My Bibliography

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Geva A, Liu M, Panickan VA, Avillach P, Cai T, Mandl KD. A high-throughput phenotyping algorithm is portable from adult to pediatric populations. J Am Med Inform Assoc. 2021 Feb 17;. doi: 10.1093/jamia/ocaa343. [Epub ahead of print] PubMed PMID: 33594412.

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Klann JG, Weber GM, Estiri H, Moal B, Avillach P, Hong C, Castro V, Maulhardt T, Tan ALM, Geva A, Beaulieu-Jones BK, Malovini A, South AM, Visweswaran S, Omenn GS, Ngiam KY, Mandl KD, Boeker M, Olson KL, Mowery DL, Morris M, Follett RW, Hanauer DA, Bellazzi R, Moore JH, Loh NW, Bell DS, Wagholikar KB, Chiovato L, Tibollo V, Rieg S, Li ALLJ, Jouhet V, Schriver E, Samayamuthu MJ, Xia Z, Hutch M, Luo Y, Kohane IS, Brat GA, Murphy SN. Validation of an Internationally Derived Patient Severity Phenotype to Support COVID-19 Analytics from Electronic Health Record Data. J Am Med Inform Assoc. 2021 Feb 10;. doi: 10.1093/jamia/ocab018. [Epub ahead of print] PubMed PMID: 33566082.

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Gutiérrez-Sacristán A, De Niz C, Kothari C, Kong SW, Mandl KD, Avillach P. GenoPheno: cataloging large-scale phenotypic and next-generation sequencing data within human datasets. Brief Bioinform. 2021 Jan 18;22(1):55-65. doi: 10.1093/bib/bbaa033. PubMed PMID: 32249310; PubMed Central PMCID: PMC7820848.

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Kohane IS, Aronow BJ, Avillach P, Beaulieu-Jones BK, Bellazzi R, Bradford RL, Brat GA, Cannataro M, Cimino JJ, García-Barrio N, Gehlenborg N, Ghassemi M, Gutiérrez-Sacristán A, Hanauer DA, Holmes JH, Hong C, Klann JG, Loh NHW, Luo Y, Mandl KD, Mohamad D, Moore JH, Murphy SN, Neuraz A, Ngiam KY, Omenn GS, Palmer N, Patel LP, Pedrera-Jiménez M, Sliz P, South AM, Tan ALM, Taylor DM, Taylor BW, Torti C, Vallejos AK, Wagholikar KB, Weber GM, Cai T. What Every Reader Should Know About Studies Using Electronic Health Record Data but May be Afraid to Ask. J Med Internet Res. 2021 Jan 10;. doi: 10.2196/22219. [Epub ahead of print] PubMed PMID: 33600347.

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Liu D, Olson KL, Manzi SF, Mandl KD. Patients dispensed medications with actionable pharmacogenomic biomarkers: rates and characteristics. Genet Med. 2021 Jan 8;. doi: 10.1038/s41436-020-01044-2. [Epub ahead of print] PubMed PMID: 33420348; NIHMSID:NIHMS1663581.

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McGraw D, Mandl KD. Privacy protections to encourage use of health-relevant digital data in a learning health system. NPJ Digit Med. 2021 Jan 4;4(1):2. doi: 10.1038/s41746-020-00362-8. Review. PubMed PMID: 33398052; PubMed Central PMCID: PMC7782585.

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Sayeed R, Jones J, Gottlieb D, Mandel JC, Mandl KD. A proposal for shoring up Federal Trade Commission protections for electronic health record-connected consumer apps under 21st Century Cures. J Am Med Inform Assoc. 2020 Dec 11;. doi: 10.1093/jamia/ocaa227. [Epub ahead of print] PubMed PMID: 33306804.

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Gordon WJ, Mandl KD. The 21st Century Cures Act: A Competitive Apps Market and the Risk of Innovation Blocking. J Med Internet Res. 2020 Dec 11;22(12):e24824. doi: 10.2196/24824. PubMed PMID: 33306034; PubMed Central PMCID: PMC7762678.

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Mandl KD, Gottlieb D, Mandel JC, Ignatov V, Sayeed R, Grieve G, Jones J, Ellis A, Culbertson A. Push Button Population Health: The SMART/HL7 FHIR Bulk Data Access Application Programming Interface. NPJ Digit Med. 2020 Nov 19;3(1):151. doi: 10.1038/s41746-020-00358-4. PubMed PMID: 33299056; PubMed Central PMCID: PMC7678833.

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Ong MS, Klann JG, Lin KJ, Maron BA, Murphy SN, Natter MD, Mandl KD. Claims-Based Algorithms for Identifying Patients With Pulmonary Hypertension: A Comparison of Decision Rules and Machine-Learning Approaches. J Am Heart Assoc. 2020 Oct 20;9(19):e016648. doi: 10.1161/JAHA.120.016648. Epub 2020 Sep 29. PubMed PMID: 32990147; PubMed Central PMCID: PMC7792386.

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Poirier C, Luo W, Majumder MS, Liu D, Mandl KD, Mooring TA, Santillana M. The role of environmental factors on transmission rates of the COVID-19 outbreak: an initial assessment in two spatial scales. Sci Rep. 2020 Oct 12;10(1):17002. doi: 10.1038/s41598-020-74089-7. PubMed PMID: 33046802; PubMed Central PMCID: PMC7552413.

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Blease C, Kharko A, Locher C, DesRoches CM, Mandl KD. US primary care in 2029: A Delphi survey on the impact of machine learning. PLoS One. 2020;15(10):e0239947. doi: 10.1371/journal.pone.0239947. eCollection 2020. PubMed PMID: 33031411; PubMed Central PMCID: PMC7544100.

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Dunn AG, Surian D, Dalmazzo J, Rezazadegan D, Steffens M, Dyda A, Leask J, Coiera E, Dey A, Mandl KD. Limited Role of Bots in Spreading Vaccine-Critical Information Among Active Twitter Users in the United States: 2017-2019. Am J Public Health. 2020 Oct;110(S3):S319-S325. doi: 10.2105/AJPH.2020.305902. PubMed PMID: 33001719; PubMed Central PMCID: PMC7532316.

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Geva A, Stedman JP, Manzi SF, Lin C, Savova GK, Avillach P, Mandl KD. Adverse drug event presentation and tracking (ADEPT): semiautomated, high throughput pharmacovigilance using real-world data. JAMIA Open. 2020 Oct;3(3):413-421. doi: 10.1093/jamiaopen/ooaa031. eCollection 2020 Oct. PubMed PMID: 33215076; PubMed Central PMCID: PMC7660953.

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Brat GA, Weber GM, Gehlenborg N, Avillach P, Palmer NP, Chiovato L, Cimino J, Waitman LR, Omenn GS, Malovini A, Moore JH, Beaulieu-Jones BK, Tibollo V, Murphy SN, Yi SL, Keller MS, Bellazzi R, Hanauer DA, Serret-Larmande A, Gutierrez-Sacristan A, Holmes JJ, Bell DS, Mandl KD, Follett RW, Klann JG, Murad DA, Scudeller L, Bucalo M, Kirchoff K, Craig J, Obeid J, Jouhet V, Griffier R, Cossin S, Moal B, Patel LP, Bellasi A, Prokosch HU, Kraska D, Sliz P, Tan ALM, Ngiam KY, Zambelli A, Mowery DL, Schiver E, Devkota B, Bradford RL, Daniar M, Daniel C, Benoit V, Bey R, Paris N, Serre P, Orlova N, Dubiel J, Hilka M, Jannot AS, Breant S, Leblanc J, Griffon N, Burgun A, Bernaux M, Sandrin A, Salamanca E, Cormont S, Ganslandt T, Gradinger T, Champ J, Boeker M, Martel P, Esteve L, Gramfort A, Grisel O, Leprovost D, Moreau T, Varoquaux G, Vie JJ, Wassermann D, Mensch A, Caucheteux C, Haverkamp C, Lemaitre G, Bosari S, Krantz ID, South A, Cai T, Kohane IS. International electronic health record-derived COVID-19 clinical course profiles: the 4CE consortium. NPJ Digit Med. 2020;3:109. doi: 10.1038/s41746-020-00308-0. eCollection 2020. PubMed PMID: 32864472; PubMed Central PMCID: PMC7438496.

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Inan OT, Tenaerts P, Prindiville SA, Reynolds HR, Dizon DS, Cooper-Arnold K, Turakhia M, Pletcher MJ, Preston KL, Krumholz HM, Marlin BM, Mandl KD, Klasnja P, Spring B, Iturriaga E, Campo R, Desvigne-Nickens P, Rosenberg Y, Steinhubl SR, Califf RM. Digitizing clinical trials. NPJ Digit Med. 2020;3:101. doi: 10.1038/s41746-020-0302-y. eCollection 2020. Review. PubMed PMID: 32821856; PubMed Central PMCID: PMC7395804.

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Miller TA, Avillach P, Mandl KD. Experiences implementing scalable, containerized, cloud-based NLP for extracting biobank participant phenotypes at scale. JAMIA Open. 2020 Jul;3(2):185-189. doi: 10.1093/jamiaopen/ooaa016. eCollection 2020 Jul. PubMed PMID: 32734158; PubMed Central PMCID: PMC7382623.

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Sathyanarayana A, El Atrache R, Jackson M, Alter AS, Mandl KD, Loddenkemper T, Bosl WJ. Nonlinear Analysis of Visually Normal EEGs to Differentiate Benign Childhood Epilepsy with Centrotemporal Spikes (BECTS). Sci Rep. 2020 May 21;10(1):8419. doi: 10.1038/s41598-020-65112-y. PubMed PMID: 32439999; PubMed Central PMCID: PMC7242341.

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Mandl KD, Kohane IS. Data Citizenship under the 21st Century Cures Act. N Engl J Med. 2020 May 7;382(19):1781-1783. doi: 10.1056/NEJMp1917640. Epub 2020 Mar 11. PubMed PMID: 32160449.

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Shapiro DJ, Barak-Corren Y, Neuman MI, Mandl KD, Harper MB, Fine AM. Identifying Patients at Lowest Risk for Streptococcal Pharyngitis: A National Validation Study. J Pediatr. 2020 May;220:132-138.e2. doi: 10.1016/j.jpeds.2020.01.030. Epub 2020 Feb 14. PubMed PMID: 32067779.

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Majumder MS, Mandl KD. Early in the epidemic: impact of preprints on global discourse about COVID-19 transmissibility. Lancet Glob Health. 2020 May;8(5):e627-e630. doi: 10.1016/S2214-109X(20)30113-3. Epub 2020 Mar 24. PubMed PMID: 32220289; PubMed Central PMCID: PMC7159059.

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Cutillo CM, Sharma KR, Foschini L, Kundu S, Mackintosh M, Mandl KD. Machine intelligence in healthcare-perspectives on trustworthiness, explainability, usability, and transparency. NPJ Digit Med. 2020;3:47. doi: 10.1038/s41746-020-0254-2. eCollection 2020. PubMed PMID: 32258429; PubMed Central PMCID: PMC7099019.

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Poirier C, Luo W, Majumder MS, Liu D, Mandl KD, Mooring TA, Santillana M. The Role of Environmental Factors on Transmission Rates of the COVID-19 Outbreak: An Initial Assessment in Two Spatial Scales. SSRN. 2020 Mar 12;:3552677. doi: 10.2139/ssrn.3552677. PubMed PMID: 32714106; PubMed Central PMCID: PMC7366806.

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Liu D, Sahu R, Ignatov V, Gottlieb D, Mandl KD. High Performance Computing on Flat FHIR Files Created with the New SMART/HL7 Bulk Data Access Standard. AMIA Annu Symp Proc. 2019;2019:592-596. eCollection 2019. PubMed PMID: 32308853; PubMed Central PMCID: PMC7153160.

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Barak-Corren Y, Castro VM, Nock MK, Mandl KD, Madsen EM, Seiger A, Adams WG, Applegate RJ, Bernstam EV, Klann JG, McCarthy EP, Murphy SN, Natter M, Ostasiewski B, Patibandla N, Rosenthal GE, Silva GS, Wei K, Weber GM, Weiler SR, Reis BY, Smoller JW. Validation of an Electronic Health Record-Based Suicide Risk Prediction Modeling Approach Across Multiple Health Care Systems. JAMA Netw Open. 2020 Mar 2;3(3):e201262. doi: 10.1001/jamanetworkopen.2020.1262. PubMed PMID: 32211868.

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Yu KH, Palmer N, Fox K, Prock L, Mandl KD, Kohane IS, Prilutsky D. The phenotypical implications of immune dysregulation in fragile X syndrome. Eur J Neurol. 2020 Mar;27(3):590-593. doi: 10.1111/ene.14146. Epub 2020 Jan 17. PubMed PMID: 31953887.

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Majumder MS, Mandl KD. Early in the Epidemic: Impact of Preprints on Global Discourse of 2019-nCoV Transmissibility. SSRN. 2020 Feb 12;:3536663. doi: 10.2139/ssrn.3536663. PubMed PMID: 32714103; PubMed Central PMCID: PMC7366820.

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Lin KJ, Rosenthal GE, Murphy SN, Mandl KD, Jin Y, Glynn RJ, Schneeweiss S. External Validation of an Algorithm to Identify Patients with High Data-Completeness in Electronic Health Records for Comparative Effectiveness Research. Clin Epidemiol. 2020;12:133-141. doi: 10.2147/CLEP.S232540. eCollection 2020. PubMed PMID: 32099479; PubMed Central PMCID: PMC7007793.

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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, Marsh E, Grimberg A, Hawkes C. The Genomics Research and Innovation Network: creating an interoperable, federated, genomics learning system. Genet Med. 2020 Feb;22(2):371-380. doi: 10.1038/s41436-019-0646-3. Epub 2019 Sep 4. PubMed PMID: 31481752; PubMed Central PMCID: PMC7000325.

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Lee IH, Negron JA, Hernandez-Ferrer C, Alvarez WJ, Mandl KD, Kong SW. The Clinical Genome and Ancestry Report: An interactive web application for prioritizing clinically implicated variants from genome sequencing data with ancestry composition. Hum Mutat. 2020 Feb;41(2):387-396. doi: 10.1002/humu.23942. Epub 2019 Nov 15. PubMed PMID: 31691385; PubMed Central PMCID: PMC7180092.

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Geva A, Abman SH, Manzi SF, Ivy DD, Mullen MP, Griffin J, Lin C, Savova GK, Mandl KD. Adverse drug event rates in pediatric pulmonary hypertension: a comparison of real-world data sources. J Am Med Inform Assoc. 2020 Feb 1;27(2):294-300. doi: 10.1093/jamia/ocz194. PubMed PMID: 31769835; PubMed Central PMCID: PMC7025334.

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Majumder MS, Mandl KD. Early Transmissibility Assessment of a Novel Coronavirus in Wuhan, China. SSRN. 2020 Jan 24;:3524675. doi: 10.2139/ssrn.3524675. PubMed PMID: 32714102; PubMed Central PMCID: PMC7366781.

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Sayeed R, Gottlieb D, Mandl KD. SMART Markers: collecting patient-generated health data as a standardized property of health information technology. NPJ Digit Med. 2020;3:9. doi: 10.1038/s41746-020-0218-6. eCollection 2020. PubMed PMID: 31993507; PubMed Central PMCID: PMC6978521.

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Kong SW, Hernandez-Ferrer C. Assessment of coverage for endogenous metabolites and exogenous chemical compounds using an untargeted metabolomics platform. Pac Symp Biocomput. 2020;25:587-598. PubMed PMID: 31797630; PubMed Central PMCID: PMC6910716.

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Shah Z, Surian D, Dyda A, Coiera E, Mandl KD, Dunn AG. Automatically Appraising the Credibility of Vaccine-Related Web Pages Shared on Social Media: A Twitter Surveillance Study. J Med Internet Res. 2019 Nov 4;21(11):e14007. doi: 10.2196/14007. PubMed PMID: 31682571; PubMed Central PMCID: PMC6862002.

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Ong MS, Abman S, Austin ED, Feinstein JA, Hopper RK, Krishnan US, Mullen MP, Natter MD, Raj JU, Rosenzweig EB, Mandl KD. Racial and Ethnic Differences in Pediatric Pulmonary Hypertension: An Analysis of the Pediatric Pulmonary Hypertension Network Registry. J Pediatr. 2019 Aug;211:63-71.e6. doi: 10.1016/j.jpeds.2019.04.046. Epub 2019 Jun 5. PubMed PMID: 31176455; PubMed Central PMCID: PMC6776463.

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Estiri H, Klann JG, Weiler SR, Alema-Mensah E, Joseph Applegate R, Lozinski G, Patibandla N, Wei K, Adams WG, Natter MD, Ofili EO, Ostasiewski B, Quarshie A, Rosenthal GE, Bernstam EV, Mandl KD, Murphy SN. A federated EHR network data completeness tracking system. J Am Med Inform Assoc. 2019 Jul 1;26(7):637-645. doi: 10.1093/jamia/ocz014. PubMed PMID: 30925587; PubMed Central PMCID: PMC6586954.

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Helbig I, Lopez-Hernandez T, Shor O, Galer P, Ganesan S, Pendziwiat M, Rademacher A, Ellis CA, Hümpfer N, Schwarz N, Seiffert S, Peeden J, Shen J, Štěrbová K, Hammer TB, Møller RS, Shinde DN, Tang S, Smith L, Poduri A, Krause R, Benninger F, Helbig KL, Haucke V, Weber YG. A Recurrent Missense Variant in AP2M1 Impairs Clathrin-Mediated Endocytosis and Causes Developmental and Epileptic Encephalopathy. Am J Hum Genet. 2019 Jun 6;104(6):1060-1072. doi: 10.1016/j.ajhg.2019.04.001. Epub 2019 May 16. PubMed PMID: 31104773; PubMed Central PMCID: PMC6556875.

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Ofili EO, Schanberg LE, Hutchinson B, Sogade F, Fergus I, Duncan P, Hargrove J, Artis A, Onyekwere O, Batchelor W, Williams M, Oduwole A, Onwuanyi A, Ojutalayo F, Cross JA, Seto TB, Okafor H, Pemu P, Immergluck L, Foreman M, Mensah EA, Quarshie A, Mubasher M, Baker A, Ngare A, Dent A, Malouhi M, Tchounwou P, Lee J, Hayes T, Abdelrahim M, Sarpong D, Fernandez-Repollet E, Sodeke SO, Hernandez A, Thomas K, Dennos A, Smith D, Gbadebo D, Ajuluchikwu J, Kong BW, McCollough C, Weiler SR, Natter MD, Mandl KD, Murphy S. The Association of Black Cardiologists (ABC) Cardiovascular Implementation Study (CVIS): A Research Registry Integrating Social Determinants to Support Care for Underserved Patients. Int J Environ Res Public Health. 2019 May 10;16(9). doi: 10.3390/ijerph16091631. PubMed PMID: 31083298; PubMed Central PMCID: PMC6539418.

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Shah Z, Martin P, Coiera E, Mandl KD, Dunn AG. Modeling Spatiotemporal Factors Associated With Sentiment on Twitter: Synthesis and Suggestions for Improving the Identification of Localized Deviations. J Med Internet Res. 2019 May 8;21(5):e12881. doi: 10.2196/12881. PubMed PMID: 31344669; PubMed Central PMCID: PMC6682275.

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Dunn AG, Orenstein L, Coiera E, Mandl KD, Bourgeois FT. The timing and frequency of trial inclusion in systematic reviews of type 2 diabetes drugs was associated with trial characteristics. J Clin Epidemiol. 2019 May;109:62-69. doi: 10.1016/j.jclinepi.2019.01.009. Epub 2019 Jan 30. PubMed PMID: 30708175.

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Taylor DM, Aronow BJ, Tan K, Bernt K, Salomonis N, Greene CS, Frolova A, Henrickson SE, Wells A, Pei L, Jaiswal JK, Whitsett J, Hamilton KE, MacParland SA, Kelsen J, Heuckeroth RO, Potter SS, Vella LA, Terry NA, Ghanem LR, Kennedy BC, Helbig I, Sullivan KE, Castelo-Soccio L, Kreigstein A, Herse F, Nawijn MC, Koppelman GH, Haendel M, Harris NL, Rokita JL, Zhang Y, Regev A, Rozenblatt-Rosen O, Rood JE, Tickle TL, Vento-Tormo R, Alimohamed S, Lek M, Mar JC, Loomes KM, Barrett DM, Uapinyoying P, Beggs AH, Agrawal PB, Chen YW, Muir AB, Garmire LX, Snapper SB, Nazarian J, Seeholzer SH, Fazelinia H, Singh LN, Faryabi RB, Raman P, Dawany N, Xie HM, Devkota B, Diskin SJ, Anderson SA, Rappaport EF, Peranteau W, Wikenheiser-Brokamp KA, Teichmann S, Wallace D, Peng T, Ding YY, Kim MS, Xing Y, Kong SW, Bönnemann CG, Mandl KD, White PS. The Pediatric Cell Atlas: Defining the Growth Phase of Human Development at Single-Cell Resolution. Dev Cell. 2019 Apr 8;49(1):10-29. doi: 10.1016/j.devcel.2019.03.001. Epub 2019 Mar 28. Review. PubMed PMID: 30930166; PubMed Central PMCID: PMC6616346.

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Blease C, Kaptchuk TJ, Bernstein MH, Mandl KD, Halamka JD, DesRoches CM. Artificial Intelligence and the Future of Primary Care: Exploratory Qualitative Study of UK General Practitioners' Views. J Med Internet Res. 2019 Mar 20;21(3):e12802. doi: 10.2196/12802. PubMed PMID: 30892270; PubMed Central PMCID: PMC6446158.

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Coravos A, Khozin S, Mandl KD. Developing and adopting safe and effective digital biomarkers to improve patient outcomes. NPJ Digit Med. 2019;2(1). doi: 10.1038/s41746-019-0090-4. Epub 2019 Mar 11. PubMed PMID: 30868107; PubMed Central PMCID: PMC6411051.

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Ning W, Chan S, Beam A, Yu M, Geva A, Liao K, Mullen M, Mandl KD, Kohane I, Cai T, Yu S. Feature extraction for phenotyping from semantic and knowledge resources. J Biomed Inform. 2019 Mar;91:103122. doi: 10.1016/j.jbi.2019.103122. Epub 2019 Feb 7. PubMed PMID: 30738949; PubMed Central PMCID: PMC6424621.

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Mandl KD, Manrai AK. Potential Excessive Testing at Scale: Biomarkers, Genomics, and Machine Learning. JAMA. 2019 Feb 26;321(8):739-740. doi: 10.1001/jama.2019.0286. PubMed PMID: 30735228; PubMed Central PMCID: PMC7572222.

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Mandl KD, Gottlieb D, Ellis A. Beyond One-Off Integrations: A Commercial, Substitutable, Reusable, Standards-Based, Electronic Health Record-Connected App. J Med Internet Res. 2019 Feb 1;21(2):e12902. doi: 10.2196/12902. PubMed PMID: 30707097; PubMed Central PMCID: PMC6376332.

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Geva A, Olson KL, Liu C, Mandl KD. Provider Connectedness to Other Providers Reduces Risk of Readmission After Hospitalization for Heart Failure. Med Care Res Rev. 2019 Feb;76(1):115-128. doi: 10.1177/1077558717718626. Epub 2017 Jul 8. PubMed PMID: 29148301; PubMed Central PMCID: PMC5748352.

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Blease C, Bernstein MH, Gaab J, Kaptchuk TJ, Kossowsky J, Mandl KD, Davis RB, DesRoches CM. Computerization and the future of primary care: A survey of general practitioners in the UK. PLoS One. 2018;13(12):e0207418. doi: 10.1371/journal.pone.0207418. eCollection 2018. PubMed PMID: 30540791; PubMed Central PMCID: PMC6291067.

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Kong SW, Lee IH, Liu X, Hirschhorn JN, Mandl KD. Measuring coverage and accuracy of whole-exome sequencing in clinical context. Genet Med. 2018 Dec;20(12):1617-1626. doi: 10.1038/gim.2018.51. Epub 2018 Apr 12. PubMed PMID: 29789557; PubMed Central PMCID: PMC6185824.