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dbgap2x: An R package to explore and extract data from the database of Genotypes and Phenotypes (dbGaP).

Versmée G, Versmée L, Dusenne M, Jalali N, Avillach P.

Bioinformatics. 2019 Aug 29. pii: btz680. doi: 10.1093/bioinformatics/btz680. [Epub ahead of print]


The Genomics Research and Innovation Network: creating an interoperable, federated, genomics learning system.

Mandl KD, Glauser T, Krantz ID, Avillach P, Bartels A, Beggs AH, Biswas S, Bourgeois FT, Corsmo J, Dauber A, Devkota B, Fleisher GR, Heath AP, Helbig I, Hirschhorn JN, Kilbourn J, Kong SW, Kornetsky S, Majzoub JA, Marsolo K, Martin LJ, Nix J, Schwarzhoff A, Stedman J, Strauss A, Sund KL, Taylor DM, White PS; Genomics Research and Innovation Network.

Genet Med. 2019 Sep 4. doi: 10.1038/s41436-019-0646-3. [Epub ahead of print]


An exploratory phenome wide association study linking asthma and liver disease genetic variants to electronic health records from the Estonian Biobank.

James G, Reisberg S, Lepik K, Galwey N, Avillach P, Kolberg L, Mägi R, Esko T, Alexander M, Waterworth D, Loomis AK, Vilo J.

PLoS One. 2019 Apr 12;14(4):e0215026. doi: 10.1371/journal.pone.0215026. eCollection 2019.


Associations of antepartum suicidal behaviour with adverse infant and obstetric outcomes.

Zhong QY, Gelaye B, Karlson EW, Avillach P, Smoller JW, Cai T, Williams MA.

Paediatr Perinat Epidemiol. 2019 Mar;33(2):137-144. doi: 10.1111/ppe.12535. Epub 2019 Feb 20.


Comparison of variation in frequency for SNPs associated with asthma or liver disease between Estonia, HapMap populations and the 1000 genome project populations.

Reisberg S, Galwey N, Avillach P, Sahlqvist AS, Kolberg L, Mägi R, Esko T, Vilo J, James G.

Int J Immunogenet. 2019 Apr;46(2):49-58. doi: 10.1111/iji.12413. Epub 2019 Jan 19.


Use of natural language processing in electronic medical records to identify pregnant women with suicidal behavior: towards a solution to the complex classification problem.

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.

Eur J Epidemiol. 2019 Feb;34(2):153-162. doi: 10.1007/s10654-018-0470-0. Epub 2018 Dec 10.


Real-world data reveal a diagnostic gap in non-alcoholic fatty liver disease.

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.

BMC Med. 2018 Aug 13;16(1):130. doi: 10.1186/s12916-018-1103-x.


Screening pregnant women for suicidal behavior in electronic medical records: diagnostic codes vs. clinical notes processed by natural language processing.

Zhong QY, Karlson EW, Gelaye B, Finan S, Avillach P, Smoller JW, Cai T, Williams MA.

BMC Med Inform Decis Mak. 2018 May 29;18(1):30. doi: 10.1186/s12911-018-0617-7.


Adverse obstetric and neonatal outcomes complicated by psychosis among pregnant women in the United States.

Zhong QY, Gelaye B, Fricchione GL, Avillach P, Karlson EW, Williams MA.

BMC Pregnancy Childbirth. 2018 May 2;18(1):120. doi: 10.1186/s12884-018-1750-0.


Adverse obstetric outcomes during delivery hospitalizations complicated by suicidal behavior among US pregnant women.

Zhong QY, Gelaye B, Smoller JW, Avillach P, Cai T, Williams MA.

PLoS One. 2018 Feb 15;13(2):e0192943. doi: 10.1371/journal.pone.0192943. eCollection 2018.


Rcupcake: an R package for querying and analyzing biomedical data through the BD2K PIC-SURE RESTful API.

Gutiérrez-Sacristán A, Guedj R, Korodi G, Stedman J, Furlong LI, Patel CJ, Kohane IS, Avillach P.

Bioinformatics. 2018 Apr 15;34(8):1431-1432. doi: 10.1093/bioinformatics/btx788.


Development of the Precision Link Biobank at Boston Children's Hospital: Challenges and Opportunities.

Bourgeois FT, Avillach P, Kong SW, Heinz MM, Tran TA, Chakrabarty R, Bickel J, Sliz P, Borglund EM, Kornetsky S, Mandl KD.

J Pers Med. 2017 Dec 15;7(4). pii: E21. doi: 10.3390/jpm7040021. Review.


Health assessment of French university students and risk factors associated with mental health disorders.

Tran A, Tran L, Geghre N, Darmon D, Rampal M, Brandone D, Gozzo JM, Haas H, Rebouillat-Savy K, Caci H, Avillach P.

PLoS One. 2017 Nov 27;12(11):e0188187. doi: 10.1371/journal.pone.0188187. eCollection 2017.


Phelan-McDermid syndrome data network: Integrating patient reported outcomes with clinical notes and curated genetic reports.

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.

Am J Med Genet B Neuropsychiatr Genet. 2018 Oct;177(7):613-624. doi: 10.1002/ajmg.b.32579. Epub 2017 Sep 1.


Dementia prevalence and incidence in a federation of European Electronic Health Record databases: The European Medical Informatics Framework resource.

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.

Alzheimers Dement. 2018 Feb;14(2):130-139. doi: 10.1016/j.jalz.2017.06.2270. Epub 2017 Jul 21.


CodeMapper: semiautomatic coding of case definitions. A contribution from the ADVANCE project.

Becker BFH, Avillach P, Romio S, van Mulligen EM, Weibel D, Sturkenboom MCJM, Kors JA; ADVANCE consortium.

Pharmacoepidemiol Drug Saf. 2017 Aug;26(8):998-1005. doi: 10.1002/pds.4245. Epub 2017 Jun 28.


The Georges Pompidou University Hospital Clinical Data Warehouse: A 8-years follow-up experience.

Jannot AS, Zapletal E, Avillach P, Mamzer MF, Burgun A, Degoulet P.

Int J Med Inform. 2017 Jun;102:21-28. doi: 10.1016/j.ijmedinf.2017.02.006. Epub 2017 Feb 16.


Combining clinical and genomics queries using i2b2 - Three methods.

Murphy SN, Avillach P, Bellazzi R, Phillips L, Gabetta M, Eran A, McDuffie MT, Kohane IS.

PLoS One. 2017 Apr 7;12(4):e0172187. doi: 10.1371/journal.pone.0172187. eCollection 2017.


A database of human exposomes and phenomes from the US National Health and Nutrition Examination Survey.

Patel CJ, Pho N, McDuffie M, Easton-Marks J, Kothari C, Kohane IS, Avillach P.

Sci Data. 2016 Oct 25;3:160096. doi: 10.1038/sdata.2016.96.


Identifying Cases of Type 2 Diabetes in Heterogeneous Data Sources: Strategy from the EMIF Project.

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.

PLoS One. 2016 Aug 31;11(8):e0160648. doi: 10.1371/journal.pone.0160648. eCollection 2016.


An informatics research agenda to support precision medicine: seven key areas.

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.

J Am Med Inform Assoc. 2016 Jul;23(4):791-5. doi: 10.1093/jamia/ocv213. Epub 2016 Apr 23.


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.

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.

EGEMS (Wash DC). 2016 Feb 8;4(1):1189. doi: 10.13063/2327-9214.1189. eCollection 2016.


Evaluating the Impact of Computerized Provider Order Entry on Medical Students Training at Bedside: A Randomized Controlled Trial.

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.

PLoS One. 2015 Sep 14;10(9):e0138094. doi: 10.1371/journal.pone.0138094. eCollection 2015.


Prevalence of Inflammatory Bowel Disease Among Patients with Autism Spectrum Disorders.

Doshi-Velez F, Avillach P, Palmer N, Bousvaros A, Ge Y, Fox K, Steinberg G, Spettell C, Juster I, Kohane I.

Inflamm Bowel Dis. 2015 Oct;21(10):2281-8. doi: 10.1097/MIB.0000000000000502.


Detection of Drug-Drug Interactions Inducing Acute Kidney Injury by Electronic Health Records Mining.

Girardeau Y, Trivin C, Durieux P, Le Beller C, Louet Agnes LL, Neuraz A, Degoulet P, Avillach P.

Drug Saf. 2015 Sep;38(9):799-809. doi: 10.1007/s40264-015-0311-y.


[Limiting a Medline/PubMed query to the "best" articles using the JCR relative impact factor].

Avillach P, Kerdelhué G, Devos P, Maisonneuve H, Darmoni SJ.

Rev Epidemiol Sante Publique. 2014 Dec;62(6):361-5. doi: 10.1016/j.respe.2014.09.008. Epub 2014 Nov 20. French.


Guide to good practices to ensure privacy protection in secondary use of medical records.

Riou C, Fresson J, Serre JL, Avillach P, Leneveut L, Quantin C; groupe de travail CIMES, CUESP, CNIM, CCTIRS, CNIL.

Rev Epidemiol Sante Publique. 2014 Jun;62(3):207-14. doi: 10.1016/j.respe.2014.03.005. Epub 2014 Jun 2. No abstract available.


Etiologies and diagnostic work-up of extreme macrocytosis defined by an erythrocyte mean corpuscular volume over 130°fL: A study of 109 patients.

Planche V, Georgin-Lavialle S, Avillach P, Ranque B, Pavie J, Caruba T, Darnige L, Pouchot J.

Am J Hematol. 2014 Jun;89(6):665-6. doi: 10.1002/ajh.23718. Epub 2014 Apr 18. No abstract available.


Translational research platforms integrating clinical and omics data: a review of publicly available solutions.

Canuel V, Rance B, Avillach P, Degoulet P, Burgun A.

Brief Bioinform. 2015 Mar;16(2):280-90. doi: 10.1093/bib/bbu006. Epub 2014 Mar 7. Review.


Signal detection of potentially drug-induced acute liver injury in children using a multi-country healthcare database network.

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; EU-ADR consortium.

Drug Saf. 2014 Feb;37(2):99-108. doi: 10.1007/s40264-013-0132-9.


Urinary retinol binding protein is a marker of the extent of interstitial kidney fibrosis.

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.

PLoS One. 2014 Jan 8;9(1):e84708. doi: 10.1371/journal.pone.0084708. eCollection 2014.


Phenome-wide association studies on a quantitative trait: application to TPMT enzyme activity and thiopurine therapy in pharmacogenomics.

Neuraz A, Chouchana L, Malamut G, Le Beller C, Roche D, Beaune P, Degoulet P, Burgun A, Loriot MA, Avillach P.

PLoS Comput Biol. 2013;9(12):e1003405. doi: 10.1371/journal.pcbi.1003405. Epub 2013 Dec 26.


Gathering and exploring scientific knowledge in pharmacovigilance.

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.

PLoS One. 2013 Dec 11;8(12):e83016. doi: 10.1371/journal.pone.0083016. eCollection 2013.


Characteristics and outcomes of sudden cardiac arrest during sports in women.

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.

Circ Arrhythm Electrophysiol. 2013 Dec;6(6):1185-91. doi: 10.1161/CIRCEP.113.000651. Epub 2013 Nov 4.


Drug-induced acute myocardial infarction: identifying 'prime suspects' from electronic healthcare records-based surveillance system.

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; EU-ADR consortium.

PLoS One. 2013 Aug 28;8(8):e72148. doi: 10.1371/journal.pone.0072148. eCollection 2013. Erratum in: PLoS One. 2013;8(9). doi:10.1371/annotation/8824e161-bf8f-4f78-81e0-a62a1540276d.


Major regional disparities in outcomes after sudden cardiac arrest during sports.

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.

Eur Heart J. 2013 Dec;34(47):3632-40. doi: 10.1093/eurheartj/eht282. Epub 2013 Aug 4.


Pilot evaluation of an automated method to decrease false-positive signals induced by co-prescriptions in spontaneous reporting databases.

Avillach P, Salvo F, Thiessard F, Miremont-Salamé G, Fourrier-Reglat A, Haramburu F, Bégaud B, Moore N, Pariente A; l'Association des Centres Régionaux de Pharmacovigilance.

Pharmacoepidemiol Drug Saf. 2014 Feb;23(2):186-94. doi: 10.1002/pds.3454. Epub 2013 May 14.


A reference standard for evaluation of methods for drug safety signal detection using electronic healthcare record databases.

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.

Drug Saf. 2013 Jan;36(1):13-23. doi: 10.1007/s40264-012-0002-x.


The EU-ADR Web Platform: delivering advanced pharmacovigilance tools.

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.

Pharmacoepidemiol Drug Saf. 2013 May;22(5):459-67. doi: 10.1002/pds.3375. Epub 2012 Dec 4.


Design and validation of an automated method to detect known adverse drug reactions in MEDLINE: a contribution from the EU-ADR project.

Avillach P, Dufour JC, Diallo G, Salvo F, Joubert M, Thiessard F, Mougin F, Trifirò G, Fourrier-Réglat A, Pariente A, Fieschi M.

J Am Med Inform Assoc. 2013 May 1;20(3):446-52. doi: 10.1136/amiajnl-2012-001083. Epub 2012 Nov 29.


Effect of competition bias in safety signal generation: analysis of a research database of spontaneous reports in France.

Pariente A, Avillach P, Salvo F, Thiessard F, Miremont-Salamé G, Fourrier-Reglat A, Haramburu F, Bégaud B, Moore N; Association Française des Centres Régionaux de Pharmacovigilance (CRPV).

Drug Saf. 2012 Oct 1;35(10):855-64. doi: 10.2165/11631780-000000000-00000.


Harmonization process for the identification of medical events in eight European healthcare databases: the experience from the EU-ADR project.

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; EU-ADR consortium.

J Am Med Inform Assoc. 2013 Jan 1;20(1):184-92. doi: 10.1136/amiajnl-2012-000933. Epub 2012 Sep 6.


Risk factors and clinical outcome of unsuspected pulmonary embolism in cancer patients: a case-control study.

Sahut D'Izarn M, Caumont Prim A, Planquette B, Revel MP, Avillach P, Chatellier G, Sanchez O, Meyer G.

J Thromb Haemost. 2012 Oct;10(10):2032-8. doi: 10.1111/j.1538-7836.2012.04868.x.


Automatic filtering and substantiation of drug safety signals.

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.

PLoS Comput Biol. 2012;8(4):e1002457. doi: 10.1371/journal.pcbi.1002457. Epub 2012 Apr 5. Erratum in: PLoS Comput Biol. 2012 May;8(5): doi/10.1371/annotation/695450aa-95a0-491d-804d-470cbfa861e8.


EU-ADR healthcare database network vs. spontaneous reporting system database: preliminary comparison of signal detection.

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 Group.

Stud Health Technol Inform. 2011;166:25-30.


A potential competition bias in the detection of safety signals from spontaneous reporting databases.

Pariente A, Didailler M, Avillach P, Miremont-Salamé G, Fourrier-Reglat A, Haramburu F, Moore N.

Pharmacoepidemiol Drug Saf. 2010 Nov;19(11):1166-71. doi: 10.1002/pds.2022.


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.

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.

Stud Health Technol Inform. 2010;160(Pt 2):1085-9.


A semantic approach for the homogeneous identification of events in eight patient databases: a contribution to the European eu-ADR project.

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.

Stud Health Technol Inform. 2009;150:190-4.


Using discharge abstracts to evaluate a regional perinatal network: assessment of the linkage procedure of anonymous data.

Quantin C, Gouyon B, Avillach P, Ferdynus C, Sagot P, Gouyon JB.

Int J Telemed Appl. 2009;2009:181842. doi: 10.1155/2009/181842. Epub 2008 Dec 23.


A model for indexing medical documents combining statistical and symbolic knowledge.

Avillach P, Joubert M, Fieschi M.

AMIA Annu Symp Proc. 2007 Oct 11:31-5.

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