http://www.gene.ucl.ac.uk/nomenclature/ashgnw_report.html>          

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Wilkins MR, Sanchez JC, Gooley AA, Appel RD, Humphery-Smith I, Hochstrasser DF, Williams KL. Progress with proteome projects : why all proteins expressed by a genome should be identified and how to do it. Biotechnol Genet Eng Rev. 1996, vol. 13, p. 19-50      

Wong Limsoon. A Protein Interaction Extraction System. Proceedings of Pacific Symposium on Biocomputing 2001, p. 520-530. 

Xenarios Ioannis, Rice Danny W, Salwinski Lukasz, Baron Marisa K, Marcotte Edward M, Eisenberg David. DIP : the Database of Interacting Proteins. Nucleic Acids Research, 2000, Vol. 28, No. 1, p. 289-291           

Yamamoto Yasunori, Ohta Yoshihiro, Uchiyama Ikuo, Takagi Toshihisa. Constructing a dictionary of biological terms for information extraction. Akutsu T, Asai K, Hagiya M., Kuhara S, Miyano S, Nakai K. Genome Informatics Workshop. Tokyo : Universal Academy Press, 1996         

Yoshida Mikio, Fukuda Ken-ichiro, Takagi Toshihisa. PNAD-CSS : a workbench for constructing a protein name abbreviation dictionary. Bioinformatics, 2000, vol.16, n° 2, p.169-175         

Yoshida Mikio; Fukuda Kenichiro, Takagi Toshihisa. Automatic Construction of Biological Abbreviation Dictionary from Abstracts of Biomedical Papers. Proceedings. of the Genome Informatics Workshop 1998, 1998, N° 9, p. 288-289

Dernière mise à jour le 9 août 2001