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Research Interests

Development and evaluation of biomedical text-mining systems: algorithms & user interfaces.

Locating, automatically, information for biological database annotation.

Document clustering based on syntactic & semantic content.

Publications

Journals:

Hearst, M.A., Divoli, A., Guturu, H., Ksikes, A., Nakov, P., Wooldridge, M.A. and Ye, J. (2007) "BioText Search Engine: beyond abstract search", Bioinformatics, 23: 2196-2197 [PubMed]

Mitchell, A.L., Divoli, A., Kim, J.-H., Hilario, M., Selimas, I. and Attwood, T.K. (2005) "METIS: Multiple Extraction Techniques for Informative Sentences", Bioinformatics, 21: 4196-4197 [PubMed]

Divoli, A. and Attwood, T.K. (2005) "BioIE: Extracting Informative Sentences from the Biomedical Literature", Bioinformatics, 21: 2138-2139 [PubMed]

Selected Conferences & Workshops:

Divoli, A., Hearst, M.A. and Wooldridge, M.A. (2008) "Evidence for Showing Gene/Protein Name Suggestions in Bioscience Literature Search", PSB 2008, The Big Island of Hawaii, HI, USA (Conference Paper) [PubMed]

Hearst, M.A., Wooldridge, M.A., Ye, J. and Divoli, A. (2007) "Showing Figures and Captions in the Biotext Journal Search Engine", ISMB/ECCB 2007, Vienna, Austria (Poster Presentation)

Schwartz, A., Divoli, A. and Hearst, M.A. (2007) "Multiple alignment of citation sentences with conditional random fields and posterior decoding", EMNLP-CoNLL 2007, Prague, Czech Republic (Conference Paper)

Hearst, M.A., Divoli, A., Wooldridge, M.A. and Ye, J. (2007) "Exploring the Efficacy of Caption Search for Bioscience Journal Search Interfaces", BioNLP Workshop at ACL 2007, Prague, Czech Republic (Workshop Paper)

Nakov, P. and Divoli, A. (2007) "BioText Report for the Second BioCreAtIvE Challenge", Proceedings of the Second BioCreative Challenge Evaluation Workshop, Madrid, Spain (Participation Report Paper)

Divoli, A., Hearst, M.A., Nakov, P.I., Schwartz, A. and Ksikes, A. (2006) "BioText Team Report for the TREC 2006 Genomics Track", The Fifteenth Text REtrieval Conference Proceedings, Gaithersburg, MD, USA (Participation Report Paper)

Divoli, A., Winter, R., Pettifer, S. and Attwood, T.K. (2005) "BioQSpace: An interactive visualisation tool for clustering MEDLINE abstracts", ECCB ISCB SC Symposium, Madrid, Spain (Oral & Poster Presentation)

Divoli, A. and Attwood, T.K. (2005) "Text-mining challenges for protein family database annotation", ISMB, Detroit, USA (Oral & Poster Presentation)

Divoli, A. and Attwood, T.K. (2005) "Protein Family Databases: Text-Mining and Annotation", ISMB BioLINK SIG Workshop, Detroit, USA (Short Paper & Poster Presentation)

Divoli, A., Mitchell, A.L., Bradley, P. and Attwood, T.K. (2004) "METIS: Multiple Extraction Techniques for Informative Sentences", ISMB/ECCB, Glasgow, UK (Poster Presentation)

Mitchell, A.L., Bradley, P., Divoli, A. and Attwood, T.K. (2004) "Sequence Analysis Workshop", MIPNETS training meeting, Liverpool, UK (Workshop Organised)

Software

BioText Search Engine: Journal Search Engine Showing Figures and Captions

The BioText Search Engine provides biologists with new ways to access information from any Open Access article available at PubMedCentral.

BioQSpace: An interactive visualisation tool for clustering PubMed abstracts

BioQSpace clusters abstracts based on similarity measures calculated on user-specified weighting of certain attributes and allows for visualisation and navigation in 3D space.

METIS: Multiple Extraction Techniques for Informative Sentences

METIS accepts Swiss-Prot identifiers or FASTA-format sequences, performs BLAST to find related sequences, and then retrieves textual information from Swiss-Prot as well as related sentences from PubMed abstracts.

BioIE: Extracting Informative Sentences from the Biomedical Literature

A rule-based system for extracting informative sentences referring to either structure, function, diseases and therapeutic compounds, localisation or familial relationships of biological entities, particularly proteins.

Background

PhD (2006) at The University of Manchester with the Protein Sequence Analysis Group supervised by Prof Terri Attwood

Thesis: "Biomedical Text Mining Approaches: Applications in Protein Family Annotation"

MSc (2001) in Biosystems and Informatics at The University of Liverpool

Thesis: "Applications of Computational Linguistics for the Investigation of the Functional Genomics of Eukaryotic Transcription Factors"
Dissertation (mini thesis): "Applications of Ideas from Linguistics to Functional Genomics: Formal Grammars for Biological Sequences"

BSc (1999) in Biomedical Sciences at The Manchester Metropolitan University