Sophia Ananiadou

Sophia Ananiadou

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Sophia Ananiadou

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An ensemble of neural models for nested adverse drug events and medication extraction with subwords.

J Am Med Inform Assoc 2020 Jan;27(1):22-30

National Centre for Text Mining, School of Computer Science, The University of Manchester, Manchester, UK.

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http://dx.doi.org/10.1093/jamia/ocz075DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6913208PMC
January 2020

Adverse drug events and medication relation extraction in electronic health records with ensemble deep learning methods.

J Am Med Inform Assoc 2020 Jan;27(1):39-46

National Centre for Text Mining, School of Computer Science, The University of Manchester, Manchester, United Kingdom.

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http://dx.doi.org/10.1093/jamia/ocz101DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6913215PMC
January 2020

The pace of modern culture.

Nat Hum Behav 2020 Jan 20. Epub 2020 Jan 20.

Department of Life Sciences, Imperial College London, London, UK.

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http://dx.doi.org/10.1038/s41562-019-0802-4DOI Listing
January 2020

Improving reference prioritisation with PICO recognition.

BMC Med Inform Decis Mak 2019 12 5;19(1):256. Epub 2019 Dec 5.

National Centre of Text Mining, School of Computer Science, University of Manchester, Princess Street, Manchester, M1 7DN, UK.

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http://dx.doi.org/10.1186/s12911-019-0992-8DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6896258PMC
December 2019

Improving clinical named entity recognition in Chinese using the graphical and phonetic feature.

BMC Med Inform Decis Mak 2019 Dec 23;19(Suppl 7):273. Epub 2019 Dec 23.

National Centre of Text Mining, University of Manchester, Manchester, UK.

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http://dx.doi.org/10.1186/s12911-019-0980-zDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6927114PMC
December 2019

Mapping anatomical related entities to human body parts based on wikipedia in discharge summaries.

BMC Bioinformatics 2019 Aug 17;20(1):430. Epub 2019 Aug 17.

State Key Laboratory of Software Development Environment and Key Laboratory of Biomechanics and Mechanobiology of Ministry of Education and Research Institute of Beihang University in Shenzhen, Beijing Advanced Innovation Center for Biomedical Engineering, Beihang University, Xueyuan Road No.37, Beijing, 100191, China.

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http://dx.doi.org/10.1186/s12859-019-3005-0DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6697955PMC
August 2019

A Text Mining Pipeline Using Active and Deep Learning Aimed at Curating Information in Computational Neuroscience.

Neuroinformatics 2019 Jul;17(3):391-406

The National Centre for Text Mining, School of Computer Science, University of Manchester, Road, M13 9PL, Oxford, UK.

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http://dx.doi.org/10.1007/s12021-018-9404-yDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6594987PMC
July 2019

Annotating and detecting phenotypic information for chronic obstructive pulmonary disease.

JAMIA Open 2019 Jul 26;2(2):261-271. Epub 2019 Apr 26.

National Centre for Text Mining, School of Computer Science, The University of Manchester, Manchester, UK.

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http://dx.doi.org/10.1093/jamiaopen/ooz009DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6951876PMC
July 2019

Quantifying risk factors in medical reports with a context-aware linear model.

J Am Med Inform Assoc 2019 Jun;26(6):537-546

National Centre for Text Mining, School of Computer Science, University of Manchester, Manchester, United Kingdom.

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http://dx.doi.org/10.1093/jamia/ocz004DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6515525PMC
June 2019

Thalia: semantic search engine for biomedical abstracts.

Bioinformatics 2019 May;35(10):1799-1801

National Centre for Text Mining, School of Computer Science, University of Manchester, Manchester, UK.

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http://dx.doi.org/10.1093/bioinformatics/bty871DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6513154PMC
May 2019

Hypothesis, analysis and synthesis, it's all Greek to me.

Elife 2019 02 20;8. Epub 2019 Feb 20.

Bioinformatics Research Laboratory, Department of Biological Sciences, University of Cyprus, Nicosia, Cyprus.

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http://dx.doi.org/10.7554/eLife.43514DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6382348PMC
February 2019

COPIOUS: A gold standard corpus of named entities towards extracting species occurrence from biodiversity literature.

Biodivers Data J 2019 22(7):e29626. Epub 2019 Jan 22.

The National Centre for Text Mining, University of Manchester, Manchester, United Kingdom The National Centre for Text Mining, University of Manchester Manchester United Kingdom.

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http://dx.doi.org/10.3897/BDJ.7.e29626DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6351503PMC
January 2019

Prioritising references for systematic reviews with RobotAnalyst: A user study.

Res Synth Methods 2018 Sep 30;9(3):470-488. Epub 2018 Jul 30.

National Centre for Text Mining, School of Computer Science, University of Manchester, Manchester, UK.

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http://dx.doi.org/10.1002/jrsm.1311DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6175382PMC
September 2018

Annotation and detection of drug effects in text for pharmacovigilance.

J Cheminform 2018 Aug 13;10(1):37. Epub 2018 Aug 13.

National Centre for Text Mining, School of Computer Science, Manchester Institute of Biotechnology, University of Manchester, 131 Princess Street, Manchester, M1 7DN, UK.

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http://dx.doi.org/10.1186/s13321-018-0290-yDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6089860PMC
August 2018

Biosimilar vs originator insulins: Systematic review and meta-analysis.

Diabetes Obes Metab 2018 07 17;20(7):1787-1792. Epub 2018 Apr 17.

Department of Diabetes and Metabolic Diseases, Graduate School of Medicine, University of Tokyo, Tokyo, Japan.

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http://doi.wiley.com/10.1111/dom.13291
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http://dx.doi.org/10.1111/dom.13291DOI Listing
July 2018

Data Visualization with Structural Control of Global Cohort and Local Data Neighborhoods.

IEEE Trans Pattern Anal Mach Intell 2018 06 15;40(6):1323-1337. Epub 2017 Jun 15.

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http://dx.doi.org/10.1109/TPAMI.2017.2715806DOI Listing
June 2018

Identification of research hypotheses and new knowledge from scientific literature.

BMC Med Inform Decis Mak 2018 06 25;18(1):46. Epub 2018 Jun 25.

National Centre for Text Mining, University of Manchester, Manchester, UK.

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http://dx.doi.org/10.1186/s12911-018-0639-1DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6019216PMC
June 2018

LitPathExplorer: a confidence-based visual text analytics tool for exploring literature-enriched pathway models.

Bioinformatics 2018 04;34(8):1389-1397

National Centre for Text Mining, School of Computer Science, University of Manchester, Manchester M1 7DN, UK.

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http://dx.doi.org/10.1093/bioinformatics/btx774DOI Listing
April 2018

Using uncertainty to link and rank evidence from biomedical literature for model curation.

Bioinformatics 2017 Dec;33(23):3784-3792

National Centre for Text Mining, School of Computer Science.

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http://dx.doi.org/10.1093/bioinformatics/btx466DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5860317PMC
December 2017

Text mining resources for the life sciences.

Database (Oxford) 2016 25;2016. Epub 2016 Nov 25.

National Centre for Text Mining, School of Computer Science, University of Manchester, Manchester, UK.

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http://dx.doi.org/10.1093/database/baw145DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5199186PMC
November 2017

Risk of bias reporting in the recent animal focal cerebral ischaemia literature.

Clin Sci (Lond) 2017 Oct 12;131(20):2525-2532. Epub 2017 Oct 12.

Centre for Clinical Brain Sciences, University of Edinburgh, Chancellor's Building, Little France Crescent, Edinburgh, U.K.

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http://dx.doi.org/10.1042/CS20160722DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5869854PMC
October 2017

biochem4j: Integrated and extensible biochemical knowledge through graph databases.

PLoS One 2017 14;12(7):e0179130. Epub 2017 Jul 14.

Manchester Centre for Synthetic Biology of Fine and Specialty Chemicals (SYNBIOCHEM), Manchester Institute of Biotechnology, The University of Manchester, Manchester, United Kingdom.

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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0179130PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5510799PMC
September 2017

Mapping Phenotypic Information in Heterogeneous Textual Sources to a Domain-Specific Terminological Resource.

PLoS One 2016 19;11(9):e0162287. Epub 2016 Sep 19.

National Centre for Text Mining, Manchester Institute of Biotechnology, Manchester University, Manchester, United Kingdom.

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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0162287PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5028053PMC
August 2017

A semi-supervised approach using label propagation to support citation screening.

J Biomed Inform 2017 08 23;72:67-76. Epub 2017 Jun 23.

National Centre for Text Mining, School of Computer Science, University of Manchester, Manchester, United Kingdom. Electronic address:

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http://dx.doi.org/10.1016/j.jbi.2017.06.018DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5726085PMC
August 2017

Constructing a biodiversity terminological inventory.

PLoS One 2017 17;12(4):e0175277. Epub 2017 Apr 17.

National Centre for Text Mining, School of Computer Science, University of Manchester, Manchester, United Kingdom.

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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0175277PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5393592PMC
May 2017

Argo: enabling the development of bespoke workflows and services for disease annotation.

Database (Oxford) 2016 17;2016. Epub 2016 May 17.

National Centre for Text Mining, School of Computer Science, University of Manchester, Manchester, UK.

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http://dx.doi.org/10.1093/database/baw066DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4869796PMC
January 2017

Topic detection using paragraph vectors to support active learning in systematic reviews.

J Biomed Inform 2016 08 10;62:59-65. Epub 2016 Jun 10.

School of Computer Science, National Centre for Text Mining, University of Manchester, Manchester, United Kingdom. Electronic address:

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http://dx.doi.org/10.1016/j.jbi.2016.06.001DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4981645PMC
August 2016

Analysis of the effect of sentiment analysis on extracting adverse drug reactions from tweets and forum posts.

J Biomed Inform 2016 08 27;62:148-58. Epub 2016 Jun 27.

Department of Biomedical Informatics, Arizona State University, Mayo Clinic, Samuel C. Johnson Research Building, 13212 East Shea Boulevard, Scottsdale, AZ 85259, United States. Electronic address:

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http://dx.doi.org/10.1016/j.jbi.2016.06.007DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4981644PMC
August 2016

Text Mining the History of Medicine.

PLoS One 2016 6;11(1):e0144717. Epub 2016 Jan 6.

National Centre for Text Mining, School of Computer Science, University of Manchester, Manchester, United Kingdom.

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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0144717PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4703377PMC
July 2016

A cross-lingual similarity measure for detecting biomedical term translations.

PLoS One 2015 1;10(6):e0126196. Epub 2015 Jun 1.

School of Computer Science, University of Manchester, Manchester, United Kingdom; National Centre for Text Mining, University of Manchester, Manchester, United Kingdom.

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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0126196PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4452086PMC
February 2016

Supporting systematic reviews using LDA-based document representations.

Syst Rev 2015 Nov 26;4:172. Epub 2015 Nov 26.

School of Computer Science, National Centre for Text Mining, The University of Manchester, Manchester, UK.

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http://dx.doi.org/10.1186/s13643-015-0117-0DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4662004PMC
November 2015

Boosting drug named entity recognition using an aggregate classifier.

Artif Intell Med 2015 Oct 17;65(2):145-53. Epub 2015 Jun 17.

National Centre for Text Mining (NaCTeM), School of Computer Science, The University of Manchester, Manchester Institute of Biotechnology, 131 Princess Street, Manchester M1 7DN, United Kingdom. Electronic address:

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http://dx.doi.org/10.1016/j.artmed.2015.05.007DOI Listing
October 2015

Erratum to: Using text mining for study identification in systematic reviews: a systematic review of current approaches.

Syst Rev 2015 Apr 28;4:59. Epub 2015 Apr 28.

The National Centre for Text Mining and School of Computer Science, Manchester Institute of Biotechnology, University of Manchester, 131 Princess Street, Manchester, M1 7DN, UK.

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http://systematicreviewsjournal.biomedcentral.com/articles/1
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http://dx.doi.org/10.1186/s13643-015-0031-5DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4411935PMC
April 2015

Supporting the annotation of chronic obstructive pulmonary disease (COPD) phenotypes with text mining workflows.

J Biomed Semantics 2015 14;6. Epub 2015 Mar 14.

National Centre for Text Mining, School of Computer Science, University of Manchester, Manchester Institute of Biotechnology, 131 Princess Street, Manchester, UK.

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http://www.jbiomedsem.com/content/6/1/8
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http://dx.doi.org/10.1186/s13326-015-0004-6DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4364458PMC
March 2015

Optimising chemical named entity recognition with pre-processing analytics, knowledge-rich features and heuristics.

J Cheminform 2015 19;7(Suppl 1 Text mining for chemistry and the CHEMDNER track):S6. Epub 2015 Jan 19.

National Centre for Text Mining, Manchester Institute of Biotechnology, 131 Princess St, Manchester, M1 7DN, UK.

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http://dx.doi.org/10.1186/1758-2946-7-S1-S6DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4331696PMC
March 2015

Processing biological literature with customizable Web services supporting interoperable formats.

Database (Oxford) 2014 8;2014. Epub 2014 Jul 8.

National Centre for Text Mining, School of Computer Science, University of Manchester, M1 7DN, UK and Department of Computer Science, University of the Philippines Diliman, Philippines 1101.

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http://dx.doi.org/10.1093/database/bau064DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4086403PMC
February 2015

Text-mining-assisted biocuration workflows in Argo.

Database (Oxford) 2014 18;2014. Epub 2014 Jul 18.

National Centre for Text Mining, School of Computer Science, University of Manchester, UK and Department of Computer Science, University of the Philippines Diliman, Philippines.

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http://dx.doi.org/10.1093/database/bau070DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4103424PMC
February 2015

Using text mining for study identification in systematic reviews: a systematic review of current approaches.

Syst Rev 2015 Jan 14;4. Epub 2015 Jan 14.

Evidence for Policy and Practice Information and Coordinating (EPPI)-Centre, Social Science Research Unit, UCL Institute of Education, University of London, London, UK.

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http://dx.doi.org/10.1186/2046-4053-4-5DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4320539PMC
January 2015

Reducing systematic review workload through certainty-based screening.

J Biomed Inform 2014 Oct 19;51:242-53. Epub 2014 Jun 19.

The National Centre for Text Mining and School of Computer Science, Manchester Institute of Biotechnology, University of Manchester, 131 Princess Street, Manchester M1 7DN, UK. Electronic address:

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https://linkinghub.elsevier.com/retrieve/pii/S15320464140014
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http://dx.doi.org/10.1016/j.jbi.2014.06.005DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4199186PMC
October 2014

Generalising semantic category disambiguation with large lexical resources for fun and profit.

J Biomed Semantics 2014 2;5:26. Epub 2014 Jun 2.

School of Computer Science, University of Manchester, Manchester, UK ; National Centre for Text Mining, University of Manchester, Manchester, UK ; Microsoft Research Asia, Beijing, People's Republic of China.

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http://dx.doi.org/10.1186/2041-1480-5-26DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4107982PMC
August 2014

Anatomical entity mention recognition at literature scale.

Bioinformatics 2014 Mar 25;30(6):868-75. Epub 2013 Oct 25.

National Centre for Text Mining and University of Manchester, Manchester, UK.

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http://dx.doi.org/10.1093/bioinformatics/btt580DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3957068PMC
March 2014

Recognising discourse causality triggers in the biomedical domain.

J Bioinform Comput Biol 2013 Dec 2;11(6):1343008. Epub 2013 Dec 2.

The National Centre for Text Mining, School of Computer Science, The University of Manchester, 131 Princess Street, Manchester M1 7DN, United Kingdom.

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http://dx.doi.org/10.1142/S0219720013430087DOI Listing
December 2013

A method for discovering and inferring appropriate eligibility criteria in clinical trial protocols without labeled data.

BMC Med Inform Decis Mak 2013 5;13 Suppl 1:S6. Epub 2013 Apr 5.

National Center for Text Mining & School of Computer Science, The University of Manchester, Manchester, M1 7DN, UK.

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http://dx.doi.org/10.1186/1472-6947-13-S1-S6DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3618207PMC
July 2013

A method for integrating and ranking the evidence for biochemical pathways by mining reactions from text.

Bioinformatics 2013 Jul;29(13):i44-52

The National Centre for Text Mining and School of Computer Science and School of Chemistry and the Manchester Institute of Biotechnology, The University of Manchester, Manchester M1 7DN, UK.

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http://dx.doi.org/10.1093/bioinformatics/btt227DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3694679PMC
July 2013

Wide coverage biomedical event extraction using multiple partially overlapping corpora.

BMC Bioinformatics 2013 Jun 3;14:175. Epub 2013 Jun 3.

The National Centre for Text Mining and School of Computer Science, Manchester Institute of Biotechnology, University of Manchester, 131 Princess Street, Manchester, M1 7DN, UK.

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http://dx.doi.org/10.1186/1471-2105-14-175DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3680179PMC
June 2013

Deploying and sharing U-Compare workflows as web services.

J Biomed Semantics 2013 Feb 18;4(1). Epub 2013 Feb 18.

National Centre for Text Mining & School of Computer Science, The University of Manchester, Manchester, M1 7DN, UK.

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http://dx.doi.org/10.1186/2041-1480-4-7DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3658995PMC
February 2013

BioCause: Annotating and analysing causality in the biomedical domain.

BMC Bioinformatics 2013 Jan 16;14. Epub 2013 Jan 16.

The National Centre for Text Mining, School of Computer Science, The University of Manchester, 131 Princess Street, Manchester M1 7DN, UK.

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http://dx.doi.org/10.1186/1471-2105-14-2DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3621543PMC
January 2013

Negated bio-events: analysis and identification.

BMC Bioinformatics 2013 Jan 16;14:14. Epub 2013 Jan 16.

National Centre for Text Mining, Manchester Interdisciplinary Biocentre, University of Manchester, 131 Princess Street, Manchester M1 7DN, UK.

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http://dx.doi.org/10.1186/1471-2105-14-14DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3561152PMC
January 2013

Proximity-based frameworks for generating embeddings from multi-output data.

IEEE Trans Pattern Anal Mach Intell 2012 Nov;34(11):2216-32

National Centre for Text Mining (NaCTeM), School of Computer Science, University of Manchester, Manchester, United Kingdom.

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http://dx.doi.org/10.1109/tpami.2012.20DOI Listing
November 2012

Event extraction across multiple levels of biological organization.

Bioinformatics 2012 Sep;28(18):i575-i581

National Centre for Text Mining and School of Computer Science, University of Manchester, Manchester, UK.

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http://dx.doi.org/10.1093/bioinformatics/bts407DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3436834PMC
September 2012

Boosting automatic event extraction from the literature using domain adaptation and coreference resolution.

Bioinformatics 2012 Jul 25;28(13):1759-65. Epub 2012 Apr 25.

The National Centre for Text Mining (NaCTeM), UK.

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http://dx.doi.org/10.1093/bioinformatics/bts237DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3381963PMC
July 2012

Argo: an integrative, interactive, text mining-based workbench supporting curation.

Database (Oxford) 2012 20;2012:bas010. Epub 2012 Mar 20.

National Centre for Text Mining and School of Computer Science, University of Manchester, 131 Princess Street, Manchester, M1 7DN, UK.

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https://academic.oup.com/database/article-lookup/doi/10.1093
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http://dx.doi.org/10.1093/database/bas010DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3308166PMC
June 2012

Overview of the ID, EPI and REL tasks of BioNLP Shared Task 2011.

BMC Bioinformatics 2012 Jun 26;13 Suppl 11:S2. Epub 2012 Jun 26.

School of Computer Science, University of Manchester, Manchester, UK.

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http://dx.doi.org/10.1186/1471-2105-13-S11-S2DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3384257PMC
June 2012

Extracting semantically enriched events from biomedical literature.

BMC Bioinformatics 2012 May 23;13:108. Epub 2012 May 23.

The National Centre for Text Mining, Manchester Interdisciplinary Biocentre, University of Manchester, Manchester, UK.

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http://dx.doi.org/10.1186/1471-2105-13-108DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3464657PMC
May 2012

ASCOT: a text mining-based web-service for efficient search and assisted creation of clinical trials.

BMC Med Inform Decis Mak 2012 Apr 30;12 Suppl 1:S3. Epub 2012 Apr 30.

National Centre for Text Mining & School of Computer Science, The University of Manchester, Manchester M1 7DN, UK.

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http://dx.doi.org/10.1186/1472-6947-12-S1-S3DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3339391PMC
April 2012

Automatic extraction of angiogenesis bioprocess from text.

Bioinformatics 2011 Oct 5;27(19):2730-7. Epub 2011 Aug 5.

National Centre for Text Mining, University of Manchester, Manchester, AstraZeneca, Alderley Park, UK.

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http://dx.doi.org/10.1093/bioinformatics/btr460DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3179660PMC
October 2011

Enriching a biomedical event corpus with meta-knowledge annotation.

BMC Bioinformatics 2011 Oct 10;12:393. Epub 2011 Oct 10.

National Centre for Text Mining, Manchester Interdisciplinary Biocentre, School of Computer Science, University of Manchester, 131 Princess Street, Manchester, M1 7DN, UK.

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http://dx.doi.org/10.1186/1471-2105-12-393DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3222636PMC
October 2011

Automatic extraction of microorganisms and their habitats from free text using text mining workflows.

J Integr Bioinform 2011 Oct 10;8(2):184. Epub 2011 Oct 10.

National Centre for Text Mining, University of Manchester, 131 Princess Street, Manchester M1 7DN, UK.

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http://dx.doi.org/10.2390/biecoll-jib-2011-184DOI Listing
October 2011

Detecting experimental techniques and selecting relevant documents for protein-protein interactions from biomedical literature.

BMC Bioinformatics 2011 Oct 3;12 Suppl 8:S11. Epub 2011 Oct 3.

National Centre for Text Mining and School of Computer Science, University of Manchester, Manchester, UK.

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http://dx.doi.org/10.1186/1471-2105-12-S8-S11DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3269934PMC
October 2011

Using workflows to explore and optimise named entity recognition for chemistry.

PLoS One 2011 25;6(5):e20181. Epub 2011 May 25.

National Centre for Text Mining, Manchester Interdisciplinary Biocentre, University of Manchester, Manchester, United Kingdom.

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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3102085PMC
September 2011

Discovering and visualizing indirect associations between biomedical concepts.

Bioinformatics 2011 Jul;27(13):i111-9

School of Information Science, Japan Advanced Institute of Science and Technology (JAIST), Nomi, Japan.

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http://dx.doi.org/10.1093/bioinformatics/btr214DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3117364PMC
July 2011

AGRA: analysis of gene ranking algorithms.

Bioinformatics 2011 Apr 23;27(8):1185-6. Epub 2011 Feb 23.

Faculty of Health Sciences, University of Maribor, Maribor, Slovenia.

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http://dx.doi.org/10.1093/bioinformatics/btr097DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3072556PMC
April 2011

Applications of text mining within systematic reviews.

Res Synth Methods 2011 Mar 11;2(1):1-14. Epub 2011 Apr 11.

University of Manchester, National Centre for Text Mining, Manchester, U.K.

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http://dx.doi.org/10.1002/jrsm.27DOI Listing
March 2011

Text mining meets workflow: linking U-Compare with Taverna.

Bioinformatics 2010 Oct 12;26(19):2486-7. Epub 2010 Aug 12.

Department of Computer Science, The University of Tokyo Hongo 7-3-1, Bunkyo-ku, Tokyo, 113-0033 Japan.

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http://dx.doi.org/10.1093/bioinformatics/btq464DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2944208PMC
October 2010

Supporting the education evidence portal via text mining.

Philos Trans A Math Phys Eng Sci 2010 Aug;368(1925):3829-44

School of Computer Science and National Centre for Text Mining, University of Manchester, 131 Princess Street, Manchester M1 7DN, UK.

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http://dx.doi.org/10.1098/rsta.2010.0152DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2981997PMC
August 2010

Event extraction for systems biology by text mining the literature.

Trends Biotechnol 2010 Jul 1;28(7):381-90. Epub 2010 Jun 1.

University of Manchester, Manchester M13 9PL, UK.

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https://linkinghub.elsevier.com/retrieve/pii/S01677799100007
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http://dx.doi.org/10.1016/j.tibtech.2010.04.005DOI Listing
July 2010

Building a high-quality sense inventory for improved abbreviation disambiguation.

Bioinformatics 2010 May 25;26(9):1246-53. Epub 2010 Mar 25.

Graduate School of Information Science and Technology, University of Tokyo, Tokyo, Japan.

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http://dx.doi.org/10.1093/bioinformatics/btq129DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2859134PMC
May 2010

Disambiguating the species of biomedical named entities using natural language parsers.

Bioinformatics 2010 Mar 6;26(5):661-7. Epub 2010 Jan 6.

National Centre for Text Mining, School of Computer Science, University of Manchester, Manchester, UK.

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http://dx.doi.org/10.1093/bioinformatics/btq002DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2828111PMC
March 2010

The value of an in-domain lexicon in genomics QA.

J Bioinform Comput Biol 2010 Feb;8(1):147-61

National Centre for Text Mining, School of Computer Science, University of Manchester, MIB, 131 Princess Street, Manchester M17DN, United Kingdom.

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http://dx.doi.org/10.1142/s0219720010004513DOI Listing
February 2010

Construction of an annotated corpus to support biomedical information extraction.

BMC Bioinformatics 2009 Oct 23;10:349. Epub 2009 Oct 23.

National Centre for Text Mining, Manchester Interdisciplinary Biocentre, University of Manchester, 131 Princess Street, Manchester, M1 7DN, UK.

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http://dx.doi.org/10.1186/1471-2105-10-349DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2774701PMC
October 2009

U-Compare: share and compare text mining tools with UIMA.

Bioinformatics 2009 Aug 4;25(15):1997-8. Epub 2009 May 4.

Department of Computer Science, University of Tokyo Hongo 7-3-1, Tokyo 113-0033, Japan.

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http://dx.doi.org/10.1093/bioinformatics/btp289DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2712335PMC
August 2009

Clinical text classification under the Open and Closed Topic Assumptions.

Int J Data Min Bioinform 2009 ;3(3):299-313

School of Computer Science, University of Manchester MIB, 131 Princess Street, Manchester, M1 7DN, UK.

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http://dx.doi.org/10.1504/ijdmb.2009.026703DOI Listing
August 2009

FACTA: a text search engine for finding associated biomedical concepts.

Bioinformatics 2008 Nov 4;24(21):2559-60. Epub 2008 Sep 4.

School of Computer Science, The University of Manchester, Manchester, UK.

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http://dx.doi.org/10.1093/bioinformatics/btn469DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2572701PMC
November 2008

Themes in biomedical natural language processing: BioNLP08.

BMC Bioinformatics 2008 Nov 19;9 Suppl 11:S1. Epub 2008 Nov 19.

US National Library of Medicine, 8600 Rockville Pike, Bethesda, MD 20894, USA.

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http://dx.doi.org/10.1186/1471-2105-9-S11-S1DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2586759PMC
November 2008

How to make the most of NE dictionaries in statistical NER.

BMC Bioinformatics 2008 Nov 19;9 Suppl 11:S5. Epub 2008 Nov 19.

School of Computer Science, University of Manchester, 131 Princess Street, Manchester M17DN, UK.

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http://dx.doi.org/10.1186/1471-2105-9-S11-S5DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2586754PMC
November 2008

Accelerating the annotation of sparse named entities by dynamic sentence selection.

BMC Bioinformatics 2008 Nov 19;9 Suppl 11:S8. Epub 2008 Nov 19.

School of Computer Science, The University of Manchester, MIB, 131 Princess Street, Manchester M17DN, UK.

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http://dx.doi.org/10.1186/1471-2105-9-S11-S8DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2586757PMC
November 2008

Normalizing biomedical terms by minimizing ambiguity and variability.

BMC Bioinformatics 2008 Apr 11;9 Suppl 3:S2. Epub 2008 Apr 11.

School of Computer Science, The University of Manchester, MIB, 131 Princess Street, Manchester, M1 7DN, UK.

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http://dx.doi.org/10.1186/1471-2105-9-S3-S2DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2352870PMC
April 2008

Filling the gaps between tools and users: a tool comparator, using protein-protein interaction as an example.

Pac Symp Biocomput 2008 :616-27

Department of Computer Science, University of Tokyo Hongo 7-3-1, Bunkyo-ku, Tokyo 113-0033, Tokyo.

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March 2008

Learning string similarity measures for gene/protein name dictionary look-up using logistic regression.

Bioinformatics 2007 Oct 12;23(20):2768-74. Epub 2007 Aug 12.

School of Computer Science, The University of Manchester, Manchester, UK.

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http://dx.doi.org/10.1093/bioinformatics/btm393DOI Listing
October 2007

Text mining and its potential applications in systems biology.

Trends Biotechnol 2006 Dec 12;24(12):571-9. Epub 2006 Oct 12.

School of Computer Science, National Centre for Text Mining, The Manchester Interdisciplinary Biocentre, The University of Manchester, 131 Princess Street, Manchester M1 7ND, UK.

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http://dx.doi.org/10.1016/j.tibtech.2006.10.002DOI Listing
December 2006

Building an abbreviation dictionary using a term recognition approach.

Bioinformatics 2006 Dec 18;22(24):3089-95. Epub 2006 Oct 18.

Graduate School of Information Science and Technology, The University of Tokyo 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8651, Japan.

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http://dx.doi.org/10.1093/bioinformatics/btl534DOI Listing
December 2006

Text mining and ontologies in biomedicine: making sense of raw text.

Brief Bioinform 2005 Sep;6(3):239-51

School of Chemistry, The University of Manchester, Sackville Street, PO Box 88, Manchester M60 1QD, UK.

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http://dx.doi.org/10.1093/bib/6.3.239DOI Listing
September 2005