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Items: 1 to 50 of 134

1.

Mining multi-site clinical data to develop machine learning MRI biomarkers: application to neonatal hypoxic ischemic encephalopathy.

Weiss RJ, Bates SV, Song Y, Zhang Y, Herzberg EM, Chen YC, Gong M, Chien I, Zhang L, Murphy SN, Gollub RL, Grant PE, Ou Y.

J Transl Med. 2019 Nov 21;17(1):385. doi: 10.1186/s12967-019-2119-5.

2.

High-throughput phenotyping with electronic medical record data using a common semi-supervised approach (PheCAP).

Zhang Y, Cai T, Yu S, Cho K, Hong C, Sun J, Huang J, Ho YL, Ananthakrishnan AN, Xia Z, Shaw SY, Gainer V, Castro V, Link N, Honerlaw J, Huang S, Gagnon D, Karlson EW, Plenge RM, Szolovits P, Savova G, Churchill S, O'Donnell C, Murphy SN, Gaziano JM, Kohane I, Cai T, Liao KP.

Nat Protoc. 2019 Dec;14(12):3426-3444. doi: 10.1038/s41596-019-0227-6. Epub 2019 Nov 20.

PMID:
31748751
3.

Rationale and design of a navigator-driven remote optimization of guideline-directed medical therapy in patients with heart failure with reduced ejection fraction.

Blood AJ, Fischer CM, Fera LE, MacLean TE, Smith KV, Dunning JR, Bosque-Hamilton JW, Aronson SJ, Gaziano TA, MacRae CA, Matta LS, Mercurio-Pinto AA, Murphy SN, Scirica BM, Wagholikar K, Desai AS.

Clin Cardiol. 2019 Nov 14. doi: 10.1002/clc.23291. [Epub ahead of print]

4.

High-throughput multimodal automated phenotyping (MAP) with application to PheWAS.

Liao KP, Sun J, Cai TA, Link N, Hong C, Huang J, Huffman JE, Gronsbell J, Zhang Y, Ho YL, Castro V, Gainer V, Murphy SN, O'Donnell CJ, Gaziano JM, Cho K, Szolovits P, Kohane IS, Yu S, Cai T.

J Am Med Inform Assoc. 2019 Nov 1;26(11):1255-1262. doi: 10.1093/jamia/ocz066.

PMID:
31613361
5.

Association of Genetic Risk of Obesity with Postoperative Complications Using Mendelian Randomization.

Robinson JR, Carroll RJ, Bastarache L, Chen Q, Mou Z, Wei WQ, Connolly JJ, Mentch F, Sleiman P, Crane PK, Hebbring SJ, Stanaway IB, Crosslin DR, Gordon AS, Rosenthal EA, Carrell D, Hayes MG, Wei W, Petukhova L, Namjou B, Zhang G, Safarova MS, Walton NA, Still C, Bottinger EP, Loos RJF, Murphy SN, Jackson GP, Kullo IJ, Hakonarson H, Jarvik GP, Larson EB, Weng C, Roden DM, Denny JC.

World J Surg. 2019 Oct 11. doi: 10.1007/s00268-019-05202-9. [Epub ahead of print]

PMID:
31605180
6.

Making work visible for electronic phenotype implementation: Lessons learned from the eMERGE network.

Shang N, Liu C, Rasmussen LV, Ta CN, Caroll RJ, Benoit B, Lingren T, Dikilitas O, Mentch FD, Carrell DS, Wei WQ, Luo Y, Gainer VS, Kullo IJ, Pacheco JA, Hakonarson H, Walunas TL, Denny JC, Wiley K, Murphy SN, Hripcsak G, Weng C.

J Biomed Inform. 2019 Nov;99:103293. doi: 10.1016/j.jbi.2019.103293. Epub 2019 Sep 19.

PMID:
31542521
7.

Use of Narrative Concepts in Electronic Health Records to Validate Associations Between Genetic Factors and Response to Treatment of Inflammatory Bowel Diseases.

Ananthakrishnan AN, Cagan A, Cai T, Gainer VS, Savova G, Shaw SY, Churchill S, Burke KE, Karlson EW, Murphy SN, Kohane I, Liao KP, Xavier RJ.

Clin Gastroenterol Hepatol. 2019 Aug 9. pii: S1542-3565(19)30861-4. doi: 10.1016/j.cgh.2019.08.005. [Epub ahead of print]

PMID:
31404664
8.

A clustering approach for detecting implausible observation values in electronic health records data.

Estiri H, Klann JG, Murphy SN.

BMC Med Inform Decis Mak. 2019 Jul 23;19(1):142. doi: 10.1186/s12911-019-0852-6.

9.

Facilitating phenotype transfer using a common data model.

Hripcsak G, Shang N, Peissig PL, Rasmussen LV, Liu C, Benoit B, Carroll RJ, Carrell DS, Denny JC, Dikilitas O, Gainer VS, Howell KM, Klann JG, Kullo IJ, Lingren T, Mentch FD, Murphy SN, Natarajan K, Pacheco JA, Wei WQ, Wiley K, Weng C.

J Biomed Inform. 2019 Aug;96:103253. doi: 10.1016/j.jbi.2019.103253. Epub 2019 Jul 17.

PMID:
31325501
10.

Correction to: Association between inflammation and systolic blood pressure in RA compared to patients without RA.

Yu Z, Kim SC, Vanni K, Huang J, Desai R, Murphy SN, Solomon DH, Liao KP.

Arthritis Res Ther. 2019 Jul 8;21(1):170. doi: 10.1186/s13075-019-1940-9.

11.

Extending i2b2 into a framework for semantic abstraction of EHR to facilitate rapid development and portability of Health IT applications.

Wagholikar KB, Ainsworth L, Vernekar VP, Pathak A, Glynn C, Zelle D, Zagade A, Karipineni N, Herrick CD, McPartlin M, Bui TV, Mendis M, Klann J, Oates M, Gordon W, Cannon C, Patel R, Aronson SJ, MacRae CA, Scirica BM, Murphy SN.

AMIA Jt Summits Transl Sci Proc. 2019 May 6;2019:370-378. eCollection 2019.

12.

Phenotyping to Facilitate Accrual for a Cardiovascular Intervention.

Wagholikar KB, Fischer CM, Goodson AP, Herrick CD, Maclean TE, Smith KV, Fera L, Gaziano TA, Dunning JR, Bosque-Hamilton J, Matta L, Toscano E, Richter B, Ainsworth L, Oates MF, Aronson S, MacRae CA, Scirica BM, Desai AS, Murphy SN.

J Clin Med Res. 2019 Jun;11(6):458-463. doi: 10.14740/jocmr3830. Epub 2019 May 10.

13.

A federated EHR network data completeness tracking system.

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.

J Am Med Inform Assoc. 2019 Jul 1;26(7):637-645. doi: 10.1093/jamia/ocz014.

14.

Automated Population of an i2b2 Clinical Data Warehouse using FHIR.

Solbrig HR, Hong N, Murphy SN, Jiang G.

AMIA Annu Symp Proc. 2018 Dec 5;2018:979-988. eCollection 2018.

15.

Data model harmonization for the All Of Us Research Program: Transforming i2b2 data into the OMOP common data model.

Klann JG, Joss MAH, Embree K, Murphy SN.

PLoS One. 2019 Feb 19;14(2):e0212463. doi: 10.1371/journal.pone.0212463. eCollection 2019.

16.

Semi-supervised encoding for outlier detection in clinical observation data.

Estiri H, Murphy SN.

Comput Methods Programs Biomed. 2019 Nov;181:104830. doi: 10.1016/j.cmpb.2019.01.002. Epub 2019 Jan 12.

PMID:
30658851
17.

Probabilistic record linkage of de-identified research datasets with discrepancies using diagnosis codes.

Hejblum BP, Weber GM, Liao KP, Palmer NP, Churchill S, Shadick NA, Szolovits P, Murphy SN, Kohane IS, Cai T.

Sci Data. 2019 Jan 8;6:180298. doi: 10.1038/sdata.2018.298.

18.

Accrual to Clinical Trials (ACT): A Clinical and Translational Science Award Consortium Network.

Visweswaran S, Becich MJ, D'Itri VS, Sendro ER, MacFadden D, Anderson NR, Allen KA, Ranganathan D, Murphy SN, Morrato EH, Pincus HA, Toto R, Firestein GS, Nadler LM, Reis SE.

JAMIA Open. 2018 Oct;1(2):147-152. doi: 10.1093/jamiaopen/ooy033. Epub 2018 Aug 21.

19.

Extraction of Ejection Fraction from Echocardiography Notes for Constructing a Cohort of Patients having Heart Failure with reduced Ejection Fraction (HFrEF).

Wagholikar KB, Fischer CM, Goodson A, Herrick CD, Rees M, Toscano E, MacRae CA, Scirica BM, Desai AS, Murphy SN.

J Med Syst. 2018 Sep 25;42(11):209. doi: 10.1007/s10916-018-1066-7.

20.

Web services for data warehouses: OMOP and PCORnet on i2b2.

Klann JG, Phillips LC, Herrick C, Joss MAH, Wagholikar KB, Murphy SN.

J Am Med Inform Assoc. 2018 Oct 1;25(10):1331-1338. doi: 10.1093/jamia/ocy093.

21.

Implementation of informatics for integrating biology and the bedside (i2b2) platform as Docker containers.

Wagholikar KB, Dessai P, Sanz J, Mendis ME, Bell DS, Murphy SN.

BMC Med Inform Decis Mak. 2018 Jul 16;18(1):66. doi: 10.1186/s12911-018-0646-2.

22.

Feasibility of Homomorphic Encryption for Sharing I2B2 Aggregate-Level Data in the Cloud.

Raisaro JL, Klann JG, Wagholikar KB, Estiri H, Hubaux JP, Murphy SN.

AMIA Jt Summits Transl Sci Proc. 2018 May 18;2017:176-185. eCollection 2018.

23.

The Ad-Hoc Uncertainty Principle of Patient Privacy.

Klann JG, Joss M, Shirali R, Natter M, Schneeweiss S, Mandl KD, Murphy SN.

AMIA Jt Summits Transl Sci Proc. 2018 May 18;2017:132-138. eCollection 2018.

24.

Automating Installation of the Integrating Biology and the Bedside (i2b2) Platform.

Wagholikar KB, Mendis M, Dessai P, Sanz J, Law S, Gilson M, Sanders S, Vangala M, Bell DS, Murphy SN.

Biomed Inform Insights. 2018 Jun 4;10:1178222618777749. doi: 10.1177/1178222618777749. eCollection 2018. Review.

25.

Association between inflammation and systolic blood pressure in RA compared to patients without RA.

Yu Z, Kim SC, Vanni K, Huang J, Desai R, Murphy SN, Solomon DH, Liao KP.

Arthritis Res Ther. 2018 Jun 1;20(1):107. doi: 10.1186/s13075-018-1597-9. Erratum in: Arthritis Res Ther. 2019 Jul 8;21(1):170.

26.

The Association Between Arthralgia and Vedolizumab Using Natural Language Processing.

Cai T, Lin TC, Bond A, Huang J, Kane-Wanger G, Cagan A, Murphy SN, Ananthakrishnan AN, Liao KP.

Inflamm Bowel Dis. 2018 Sep 15;24(10):2242-2246. doi: 10.1093/ibd/izy127.

27.

Genetic validation of bipolar disorder identified by automated phenotyping using electronic health records.

Chen CY, Lee PH, Castro VM, Minnier J, Charney AW, Stahl EA, Ruderfer DM, Murphy SN, Gainer V, Cai T, Jones I, Pato CN, Pato MT, Landén M, Sklar P, Perlis RH, Smoller JW.

Transl Psychiatry. 2018 Apr 18;8(1):86. doi: 10.1038/s41398-018-0133-7.

28.

Field of View Normalization in Multi-Site Brain MRI.

Ou Y, Zöllei L, Da X, Retzepi K, Murphy SN, Gerstner ER, Rosen BR, Grant PE, Kalpathy-Cramer J, Gollub RL.

Neuroinformatics. 2018 Oct;16(3-4):431-444. doi: 10.1007/s12021-018-9359-z.

PMID:
29353341
29.

Male-male aggression is unlikely to stabilize a poison frog polymorphism.

Yang Y, Dugas MB, Sudekum HJ, Murphy SN, Richards-Zawacki CL.

J Evol Biol. 2018 Mar;31(3):457-468. doi: 10.1111/jeb.13243. Epub 2018 Feb 8.

PMID:
29345026
30.

Out-of-system Care and Recording of Patient Characteristics Critical for Comparative Effectiveness Research.

Lin KJ, Glynn RJ, Singer DE, Murphy SN, Lii J, Schneeweiss S.

Epidemiology. 2018 May;29(3):356-363. doi: 10.1097/EDE.0000000000000794.

31.

Enabling phenotypic big data with PheNorm.

Yu S, Ma Y, Gronsbell J, Cai T, Ananthakrishnan AN, Gainer VS, Churchill SE, Szolovits P, Murphy SN, Kohane IS, Liao KP, Cai T.

J Am Med Inform Assoc. 2018 Jan 1;25(1):54-60. doi: 10.1093/jamia/ocx111.

32.

Exploring completeness in clinical data research networks with DQe-c.

Estiri H, Stephens KA, Klann JG, Murphy SN.

J Am Med Inform Assoc. 2018 Jan 1;25(1):17-24. doi: 10.1093/jamia/ocx109.

33.

Biases introduced by filtering electronic health records for patients with "complete data".

Weber GM, Adams WG, Bernstam EV, Bickel JP, Fox KP, Marsolo K, Raghavan VA, Turchin A, Zhou X, Murphy SN, Mandl KD.

J Am Med Inform Assoc. 2017 Nov 1;24(6):1134-1141. doi: 10.1093/jamia/ocx071.

34.

Identifying Patients With High Data Completeness to Improve Validity of Comparative Effectiveness Research in Electronic Health Records Data.

Lin KJ, Singer DE, Glynn RJ, Murphy SN, Lii J, Schneeweiss S.

Clin Pharmacol Ther. 2018 May;103(5):899-905. doi: 10.1002/cpt.861. Epub 2017 Oct 10.

35.

Evolving Research Data Sharing Networks to Clinical App Sharing Networks.

Wagholikar KB, Jain R, Oliveira E, Mandel J, Klann J, Colas R, Patil P, Yadav K, Mandl KD, Carton T, Murphy SN.

AMIA Jt Summits Transl Sci Proc. 2017 Jul 26;2017:302-307. eCollection 2017.

36.

A Computable Phenotype Improves Cohort Ascertainment in a Pediatric Pulmonary Hypertension Registry.

Geva A, Gronsbell JL, Cai T, Cai T, Murphy SN, Lyons JC, Heinz MM, Natter MD, Patibandla N, Bickel J, Mullen MP, Mandl KD; Pediatric Pulmonary Hypertension Network and National Heart, Lung, and Blood Institute Pediatric Pulmonary Vascular Disease Outcomes Bioinformatics Clinical Coordinating Center Investigators.

J Pediatr. 2017 Sep;188:224-231.e5. doi: 10.1016/j.jpeds.2017.05.037. Epub 2017 Jun 16.

37.

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.

38.

Using clinically acquired MRI to construct age-specific ADC atlases: Quantifying spatiotemporal ADC changes from birth to 6-year old.

Ou Y, Zöllei L, Retzepi K, Castro V, Bates SV, Pieper S, Andriole KP, Murphy SN, Gollub RL, Grant PE.

Hum Brain Mapp. 2017 Jun;38(6):3052-3068. doi: 10.1002/hbm.23573. Epub 2017 Mar 31.

39.

Surrogate-assisted feature extraction for high-throughput phenotyping.

Yu S, Chakrabortty A, Liao KP, Cai T, Ananthakrishnan AN, Gainer VS, Churchill SE, Szolovits P, Murphy SN, Kohane IS, Cai T.

J Am Med Inform Assoc. 2017 Apr 1;24(e1):e143-e149. doi: 10.1093/jamia/ocw135.

40.

SMART-on-FHIR implemented over i2b2.

Wagholikar KB, Mandel JC, Klann JG, Wattanasin N, Mendis M, Chute CG, Mandl KD, Murphy SN.

J Am Med Inform Assoc. 2017 Mar 1;24(2):398-402. doi: 10.1093/jamia/ocw079.

41.

Comparative Effectiveness of Infliximab and Adalimumab in Crohn's Disease and Ulcerative Colitis.

Ananthakrishnan AN, Cagan A, Cai T, Gainer VS, Shaw SY, Savova G, Churchill S, Karlson EW, Kohane I, Liao KP, Murphy SN.

Inflamm Bowel Dis. 2016 Apr;22(4):880-5. doi: 10.1097/MIB.0000000000000754.

42.

The Biobank Portal for Partners Personalized Medicine: A Query Tool for Working with Consented Biobank Samples, Genotypes, and Phenotypes Using i2b2.

Gainer VS, Cagan A, Castro VM, Duey S, Ghosh B, Goodson AP, Goryachev S, Metta R, Wang TD, Wattanasin N, Murphy SN.

J Pers Med. 2016 Feb 26;6(1). pii: E11. doi: 10.3390/jpm6010011.

43.

Data interchange using i2b2.

Klann JG, Abend A, Raghavan VA, Mandl KD, Murphy SN.

J Am Med Inform Assoc. 2016 Sep;23(5):909-15. doi: 10.1093/jamia/ocv188. Epub 2016 Feb 5.

44.

Statin Use Is Associated With Reduced Risk of Colorectal Cancer in Patients With Inflammatory Bowel Diseases.

Ananthakrishnan AN, Cagan A, Cai T, Gainer VS, Shaw SY, Churchill S, Karlson EW, Murphy SN, Liao KP, Kohane I.

Clin Gastroenterol Hepatol. 2016 Jul;14(7):973-9. doi: 10.1016/j.cgh.2016.02.017. Epub 2016 Feb 22.

45.

An eMERGE Clinical Center at Partners Personalized Medicine.

Smoller JW, Karlson EW, Green RC, Kathiresan S, MacArthur DG, Talkowski ME, Murphy SN, Weiss ST.

J Pers Med. 2016 Jan 20;6(1). pii: E5. doi: 10.3390/jpm6010005.

46.

A numerical similarity approach for using retired Current Procedural Terminology (CPT) codes for electronic phenotyping in the Scalable Collaborative Infrastructure for a Learning Health System (SCILHS).

Klann JG, Phillips LC, Turchin A, Weiler S, Mandl KD, Murphy SN.

BMC Med Inform Decis Mak. 2015 Dec 11;15:104. doi: 10.1186/s12911-015-0223-x.

47.

Identification of subjects with polycystic ovary syndrome using electronic health records.

Castro V, Shen Y, Yu S, Finan S, Pau CT, Gainer V, Keefe CC, Savova G, Murphy SN, Cai T, Welt CK.

Reprod Biol Endocrinol. 2015 Oct 29;13:116. doi: 10.1186/s12958-015-0115-z.

48.

Identification of Nonresponse to Treatment Using Narrative Data in an Electronic Health Record Inflammatory Bowel Disease Cohort.

Ananthakrishnan AN, Cagan A, Cai T, Gainer VS, Shaw SY, Savova G, Churchill S, Karlson EW, Murphy SN, Liao KP, Kohane I.

Inflamm Bowel Dis. 2016 Jan;22(1):151-8. doi: 10.1097/MIB.0000000000000580.

49.

Methods to Develop an Electronic Medical Record Phenotype Algorithm to Compare the Risk of Coronary Artery Disease across 3 Chronic Disease Cohorts.

Liao KP, Ananthakrishnan AN, Kumar V, Xia Z, Cagan A, Gainer VS, Goryachev S, Chen P, Savova GK, Agniel D, Churchill S, Lee J, Murphy SN, Plenge RM, Szolovits P, Kohane I, Shaw SY, Karlson EW, Cai T.

PLoS One. 2015 Aug 24;10(8):e0136651. doi: 10.1371/journal.pone.0136651. eCollection 2015.

50.

Brain extraction in pediatric ADC maps, toward characterizing neuro-development in multi-platform and multi-institution clinical images.

Ou Y, Gollub RL, Retzepi K, Reynolds N, Pienaar R, Pieper S, Murphy SN, Grant PE, Zöllei L.

Neuroimage. 2015 Nov 15;122:246-61. doi: 10.1016/j.neuroimage.2015.08.002. Epub 2015 Aug 7.

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