Anita Burgun

Directrice du laboratoire « Sciences de l’information et médecine personnalisée » de l’Unité 1138 Centre de recherche des Cordeliers de l’INSERM et de l’Université Paris Descartes

Professeure en informatique biomédicale à l’Université Paris Descartes

Professeure d’informatique biomédicale à l’Université Paris Descartes, Anita Burgun s’intéresse particulièrement aux ontologies, aux terminologies biomédicales, à la bio-informatique et à l’intégration de données. Elle est directrice des départements d’informatique biomédicale à l’hôpital Necker — Enfants malades et à l’hôpital européen Georges-Pompidou. Elle réalise de la recherche translationnelle en informatique de la santé en lien avec l’intégration de données cliniques, l’utilisation secondaire de données de santé de routine, et les systèmes d’aide à la décision.

Les travaux de recherche d’Anita Burgun portent sur les interfaces entre les représentations de la connaissance et la collecte de données. Elle dirige une équipe interdisciplinaire spécialisée en informatique biomédicale et en méthodes statistiques. Cette équipe développe des méthodes combinant des approches basées à la fois sur les connaissances et sur les données, afin de soutenir la médecine personnalisée. Les thèmes de recherche qu’affectionne Anita Burgun sont l’intégration de données de santé de masse et les outils d’aide à la décision basés sur les données et les ontologies.

Anita Burgun a dirigé le groupe de recherche UMR 936, à l’INSERM, dont les travaux portaient sur les ontologies biomédicales, les représentations de la connaissance et les méthodes d’intégration de données (p. ex. génomiques et cliniques). À l’université et à l’hôpital de Rennes, elle a été professeure de biostatistiques et d’informatique biomédicale.

Formation

Ph. D., Université de Rennes 1, informatique médicale

M. Sc., Institut de formation supérieure en informatique et communication (IFSIC)–Université de Rennes 1, informatique

M. Sc., Université Pierre et Marie Curie — Paris 6, biostatistiques et informatique de la santé

M.D., Université de Rennes 1, doctorat en médecine

Publications

Abdoul C, Cros P, Coutier L, Hadchouel A, Neuraz A, Burgun A, Giovannini-Chami L, Drummond D (2020) Parents’ views on artificial intelligence for the daily management of childhood  asthma: a survey. J Allergy Clin Immunol Pract. https://doi.org/10.1016/j.jaip.2020.11.048 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
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
Faviez C, Chen X, Garcelon N, Neuraz A, Knebelmann B, Salomon R, Lyonnet S, Saunier S, Burgun A (2020) Diagnosis support systems for rare diseases: a scoping review. Orphanet J Rare Dis 15:94 . https://doi.org/10.1186/s13023-020-01374-z Cite
Garcelon N, Burgun A, Salomon R, Neuraz A (2020) Electronic health records for the diagnosis of rare diseases. Kidney Int 97:676–686 . https://doi.org/10.1016/j.kint.2019.11.037 Cite
Boulet S, Ursino M, Thall P, Landi B, Lepère C, Pernot S, Burgun A, Taieb J, Zaanan A, Zohar S, Jannot A-S (2020) Integration of elicited expert information via a power prior in Bayesian variable  selection: Application to colon cancer data. Stat Methods Med Res 29:541–567 . https://doi.org/10.1177/0962280219841082 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
Brat GA, Weber GM, Gehlenborg N, Avillach P, Palmer NP, Chiovato L, Cimino J, Waitman LR, Omenn GS, Malovini A, Moore JH, Beaulieu-Jones BK, Tibollo V, Murphy SN, Yi SL, Keller MS, Bellazzi R, Hanauer DA, Serret-Larmande A, Gutierrez-Sacristan A, Holmes JJ, Bell DS, Mandl KD, Follett RW, Klann JG, Murad DA, Scudeller L, Bucalo M, Kirchoff K, Craig J, Obeid J, Jouhet V, Griffier R, Cossin S, Moal B, Patel LP, Bellasi A, Prokosch HU, Kraska D, Sliz P, Tan ALM, Ngiam KY, Zambelli A, Mowery DL, Schiver E, Devkota B, Bradford RL, Daniar M, Daniel C, Benoit V, Bey R, Paris N, Serre P, Orlova N, Dubiel J, Hilka M, Jannot AS, Breant S, Leblanc J, Griffon N, Burgun A, Bernaux M, Sandrin A, Salamanca E, Cormont S, Ganslandt T, Gradinger T, Champ J, Boeker M, Martel P, Esteve L, Gramfort A, Grisel O, Leprovost D, Moreau T, Varoquaux G, Vie J-J, Wassermann D, Mensch A, Caucheteux C, Haverkamp C, Lemaitre G, Bosari S, Krantz ID, South A, Cai T, Kohane IS (2020) International electronic health record-derived COVID-19 clinical course profiles:  the 4CE consortium. NPJ Digit Med 3:109 . https://doi.org/10.1038/s41746-020-00308-0 Cite
Chen X, Garcelon N, Neuraz A, Billot K, Lelarge M, Bonald T, Garcia H, Martin Y, Benoit V, Vincent M, Faour H, Douillet M, Lyonnet S, Saunier S, Burgun A (2019) Phenotypic similarity for rare disease: Ciliopathy diagnoses and subtyping. J Biomed Inform 100:103308 . https://doi.org/10.1016/j.jbi.2019.103308 Cite
Looten V, Kong Win Chang L, Neuraz A, Landau-Loriot M-A, Vedie B, Paul J-L, Mauge L, Rivet N, Bonifati A, Chatellier G, Burgun A, Rance B (2019) What can millions of laboratory test results tell us about the temporal aspect of  data quality? Study of data spanning 17 years in a clinical data warehouse. Comput Methods Programs Biomed 181:104825 . https://doi.org/10.1016/j.cmpb.2018.12.030 Cite
Digan W, Wack M, Looten V, Neuraz A, Burgun A, Rance B (2019) Evaluating the Impact of Text Duplications on a Corpus of More than 600,000 Clinical  Narratives in a French Hospital. Stud Health Technol Inform 264:103–107 . https://doi.org/10.3233/SHTI190192 Cite
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
Arnoux-Guenegou A, Girardeau Y, Chen X, Deldossi M, Aboukhamis R, Faviez C, Dahamna B, Karapetiantz P, Guillemin-Lanne S, Lillo-Le Louët A, Texier N, Burgun A, Katsahian S (2019) The Adverse Drug Reactions From Patient Reports in Social Media Project: Protocol  for an Evaluation Against a Gold Standard. JMIR Res Protoc 8:e11448 . https://doi.org/10.2196/11448 Cite
Bussy S, Veil R, Looten V, Burgun A, Gaïffas S, Guilloux A, Ranque B, Jannot A-S (2019) Comparison of methods for early-readmission prediction in a high-dimensional  heterogeneous covariates and time-to-event outcome framework. BMC Med Res Methodol 19:50 . https://doi.org/10.1186/s12874-019-0673-4 Cite
Cohen S, Jannot A-S, Iserin L, Bonnet D, Burgun A, Escudié J-B (2019) Accuracy of claim data in the identification and classification of adults with  congenital heart diseases in electronic medical records. Arch Cardiovasc Dis 112:31–43 . https://doi.org/10.1016/j.acvd.2018.07.002 Cite
Giraud P, Giraud P, Gasnier A, El Ayachy R, Kreps S, Foy J-P, Durdux C, Huguet F, Burgun A, Bibault J-E (2019) Radiomics and Machine Learning for Radiotherapy in Head and Neck Cancers. Front Oncol 9:174 . https://doi.org/10.3389/fonc.2019.00174 Cite
Khnaisser C, Lavoie L, Fraikin B, Barton A, Burgun A, Ethier J-F (2019) Advanced ontology-driven relational database generation for heterogeneous data : Ontorelα. Journal on Data Semantics (JODS) [Submitted 2019-09-20] Cite
Khnaisser C, Looten V, Lavoie L, Ethier J-F, Burgun A (2019) Combining ontology and temporal databases for data reuse: the example of hospital organizational structures. International Journal of Medical Informatics (IJMI) [To be publised] Cite
Gruson D, Petrelluzzi J, Mehl J, Burgun A, Garcelon N (2018) [Ethical, legal and operational issues of artificial intelligence]. Rev Prat 68:1145–1148 Cite
Bibault J-E, Giraud P, Housset M, Durdux C, Taieb J, Berger A, Coriat R, Chaussade S, Dousset B, Nordlinger B, Burgun A (2018) Author Correction: Deep Learning and Radiomics predict complete response after  neo-adjuvant chemoradiation for locally advanced rectal cancer. Sci Rep 8:16914 . https://doi.org/10.1038/s41598-018-35359-7 Cite
Bibault J-E, Giraud P, Housset M, Durdux C, Taieb J, Berger A, Coriat R, Chaussade S, Dousset B, Nordlinger B, Burgun A (2018) Deep Learning and Radiomics predict complete response after neo-adjuvant  chemoradiation for locally advanced rectal cancer. Sci Rep 8:12611 . https://doi.org/10.1038/s41598-018-30657-6 Cite
Cohen S, Gilutz H, Marelli AJ, Iserin L, Benis A, Bonnet D, Burgun A (2018) Administrative health databases for addressing emerging issues in adults with CHD: a  systematic review. Cardiol Young 28:844–853 . https://doi.org/10.1017/S1047951118000446 Cite
Garcelon N, Neuraz A, Salomon R, Bahi-Buisson N, Amiel J, Picard C, Mahlaoui N, Benoit V, Burgun A, Rance B (2018) Next generation phenotyping using narrative reports in a rare disease clinical data  warehouse. Orphanet J Rare Dis 13:85 . https://doi.org/10.1186/s13023-018-0830-6 Cite
Ethier J-F, McGilchrist M, Barton A, Cloutier A-M, Curcin V, Delaney BC, Burgun A (2018) The TRANSFoRm project: Experience and lessons learned regarding functional and  interoperability requirements to support primary care. Learn Health Syst 2:e10037 . https://doi.org/10.1002/lrh2.10037 Cite
Deborde T, Amar L, Bobrie G, Postel-Vinay N, Battaglia C, Tache A, Chedid A, Dhib M-M, Chatellier G, Plouin P-F, Burgun A, Azizi M, Jannot A-S (2018) Sex differences in antihypertensive treatment in France among 17 856 patients in a  tertiary hypertension unit. J Hypertens 36:939–946 . https://doi.org/10.1097/HJH.0000000000001607 Cite
Garcelon N, Neuraz A, Salomon R, Faour H, Benoit V, Delapalme A, Munnich A, Burgun A, Rance B (2018) A clinician friendly data warehouse oriented toward narrative reports: Dr.  Warehouse. J Biomed Inform 80:52–63 . https://doi.org/10.1016/j.jbi.2018.02.019 Cite
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
Abdellaoui R, Foulquié P, Texier N, Faviez C, Burgun A, Schück S (2018) Detection of Cases of Noncompliance to Drug Treatment in Patient Forum Posts: Topic  Model Approach. J Med Internet Res 20:e85 . https://doi.org/10.2196/jmir.9222 Cite
Bibault J-E, Zapletal E, Rance B, Giraud P, Burgun A (2018) Labeling for Big Data in radiation oncology: The Radiation Oncology Structures  ontology. PLoS One 13:e0191263 . https://doi.org/10.1371/journal.pone.0191263 Cite
Jantzen R, Rance B, Katsahian S, Burgun A, Looten V (2018) The Need of an Open Data Quality Policy: The Case of the “Transparency - Health”  Database in the Prevention of Conflict of Interest. Stud Health Technol Inform 247:611–615 Cite
Karapetiantz P, Bellet F, Audeh B, Lardon J, Leprovost D, Aboukhamis R, Morlane-Hondère F, Grouin C, Burgun A, Katsahian S, Jaulent M-C, Beyens M-N, Lillo-Le Louët A, Bousquet C (2018) Descriptions of Adverse Drug Reactions Are Less Informative in Forums Than in the  French Pharmacovigilance Database but Provide More Unexpected Reactions. Front Pharmacol 9:439 . https://doi.org/10.3389/fphar.2018.00439 Cite
Chen X, Faviez C, Schuck S, Lillo-Le-Louët A, Texier N, Dahamna B, Huot C, Foulquié P, Pereira S, Leroux V, Karapetiantz P, Guenegou-Arnoux A, Katsahian S, Bousquet C, Burgun A (2018) Mining Patients’ Narratives in Social Media for Pharmacovigilance: Adverse Effects  and Misuse of Methylphenidate. Front Pharmacol 9:541 . https://doi.org/10.3389/fphar.2018.00541 Cite
Khnaisser C, Lavoie L, Burgun A, Ethier J-F (2018) Generating relational database using ontology review : Issues, challenges and trends. International Journal of Advanced Computer Science and Applications (IJACSA) 9: . https://doi.org/10.14569/IJACSA.2018.090620 Cite Download
Dunn WJ, Burgun A, Krebs M-O, Rance B (2017) Exploring and visualizing multidimensional data in translational research platforms. Brief Bioinform 18:1044–1056 . https://doi.org/10.1093/bib/bbw080 Cite
Ethier J-F, Curcin V, McGilchrist MM, Choi Keung SNL, Zhao L, Andreasson A, Bródka P, Michalski R, Arvanitis TN, Mastellos N, Burgun A, Delaney BC (2017) eSource for clinical trials: Implementation and evaluation of a standards-based  approach in a real world trial. Int J Med Inform 106:17–24 . https://doi.org/10.1016/j.ijmedinf.2017.06.006 Cite
Escudié J-B, Rance B, Malamut G, Khater S, Burgun A, Cellier C, Jannot A-S (2017) A novel data-driven workflow combining literature and electronic health records to  estimate comorbidities burden for a specific disease: a case study on autoimmune  comorbidities in patients with celiac disease. BMC Med Inform Decis Mak 17:140 . https://doi.org/10.1186/s12911-017-0537-y Cite
Garcelon N, Neuraz A, Benoit V, Salomon R, Kracker S, Suarez F, Bahi-Buisson N, Hadj-Rabia S, Fischer A, Munnich A, Burgun A (2017) Finding patients using similarity measures in a rare diseases-oriented clinical data  warehouse: Dr. Warehouse and the needle in the needle stack. J Biomed Inform 73:51–61 . https://doi.org/10.1016/j.jbi.2017.07.016 Cite
Abdellaoui R, Schück S, Texier N, Burgun A (2017) Filtering Entities to Optimize Identification of Adverse Drug Reaction From Social  Media: How Can the Number of Words Between Entities in the Messages Help? JMIR Public Health Surveill 3:e36 . https://doi.org/10.2196/publichealth.6577 Cite
Jannot A-S, Burgun A, Thervet E, Pallet N (2017) The Diagnosis-Wide Landscape of Hospital-Acquired AKI. Clin J Am Soc Nephrol 12:874–884 . https://doi.org/10.2215/CJN.10981016 Cite
Jannot A-S, Zapletal E, Avillach P, Mamzer M-F, Burgun A, Degoulet P (2017) The Georges Pompidou University Hospital Clinical Data Warehouse: A 8-years  follow-up experience. Int J Med Inform 102:21–28 . https://doi.org/10.1016/j.ijmedinf.2017.02.006 Cite
Garcelon N, Neuraz A, Benoit V, Salomon R, Burgun A (2017) Improving a full-text search engine: the importance of negation detection and family  history context to identify cases in a biomedical data warehouse. J Am Med Inform Assoc 24:607–613 . https://doi.org/10.1093/jamia/ocw144 Cite
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) Erratum to: Partnering with patients in translational oncology research: ethical  approach. J Transl Med 15:80 . https://doi.org/10.1186/s12967-017-1181-0 Cite
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
Girardeau Y, Doods J, Zapletal E, Chatellier G, Daniel C, Burgun A, Dugas M, Rance B (2017) Leveraging the EHR4CR platform to support patient inclusion in academic studies:  challenges and lessons learned. BMC Med Res Methodol 17:36 . https://doi.org/10.1186/s12874-017-0299-3 Cite
Barton A, Ethier J-F, Duvauferrier R, Burgun A (2017) An ontological analysis of medical Bayesian indicators of performance. J Biomed Semantics 8:1 . https://doi.org/10.1186/s13326-016-0099-4 Cite
Chen X, Deldossi M, Aboukhamis R, Faviez C, Dahamna B, Karapetiantz P, Guenegou-Arnoux A, Girardeau Y, Guillemin-Lanne S, Lillo-Le-Louët A, Texier N, Burgun A, Katsahian S (2017) Mining Adverse Drug Reactions in Social Media with Named Entity Recognition and  Semantic Methods. Stud Health Technol Inform 245:322–326 Cite
Ethier J-F, Curcin V, McGilchrist MM, Lim Choi Keung SN, Zhao L, Andreasson A, Bródka P, Michalski R, Arvanitis TN, Mastellos N, Burgun A, Delaney BC (2017) eSource for clinical trials: Implementation and evaluation of a standards-based approach in a real world trial. Int J Med Inform 106:17–24 . https://doi.org/10.1016/j.ijmedinf.2017.06.006 Cite Download Download
Barton A, Ethier J-F, Duvauferrier R, Burgun A (2017) An ontological analysis of medical Bayesian indicators of performance. J Biomed Semant 8:1 . Cite Download
Ethier J-F, McGilchrist MM, Barton A, Cloutier A-M, Curcin V, Delaney BC, Burgun A (2017) The TRANSFoRm project: Experience and lessons learned regarding functional and interoperability requirements to support primary care. Learn Health Sys. https://doi.org/10.1002/lrh2.10037 Cite Download
Bibault J-E, Giraud P, Burgun A (2016) Big Data and machine learning in radiation oncology: State of the art and future  prospects. Cancer Lett 382:110–117 . https://doi.org/10.1016/j.canlet.2016.05.033 Cite
Khnaisser C, Lavoie L, Burgun A, Ethier J-F (2017) Past indeterminacy in data warehouse design. In: Database and Expert Systems Applications. Springer, Cham, pp 90–100 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
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
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
Barton A, Duvauferrier R, Burgun A (2015) Formalization of indicators of diagnostic performance in a realist ontology. In: Proceedings of 6th International Conference on Biomedical Ontology (ICBO-2015). CEUR Workshop Proceedings, pp 63–70 Cite Download
Barton A, Rosier A, Burgun A, Ethier J-F (2014) The cardiovascular disease ontology. In: Garbacz P, Kutz O (eds) Formal Ontology in Information Systems. Proceedings of the 8th International Conference (FOIS 2014). IOS Press, Amsterdam, pp 409–414 Cite Download
Barton A, Rosier A, Burgun A, Ethier J-F (2014) The cardiovascular disease ontology. In: Proceedings of the 8th conference on Formal Ontology in Information Systems (FOIS). IOS Press, Amsterdam, pp 409–414 Cite Download
Barton A, Burgun A, Duvauferrier R (2012) Probability assignments to dispositions in ontologies. In: Donnelly M, Guizzardi G (eds) Proceedings of the 7th International Conference on Formal Ontology in Information Systems (FOIS2012). IOS Press, Amsterdam, pp 3–14 Cite Download
Khnaisser C, Lavoie L, Burgun A, Ethier J-F (2017) Healthcare trajectories reconstruction with i2b2: issues and recommandations Cite Download
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
Khnaisser C, Lavoie L, Burgun A, Ethier J-F (2016) Méthode de construction d’entrepôts de données temporalissées guidée par les ontologies Cite Download
Curcin V, Arvanitis TN, Ethier J-F, Fraczkowsk K, Kazienko P, Brodka P, Andreasson A, Blizniuk G, Lim Choi Keung SN, Zhao L, Misiaszek A, McGilchrist MM, Delaney BC, Burgun A (2014) Semantic approach to achieving interoperability between clinical care and clinical research 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
Khnaisser C, Lavoie L, Burgun A, Ethier J-F (2017) Unified bitemporal historicization framework. Université de Sherbrooke (GRIIS), Sherbrooke, Québec, Canada Cite
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