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Anni 2.0: a multipurpose text-mining tool for the life sciences
Rob Jelier, Martijn J Schuemie, Antoine Veldhoven, Lambert CJ Dorssers, Guido Jenster, Jan A Kors
Genome Biol. 2008; 9(6): R96. Published online 2008 June 12. doi: 10.1186/gb-2008-9-6-r96
PMCID:
PMC2481428
Abstract Full Text PDF–746K Supplementary Material

Is Cited by the Following 24 Articles in this Archive:

Exploring the Transcriptome of Ciliated Cells Using In Silico Dissection of Human Tissues
Alexander E. Ivliev, Peter A. C. 't Hoen, Willeke M. C. van Roon-Mom, Dorien J. M. Peters, Marina G. Sergeeva
PLoS One. 2012; 7(4): e35618. Published online 2012 April 25. doi: 10.1371/journal.pone.0035618
PMCID:
PMC3338421
Abstract Full Text PDF–4.3M Supplementary Material
Text Mining for Literature Review and Knowledge Discovery in Cancer Risk Assessment and Research
Anna Korhonen, Diarmuid Ó Séaghdha, Ilona Silins, Lin Sun, Johan Högberg, Ulla Stenius
PLoS One. 2012; 7(4): e33427. Published online 2012 April 12. doi: 10.1371/journal.pone.0033427
PMCID:
PMC3325219
Abstract Full Text PDF–1.6M Supplementary Material
Transcriptional Profiling of Human Familial Longevity Indicates a Role for ASF1A and IL7R
Willemijn M. Passtoors, Judith M. Boer, Jelle J. Goeman, Erik B. van den Akker, Joris Deelen, Bas J. Zwaan, Ann Scarborough, Ruud van der Breggen, Rolf H. A. M. Vossen, Jeanine J. Houwing-Duistermaat, Gert Jan B. van Ommen, Rudi G. J. Westendorp, Diana van Heemst, Anton J. M. de Craen, Andrew J. White, David A. Gunn, Marian Beekman, P. Eline Slagboom
PLoS One. 2012; 7(1): e27759. Published online 2012 January 11. doi: 10.1371/journal.pone.0027759
Correction in:
PLoS One. 2012; 7(5): 10.1371/annotation/d4d3b1fb-35e0-4c4d-89bc-e6a839504e54.
PMCID:
PMC3256132
Abstract Full Text PDF–2.1M Supplementary Material Correction
Data mining of mental health issues of non-bone marrow donor siblings
Morihito Takita, Yuji Tanaka, Yuko Kodama, Naoko Murashige, Nobuyo Hatanaka, Yukiko Kishi, Tomoko Matsumura, Yukio Ohsawa, Masahiro Kami
J Clin Bioinforma. 2011; 1: 19. Published online 2011 July 20. doi: 10.1186/2043-9113-1-19
PMCID:
PMC3164612
Abstract Full Text PDF–1005K
Systemic Signature of the Lung Response to Respiratory Syncytial Virus Infection
Jeroen L. A. Pennings, Annemieke Schuurhof, Hennie M. Hodemaekers, Annemarie Buisman, Lia C. G. H. de Rond, Myra N. Widjojoatmodjo, Willem Luytjes, Jan L. L. Kimpen, Louis Bont, Riny Janssen
PLoS One. 2011; 6(6): e21461. Published online 2011 June 24. doi: 10.1371/journal.pone.0021461
PMCID:
PMC3123345
Abstract Full Text PDF–342K
Discovering and visualizing indirect associations between biomedical concepts
Yoshimasa Tsuruoka, Makoto Miwa, Kaisei Hamamoto, Jun'ichi Tsujii, Sophia Ananiadou
Bioinformatics. 2011 July 1; 27(13): i111–i119. Published online 2011 June 14. doi: 10.1093/bioinformatics/btr214
PMCID:
PMC3117364
Abstract Full Text
Deregulation of the ubiquitin-proteasome system is the predominant molecular pathology in OPMD animal models and patients
Seyed Yahya Anvar, Peter AC 't Hoen, Andrea Venema, Barbara van der Sluijs, Baziel van Engelen, Marc Snoeck, John Vissing, Capucine Trollet, George Dickson, Aymeric Chartier, Martine Simonelig, Gert-Jan B van Ommen, Silvere M van der Maarel, Vered Raz
Skelet Muscle. 2011; 1: 15. Published online 2011 April 4. doi: 10.1186/2044-5040-1-15
PMCID:
PMC3156638
Abstract Full Text PDF–5.5M Supplementary Material
Human Papillomavirus Deregulates the Response of a Cellular Network Comprising of Chemotactic and Proinflammatory Genes
Rezaul Karim, Craig Meyers, Claude Backendorf, Kristina Ludigs, Rienk Offringa, Gert-Jan B. van Ommen, Cornelis J. M. Melief, Sjoerd H. van der Burg, Judith M. Boer
PLoS One. 2011; 6(3): e17848. Published online 2011 March 14. doi: 10.1371/journal.pone.0017848
PMCID:
PMC3056770
Abstract Full Text PDF–1.7M Supplementary Material
AGRA: analysis of gene ranking algorithms
Simon Kocbek, Rune Sætre, Gregor Stiglic, Jin-Dong Kim, Igor Pernek, Yoshimasa Tsuruoka, Peter Kokol, Sophia Ananiadou, Jun'ichi Tsujii
Bioinformatics. 2011 April 15; 27(8): 1185–1186. Published online 2011 February 23. doi: 10.1093/bioinformatics/btr097
PMCID:
PMC3072556
Abstract Full Text PDF–134K
Comprehensive Gene-Expression Survey Identifies Wif1 as a Modulator of Cardiomyocyte Differentiation
Henk P. J. Buermans, Bram van Wijk, Margriet A. Hulsker, Niels C. H. Smit, Johan T. den Dunnen, Gertjan B. van Ommen, Antoon F. Moorman, Maurice J. van den Hoff, Peter A. C. 't Hoen
PLoS One. 2010; 5(12): e15504. Published online 2010 December 13. doi: 10.1371/journal.pone.0015504
PMCID:
PMC3001492
Abstract Full Text PDF–1.7M Supplementary Material
Recent progress in automatically extracting information from the pharmacogenomic literature
Yael Garten, Adrien Coulet, Russ B Altman
Pharmacogenomics. Author manuscript; available in PMC 2011 August 1.
Published in final edited form as: Pharmacogenomics. 2010 October; 11(10): 1467–1489. doi: 10.2217/pgs.10.136
PMCID:
PMC3035632
Abstract Full Text PDF–990K
Literature Mining for the Discovery of Hidden Connections between Drugs, Genes and Diseases
Raoul Frijters, Marianne van Vugt, Ruben Smeets, René van Schaik, Jacob de Vlieg, Wynand Alkema
PLoS Comput Biol. 2010 September; 6(9): e1000943. Published online 2010 September 23. doi: 10.1371/journal.pcbi.1000943
PMCID:
PMC2944780
Abstract Full Text PDF–817K Supplementary Material
eGIFT: Mining Gene Information from the Literature
Catalina O Tudor, Carl J Schmidt, K Vijay-Shanker
BMC Bioinformatics. 2010; 11: 418. Published online 2010 August 9. doi: 10.1186/1471-2105-11-418
PMCID:
PMC2929241
Abstract Full Text PDF–677K Supplementary Material
Calpain 3 Is a Rapid-Action, Unidirectional Proteolytic Switch Central to Muscle Remodeling
Antoine de Morrée, David Lutje Hulsik, Antonietta Impagliazzo, Herman H. H. B. M. van Haagen, Paula de Galan, Alexandra van Remoortere, Peter A. C. 't Hoen, GertJan B. van Ommen, Rune R. Frants, Silvère M. van der Maarel
PLoS One. 2010; 5(8): e11940. Published online 2010 August 4. doi: 10.1371/journal.pone.0011940
PMCID:
PMC2915920
Abstract Full Text PDF–822K Supplementary Material
Tissue-specific transcript annotation and expression profiling with complementary next-generation sequencing technologies
Matthew S. Hestand, Andreas Klingenhoff, Matthias Scherf, Yavuz Ariyurek, Yolande Ramos, Wilbert van Workum, Makoto Suzuki, Thomas Werner, Gert-Jan B. van Ommen, Johan T. den Dunnen, Matthias Harbers, Peter A.C. 't Hoen
Nucleic Acids Res. 2010 September; 38(16): e165. Published online 2010 July 7. doi: 10.1093/nar/gkq602
PMCID:
PMC2938216
Abstract Full Text PDF–4.0M
BSQA: integrated text mining using entity relation semantics extracted from biological literature of insects
Xin He, Yanen Li, Radhika Khetani, Barry Sanders, Yue Lu, Xu Ling, ChengXiang Zhai, Bruce Schatz
Nucleic Acids Res. 2010 July 1; 38(Web Server issue): W175–W181. Published online 2010 June 21. doi: 10.1093/nar/gkq544
PMCID:
PMC2896161
Abstract Full Text PDF–6.1M
Identifying overrepresented concepts in gene lists from literature: a statistical approach based on Poisson mixture model
Xin He, Moushumi Sen Sarma, Xu Ling, Brant Chee, Chengxiang Zhai, Bruce Schatz
BMC Bioinformatics. 2010; 11: 272. Published online 2010 May 20. doi: 10.1186/1471-2105-11-272
PMCID:
PMC2885378
Abstract Full Text PDF–1.6M Supplementary Material
The identification of informative genes from multiple datasets with increasing complexity
S Yahya Anvar, Peter AC 't Hoen, Allan Tucker
BMC Bioinformatics. 2010; 11: 32. Published online 2010 January 15. doi: 10.1186/1471-2105-11-32
PMCID:
PMC2822754
Abstract Full Text PDF–433K Supplementary Material
Martini: using literature keywords to compare gene sets
Theodoros G. Soldatos, Seán I. O’Donoghue, Venkata P. Satagopam, Lars J. Jensen, Nigel P. Brown, Adriano Barbosa-Silva, Reinhard Schneider
Nucleic Acids Res. 2010 January; 38(1): 26–38. Published online 2010 January. doi: 10.1093/nar/gkp876
PMCID:
PMC2800231
Abstract Full Text PDF–4.3M
Biomedical Text Mining and Its Applications
Raul Rodriguez-Esteban
PLoS Comput Biol. 2009 December; 5(12): e1000597. Published online 2009 December 24. doi: 10.1371/journal.pcbi.1000597
PMCID:
PMC2791166
Full Text PDF–542K
Discovery of Novel Serum Biomarkers for Prenatal Down Syndrome Screening by Integrative Data Mining
Jeroen L. A. Pennings, Maria P. H. Koster, Wendy Rodenburg, Peter C. J. I. Schielen, Annemieke de Vries
PLoS One. 2009; 4(11): e8010. Published online 2009 November 24. doi: 10.1371/journal.pone.0008010
PMCID:
PMC2777317
Abstract Full Text PDF–216K
Novel Protein-Protein Interactions Inferred from Literature Context
Herman H. H. B. M. van Haagen, Peter A. C. 't Hoen, Alessandro Botelho Bovo, Antoine de Morrée, Erik M. van Mulligen, Christine Chichester, Jan A. Kors, Johan T. den Dunnen, Gert-Jan B. van Ommen, Silvère M. van der Maarel, Vinícius Medina Kern, Barend Mons, Martijn J. Schuemie
PLoS One. 2009; 4(11): e7894. Published online 2009 November 18. doi: 10.1371/journal.pone.0007894
PMCID:
PMC2774517
Abstract Full Text PDF–128K Supplementary Material
Structuring and extracting knowledge for the support of hypothesis generation in molecular biology
Marco Roos, M Scott Marshall, Andrew P Gibson, Martijn Schuemie, Edgar Meij, Sophia Katrenko, Willem Robert van Hage, Konstantinos Krommydas, Pieter W Adriaans
BMC Bioinformatics. 2009; 10(Suppl 10): S9. Published online 2009 October 1. doi: 10.1186/1471-2105-10-S10-S9
PMCID:
PMC2755830
Abstract Full Text PDF–1.4M
Evaluation of genome-wide association study results through development of ontology fingerprints
Lam C. Tsoi, Michael Boehnke, Richard L. Klein, W. Jim Zheng
Bioinformatics. 2009 May 15; 25(10): 1314–1320. Published online 2009 April 5. doi: 10.1093/bioinformatics/btp158
PMCID:
PMC2732313
Abstract Full Text PDF–127K Supplementary Material
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