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profileShawn Norman Murphy, M.D., Ph.D.

TitleAssociate Professor of Neurology
InstitutionMassachusetts General Hospital
DepartmentNeurology
AddressPartners HealthCare System, Inc
Research Computing
One Constitution Center 299
Charlestown MA 02129
Phone617/724-7980
Fax617/726-8481
vCardDownload vCard (login for email)
Other Positions
TitleAssociate Professor of Biomedical Informatics
InstitutionHarvard Medical School
DepartmentBiomedical Informatics


Collapse Research 
Collapse research activities and funding
The research activities and funding listed below are automatically derived from NIH ExPORTER and other sources, which might result in incorrect or missing items. Faculty can login to make corrections and additions.
R01HG009174     (MURPHY, SHAWN N)Sep 28, 2016 - Aug 31, 2020
NIH/NHGRI
Developing i2b2 into a Health Innovation Platform for Clinical Decision Support in the Genomics Era
Role: Co-Principal Investigator

OT2OD024612     (SMOLLER, JORDAN W)Sep 27, 2016 - Aug 31, 2017
NIH
A New England Enrollment Center for PMI Cohort Program
Role: Co-Principal Investigator

U01HG008685     (KARLSON, ELIZABETH W)Sep 1, 2015 - May 31, 2019
NIH/NHGRI
EMERGE PHASE III CLINICAL CENTER AT PARTNERS HEALTHCARE
Role: Co-Principal Investigator

U54HG007963     (KOHANE, ISAAC S.)Sep 29, 2014 - Aug 31, 2018
NIH/NHGRI
Patient-Centered Information Commons
Role: Co-Principal Investigator

R01EB014947     (MURPHY, SHAWN N)Aug 1, 2012 - Jul 31, 2016
NIH/NIBIB
mi2b2 Enabled Pediatric Radiological Decision Support
Role: Co-Principal Investigator

Collapse Bibliographic 
Collapse selected publications
Publications listed below are automatically derived from MEDLINE/PubMed and other sources, which might result in incorrect or missing publications. Faculty can login to make corrections and additions.
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  1. Murphy SN, Avillach P, Bellazzi R, Phillips L, Gabetta M, Eran A, McDuffie MT, Kohane IS. Combining clinical and genomics queries using i2b2 - Three methods. PLoS One. 2017; 12(4):e0172187. PMID: 28388645.
    View in: PubMed
  2. Yu S, Chakrabortty A, Liao KP, Cai T, Ananthakrishnan AN, Gainer VS, Churchill SE, Szolovits P, Murphy SN, Kohane IS, Cai T. Surrogate-assisted feature extraction for high-throughput phenotyping. J Am Med Inform Assoc. 2017 Apr 01; 24(e1):e143-e149. PMID: 27632993.
    View in: PubMed
  3. Ou Y, Zöllei L, Retzepi K, Castro V, Bates SV, Pieper S, Andriole KP, Murphy SN, Gollub RL, Grant PE. Using clinically acquired MRI to construct age-specific ADC atlases: Quantifying spatiotemporal ADC changes from birth to 6-year old. Hum Brain Mapp. 2017 Jun; 38(6):3052-3068. PMID: 28371107.
    View in: PubMed
  4. Wagholikar KB, Mandel JC, Klann JG, Wattanasin N, Mendis M, Chute CG, Mandl KD, Murphy SN. SMART-on-FHIR implemented over i2b2. J Am Med Inform Assoc. 2017 Mar 01; 24(2):398-402. PMID: 27274012.
    View in: PubMed
  5. Ananthakrishnan AN, Cagan A, Cai T, Gainer VS, Shaw SY, Savova G, Churchill S, Karlson EW, Kohane I, Liao KP, Murphy SN. Comparative Effectiveness of Infliximab and Adalimumab in Crohn's Disease and Ulcerative Colitis. Inflamm Bowel Dis. 2016 Apr; 22(4):880-5. PMID: 26933751; PMCID: PMC4792716 [Available on 04/01/17].
  6. Gainer VS, Cagan A, Castro VM, Duey S, Ghosh B, Goodson AP, Goryachev S, Metta R, Wang TD, Wattanasin N, Murphy SN. The Biobank Portal for Partners Personalized Medicine: A Query Tool for Working with Consented Biobank Samples, Genotypes, and Phenotypes Using i2b2. J Pers Med. 2016 Feb 26; 6(1). PMID: 26927184; PMCID: PMC4810390.
  7. Ananthakrishnan AN, Cagan A, Cai T, Gainer VS, Shaw SY, Churchill S, Karlson EW, Murphy SN, Liao KP, Kohane I. Statin Use Is Associated With Reduced Risk of Colorectal Cancer in Patients With Inflammatory Bowel Diseases. Clin Gastroenterol Hepatol. 2016 Jul; 14(7):973-9. PMID: 26905907; PMCID: PMC4912917 [Available on 07/01/17].
  8. Klann JG, Abend A, Raghavan VA, Mandl KD, Murphy SN. Data interchange using i2b2. J Am Med Inform Assoc. 2016 Sep; 23(5):909-15. PMID: 26911824; PMCID: PMC4997035 [Available on 09/01/17].
  9. Smoller JW, Karlson EW, Green RC, Kathiresan S, MacArthur DG, Talkowski ME, Murphy SN, Weiss ST. An eMERGE Clinical Center at Partners Personalized Medicine. J Pers Med. 2016 Jan 20; 6(1). PMID: 26805891; PMCID: PMC4810384.
  10. Klann JG, Phillips LC, Turchin A, Weiler S, Mandl KD, Murphy SN. 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). BMC Med Inform Decis Mak. 2015 Dec 11; 15:104. PMID: 26655696.
    View in: PubMed
  11. Klann JG, Pfiffner PB, Natter MD, Conner E, Blazejewski P, Murphy SN, Mandl KD. Supporting Multi-sourced Medication Information in i2b2. AMIA Annu Symp Proc. 2015; 2015:747-55. PMID: 26958210; PMCID: PMC4765563.
  12. Ananthakrishnan AN, Cagan A, Cai T, Gainer VS, Shaw SY, Churchill S, Karlson EW, Murphy SN, Kohane I, Liao KP, Xavier RJ. Common Genetic Variants Influence Circulating Vitamin D Levels in Inflammatory Bowel Diseases. Inflamm Bowel Dis. 2015 Nov; 21(11):2507-14. PMID: 26241000; PMCID: PMC4615315 [Available on 11/01/16].
  13. Castro V, Shen Y, Yu S, Finan S, Pau CT, Gainer V, Keefe CC, Savova G, Murphy SN, Cai T, Welt CK. Identification of subjects with polycystic ovary syndrome using electronic health records. Reprod Biol Endocrinol. 2015 Oct 29; 13:116. PMID: 26510685; PMCID: PMC4625743.
  14. 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. Methods to Develop an Electronic Medical Record Phenotype Algorithm to Compare the Risk of Coronary Artery Disease across 3 Chronic Disease Cohorts. PLoS One. 2015; 10(8):e0136651. PMID: 26301417; PMCID: PMC4547801.
  15. Ou Y, Gollub RL, Retzepi K, Reynolds N, Pienaar R, Pieper S, Murphy SN, Grant PE, Zöllei L. Brain extraction in pediatric ADC maps, toward characterizing neuro-development in multi-platform and multi-institution clinical images. Neuroimage. 2015 Nov 15; 122:246-61. PMID: 26260429; PMCID: PMC4966541 [Available on 11/15/16].
  16. Yu S, Liao KP, Shaw SY, Gainer VS, Churchill SE, Szolovits P, Murphy SN, Kohane IS, Cai T. Toward high-throughput phenotyping: unbiased automated feature extraction and selection from knowledge sources. J Am Med Inform Assoc. 2015 Sep; 22(5):993-1000. PMID: 25929596; PMCID: PMC4986664.
  17. Liao KP, Cai T, Savova GK, Murphy SN, Karlson EW, Ananthakrishnan AN, Gainer VS, Shaw SY, Xia Z, Szolovits P, Churchill S, Kohane I. Development of phenotype algorithms using electronic medical records and incorporating natural language processing. BMJ. 2015 Apr 24; 350:h1885. PMID: 25911572; PMCID: PMC4707569.
  18. Ananthakrishnan AN, Cagan A, Cai T, Gainer VS, Shaw SY, Churchill S, Karlson EW, Murphy SN, Kohane I, Liao KP. Diabetes and the risk of infections with immunomodulator therapy in inflammatory bowel diseases. Aliment Pharmacol Ther. 2015 Jun; 41(11):1141-8. PMID: 25864945; PMCID: PMC4420684.
  19. Diogo D, Bastarache L, Liao KP, Graham RR, Fulton RS, Greenberg JD, Eyre S, Bowes J, Cui J, Lee A, Pappas DA, Kremer JM, Barton A, Coenen MJ, Franke B, Kiemeney LA, Mariette X, Richard-Miceli C, Canhão H, Fonseca JE, de Vries N, Tak PP, Crusius JB, Nurmohamed MT, Kurreeman F, Mikuls TR, Okada Y, Stahl EA, Larson DE, Deluca TL, O'Laughlin M, Fronick CC, Fulton LL, Kosoy R, Ransom M, Bhangale TR, Ortmann W, Cagan A, Gainer V, Karlson EW, Kohane I, Murphy SN, Martin J, Zhernakova A, Klareskog L, Padyukov L, Worthington J, Mardis ER, Seldin MF, Gregersen PK, Behrens T, Raychaudhuri S, Denny JC, Plenge RM. TYK2 protein-coding variants protect against rheumatoid arthritis and autoimmunity, with no evidence of major pleiotropic effects on non-autoimmune complex traits. PLoS One. 2015; 10(4):e0122271. PMID: 25849893; PMCID: PMC4388675.
  20. Murphy SN, Herrick C, Wang Y, Wang TD, Sack D, Andriole KP, Wei J, Reynolds N, Plesniak W, Rosen BR, Pieper S, Gollub RL. High throughput tools to access images from clinical archives for research. J Digit Imaging. 2015 Apr; 28(2):194-204. PMID: 25316195; PMCID: PMC4359193.
  21. Castro VM, Minnier J, Murphy SN, Kohane I, Churchill SE, Gainer V, Cai T, Hoffnagle AG, Dai Y, Block S, Weill SR, Nadal-Vicens M, Pollastri AR, Rosenquist JN, Goryachev S, Ongur D, Sklar P, Perlis RH, Smoller JW. Validation of electronic health record phenotyping of bipolar disorder cases and controls. Am J Psychiatry. 2015 Apr; 172(4):363-72. PMID: 25827034; PMCID: PMC4441333.
  22. Klann JG, Mendis M, Phillips LC, Goodson AP, Rocha BH, Goldberg HS, Wattanasin N, Murphy SN. Taking advantage of continuity of care documents to populate a research repository. J Am Med Inform Assoc. 2015 Mar; 22(2):370-9. PMID: 25352566.
    View in: PubMed
  23. Castro VM, McCoy TH, Cagan A, Rosenfield HR, Murphy SN, Churchill SE, Kohane IS, Perlis RH. Stratification of risk for hospital admissions for injury related to fall: cohort study. BMJ. 2014 Oct 24; 349:g5863. PMID: 25954985; PMCID: PMC4208628.
  24. Ananthakrishnan AN, Cheng A, Cagan A, Cai T, Gainer VS, Shaw SY, Churchill S, Karlson EW, Murphy SN, Kohane I, Liao KP. Mode of childbirth and long-term outcomes in women with inflammatory bowel diseases. Dig Dis Sci. 2015 Feb; 60(2):471-7. PMID: 25213079; PMCID: PMC4304947.
  25. Murphy S, Wilcox A. Mission and Sustainability of Informatics for Integrating Biology and the Bedside (i2b2). EGEMS (Wash DC). 2014; 2(2):1074. PMID: 25848608; PMCID: PMC4371505.
  26. Castro VM, Apperson WK, Gainer VS, Ananthakrishnan AN, Goodson AP, Wang TD, Herrick CD, Murphy SN. Evaluation of matched control algorithms in EHR-based phenotyping studies: a case study of inflammatory bowel disease comorbidities. J Biomed Inform. 2014 Dec; 52:105-11. PMID: 25196084; PMCID: PMC4261034.
  27. Clements CC, Castro VM, Blumenthal SR, Rosenfield HR, Murphy SN, Fava M, Erb JL, Churchill SE, Kaimal AJ, Doyle AE, Robinson EB, Smoller JW, Kohane IS, Perlis RH. Prenatal antidepressant exposure is associated with risk for attention-deficit hyperactivity disorder but not autism spectrum disorder in a large health system. Mol Psychiatry. 2015 Jun; 20(6):727-34. PMID: 25155880; PMCID: PMC4427538.
  28. Blumenthal SR, Castro VM, Clements CC, Rosenfield HR, Murphy SN, Fava M, Weilburg JB, Erb JL, Churchill SE, Kohane IS, Smoller JW, Perlis RH. An electronic health records study of long-term weight gain following antidepressant use. JAMA Psychiatry. 2014 Aug; 71(8):889-96. PMID: 24898363.
    View in: PubMed
  29. Sinnott JA, Dai W, Liao KP, Shaw SY, Ananthakrishnan AN, Gainer VS, Karlson EW, Churchill S, Szolovits P, Murphy S, Kohane I, Plenge R, Cai T. Improving the power of genetic association tests with imperfect phenotype derived from electronic medical records. Hum Genet. 2014 Nov; 133(11):1369-82. PMID: 25062868; PMCID: PMC4185241.
  30. Ananthakrishnan AN, Cagan A, Cai T, Gainer VS, Shaw SY, Churchill S, Karlson EW, Murphy SN, Kohane I, Liao KP. Colonoscopy is associated with a reduced risk for colon cancer and mortality in patients with inflammatory bowel diseases. Clin Gastroenterol Hepatol. 2015 Feb; 13(2):322-329.e1. PMID: 25041865; PMCID: PMC4297589.
  31. Mandl KD, Kohane IS, McFadden D, Weber GM, Natter M, Mandel J, Schneeweiss S, Weiler S, Klann JG, Bickel J, Adams WG, Ge Y, Zhou X, Perkins J, Marsolo K, Bernstam E, Showalter J, Quarshie A, Ofili E, Hripcsak G, Murphy SN. Scalable Collaborative Infrastructure for a Learning Healthcare System (SCILHS): architecture. J Am Med Inform Assoc. 2014 Jul-Aug; 21(4):615-20. PMID: 24821734; PMCID: PMC4078286.
  32. Klann JG, Buck MD, Brown J, Hadley M, Elmore R, Weber GM, Murphy SN. Query Health: standards-based, cross-platform population health surveillance. J Am Med Inform Assoc. 2014 Jul-Aug; 21(4):650-6. PMID: 24699371; PMCID: PMC4078284.
  33. Ananthakrishnan AN, Cagan A, Gainer VS, Cheng SC, Cai T, Szolovits P, Shaw SY, Churchill S, Karlson EW, Murphy SN, Kohane I, Liao KP. Higher plasma vitamin D is associated with reduced risk of Clostridium difficile infection in patients with inflammatory bowel diseases. Aliment Pharmacol Ther. 2014 May; 39(10):1136-42. PMID: 24641590; PMCID: PMC4187206.
  34. Ananthakrishnan AN, Cagan A, Gainer VS, Cheng SC, Cai T, Scoville E, Konijeti GG, Szolovits P, Shaw SY, Churchill S, Karlson EW, Murphy SN, Kohane I, Liao KP. Thromboprophylaxis is associated with reduced post-hospitalization venous thromboembolic events in patients with inflammatory bowel diseases. Clin Gastroenterol Hepatol. 2014 Nov; 12(11):1905-10. PMID: 24632349; PMCID: PMC4162859.
  35. Ananthakrishnan AN, Cagan A, Gainer VS, Cheng SC, Cai T, Szolovits P, Shaw SY, Churchill S, Karlson EW, Murphy SN, Kohane I, Liao KP. Mortality and extraintestinal cancers in patients with primary sclerosing cholangitis and inflammatory bowel disease. J Crohns Colitis. 2014 Sep; 8(9):956-63. PMID: 24559536; PMCID: PMC4136996.
  36. O'Dushlaine C, Ripke S, Ruderfer DM, Hamilton SP, Fava M, Iosifescu DV, Kohane IS, Churchill SE, Castro VM, Clements CC, Blumenthal SR, Murphy SN, Smoller JW, Perlis RH. Rare copy number variation in treatment-resistant major depressive disorder. Biol Psychiatry. 2014 Oct 01; 76(7):536-41. PMID: 24529801; PMCID: PMC4104153.
  37. Ananthakrishnan AN, Cheng SC, Cai T, Cagan A, Gainer VS, Szolovits P, Shaw SY, Churchill S, Karlson EW, Murphy SN, Kohane I, Liao KP. Serum inflammatory markers and risk of colorectal cancer in patients with inflammatory bowel diseases. Clin Gastroenterol Hepatol. 2014 Aug; 12(8):1342-8.e1. PMID: 24407106; PMCID: PMC4085150.
  38. Liao KP, Cai T, Gainer VS, Cagan A, Murphy SN, Liu C, Churchill S, Shaw SY, Kohane I, Solomon DH, Plenge RM, Karlson EW. Lipid and lipoprotein levels and trend in rheumatoid arthritis compared to the general population. Arthritis Care Res (Hoboken). 2013 Dec; 65(12):2046-50. PMID: 23925980; PMCID: PMC4060244.
  39. Xia Z, Secor E, Chibnik LB, Bove RM, Cheng S, Chitnis T, Cagan A, Gainer VS, Chen PJ, Liao KP, Shaw SY, Ananthakrishnan AN, Szolovits P, Weiner HL, Karlson EW, Murphy SN, Savova GK, Cai T, Churchill SE, Plenge RM, Kohane IS, De Jager PL. Modeling disease severity in multiple sclerosis using electronic health records. PLoS One. 2013; 8(11):e78927. PMID: 24244385; PMCID: PMC3823928.
  40. Hripcsak G, Bloomrosen M, FlatelyBrennan P, Chute CG, Cimino J, Detmer DE, Edmunds M, Embi PJ, Goldstein MM, Hammond WE, Keenan GM, Labkoff S, Murphy S, Safran C, Speedie S, Strasberg H, Temple F, Wilcox AB. Health data use, stewardship, and governance: ongoing gaps and challenges: a report from AMIA's 2012 Health Policy Meeting. J Am Med Inform Assoc. 2014 Mar-Apr; 21(2):204-11. PMID: 24169275; PMCID: PMC3932468.
  41. Ananthakrishnan AN, Cheng SC, Cai T, Cagan A, Gainer VS, Szolovits P, Shaw SY, Churchill S, Karlson EW, Murphy SN, Kohane I, Liao KP. Association between reduced plasma 25-hydroxy vitamin D and increased risk of cancer in patients with inflammatory bowel diseases. Clin Gastroenterol Hepatol. 2014 May; 12(5):821-7. PMID: 24161349; PMCID: PMC3995841.
  42. Ananthakrishnan AN, Cagan A, Gainer VS, Cai T, Cheng SC, Savova G, Chen P, Szolovits P, Xia Z, De Jager PL, Shaw SY, Churchill S, Karlson EW, Kohane I, Plenge RM, Murphy SN, Liao KP. Normalization of plasma 25-hydroxy vitamin D is associated with reduced risk of surgery in Crohn's disease. Inflamm Bowel Dis. 2013 Aug; 19(9):1921-7. PMID: 23751398; PMCID: PMC3720838.
  43. Ananthakrishnan AN, Cai T, Savova G, Cheng SC, Chen P, Perez RG, Gainer VS, Murphy SN, Szolovits P, Xia Z, Shaw S, Churchill S, Karlson EW, Kohane I, Plenge RM, Liao KP. Improving case definition of Crohn's disease and ulcerative colitis in electronic medical records using natural language processing: a novel informatics approach. Inflamm Bowel Dis. 2013 Jun; 19(7):1411-20. PMID: 23567779; PMCID: PMC3665760.
  44. Klann JG, McCoy AB, Wright A, Wattanasin N, Sittig DF, Murphy SN. Health care transformation through collaboration on open-source informatics projects: integrating a medical applications platform, research data repository, and patient summarization. Interact J Med Res. 2013 May 30; 2(1):e11. PMID: 23722634; PMCID: PMC3668611.
  45. Liao KP, Diogo D, Cui J, Cai T, Okada Y, Gainer VS, Murphy SN, Gupta N, Mirel D, Ananthakrishnan AN, Szolovits P, Shaw SY, Raychaudhuri S, Churchill S, Kohane I, Karlson EW, Plenge RM. Association between low density lipoprotein and rheumatoid arthritis genetic factors with low density lipoprotein levels in rheumatoid arthritis and non-rheumatoid arthritis controls. Ann Rheum Dis. 2014 Jun; 73(6):1170-5. PMID: 23716066; PMCID: PMC3815491.
  46. Klann JG, Murphy SN. Computing health quality measures using Informatics for Integrating Biology and the Bedside. J Med Internet Res. 2013 Apr 19; 15(4):e75. PMID: 23603227; PMCID: PMC3636801.
  47. Klann JG, Murphy SN. Supporting the Health Quality Measures Format in i2b2. AMIA Jt Summits Transl Sci Proc. 2013; 2013:124. PMID: 24303250.
    View in: PubMed
  48. McMurry AJ, Murphy SN, MacFadden D, Weber G, Simons WW, Orechia J, Bickel J, Wattanasin N, Gilbert C, Trevvett P, Churchill S, Kohane IS. SHRINE: enabling nationally scalable multi-site disease studies. PLoS One. 2013; 8(3):e55811. PMID: 23533569; PMCID: PMC3591385.
  49. Liao KP, Kurreeman F, Li G, Duclos G, Murphy S, Guzman R, Cai T, Gupta N, Gainer V, Schur P, Cui J, Denny JC, Szolovits P, Churchill S, Kohane I, Karlson EW, Plenge RM. Associations of autoantibodies, autoimmune risk alleles, and clinical diagnoses from the electronic medical records in rheumatoid arthritis cases and non-rheumatoid arthritis controls. Arthritis Rheum. 2013 Mar; 65(3):571-81. PMID: 23233247; PMCID: PMC3582761.
  50. Castro VM, Clements CC, Murphy SN, Gainer VS, Fava M, Weilburg JB, Erb JL, Churchill SE, Kohane IS, Iosifescu DV, Smoller JW, Perlis RH. QT interval and antidepressant use: a cross sectional study of electronic health records. BMJ. 2013 Jan 29; 346:f288. PMID: 23360890; PMCID: PMC3558546.
  51. Ananthakrishnan AN, Gainer VS, Cai T, Perez RG, Cheng SC, Savova G, Chen P, Szolovits P, Xia Z, De Jager PL, Shaw S, Churchill S, Karlson EW, Kohane I, Perlis RH, Plenge RM, Murphy SN, Liao KP. Similar risk of depression and anxiety following surgery or hospitalization for Crohn's disease and ulcerative colitis. Am J Gastroenterol. 2013 Apr; 108(4):594-601. PMID: 23337479; PMCID: PMC3627544.
  52. Ananthakrishnan AN, Gainer VS, Perez RG, Cai T, Cheng SC, Savova G, Chen P, Szolovits P, Xia Z, De Jager PL, Shaw SY, Churchill S, Karlson EW, Kohane I, Perlis RH, Plenge RM, Murphy SN, Liao KP. Psychiatric co-morbidity is associated with increased risk of surgery in Crohn's disease. Aliment Pharmacol Ther. 2013 Feb; 37(4):445-54. PMID: 23289600; PMCID: PMC3552092.
  53. Hoogenboom WS, Perlis RH, Smoller JW, Zeng-Treitler Q, Gainer VS, Murphy SN, Churchill SE, Kohane IS, Shenton ME, Iosifescu DV. Feasibility of studying brain morphology in major depressive disorder with structural magnetic resonance imaging and clinical data from the electronic medical record: a pilot study. Psychiatry Res. 2013 Mar 30; 211(3):202-13. PMID: 23149041; PMCID: PMC3574623.
  54. Wattanasin N, Porter A, Ubaha S, Mendis M, Phillips L, Mandel J, Ramoni R, Mandl K, Kohane I, Murphy SN. Apps to display patient data, making SMART available in the i2b2 platform. AMIA Annu Symp Proc. 2012; 2012:960-9. PMID: 23304371; PMCID: PMC3540423.
  55. Gallagher PJ, Castro V, Fava M, Weilburg JB, Murphy SN, Gainer VS, Churchill SE, Kohane IS, Iosifescu DV, Smoller JW, Perlis RH. Antidepressant response in patients with major depression exposed to NSAIDs: a pharmacovigilance study. Am J Psychiatry. 2012 Oct; 169(10):1065-72. PMID: 23032386; PMCID: PMC3787520.
  56. Sittig DF, Hazlehurst BL, Brown J, Murphy S, Rosenman M, Tarczy-Hornoch P, Wilcox AB. A survey of informatics platforms that enable distributed comparative effectiveness research using multi-institutional heterogenous clinical data. Med Care. 2012 Jul; 50 Suppl:S49-59. PMID: 22692259; PMCID: PMC3415281.
  57. Hoogenboom WS, Perlis RH, Smoller JW, Zeng-Treitler Q, Gainer VS, Murphy SN, Churchill SE, Kohane IS, Shenton ME, Iosifescu DV. Limbic system white matter microstructure and long-term treatment outcome in major depressive disorder: a diffusion tensor imaging study using legacy data. World J Biol Psychiatry. 2014 Feb; 15(2):122-34. PMID: 22540406.
    View in: PubMed
  58. Kohane IS, McMurry A, Weber G, MacFadden D, Rappaport L, Kunkel L, Bickel J, Wattanasin N, Spence S, Murphy S, Churchill S. The co-morbidity burden of children and young adults with autism spectrum disorders. PLoS One. 2012; 7(4):e33224. PMID: 22511918; PMCID: PMC3325235.
  59. Ripke S, Wray NR, Lewis CM, Hamilton SP, Weissman MM, Breen G, Byrne EM, Blackwood DH, Boomsma DI, Cichon S, Heath AC, Holsboer F, Lucae S, Madden PA, Martin NG, McGuffin P, Muglia P, Noethen MM, Penninx BP, Pergadia ML, Potash JB, Rietschel M, Lin D, Müller-Myhsok B, Shi J, Steinberg S, Grabe HJ, Lichtenstein P, Magnusson P, Perlis RH, Preisig M, Smoller JW, Stefansson K, Uher R, Kutalik Z, Tansey KE, Teumer A, Viktorin A, Barnes MR, Bettecken T, Binder EB, Breuer R, Castro VM, Churchill SE, Coryell WH, Craddock N, Craig IW, Czamara D, De Geus EJ, Degenhardt F, Farmer AE, Fava M, Frank J, Gainer VS, Gallagher PJ, Gordon SD, Goryachev S, Gross M, Guipponi M, Henders AK, Herms S, Hickie IB, Hoefels S, Hoogendijk W, Hottenga JJ, Iosifescu DV, Ising M, Jones I, Jones L, Jung-Ying T, Knowles JA, Kohane IS, Kohli MA, Korszun A, Landen M, Lawson WB, Lewis G, Macintyre D, Maier W, Mattheisen M, McGrath PJ, McIntosh A, McLean A, Middeldorp CM, Middleton L, Montgomery GM, Murphy SN, Nauck M, Nolen WA, Nyholt DR, O'Donovan M, Oskarsson H, Pedersen N, Scheftner WA, Schulz A, Schulze TG, Shyn SI, Sigurdsson E, Slager SL, Smit JH, Stefansson H, Steffens M, Thorgeirsson T, Tozzi F, Treutlein J, Uhr M, van den Oord EJ, Van Grootheest G, Völzke H, Weilburg JB, Willemsen G, Zitman FG, Neale B, Daly M, Levinson DF, Sullivan PF. A mega-analysis of genome-wide association studies for major depressive disorder. Mol Psychiatry. 2013 Apr; 18(4):497-511. PMID: 22472876; PMCID: PMC3837431.
  60. Castro VM, Gallagher PJ, Clements CC, Murphy SN, Gainer VS, Fava M, Weilburg JB, Churchill SE, Kohane IS, Iosifescu DV, Smoller JW, Perlis RH. Incident user cohort study of risk for gastrointestinal bleed and stroke in individuals with major depressive disorder treated with antidepressants. BMJ Open. 2012; 2(2):e000544. PMID: 22466034; PMCID: PMC3330255.
  61. Mandl KD, Mandel JC, Murphy SN, Bernstam EV, Ramoni RL, Kreda DA, McCoy JM, Adida B, Kohane IS. The SMART Platform: early experience enabling substitutable applications for electronic health records. J Am Med Inform Assoc. 2012 Jul-Aug; 19(4):597-603. PMID: 22427539; PMCID: PMC3384120.
  62. Carroll RJ, Thompson WK, Eyler AE, Mandelin AM, Cai T, Zink RM, Pacheco JA, Boomershine CS, Lasko TA, Xu H, Karlson EW, Perez RG, Gainer VS, Murphy SN, Ruderman EM, Pope RM, Plenge RM, Kho AN, Liao KP, Denny JC. Portability of an algorithm to identify rheumatoid arthritis in electronic health records. J Am Med Inform Assoc. 2012 Jun; 19(e1):e162-9. PMID: 22374935; PMCID: PMC3392871.
  63. Murphy SN, Dubey A, Embi PJ, Harris PA, Richter BG, Turisco F, Weber GM, Tcheng JE, Keogh D. Current state of information technologies for the clinical research enterprise across academic medical centers. Clin Transl Sci. 2012 Jun; 5(3):281-4. PMID: 22686207.
    View in: PubMed
  64. Ananthakrishnan AN, Guzman-Perez R, Gainer V, Cai T, Churchill S, Kohane I, Plenge RM, Murphy S. Predictors of severe outcomes associated with Clostridium difficile infection in patients with inflammatory bowel disease. Aliment Pharmacol Ther. 2012 Apr; 35(7):789-95. PMID: 22360370; PMCID: PMC3716251.
  65. Kohane IS, Churchill SE, Murphy SN. A translational engine at the national scale: informatics for integrating biology and the bedside. J Am Med Inform Assoc. 2012 Mar-Apr; 19(2):181-5. PMID: 22081225; PMCID: PMC3277623.
  66. Murphy SN, Gainer V, Mendis M, Churchill S, Kohane I. Strategies for maintaining patient privacy in i2b2. J Am Med Inform Assoc. 2011 Dec; 18 Suppl 1:i103-8. PMID: 21984588; PMCID: PMC3241166.
  67. Perlis RH, Iosifescu DV, Castro VM, Murphy SN, Gainer VS, Minnier J, Cai T, Goryachev S, Zeng Q, Gallagher PJ, Fava M, Weilburg JB, Churchill SE, Kohane IS, Smoller JW. Using electronic medical records to enable large-scale studies in psychiatry: treatment resistant depression as a model. Psychol Med. 2012 Jan; 42(1):41-50. PMID: 21682950; PMCID: PMC3837420.
  68. Tatonetti NP, Denny JC, Murphy SN, Fernald GH, Krishnan G, Castro V, Yue P, Tsao PS, Tsau PS, Kohane I, Roden DM, Altman RB. Detecting drug interactions from adverse-event reports: interaction between paroxetine and pravastatin increases blood glucose levels. Clin Pharmacol Ther. 2011 Jul; 90(1):133-42. PMID: 21613990; PMCID: PMC3216673.
  69. Kurreeman F, Liao K, Chibnik L, Hickey B, Stahl E, Gainer V, Li G, Bry L, Mahan S, Ardlie K, Thomson B, Szolovits P, Churchill S, Murphy SN, Cai T, Raychaudhuri S, Kohane I, Karlson E, Plenge RM. Genetic basis of autoantibody positive and negative rheumatoid arthritis risk in a multi-ethnic cohort derived from electronic health records. Am J Hum Genet. 2011 Jan 07; 88(1):57-69. PMID: 21211616; PMCID: PMC3014362.
  70. Turchin A, Shubina M, Murphy SN. I am Not Dead Yet: Identification of False-Positive Matches to Death Master File. AMIA Annu Symp Proc. 2010 Nov 13; 2010:807-11. PMID: 21347090; PMCID: PMC3041274.
  71. Liao KP, Cai T, Gainer V, Goryachev S, Zeng-treitler Q, Raychaudhuri S, Szolovits P, Churchill S, Murphy S, Kohane I, Karlson EW, Plenge RM. Electronic medical records for discovery research in rheumatoid arthritis. Arthritis Care Res (Hoboken). 2010 Aug; 62(8):1120-7. PMID: 20235204; PMCID: PMC3121049.
  72. Murphy SN, Weber G, Mendis M, Gainer V, Chueh HC, Churchill S, Kohane I. Serving the enterprise and beyond with informatics for integrating biology and the bedside (i2b2). J Am Med Inform Assoc. 2010 Mar-Apr; 17(2):124-30. PMID: 20190053; PMCID: PMC3000779.
  73. Brownstein JS, Murphy SN, Goldfine AB, Grant RW, Sordo M, Gainer V, Colecchi JA, Dubey A, Nathan DM, Glaser JP, Kohane IS. Rapid identification of myocardial infarction risk associated with diabetes medications using electronic medical records. Diabetes Care. 2010 Mar; 33(3):526-31. PMID: 20009093; PMCID: PMC2827502.
  74. Sordo, M., Ochoa, G., Murphy, S.N. A PSO/ACO approach to knowledge discovery in a pharmacovigilance context. Genetic and Evolutionary Computation Conference - GECCO. 2009; 2679-2684.
  75. Murphy S, Churchill S, Bry L, Chueh H, Weiss S, Lazarus R, Zeng Q, Dubey A, Gainer V, Mendis M, Glaser J, Kohane I. Instrumenting the health care enterprise for discovery research in the genomic era. Genome Res. 2009 Sep; 19(9):1675-81. PMID: 19602638; PMCID: PMC2752136.
  76. Weber GM, Murphy SN, McMurry AJ, Macfadden D, Nigrin DJ, Churchill S, Kohane IS. The Shared Health Research Information Network (SHRINE): a prototype federated query tool for clinical data repositories. J Am Med Inform Assoc. 2009 Sep-Oct; 16(5):624-30. PMID: 19567788; PMCID: PMC2744712.
  77. Wang, T., Plaisant, C., Quinn, A., Stanchak, R., Murphy, S.N., Shneiderman, B. Aligning temporal data by sentinel events: discovering patterns in electronic health records. ACM Computer-Human Interaction. 2008; 457-466.
  78. Mendis M, Phillips LC, Kuttan R, Pan W, Gainer V, Kohane I, Murphy SN. Integrating outside modules into the i2b2 architecture. AMIA Annu Symp Proc. 2008 Nov 06; 1054. PMID: 18999021.
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  79. Sordo M, Colecchi J, Dubey A, Dubey AK, Gainer V, Murphy SN. STROBE-based methodology for detection of adverse events across multiple communities. AMIA Annu Symp Proc. 2008 Nov 06; 1144. PMID: 18998965.
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  80. Dubey AK, Gainer V, Murphy SN. Simulated yields of prospective specimen collection from specific patient cohorts using retrospective data from a research patient data repository. AMIA Annu Symp Proc. 2008 Nov 06; 935. PMID: 18999309.
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  81. Scheufele EL, Scheufele EL, Dubey A, Dubey AK, Murphy SN. A study of the age attribute in a query tool for a clinical data warehouse. AMIA Annu Symp Proc. 2008 Nov 06; 1123. PMID: 18999019.
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  82. Wattanasin N, Peng Z, Raine C, Mitchell M, Wang C, Murphy SN. E-facts: business process management in clinical data repositories. AMIA Annu Symp Proc. 2008 Nov 06; 1170. PMID: 18999043.
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  83. Dinov ID, Rubin D, Lorensen W, Dugan J, Ma J, Murphy S, Kirschner B, Bug W, Sherman M, Floratos A, Kennedy D, Jagadish HV, Schmidt J, Athey B, Califano A, Musen M, Altman R, Kikinis R, Kohane I, Delp S, Parker DS, Toga AW. iTools: a framework for classification, categorization and integration of computational biology resources. PLoS One. 2008 May 28; 3(5):e2265. PMID: 18509477; PMCID: PMC2386255.
  84. Keator, D.B., Grethe, J.S., Marcus, D., Ozyurt, B., Gadde, S., Murphy, S.N., Pieper, S., Greve, D., Notestine, R., Bockholt, H.J., Papadopoulos, P. A national neuroimaging collaboratory enabled by The Biomedical Informatics Research Network (BIRN). IEEE Transactions on Information Technology in Biomedicine, Special Bio-Grid edition. 2007; 2(12):162-172.
  85. Weiner, M., Lymon, J., Murphy, S.N. Electronic health records: high-quality electronic data for higher-quality clinical research. Informatics in Primary Care. 2007; 2(15):121-127.
  86. Mendis M, Wattanasin N, Kuttan R, Pan W, Philips L, Hackett K, Gainer V, Chueh HC, Murphy S. Integration of Hive and cell software in the i2b2 architecture. AMIA Annu Symp Proc. 2007 Oct 11; 1048. PMID: 18694146.
    View in: PubMed
  87. Murphy SN, Mendis M, Hackett K, Kuttan R, Pan W, Phillips LC, Gainer V, Berkowicz D, Glaser JP, Kohane I, Chueh HC. Architecture of the open-source clinical research chart from Informatics for Integrating Biology and the Bedside. AMIA Annu Symp Proc. 2007 Oct 11; 548-52. PMID: 18693896; PMCID: PMC2655844.
  88. Gainer V, Hackett K, Mendis M, Kuttan R, Pan W, Phillips LC, Chueh HC, Murphy S. Using the i2b2 hive for clinical discovery: an example. AMIA Annu Symp Proc. 2007 Oct 11; 959. PMID: 18694059.
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  89. Dubey AK, Herrick C, Murphy SN. Mining for associations between categorical data items in a clinical data repository. AMIA Annu Symp Proc. 2007 Oct 11; 945. PMID: 18694045.
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  90. Frank NY, Kho AT, Schatton T, Murphy GF, Molloy MJ, Zhan Q, Ramoni MF, Frank MH, Kohane IS, Gussoni E. Regulation of myogenic progenitor proliferation in human fetal skeletal muscle by BMP4 and its antagonist Gremlin. J Cell Biol. 2006 Oct 09; 175(1):99-110. PMID: 17015616; PMCID: PMC2064502.
  91. Zeng QT, Goryachev S, Weiss S, Sordo M, Murphy SN, Lazarus R. Extracting principal diagnosis, co-morbidity and smoking status for asthma research: evaluation of a natural language processing system. BMC Med Inform Decis Mak. 2006 Jul 26; 6:30. PMID: 16872495; PMCID: PMC1553439.
  92. Hackett KL, Kohane IS, Chueh HC, Murphy SN. Mapping tool for maintaining vocabulary relationships. AMIA Annu Symp Proc. 2006; 939. PMID: 17238558; PMCID: PMC1839260.
  93. Murphy SN, Mendis ME, Berkowitz DA, Kohane I, Chueh HC. Integration of clinical and genetic data in the i2b2 architecture. AMIA Annu Symp Proc. 2006; 1040. PMID: 17238659; PMCID: PMC1839291.
  94. Nalichowski R, Keogh D, Chueh HC, Murphy SN. Calculating the benefits of a Research Patient Data Repository. AMIA Annu Symp Proc. 2006; 1044. PMID: 17238663; PMCID: PMC1839563.
  95. Murphy SN, Mendis ME, Grethe JS, Gollub RL, Kennedy D, Rosen BR. A web portal that enables collaborative use of advanced medical image processing and informatics tools through the Biomedical Informatics Research Network (BIRN). AMIA Annu Symp Proc. 2006; 579-83. PMID: 17238407; PMCID: PMC1839506.
  96. Chung J, Murphy S. Concept-value pair extraction from semi-structured clinical narrative: a case study using echocardiogram reports. AMIA Annu Symp Proc. 2005; 131-5. PMID: 16779016; PMCID: PMC1560613.
  97. Murphy SN, Gainer V, Chueh HC. A visual interface designed for novice users to find research patient cohorts in a large biomedical database. AMIA Annu Symp Proc. 2003; 489-93. PMID: 14728221; PMCID: PMC1480150.
  98. Murphy SN, Chueh HC. A security architecture for query tools used to access large biomedical databases. Proc AMIA Symp. 2002; 552-6. PMID: 12463885; PMCID: PMC2244204.
  99. Murphy SN, Barnett GO, Chueh HC. Visual query tool for finding patient cohorts from a clinical data warehouse of the partners HealthCare system Proc AMIA Symp. 2000; 1174. PMID: 11080028.
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  100. Murphy SN, Morgan MM, Barnett GO, Chueh HC. Optimizing healthcare research data warehouse design through past COSTAR query analysis. Proc AMIA Symp. 1999; 892-6. PMID: 10566489; PMCID: PMC2232518.
  101. Ohno-Machado L, Gennari JH, Murphy SN, Jain NL, Tu SW, Oliver DE, Pattison-Gordon E, Greenes RA, Shortliffe EH, Barnett GO. The guideline interchange format: a model for representing guidelines. J Am Med Inform Assoc. 1998 Jul-Aug; 5(4):357-72. PMID: 9670133; PMCID: PMC61313.
  102. Murphy SN, Ng T, Sittig DF, Barnett GO. Using web technology and Java mobile software agents to manage outside referrals. Proc AMIA Symp. 1998; 101-5. PMID: 9929190; PMCID: PMC2232210.
  103. Murphy, S.N., Rabanni, U., Barnett, G.O. Using software agents to maintain autonomous patient registries for clinical research. Journal of the American Informatics Association, Symposium Supplement. 1997; 71-75.
  104. DeEstrada, W.D., Murphy, S.N., Barnett, G.O. Puya: An added-value clinical note retrieval and display system. Journal of the American Informatics Association, Symposium Supplement, 1997. 1997; 509-513.
  105. Murphy SN, Barnett GO. Achieving automated narrative text interpretation using phrases in the electronic medical record. Proc AMIA Annu Fall Symp. 1996; 532-6. PMID: 8947723; PMCID: PMC2233147.
  106. van Wingerde FJ, Schindler J, Kilbridge P, Szolovits P, Safran C, Rind D, Murphy S, Barnett GO, Kohane IS. Using HL7 and the World Wide Web for unifying patient data from remote databases. Proc AMIA Annu Fall Symp. 1996; 643-7. PMID: 8947745; PMCID: PMC2233237.
  107. Kohane IS, van Wingerde FJ, Fackler JC, Cimino C, Kilbridge P, Murphy S, Chueh H, Rind D, Safran C, Barnett O, Szolovits P. Sharing electronic medical records across multiple heterogeneous and competing institutions. Proc AMIA Annu Fall Symp. 1996; 608-12. PMID: 8947738; PMCID: PMC2233175.
  108. Blotner M, Shangold GA, Lee EY, Murphy SN, Miller RJ. Nitrendipine and omega-conotoxin modulate gonadotropin release and gonadotrope [Ca2+]i. Mol Cell Endocrinol. 1990 Jul 09; 71(3):205-16. PMID: 2170211.
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  109. Murphy SN, Miller RJ. Two distinct quisqualate receptors regulate Ca2+ homeostasis in hippocampal neurons in vitro. Mol Pharmacol. 1989 May; 35(5):671-80. PMID: 2566904.
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  110. Murphy SN, Miller RJ. Regulation of Ca++ influx into striatal neurons by kainic acid. J Pharmacol Exp Ther. 1989 Apr; 249(1):184-93. PMID: 2565388.
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  111. Murphy SN, Miller RJ. A glutamate receptor regulates Ca2+ mobilization in hippocampal neurons. Proc Natl Acad Sci U S A. 1988 Nov; 85(22):8737-41. PMID: 2903505; PMCID: PMC282536.
  112. Shangold GA, Murphy SN, Miller RJ. Gonadotropin-releasing hormone-induced Ca2+ transients in single identified gonadotropes require both intracellular Ca2+ mobilization and Ca2+ influx. Proc Natl Acad Sci U S A. 1988 Sep; 85(17):6566-70. PMID: 3045819; PMCID: PMC282014.
  113. Murphy SN, Thayer SA, Miller RJ. The effects of excitatory amino acids on intracellular calcium in single mouse striatal neurons in vitro. J Neurosci. 1987 Dec; 7(12):4145-58. PMID: 3320284.
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  114. Reynolds IJ, Murphy SN, Miller RJ. 3H-labeled MK-801 binding to the excitatory amino acid receptor complex from rat brain is enhanced by glycine. Proc Natl Acad Sci U S A. 1987 Nov; 84(21):7744-8. PMID: 2823273; PMCID: PMC299377.
  115. Thayer SA, Murphy SN, Miller RJ. Widespread distribution of dihydropyridine-sensitive calcium channels in the central nervous system. Mol Pharmacol. 1986 Dec; 30(6):505-9. PMID: 2431262.
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  116. Winicur, D.H., Hardwick, J.L., Murphy, S.N. . Spectroscopic studies of the helium-acetylene flame. Combustion and Flame. 1983; 53:93-102.
  117. Miller JD, McKusick VA, Malvaux P, Temtamy S, Salinas C. The 3-M syndrome: a heritable low birthweight dwarfism. Birth Defects Orig Artic Ser. 1975; 11(5):39-47. PMID: 1218233.
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