Background

Paul Avillach holds an MD in public health and epidemiology from the University of Bordeaux and a PhD in biomedical informatics from the University of Marseilles. Avillach's research focuses on the development of novel methods and techniques for the integration of multiple heterogeneous clinic cohorts, electronic health records data, and multiple types of genomics data to encompass biological observations. He is PI and Co-Investigator on several large projects at DBMI, including the BD2K PIC-SURE Center of Excellence, the Global Rare Diseases Registry project, the PCORI ARCH project, and the PCORI Phelan-Mcdermid Syndrome project.

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PUBLICATIONS

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  1. Alexander M, Loomis AK, van der Lei J, Duarte-Salles T, Prieto-Alhambra D, Ansell D, Pasqua A, Lapi F, Rijnbeek P, Mosseveld M, Avillach P, Egger P, Dhalwani NN, Kendrick S, Celis-Morales C, Waterworth DM, Alazawi W, Sattar N. Non-alcoholic fatty liver disease and risk of incident acute myocardial infarction and stroke: findings from matched cohort study of 18 million European adults. BMJ. 2019 10 08; 367:l5367. View abstract
  2. Zhong QY, Mittal LP, Nathan MD, Brown KM, Knudson González D, Cai T, Finan S, Gelaye B, Avillach P, Smoller JW, Karlson EW, Cai T, Williams MA. Use of natural language processing in electronic medical records to identify pregnant women with suicidal behavior: towards a solution to the complex classification problem. Eur J Epidemiol. 2019 Feb; 34(2):153-162. View abstract
  3. Alexander M, Loomis AK, Fairburn-Beech J, van der Lei J, Duarte-Salles T, Prieto-Alhambra D, Ansell D, Pasqua A, Lapi F, Rijnbeek P, Mosseveld M, Avillach P, Egger P, Kendrick S, Waterworth DM, Sattar N, Alazawi W. Real-world data reveal a diagnostic gap in non-alcoholic fatty liver disease. BMC Med. 2018 08 13; 16(1):130. View abstract
  4. Zhong QY, Karlson EW, Gelaye B, Finan S, Avillach P, Smoller JW, Cai T, Williams MA. Screening pregnant women for suicidal behavior in electronic medical records: diagnostic codes vs. clinical notes processed by natural language processing. BMC Med Inform Decis Mak. 2018 05 29; 18(1):30. View abstract
  5. Zhong QY, Gelaye B, Fricchione GL, Avillach P, Karlson EW, Williams MA. Adverse obstetric and neonatal outcomes complicated by psychosis among pregnant women in the United States. BMC Pregnancy Childbirth. 2018 05 02; 18(1):120. View abstract
  6. Gutiérrez-Sacristán A, Guedj R, Korodi G, Stedman J, Furlong LI, Patel CJ, Kohane IS, Avillach P. Rcupcake: an R package for querying and analyzing biomedical data through the BD2K PIC-SURE RESTful API. Bioinformatics. 2018 04 15; 34(8):1431-1432. View abstract
  7. Zhong QY, Gelaye B, Smoller JW, Avillach P, Cai T, Williams MA. Adverse obstetric outcomes during delivery hospitalizations complicated by suicidal behavior among US pregnant women. PLoS One. 2018; 13(2):e0192943. View abstract
  8. Tran A, Tran L, Geghre N, Darmon D, Rampal M, Brandone D, Gozzo JM, Haas H, Rebouillat-Savy K, Caci H, Avillach P. Health assessment of French university students and risk factors associated with mental health disorders. PLoS One. 2017; 12(11):e0188187. View abstract
  9. Kothari C, Wack M, Hassen-Khodja C, Finan S, Savova G, O'Boyle M, Bliss G, Cornell A, Horn EJ, Davis R, Jacobs J, Kohane I, Avillach P. Phelan-McDermid syndrome data network: Integrating patient reported outcomes with clinical notes and curated genetic reports. Am J Med Genet B Neuropsychiatr Genet. 2018 10; 177(7):613-624. View abstract
  10. Perera G, Pedersen L, Ansel D, Alexander M, Arrighi HM, Avillach P, Foskett N, Gini R, Gordon MF, Gungabissoon U, Mayer MA, Novak G, Rijnbeek P, Trifirò G, van der Lei J, Visser PJ, Stewart R. Dementia prevalence and incidence in a federation of European Electronic Health Record databases: The European Medical Informatics Framework resource. Alzheimers Dement. 2018 02; 14(2):130-139. View abstract
  11. Becker BFH, Avillach P, Romio S, van Mulligen EM, Weibel D, Sturkenboom MCJM, Kors JA. CodeMapper: semiautomatic coding of case definitions. A contribution from the ADVANCE project. Pharmacoepidemiol Drug Saf. 2017 Aug; 26(8):998-1005. View abstract
  12. Jannot AS, Zapletal E, Avillach P, Mamzer MF, Burgun A, Degoulet P. The Georges Pompidou University Hospital Clinical Data Warehouse: A 8-years follow-up experience. Int J Med Inform. 2017 06; 102:21-28. View abstract
  13. Roberto G, Leal I, Sattar N, Loomis AK, Avillach P, Egger P, van Wijngaarden R, Ansell D, Reisberg S, Tammesoo ML, Alavere H, Pasqua A, Pedersen L, Cunningham J, Tramontan L, Mayer MA, Herings R, Coloma P, Lapi F, Sturkenboom M, van der Lei J, Schuemie MJ, Rijnbeek P, Gini R. Identifying Cases of Type 2 Diabetes in Heterogeneous Data Sources: Strategy from the EMIF Project. PLoS One. 2016; 11(8):e0160648. View abstract
  14. Tenenbaum JD, Avillach P, Benham-Hutchins M, Breitenstein MK, Crowgey EL, Hoffman MA, Jiang X, Madhavan S, Mattison JE, Nagarajan R, Ray B, Shin D, Visweswaran S, Zhao Z, Freimuth RR. An informatics research agenda to support precision medicine: seven key areas. J Am Med Inform Assoc. 2016 07; 23(4):791-5. View abstract
  15. Gini R, Schuemie M, Brown J, Ryan P, Vacchi E, Coppola M, Cazzola W, Coloma P, Berni R, Diallo G, Oliveira JL, Avillach P, Trifirò G, Rijnbeek P, Bellentani M, van Der Lei J, Klazinga N, Sturkenboom M. Data Extraction and Management in Networks of Observational Health Care Databases for Scientific Research: A Comparison of EU-ADR, OMOP, Mini-Sentinel and MATRICE Strategies. EGEMS (Wash DC). 2016; 4(1):1189. View abstract
  16. Wack M, Puymirat E, Ranque B, Georgin-Lavialle S, Pierre I, Tanguy A, Ackermann F, Mallet C, Pavie J, Boultache H, Durieux P, Avillach P. Evaluating the Impact of Computerized Provider Order Entry on Medical Students Training at Bedside: A Randomized Controlled Trial. PLoS One. 2015; 10(9):e0138094. View abstract
  17. Girardeau Y, Trivin C, Durieux P, Le Beller C, Louet Agnes LL, Neuraz A, Degoulet P, Avillach P. Detection of Drug-Drug Interactions Inducing Acute Kidney Injury by Electronic Health Records Mining. Drug Saf. 2015 Sep; 38(9):799-809. View abstract
  18. Avillach P, Kerdelhué G, Devos P, Maisonneuve H, Darmoni SJ. [Limiting a Medline/PubMed query to the "best" articles using the JCR relative impact factor]. Rev Epidemiol Sante Publique. 2014 Dec; 62(6):361-5. View abstract
  19. Riou C, Fresson J, Serre JL, Avillach P, Leneveut L, Quantin C. Guide to good practices to ensure privacy protection in secondary use of medical records. Rev Epidemiol Sante Publique. 2014 Jun; 62(3):207-14. View abstract
  20. Planche V, Georgin-Lavialle S, Avillach P, Ranque B, Pavie J, Caruba T, Darnige L, Pouchot J. Etiologies and diagnostic work-up of extreme macrocytosis defined by an erythrocyte mean corpuscular volume over 130°fL: A study of 109 patients. Am J Hematol. 2014 Jun; 89(6):665-6. View abstract
  21. Canuel V, Rance B, Avillach P, Degoulet P, Burgun A. Translational research platforms integrating clinical and omics data: a review of publicly available solutions. Brief Bioinform. 2015 Mar; 16(2):280-90. View abstract
  22. Ferrajolo C, Coloma PM, Verhamme KM, Schuemie MJ, de Bie S, Gini R, Herings R, Mazzaglia G, Picelli G, Giaquinto C, Scotti L, Avillach P, Pedersen L, Rossi F, Capuano A, van der Lei J, Trifiró G, Sturkenboom MC. Signal detection of potentially drug-induced acute liver injury in children using a multi-country healthcare database network. Drug Saf. 2014 Feb; 37(2):99-108. View abstract
  23. Pallet N, Chauvet S, Chassé JF, Vincent M, Avillach P, Levi C, Meas-Yedid V, Olivo-Marin JC, Nga-Matsogo D, Beaune P, Thervet E, Karras A. Urinary retinol binding protein is a marker of the extent of interstitial kidney fibrosis. PLoS One. 2014; 9(1):e84708. View abstract
  24. Neuraz A, Chouchana L, Malamut G, Le Beller C, Roche D, Beaune P, Degoulet P, Burgun A, Loriot MA, Avillach P. Phenome-wide association studies on a quantitative trait: application to TPMT enzyme activity and thiopurine therapy in pharmacogenomics. PLoS Comput Biol. 2013; 9(12):e1003405. View abstract
  25. Lopes P, Nunes T, Campos D, Furlong LI, Bauer-Mehren A, Sanz F, Carrascosa MC, Mestres J, Kors J, Singh B, van Mulligen E, Van der Lei J, Diallo G, Avillach P, Ahlberg E, Boyer S, Diaz C, Oliveira JL. Gathering and exploring scientific knowledge in pharmacovigilance. PLoS One. 2013; 8(12):e83016. View abstract
  26. Marijon E, Bougouin W, Celermajer DS, Périer MC, Dumas F, Benameur N, Karam N, Lamhaut L, Tafflet M, Mustafic H, de Deus NM, Le Heuzey JY, Desnos M, Avillach P, Spaulding C, Cariou A, Prugger C, Empana JP, Jouven X. Characteristics and outcomes of sudden cardiac arrest during sports in women. Circ Arrhythm Electrophysiol. 2013 Dec; 6(6):1185-91. View abstract
  27. Coloma PM, Schuemie MJ, Trifirò G, Furlong L, van Mulligen E, Bauer-Mehren A, Avillach P, Kors J, Sanz F, Mestres J, Oliveira JL, Boyer S, Helgee EA, Molokhia M, Matthews J, Prieto-Merino D, Gini R, Herings R, Mazzaglia G, Picelli G, Scotti L, Pedersen L, van der Lei J, Sturkenboom M. Drug-induced acute myocardial infarction: identifying 'prime suspects' from electronic healthcare records-based surveillance system. PLoS One. 2013; 8(8):e72148. View abstract
  28. Marijon E, Bougouin W, Celermajer DS, Perier MC, Benameur N, Lamhaut L, Karam N, Dumas F, Tafflet M, Prugger C, Mustafic H, Rifler JP, Desnos M, Le Heuzey JY, Spaulding CM, Avillach P, Cariou A, Empana JP, Jouven X. Major regional disparities in outcomes after sudden cardiac arrest during sports. Eur Heart J. 2013 Dec; 34(47):3632-40. View abstract
  29. Avillach P, Salvo F, Thiessard F, Miremont-Salamé G, Fourrier-Reglat A, Haramburu F, Bégaud B, Moore N, Pariente A. Pilot evaluation of an automated method to decrease false-positive signals induced by co-prescriptions in spontaneous reporting databases. Pharmacoepidemiol Drug Saf. 2014 Feb; 23(2):186-94. View abstract
  30. Coloma PM, Avillach P, Salvo F, Schuemie MJ, Ferrajolo C, Pariente A, Fourrier-Réglat A, Molokhia M, Patadia V, van der Lei J, Sturkenboom M, Trifirò G. A reference standard for evaluation of methods for drug safety signal detection using electronic healthcare record databases. Drug Saf. 2013 Jan; 36(1):13-23. View abstract
  31. Oliveira JL, Lopes P, Nunes T, Campos D, Boyer S, Ahlberg E, van Mulligen EM, Kors JA, Singh B, Furlong LI, Sanz F, Bauer-Mehren A, Carrascosa MC, Mestres J, Avillach P, Diallo G, Díaz Acedo C, van der Lei J. The EU-ADR Web Platform: delivering advanced pharmacovigilance tools. Pharmacoepidemiol Drug Saf. 2013 May; 22(5):459-67. View abstract
  32. Avillach P, Dufour JC, Diallo G, Salvo F, Joubert M, Thiessard F, Mougin F, Trifirò G, Fourrier-Réglat A, Pariente A, Fieschi M. Design and validation of an automated method to detect known adverse drug reactions in MEDLINE: a contribution from the EU-ADR project. J Am Med Inform Assoc. 2013 May 01; 20(3):446-52. View abstract
  33. Pariente A, Avillach P, Salvo F, Thiessard F, Miremont-Salamé G, Fourrier-Reglat A, Haramburu F, Bégaud B, Moore N. Effect of competition bias in safety signal generation: analysis of a research database of spontaneous reports in France. Drug Saf. 2012 Oct 01; 35(10):855-64. View abstract
  34. Sahut D'Izarn M, Caumont Prim A, Planquette B, Revel MP, Avillach P, Chatellier G, Sanchez O, Meyer G. Risk factors and clinical outcome of unsuspected pulmonary embolism in cancer patients: a case-control study. J Thromb Haemost. 2012 Oct; 10(10):2032-8. View abstract
  35. Avillach P, Coloma PM, Gini R, Schuemie M, Mougin F, Dufour JC, Mazzaglia G, Giaquinto C, Fornari C, Herings R, Molokhia M, Pedersen L, Fourrier-Réglat A, Fieschi M, Sturkenboom M, van der Lei J, Pariente A, Trifirò G. Harmonization process for the identification of medical events in eight European healthcare databases: the experience from the EU-ADR project. J Am Med Inform Assoc. 2013 Jan 01; 20(1):184-92. View abstract
  36. Bauer-Mehren A, van Mullingen EM, Avillach P, Carrascosa Mdel C, Garcia-Serna R, Piñero J, Singh B, Lopes P, Oliveira JL, Diallo G, Ahlberg Helgee E, Boyer S, Mestres J, Sanz F, Kors JA, Furlong LI. Automatic filtering and substantiation of drug safety signals. PLoS Comput Biol. 2012; 8(4):e1002457. View abstract
  37. Trifirò G, Patadia V, Schuemie MJ, Coloma PM, Gini R, Herings R, Hippisley-Cox J, Mazzaglia G, Giaquinto C, Scotti L, Pedersen L, Avillach P, Sturkenboom MC, van der Lei J. EU-ADR healthcare database network vs. spontaneous reporting system database: preliminary comparison of signal detection. Stud Health Technol Inform. 2011; 166:25-30. View abstract
  38. Pariente A, Didailler M, Avillach P, Miremont-Salamé G, Fourrier-Reglat A, Haramburu F, Moore N. A potential competition bias in the detection of safety signals from spontaneous reporting databases. Pharmacoepidemiol Drug Saf. 2010 Nov; 19(11):1166-71. View abstract
  39. Avillach P, Joubert M, Thiessard F, Trifirò G, Dufour JC, Pariente A, Mougin F, Polimeni G, Catania MA, Giaquinto C, Mazzaglia G, Fornari C, Herings R, Gini R, Hippisley-Cox J, Molokhia M, Pedersen L, Fourrier-Réglat A, Sturkenboom M, Fieschi M. Design and evaluation of a semantic approach for the homogeneous identification of events in eight patient databases: a contribution to the European EU-ADR project. Stud Health Technol Inform. 2010; 160(Pt 2):1085-9. View abstract
  40. Avillach P, Mougin F, Joubert M, Thiessard F, Pariente A, Dufour JC, Trifirò G, Polimeni G, Catania MA, Giaquinto C, Mazzaglia G, Baio G, Herings R, Gini R, Hippisley-Cox J, Molokhia M, Pedersen L, Fourrier-Réglat A, Sturkenboom M, Fieschi M. A semantic approach for the homogeneous identification of events in eight patient databases: a contribution to the European eu-ADR project. Stud Health Technol Inform. 2009; 150:190-4. View abstract
  41. Quantin C, Gouyon B, Avillach P, Ferdynus C, Sagot P, Gouyon JB. Using discharge abstracts to evaluate a regional perinatal network: assessment of the linkage procedure of anonymous data. Int J Telemed Appl. 2009; 2009:181842. View abstract
  42. Avillach P, Joubert M, Fieschi M. Improving the quality of the coding of primary diagnosis in standardized discharge summaries. Health Care Manag Sci. 2008 Jun; 11(2):147-51. View abstract
  43. Joubert M, Darmoni SJ, Avillach P, Dahamna B, Fieschi M. Using knowledge for indexing health web resources in a quality-controlled gateway. Stud Health Technol Inform. 2008; 136:205-10. View abstract
  44. Quantin C, Allaert FA, Avillach P, Fassa M, Riandey B, Trouessin G, Cohen O. Building application-related patient identifiers: what solution for a European country? Int J Telemed Appl. 2008; 678302. View abstract
  45. Avillach P, Joubert M, Fieschi M. A model for indexing medical documents combining statistical and symbolic knowledge. AMIA Annu Symp Proc. 2007 Oct 11; 31-5. View abstract
  46. Quantin C, Allaert F, Fassa M, Avillach P, Fieschi M, Cohen O. Interoperability issues regarding patient identification in Europe. Conf Proc IEEE Eng Med Biol Soc. 2007; 2007:6161. View abstract
  47. Quantin C, Allaert FA, Avillach P, Riandey B, Fieschi M, Fassa M, Cohen O. Proposal of a French health identification number interoperable at the European level. Stud Health Technol Inform. 2007; 129(Pt 1):503-7. View abstract
  48. Quantin C, Allaert FA, Fassa M, Riandey B, Avillach P, Cohen O. How to manage secure direct access of European patients to their computerized medical record and personal medical record. Stud Health Technol Inform. 2007; 127:246-55. View abstract