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Journal articles

Zwanenburg A, Vallieres M, Abdalah MA, Aerts HJWL, Andrearczyk V, Apte A, Ashrafinia S, Bakas S, Beukinga RJ, Boellaard R, Bogowicz M, Boldrini L, Buvat I, Cook GJR, Davatzikos C, Depeursinge A, Desseroit M-C, Dinapoli N, Dinh CV, Echegaray S, El Naqa I, Fedorov AY, Gatta R, Gillies RJ, Goh V, Götz M, Guckenberger M, Ha SM, Hatt M, Isensee F, Lambin P, Leger S, Leijenaar RTH, Lenkowicz J, Lippert F, Losnegård A, Maier-Hein KH, Morin O, Müller H, Napel S, Nioche C, Orlhac F, Pati S, Pfaehler EAG, Rahmim A, Rao AUK, Scherer J, Siddique MM, Sijtsema NM, Socarras Fernandez J, Spezi E, Steenbakkers RJHM, Tanadini-Lang S, Thorwarth D, Troost EGC, Upadhaya T, Valentini V, van Dijk LV, van Griethuysen J, van Velden FHP, Whybra P, Richter C, Löck S (2020) The Image Biomarker Standardization Initiative: standardized quantitative radiomics for high-throughput image-based phenotyping. Radiology 191145. https://doi.org/10.1148/radiol.2020191145 Cite Download
Zhou H, Chang K, Bai HX, Xiao B, Su C, Bi WL, Zhang PJ, Senders JT, Vallieres M, Kavouridis VK, Boaro A, Arnaout O, Yang L, Huang RY (2019) Machine learning reveals multimodal MRI patterns predictive of isocitrate dehydrogenase and 1p/19q status in diffuse low- and high-grade gliomas. J Neurooncol 142:299–307. Cite Download
Zhao Y, Chang M, Wang R, Xi IL, Chang K, Huang RY, Vallieres M, Habibollahi P, Dagli MS, Palmer M, Zhang PJ, Silva AC, Yang L, Soulen MC, Zhang Z, Bai HX, Stavropoulos SW (2020) Deep Learning Based on MRI for Differentiation of Low- and High-Grade in Low-Stage Renal Cell Carcinoma. Journal of Magnetic Resonance Imaging. https://doi.org/10.1002/jmri.27153 Cite Download
Zapletal E, Bibault J-E, Giraud P, Burgun A (2018) Integrating Multimodal Radiation Therapy Data into i2b2. Appl Clin Inform 9:377–390. https://doi.org/10.1055/s-0038-1651497 Cite
Yousif A, Dault R, Courteau M, Blais L, Cloutier A-M, Lacasse A, Vanasse A, Bartlett G, Benigeri M, Blais L, Borja J, Buckeridge D, Choinière M, Côté-Marcil M-A, Courteau J, Courteau M, Dorais M, Dubé F, Ethier J-F, Émond V, Giguère A, Hudon C, Jean S, Lacasse A, Lamarche B, Lebel A, Leroux I, Néron A, Plante S, Pomey M-P, Quesnel-Vallée A, Quirion S, Rheaume J, Roberge P, Roy D, Tremblay P, on behalf of the TorSaDE Cohort Working Group (2022) The validity of diagnostic algorithms to identify asthma patients in healthcare administrative databases: a systematic literature review. J Asthma 59:152–168. https://doi.org/10.1080/02770903.2020.1827425 Cite
Yang DD, Baujat G, Neuraz A, Garcelon N, Messiaen C, Sandrin A, Cheron G, Burgun A, Pejin Z, Cormier-Daire V, Angoulvant F (2020) Healthcare trajectory of children with rare bone disease attending pediatric  emergency departments. Orphanet J Rare Dis 15:2. https://doi.org/10.1186/s13023-019-1284-1 Cite
Xi IL, Zhao Y, Wang R, Chang M, Purkayastha S, Chang K, Huang RY, Silva AC, Vallieres M, Habibollahi P, Fan Y, Zou B, Gade TP, Zhang PJ, Soulen MC, Zhang Z, Bai HX, Stavropoulos SW (2020) Deep Learning to Distinguish Benign from Malignant Renal Lesions Based on Routine MR Imaging. Clin Cancer Res. https://doi.org/10.1158/1078-0432.CCR-19-0374 Cite Download
Wouterlood MA, Malhamé I, Lévesque K, Dayan N, Mahone M, Côté A-M, Cumyn A, Malick M, Sauvé N (2021) Pregnancy‐associated pelvic vein thrombosis: Insights from a multicenter case series. Journal of Thrombosis and Haemostasis 19:1926–1931. https://doi.org/https://doi.org/10.1111/jth.15333 Cite
Witham MD, Frost H, McMurdo M, Donnan PT, McGilchrist MM (2015) Construction of a linked health and social care database resource—lessons on process, content and culture. Inform Health Soc Care 40:229–239. Cite
Wei L, Rosen B, Vallieres M, Chotchutipan T, Mierzwa M, Eisbruch A, El Naqa I (2019) Automatic recognition and analysis of metal streak artifacts in head and neck computed tomography for radiomics modeling. Physics and Imaging in Radiation Oncology 10:49–54. https://doi.org/10.1016/j.phro.2019.05.001 Cite Download
Vincenot M, Coulombe-Lévêque A, Sean M, Camirand Lemyre F, Gendron L, Marchand S, Léonard G (2021) Development and Validation of a Predictive Model of Pain Modulation Profile to Guide Chronic Pain Treatment: A Study Protocol. Frontiers in Pain Research 2. https://doi.org/10.3389/fpain.2021.606422 Cite Download
Verheij RA, Curcin V, Delaney BC, McGilchrist MM (2018) Possible sources of bias in primary care electronic health record data use and reuse. J Med Internet Res 20:e185. Cite
Vanasse A, Courteau M, Ethier J-F (2018) The "6W" multidimensional model of care trajectories for patients with chronic ambulatory care sensitive conditions and hospital readmissions. Public Health 157:53–61. Cite Download
Ure J, Procter R, Martone M, Porteous D, Lloyd S, Lawrie S, Job D, Baldock R, Philp A, Liewald D, Rakebrandt F, Blaikie A, McKay C, Anderson S, Ainsworth J, van Hemert J, Blanquer I, Sinnott R, Barillot C, Gibaud FB, Williams A, Hartswood M, Watson P, Smith L, Burger A, Kennedy J, Gonzalez-Velez H, Stevens R, Corcho O, Morton R, Linksted P, Deschenes M, McGilchrist MM, Johnson P, Voss A, Gertz R, Wardlaw J (2007) Data integration in eHealth: a domain/disease specific roadmap. Stud Health Technol Inform 126:144–153 Cite
Traverso A, Vallieres M, Van Soest J, Wee L, Morin O, Dekker A (2020) Publishing linked and FAIR radiomics data in radiation oncology via ontologies and Semantic Web. Radiotherapy and Oncology 152:S827–S827 Cite
Trahan M-J, Cumyn A, Cheng MP, McDonald EG, Lapinsky SE, Daneman N, Abenhaim HA, Malhamé I (2021) Physician Perspectives on Including Pregnant Women in Covid-19 Clinical Trials: Time for a Paradigm Change. Ethics & Human Research 43:19–27. https://doi.org/https://doi.org/10.1002/eahr.500107 Cite
Toyoshima F, Barton A, Ethier J-F (2022) Affordances and their ontological core. Applied Ontology 17:285–320. Cite
Toyoshima F (2021) Roles and their three facets: A foundational perspective. Applied Ontology 16:161–192. https://doi.org/10.3233/AO-210244 Cite
Taseen R, Ethier J-F (2021) Expected clinical utility of automatable prediction models for improving palliative and end-of-life care outcomes: Toward routine decision analysis before implementation. Journal of the American Medical Informatics Association 28:2366–2378. Cite
Tarbouriech C, Vieu L, Barton A, Ethier J-F (2024) From slot mereology to a mereology of slots. Applied Ontology Preprint:1–50. https://doi.org/10.3233/AO-230051 Cite
St-Arnaud C, Ethier J-F, Hamielec C, Bersten A, Guyatt G, Meade M, Zhou Q, Leclair M-A, Patel A, Lamontagne F (2013) Prescribed targets for titration of vasopressors in septic shock: a retrospective cohort study. Canadian Medical Association Open Access Journal 1:E127–E133. Cite
Smith BH, Campbell A, Linksted P, Fitzpatrick B, Jackson C, Kerr SM, Deary IJ, Macintyre DJ, Campbell H, McGilchrist MM, Hocking LJ, Wisely L, Ford I, Lindsay RS, Morton R, Palmer CNA, Dominiczak AF, Porteous DJ, Morris AD (2013) Cohort Profile: Generation Scotland: Scottish Family Health Study (GS:SFHS). The study, its participants and their potential for genetic research on health and illness. International Journal of Epidemiology 42:689–700. Cite Download
Smith BH, Campbell H, Blackwood D, Connell J, Connor M, Deary IJ, Dominiczak AF, Fitzpatrick B, Ford I, Jackson C, Haddow G, Kerr S, Lindsay R, McGilchrist MM, Morton R, Murray G, Palmer CNA, Pell JP, Ralston SH, St Clair D, Sullivan F, Watt G, Wolf R, Wright A, Porteous D, Morris AD (2006) Generation Scotland: the Scottish Family Health Study; a new resource for researching genes and heritability. BMC Med Genet 7:74. https://doi.org/10.1186/1471-2350-7-74 Cite Download
Sauvé N, Rey É, Cumyn A (2017) Atrial fibrillation in a structurally normal heart during pregnancy: A review of cases from a registry and from the literature. J Obstet Gynaecol Can 39:18–24. https://doi.org/10.1016/j.jogc.2016.09.076 Cite
Samadoulougou S, Idzerda L, Dault R, Lebel A, Cloutier A-M, Vanasse A (2020) Validated methods for identifying individuals with obesity in health care administrative databases: A systematic review. Obes Sci Pract 6:677–693. https://doi.org/10.1002/osp4.450 Cite
Rosier A, Mabo P, Temal L, Van Hille P, Dameron O, Deleger L, Grouin C, Zweigenbaum P, Jacques J, Chazard E, Laporte L, Henry C, Burgun A (2016) Remote Monitoring of Cardiac Implantable Devices: Ontology Driven Classification of  the Alerts. Stud Health Technol Inform 221:59–63 Cite
Rosier A, Mabo P, Temal L, Van Hille P, Dameron O, Deléger L, Grouin C, Zweigenbaum P, Jacques J, Chazard E, Laporte L, Henry C, Burgun A (2016) Personalized and automated remote monitoring of atrial fibrillation. Europace 18:347–352. https://doi.org/10.1093/europace/euv234 Cite
Roberge P, Houle J, Provost J-R, Coulombe S, Beaudin A, Bower P, Camirand Lemyre F, Drapeau M, Drouin M-S, Hudon C, Provencher MD, Vasiliadis H-M (2022) A pragmatic randomized controlled trial of a group self-management support program versus treatment-as-usual for anxiety disorders: study protocol. BMC Psychiatry 22:135. Cite Download
Rance B, Canuel V, Countouris H, Laurent-Puig P, Burgun A (2016) Integrating Heterogeneous Biomedical Data for Cancer Research: the CARPEM  infrastructure. Appl Clin Inform 7:260–274. https://doi.org/10.4338/ACI-2015-09-RA-0125 Cite
Purkayastha S, Xiao Y, Jiao Z, Thepumnoeysuk R, Halsey K, Wu J, Tran TML, Hsieh B, Choi JW, Wang D, Vallieres M (2021) Machine Learning-Based Prediction of COVID-19 Severity and Progression to Critical Illness Using CT Imaging and Clinical Data. Korean Journal of Radiology 22:1213. https://doi.org/10.3348/kjr.2020.1104 Cite
Prach AT, McGilchrist MM, Murray FE, Johnston DA, MacDonald TM (1999) Prescription of acid-suppressing drugs in relation to endoscopic diagnosis: a record-linkage study. Aliment Pharmacol Ther 13:397–405 Cite
Pouliot F, Beauregard J-M, Saad F, Trudel D, Richard PO, Turcotte É, Rousseau É, Probst S, Kassouf W, Anidjar M, Camirand Lemyre F, Bouvet GF, Neveu B, Tétu A, Guérin B (2022) The Triple-Tracer strategy against Metastatic PrOstate cancer (3TMPO) study protocol. BJU International 130:314–322. Cite Download
Parfenova M, Côté A-M, Cumyn A, Pesant M-H, Champagne M, Roy-Lacroix M-È, Malick M, Sauvé N (2020) Impact of an Educational Pamphlet on Knowledge about Health Risks after Hypertensive Disorders of Pregnancy: A Randomized Trial. Journal of Obstetrics and Gynaecology Canada 43:182–190 Cite
Paré-Beauchemin R, Madar H, Dorion A-S, Angrand R, Chapdelaine A, Saucier D, Hernández-Hernández A, Mendoza J, Idrissi Z (2022) La nécessité de débuter les apprentissages en mobilisation de connaissances dès le début des études universitaires : points de vue d’étudiants et d’étudiantes gradués. 6:1–8. https://doi.org/10.18166/tuc.2022.6.1.24 Cite
Oreiller V, Andrearczyk V, Jreige M, Boughdad S, Elhalawani H, Castelli J, Vallieres M, Zhu S, Xie J, Peng Y, others (2022) Head and neck tumor segmentation in PET/CT: the HECKTOR challenge. Medical Image Analysis 77:102336 Cite
Olivier Grenier, Adrien Barton (2021) Vers une ontologie dispositionnelle du risque. Lato Sensu 8:57–69. https://doi.org/10.20416/LSRSPS.V8I2.6 Cite Download
Neuraz A, Looten V, Rance B, Daniel N, Garcelon N, Llanos LC, Burgun A, Rosset S (2019) Do You Need Embeddings Trained on a Massive Specialized Corpus for Your Clinical  Natural Language Processing Task? Stud Health Technol Inform 264:1558–1559. https://doi.org/10.3233/SHTI190533 Cite
Neuraz A, Rance B, Garcelon N, Llanos LC, Burgun A, Rosset S (2020) The Impact of Specialized Corpora for Word Embeddings in Natural Langage  Understanding. Stud Health Technol Inform 270:432–436. https://doi.org/10.3233/SHTI200197 Cite
Neuraz A, Lerner I, Digan W, Paris N, Tsopra R, Rogier A, Baudoin D, Cohen KB, Burgun A, Garcelon N, Rance B (2020) Natural Language Processing for Rapid Response to Emergent Diseases: Case Study of  Calcium Channel Blockers and Hypertension in the COVID-19 Pandemic. J Med Internet Res 22:e20773. https://doi.org/10.2196/20773 Cite
Nair JKR, Vallieres M, Mascarella MA, Sabbagh NE, Duchatellier CF, Zeitouni A, Shenouda G, Chankowsky J (2020) Magnetic resonance imaging texture analysis predicts recurrence in patients with nasopharyngeal carcinoma. Canadian Association of Radiologists Journal. https://doi.org/10.1016/j.carj.2019.06.009 Cite Download
Morin O, Vallieres M, Braunstein S, Ginart JB, Upadhaya T, Woodruff HC, Zwanenburg A, Chatterjee A, Villanueva-Meyer JE, Valdes G, others (2021) An artificial intelligence framework integrating longitudinal electronic health records with real-world data enables continuous pan-cancer prognostication. Nature Cancer 2:709–722 Cite
Morin O, Chen WC, Nassiri F, Susko M, Magill ST, Vasudevan HN, Wu A, Vallieres M, Gennatas ED, Valdes G, Pekmezci M, Alcaide-Leon P, Choudhury A, Interian Y, Mortezavi S, Turgutlu K, Bush NAO, Solberg TD, Braunstein SE, Sneed PK, Perry A, Zadeh G, McDermott MW, Villanueva-Meyer JE, Raleigh DR (2019) Integrated models incorporating radiologic and radiomic features predict meningioma grade, local failure, and overall survival. Neuro Oncol Adv 1. https://doi.org/10.1093/noajnl/vdz011 Cite Download
Millar HL, Clunie FS, McGilchrist MM, McMahon AD, MacDonald TM (1997) The impact on community benzodiazepine prescribing of hospitalization. J Psychosom Res 42:61–69 Cite
McMahon AD, Evans JM, McGilchrist MM, McDevitt DG, MacDonald TM (1998) Drug exposure risk windows and unexposed comparator groups for cohort studies in pharmacoepidemiology. Pharmacoepidemiol Drug Saf 7:275–280. https://doi.org/10.1002/(SICI)1099-1557(199807/08)7:4<275::AID-PDS363>3.0.CO;2-N Cite
McMahon AD, Evans JM, White G, Murray FE, McGilchrist MM, McDevitt DG, MacDonald TM (1997) A cohort study (with re-sampled comparator groups) to measure the association between new NSAID prescribing and upper gastrointestinal hemorrhage and perforation. J Clin Epidemiol 50:351–356 Cite
McLeish NJ, Simmonds P, Robertson C, Handel I, McGilchrist MM, Singh BK, Kerr S, Chase-Topping ME, Sinka K, Bronsvoort M, Porteous DJ, Carman W, McMenamin J, Leigh-Brown A, Woolhouse MEJ (2011) Sero-prevalence and incidence of A/H1N1 2009 influenza infection in Scotland in winter 2009-2010. PLoS ONE 6:e20358. https://doi.org/10.1371/journal.pone.0020358 Cite Download
McKay R, Letarte L, Lebel A, Quesnel-Vallée A, Vanasse A, Bartlett G, Blais L, Buckeridge D, Choinière M, Hudon C, Lacasse A, Lamarche B, Lebel A, Quesnel-Vallée A, Roberge P, Émond V, Pomey M-P, Benigeri M, Cloutier A-M, Dorais M, Courteau J, Courteau M, Plante S, Cambon P, Giguère A, Leroux I, St-Laurent D, Roy D, Borja J, Néron A, Landry G, Ethier J-F, Dault R, Côté-Marcil M-A, Tremblay P, Quirion S, on behalf of the TorSaDE Cohort Working Group (2022) Exploring social inequalities in healthcare trajectories following diagnosis of diabetes: a state sequence analysis of linked survey and administrative data. BMC Health Services Research 22:131. Cite
McGilchrist MM, Sullivan F, Kalra D (2007) Assuring the confidentiality of shared electronic health records. BMJ 335:1223–1224. https://doi.org/10.1136/bmj.39421.544063.BE Cite Download
Mastellos N, Bliźniuk G, Czopnik D, McGilchrist MM, Misiaszek A, Bródka P, Curcin V, Car J, Delaney BC, Andreasson A (2016) Feasibility and acceptability of TRANSFoRm to improve clinical trial recruitment in primary care. Fam Pract 33:186–191. https://doi.org/10.1093/fampra/cmv102 Cite Download
Mamzer M-F, Duchange N, Darquy S, Marvanne P, Rambaud C, Marsico G, Cerisey C, Scotté F, Burgun A, Badoual C, Laurent-Puig P, Hervé C (2017) Partnering with patients in translational oncology research: ethical approach. J Transl Med 15:74. https://doi.org/10.1186/s12967-017-1177-9 Cite

Book chapters

Nano T, Lafrenière M, Ziemer B, Witztum A, Barrios J, Upadhaya T, Vallieres M, Interian Y, Valdes G, Morin O (2020) Artificial Intelligence in Radiation Oncology. In: The Modern Technology of Radiation Oncology. Jacob Van Dyk, p 522 Cite
Khnaisser C, Lavoie L, Diab H, Ethier J-F (2015) Data warehouse design methods review: Trends, challenges and future directions for the healthcare domain. In: Morzy T, Valduriez P, Bellatreche L (eds) New Trends in Databases and Information Systems. Springer International Publishing, pp 76–87 Cite Download Download
Khnaisser C, Hamrouni H, Blumenthal D, Dignös A, Gamper J (2022) Querying Temporal Anomalies in Healthcare Information Systems and Beyond. In: Advances in Databases and Information Systems. Springer International Publishing Cite
Barton A, Ethier J-F (2016) The two ontological faces of velocity. In: Ferrario R, Kuhn W (eds) Formal Ontology in Information Systems. Proceedings of the 9th International Conference (FOIS 2016). IOS Press, Amsterdam, Pays-Bas, pp 123–136 Cite Download Download
Barton A (2017) L’ontologie est-elle une science? In: Silberstein M (ed) Qu’est-ce que la science... pour vous?, Editions Matériologiques. Paris, France, pp 21–26 Cite
Barton A (2020) L'ontologie appliquée : un dialogue entre métaphysique analytique et traitement de l'information. In: Lacroix A (ed) La philosophie pratique : un passage obligé pour penser la société. Presses de l'Université Laval, pp 87–108 Cite
Barton A (2016) La nature des probabilités dans les systèmes de raisonnement médical bayésien. In: Drouet I (ed) Les Approches et méthodes bayésiennes, fondements et pratiques, Editions Matériologiques. pp 53–86 Cite

Conference papers

Zhao L, Lim Choi Keung SN, Golby C, Ethier J-F, Curcin V, Bastiaens H, Burgun A, Delaney BC, Arvanitis TN (2015) EU FP7 TRANSFoRm Project: query workbench for participant identification and data extraction. In: AMIA CRI 2015. San Francisco, États-Unis Cite Download
Traverso A, Vallieres M, van Soest J, Wee L, Morin O, Dekker A (2019) Publishing Linked and FAIR-compliant Radiomics Data in Radiation Oncology via Ontologies and Semantic Web Techniques. In: SWAT4HCLS. pp 143–144 Cite
Toyoshima F, Barton A, Fabry P, Ethier J-F (2022) Representing Gender in Ontologies: A Dispositional Perspective. In: Proceedings of the 12th International Conference on Biomedical Ontology (ICBO 2021). CEUR Workshop Proceedings, Bolzano, Italie, pp 1–12 Cite Download
Toyoshima F, Barton A, Jansen L, Ethier J-F (2021) Towards a Unified Dispositional Framework for Realizable Entities. In: Proceedings of the 12th International Conference on Formal Ontology in Information Systems (FOIS 2021). IOS Press, Bolzano, Italie, pp 64–78 Cite Download
Toyoshima F, Barton A, Jansen L, Ethier J-F (2021) How an Aggregate View of Social Roles Meets Dispositions. In: Proceedings of the 7th Joint Ontology Workshops (JOWO 2021). CEUR Workshop Proceedings, Bolzano, Italie Cite Download
Toyoshima F, Barton A, Ethier J-F (2020) Functional Parthood: A Dispositional Perspective. In: Proceedings of the 6th Joint Ontology Workshops (JOWO 2020). CEUR Workshop Proceedings, Bolzano, Italie (évènement virtuel), p 8 Cite Download
Toyoshima F, Barton A, Ethier J-F (2022) Investigating Functions in BFO from the Viewpoint of Extrinsic Dispositions. In: CEUR Workshop Proceedings Cite
Toyoshima F, Barton A, Grenier O (2020) Foundations for an Ontology of Belief, Desire and Intention. In: Brodaric B, Neuhaus F (eds) Frontiers in Artificial Intelligence and Applications. IOS Press, pp 140–154 Cite
Toyoshima F, Niki S (2021) Semantics Matters: A New Light on Ontological Commitments of Logics. In: Proceedings of the 7th Joint Ontology Workshops (JOWO 2021). CEUR Workshop Proceedings, Bolzano, Italie, p 16 Cite Download
Toyoshima F, Barton A (2019) Linking image schemas with affordances: An ontological approach. In: Seppälä S, Porello D (eds) Proceedings of the 5th Joint Ontology Workshops (JOWO 2019). CEUR Workshop Proceedings, Graz, Autriche, pp 1–9 Cite
Toyoshima F, Barton A (2019) A formal representation of affordances as reciprocal dispositions. In: Kutz O, Hedblom MM (eds) Proceedings of TriCoLore 2018: The 7th International Workshop on Computational Creativity, Concept Invention, and General Intelligence (C3GI 2018), The 4th Image Schema Day (ISD4), and SCORE. CEUR Workshop Proceedings, Bolzano, Italie, pp 1–9 Cite
Toyoshima F (2020) Foundations for Ontology of Persistence: Beyond Talk of Temporal Parts. In: Brodaric B, Neuhaus F (eds) Frontiers in Artificial Intelligence and Applications. IOS Press, pp 17–31 Cite
Tarbouriech C, Bernard D, Vieu L, Barton A, Ethier J-F (2021) Flight Procedures Description Using Semantic Roles. In: Proceedings of the Joint Ontology Workshops 2021 (JOWO 2021). CEUR Workshop Proceedings Cite
Tarbouriech C, Barton A, Vieu L, Ethier J-F (2021) The Counting Problem of Slot Mereology. In: Proceedings of the Joint Ontology Workshops 2021 (JOWO 2021) Cite
St-Arnaud C, Ethier J-F, Hamielec C, Leclair M-A, Lamontagne F (2011) Prescribed targets for vasopressors titration in septic shock: a retrospective cohort study. In: European Society of Intensive Care Medicine. Berlin, Allemagne Cite
McGilchrist MM, Curcin V, Ethier J-F, Arvanitis TN, Delaney BC (2015) TRANSFoRm: Connectivity infrastructure to embed eCRFs into EHRs. In: AMIA CRI 2015. San Francisco, États-Unis Cite Download
Masolo C, Barton A (2019) The identity of property particulars. In: Proceedings of the Joint Ontology Workshops 2019 (JOWO 2019). Graz, Autriche, pp 1–10 Cite
Madar HM, Brown C, Baillargeon J-P, Langlois M-F (2016) Targeting gaps in the quality of care for patients with diabetes in community chronic care programs. Ottawa, Canada Cite
Madar H, Lebrun V, Brown C, Baillargeon J-P, Langlois M-F (2013) Évaluation de la qualité organisationnelle des soins pour les maladies chroniques cardiométaboliques en première ligne. Sherbrooke, Canada Cite
Madar HM, Lebrun V, Brown C, Baillargeon J-P, Langlois M-F (2013) Évaluation de la qualité des soins pour les maladies chroniques cardiométaboliques en première ligne. Sherbrooke, Canada Cite
Madar HM, Lebrun V, Brown C, Baillargeon J-P, Langlois M-F (2013) Accessibilité aux soins pour les maladies chroniques cardiométaboliques dans les Centres de santé et services sociaux de l’Estrie. Québec, Canada Cite
Madar HM, Lebrun V, Brown C, Baillargeon J-P, Langlois M-F (2015) Agir Sur Sa SantÉ : An evaluation-informed integrated care framework for the prevention and management of cardio-metabolic chronic diseases in primary care. Montréal, Canada Cite
Madar HM, Baillargeon J-P, Brown C, Langlois M-F (2016) Quality of Care Received by Patients Living with Obesity in Community Health Centers of the Eastern Townships in Québec, Canada. Vancouver, Canada Cite
Madar HM, Brown C, Baillargeon J-P, Langlois M-F (2018) Improved obesity screening and management using integrated community-based chronic diseases program. Nashville, Tennessee, USA Cite
Madar H, Brown C, Baillargeon J-P, Langlois M-F (2021) Programme Agir Sur Sa Santé : Effets sur la qualité des soins des patients à risque ou atteints de maladies chroniques cardiométaboliques dans les soins de première ligne en Estrie. Congrès annuel du Réseau de recherche en santé cardiométabolique, diabète et obésité/ Société québécoise de lipidologie, de nutrition et de métabolisme Cite
Lim Choi Keung SN, Zhao L, Ethier J-F, Curcin V, Burgun A, Delaney BC, Arvanitis TN (2015) Semantic enrichment of CDISC operational data model. In: AMIA Joint Summits on Translational Science proceedings AMIA Summit on Translational Science. American Medical Informatics Association, San Francisco, États-Unis Cite Download
Lim Choi Keung SN, Ethier J-F, Zhao L, Curcin V, Arvanitis TN (2014) The integration challenges in bridging patient care and clinical research in a learning healthcare system. In: European Medical Informatics Conference. Istanbul, Turquie Cite Download
Lim Choi Keung SN, Zhao L, Rossiter J, McGilchrist MM, Culross F, Ethier J-F, Burgun A, Verheij RA, Khan N, Taweel A, Curcin V, Delaney BC, Arvanitis TN (2014) Detailed clinical modelling approach to data extraction from heterogeneous data sources for clinical research. In: AMIA Joint Summits on Translational Science proceedings. AMIA Joint Summits on Translational Science. pp 55–59 Cite Download
Lim Choi Keung SN, Zhao L, Arvanitis TN, Curcin V, Delaney BC, Ethier J-F, Burgun A, McGilchrist MM, Bródka P, Tuligowicz W, Andreasson A (2015) TRANSFoRm: Implementing a learning healthcare system in Europe through embedding clinical research into clinical practice. In: 2015 48th Hawaii International Conference on System Sciences. Hawaii, États-Unis, pp 3176–3185 Cite Download
Liang SF, Ethier J-F, Porat T, Tapuria A, Delaney BC, Curcin V (2016) MeTMapS—Medical terminology mapping system. In: 7th Workshop on Ontologies and Data in Life Sciences. Halle, Allemagne Cite Download
Liang SF, Porat T, Tapuria A, Ethier J-F, Delaney BC, Curcin V (2016) A dynamic medical terminology mapping system—MeTMapS. In: Data Mining for Medical Informatics workshop. Chicago, États-Unis Cite Download
Khnaisser C, Lavoie L, Burgun A, Ethier J-F (2017) Past Indeterminacy in Data Warehouse Design. In: Benslimane D, Damiani E, Grosky WI, Hameurlain A, Sheth A, Wagner RR (eds) Database and Expert Systems Applications. Springer, Cham, pp 90–100 Cite Download
Khnaisser C, Lavoie L, Diab H, Ethier J-F (2015) Data Warehouse Design Methods Review: Trends, Challenges and Future Directions for the Healthcare Domain. In: Morzy T, Valduriez P, Bellatreche L (eds) New Trends in Databases and Information Systems. Springer International Publishing, pp 76–87 Cite
Khnaisser C, Hamrouni H, Blumenthal DB, Dignös A, Gamper J (2022) Querying Temporal Anomalies in Healthcare Information Systems and Beyond [BEST PAPER AWARD]. In: Chiusano S, Cerquitelli T, Wrembel R (eds) Advances in Databases and Information Systems. Springer International Publishing, pp 209–222 Cite
Khnaisser C, Lavoie L, Ethier J-F (2017) Unified bitemporal modelling framework for automatic data warehouse design. In: 28th International Conference on Database and Expert Systems Applications DEXA 2017. Lyon, France Cite
Hulin A-S, Burgun A, Combes S, De Grove-Valdeyron N, Guillot C, Priol J, Solofrizzo J, Valat G (2024) Entre gouvernance des données et intelligence artificielle : quelle place pour la poursuite de l'intérêt général? In: Actes du colloque de clôture des travaux de la Chaire Justice sociale et IA. Paris, France Cite
Goyer F, Fabry P, Barton A, Ethier J-F (2022) An ontology for healthcare systems. In: Proceedings of the 13th International Conference on Biomedical Ontology (ICBO 2022). Ann Arbor, États-Unis Cite
Fougères A, Canalda P, Ecarot T, Samaali A, Guglielmetti L (2012) A push service for carpooling. In: 2012 IEEE International Conference on Green Computing and Communications. pp 685–691 Cite Download
Fabry P, Goyer F, Barton A, Ethier J-F (2021) An Ontological Analysis of Health Procedure Information. In: Proceedings of the 12th International Conference on Biological Ontology (ICBO 2021). CEUR Workshop Proceedings, Bolzano, Italie, pp 36–47 Cite
Fabry P, Barton A, Ethier J-F (2020) QUESTO – An ontology for questionnaires. In: ICBO|ODLS 2020 International Conference on Biomedical Ontologies 2020. CEUR-WS.org, Bolzano, Italie, p B.1-12 Cite Download
Fabry P, Goyer F, Barton A, Ethier J-F (2022) An informational perspective on the ontology of services. In: CEUR Workshop Proceedings Cite
Fabry P, Barton A, Ethier J-F (2020) An Ontological Representation of Sex and Gender Information. In: Hastings J, Loebe F (eds) ICBO|ODLS 2020 International Conference on Biomedical Ontologies 2020. CEUR-WS.org, Bolzano, Italy, p O.1-5 Cite Download
Ethier J-F, Taseen R, Lavoie L, Barton A (2016) Improving the semantics of drug prescriptions with a realist ontology. In: Jaiswal P, Hoehndorf R, Arighi C, Meier A (eds) Proceedings of the Joint International Conference on Biological Ontology and BioCreative. Oregon, États-Unis, p IT603:1-6 Cite Download
Ecarot T, Fraikin B, Ouellet F, Lavoie L, McGilchrist MM, Ethier J-F (2020) Sensitive Data Exchange Protocol Suite for Healthcare. In: IEEE Symposium on Computers and Communications. Rennes, France Cite Download
Ecarot T, Dussault S, Souid A, Lavoie L, Ethier J-F (2020) AppArmor For Health Data Access Control: Assessing Risks and Benefits. In: 2020 7th International Conference on Internet of Things: Systems, Management and Security (IOTSMS). Paris, France, pp 1–7 Cite Download Download
Ecarot T, Fraikin B, Lavoie L, McGilchrist MM, Ethier J-F (2021) Learning health systems: An anonymous network routing protocol. In: Almeida JR, Gonzalez AR, Shen L, Kane B, Soda P, Oliveira JL (eds) Proceedings of the IEEE Symposium on Computer-Based Medical Systems. pp 562–567 Cite
Ecarot T, Zeghlache D, Brandily C (2017) Consumer-and-provider-oriented efficient IaaS resource allocation. In: 2017 IEEE International Parallel and Distributed Processing Symposium Workshops (IPDPSW). pp 77–85 Cite Download
Diamant A, Chatterjee A, Vallieres M, Shenouda G, Seuntjens J (2019) Multi-Modal Deep Learning Framework for Head & Neck Cancer Outcome Prediction. In: MEDICAL PHYSICS. WILEY 111 RIVER ST, HOBOKEN 07030-5774, NJ USA, pp 5372–5372 Cite
Diamant A, Chatterjee A, Vallieres M, Shenouda G, Seuntjens J (2019) Multi-Branch Convolutional Neural Network Combines Unregistered PET and CT Images for Head & Neck Cancer Outcome Prediction. In: MEDICAL PHYSICS. WILEY 111 RIVER ST, HOBOKEN 07030-5774, NJ USA, pp E294–E294 Cite
Delaney BC, Ethier J-F, Curcin V, Corrigan D, Friedman C (2013) International perspectives on the digital infrastructure for The Learning Healthcare System. In: Panel at AMIA annual symposium. Washington DC, États-Unis Cite

Presentations

Vanasse A, Benigeri M, Courteau J, Dorais M, Ethier J-F (2018) Linking canadian community health surveys to administrative data in Quebec: A unique opportunity for health care trajectories research on ambulatory care sensitive conditions Cite
Vanasse A, Boivin A, Dumez V, Ethier J-F, Leblanc A, Légaré F, Pluye P, Belec G, Pelletier J-G (2019) A learning health system oriented toward care trajectories Cite Download
Vanasse A, Ethier J-F, Dault R, Benigeri M, Cloutier A-M (2019) Validated case selection algorithms to identify 7 ambulatory care sensitive conditions Cite Download
Vallieres M (2019) MEDomics: synergie entre analyse d’images médicales, apprentissage automatique, apprentissage profond, traitement automatique des langues naturelles et apprentissage distribué Cite
Vallieres M (2019) Radiomics: the Image Biomarker Standardisation Initiative (IBSI) Cite
Vallieres M (2019) Radiomics: the Image Biomarker Standardisation Initiative (IBSI) Cite
Vallieres M (2019) MEDomicsLab: an open-source computation platform for integrative data modeling in medicine Cite
Vallieres M (2019) Radiomics: the Image Biomarker Standardisation Initiative (IBSI) Cite
Touré AW, Lavoie L (2021) Étude comparative de serveurs multi-terminologiques dans le contexte d'une plateforme d'échange de données ontologiquement annotées Cite
Taseen R, Ethier J-F, Barton A (2016) On prescribing drug prescriptions Cite
Taseen R (2021) Au-delà des métriques de performance usuelles : utilité clinique d’un modèle de prédiction pour stimuler les discussions des objectifs de soins chez les patients hospitalisés Cite Download
Souid A, Ecarot T (2021) Formalisation du cycle de vie et des propriétés de sécurité associées aux informations classifiées dans une stratégie de défense en profondeur Cite
Quirion R, Plante J-F, Rousseau L-M, Ethier J-F (2016) À la recherche du patient au coeur des données massives — Looking for the patient at the core of big data Cite
Ménard J-F (2024) Attentes sociétales et déploiement d'une nouvelle conception de l'utilisation des renseignements de santé en recherche : regard sur le processus québécois Cite
Ménard J-F (2021) Peut-on prendre n’importe quel moyen pour y arriver? Intérêt supérieur, influence et manipulation. Cite
Ménard J-F (2022) Modèles de consentement dans le PL19 : l'exemple de la recherche utilisant des renseignements de santé et de services sociaux Cite
Madar HM, Pomey M-P, Ethier J-F, Gauvin L (2021) Programme CoMPAS+ diabète : Amélioration de la trajectoire et de la qualité des soins du diabète dans les soins et services de proximité dans un système de santé apprenant Cite
Looten V, Khnaisser C, Burgun A, Rance B (2017) Storing biological data in i2b2: extending the representation of laboratory exams beyond the sheer result Cite
Lim Choi Keung SN, Zhao L, Rossiter J, Ogunsina I, Curcin V, Danger R, McGilchrist MM, Ethier J-F, Ohmann C, Kuchinke W, Taweel A, Delaney BC, Arvanitis TN (2013) Provenance-aware query formulation tool to identify eligible clinical research participants Cite
Lévesque S, Camirand Lemyre F, Ethier J-F (2023) Inférence distribuée pour les modèles linéaires généralisés Cite
Lévesque F, Cumyn A, Ménard J-F, Dault R, Barton A, Ethier J-F (2022) CLARET Transparence - vers un portail citoyen de transparence sur l'accès et l'utilisation secondaire des données de santé Cite
Khnaisser C, Lavoie L, Ethier J-F (2021) Partage des données de santé au Québec avec PARS3 : les systèmes de santé apprenants au service des citoyens Cite Download
Khnaisser C, Lavoie L, Diab H, Ethier J-F (2015) Architecture et méthode de construction d’entrepôts de données au coeur des systèmes informationnels régionaux de santé. Cite
Khnaisser C, Lavoie L, Burgun A, Ethier J-F (2015) Étude comparative des modèles temporels BCDM et DDLM dans le contexte d’entrepôt de données. Cite
Khnaisser C, Lavoie L, Burgun A, Ethier J-F (2014) Génération automatisée de schémas relationnels bitemporels dans un contexte d’entrepôt de données Cite
Khnaisser C, Lavoie L, Burgun A, Ethier J-F (2017) Unification des données par les connaissances. Méthode de construction d’un entrepôt de données historicisé de santé guidée par les ontologies Cite Download
Khnaisser C, Lavoie L, Burgun A, Ethier J-F (2016) Méthode de construction d’entrepôts de données temporalisées guidée par les ontologies Cite Download
Khnaisser C, Lavoie L, Burgun A, Ethier J-F (2017) Healthcare trajectories reconstruction with i2b2: issues and recommandations Cite Download
Khnaisser C Data Warehouse Design Methods Review: Trends, Challenges and Future Directions for the Healthcare Domain Cite
Khnaisser C (2017) Past Indeterminacy in Data Warehouse Design Cite
Khnaisser C (2022) Querying Temporal Anomalies in Healthcare Information Systems and Beyond Cite
Khnaisser C (2022) Modèle de données historicisées pour les systèmes de santé apprenants Cite
Khnaisser C (2023) Modèle de données historicisées pour les systèmes de santé apprenants Cite
Khnaisser C (2022) Modélisation de données temporalisées à partir d'une ontologie au sein d'un système de santé apprenant Cite
Goyer F, Ethier J-F (2021) La pratique réflexive pour faire une différence dans la vie de nos patients Cite Download
Gagnon G, Carreau A-M, Cloutier-Langevin C, Plante A-S, Weisnagel SJ, Marceau S, Biertho L, Hould FS, Camirand Lemyre F, Morisset A-S (2020) Gain de poids gestationnel total et trimestriel chez les femmes ayant eu une chirurgie bariatrique malabsorptive Cite
Gagnon G, Carreau A-M, Cloutier-Langevin C, Plante A-S, Weisnagel SJ, Marceau S, Biertho L, Camirand Lemyre F, Tchernof A, Morisset A-S (2020) Gain de poids gestationnel total et trimestriel chez les femmes ayant eu une chirurgie bariatrique malabsorptive Cite
Fabry P, Barton A, Ethier J-F (2019) LABO: an ontology for laboratory test prescription and reporting Cite Download Download
Fabry P (2022) An ontology for healthcare systems Cite
Fabry P (2021) Vers une ontologie des procédures de santé Cite Download
Ethier J-F, McGilchrist M, Yang D, La C, DASH Working Group, Algorithms and Harmonized (AHD) Data Working Group, Anis A, Whyte C-A (2024) HDRN Canada: Development of an information items dictionary to support research data access requests in Canada Cite
Ethier J-F, McGilchrist MM, Fabry P (2021) Introduction to Formal Ontologies Cite
Ethier J-F, McGrail K (2021) Learning health systems to support data intensive research: a Canadian perspective Cite
Ethier J-F, Lavoie L (2021) PARS3 : Relier les données de santé au sein du réseau Ensemble Cite Download
Ethier J-F, Ibara M (2018) Use of Electronic Health Records (EHRs) as eSource in Clinical Investigations Cite
Ethier J-F (2023) La collaboration au cœur des systèmes de santé apprenants Cite
Ethier J-F (2020) Partage des données de santé au Québec : Permettons de changer le devenir des patients avec PARS3 Cite
Ethier J-F (2019) Learning health systems: challenges and opportunities Cite
Ethier J-F (2017) The learning health and social services research platform (PARS3). Truly putting the patient at the core Cite
Ethier J-F (2023) Learning health systems coming of age: How to deploy them in clinic so they truly become more than the sum of their parts Cite

Reports

Zwanenburg A, Leger S, Vallieres M, Löck S (2020) Image biomarker standardisation initiative Cite Download
Paprica PA, Maillet DC, Dahl L, Diverty B, Ethier J-F, Gavin F, Katz A, Lix LM, MacDonald D, McDonald T, McGrail K, Quan H, Rowe R, Schull MJ, Street C, Victor JC, Walker J, Wu J, Yada N (2020) Infrastructure de recherche numérique sur la santé des populations : s'appuyer sur un réseau d'apprentissage collaboratif. Réseau de recherche sur les données de santé du Canada (RRDS Canada) Cite
Khnaisser C, Lavoie L, Burgun A, Ethier J-F (2017) Unified bitemporal historicization framework. Université de Sherbrooke (GRIIS), Sherbrooke, Canada Cite
Khnaisser C, Lavoie L, Diab H, Ethier J-F (2015) Data warehouse design methods review for the healthcare domain. Université de Sherbrooke, Sherbrooke, Canada Cite Download
Khnaisser C, Lavoie L, Burgun A, Ethier J-F (2017) Automated bitemporal database schema design with a unified framework. Université de Sherbrooke, Sherbrooke, Canada Cite Download
Khnaisser C, Lavoie L, Fraikin B, Barton A, Burgun A, Ethier J-F (2019) Generating a relational database for heterogeneous data using an ontology Cite Download
Khanji C, Cloutier A-M, Dault R, Roy D, Beaulieu M-D, Vanasse A, Ethier J-F (2017) Utilisation des données contenues dans les dossiers médicaux électroniques: revue rapide de la littérature. Unité Soutien SRAP du Québec, Sherbrooke, Canada Cite Download
Fisette J-F, Ethier J-F, Leclair M-A, Ramon-Moliner P (2015) Transfert de l'information aux points de transition. Unité d'évaluation des technologies et des modes d'intervention en santé, CIUSSS de l'Estrie - CHUS, Installation CHUS, Sherbrooke, Canada Cite
Collin J, Deschênes M, Désilets F, Després P, Ethier J-F, Giroux Blanchet S, Frenette C, Carbonneau M, Gagnon M-A, Ganache I, Zawati MH, Loum N, Maclure J (2022) Mériter et renforcer la confiance des citoyens dans la gestion et la valorisation des données de santé : pour une gouvernance transparente et responsable, soucieuse de la dignité des personnes et de l'intérêt public. Comité de travail sur l'accès aux données gouvernementales par le secteur privé et les OBNL de la Commission de l'éthique en science et en technologie du Québec Cite Download
Beaulieu M-D, Cloutier A-M, Dault R, Ethier J-F, Goetghebeur M, Khanji C, Roy D, Vanasse A (2018) Utilisation des données cliniques issues des dossiers médicaux électroniques à des fins de recherche et d'amélioration continue de la qualité des soins et services de première ligne. Unité Soutien SRAP du Québec et INESSS Cite Download

Theses

Souid A (2024) Proposition de modélisation de la défense en profondeur des actifs informationnels appuyée par une ontologie. Mémoire de maitrise, Université de Sherbrooke Cite
Madar H (2020) Effets du programme " Agir Sur Sa Santé " sur la qualité des soins des patients à risque ou atteints de maladies chroniques cardiométaboliques dans les Centres de santé et de services sociaux de l'Estrie. Université de Sherbrooke Cite
Khnaisser C, Lavoie L (dir.) et Ethier J-F (dir.) (2016) Méthode de construction d'entrepôt de données temporalisé pour un système informationnel de santé. Mémoire de maitrise, Université de Sherbrooke Cite Download
Khnaisser C (2019) Construction de modèles de données relationnels temporalisés guidée par les ontologies. Thèse de doctorat Cite
Ethier J-F (2016) Integrating resources for translational research: a unified approach for learning health systems. Thèse de doctorat, Université Pierre-Marie Curie - Paris VI Cite Download
Ecarot T (2016) Efficient allocation for distributed and connected cloud. Thèse de doctorat, Telecom Sud Paris et Université Pierre et Marie Curie Cite Download
Camirand Lemyre F (2016) Sur des estimateurs et des tests non-paramétriques pour des distributions et copules conditionnelles. Thèse de doctorat, Université de Sherbrooke Cite Download
Baillargeon R-L (2023) La catégorie dérivée d'une catégorie exacte. Mémoire de maitrise, Université de Sherbrooke Cite

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