All Stories

  1. BioHackathon series in 2013 and 2014: improvements of semantic interoperability in life science data and services

    Article • F1000Research, September 2019, Faculty of 1000, Ltd.

    Dr. Yasset Perez-Riverol, Dr Kevin Bretonnel Cohen, Robert Hoehndorf, Karin M Verspoor, Yusuke Komiyama, Dr. Hidemasa Bono, Katsuhiko Murakami, Hiromasa Ono, Shin Kawano, Shuichi Kawashima, Tatsuya Kushida, Yosuke Nishimura, Kazuharu Arakawa, hongyan Wu

  2. Learning Biological Sequence Types Using the Literature

    Article • November 2017, ACM (Association for Computing Machinery)

    Karin M Verspoor

  3. Comparative Analysis of Sequence Clustering Methods for Deduplication of Biological Databases

    Article • Journal of Data and Information Quality, September 2017, ACM (Association for Computing Machinery)

    Karin M Verspoor

  4. The randomized information coefficient: assessing dependencies in noisy data

    Article • Machine Learning, September 2017, Springer Science + Business Media

    Karin M Verspoor

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

    Article • Journal of Biomedical Informatics, July 2017, Elsevier

    Karin M Verspoor

  6. CommViz: Visualization of semantic patterns in large social communication networks

    Article • Information Visualization, February 2017, SAGE Publications

    Karin M Verspoor

  7. Literature Consistency of Bioinformatics Sequence Databases is Effective for Assessing Record Quality

    Article • January 2017, Cold Spring Harbor Laboratory Press

    Karin M Verspoor

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

    Article • Database, January 2017, Oxford University Press (OUP)

    Karin M Verspoor

  9. Thematic issue of the Second combined Bio-ontologies and Phenotypes Workshop

    Article • Journal of Biomedical Semantics, December 2016, Springer Science + Business Media

    Karin M Verspoor

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

    Article • Journal of Biomedical Informatics, December 2016, Elsevier

    Karin M Verspoor

  11. Benchmarks for Measurement of Duplicate Detection Methods in Nucleotide Databases

    Article • November 2016, Cold Spring Harbor Laboratory Press

    Karin M Verspoor

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

    Article • November 2016, Cold Spring Harbor Laboratory Press

    Karin M Verspoor

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

    Article • BMC Medical Informatics and Decision Making, July 2016, Springer Science + Business Media

    Karin M Verspoor

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

    Article • Journal of Medical Internet Research, June 2016, JMIR Publications Inc.

    Karin M Verspoor

  15. Better Health Explorer

    Article • December 2015, ACM (Association for Computing Machinery)

    Karin M Verspoor

  16. Special issue on bio-ontologies and phenotypes

    Article • Journal of Biomedical Semantics, December 2015, Springer Science + Business Media

    Karin M Verspoor

  17. DTMBIO 2015

    Article • October 2015, ACM (Association for Computing Machinery)

    Min Song, Karin M Verspoor

  18. A close look at protein function prediction evaluation protocols

    Article • GigaScience, September 2015, Springer Science + Business Media

    Karin M Verspoor, Indika Kahanda

  19. Phenotype prediction incorporating literature mining

    Article • F1000Research, July 2015, Faculty of 1000, Ltd.

    Karin M Verspoor, Asa Ben-Hur, Indika Kahanda, Indika Kahanda

  20. Assessing the Impact of Case Sensitivity and Term Information Gain on Biomedical Concept Recognition

    Article • PLoS ONE, March 2015, PLOS

    Karin M Verspoor

  21. Conceptualising health information seeking behaviours and exploratory search: result of a qualitative study

    Article • Health and Technology, February 2015, Springer Science + Business Media

    Karin M Verspoor

  22. The CHEMDNER corpus of chemicals and drugs and its annotation principles

    Article • Journal of Cheminformatics, January 2015, Springer Science + Business Media

    Karin M Verspoor

  23. Optimizing graph-based patterns to extract biomedical events from the literature

    Article • BMC Bioinformatics, January 2015, Springer Science + Business Media

    Karin M Verspoor

  24. Interoperability of text corpus annotations with the semantic web

    Article • BMC Proceedings, January 2015, Springer Science + Business Media

    Karin M Verspoor

  25. Evaluation of a Machine Learning Duplicate Detection Method for Bioinformatics Databases

    Article • January 2015, ACM (Association for Computing Machinery)

    Karin M Verspoor

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

    Article • Journal of Biomedical Semantics, January 2015, Springer Science + Business Media

    Karin M Verspoor, Asa Ben-Hur

  27. CQADupStack

    Article • January 2015, ACM (Association for Computing Machinery)

    Karin M Verspoor

  28. Better health information exploration

    Article • January 2015, ACM (Association for Computing Machinery)

    Karin M Verspoor

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

    Article • PeerJ, October 2014, PeerJ

    Karin M Verspoor

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

    Article • Bioinformatics, July 2014, Oxford University Press (OUP)

    Karin M Verspoor

  31. BioC interoperability track overview

    Article • Database, June 2014, Oxford University Press (OUP)

    Karin M Verspoor

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

    Article • F1000Research, June 2014, Faculty of 1000, Ltd.

    Karin M Verspoor

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

    Article • Database, February 2014, Oxford University Press (OUP)

    Karin M Verspoor

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

    Article • F1000Research, January 2014, F1000Research

    Karin M Verspoor

  35. What Can We Get From 1000 Tokens? A Case Study of Multilingual POS Tagging For Resource-Poor Languages

    Article • January 2014, Association for Computational Linguistics (ACL)

    Karin M Verspoor

  36. Roles for Text Mining in Protein Function Prediction

    Article • January 2014, Springer Science + Business Media

    Karin M Verspoor

  37. Large-scale biomedical concept recognition: an evaluation of current automatic annotators and their parameters

    Article • BMC Bioinformatics, January 2014, Springer Science + Business Media

    Karin M Verspoor

  38. Integrating UIMA with Alveo, a human communication science virtual laboratory

    Article • January 2014, Association for Computational Linguistics (ACL)

    Karin M Verspoor

  39. Biomedical Text Mining: State-of-the-Art, Open Problems and Future Challenges

    Article • January 2014, Springer Science + Business Media

    Karin M Verspoor

  40. Big Data in Medicine Is Driving Big Changes

    Article • Yearbook of Medical Informatics, January 2014, Schattauer GmbH

    Karin M Verspoor

  41. Annokey: an annotation tool based on key term search of the NCBI Entrez Gene database

    Article • Source Code for Biology and Medicine, January 2014, Springer Science + Business Media

    Karin M Verspoor

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

    Article • Database, September 2013, Oxford University Press (OUP)

    Karin M Verspoor

  43. Approximate Subgraph Matching-Based Literature Mining for Biomedical Events and Relations

    Article • PLoS ONE, April 2013, PLOS

    Karin M Verspoor

  44. Annotating the biomedical literature for the human variome

    Article • Database, April 2013, Oxford University Press (OUP)

    Karin M Verspoor

  45. Approaches to verb subcategorization for biomedicine

    Article • Journal of Biomedical Informatics, April 2013, Elsevier

    Karin M Verspoor

  46. Acquisition and evaluation of verb subcategorization resources for biomedicine

    Article • Journal of Biomedical Informatics, April 2013, Elsevier

    Karin M Verspoor

  47. A large-scale evaluation of computational protein function prediction

    Article • Nature Methods, January 2013, Nature

    Karin M Verspoor, Dr Serkan Erdin

  48. Unstructured Information Management Architecture (UIMA)

    Article • January 2013, Springer Science + Business Media

    Karin M Verspoor

  49. Representing annotation compositionality and provenance for the Semantic Web

    Article • Journal of Biomedical Semantics, January 2013, Springer Science + Business Media

    Karin M Verspoor

  50. Natural Language Processing

    Article • January 2013, Springer Science + Business Media

    Karin M Verspoor

  51. Towards human-computer synergetic analysis of large-scale biological data

    Article • BMC Bioinformatics, January 2013, Springer Science + Business Media

    Karin M Verspoor

  52. Applied Text Mining

    Article • January 2013, Springer Science + Business Media

    Karin M Verspoor

  53. DETECTION OF PROTEIN CATALYTIC SITES IN THE BIOMEDICAL LITERATURE

    Article • November 2012, World Scientific Pub Co Pte Lt

    Karin M Verspoor

  54. Text Mining Improves Prediction of Protein Functional Sites

    Article • PLoS ONE, February 2012, PLOS

    Karin M Verspoor

  55. Extracting structured information from free-text medication prescriptions using dependencies

    Article • January 2012, ACM (Association for Computing Machinery)

    Karin M Verspoor

  56. Concept annotation in the CRAFT corpus

    Article • BMC Bioinformatics, January 2012, Springer Science + Business Media

    Karin M Verspoor

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

    Article • Journal of Biomedical Semantics, January 2012, Springer Science + Business Media

    Karin M Verspoor

  58. A corpus of full-text journal articles is a robust evaluation tool for revealing differences in performance of biomedical natural language processing tools

    Article • BMC Bioinformatics, January 2012, Springer Science + Business Media

    Karin M Verspoor

  59. Pattern Learning through Distant Supervision for Extraction of Protein-Residue Associations in the Biomedical Literature

    Article • December 2011, Institute of Electrical & Electronics Engineers (IEEE)

    Karin M Verspoor

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

    Article • Computational Intelligence, November 2011, Wiley

    Karin M Verspoor

  61. The gene normalization task in BioCreative III

    Article • BMC Bioinformatics, October 2011, Springer Science + Business Media

    Dr Feifan Liu, Karin M Verspoor

  62. U-Compare bio-event meta-service: compatible BioNLP event extraction services

    Article • BMC Bioinformatics, January 2011, Springer Science + Business Media

    Karin M Verspoor

  63. Leveraging Gene Ontology Annotations to Improve a Memory-Based Language Understanding System

    Article • September 2010, Institute of Electrical & Electronics Engineers (IEEE)

    Karin M Verspoor

  64. Exploring Species-Based Strategies for Gene Normalization

    Article • IEEE/ACM Transactions on Computational Biology and Bioinformatics, July 2010, Institute of Electrical & Electronics Engineers (IEEE)

    Karin M Verspoor

  65. A UIMA wrapper for the NCBO annotator

    Article • Bioinformatics, May 2010, Oxford University Press (OUP)

    Karin M Verspoor

  66. Visualization and Language Processing for Supporting Analysis across the Biomedical Literature

    Article • January 2010, Springer Science + Business Media

    Karin M Verspoor

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

    Article • BMC Bioinformatics, January 2010, Springer Science + Business Media

    Karin M Verspoor

  68. Ontology quality assurance through analysis of term transformations

    Article • Bioinformatics, May 2009, Oxford University Press (OUP)

    Karin M Verspoor

  69. The textual characteristics of traditional and Open Access scientific journals are similar

    Article • BMC Bioinformatics, January 2009, Springer Science + Business Media

    Karin M Verspoor

  70. High-precision biological event extraction with a concept recognizer

    Article • January 2009, Association for Computational Linguistics (ACL)

    Karin M Verspoor

  71. Exploiting Term Relations for Semantic Hierarchy Construction

    Article • August 2008, Institute of Electrical & Electronics Engineers (IEEE)

    Karin M Verspoor

  72. Uncovering protein interaction in abstracts and text using a novel linear model and word proximity networks

    Article • Genome Biology, January 2008, Springer Science + Business Media

    Karin M Verspoor

  73. Knowledge Integration in OpenWorlds: Utilizing the Mathematics of Hierarchical Structure

    Article • September 2007, Institute of Electrical & Electronics Engineers (IEEE)

    Karin M Verspoor

  74. A categorization approach to automated ontological function annotation

    Article • Protein Science, June 2006, Wiley

    Karin M Verspoor

  75. LARGE-SCALE TESTING OF BIBLIOME INFORMATICS USING PFAM PROTEIN FAMILIES

    Article • December 2005, World Scientific Pub Co Pte Lt

    Karin M Verspoor

  76. Towards a Semantic Lexicon for Biological Language Processing

    Article • Comparative and Functional Genomics, January 2005, Hindawi Publishing Corporation

    Karin M Verspoor

  77. Protein annotation as term categorization in the gene ontology using word proximity networks

    Article • BMC Bioinformatics, January 2005, Springer Science + Business Media

    Karin M Verspoor

  78. Automatic English-Chinese name transliteration for development of multilingual resources

    Article • January 1998, Association for Computational Linguistics (ACL)

    Karin M Verspoor

  79. Automatic English-Chinese name transliteration for development of multilingual resources

    Article • January 1998, Association for Computational Linguistics (ACL)

    Karin M Verspoor

  80. A Semantics-Enhanced Language Model for Unsupervised Word Sense Disambiguation

    Article • Springer Science + Business Media

    Karin M Verspoor

  81. Dynamic document delivery: generating natural language texts on demand

    Article • Institute of Electrical & Electronics Engineers (IEEE)

    Karin M Verspoor