Karin Verspoor

Karin Verspoor

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Karin Verspoor

Publications by authors named "Karin Verspoor"

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DrKnow: A Diagnostic Learning Tool with Feedback from Automated Clinical Decision Support.

AMIA Annu Symp Proc 2018 5;2018:1348-1357. Epub 2018 Dec 5.

School of Computing and Information Systems, Melbourne School of Engineering, University of Melbourne, Australia.

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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6371235PMC
January 2020

The current scope of healthcare-associated infection surveillance activities in hospitalized immunocompromised patients: a systematic review.

Int J Epidemiol 2019 12;48(6):1768-1782

Sir Peter MacCallum Department of Oncology, Victorian Comprehensive Cancer Centre, University of Melbourne, Melbourne, Victoria, Australia.

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https://academic.oup.com/ije/advance-article/doi/10.1093/ije
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http://dx.doi.org/10.1093/ije/dyz162DOI Listing
December 2019

Quantifying semantic similarity of clinical evidence in the biomedical literature to facilitate related evidence synthesis.

J Biomed Inform 2019 Dec 30;100:103321. Epub 2019 Oct 30.

School of Computing and Information Systems, University of Melbourne, Melbourne, VIC, Australia. Electronic address:

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http://dx.doi.org/10.1016/j.jbi.2019.103321DOI Listing
December 2019

Exploring effective approaches for haplotype block phasing.

BMC Bioinformatics 2019 Oct 30;20(1):540. Epub 2019 Oct 30.

Centre for Epidemiology and Biostatistics, The University of Melbourne, Parkville, 3010, Australia.

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http://dx.doi.org/10.1186/s12859-019-3095-8DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6822470PMC
October 2019

Characterizing the Scope of Exposome Research Through Topic Modeling and Ontology Analysis.

Stud Health Technol Inform 2019 Aug;264:1530-1531

Health and Biomedical Informatics Centre, The University of Melbourne, Parkville, Victoria, Australia.

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http://dx.doi.org/10.3233/SHTI190519DOI Listing
August 2019

Search Effectiveness in Nonredundant Sequence Databases: Assessments and Solutions.

J Comput Biol 2019 Jun 24;26(6):605-617. Epub 2018 Dec 24.

1 School of Computing and Information Systems, The University of Melbourne, Parkville, Australia.

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http://dx.doi.org/10.1089/cmb.2018.0198DOI Listing
June 2019

Automated assessment of biological database assertions using the scientific literature.

BMC Bioinformatics 2019 Apr 29;20(1):216. Epub 2019 Apr 29.

School of Computing and Information Systems, University of Melbourne, Melbourne, 3010, Australia.

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http://dx.doi.org/10.1186/s12859-019-2801-xDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6489365PMC
April 2019

From POS tagging to dependency parsing for biomedical event extraction.

BMC Bioinformatics 2019 Feb 12;20(1):72. Epub 2019 Feb 12.

School of Computing and Information Systems, The University of Melbourne, Melbourne, Australia.

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http://dx.doi.org/10.1186/s12859-019-2604-0DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6373122PMC
February 2019

Crowdsourcing critical appraisal of research evidence (CrowdCARE) was found to be a valid approach to assessing clinical research quality.

J Clin Epidemiol 2018 12 1;104:8-14. Epub 2018 Aug 1.

Department of Optometry and Vision Sciences, University of Melbourne, Parkville, Victoria, Australia 3010. Electronic address:

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http://dx.doi.org/10.1016/j.jclinepi.2018.07.015DOI Listing
December 2018

Appraising the Quality of Systematic Reviews for Age-Related Macular Degeneration Interventions: A Systematic Review.

JAMA Ophthalmol 2018 09;136(9):1051-1061

Department of Optometry and Vision Sciences, University of Melbourne, Parkville, Victoria, Australia.

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http://dx.doi.org/10.1001/jamaophthalmol.2018.2620DOI Listing
September 2018

Diagnostic Machine Learning Models for Acute Abdominal Pain: Towards an e-Learning Tool for Medical Students.

Stud Health Technol Inform 2017 ;245:447-451

Dept of Computing and Information Systems, School of Engineering, University of Melbourne, Melbourne, Australia.

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June 2018

Characterising the Scope of Exposome Research: A Generalisable Approach.

Stud Health Technol Inform 2017 ;245:457-461

Health and Biomedical Informatics Centre, The University of Melbourne, Parkville, Victoria, Australia.

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June 2018

Understanding the Context of Learning in an Online Social Network for Health Professionals' Informal Learning.

Stud Health Technol Inform 2017 ;235:353-357

General Practice Academic Unit, Graduate School of Medicine, University of Wollongong.

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April 2018

Understanding Health Professionals' Informal Learning in Online Social Networks: A Cross-Sectional Survey.

Stud Health Technol Inform 2017 ;239:77-83

General Practice Academic Unit, Graduate School of Medicine, University of Wollongong.

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April 2018

A Semantic-Based K-Anonymity Scheme for Health Record Linkage.

Stud Health Technol Inform 2017 ;239:84-90

Department of Computing and Information System, The University of Melbourne, Melbourne, Australia.

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April 2018

A two-tiered unsupervised clustering approach for drug repositioning through heterogeneous data integration.

BMC Bioinformatics 2018 04 11;19(1):129. Epub 2018 Apr 11.

Research School of Engineering, College of Engineering & Computer Science, The Australian National University, Canberra, ACT, 2601, Australia.

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http://dx.doi.org/10.1186/s12859-018-2123-4DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5896044PMC
April 2018

Analysing Health Professionals' Learning Interactions in an Online Social Network: A Longitudinal Study.

Stud Health Technol Inform 2016 ;227:93-9

General Practice Academic Unit, Graduate School of Medicine, University of Wollongong.

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February 2018

Finding and Exploring Health Information with a Slider-Based User Interface.

Stud Health Technol Inform 2016 ;227:106-12

Department of Computing and Information Systems, The University of Melbourne, Melbourne, Australia.

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February 2018

Exploiting graph kernels for high performance biomedical relation extraction.

J Biomed Semantics 2018 01 30;9(1). Epub 2018 Jan 30.

School of Computing and Information Systems, University of Melbourne, Melbourne, Australia.

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http://dx.doi.org/10.1186/s13326-017-0168-3DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5791373PMC
January 2018

BioCreative VI Precision Medicine Track system performance is constrained by entity recognition and variations in corpus characteristics.

Database (Oxford) 2018 01 1;2018. Epub 2018 Jan 1.

School of Computing and Information Systems, The University of Melbourne, Parkville VIC Australia.

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http://dx.doi.org/10.1093/database/bay122DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6301335PMC
January 2018

Coreference resolution improves extraction of Biological Expression Language statements from texts.

Database (Oxford) 2016 3;2016. Epub 2016 Jul 3.

Department of Computing and Information Systems, the University of Melbourne

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http://dx.doi.org/10.1093/database/baw076DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4930833PMC
November 2017

Duplicates, redundancies and inconsistencies in the primary nucleotide databases: a descriptive study.

Database (Oxford) 2017 10;2017. Epub 2017 Jan 10.

Department of Computing and Information Systems, The University of Melbourne, Parkville, VIC, 3010, Australia.

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http://dx.doi.org/10.1093/database/baw163DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5225397PMC
November 2017

Developing a Manually Annotated Corpus of Clinical Letters for Breast Cancer Patients on Routine Follow-Up.

Stud Health Technol Inform 2017 ;235:196-200

The University of Melbourne, Melbourne VIC Australia.

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October 2017

Supervised Learning for Detection of Duplicates in Genomic Sequence Databases.

PLoS One 2016 4;11(8):e0159644. Epub 2016 Aug 4.

Department of Computing and Information Systems, The University of Melbourne, Melbourne, Australia.

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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0159644PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4973881PMC
August 2017

Automated detection of records in biological sequence databases that are inconsistent with the literature.

J Biomed Inform 2017 07 15;71:229-240. Epub 2017 Jun 15.

Department of Computing and Information Systems, The University of Melbourne, Parkville 3053, Australia. Electronic address:

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http://dx.doi.org/10.1016/j.jbi.2017.06.015DOI Listing
July 2017

The Pre-Eclampsia Ontology: A Disease Ontology Representing the Domain Knowledge Specific to Pre-Eclampsia.

PLoS One 2016 27;11(10):e0162828. Epub 2016 Oct 27.

Department of Clinical Informatics, Tohoku University Graduate School of Medicine 2-1, Seiryo-machi, Aoba-ku, Sendai, Miyagi, Japan.

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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0162828PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5082890PMC
June 2017

Mapping biomedical vocabularies: a semi-automated term matching approach.

Stud Health Technol Inform 2014 ;202:16-9

Dept. of Computing and Information Systems, The University of Melbourne, Australia.

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April 2017

Positive-Unlabeled Learning for inferring drug interactions based on heterogeneous attributes.

BMC Bioinformatics 2017 Mar 1;18(1):140. Epub 2017 Mar 1.

Research School of Engineering, College of Engineering and Computer Science, The Australian National University, Canberra, 2601, ACT, Australia.

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http://dx.doi.org/10.1186/s12859-017-1546-7DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5333429PMC
March 2017

Benchmarks for measurement of duplicate detection methods in nucleotide databases.

Database (Oxford) 2017 Jan 8. Epub 2017 Jan 8.

Department of Computing and Information Systems, The University of Melbourne, Parkville, VIC 3010, Australia.

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http://dx.doi.org/10.1093/database/baw164DOI Listing
January 2017

Multi-field query expansion is effective for biomedical dataset retrieval.

Database (Oxford) 2017 01;2017

School of Computing and Information Systems, The University of Melbourne, Parkville, VIC, 3010, Australia.

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http://dx.doi.org/10.1093/database/bax062DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5737205PMC
January 2017

Text mining electronic hospital records to automatically classify admissions against disease: Measuring the impact of linking data sources.

J Biomed Inform 2016 12 11;64:158-167. Epub 2016 Oct 11.

Department of Computing and Information Systems, University of Melbourne, Melbourne, Australia.

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http://dx.doi.org/10.1016/j.jbi.2016.10.008DOI Listing
December 2016

A physarum-inspired prize-collecting steiner tree approach to identify subnetworks for drug repositioning.

BMC Syst Biol 2016 Dec 5;10(Suppl 5):128. Epub 2016 Dec 5.

Research School of Engineering, College of Engineering & Computer Science, The Australian National University, Canberra, 2601, ACT, Australia.

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http://dx.doi.org/10.1186/s12918-016-0371-3DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5249043PMC
December 2016

TOWARDS EARLY DISCOVERY OF SALIENT HEALTH THREATS: A SOCIAL MEDIA EMOTION CLASSIFICATION TECHNIQUE.

Pac Symp Biocomput 2016 ;21:504-15

Department of Computing and Information Systems, Australia.

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October 2016

An expanded evaluation of protein function prediction methods shows an improvement in accuracy.

Authors:
Yuxiang Jiang Tal Ronnen Oron Wyatt T Clark Asma R Bankapur Daniel D'Andrea Rosalba Lepore Christopher S Funk Indika Kahanda Karin M Verspoor Asa Ben-Hur Da Chen Emily Koo Duncan Penfold-Brown Dennis Shasha Noah Youngs Richard Bonneau Alexandra Lin Sayed M E Sahraeian Pier Luigi Martelli Giuseppe Profiti Rita Casadio Renzhi Cao Zhaolong Zhong Jianlin Cheng Adrian Altenhoff Nives Skunca Christophe Dessimoz Tunca Dogan Kai Hakala Suwisa Kaewphan Farrokh Mehryary Tapio Salakoski Filip Ginter Hai Fang Ben Smithers Matt Oates Julian Gough Petri Törönen Patrik Koskinen Liisa Holm Ching-Tai Chen Wen-Lian Hsu Kevin Bryson Domenico Cozzetto Federico Minneci David T Jones Samuel Chapman Dukka Bkc Ishita K Khan Daisuke Kihara Dan Ofer Nadav Rappoport Amos Stern Elena Cibrian-Uhalte Paul Denny Rebecca E Foulger Reija Hieta Duncan Legge Ruth C Lovering Michele Magrane Anna N Melidoni Prudence Mutowo-Meullenet Klemens Pichler Aleksandra Shypitsyna Biao Li Pooya Zakeri Sarah ElShal Léon-Charles Tranchevent Sayoni Das Natalie L Dawson David Lee Jonathan G Lees Ian Sillitoe Prajwal Bhat Tamás Nepusz Alfonso E Romero Rajkumar Sasidharan Haixuan Yang Alberto Paccanaro Jesse Gillis Adriana E Sedeño-Cortés Paul Pavlidis Shou Feng Juan M Cejuela Tatyana Goldberg Tobias Hamp Lothar Richter Asaf Salamov Toni Gabaldon Marina Marcet-Houben Fran Supek Qingtian Gong Wei Ning Yuanpeng Zhou Weidong Tian Marco Falda Paolo Fontana Enrico Lavezzo Stefano Toppo Carlo Ferrari Manuel Giollo Damiano Piovesan Silvio C E Tosatto Angela Del Pozo José M Fernández Paolo Maietta Alfonso Valencia Michael L Tress Alfredo Benso Stefano Di Carlo Gianfranco Politano Alessandro Savino Hafeez Ur Rehman Matteo Re Marco Mesiti Giorgio Valentini Joachim W Bargsten Aalt D J van Dijk Branislava Gemovic Sanja Glisic Vladmir Perovic Veljko Veljkovic Nevena Veljkovic Danillo C Almeida-E-Silva Ricardo Z N Vencio Malvika Sharan Jörg Vogel Lakesh Kansakar Shanshan Zhang Slobodan Vucetic Zheng Wang Michael J E Sternberg Mark N Wass Rachael P Huntley Maria J Martin Claire O'Donovan Peter N Robinson Yves Moreau Anna Tramontano Patricia C Babbitt Steven E Brenner Michal Linial Christine A Orengo Burkhard Rost Casey S Greene Sean D Mooney Iddo Friedberg Predrag Radivojac

Genome Biol 2016 09 7;17(1):184. Epub 2016 Sep 7.

Department of Computer Science and Informatics, Indiana University, Bloomington, IN, USA.

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http://dx.doi.org/10.1186/s13059-016-1037-6DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5015320PMC
September 2016

Gene Ontology synonym generation rules lead to increased performance in biomedical concept recognition.

J Biomed Semantics 2016 Sep 9;7:52. Epub 2016 Sep 9.

Department of Computing and Information Systems, University of Melbourne, Parkville, Melbourne, 3010, Australia.

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http://dx.doi.org/10.1186/s13326-016-0096-7DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5018193PMC
September 2016

A close look at protein function prediction evaluation protocols.

Gigascience 2015 14;4:41. Epub 2015 Sep 14.

Department of Computer Science, Colorado State University, Fort Collins, 80523 CO USA.

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http://dx.doi.org/10.1186/s13742-015-0082-5DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4570743PMC
July 2016

Establishing a baseline for literature mining human genetic variants and their relationships to disease cohorts.

BMC Med Inform Decis Mak 2016 07 18;16 Suppl 1:68. Epub 2016 Jul 18.

Department of Library and Information Science, Yonsei University, Seoul, Korea.

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http://dx.doi.org/10.1186/s12911-016-0294-3DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4959367PMC
July 2016

Designing Health Websites Based on Users' Web-Based Information-Seeking Behaviors: A Mixed-Method Observational Study.

J Med Internet Res 2016 06 6;18(6):e145. Epub 2016 Jun 6.

Department of Computing and Information Systems, The University of Melbourne, Parkville, Australia.

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http://dx.doi.org/10.2196/jmir.5661DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4914778PMC
June 2016

A categorical analysis of coreference resolution errors in biomedical texts.

J Biomed Inform 2016 Apr 27;60:309-18. Epub 2016 Feb 27.

Department of Computing and Information Systems, The University of Melbourne, Melbourne, Australia. Electronic address:

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http://dx.doi.org/10.1016/j.jbi.2016.02.015DOI Listing
April 2016

Assessing the impact of case sensitivity and term information gain on biomedical concept recognition.

PLoS One 2015 19;10(3):e0119091. Epub 2015 Mar 19.

Department of Computing and Information Systems, The University of Melbourne, Melbourne, Australia; Health and Biomedical Informatics Centre, The University of Melbourne, Melbourne, Australia.

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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0119091PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4366016PMC
February 2016

PHENOstruct: Prediction of human phenotype ontology terms using heterogeneous data sources.

F1000Res 2015 16;4:259. Epub 2015 Jul 16.

Department of Computer Science, Colorado State University, Fort Collins, CO, 80523, USA.

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http://dx.doi.org/10.12688/f1000research.6670.1DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4722686PMC
February 2016

Roles for text mining in protein function prediction.

Authors:
Karin M Verspoor

Methods Mol Biol 2014 ;1159:95-108

Department of Computing and Information Systems, The University of Melbourne, Melbourne, VIC, 3010, Australia,

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http://dx.doi.org/10.1007/978-1-4939-0709-0_6DOI Listing
May 2015

Evaluating a variety of text-mined features for automatic protein function prediction with GOstruct.

J Biomed Semantics 2015 18;6. Epub 2015 Mar 18.

Department of Computing and Information Systems, University of Melbourne, Parkville, 3010 Victoria Australia ; Health and Biomedical Informatics Centre, University of Melbourne, Parkville, 3010 Victoria Australia.

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http://dx.doi.org/10.1186/s13326-015-0006-4DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4441003PMC
May 2015

BioC interoperability track overview.

Database (Oxford) 2014 30;2014. Epub 2014 Jun 30.

National Center for Biotechnology Information, National Library of Medicine, Bethesda, MD 20894, USA, National Centre for Text Mining and School of Computer Science, University of Manchester, Manchester M1 7DN, UK, Graduate Institute of BioMedical Informatics, College of Medical Science and Technology, Taipei Medical University, Taipei 110, Taiwan, R.O.C., Department of Computing and Information Systems, The University of Melbourne, Parkville, Victoria Australia 3010, Institute of Computational Linguistics, University of Zurich, Zurich 8050, Switzerland, Department of Biological Sciences, North Carolina State University, Raleigh, NC 27695-7617, USA, WBI, Institute for Computer Science, Humboldt-Universität zu Berlin, Berlin 10099, Germany, Berlin Brandenburg Center for Regenerative Therapies, Charité - Universitätsmedizin Berlin, Berlin 13353, Germany, Department of Computer and Information Sciences, University of Delaware, Newark, DE 19711, USA, Department of Computer Science and Information Engineering, National Central University, Taoyuan 32001, Taiwan, R.O.C., Health and Biomedical Informatics Centre, The University of Melbourne, Parkville, Victoria Australia 3010, Center for Bioinformatics and Computational Biology, University of Delaware, Newark, DE 19711, USA.

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http://dx.doi.org/10.1093/database/bau053DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4074764PMC
February 2015

Summary of the BioLINK SIG 2013 meeting at ISMB/ECCB 2013.

Bioinformatics 2015 Jan 14;31(2):297-8. Epub 2014 Jul 14.

Department of Computing and Information Systems, The University of Melbourne, Parkville VIC 3010, Australia Department of Computer and Information Sciences, University of Delaware, Newark, DE 19716, USA, MITRE Corporation, Bedford, MA 01730, USA, Spanish Institute of Bioinformatics, Madrid, Spain and Spanish National Centre for Cancer Research, Madrid, Spain.

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https://academic.oup.com/bioinformatics/article-lookup/doi/1
Publisher Site
http://dx.doi.org/10.1093/bioinformatics/btu412DOI Listing
January 2015

Associating disease-related genetic variants in intergenic regions to the genes they impact.

PeerJ 2014 23;2:e639. Epub 2014 Oct 23.

Department of Computing and Information Systems, The University of Melbourne, VIC, Australia.

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http://dx.doi.org/10.7717/peerj.639DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4217187PMC
November 2014

Mutation extraction tools can be combined for robust recognition of genetic variants in the literature.

F1000Res 2014 21;3:18. Epub 2014 Jan 21.

National ICT Australia, Victoria Research Laboratory, Melbourne, Australia ; Department of Computing and Information Systems, The University of Melbourne, Melbourne, Australia.

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http://dx.doi.org/10.12688/f1000research.3-18.v2DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4176422PMC
October 2014

Representing annotation compositionality and provenance for the Semantic Web.

J Biomed Semantics 2013 22;4:38. Epub 2013 Nov 22.

National ICT Australia, Victoria Research Laboratory, Melbourne, VIC, 3010, Australia ; Department of Computing and Information Systems, The University of Melbourne, Melbourne 3010 VIC, Australia.

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http://dx.doi.org/10.1186/2041-1480-4-38DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4129183PMC
September 2014

Literature mining of genetic variants for curation: quantifying the importance of supplementary material.

Database (Oxford) 2014 10;2014:bau003. Epub 2014 Feb 10.

National ICT Australia, Victoria Research Laboratory, Melbourne, Australia and Department of Computing and Information Systems, The University of Melbourne, Melbourne, Australia.

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http://dx.doi.org/10.1093/database/bau003DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3920087PMC
August 2014

BioC: a minimalist approach to interoperability for biomedical text processing.

Database (Oxford) 2013 18;2013:bat064. Epub 2013 Sep 18.

National Center for Biotechnology Information, National Library of Medicine, Bethesda, MD 20894, USA, Department of Neurology, Massachusetts General Hospital, Boston, MA 02114, Harvard Medical School, Harvard University, Boston, MA 02115 USA, Center for Computational Pharmacology, University of Colorado Denver School of Medicine, Aurora, CO 80045, USA, Structural and Computational Biology Group, Spanish National Cancer Research Centre, Madrid E-28029, Spain, Center for Bioinformatics and Computational Biology, Department of Computer and Information Sciences, University of Delaware, Newark, DE 19711, USA, Institute of Computational Linguistics, University of Zurich, Zurich 8050, Switzerland, National ICT Australia (NICTA), Victoria Research Laboratory, The University of Melbourne, Parkville VIC 3010, Australia and Department of Biology, North Carolina State University, Raleigh, NC 27695, USA.

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http://dx.doi.org/10.1093/database/bat064DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3889917PMC
March 2014

Detection of protein catalytic sites in the biomedical literature.

Pac Symp Biocomput 2013 :433-44

National ICT Australia, Victoria Research Lab, Parkville, VIC 3010, Australia.

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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3664919PMC
December 2013

Approximate subgraph matching-based literature mining for biomedical events and relations.

PLoS One 2013 17;8(4):e60954. Epub 2013 Apr 17.

National Center for Biotechnology Information, Bethesda, Maryland, United States of America.

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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0060954PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3629260PMC
November 2013

Combining heterogeneous data sources for accurate functional annotation of proteins.

BMC Bioinformatics 2013 28;14 Suppl 3:S10. Epub 2013 Feb 28.

Department of Biomolecular Engineering, University of California Santa Cruz, Santa Cruz, California 95064, USA.

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http://dx.doi.org/10.1186/1471-2105-14-S3-S10DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3584846PMC
July 2013

Annotating the biomedical literature for the human variome.

Database (Oxford) 2013 12;2013:bat019. Epub 2013 Apr 12.

National ICT Australia (NICTA), Victoria Research Laboratory, Level 2, Building 193, The University of Melbourne, Parkville VIC 3010, Australia.

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http://dx.doi.org/10.1093/database/bat019DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3676157PMC
June 2013

Approaches to verb subcategorization for biomedicine.

J Biomed Inform 2013 Apr 28;46(2):212-27. Epub 2012 Dec 28.

Computer Laboratory, University of Cambridge, 15 JJ Thomson Avenue, Cambridge CB3 0FD, UK.

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http://dx.doi.org/10.1016/j.jbi.2012.12.001DOI Listing
April 2013

Acquisition and evaluation of verb subcategorization resources for biomedicine.

J Biomed Inform 2013 Apr 22;46(2):228-37. Epub 2013 Jan 22.

Computer Laboratory, University of Cambridge, 15 JJ Thomson Avenue, Cambridge CB3 0FD, UK.

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http://dx.doi.org/10.1016/j.jbi.2013.01.001DOI Listing
April 2013

A large-scale evaluation of computational protein function prediction.

Authors:
Predrag Radivojac Wyatt T Clark Tal Ronnen Oron Alexandra M Schnoes Tobias Wittkop Artem Sokolov Kiley Graim Christopher Funk Karin Verspoor Asa Ben-Hur Gaurav Pandey Jeffrey M Yunes Ameet S Talwalkar Susanna Repo Michael L Souza Damiano Piovesan Rita Casadio Zheng Wang Jianlin Cheng Hai Fang Julian Gough Patrik Koskinen Petri Törönen Jussi Nokso-Koivisto Liisa Holm Domenico Cozzetto Daniel W A Buchan Kevin Bryson David T Jones Bhakti Limaye Harshal Inamdar Avik Datta Sunitha K Manjari Rajendra Joshi Meghana Chitale Daisuke Kihara Andreas M Lisewski Serkan Erdin Eric Venner Olivier Lichtarge Robert Rentzsch Haixuan Yang Alfonso E Romero Prajwal Bhat Alberto Paccanaro Tobias Hamp Rebecca Kaßner Stefan Seemayer Esmeralda Vicedo Christian Schaefer Dominik Achten Florian Auer Ariane Boehm Tatjana Braun Maximilian Hecht Mark Heron Peter Hönigschmid Thomas A Hopf Stefanie Kaufmann Michael Kiening Denis Krompass Cedric Landerer Yannick Mahlich Manfred Roos Jari Björne Tapio Salakoski Andrew Wong Hagit Shatkay Fanny Gatzmann Ingolf Sommer Mark N Wass Michael J E Sternberg Nives Škunca Fran Supek Matko Bošnjak Panče Panov Sašo Džeroski Tomislav Šmuc Yiannis A I Kourmpetis Aalt D J van Dijk Cajo J F ter Braak Yuanpeng Zhou Qingtian Gong Xinran Dong Weidong Tian Marco Falda Paolo Fontana Enrico Lavezzo Barbara Di Camillo Stefano Toppo Liang Lan Nemanja Djuric Yuhong Guo Slobodan Vucetic Amos Bairoch Michal Linial Patricia C Babbitt Steven E Brenner Christine Orengo Burkhard Rost Sean D Mooney Iddo Friedberg

Nat Methods 2013 Mar 27;10(3):221-7. Epub 2013 Jan 27.

School of Informatics and Computing, Indiana University, Bloomington, Indiana, USA.

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http://dx.doi.org/10.1038/nmeth.2340DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3584181PMC
March 2013

Literature mining of protein-residue associations with graph rules learned through distant supervision.

J Biomed Semantics 2012 Oct 5;3 Suppl 3:S2. Epub 2012 Oct 5.

University of Colorado School of Medicine, Aurora, CO 80045, USA.

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http://dx.doi.org/10.1186/2041-1480-3-S3-S2DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3465209PMC
October 2012

Text mining improves prediction of protein functional sites.

PLoS One 2012 29;7(2):e32171. Epub 2012 Feb 29.

University of Colorado School of Medicine, Aurora, Colorado, United States of America.

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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0032171PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3290545PMC
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Concept annotation in the CRAFT corpus.

BMC Bioinformatics 2012 Jul 9;13:161. Epub 2012 Jul 9.

Department of Pharmacology, University of Colorado Anschutz Medical Campus, Aurora, CO, USA.

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http://dx.doi.org/10.1186/1471-2105-13-161DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3476437PMC
July 2012

BioLemmatizer: a lemmatization tool for morphological processing of biomedical text.

J Biomed Semantics 2012 Apr 1;3. Epub 2012 Apr 1.

Colorado Computational Pharmacology, University of Colorado School of Medicine, Aurora, CO 80045, USA.

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http://dx.doi.org/10.1186/2041-1480-3-3DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3359276PMC
April 2012

HIGH-PRECISION BIOLOGICAL EVENT EXTRACTION: EFFECTS OF SYSTEM AND OF DATA.

Comput Intell 2011 Nov;27(4):681-701

Center for Computational Pharmacology, University of Colorado Denver School of Medicine, Aurora, CO, USA.

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http://dx.doi.org/10.1111/j.1467-8640.2011.00405.xDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4414063PMC
November 2011

Exploring species-based strategies for gene normalization.

IEEE/ACM Trans Comput Biol Bioinform 2010 Jul-Sep;7(3):462-71

Center for Computational Pharmacology, University of Colorado Denver, Aurora, CO 80045, USA.

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http://dx.doi.org/10.1109/TCBB.2010.48DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2929766PMC
December 2010

The structural and content aspects of abstracts versus bodies of full text journal articles are different.

BMC Bioinformatics 2010 Sep 29;11:492. Epub 2010 Sep 29.

Department of Pharmacology, Center for Computational Pharmacology, University of Colorado School of Medicine, Aurora, Colorado, USA.

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http://dx.doi.org/10.1186/1471-2105-11-492DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3098079PMC
September 2010

A UIMA wrapper for the NCBO annotator.

Bioinformatics 2010 Jul 26;26(14):1800-1. Epub 2010 May 26.

Center for Computational Pharmacology, University of Colorado School of Medicine, Aurora, CO, USA.

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http://dx.doi.org/10.1093/bioinformatics/btq250DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2894505PMC
July 2010

Towards a semantic lexicon for biological language processing.

Authors:
Karin Verspoor

Comp Funct Genomics 2005 ;6(1-2):61-6

Los Alamos National Laboratory, Los Alamos, NM 87545, USA.

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http://dx.doi.org/10.1002/cfg.451DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2448606PMC
June 2010

Ontology quality assurance through analysis of term transformations.

Bioinformatics 2009 Jun;25(12):i77-84

Center for Computational Pharmacology, University of Colorado Denver, Aurora, CO 80045, USA.

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http://dx.doi.org/10.1093/bioinformatics/btp195DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2687949PMC
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The textual characteristics of traditional and Open Access scientific journals are similar.

BMC Bioinformatics 2009 Jun 15;10:183. Epub 2009 Jun 15.

Center for Computational Pharmacology, University of Colorado Denver School of Medicine, Aurora, CO 80045, USA.

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http://www.biomedcentral.com/1471-2105/10/183
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http://dx.doi.org/10.1186/1471-2105-10-183DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2714574PMC
June 2009

Large-scale testing of bibliome informatics using Pfam protein families.

Pac Symp Biocomput 2006 :76-87

School of Informatics, Indiana University 1900 East Tenth Street, Bloomington, IN 47408, USA.

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January 2007

A categorization approach to automated ontological function annotation.

Protein Sci 2006 Jun 2;15(6):1544-9. Epub 2006 May 2.

Los Amos National Laboratory, Los Almos, New Mexico 87454, USA.

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http://dx.doi.org/10.1110/ps.062184006DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2242540PMC
June 2006