PuReD-MCL: A graph-based PubMed document clustering methodology

Bioinformatics

Volumn 24, Issue 17, 2008, Pages 1935-1941

  Theodosiou, T ^a,b   Darzentas, N ^b   Angelis, L ^a   Ouzounis, C A ^b,c  

^a ARISTOTLE UNIVERSITY OF THESSALONIKI   (Greece)

^b INFORMATION TECHNOLOGIES INSTITUTE   (Greece)

^c KING'S COLLEGE LONDON   (United Kingdom)

Author keywords

[No Author keywords available]

Indexed keywords

ALGORITHM; ARTICLE; CLINICAL DATA REPOSITORY; DATA ANALYSIS; DATA MINING; DOCUMENTATION; ESCHERICHIA COLI; FACTUAL DATABASE; INFORMATION PROCESSING; INFORMATION RETRIEVAL; MACHINE LEARNING; MEDLINE; METHODOLOGY; PRIORITY JOURNAL; VALIDATION PROCESS; YEAST;

ALGORITHMS; ARTIFICIAL INTELLIGENCE; CLUSTER ANALYSIS; DATABASE MANAGEMENT SYSTEMS; INFORMATION STORAGE AND RETRIEVAL; NATURAL LANGUAGE PROCESSING; PATTERN RECOGNITION, AUTOMATED; PUBMED; SOFTWARE;

ESCHERICHIA COLI;

EID: 50549101908     PISSN: 13674803     EISSN: 14602059     Source Type: Journal    
DOI: 10.1093/bioinformatics/btn318     Document Type: Article

References (33)

1. Ananiadou,S. et al. (2006) Text mining and its potential applications in systems biology. Trends Biotechnol., 24, 571-579.
2. Brohee,S. and van Helden,J. (2006) Evaluation of clustering algorithm for protein-protein interaction networks. BMC Bioinformatics, 7 488.
3. Dorow,B. et al. (2005) Using curvature and Martov clustering in graphs for lexical acquisition and word sense discrimination. In MEANING-2005, 2nd Workshop organized by the MEANING Project, February 3-4, 2005, Trento, Italy.
4. Enright,A.J. et al. (2002) An efficient algorithm for large-scale detection of protein families. Nucleic Acids Res., 30, 1575-1584.
5. Gfeller,D. et al. (2005) Synonym dictionary improvement through Markov clustering and clustering stability. In International Symposium on Applied Stochastic Models and Data Analysis 2005, Brest, France. pp. 106-113.
6. Goldovsky.L. et al. (2005) BioLayout(Java): Versatile network visualisation of structural and functional relationships. Appl. Bioinform., 4, 71-74.
7. Hirschman,L. et al. (2005) Overview of BioCreAtIve: Critical assessment of information extraction for biology. BMC Bioinformatics 6 (Suppl. 1), S1.
8. Hope,A.C.C. (1968) A simplified Monte Carlo significance test procedure. J. R. Stat. Soc. B, 30, 582-598.
9. Hu,Z.Z. et al. (2005) Literature mining and database annotation of protein phosphorylation using a rule-based system. Bioinformatics, 21, 2759-2765.
10. Iliopoulos,I. et al. (2001) TextQuest: Document clustering of medline abstracts for concept discovery in molecular biology. Pac. Symp. Biocomput., 6, 384-395.
11. Izumitani,T. et al. (2004) Assigning gene ontology categories (GO) to yeast genes using text-based supervised learning methods. In Proceedings of the IEEE Computational Systems Bioinformatics Conference (CSB 2004), IEEE Computer Society, Stanford, USA, pp. 503-504.
12. Kim,D.J. et al. (2003) GENIA corpus - a semantically annotated corpus for biotextmining. Bioinformatics, 19, i180-i182.
13. Lappin,T.R. et al. (2006) HOX genes: Seductive science, mysterious mechanism. Ulster Med. J., 75, 23-31.
14. Manning,C.D. and Schutze,H. (1999) Foundations of Statistical Natural Language Processing. The MIT Press, Cambridge, MA, USA.
15. Marigo,V. et al. (1996) Sonic hedgehog differentially regulates expression of GLI and GLI3 during limb development. Dev. Biol., 180, 273-283.
16. Mochihashi,D. et al. (2006) Learning an optimal distance metric in a linguistic vector space. Syst. Comput. Jpn., 37, 12-21.
17. Nenadic,G. et al. (2003) Terminology-driven mining of biomedical literature. In Proceedings of the 2003 ACM Symposium on Applied Computing, ACM, Florida, USA, pp. 83-87.
18. Passner,J.M. et al. (1999) Structure of a DNA-bound ultrabithorax-extradenticle homeodomain complex. Nature, 397 714-719.
19. R Development Core Team (2007) R: A language and Enviroment for Statistical Computing. R Foundation for Statistical Computing, Vienna, Austria.
20. Radhakrishna,C.R. and Bhaskara,M.R. (1998) Matrix Algebra and its Applications to Statistics and Econometrics. World Scientific Pub Co, Inc.; Singapore.
21. Rawls,A. et al. (2000) Genetic regulation of somite formation. Curr. Top. Dev. Biol., 47:131-54.
22. Raychaudhuri,S. et al. (2002) Associating genes with gene ontology codes using a maximum entropy analysis of biomedical literature. Genome Res., 12, 203-214.
23. Salton,G. (1970) Automatic text analysis. Science, 168, 335-343.
24. Schier,A.F. et al. (1996) Mutations affecting the development of the embryonic zebrafish brain. Development. 123, 165-78.
25. Struble,C.A. and Dharmanolla,C. (2004) Clustering MeSH representations of biomedical literature. In Proceedings of BioLINK 2004, Association for Computational Linguistics, Boston, May 6 2004, pp. 41-47.
26. Theodosiou,T. et al. (2007) Gene functional annotation by statistical analysis of biomedical articles. Int. J. Med. Inform., 76, 601-613.
27. van Dongen,S. (2000) Graph clustering by flow simulation. PhD thesis, University of Utrecht. Available at http://micans.org/mc1/lit/ svdthesis.pdf.gz (last accessed on July 17 2008).
28. Weiss,N.A. (2002) Introductory Statistics. 6th edn. Addison-Wesley, USA.
29. Wheeler,D.L. et al. (2007) Database resources of the National Centre for Biotechnology Information. Nucleic Acids Res., 35(Database issue), D5-D12.
30. Wilbur,W.J. and Yang,Y. (1996) An analysis of statistical term strength and its use in the indexing and retrieval of molecular biology texts. Comput. Biol. Med., 26, 209-222.
31. Xiang,Y. (2003) A wingless flight. PLoS Biol., 1, e49.
32. Yamamoto,Y. and Takagi,T. (2007) Biomedical knowledge navigation by literature clustering. J. Biomed. Inform., 40, 114-130.
33. Zhang,J. and Carthew,R.W. (1998) Interactions between Wingless and DFz2 during Drosophila development. Development, 125, 3075-85.