Anita Burgun


Anita Burgun
 PUPH,
AP-HP – UP
email: first name dot last name at aphp dot fr
postal address:
web page: linkedin
bio:I am a professor of biomedical informatics at Paris University with interests in ontologies, biomedical terminologies, bioinformatics and data integration. I am the head of the Department of Biomedical Informatics at Necker Children’s Hospital and Georges Pompidou European Hospital, developing translational research in biomedical informatics regarding clinical/omic data Integration, secondary use of routine care data, and data driven decision support systems. As a researcher, I have been focusing on the interface between knowledge representation, and data collection. I lead a multi-disciplinary research team that is deep in biomedical informatics and statistical methodology. Our objective is to develop new methods that combine knowledge-driven and data-driven approaches to support precision medicine. My favorite topics include: integration of large-scale health data as well as data driven and ontology driven decision support.Specialties: health and biomedical informatics, e-health, public health, connected health, ontologies, biomedical terminologies, clinical informatics.

Research projects


Publications

Publications HAL de anita, burgun

2024

Journal articles

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Julie Michel, Aurélia Manns, Sofia Boudersa, Côme Jaubert, Laurent Dupic, et al.. Clinical decision support system in emergency telephone triage: A scoping review of technical design, implementation and evaluation. International Journal of Medical Informatics, 2024, 184, pp.105347. ⟨10.1016/j.ijmedinf.2024.105347⟩. ⟨hal-04434604⟩
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Carole Faviez, Marc Vincent, Nicolas Garcelon, Olivia Boyer, Bertrand Knebelmann, et al.. Performance and clinical utility of a new supervised machine-learning pipeline in detecting rare ciliopathy patients based on deep phenotyping from electronic health records and semantic similarity. Orphanet Journal of Rare Diseases, 2024, 19 (1), pp.55. ⟨10.1186/s13023-024-03063-7⟩. ⟨hal-04455861⟩
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https://hal.sorbonne-universite.fr/hal-04455861/file/s13023-024-03063-7.pdf BibTex

2023

Journal articles

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Friederike Petzold, Katy Billot, Xiaoyi Chen, Charline Henry, Emilie Filhol, et al.. The genetic landscape and clinical spectrum of nephronophthisis and related ciliopathies. Kidney International, 2023, 104 (2), pp.378-387. ⟨10.1016/j.kint.2023.05.007⟩. ⟨hal-04339478⟩
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Xiaoyi Chen, Carole Faviez, Marc Vincent, Sophie Saunier, Nicolas Garcelon, et al.. Improving Patient Similarity Using Different Modalities of Phenotypes Extracted from Clinical Narratives. Studies in Health Technology and Informatics, 2023, Studies in Health Technology and Informatics, ⟨10.3233/SHTI230342⟩. ⟨hal-04339484⟩
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Sophie Quennelle, Maxime Douillet, Lisa Friedlander, Olivia Boyer, Antoine Neuraz, et al.. The Smart Data Extractor, a Clinician Friendly Solution to Accelerate and Improve the Data Collection During Clinical Trials. Studies in Health Technology and Informatics, 2023, Studies in Health Technology and Informatics, ⟨10.3233/SHTI230112⟩. ⟨hal-04339483⟩
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https://arxiv.org/pdf/2308.16537 BibTex
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Philippe Martin, Corinne Alberti, Auréline Bourmaud, Anita Burgun, Elise de La Rochebrochard. Communauté interactive et participative en ligne, menée avec les pairs, comme outil de promotion de la santé sexuelle et reproductive des adolescents et jeunes adultes: la recherche-action Sexpairs. Epidemiology and Public Health = Revue d’Epidémiologie et de Santé Publique, 2023, 71 (Supplement 2), pp.6-7. ⟨10.1016/j.respe.2023.101609⟩. ⟨hal-04208892⟩
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https://hal.science/hal-04208892/file/Martin%202023%2C%20RESP.pdf BibTex
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Rosy Tsopra, Nathan Peiffer-Smadja, Caroline Charlier, Florence Campeotto, Cédric Lemogne, et al.. Putting undergraduate medical students in AI-CDSS designers’ shoes: An innovative teaching method to develop digital health critical thinking. International Journal of Medical Informatics, 2023, 171, 10 p. ⟨10.1016/j.ijmedinf.2022.104980⟩. ⟨hal-04162799⟩
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Carole Faviez, Manissa Talmatkadi, Pierre Foulquié, Adel Mebarki, Stéphane Schück, et al.. Assessment of the Early Detection of Anosmia and Ageusia Symptoms in COVID-19 on Twitter: Retrospective Study. JMIR Infodemiology, 2023, 3, pp.e41863. ⟨10.2196/41863⟩. ⟨hal-04227117⟩
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https://inria.hal.science/hal-04227117/file/infodemiology_v3i1e41863.pdf BibTex
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Tan Mai Nguyen, Chloé Bertolus, Paul Giraud, Anita Burgun, Pierre Saintigny, et al.. A Radiomics Approach to Identify Immunologically Active Tumor in Patients with Head and Neck Squamous Cell Carcinomas. Cancers, 2023, 15 (22), pp.5369. ⟨10.3390/cancers15225369⟩. ⟨hal-04459206⟩
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https://hal.science/hal-04459206/file/cancers-15-05369.pdf BibTex

Book sections

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Sophie Quennelle, Maxime Douillet, Lisa Friedlander, Olivia Boyer, Antoine Neuraz, et al.. The Smart Data Extractor, a Clinician Friendly Solution to Accelerate and Improve the Data Collection During Clinical Trials. Caring is Sharing – Exploiting the Value in Data for Health and Innovation, 302, 2023, Studies in Health Technology and Informatics, ⟨10.3233/SHTI230112⟩. ⟨hal-04191423⟩
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https://hal.science/hal-04191423/file/SmartDataExtractor-Final-MIE-Submission.pdf BibTex

2022

Journal articles

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Rosy Tsopra, Nathan Peiffer-Smadja, Caroline Charlier, Florence Campeotto, Cédric Lemogne, et al.. Putting undergraduate medical students in AI-CDSS designers’ shoes: An innovative teaching method to develop digital health critical thinking. International Journal of Medical Informatics, 2022, 171, pp.104980. ⟨10.1016/j.ijmedinf.2022.104980⟩. ⟨hal-04094111⟩
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https://u-paris.hal.science/hal-04094111/file/digital_health_critical_thinking.pdf BibTex
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Griffin Weber, Chuan Hong, Zongqi Xia, Nathan Palmer, Paul Avillach, et al.. International comparisons of laboratory values from the 4CE collaborative to predict COVID-19 mortality. npj Digital Medicine, 2022, 5 (1), pp.74. ⟨10.1038/s41746-022-00601-0⟩. ⟨hal-03886991⟩
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Nicolas Hoertel, David Boulware, Marina Sánchez-Rico, Anita Burgun, Frédéric Limosin. Prevalence of Contraindications to Nirmatrelvir-Ritonavir Among Hospitalized Patients With COVID-19 at Risk for Progression to Severe Disease. JAMA Network Open, 2022, 5 (11), pp.e2242140. ⟨10.1001/jamanetworkopen.2022.42140⟩. ⟨hal-03889233⟩
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Lucien Lahmi, Marie-France Mamzer, Anita Burgun, Catherine Durdux, Jean-Emmanuel Bibault. Ethical Aspects of Artificial Intelligence in Radiation Oncology. Seminars in Radiation Oncology, 2022, 32 (4), pp.442-448. ⟨10.1016/j.semradonc.2022.06.013⟩. ⟨hal-03889231⟩
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Christina Khnaisser, Luc Lavoie, Benoit Fraikin, Adrien Barton, Samuel Dussault, et al.. Using an ontology to derive a sharable and interoperable relational data model for heterogeneous healthcare data and various applications. Methods of Information in Medicine, 2022, ⟨10.1055/a-1877-9498⟩. ⟨hal-03759575⟩
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https://hal.science/hal-03759575/file/OntoRela-methods.pdf BibTex
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Maxime Wack, David Veyer, Camille Peneau, Sonia Lameiras, William Digan, et al.. viroCapt: A Bioinformatics Pipeline for Identifying Viral Insertion in Human Host Genome. Studies in Health Technology and Informatics, 2022, Studies in Health Technology and Informatics, ⟨10.3233/SHTI220602⟩. ⟨hal-04147996⟩
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https://hal.science/hal-04147996/file/SHTI-294-SHTI220602.pdf BibTex
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Xiaoyi Chen, Carole Faviez, Marc Vincent, Luis Briseño-Roa, Hassan Faour, et al.. Patient-Patient Similarity-Based Screening of a Clinical Data Warehouse to Support Ciliopathy Diagnosis. Frontiers in Pharmacology, 2022, 13, ⟨10.3389/fphar.2022.786710⟩. ⟨hal-03629207⟩
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Ivan Lerner, Arnaud Serret-Larmande, Bastien Rance, Nicolas Garcelon, Anita Burgun, et al.. Mining Electronic Health Records for Drugs Associated With 28-day Mortality in COVID-19: Pharmacopoeia-wide Association Study (PharmWAS). JMIR Medical Informatics, 2022, 10 (3), pp.e35190. ⟨10.2196/35190⟩. ⟨hal-03792405v2⟩
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https://hal.science/hal-03792405/file/Mining%20Electronic%20Health%20Records%20for%20Drugs%20Associated%20With.pdf BibTex
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Adrien Boukobza, Anita Burgun, Bertrand Roudier, Rosy Tsopra. Deep Neural Networks for Simultaneously Capturing Public Topics and Sentiments During a Pandemic: Application on a COVID-19 Tweet Data Set. JMIR Medical Informatics, 2022, 10 (5), pp.e34306. ⟨10.2196/34306⟩. ⟨hal-03738943⟩
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https://hal.science/hal-03738943/file/PDF%282%29.pdf BibTex

Conference papers

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Safa Alsaidi, Miguel Couceiro, Esteban Marquer, Sophie Quennelle, Anita Burgun, et al.. An analogy based framework for patient-stay identification in healthcare. ATA@ICCBR 2022 – Workshop Analogies: from Theory to Applications, Sep 2022, Nancy, France. ⟨hal-03763772⟩
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https://inria.hal.science/hal-03763772/file/ICCBR_2022_Workshop_paper_76%20%281%29.pdf BibTex
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Safa Alsaidi, Miguel Couceiro, Sophie Quennelle, Anita Burgun, Nicolas Garcelon, et al.. Exploring Analogical Inference in Healthcare. IARML@IJCAI-ECAI’2022: Workshop on the Interactions between Analogical Reasoning and Machine Learning, at IJCAI-ECAI’2022, Jul 2022, Vienna, Austria. ⟨hal-03955354⟩
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https://inria.hal.science/hal-03955354/file/paper4.pdf BibTex

Book sections

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Adrien Boukobza, Maxime Wack, Antoine Neuraz, Daniela Geromin, Cécile Badoual, et al.. Determining the Set of Items to Include in Breast Operative Reports, Using Clustering Algorithms on Retrospective Data Extracted from Clinical DataWarehouse. Advances in Informatics, Management and Technology in Healthcare, 295, IOS Press, pp.45-48, 2022, Studies in Health Technology and Informatics, ⟨10.3233/SHTI220656⟩. ⟨hal-03738958⟩
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Alexandre Saadi, Alice Rogier, Anita Burgun, Rosy Tsopra. Design of an ontology-based triage system for painful patients. MEDINFO 2021: One World, One Health – Global Partnership for Digital Innovation, 290, IOS Press; IOS Press, pp.81-85, 2022, Studies in Health Technology and Informatics, ⟨10.3233/SHTI220036⟩. ⟨hal-03694355⟩
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https://hal.sorbonne-universite.fr/hal-03694355/file/209_SAADI_A_Medinfo2021_Final_Review1.pdf BibTex
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Marc Vincent, Maxime Douillet, Ivan Lerner, Antoine Neuraz, Anita Burgun, et al.. Using Deep Learning to Improve Phenotyping from Clinical Reports. MEDINFO 2021: One World, One Health – Global Partnership for Digital Innovation, IOS Press, 2022, Studies in Health Technology and Informatics, ⟨10.3233/SHTI220079⟩. ⟨hal-03887001⟩
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Marc Vincent, Maxime Douillet, Ivan Lerner, Antoine Neuraz, Anita Burgun, et al.. Using Deep Learning to Improve Phenotyping from Clinical Reports. MEDINFO 2021: One World, One Health – Global Partnership for Digital Innovation, IOS Press, 2022, Studies in Health Technology and Informatics, ⟨10.3233/SHTI220079⟩. ⟨hal-03880500⟩
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Claire Durchon, Stephi Vanderlan, Alice Jegard, Hasini Saram, Marina Falchi, et al.. An Interactive Interface for Displaying Recommendations on Emergency Phone Triage in Pediatrics. Challenges of Trustable AI and Added-Value on Health, 294, IOS Press, pp.430-434, 2022, Studies in Health Technology and Informatics, ⟨10.3233/SHTI220495⟩. ⟨hal-03738948⟩
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Edouard Michot, Jules Woo, Louis Mouline, Catherine Sinnappan, Adrien Boukobza, et al.. Towards a Clinical Decision Support System for Helping Medical Students in Emergency Call Centers. Challenges of Trustable AI and Added-Value on Health, 294, IOS Press, pp.425-429, 2022, Studies in Health Technology and Informatics, ⟨10.3233/SHTI220494⟩. ⟨hal-03738946⟩
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Carole Faviez, Marc Vincent, Nicolas Garcelon, Caroline Michot, Genevieve Baujat, et al.. Enriching UMLS-Based Phenotyping of Rare Diseases Using Deep-Learning: Evaluation on Jeune Syndrome. Challenges of Trustable AI and Added-Value on Health, IOS Press, 2022, Studies in Health Technology and Informatics, ⟨10.3233/SHTI220604⟩. ⟨hal-03886930⟩
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Carole Faviez, Marc Vincent, Nicolas Garcelon, Caroline Michot, Genevieve Baujat, et al.. Enriching UMLS-Based Phenotyping of Rare Diseases Using Deep-Learning: Evaluation on Jeune Syndrome. Challenges of Trustable AI and Added-Value on Health, 294, IOS Press; IOS Press, pp.844-848, 2022, Studies in Health Technology and Informatics, ⟨10.3233/SHTI220604⟩. ⟨hal-03790710⟩
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Maxime Wack, David Veyer, Camille Peneau, Sonia Lameiras, William Digan, et al.. viroCapt: A Bioinformatics Pipeline for Identifying Viral Insertion in Human Host Genome. Challenges of Trustable AI and Added-Value on Health, 294, IOS Press, pp.834-838, 2022, Studies in Health Technology and Informatics, ⟨10.3233/SHTI220602⟩. ⟨inserm-03772185⟩
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https://inserm.hal.science/inserm-03772185/file/SHTI-294-SHTI220602.pdf BibTex

2021

Journal articles

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Marina Sánchez-Rico, Frédéric Limosin, Raphaël Vernet, Nathanaël Beeker, Antoine Neuraz, et al.. Hydroxyzine Use and Mortality in Patients Hospitalized for COVID-19: A Multicenter Observational Study. Journal of Clinical Medicine, 2021, 10 (24), pp.5891. ⟨10.3390/jcm10245891⟩. ⟨hal-03519439⟩
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https://hal.sorbonne-universite.fr/hal-03519439/file/jcm-10-05891.pdf BibTex
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Hossein Estiri, Zachary Strasser, Gabriel Brat, Yevgeniy Semenov, Chirag Patel, et al.. Evolving phenotypes of non-hospitalized patients that indicate long COVID. BMC Medicine, 2021, 19 (1), pp.249. ⟨10.1186/s12916-021-02115-0⟩. ⟨hal-03476717⟩
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Rosy Tsopra, Paul Frappe, Sven Streit, Ana Luisa Neves, Persijn Honkoop, et al.. Reorganisation of GP surgeries during the COVID-19 outbreak: analysis of guidelines from 15 countries. BMC Family Practice, 2021, 22 (1), pp.96. ⟨10.1186/s12875-021-01413-z⟩. ⟨hal-03738914⟩
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Trang Le, Alba Gutiérrez-Sacristán, Jiyeon Son, Chuan Hong, Andrew South, et al.. Multinational characterization of neurological phenotypes in patients hospitalized with COVID-19. Scientific Reports, 2021, 11 (1), pp.20238. ⟨10.1038/s41598-021-99481-9⟩. ⟨hal-03476703⟩
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Marina Sánchez-Rico, Frédéric Limosin, Raphaël Vernet, Nathanaël Beeker, Antoine Neuraz, et al.. Hydroxyzine Use and Mortality in Patients Hospitalized for COVID-19: A Multicenter Observational Study. Journal of Clinical Medicine, 2021, 10 (24), pp.5891. ⟨10.3390/jcm10245891⟩. ⟨hal-03887044⟩
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Yannis Lombardi, Loris Azoyan, Piotr Szychowiak, Ali Bellamine, Guillaume Lemaitre, et al.. External validation of prognostic scores for COVID-19: a multicenter cohort study of patients hospitalized in Greater Paris University Hospitals. Intensive Care Medicine, 2021, 47 (12), pp.1426-1439. ⟨10.1007/s00134-021-06524-w⟩. ⟨hal-03967472v2⟩
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https://inria.hal.science/hal-03967472/file/s00134-021-06524-w.pdf BibTex
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Rosy Tsopra, Xose Fernandez, Claudio Luchinat, Lilia Alberghina, Hans Lehrach, et al.. A framework for validating AI in precision medicine: considerations from the European ITFoC consortium. BMC Medical Informatics and Decision Making, 2021, 21 (1), pp.274. ⟨10.1186/s12911-021-01634-3⟩. ⟨inserm-03373629⟩
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https://inserm.hal.science/inserm-03373629/file/s12911-021-01634-3.pdf BibTex
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Nicolas Hoertel, Marina Sánchez-Rico, Raphaël Vernet, Nathanaël Beeker, Antoine Neuraz, et al.. Dexamethasone Use and Mortality in Hospitalized Patients with Coronavirus Disease 2019: a Multicenter Retrospective Observational Study. British Journal of Clinical Pharmacology, 2021, 87 (10), pp.3766-3775. ⟨10.1111/bcp.14784⟩. ⟨hal-03463231⟩
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https://inria.hal.science/hal-03463231/file/Dexamethasone%20use%20and%20Mortality%20in%20Hospitalized%20Patients%20with%20Coronavirus%20Disease%202019.pdf BibTex
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Nicolas Hoertel, Marina Sánchez-Rico, Raphaël Vernet, Nathanaël Beeker, Anne-Sophie Jannot, et al.. Association between antidepressant use and reduced risk of intubation or death in hospitalized patients with COVID-19: results from an observational study. Molecular Psychiatry, 2021, 26 (9), pp.5199-5212. ⟨10.1038/s41380-021-01021-4⟩. ⟨hal-03887177⟩
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Anne-Sophie Jannot, Hector Countouris, Alexis van Straaten, Anita Burgun, Sandrine Katsahian, et al.. Low-income neighbourhood was a key determinant of severe COVID-19 incidence during the first wave of the epidemic in Paris. Journal of Epidemiology and Community Health, 2021, pp.jech-2020-216068. ⟨10.1136/jech-2020-216068⟩. ⟨hal-03335290⟩
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Florence Bourgeois, Alba Gutiérrez-Sacristán, Mark Keller, Molei Liu, Chuan Hong, et al.. International Analysis of Electronic Health Records of Children and Youth Hospitalized With COVID-19 Infection in 6 Countries. JAMA Network Open, 2021, 4 (6), pp.e2112596. ⟨10.1001/jamanetworkopen.2021.12596⟩. ⟨hal-03476737⟩
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Carole Faviez, Pierre Foulquié, Xiaoyi Chen, Adel Mebarki, Sophie Quennelle, et al.. Fuzzy Matching for Symptom Detection in Tweets: Application to Covid-19 During the First Wave of the Pandemic in France. Studies in Health Technology and Informatics, 2021, ⟨10.3233/shti210308⟩. ⟨hal-03253247⟩
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https://hal.science/hal-03253247/file/SHTI-281-SHTI210308.pdf BibTex
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Xiaoyi Chen, Carole Faviez, Marc Vincent, Nicolas Garcelon, Sophie Saunier, et al.. Identification of Similar Patients Through Medical Concept Embedding from Electronic Health Records: A Feasibility Study for Rare Disease Diagnosis. Studies in Health Technology and Informatics, 2021, ⟨10.3233/shti210241⟩. ⟨hal-03253313⟩
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https://hal.science/hal-03253313/file/SHTI-281-SHTI210241.pdf BibTex
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Radouane El Ayachy, Nicolas Giraud, Paul Giraud, Catherine Durdux, Philippe Giraud, et al.. The Role of Radiomics in Lung Cancer: From Screening to Treatment and Follow-Up. Frontiers in Oncology, 2021, 11, ⟨10.3389/fonc.2021.603595⟩. ⟨hal-03236180⟩
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https://hal.sorbonne-universite.fr/hal-03236180/file/fonc-11-603595.pdf BibTex
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Adrien Coulet, Stéphanie Allassonniere, François Angoulvant, Anita Burgun, Xiaoyi Chen, et al.. L’équipe-projet HeKA. Bulletin de l’Association Française pour l’Intelligence Artificielle, 2021, 112, pp.29-32. ⟨hal-03485904⟩
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https://inria.hal.science/hal-03485904/file/equipe-projet_heka.pdf BibTex
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Stéphane Schück, Pierre Foulquié, Adel Mebarki, Carole Faviez, Mickaïl Khadhar, et al.. Concerns Discussed on Chinese and French Social Media During the COVID-19 Lockdown: Comparative Infodemiology Study Based on Topic Modeling. JMIR Formative Research, 2021, 5 (4), pp.e23593. ⟨10.2196/23593⟩. ⟨hal-03253371⟩
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Cindy Abdoul, Pierrick Cros, Laurianne Coutier, Alice Hadchouel, Antoine Neuraz, et al.. Parents’ views on artificial intelligence for the daily management of childhood asthma: a survey. Journal of Allergy and Clinical Immunology: In Practice, 2021, 9 (4), pp.1728-1730.e3. ⟨10.1016/j.jaip.2020.11.048⟩. ⟨hal-03476824⟩
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https://inria.hal.science/hal-03476824/file/S221321982031271X.pdf BibTex
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William Digan, Aurélie Névéol, Antoine Neuraz, Maxime Wack, David Baudoin, et al.. Can reproducibility be improved in clinical natural language processing? A study of 7 clinical NLP suites. Journal of the American Medical Informatics Association, 2021, 28 (3), pp.504-515. ⟨10.1093/jamia/ocaa261⟩. ⟨hal-03887189⟩
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Elise Jacquier, Pierre Laurent-Puig, Cécile Badoual, Anita Burgun, Marie-France Mamzer. Facing new challenges to informed consent processes in the context of translational research: the case in CARPEM consortium. BMC Medical Ethics, 2021, 22 (1), ⟨10.1186/s12910-021-00592-9⟩. ⟨hal-03159272⟩
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https://hal.sorbonne-universite.fr/hal-03159272/file/Jacquier2021_Article_FacingNewChallengesToInformedC.pdf BibTex
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Laurent Chouchana, Nathanaël Beeker, Nathanaël Beeker, Nicolas Garcelon, Nicolas Garcelon, et al.. Association of Antihypertensive Agents with the Risk of In-Hospital Death in Patients with Covid-19. Cardiovascular Drugs and Therapy, 2021, 36 (3), pp.483-488. ⟨10.1007/s10557-021-07155-5⟩. ⟨hal-04360151⟩
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Laurent Chouchana, Nathanaël Beeker, Nicolas Garcelon, Bastien Rance, Nicolas Paris, et al.. Association of Antihypertensive Agents with the Risk of In-Hospital Death in Patients with Covid-19. Cardiovascular Drugs and Therapy, 2021, ⟨10.1007/s10557-021-07155-5⟩. ⟨hal-03476800⟩
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Paul Giraud, Philippe Giraud, Eliot Nicolas, Pierre Boisselier, Marc Alfonsi, et al.. Interpretable Machine Learning Model for Locoregional Relapse Prediction in Oropharyngeal Cancers. Cancers, 2021, 13 (1), pp.57. ⟨10.3390/cancers13010057⟩. ⟨halshs-03428057⟩
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Jordan Jouffroy, Sarah Feldman, Ivan Lerner, Bastien Rance, Anita Burgun, et al.. Hybrid Deep Learning for Medication-Related Information Extraction From Clinical Texts in French: MedExt Algorithm Development Study. JMIR Medical Informatics, 2021, 9 (3), pp.e17934. ⟨10.2196/17934⟩. ⟨hal-03476758⟩
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Vincent Looten, Antoine Neuraz, Nicolas Garcelon, Anita Burgun, Gilles Chatellier, et al.. The Epidemiology of Patients’ Email Addresses in a French University Hospital: Case-Control Study. Journal of Medical Internet Research, 2021, 23 (2), pp.e13992. ⟨10.2196/13992⟩. ⟨hal-03476768⟩
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https://inria.hal.science/hal-03476768/file/PDF.pdf BibTex
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Rosy Tsopra, Paul Frappe, Sven Streit, Ana Luisa Neves, Persijn J Honkoop, et al.. Reorganisation of GP surgeries during the COVID-19 outbreak: analysis of guidelines from 15 countries. BMC Family Practice, 2021, 22, pp.96. ⟨10.1186/s12875-021-01413-z⟩. ⟨hal-03230768⟩
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https://hal.sorbonne-universite.fr/hal-03230768/file/s12875-021-01413-z.pdf BibTex

Book sections

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Jean-Patrick Vrel, Samy Oulmane, Adrien Boukobza, Anita Burgun, Rosy Tsopra. A COVID-19 Decision Support System for Phone Call Triage, Designed by and for Medical Students. Public Health and Informatics, 281, IOS Press, pp.525-529, 2021, Studies in Health Technology and Informatics, 978-1-64368-185-6. ⟨10.3233/SHTI210226⟩. ⟨hal-03738916⟩
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2020

Journal articles

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Valentin Calugaru, Pascal Pommier, Paul Giraud, Philippe Giraud, Eliot Nicolas, et al.. Interpretable Machine Learning Model for Locoregional Relapse Prediction in Oropharyngeal Cancers. Cancers, 2020, 13 (1), pp.57. ⟨10.3390/cancers13010057⟩. ⟨hal-03146371⟩
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William Digan, Aurélie Névéol, Antoine Neuraz, Maxime Wack, David Baudoin, et al.. Can reproducibility be improved in clinical natural language processing? A study of 7 clinical NLP suites. Journal of the American Medical Informatics Association, 2020, ⟨10.1093/jamia/ocaa261⟩. ⟨hal-03118455⟩
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Sébastien Czernichow, Nathanael Beeker, Claire Rives‐lange, Emmanuel Guerot, Jean‐luc Diehl, et al.. Obesity Doubles Mortality in Patients Hospitalized for Severe Acute Respiratory Syndrome Coronavirus 2 in Paris Hospitals, France: A Cohort Study on 5,795 Patients. Obesity, 2020, 28 (12), pp.2282-2289. ⟨10.1002/oby.23014⟩. ⟨hal-03677189⟩
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Sébastien Czernichow, Nathanael Beeker, Claire Rives-Lange, Emmanuel Guerot, Jean‐luc Diehl, et al.. Obesity Doubles Mortality in Patients Hospitalized for Severe Acute Respiratory Syndrome Coronavirus 2 in Paris Hospitals, France: A Cohort Study on 5,795 Patients. Obesity, 2020, 28 (12), pp.2282-2289. ⟨10.1002/oby.23014⟩. ⟨hal-03967463⟩
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Gabriel A. Brat, Griffin M. Weber, Nils Gehlenborg, Paul Avillach, Nathan P. Palmer, et al.. International electronic health record-derived COVID-19 clinical course profiles: the 4CE consortium. npj Digital Medicine, 2020, 3 (1), pp.#109. ⟨10.1038/s41746-020-00308-0⟩. ⟨hal-02918344⟩
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David Dawei Yang, Geneviève Baujat, Antoine Neuraz, Nicolas Garcelon, Claude Messiaen, et al.. Healthcare trajectory of children with rare bone disease attending pediatric emergency departments. Orphanet Journal of Rare Diseases, 2020, 15 (1), pp.2. ⟨10.1186/s13023-019-1284-1⟩. ⟨hal-03887220⟩
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David Dawei Yang, Geneviève Baujat, Antoine Neuraz, Nicolas Garcelon, Claude Messiaen, et al.. Healthcare trajectory of children with rare bone disease attending pediatric emergency departments. Orphanet Journal of Rare Diseases, 2020, 15 (1), pp.2. ⟨10.1186/s13023-019-1284-1⟩. ⟨hal-03962408⟩
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David Dawei Yang, Geneviève Baujat, Antoine Neuraz, Nicolas Garcelon, Claude Messiaen, et al.. Healthcare trajectory of children with rare bone disease attending pediatric emergency departments. Orphanet Journal of Rare Diseases, 2020, 15 (1), pp.2. ⟨10.1186/s13023-019-1284-1⟩. ⟨hal-03944517⟩
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Antoine Neuraz, Bastien Rance, Nicolas Garcelon, Leonardo Campillos Llanos, Anita Burgun, et al.. The Impact of Specialized Corpora for Word Embeddings in Natural Langage Understanding.. Studies in Health Technology and Informatics, 2020, 270, pp.432-436. ⟨10.3233/SHTI200197⟩. ⟨hal-04360200⟩
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Antoine Neuraz, Bastien Rance, Nicolas Garcelon, Leonardo Campillos Llanos, Anita Burgun, et al.. The Impact of Specialized Corpora for Word Embeddings in Natural Langage Understanding.. Studies in Health Technology and Informatics, 2020, 270, pp.432-436. ⟨10.3233/SHTI200197⟩. ⟨hal-03476839⟩
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Carole Faviez, Xiaoyi Chen, Nicolas Garcelon, Antoine Neuraz, Bertrand Knebelmann, et al.. Diagnosis support systems for rare diseases: a scoping review. Orphanet Journal of Rare Diseases, 2020, 15 (1), pp.94. ⟨10.1186/s13023-020-01374-z⟩. ⟨hal-04360206⟩
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Nicolas Garcelon, Anita Burgun, Rémi Salomon, Antoine Neuraz. Electronic health records for the diagnosis of rare diseases. Kidney International, 2020, 97 (4), pp.676-686. ⟨10.1016/j.kint.2019.11.037⟩. ⟨hal-03476852⟩
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Sandrine Boulet, Moreno Ursino, Peter F Thall, Bruno Landi, Céline Lepere, et al.. Integration of elicited expert information via a power prior in Bayesian variable selection: Application to colon cancer data. Statistical Methods in Medical Research, 2020, 38 (12), Ahead of print. ⟨10.1177/0962280219841082⟩. ⟨inserm-02456624⟩
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Antoine Neuraz, Ivan Lerner, William Digan, Nicolas Paris, Rosy Tsopra, et al.. Natural Language Processing for Rapid Response to Emergent Diseases: Case Study of Calcium Channel Blockers and Hypertension in the COVID-19 Pandemic. Journal of Medical Internet Research, 2020, 22 (8), pp.e20773. ⟨10.2196/20773⟩. ⟨hal-03738905⟩
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Carole Faviez, Xiaoyi Chen, Nicolas Garcelon, Antoine Neuraz, Bertrand Knebelmann, et al.. Diagnosis support systems for rare diseases: a scoping review. Orphanet Journal of Rare Diseases, 2020, 15 (1), pp.94. ⟨10.1186/s13023-020-01374-z⟩. ⟨hal-02570643⟩
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Antoine Neuraz, Ivan Lerner, William Digan, Nicolas Paris, Rosy Tsopra, et al.. Natural Language Processing for Rapid Response to Emergent Diseases: Case Study of Calcium Channel Blockers and Hypertension in the COVID-19 Pandemic. Journal of Medical Internet Research, 2020, 22 (8), pp.e20773. ⟨10.2196/20773⟩. ⟨hal-03119925⟩
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2019

Journal articles

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Xiaoyi Chen, Nicolas Garcelon, Antoine Neuraz, Katy Billot, Marc Lelarge, et al.. Phenotypic similarity for rare disease: Ciliopathy diagnoses and subtyping. Journal of Biomedical Informatics, 2019, 100, pp.103308. ⟨10.1016/j.jbi.2019.103308⟩. ⟨hal-03962406⟩
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Xiaoyi Chen, Nicolas Garcelon, Antoine Neuraz, Katy Billot, Marc Lelarge, et al.. Phenotypic similarity for rare disease: Ciliopathy diagnoses and subtyping. Journal of Biomedical Informatics, 2019, 100, pp.103308. ⟨10.1016/j.jbi.2019.103308⟩. ⟨hal-03253410⟩
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Vincent Looten, Liliane Kong Win Chang, Antoine Neuraz, Marie-Anne Landau-Loriot, Benoit Vedie, et al.. 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. Computer Methods and Programs in Biomedicine, 2019, 181, pp.1-20. ⟨10.1016/j.cmpb.2018.12.030⟩. ⟨hal-01978796⟩
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Antoine Neuraz, Vincent Looten, Bastien Rance, Nicolas Daniel, Nicolas Garcelon, et al.. Do You Need Embeddings Trained on a Massive Specialized Corpus for Your Clinical Natural Language Processing Task?. Studies in Health Technology and Informatics, 2019, 264, pp.1558-1559. ⟨10.3233/SHTI190533⟩. ⟨hal-03962397⟩
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Sarah Cohen, Anne-Sophie Jannot, Laurence Iserin, Damien Bonnet, Anita Burgun, et al.. Accuracy of claim data in the identification and classification of adults with congenital heart diseases in electronic medical records. Archives of cardiovascular diseases, 2019, 112, pp.31 – 43. ⟨10.1016/j.acvd.2018.07.002⟩. ⟨hal-03486373⟩
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Sarah Cohen, Anne-Sophie Jannot, Laurence Iserin, Damien Bonnet, Anita Burgun, et al.. Accuracy of claim data in the identification and classification of adults with congenital heart diseases in electronic medical records. Archives of cardiovascular diseases, 2019, 112 (1), pp.31-43. ⟨10.1016/j.acvd.2018.07.002⟩. ⟨hal-03886379⟩
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Xiaoyi Chen, Nicolas Garcelon, Antoine Neuraz, Katy Billot, Marc Lelarge, et al.. Phenotypic similarity for rare disease: ciliopathy diagnoses and subtyping. Journal of Biomedical Informatics, 2019. ⟨hal-02893160⟩
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Armelle Arnoux-Guenegou, Yannick Girardeau, Xiaoyi Chen, Myrtille Deldossi, Rim Aboukhamis, et al.. The Adverse Drug Reactions From Patient Reports in Social Media Project: Protocol for an Evaluation Against a Gold Standard. JMIR Research Protocols, 2019, 8 (5), pp.e11448. ⟨10.2196/11448⟩. ⟨hal-03253382⟩
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Paul Giraud, Philippe Giraud, Anne Gasnier, Radouane El Ayachy, Sarah Kreps, et al.. Radiomics and Machine Learning for Radiotherapy in Head and Neck Cancers. Frontiers in Oncology, 2019, 9, pp.174. ⟨10.3389/fonc.2019.00174⟩. ⟨hal-02094643⟩
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Simon Bussy, Raphaël Veil, Vincent Looten, Anita Burgun, Stéphane Gaiffas, et al.. Comparison of methods for early-readmission prediction in a high-dimensional heterogeneous covariates and time-to-event outcome framework. BMC Medical Research Methodology, 2019, 19 (1), pp.50. ⟨10.1186/s12874-019-0673-4⟩. ⟨hal-02082787⟩
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Conference papers

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Antoine Neuraz, Vincent Looten, Bastien Rance, Nicolas Daniel, Nicolas Garcelon, et al.. Do You Need Embeddings Trained on a Massive Specialized Corpus for Your Clinical Natural Language Processing Task?. 17th World Congress on Medical and Health Informatics (MEDINFO), MCO Congress Group, Aug 2019, Lyon, France. pp.1558-1559, ⟨10.3233/SHTI190533⟩. ⟨hal-03887246⟩
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William Digan, Maxime Wack, Vincent Looten, Antoine Neuraz, Anita Burgun, et al.. Evaluating the impact of text duplications on a corpus of more than 600,000 clinical narratives in a French Hospital. medinfo 2019, Aug 2019, Lyon, France. ⟨hal-02265124⟩
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Vincent Looten, Jérôme Gariépy, Marie Simon, Virginie Villey, Anita Burgun, et al.. L’entrepôt de données cliniques comme nouvel acteur du codage partagé : l’exemple de la dénutrition à l’hôpital européen Georges-Pompidou, Paris, France. EMOIS 2019, Mar 2019, Nancy, France. pp.S17-S18, ⟨10.1016/j.respe.2013.01.043⟩. ⟨hal-02069178⟩
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Poster communications

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Vincent Looten, Antoine Neuraz, Nicolas Garcelon, Anita Burgun, Gilles Chatellier, et al.. Description des courriels des patients pris en charge à l’Hôpital Européen Georges Pompidou, Paris, France. EMOIS 2019, Mar 2019, Nancy, France. 67, pp.S104, 2019. ⟨hal-02069234⟩
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Proceedings

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William Digan, Maxime Wack, Vincent Looten, Antoine Neuraz, Anita Burgun, et al.. Evaluating the Impact of Text Duplications on a Corpus of More than 600,000 Clinical Narratives in a French Hospital.. Studies in Health Technology and Informatics, 264, pp.103-107, 2019, ⟨10.3233/SHTI190192⟩. ⟨hal-03887250⟩
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2018

Journal articles

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David Gruson, Julia Petrelluzzi, Judith Mehl, Anita Burgun, Nicolas Garcelon. [Ethical, legal and operational issues of artificial intelligence].. La Revue du Praticien Médecine Générale, 2018, 68 (10), pp.1145-1148. ⟨hal-04360216⟩
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David Gruson, Julia Petrelluzzi, Judith Mehl, Anita Burgun, Nicolas Garcelon. Ethical, legal and operational issues of artificial intelligence. Revue du Praticien (La), 2018, 68 (10), pp.1145-1148. ⟨hal-03886592⟩
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Jean-Emmanuel Bibault, Philippe Giraud, Martin Housset, Catherine Durdux, Julien Taieb, et al.. Deep Learning and Radiomics predict complete response after neo-adjuvant chemoradiation for locally advanced rectal cancer. Scientific Reports, 2018, 8 (1), pp.12611. ⟨10.1038/s41598-018-30657-6⟩. ⟨hal-03868467⟩
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Nicolas Garcelon, Antoine Neuraz, Rémi Salomon, Nadia Bahi-Buisson, Jeanne Amiel, et al.. Next generation phenotyping using narrative reports in a rare disease clinical data warehouse. Orphanet Journal of Rare Diseases, 2018, 13 (1), pp.85. ⟨10.1186/s13023-018-0830-6⟩. ⟨hal-03962363⟩
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Nicolas Garcelon, Antoine Neuraz, Rémi Salomon, Nadia Bahi-Buisson, Jeanne Amiel, et al.. Next generation phenotyping using narrative reports in a rare disease clinical data warehouse. Orphanet Journal of Rare Diseases, 2018, 13 (1), pp.85. ⟨10.1186/s13023-018-0830-6⟩. ⟨hal-03868336⟩
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Xiaoyi Chen, Carole Faviez, Stéphane Schuck, Agnès Lillo-Le-Louët, Nathalie Texier, et al.. Mining Patients’ Narratives in Social Media for Pharmacovigilance: Adverse Effects and Misuse of Methylphenidate. Frontiers in Pharmacology, 2018, 9, pp.541. ⟨10.3389/fphar.2018.00541⟩. ⟨hal-02103689⟩
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Sarah Cohen, Harel Gilutz, Ariane Marelli, Laurence Iserin, Arriel Benis, et al.. The Need of an Open Data Quality Policy: the Case of the “Transparency -Health” Database in the Prevention of Conflict of Interest. Studies in Health Technology and Informatics, 2018, 247 (6), pp.611-615. ⟨10.3233/978-1-61499-852-5-611⟩. ⟨hal-03868308⟩
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Eric Zapletal, Jean-Emmanuel Bibault, Philippe Giraud, Anita Burgun. Integrating Multimodal Radiation Therapy Data into i2b2. Applied Clinical Informatics, 2018, 09 (02), pp.377-390. ⟨10.1055/s-0038-1651497⟩. ⟨hal-03868317⟩
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Nicolas Garcelon, Antoine Neuraz, Rémi Salomon, Hassan Faour, Vincent Benoit, et al.. A clinician friendly data warehouse oriented toward narrative reports: Dr. Warehouse. Journal of Biomedical Informatics, 2018, 80, pp.52-63. ⟨10.1016/j.jbi.2018.02.019⟩. ⟨hal-03865704⟩
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Nicolas Garcelon, Antoine Neuraz, Rémi Salomon, Hassan Faour, Vincent Benoit, et al.. A clinician friendly data warehouse oriented toward narrative reports: Dr. Warehouse. Journal of Biomedical Informatics, 2018, 80, pp.52-63. ⟨10.1016/j.jbi.2018.02.019⟩. ⟨hal-03962360⟩
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Redhouane Abdellaoui, Pierre Foulquié, Nathalie Texier, Carole Faviez, Anita Burgun, et al.. Detection of Cases of Noncompliance to Drug Treatment in Patient Forum Posts: Topic Model Approach. Journal of Medical Internet Research, 2018, 20 (3), pp.e85. ⟨10.2196/jmir.9222⟩. ⟨hal-01768659⟩
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Jean-Emmanuel Bibault, Eric Zapletal, Bastien Rance, Philippe Giraud, Anita Burgun. Labeling for Big Data in radiation oncology: The Radiation Oncology Structures ontology. PLoS ONE, 2018, 13 (1), pp.e0191263. ⟨10.1371/journal.pone.0191263⟩. ⟨hal-03865701⟩
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Jean-François Ethier, Mark Mcgilchrist, Adrien Barton, Anne-Marie Cloutier, Vasa Curcin, et al.. The TRANSFoRm project: Experience and lessons learned regarding functional and interoperability requirements to support primary care. Learning Health Systems, 2018, 2 (2), pp.1–7. ⟨10.1002/lrh2.10037⟩. ⟨hal-02983146⟩
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Pierre Karapetiantz, Florelle Bellet, Bissan Audeh, Jérémy Lardon, Damien Leprovost, et al.. Descriptions of Adverse Drug Reactions are Less Informative in Forums than in the French Pharmacovigilance Database but Provide More Unexpected Reactions. Frontiers in Pharmacology, 2018, 9, pp.23. ⟨10.3389/fphar.2018.00439⟩. ⟨hal-01831145⟩
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Thérèse Deborde, Laurence Amar, Guillaume Bobrie, Nicolas Postel-Vinay, Christiane Battaglia, et al.. Sex differences in antihypertensive treatment in France among 17 856 patients in a tertiary hypertension unit. Journal of Hypertension, 2018, 36 (4), pp.939-946. ⟨10.1097/HJH.0000000000001607⟩. ⟨hal-03868256⟩
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Conference papers

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Antoine Neuraz, Leonardo Campillos Llanos, Anita Burgun, Sophie Rosset. Natural language understanding for task oriented dialog in the biomedical domain in a low ressources context, NIPS Workshop. Machine Learning for Health, Dec 2018, Montréal, Québec, Canada. ⟨hal-02358037⟩
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2017

Journal articles

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William Digan, Hector Countouris, Marc Barritault, David Baudoin, Pierre Laurent-Puig, et al.. An architecture for genomics analysis in a clinical setting using Galaxy and Docker. GigaScience, 2017, 6 (11), ⟨10.1093/gigascience/gix099⟩. ⟨inserm-01958151⟩
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Jean-Francois Ethier, Vasa Curcin, Mark Mcgilchrist, Sarah Choi Keung, Lei Zhao, et al.. eSource for clinical trials: Implementation and evaluation of a standards-based approach in a real world trial. International Journal of Medical Informatics, 2017, 106, pp.17-24. ⟨10.1016/j.ijmedinf.2017.06.006⟩. ⟨hal-03868238⟩
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Jean-Baptiste Escudié, Bastien Rance, Georgia Malamut, Sherine Khater, Anita Burgun, et al.. 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 Medical Informatics and Decision Making, 2017, 17 (1), pp.140. ⟨10.1186/s12911-017-0537-y⟩. ⟨inserm-02307407⟩
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Nicolas Garcelon, Antoine Neuraz, Vincent Benoit, Rémi Salomon, Sven Kracker, et al.. Finding patients using similarity measures in a rare diseases-oriented clinical data warehouse: Dr. Warehouse and the needle in the needle stack. Journal of Biomedical Informatics, 2017, 73, pp.51-61. ⟨10.1016/j.jbi.2017.07.016⟩. ⟨hal-03868233⟩
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Nicolas Garcelon, Antoine Neuraz, Vincent Benoit, Rémi Salomon, Sven Kracker, et al.. Finding patients using similarity measures in a rare diseases-oriented clinical data warehouse: Dr. Warehouse and the needle in the needle stack. Journal of Biomedical Informatics, 2017, 73, pp.51-61. ⟨10.1016/j.jbi.2017.07.016⟩. ⟨hal-03962341⟩
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Xiaoyi Chen, Myrtille Deldossi, Rim Aboukhamis, Carole Faviez, Badisse Dahamna, et al.. Mining Adverse Drug Reactions in Social Media with Named Entity Recognition and Semantic Methods.. Studies in Health Technology and Informatics, 2017, 245, pp.322-326. ⟨10.3233/978-1-61499-830-3-322⟩. ⟨hal-03251581⟩
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Anne-Sophie Jannot, Anita Burgun, Eric Thervet, Nicolas Pallet. The Diagnosis-Wide Landscape of Hospital-Acquired AKI. Clinical Journal of the American Society of Nephrology, 2017, 12 (6), pp.874-884. ⟨10.2215/CJN.10981016⟩. ⟨hal-03868197⟩
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Anne-Sophie Jannot, Eric Zapletal, Paul Avillach, Marie-France Mamzer, Anita Burgun, et al.. The Georges Pompidou University Hospital Clinical Data Warehouse: A 8-years follow-up experience. International Journal of Medical Informatics, 2017, 102, pp.21-28. ⟨10.1016/j.ijmedinf.2017.02.006⟩. ⟨hal-03868186⟩
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Nicolas Garcelon, Antoine Neuraz, Vincent Benoit, Rémi Salomon, Anita Burgun. Improving a full-text search engine: the importance of negation detection and family history context to identify cases in a biomedical data warehouse. Journal of the American Medical Informatics Association, 2017, 24 (3), pp.607-613. ⟨10.1093/jamia/ocw144⟩. ⟨hal-03962335⟩
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Nicolas Garcelon, Antoine Neuraz, Vincent Benoit, Rémi Salomon, Anita Burgun. Improving a full-text search engine: the importance of negation detection and family history context to identify cases in a biomedical data warehouse. Journal of the American Medical Informatics Association, 2017, 24 (3), pp.607-613. ⟨10.1093/jamia/ocw144⟩. ⟨hal-03868144⟩
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Marie-France Mamzer, Nathalie Duchange, Sylviane Darquy, Patrice Marvanne, Claude Rambaud, et al.. Partnering with patients in translational oncology research: ethical approach. Journal of Translational Medicine, 2017, 15 (1), pp.74. ⟨10.1186/s12967-017-1177-9⟩. ⟨inserm-01504029⟩
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Yannick Girardeau, Justin Doods, Eric Zapletal, Gilles Chatellier, Christel Daniel, et al.. Leveraging the EHR4CR platform to support patient inclusion in academic studies: challenges and lessons learned. BMC Medical Research Methodology, 2017, 17 (1), pp.37 – 37. ⟨10.1186/s12874-017-0299-3⟩. ⟨hal-01485291⟩
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Raphael Metral, Laurent Deliere, David Lafond, Anita Burgun, Christel Chevrier, et al.. Conception de systèmes viticoles innovants à bas intrants phytosanitaires pour répondre aux attentes du plan Ecophyto : synthèse des premiers résultats et perspectives. Revue Française d’Oenologie, 2017, 283, pp.16-19. ⟨hal-02016729⟩
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Adrien Barton, Jean-Francois Ethier, Régis Duvauferrier, Anita Burgun. An ontological analysis of medical Bayesian indicators of performance. Journal of Biomedical Semantics, 2017, 8 (1), ⟨10.1186/s13326-016-0099-4⟩. ⟨hal-01479221⟩
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Redhouane Abdellaoui, Stéphane Schück, Nathalie Texier, Anita Burgun. 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 and Surveillance, 2017, 3 (2), pp.e36. ⟨10.2196/publichealth.6577⟩. ⟨hal-03868207⟩
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Poster communications

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Vincent Looten, Chistina Khnaisser, Anita Burgun, Bastien Rance. Storing biological data in i2b2:Extending the representation of laboratory exams beyond the sheer result. i2b2 and tranSMART european meeting, Oct 2017, Paris, France. ⟨hal-01702475⟩
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2016

Journal articles

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William Dunn, Anita Burgun, Marie-Odile Krebs, Bastien Rance. Exploring and visualizing multidimensional data in translational research platforms. Briefings in Bioinformatics, 2016, pp.bbw080. ⟨10.1093/bib/bbw080⟩. ⟨hal-03865659⟩
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Arnaud Rosier, Philippe Mabo, Lynda Temal, Pascal van Hille, Olivier Dameron, et al.. Personalized and automated remote monitoring of atrial fibrillation. EP-Europace, 2016, 18 (3), pp.347-352. ⟨10.1093/europace/euv234⟩. ⟨hal-01331019⟩
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Arnaud Rosier, Philippe Mabo, Lynda Temal, Pascal van Hille, Olivier Dameron, et al.. Remote Monitoring of Cardiac Implantable Devices: Ontology Driven Classification of the Alerts. Studies in Health Technology and Informatics, 2016, 221, pp.59–63. ⟨10.3233/978-1-61499-633-0-59⟩. ⟨hal-01319949⟩
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Conference papers

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Anita Burgun, Dina V Oksen, Wolfgang Kuchinke, Hans-Ulrich Prokosch, Thomas Ganslandt, et al.. Linking health and administrative data for maternal, child and young adult health. 9. European Public Health Conference, Nov 2016, Vienne, Austria. ⟨10.1093/eurpub/ckw168.038⟩. ⟨hal-01861720⟩
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2015

Journal articles

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Sandrine Katsahian, Erica Simond Moreau, Damien Leprovost, Jérémy Lardon, Cédric Bousquet, et al.. Evaluation of Internet Social Networks using Net scoring Tool: A Case Study in Adverse Drug Reaction Mining. Studies in Health Technology and Informatics, 2015, 210, pp.526-30. ⟨hal-02103617⟩
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Anita Burgun, Dina V Oksen, Wolfgang Kuchinke, Hans-Ulrich Prokosch, Thomas Ganslandt, et al.. Proposal for a European Public Health Research Infrastructure for Sharing of health and Medical administrative data (PHRIMA).. Studies in Health Technology and Informatics, 2015, 216, pp.1005. ⟨10.3233/978-1-61499-564-7-1005⟩. ⟨hal-01232643⟩
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Jérémy Lardon, Redhouane Abdellaoui, Florelle Bellet, Hadyl Asfari, Julien Souvignet, et al.. Adverse Drug Reaction Identification and Extraction in Social Media: A Scoping Review. Journal of Medical Internet Research, 2015, 17 (7), pp.e171. ⟨10.2196/jmir.4304⟩. ⟨hal-03696358⟩
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Arnaud Rosier, Philippe Mabo, Michel Chauvin, Anita Burgun. An ontology-based annotation of cardiac implantable electronic devices to detect therapy changes in a national registry. IEEE Journal of Biomedical and Health Informatics, 2015, 19 (3), pp.971–978. ⟨10.1109/JBHI.2014.2338741⟩. ⟨hal-01154235⟩
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2013

Journal articles

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Antoine Neuraz, Laurent Chouchana, Georgia Malamut, Christine Le Beller, Denis Roche, et al.. Phenome-Wide Association Studies on a Quantitative Trait: Application to TPMT Enzyme Activity and Thiopurine Therapy in Pharmacogenomics. PLoS Computational Biology, 2013, 9 (12), pp.e1003405. ⟨10.1371/journal.pcbi.1003405⟩. ⟨inserm-02150166⟩
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Anne-Dominique Pham, Aurélie Névéol, Thomas Lavergne, Daisuke Yasunaga, Olivier Clément, et al.. Natural language processing of radiology reports for the detection of thromboembolic diseases and clinically relevant incidental findings.. BMC Bioinformatics, 2013, pp.266. ⟨inserm-01094167⟩
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Olivier Dameron, Paolo Besana, Oussama Zekri, Annabel Bourdé, Anita Burgun, et al.. OWL model of clinical trial eligibility criteria compatible with partially-known information.. Journal of Biomedical Semantics, 2013, 4 (1), pp.17. ⟨10.1186/2041-1480-4-17⟩. ⟨inserm-00874968⟩
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Jean-François Ethier, Olivier Dameron, Vasa Curcin, Mark M Mcgilchrist, Robert A Verheij, et al.. A unified structural/terminological interoperability framework based on LexEVS: application to TRANSFoRm.. Journal of the American Medical Informatics Association, 2013, 20 (5), pp.986-94. ⟨10.1136/amiajnl-2012-001312⟩. ⟨hal-00913132⟩
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2012

Journal articles

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Charles Bettembourg, Christian Diot, Anita Burgun, Olivier Dameron. GO2PUB: Querying PubMed with semantic expansion of gene ontology terms.. Journal of Biomedical Semantics, 2012, 3 (1), pp.7. ⟨10.1186/2041-1480-3-7⟩. ⟨inserm-00801230⟩
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Jeremy Lasbleiz, John Morelli, Nicolas Schnel, Anita Burgun, Régis Duvauferrier, et al.. MRI image artifact ontology: A Proposed Method for Improved Recognition.. Studies in Health Technology and Informatics, 2012, 180, pp.103-7. ⟨10.3233/978-1-61499-101-4-103⟩. ⟨inserm-00748002⟩
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Conference papers

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Fleur Mougin, Anita Burgun, Olivier Bodenreider. Comparing drug-class membership in ATC and NDF-RT. ACM International Health Informatics Symposium, Jan 2012, Miami, United States. pp.437-444, ⟨10.1145/2110363.2110413⟩. ⟨hal-02987907⟩
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Anita Burgun, Philippe Mabo, Pascal van Hille, Louise Deléger, Cyril Grouin, et al.. Computerized CHA2DS2Vasc classification in remote atrial fibrillation alerts: an ontology-based approach. Congrès Mondial d’Electrophysiologie et de Techniques Cardiaques, Jan 2012, Nice, France. ⟨hal-01831252⟩
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Other publications

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Charles Bettembourg, Olivier Dameron, Christian Diot, Anita Burgun. GO2PUB. 2012. ⟨hal-01210572⟩
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Poster communications

ref_biblio
Charles Bettembourg, Christian Diot, Anita Burgun, Olivier Dameron. GO2PUB: Querying PubMed with Semantic Expansion of Gene Ontology Terms. Journées Ouvertes en Biologie, Informatique et Mathématiques – JOBIM 2012, Jul 2012, Rennes, France. LIRMM UMR CNRS/UM2 5506, 2012, Journées Ouvertes de Biologie, Informatique et Mathématiques. ⟨hal-01210643⟩
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2011

Journal articles

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Fanny Jadeau, Annick Barthelaix, Anita Burgun, Charles Deleval, Nicolas Garcelon, et al.. [The directory of French biological resources centres/biobanks].. Médecine/Sciences, 2011, 27 (10), pp.895-7. ⟨10.1051/medsci/20112710019⟩. ⟨hal-00748797⟩
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Anita Burgun, A. Rosier, L. Temal, Julien Jacques, R. Messai, et al.. Aide à la décision en télécardiologie par une approche basée ontologie et centrée patient . [Decision Support in Telecardiology: An Ontology-Based Patient-Centered Approach.]. Innovation and Research in BioMedical engineering, 2011, 32 (3), pp.191-194. ⟨10.1016/j.irbm.2011.01.035⟩. ⟨hal-00907010⟩
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Cyril Grouin, Louise Deléger, Arnaud Rosier, Lynda Temal, Olivier Dameron, et al.. Automatic computation of CHA2DS2-VASc score: information extraction from clinical texts for thromboembolism risk assessment.. AMIA .. Annual Symposium proceedings [electronic resource] / AMIA Symposium. AMIA Symposium., 2011, 2011, pp.501-10. ⟨hal-00748588⟩
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Jérémy Lasbleiz, Hervé Saint-Jalmes, Régis Duvauferrier, Anita Burgun. Creating a magnetic resonance imaging ontology.. Studies in Health Technology and Informatics, 2011, 169, pp.784-8. ⟨inserm-00664038⟩
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Olivier Dameron, Pascal van Hille, Lynda Temal, Arnaud Rosier, Louise Deléger, et al.. Comparison of OWL and SWRL-based ontology modeling strategies for the determination of pacemaker alerts severity. Proceedings of the American Medical Informatics Association Conference AMIA, 2011, pp.284. ⟨hal-00748796⟩
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Vianney Jouhet, Georges Defossez, Anita Burgun, Pierre Le Beux, P. Levillain, et al.. Automated Classification of Free-text Pathology Reports for Registration of Incident Cases of Cancer. Methods of Information in Medicine, 2011, 50. ⟨hal-00643819⟩
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Conference papers

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Charles Bettembourg, Olivier Dameron, Anita Burgun, Christian Diot. Comparaison inter-espèces de voies métaboliques par mesure de similarité sémantique : Application au métabolisme des lipides chez le poulet, la souris et l’homme. Ecole chercheurs en Biologie Intégrative et Génomique dans le Grand Ouest (BIGOU), Nov 2011, Auray, France. ⟨hal-02807223⟩
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2010

Journal articles

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Lynda Temal, Arnaud Rosier, Olivier Dameron, Anita Burgun. Mapping BFO and DOLCE.. Studies in Health Technology and Informatics, 2010, 160 (Pt 2), pp.1065-9. ⟨10.3233/978-1-60750-588-4-1065⟩. ⟨hal-00748818⟩
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Denis Delamarre, Agnès Lillo-Le Louët, Laetitia Guillot, Anne Jamet, Eric Sadou, et al.. Documentation in pharmacovigilance: using an ontology to extend and normalize Pubmed queries.. Studies in Health Technology and Informatics, 2010, 160 (Pt 1), pp.518-22. ⟨10.3233/978-1-60750-588-4-518⟩. ⟨hal-00748892⟩
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Olivier Bodenreider, Anita Burgun. A framework for comparing phenotype annotations of orthologous genes.. Studies in Health Technology and Informatics, 2010, 160 (Pt 2), pp.1309-13. ⟨10.3233/978-1-60750-588-4-1309⟩. ⟨hal-00748838⟩
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Fleur Mougin, Olivier Bodenreider, Anita Burgun. Looking for Anemia (and Other Disorders) in SNOMED CT: Comparison of Three Approaches and Practical Implications.. AMIA .. Annual Symposium proceedings [electronic resource] / AMIA Symposium. AMIA Symposium., 2010, 2010, pp.527-31. ⟨hal-00748898⟩
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Conference papers

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Nicolas Lebreton, Chistophe Blanchet, Daniela Barreiro Claro, Julie Chabalier, Anita Burgun, et al.. Verification of parameters semantic compatibility for semi-automatic web service composition: a generic case study. Emerging Research and Projects Applications and Services symposium (ERPAS2010), Nov 2010, Paris, France. ⟨hal-00749032⟩
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Paolo Besana, Marc Cuggia, Oussama Zekri, Annabel Bourdé, Anita Burgun. Using Semantic Web Technologies for Clinical Trial Recruitment. 9th International Semantic Web Conference, ISWC 2010, Nov 2010, Shangai, China. pp.34-49, ⟨10.1007/978-3-642-17749-1_3⟩. ⟨hal-00748985⟩
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Olivier Bodenreider, Fleur Mougin, Anita Burgun. Automatic determination of anticoagulation status with NDF-RT. 13th ISMB’2010 SIG meeting “Bio-ontologies”, 2010, Aberystwyth, United Kingdom. pp.140-143. ⟨hal-02987935⟩
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2009

Journal articles

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Anita Burgun, Fleur Mougin, Olivier Bodenreider. Two approaches to integrating phenotype and clinical information. AMIA Annual Symposium Proceedings, 2009, pp.75-9. ⟨hal-02987803⟩
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Fleur Mougin, Olivier Bodenreider, Anita Burgun. Analyzing polysemous concepts from a clinical perspective: Application to auditing concept categorization in the UMLS. Journal of Biomedical Informatics, 2009, 42 (3), pp.440-451. ⟨10.1016/j.jbi.2009.03.008⟩. ⟨hal-01135073⟩
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Conference papers

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Florence Amardeilh, Cédric Bousquet, Sylvie Guillemin-Lanne, Mathilde Wiss-Thébault, Laetitia Guillot, et al.. A Knowledge Management Platform for Documentation of Case Reports in Pharmacovigilance. The XXII International Medical Informatics Europe Conference (MIE’09), Aug 2009, Sarajevo, Bosnia and Herzegovina. ⟨hal-00411266⟩
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2008

Journal articles

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Valérie Bertaud, Jérémy Lasbleiz, Fleur Mougin, Anita Burgun, Régis Duvauferrier. A unified representation of findings in clinical radiology using the UMLS and DICOM. International Journal of Medical Informatics, 2008, 77 (9), pp.621-629. ⟨10.1016/j.ijmedinf.2007.11.003⟩. ⟨hal-02987785⟩
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Marc Aubry, Annabelle Monnier, Céline Chicault, Marie-Dominique Galibert, Anita Burgun, et al.. Iron-related transcriptomic variations in Caco-2 cells: in silico perspectives.. Biochimie, 2008, 90 (4), pp.669-78. ⟨10.1016/j.biochi.2008.01.002⟩. ⟨hal-00235440⟩
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Delphine Rossille, Anita Burgun, Céline Pangault-Lorho, Thierry Fest. Integrating clinical, gene expression, protein expression and preanalytical data for in silico cancer research.. Studies in Health Technology and Informatics, 2008, 136, pp.455-60. ⟨inserm-00869488⟩
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Arnaud Rosier, Anita Burgun, Philippe Mabo. Using regular expressions to extract information on pacemaker implantation procedures from clinical reports.. AMIA .. Annual Symposium proceedings [electronic resource] / AMIA Symposium. AMIA Symposium., 2008, pp.81-5. ⟨inserm-00413991⟩
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Book sections

ref_biblio
Fleur Mougin, Anita Burgun, Olivier Bodenreider, Julie Chabalier, Olivier Loréal, et al.. Automatic Methods for Integrating Biomedical Data Sources in a Mediator-Based System. Lecture Notes in Computer Science, vol. 5109, pp.61-76, 2008, ⟨10.1007/978-3-540-69828-9_7⟩. ⟨hal-02987891⟩
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2007

Conference papers

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Fleur Mougin, Julie Chabalier, Olivier Bodenreider, Anita Burgun. Méthodes de mapping situées aux niveaux instance et schéma pour l’intégration de sources de données hétérogènes. Ingénierie des Connaissances 2007, Jul 2007, Grenoble, France. pp.37-48. ⟨hal-00380907⟩
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2006

Journal articles

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Fleur Mougin, Anita Burgun, Olivier Bodenreider. Mapping data elements to terminological resources for integrating biomedical data sources. BMC Bioinformatics, 2006, 7 (S3), pp.S6. ⟨10.1186/1471-2105-7-S3-S6⟩. ⟨hal-02987759⟩
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Anita Burgun, Stéfan Darmoni, Franck Le Duff, J. Weber. Problem-based learning in medical informatics for undergraduate medical students: An experiment in two medical schools. International Journal of Medical Informatics, 2006, 75 (5), pp.396-402. ⟨hal-00499581⟩
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Marc Aubry, Annabelle Monnier, Céline Chicault, Marie de Tayrac, Marie-Dominique Galibert, et al.. Combining evidence, biomedical literature and statistical dependence: new insights for functional annotation of gene sets.. BMC Bioinformatics, 2006, 7, pp.241. ⟨10.1186/1471-2105-7-241⟩. ⟨hal-00094484⟩
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Fleur Mougin, Anita Burgun, Olivier Bodenreider. Using WordNet to improve the mapping of data elements to UMLS for data sources integration. AMIA Annual Symposium Proceedings, 2006, pp.574-8. ⟨hal-02987780⟩
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Nicolas Garcelon, Fleur Mougin, Cédric Bousquet, Anita Burgun. Evidence in pharmacovigilance: extracting adverse drug reactions articles from MEDLINE to link them to case databases. Studies in Health Technology and Informatics, 2006, 124, pp.528-33. ⟨hal-02987766⟩
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2005

Journal articles

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Pierre Zweigenbaum, Robert Baud, Anita Burgun, Fiammetta Namer, Eric Jarrousse, et al.. UMLF : a unified medical lexicon for French. International Journal of Medical Informatics, 2005, 74 (2-4), pp.119-124. ⟨10.1016/j.ijmedinf.2004.03.010⟩. ⟨halshs-00157557⟩
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Anita Burgun, Olivier Bodenreider, Fleur Mougin. Classifying diseases with respect to anatomy: a study in SNOMED CT. AMIA Annual Symposium Proceedings, 2005, pp.91-5. ⟨hal-02987756⟩
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Conference papers

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Émilie Guerin, G. Marquet, Anita Burgun, Olivier Loréal, Laure Berti-Équille, et al.. Integrating and Warehousing Liver Gene Expression Data and Related Biomedical Resources in GEDAW. DILS 2005 – 2nd International Workshop on Data Integration in the Life Sciences, Jul 2005, San Diego, United States. pp.158-174, ⟨10.1007/11530084_14⟩. ⟨hal-01856023⟩
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2004

Journal articles

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Fleur Mougin, Anita Burgun, Olivier Loréal, Pierre Le Beux. Towards the automatic generation of biomedical sources schema. Studies in Health Technology and Informatics, 2004, 107 (Pt 2), pp.783-7. ⟨hal-02987859⟩
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2003

Conference papers

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Fiammetta Namer, Robert Baud, Anita Burgun, Stéfan J. Darmoni, Natalia Grabar, et al.. UMLF : construction d’un lexique médical francophone unifié. Journée Francophone d’informatique médicale, Sep 2003, Tunis, Tunisie. ⟨halshs-00157780⟩
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Pierre Zweigenbaum, Robert Baud, Anita Burgun, Fiammetta Namer, Eric Jarrousse, et al.. Towards a unified medical lexicon for French. Medical Informatics Europe (MIE), May 2003, Saint-Malô, France. pp.415-420. ⟨halshs-00157662⟩
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Pierre Zweigenbaum, Robert Baud, Anita Burgun, Fiammetta Namer, Eric Jarousse, et al.. UMLF: construction d’un lexique médical francophone unifié.. Journée Francophone d’Informatique médicale, Tunis, 2003, France. ⟨halshs-00006141⟩
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2000

Journal articles

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Pierre Beux, Franck Duff, Annie Fresnel, Yvon Berland, Régis Beuscart, et al.. The French Virtual Medical University.. Studies in Health Technology and Informatics, 2000, 77, pp.554-62. ⟨hal-02007721⟩
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1996

Conference papers

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Patrick Denier, Bruno Pouliquen, Denis Delamarre, Mireille Cleret, Christophe Courtin, et al.. A Web Server for Teaching Clinical Students in a Medical School and University Hospital. European Congress of the Internet in Medicine, Oct 1996, Brighton, United Kingdom. ⟨hal-02885560⟩
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