Scientific excellence

Publications

Here is a non-exhaustive list of publications (scientific communications, patents, software libraries) to which DNAlytics collaborators have contributed.

• Vaccinology in the artificial intelligence era.
  G. Gasperini, N. Baylor, S. Black, D.E. Bloom, J. Cramer, G. de Lannoy, P. Denoel, M. Feinberg, T. Helleputte, G. Kang, W.R. Schief, L. Stuart, C. Weller, M. Zwierzyna, R. Rappuoli, Science Translational Medicine, 17. 10.1126/scitranslmed.adu3791
• Structured and unstructured data from first and second line care combined in OMOP datawarehouses                             
  T.Helleputte, M. Borshchivska, A. Kanfoud, P. Olivier, G. Vanhalst, T. Klein, European OHDSI Symposium 2024, Rotterdam.
• Institute of Analytics for Health
  M. Borshchivska, A. Kanfoud, T.Helleputte, European OHDSI Symposium 2024, Rotterdam.
• IODA, an ATLAS-based software for the INAH Community
  A. Kanfoud, M. Borshchivska, T.Helleputte, European OHDSI Symposium 2024, Rotterdam.
• Feature selection with prior knowledge improves interpretability of chemometrics models
  Thomas Des Touches, Marco Munda, Thomas Cornet, Pascal Gerkens, Thibault Helleputte, Chemometrics and Intelligent Laboratory Systems, 2023.
• Immune Response Evolution in Peanut Epicutaneous Immunotherapy for Peanut-Allergic Children
  Marie Bastin, Warner W. Carr, Carla M. Davis, David M. Fleischer, Jay A. Lieberman, S. Shahzad Mustafa, Thibault Helleputte, Timothée Bois, Dianne E. Campbell, Todd D. Green, Matthew Greenhawt, European Journal of Allergy and Clinical Immunology, 14 March 2023.
• Viscosupplementation in Osteoarthritis 
  Yves Henrotin, Cedric Tits, Jérôme Paul, Pierre Gramme, Thibault Helleputte, Alberto Migliore, Pascal Richette, Xavier Chevalier, Jordi Monfort, Demirhan Diracoglu, Hervé Bard, Jörg Jerosch, Dominique Baron, Raman Raghu, Thierry Conrozier, Cartilage 13 (2021) 1696S.
• Machine Learning in the biopharma industry
  Thibault Helleputte, Gaël de Lannoy, Paul Smyth – ESANN proceedings. European Symposium on Artificial Neural Networks, Computational Intelligence and Machine Learning.
• Trends and preferences in RA clinical scores worldwide
  Thibault Helleputte, Damien Bertrand – Annals of the Rheumatic Diseases 2020;79:257-258.
• Cartilage biomarkers s-Coll2-1 and s-Coll2-1NO2 are helpful in identifying knee osteoarthritis patients at risk of disease worsening
  Yves Henrotin, Bérénice Costes, Michel Malaise, Damien Loeuille, Thierry Conrozier, Yves Maugars, Franz Pelousse, Jean-Marc Lemaire, Thibault Helleputte, Cédric Tits, Alain Labasse, Anne-Christine Hick – ACR 2020 – Customer : Artialis
• Feedback Adaptation to Unpredictable Force Fields in 250 ms
  Frédéric Crevecoeur, James Mathew, Marie Bastin, Philippe Lefèvre, eNeuro, 21 April 2020, 7 (2).
• Assessment of the Most Impactful Combination of Factors Associated with Nocturia and to Define Nocturnal Polyuria by Multivariate Modelling
  Olesen, T.; Paul, J.; Gramme, P.; Drake, M.J.; Vandewalle, J.; Everaert, K. – J. Clin. Med.2020, 9, 2262. – Customer : Ferring
• Clinical Innovation
  Partner : Biowin – Authors : Sylvie Ponchaut, Marianne Ghyoot & Thibault Helleputte. 
• Mapping acute HIV-1 infection: designing a webtool to capture multicentric and multidisciplinary data
  Jozefien De Clercq, Cedric Tits, Damien Bertrand, Sophie Vanherrewege, Sofie Rutsaert, Laura De Clercq, Marie-Angélique De Scheerder, Linos Vandekerckhove – Poster presentation @ Flanders Bio – Knowledge for Growth, Ghent, May 2019. 
• Data science, artificial intelligence, and machine learning: Opportunities for laboratory medicine and the value of positive regulation.
  Damien Gruson, Thibault Helleputte, Patrick Rousseau, David Gruson – Clinical Biochemistry – Customer : Cliniques Universitaires Saint-Luc
• More efficient DMOAD trials through innovative screening strategies
  Thibault Helleputte, Yves Henrotin – Annals of Rheumatic Diseases 78 (2019) A646 – Customer : Artialis
• Dominance of drug target mechanisms in Rheumatoid Arthritis
  Jérôme Paul, Pierre Gramme, Thibault Helleputte – Annals of Rheumatic Diseases 78 (2019) A284 – Customer : Sanofi Genzyme
• Novel insights into the assessment of risk of upper gastrointestinal bleeding in decompensated cirrhotic children.
  N Bonnet, J Paul, T Helleputte, et al. Novel insights into the assessment of risk of upper gastrointestinal bleeding in decompensated cirrhotic children – Pediatric Transplantation 2019 – e13390 – Customer : UCL/BELCRO – Online Calculator
• Discovery and validation of a serum microRNA signature to characterize oligo- and polymetastatic prostate cancer: not ready for prime time
  Bert Dhondt, Elise De Bleser, Tom Claeys, Sarah Buelens, Nicolaas Lumen, Jo Vandesompele, Anneleen Beckers, Valerie Fonteyne, Kim Van der Eecken, Aurélie De Bruycker, Jérôme Paul, Pierre Gramme, Piet Ost – World Journal of Urology (2019) – Customer : UGent
• Development of a multivariate prediction model for nocturia, based on urinary tract etiologies
  Olesen TK, Denys MA, Goessaert AS, Bruneel E, Decalf V, Helleputte T, Paul J, Gramme P, Everaert K – International Journal of Clinical Practice (2019) – Customer : Ferring – Online Calculator
  
• Serum Biomarkers of Immunomodulation During Peanut Epicutaneous Immunotherapy (EPIT) in Peanut-Allergic Subjects
  ACAAI Annual Meeting, November 15-19, 2018, Seattle, Washington. (2018) – Customer : DBV Technologies
• Serum Biomarkers of Immunomodulation During PeanutEpicutaneous Immunotherapy (EPIT) in Peanut-Allergic Subjects
  Matthew Greenhawt, Warner Carr, Carla M. Davis, Jay A. Lieberman, S. Shahzad Mustafa, Todd D. Green, Thibault Helleputte, Romain Lambert, David M. Fleischer – FAAM 2018, Food Allergy and Anaphylaxis Meeting; Copenhagen, Denmark; October 18–20, 2018 (2018) – Customer : DBV Technologies
• Development of a multivariate prediction model for nocturia, based on the most important etiologies of the urinary tract
  Roggeman S., Olesen T.K., Denys M-A., Goessaert A-S., Bruneel E., Decalf V., Helleputte T., Gramme P., Everaert K., European Urology. Supplements Volume 17, Issue 2, March 2018, Page e347 (2018) – Customer : Ferring
• Long-term Outcomes with Anti-TNF Therapy and Accelerated Step-up in the Prospective Pediatric Belgian Crohn’s Disease Registry (BELCRO)
  Lucas Wauters, Françoise Smets, Elisabeth De Greef, Patrick Bontems, Ilse Hoffman, Bruno Hauser, Philippe Alliet, Wim Arts, Harald Peeters, Stephanie Van Biervliet, Isabelle Paquot, Els Van de Vijver, Martine De Vos, Peter Bossuyt, Jean-François Rahier, Olivier Dewit, Tom Moreels, Denis Franchimont, Vincianne Muls, Fernand Fontaine, Edouard Louis, Jean-Charles Coche, Filip Baert, Jérôme Paul, Séverine Vermeire, Geneviève Veereman, Inflammatory Bowel Diseases (2017) – Customer : UCL/BELCRO
• Routine Use of Synovial Biopsies for Diagnosis and Treatment Guidance
  Thibault Helleputte, Pierre Gramme, Annals of the Rheumatic Diseases (2016)
• Prediction of peanut-challenge outcome with biomarkers
  Peillon A., Thébault C., Helleputte T., Gramme P., Agbotounou W.K., Martin L., Prof. Dupont C., Benhamou P.-H., H.A. Sampson, Ruban C., EAACI 2016 –Vienna, Austria (2016) – Customer : DBV Technologies
• Monitoring viaskin peanut treatment progression with a biomarker-based model
  L. Salmun, A. Peillon, C. Thebault, C. Ruban, R. Lambert, T. Helleputte, P. Gramme, Annallergy, Volume 117, Issue 5, Supplement, Page S102 (2016) – Customer : DBV Technologies
• Evaluating risk of esophageal variceal bleed in children with cirrhosis and waitlisted for liver transplantation
  Stephenne X., Bonnet N., Varma S., Helleputte T., Smets F., Veyckemans F., Eeckhoudt S., Hermans C., Sokal E., Journal of Pediatric Gastroenterology and Nutrition (2016) – Customer : Cliniques Universitaires St Luc, service of paediatrics – See the resulting web app : Online Calculator
• Type of treating physician is associated with long-term disease outcome in the prospective Belgian paediatric Crohn’s disease registry
  L Wauters, F Smets, E De Greef, P Bontems, I Hoffman, B Hauser, P Alliet, W Arts, H Peeters, S Van Biervliet, I Paquot, E Van de Vijver,            M De Vos, P Bossuyt, J-F ahier, O Dewit, T Moreels, D Franchimont, V Muls, F Fontaine, E Louis, J-C Coche, J Paul, F Baert, S Vermeire, G Veereman, Journal of Cronhs & Colitis (2016) – Customer : UCL/BELCRO
• Heterogeneity of Synovial Molecular Patterns in Patients with Arthritis
  Bernard R. Lauwerys , Daniel Hernández-Lobato, Pierre Gramme, Julie Ducreux, Adrien Dessy, Isabelle Focant, Jérôme Ambroise, Bertrand Bearzatto, Adrien Nzeusseu Toukap, Benoît J. Van den Eynde, Dirk Elewaut, Jean-Luc Gala, Patrick Durez, Frédéric A. Houssiau, Thibault Helleputte, Pierre Dupont, PLoS One (2015)
• DNA Methylation-Guided Prediction of Clinical Failure in High-Risk Prostate Cancer
  Kirill Litovkin, Aleyde Van Eynde, Steven Joniau, Evelyne Lerut, Annouschka Laenen, Thomas Gevaert, Olivier Gevaert, Martin Spahn, Burkhard Kneitz, Pierre Gramme, Thibault Helleputte, Sofie Isebaert, Karin Haustermans, Mathieu Bollen, PLoS One (2015) – Customer : FFMI/KULeuven
• Inferring statistically significant features from random forests
  J. Paul and P. Dupont, Neurocomputing (2015)
• Clinical Parameters vs Cytokine Profiles as Predictive Markers of IgE-Mediated Allergy in Young Children
  Catherine Lombard, Floriane André, Jérôme Paul, Catherine Wanty, Olivier Vosters, Pierre Bernard, Charles Pilette, Pierre Dupont, Etienne Sokal and Françoise Smets, PLoS ONE (2015)
• Kernel methods for heterogeneous feature selection
  J. Paul, R. D’Ambrosio and P. Dupont, Neurocomputing (2015)
• A generic cycling hypoxia-derived prognostic gene signature: application to breast cancer profiling.
  Boidot R., Branders S., Helleputte T., Rubio L.I., Dupont P. and Feron O., Oncotarget, Vol. 5, No. 16, 2014. (2014) – Customer : UCL/PHARMA
• Baseline measurements of Coll2-1 and Coll2-1NO2 in urine are highly predictive of joint space narrowing in knee osteoarthritis.
  Henrotin Y., Kraus V., Huebner J., Helleputte T., Deberg M., EULAR Congress, Madrid, Spain, 2013. (2013) – Customer : Artialis
• RheumaKit, a new early diagnostic tool for patients with arthritis.
  Helleputte T., Dessy A., Hernandez-Lobato D., Dupont P., Lauwerys B., Knowledge for Growth, Ghent, Belgium, 30 May 2013. (2013) – Winner of the Inspiring Young Scientist Award
• Assessment of risk of bleeding from esophageal varices during management of biliary atresia in children.
  Stephenne X., Wanty C., Helleputte T., Smets F., Sokal E., 63rd Annual Meeting of the American Association for the Study of Liver Diseases (AASLD), Boston, Massachusetts, USA, November 9-13 2012 (2012) – Cliniques Universitaires St Luc, service of paediatrics – See the resulting web app : Online Calculator
• Assessment of risk of bleeding from esophageal varices during management of biliary atresia in children.
  Wanty C., Helleputte T., Smets F., Sokal EM., Stephenne X., Journal of Pediatric Gastroenterology and Nutrition. December 20, 2012 (2012) – Customer : Cliniques Universitaires St Luc, service of paediatrics – See the resulting web app : Online Calculator
• Strategic Overview of Personalised Medicine.
  Helleputte T., International Pharmaceutical Industry, Volume 4, No. 2, Spring 2012. (2012)
• Differences in the cytokine profiles of cord blood mononuclear cells from allergic and non-allergic infants
  C. Lombard, F. André, C. Wanty, J. Paul, P. Dupont, E. Sokal, F. Smets, European Society for Paediatric Gastroenterology, Hepatology, and Nutrition (ESPGHAN’12), Stockholm, Sweden, April 27-28, 2012 (2012) – Customer : Cliniques Universitaires St Luc, service of paediatrics.
• Expectation Propagation for Bayesian Multi-task Feature Selection
  Hernandez-Lobato, D., Hernandez-Lobato, J., Helleputte, T. and Dupont, P., European Conference on Machine Learning (ECML), Barcelona, Spain, September, 2010. (2010)
• Robust biomarker identification for cancer diagnosis with ensemble feature selection methods.
  Abeel T., Helleputte T., Van de Peer Y. and Saeys Y., Bioinformatics Advance Access published on February 1, 2010. Bioinformatics, Volume 26, No. 3, pp. 392-398. (2010) – Partnering with Ugent/Y.Saeys – Supp Material
• Expectation Propagation for Bayesian Multi-task Feature Selection.
  Hernández-Lobato D., Hernández-Lobato J.M., Helleputte T., Dupont P., Machine Learning and Knowledge Discovery in Databases. ECML/PKDD 2010. Lecture Notes in Computer Science, vol 6321. Springer, Berlin, Heidelberg (2010)
• Inductive Biases for Stable Feature Selection in High Dimensional Spaces: Applications to Gene Profiling and Diagnosis from DNA Microarrays.
  Helleputte T., PhD Thesis, University of Louvain, September 2010. (2010) – Video
• Robust biomarker identification for cancer diagnosis using ensemble feature selection methods.
  Abeel T., Helleputte T., Van de Peer Y., Dupont P., and Saeys Y., Third International Workshop on Machine Learning in Systems Biology (MLSB), pp. 135, Ljubljana, Slovenia, September 5-6, 2009. (2009) – Partnering with Ugent/Y.Saeys – Poster
• Biomarker Selection by Transfer Learning with Linear Regularized Models
  Helleputte T. and Dupont P., Third International Workshop on Machine Learning in Systems Biology (MLSB), pp. 159-160, Ljubljana, Slovenia, September 5-6, 2009. (2009) – Poster
• Feature Selection by Transfer Learning with Linear Regularized Models
  Helleputte T. and Dupont P., European Conference on Machine Learning (ECML), Bled, Slovenia, September 7-11, 2009. (2009) – Poster – Video
• Partially Supervised Feature Selection with Regularized Linear Models
  Helleputte T. and Dupont P., 26th International Conference on Machine Learning (ICML), Montreal, Canada, June 14-18, 2009. (2009) – Poster – Video
• Clinical response to the MAGE-3 immunotherapeutic in metastatic melanoma patients is associated with a specific gene profile present prior to treatment
  Louahed J., Gaulis S., Helleputte T., Dupont P., Gruselle O., Spatz A., Kruit Wim H J, Dreno B, Lehmann F, Brichard V, 33th European Society for Medical Oncology (ESMO) Congress, Stockholm, Sweden, September 12-16, 2008, 470129. (2008) – Customer : GSK

Patents

To which we contributed as (co-)inventors, or on which we have a license:

• Signature of cycling hypoxia and use thereof for the prognosis of cancer.
  Feron O., Boidot R., Branders S., Dupont P., Helleputte T. (2015) – This patent has been invented in the context of a collaboration with Prof. Olivier Feron (UCL)
• Method and tools for predicting a pain response in a subject suffering from cancer-induced bone pain
  Alvaro Pereira, Chantal Gossuin, Dominique Demolle, Denis Gossen, Thibault Helleputte (2014) -This patent has been invented in the context of a collaboration with our customer Tools4Patients
• Method for prediction of a placebo response in a individual suffering from or at risk to a pain disorder
  Thibault Helleputte, Alvaro Pereira, Chantal Gossuin, Dominique Demolle (2014) – This patent has been invented in the context of a collaboration with our customer Tools4Patients.
• Method for classifying a cancer patient as responder or non-responder to immunotherapy
  Dupont P., Gaulis S. and Helleputte T. (2010) – This patent has been invented in the context of a collaboration with GSK.

Software

LiblineaR – an R package for large-scale linear modeling  supporting classification and regression of large datasets. The original software in C/C++ was developed by Prof. Chih-Jen Lin and his team at the Machine Learning Group of the Taiwan University. As most of our developments are done in the open source R language, we have developed the R library LiblineaR, making all the functionalities of the original library available in the R environment. This software library thus offers to bioinformaticians, machine learners, data miners, to process data sets with very large number of features and/or large number of observations right in their favorite language. Recent versions of our package offers not only support for classification, but also for regression. The use of sparse matrices is also supported. We continue maintaining it as an open source software : it is freely available and has been downloaded more than 450.000 times around the world !