Publications

  • Rewriting and suppressing UMLS terms for improved biomedical term identification.
    Hettne KM, van Mulligen EM, Schuemie MJ, Schijvenaars BJ, Kors JA.
    Journal of Biomedical Semantics 2010, 1:1.
    [Journal of Biomedical Semantics]
  • Automatic vs. manual curation of a multi-source chemical dictionary: the impact on text mining.
    Hettne KM, Williams AJ, van Mulligen EM, Kleinjans J, Tkachenko V, Kors JA.
    Journal of Cheminformatics. 2010 Mar 23;2(1):3.
    [PubMed][Journal of Cheminformatics]
  • Novel Protein-Protein Interactions Inferred from Literature Context.
    van Haagen HH, 't Hoen PA, Botelho Bovo A, de Morrée A, van Mulligen EM, Chichester C, Kors JA, den Dunnen JT, van Ommen GJ, van der Maarel SM, Kern VM, Mons B, Schuemie MJ
    PLos ONE 2009, November 18
    [PubMed]
  • GeneE: Gene and protein query expansion with disambiguation.
    Schuemie MJ, Kang N, Hekkelman ML, Kors JA
    Bioinformatics 2009, October 16
    [PubMed]
  • Structuring and extracting knowledge for the support of hypothesis generation in molecular biology.
    Roos M, Marshall MS, Gibson AP, Schuemie MJ, Meij E, Katrenko S, van Hage WR, Krommydas K, Adriaans PW
    BMC Bioinformatics 2009 Oct 1;10(Suppl 10):S9
    [BMC Bioinformatics]
  • A Dictionary to Identify Small Molecules and Drugs in Free Text.
    Hettne KM, Stierum RH, Schuemie MJ, Hendriksen PJ, Schijvenaars BJ, van Mulligen EM, Kleinjans J, Kors J.
    Bioinformatics 2009 Nov 15;25(22):2983-91
    [PubMed]
  • An Inventory of Publicationson Electronic Medical Records Revisited.
    Moorman PW, Schuemie MJ, van der Lei J
    Methods of Information in Medicine 2009 May 15;48(4)
    [PubMed]
  • Literature-based priors for gene regulatory networks.
    Steele E, Tucker A, 't Hoen PA, Schuemie MJ
    Bioinformatics 2009, Jul 15;25(14):1768-74
    [PubMed]
  • Mapping the domain of medical informatics.
    Schuemie MJ, Talmon JL, Moorman PW, Kors JA
    Methods of Information in Medicine 2009, 48(1):76-83
    [PubMed]
  • Text mining for biology - the way forward: opinions from leading scientists.
    Altman RB, Bergman CM, Blake J, Blaschke C, Cohen A, Gannon F, Grivell L, Hahn U, Hersh W, Hirschman L, Jensen LJ, Krallinger M, Mons B, O'Donoghue SI, Peitsch MC, Rebholz-Schuhmann D, Shatkay H, Valencia A
    Genome Biology 2008 Sep 1, 9(Suppl 2):S7
    [Genome Biology]
  • Overview of BioCreative II gene normalization.
    Morgan AA, Lu Z, Wang X, Cohen AM, Fluck J, Ruch P, Divoli A, Fundel K, Leaman R, Hakenberg J, Sun C, Liu H, Torres R, Krauthammer M, Lau WW, Liu H, Hsu C, Schuemie MJ, Cohen CB, Hirschman L
    Genome Biology 2008 Sep 1, 9(Suppl 2):S3
    [Genome Biology]
  • Literature-aided meta-analysis of microarray data: a compendium study on muscle development and disease.
    Jelier R, 't Hoen PAC, Sterrenburg E, den Dunnen JT, van Ommen GJ, Kors JA, Mons B.
    BMC Bioinformatics 2008 Jun 24, 9(1):291
    [PubMed]
  • Anni 2.0: a multipurpose text-mining tool for the life sciences.
    Jelier R, Schuemie MJ, Veldhoven A, Dorssers LC, Jenster G, Kors JA
    Genome Biology 2008 Jun 12, 9(6):R96
    [PubMed]
  • Calling on a million minds for community annotation in WikiProteins.
    Mons B, Ashburner M, Chichester C, van Mulligen E, Weeber M, den Dunnen J, van Ommen GJ, Musen M, Cockerill M, Hermjakob H, Mons A, Packer A, Pacheco R, Lewis S, Berkeley A, Melton W, Barris N, Wales J, Meijssen G, Moeller E, Roes PJ, Borner K, Bairoch A.
    Genome Biology 2008 May 28, 9(5):R89
    [PubMed]
  • Literature-based concept profiles for gene annotation: the issue of weighting.
    Jelier R, Schuemie MJ, Roes PJ, van Mulligen EM, Kors JA
    International Journal of Medical Informatics 2008 May, 77(5):354-62
    [PubMed]
  • Jane: Suggesting Journals, Finding Experts.
    Schuemie MJ, Kors JA
    Bioinformatics 2008 Jan, Mar 1, 24(5):727-8
    [PubMed]
  • Automatic mining of the literature to generate new hypotheses for the possible link between periodontitis and atherosclerosis: lipopolysaccharide as a case study.
    Hettne KM, Weeber M, Laine ML, ten Cate H, Boyer S, Kors JA, Loos BG
    Journal of Clinical Periodontology 2007 Dec, 34(12):1016-24
    [PubMed]
  • Cross Language Information Retrieval for Biomedical Literature.
    Schuemie MJ, Trieschnigg D, Kraaij W
    The Sixteenth Text REtrieval Conference (TREC 2007) November 6-9, Gaithersburg
    [PDF]
  • Connecting small molecules to nuclear receptor pathways.
    Hettne K, Cases M, Boyer S, Mestres J
    Current Topics in Medicinal Chemistry 2007 Aug, 7(15):1030-6
    [PubMed]
  • Evaluation of techniques for increasing recall in a dictionary approach to gene and protein name identification.
    Schuemie MJ, Mons B, Weeber M, Kors JA
    Journal of Biomedical Informatics 2007 Jun, 40(3):316-24
    [PubMed]
  • Medical informatics and bioinformatics: a bibliometric study.
    Bansard JY, Rebholz-Schuhmann D, Cameron G, Clark D, van Mulligen E, Beltrame E, Barbolla E, Martin-Sanchez Fdel H, Milanesi L, Tollis I, van der Lei J, Coatrieux JL
    IEEE transactions on information technology in biomedicine 2007 May, 11(3):237-43
    [PubMed]
  • Applied information retrieval and multidisciplinary research: new mechanistic hypotheses in complex regional pain syndrome.
    Hettne KM, de Mos M, de Bruijn AG, Weeber M, Boyer S, van Mulligen EM, Cases M, Mestres J, van der Lei J
    Journal of biomedical discovery and collaboration 2007 May 4, 2:2
    [PubMed]
  • Peregrine: Lightweight gene name normalization by dictionary lookup.
    Schuemie M, Jelier R, Kors JA
    Proceedings of the Biocreative 2 workshop 2007 April 23-25, Madrid, 131-140
    [PDF]
  • SYMBIOmatics: synergies in Medical Informatics and Bioinformatics--exploring current scientific literature for emerging topics.
    Rebholz-Schuhman D, Cameron G, Clark D, van Mulligen E, Coatrieux JL, Del Hoyo Barbolla E, Martin-Sanchez F, Milanesi L, Porro I, Beltrame F, Tollis I, Van der Lei J
    BMC Bioinformatics 2007 Mar 8, 8 Suppl 1:S18
    [PubMed][BMC Bioinformatics]
  • Assignment of protein function and discovery of novel nucleolar proteins based on automatic analysis of MEDLINE.
    Schuemie M, Chichester C, Lisacek F, Coute Y, Roes PJ, Sanchez JC, Kors JA, Mons B
    Proteomics 2007 Mar, 7(6):921-31
    [PubMed]
  • Text-derived concept profiles support assessment of DNA microarray data for acute myeloid leukemia and for androgen receptor stimulation.
    Jelier R, Jenster G, Dorssers LC, Wouters BJ, Hendriksen PJ, Mons B, Delwel R, Kors JA
    BMC Bioinformatics 2007 Jan 18, 8:14
    [PubMed][BMC Bioinformatics]
  • Databases for knowledge discovery. Examples from biomedicine and health care.
    van Bemmel JH, van Mulligen EM, Mons B, van Wijk M, Kors JA, van der Lei J
    International Journal of Medical Informatics 2006 Mar-Apr, 75(3-4):257-67
    [PubMed]
  • Concept Based Document Retrieval for Genomics Literature.
    Trieschnigg D, Kraaij W, Schuemie MJ
    The Fifteenth Text REtrieval Conference (TREC 2006) November 14-17, Gaithersburg
    [PDF]
  • Storing, linking, and mining microarray databases using SRS.
    Veldhoven A, de Lange D, Smid M, de Jager V, Kors JA, Jenster G
    BMC Bioinformatics 2005 Jul 27, 6(1):192
    [PubMed] [BMC Bioinformatics]
  • CoPub Mapper: mining MEDLINE based on search term co-publication.
    Alako BT, Veldhoven A, van Baal S, Jelier R, Verhoeven S, Rullmann T, Polman J, Jenster G
    BMC Bioinformatics 2005 Mar 11, 6:51
    [PubMed][BMC Bioinformatics]
  • Chemical and Biological profiling of an Annotated Compound Library directed to the Nuclear Receptor Family.
    Cases M, Garcia-Serna R, Hettne K, Weeber M, Van der Lei J, Boyer S, Mestres J
    Current Topics in Medicinal Chemistry 2005, 5:763-772
    [PubMed]
  • Combination of genetic databases for improving identification of genes and proteins in text.
    Kors JA, Schuemie MJ, Schijvenaars BJA, Weeber M, Mons B
    Proceedings of BioLINK, 2005 June 24, Detroit
    [BioLink]
  • Mapping OpenSDE domain models to SNOMED CT: Applied to the domain of cardiovascular disease.
    Min Z, Weeber M, Baofen D, Van Ginneken AM
    Methods of Information in Medicine 2005, 45(1):4-9
    [PubMed]
  • Online text mining tools to support discovery in the life sciences.
    Weeber M, Kors JA, Mons B
    Briefings in Bioinformatics 2005, 6(3):277-86
    [PubMed]
  • Thesaurus-based disambiguation of gene symbols.
    Schijvenaars BJ, Mons B, Weeber M, Schuemie MJ, van Mulligen EM, Wain HM, Kors JA
    BMC Bioinformatics 2005 Jun 16, 6:149
    [PubMed]
  • Word sense disambiguation in the biomedical domain: an overview.
    Schuemie MJ, Kors JA, Mons B
    Journal of Computational Biology 2005 Jun, 12:554-65
    [PubMed]
  • Which gene did you mean?
    Mons B
    BMC Bioinformatics 2005 Jun 7, 6:142
    [PubMed]
  • Co-occurrence based meta-analysis of scientific texts: retrieving biological relationships between genes.
    Jelier R, Jenster G, Dorssers LC, van der Eijk CC, van Mulligen EM, Mons B, Kors JA
    Bioinformatics 2005 May 1, 21:2049-58
    [PubMed]
  • Contextual annotation of web pages for interactive browsing.
    van Mulligen E, Diwersy M, Schijvenaars B, Weeber M, van der Eijk CC, Jelier R, Schuemie M, Kors J, Mons B
    Medinfo 2004, 11:94-8
    [PubMed]
  • Distribution of information in biomedical abstracts and full-text publications.
    Schuemie MJ, Weeber M, Schijvenaars BJ, van Mulligen EM, van der Eijk CC, Jelier R, Mons B, Kors JA
    Bioinformatics 2004 Nov 1, 20:2597-604
    [PubMed]
  • Constructing an Associative Concept Space for Literature-based Discovery.
    van der Eijk CC, van Mulligen EM, Kors JA, Mons B, van den Berg J
    Journal of the American Society for Information Science and Technology 2004, 55(5): 436-444
    [PDF]
  • Zoeken naar Impliciete kennis in Wetenschappelijke Literatuur.
    van der Eijk CC, van Mulligen EM, Kors JA, Mons B, van den Berg J
    Informatie & Zorg 2003, 32(1): 9-13
  • Ambiguity of Human Gene Symbols in LocusLink and MEDLINE: Creating an Inventory and a Disambiguation Test Collection.
    Weeber M, Schijvenaars RJA, van Mulligen EM, Mons B, Jelier R, van der Eijk CC, Kors JA
    Proceedings of AMIA Symposium 2003, 704-708
    [PubMed] [PDF] [Test Collection]
  • Using contextual queries.
    Schijvenaars B, Van Mulligen E, Diwersy M, Weeber M, Van Der Eijk C, Jelier R, Kors J, Mons B
    Proceedings of AMIA Symposium 2003, 998
    [PubMed]
  • Mining microarray datasets aided by knowledge stored in literature.
    Jelier R, Jenster G, Dorssers LC, Van Mulligen EM, Mons B, Kors JA
    Proceedings of AMIA Symposium 2003, 879
    [PubMed]
  • Research for research: tools for knowledge discovery and visualization.
    van Mulligen EM, van der Eijk CC, Kors JA, Schijvenaars RJA, Mons B
    Proceedings of AMIA Symposium 2002, 835-9
    [PubMed]
  • Finding Complementary Scientific Concepts Using a Conceptual Associative Spatial Graph.
    van der Eijk CC, van Mulligen EM, van den Berg J
    Proceedings of SCI 2002 2002, XIII: 46-50
  • Facilitating networks of information.
    van Mulligen EM, Diwersy M, Schmidt M, Buurman H, Mons B
    Proceedings of AMIA Symposium 2000, 868-72

    • Theses

  • Literature-based knowledge discovery using an associative concept space.
    van der Lans, BF
    M. Sc. Thesis 2004, Erasmus University, Rotterdam
    [PDF]
  • Knowledge Discovery in Scientific Literature.
    van der Eijk, CC
    M. Sc. Thesis 2001, Erasmus University, Rotterdam
    [PDF]

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