Journal articles

  1. Vromen, T., Kraal, J. J., Kuiper, J., Spee, R. F., Peek, N., & Kemps, H. M. (2016). The influence of training characteristics on the effect of aerobic exercise training in patients with chronic heart failure: A meta-regression analysis. International Journal of Cardiology. [doi]
  2. Wallace, B. C., Kuiper, J., Sharma, A., Marshall, I. J., & Zhu, M. (B. (2016). Extracting PICO Sentences from Clinical Trial Reports using Supervised Distant Supervision. Journal of Machine Learning Research. [preprint]
  3. Kuiper, J., van den Heuvel, E. R., & Swertz, M. A. (2015). The Hybrid Synthetic Microdata Platform: A Method for Statistical Disclosure Control. Biopreservation and Biobanking, 13(3), 178–182. [preprint] [doi]
  4. van der Velde, K. J., Kuiper, J., Thompson, B. A., Plazzer, J.-P., van Valkenhoef, G., de Haan, M., … Swertz, M. A. (2015). Evaluation of CADD Scores in Curated Mismatch Repair Gene Variants Yields a Model for Clinical Validation and Prioritization. Human Mutation, 36(7), 712–719. [preprint] [doi]
  5. Pang, C., Hendriksen, D., Dijkstra, M., van der Velde, K. J., Kuiper, J., Hillege, H. L., & Swertz, M. A. (2015). BiobankConnect: software to rapidly connect data elements for pooled analysis across biobanks using ontological and lexical indexing. Journal of the American Medical Informatics Association, 22(1), 65–75. [doi]
  6. Marshall, I. J., Kuiper, J., & Wallace, B. C. (2015). Automating Risk of Bias Assessment for Clinical Trials. IEEE Journal of Biomedical and Health Informatics (JBHI), 19(4), 1406–1412. [doi]
  7. Marshall, I. J., Noel-Storr, A., Kuiper, J., Thomas, J., & Wallace, B. C. (2018). Machine learning for identifying Randomized Controlled Trials: An evaluation and practitioner’s guide. Research synthesis methods. [preprint]
  8. Marshall, I. J., Kuiper, J., & Wallace, B. C. (2015). RobotReviewer: evaluation of a system for automatically assessing bias in clinical trials. Journal of the American Medical Informatics Association. [preprint] [doi]
  9. Kanterakis, A., Kuiper, J., Potamias, G., & Swertz, M. A. (2015). PyPedia: using the wiki paradigm as crowd sourcing environment for bioinformatics protocols. Source Code for Biology and Medicine, 10(1), 1. [doi]

Conference proceedings

  1. Marshall, I. J., Kuiper, J., Banner, E., & Wallace, B. C. (2017). Automating biomedical evidence synthesis: RobotReviewer. In Proceedings of the conference. Association for Computational Linguistics. Meeting (Vol. 2017, pp. 7–12). Association for Computational Linguistics. [preprint]
  2. Kuiper, J., Marshall, I. J., Wallace, B. C., & Swertz, M. A. (2014). Spá: A Web-Based Viewer for Text Mining in Evidence Based Medicine. In Proceedings of the European Conference on Machine Learning and Principles and Practice of Knowledge Discovery in Databases (ECML-PKDD 2014) (Vol. 8726, pp. 452–455). Springer Berlin Heidelberg. [preprint] [doi]
  3. Marshall, I. J., Kuiper, J., & Wallace, B. C. (2014). Automating Risk of Bias Assessment for Clinical Trials. In Proceedings of the ACM Conference on Bioinformatics, Computational Biology, and Health Informatics (ACM-BCB) (pp. 88–95). ACM. [invited resubmission to JBHI]. [preprint] [doi]
  4. van Valkenhoef, G., & Kuiper, J. (2014). Crowdsourcing a Comprehensive Clinical Trial Repository. In Proceedings of the AAAI Workshop on Modern Artificial Intelligence for Health Analytics (MAIHA 2014). [preprint]
  5. Kuiper, J., & van Valkenhoef, G. (2013). Top-Level MeSH Disease Terms Are Not Linearly Separable in Clinical Trial Abstracts. In Proceedings of the conference on Artificial Intelligence in Medicine (AIME 2013) (Vol. 7885, pp. 130–134). Springer Berlin Heidelberg. [preprint] [slides] [poster] [doi]

Abstracts and presentations

  1. Kuiper, J. (2014). Collaborating on knowledge. [slides]
  2. Kuiper, J. (2014). Sharing knowledge in institutions. [slides]
  3. Kuiper, J. (2014). From data to publication, and back again. [Presentation at the annual BioSHaRE meeting, 12 November 2014, Athens, Greece].
  4. Kuiper, J. (2014). (Re)imposing Structure. [Presentation at Genetics Coordination Center, University Medical Center Groningen, 21 September 2014, Groningen, The Netherlands]. [slides] [doi]
  5. Kuiper, J. (2014). Resurrecting documents – automatically extracting structure from PDFs. [Presentation at the Social Epidemiology unit meeting, University Medical Center Groningen, 16 June 2014, Groningen, The Netherlands]. [slides]
  6. Kuiper, J. (2013). Reproducible Science: how to deal with the entanglement of data, methods, code and publications. [Presentation at Epidemiology, University Medical Center Groningen, 14 November 2013, Groningen, The Netherlands]. [slides]
  7. Kuiper, J. (2011). As we may remember — a conjunction between memory & consciousness. [BSc. thesis in Artificial Intelligence, 4 July 2011, Groningen, The Netherlands]. [slides]