Research IT publications

Authorship in peer reviewed journals

2018

  1. Higher Absolute Lymphocyte Counts Predict Lower Mortality from Early-Stage Triple-Negative Breast Cancer. Clinical cancer research : an official journal of the American Association for Cancer Research, Afghahi, A., Purington, N., Han, S. S., Desai, M., Pierson, E., Mathur, M. B., Seto, T., Thompson, C. A., Rigdon, J., Telli, M. L., Badve, S. S., Curtis, C., West, R. B., Horst, K., Gomez, S. L., Ford, J. M., Sledge, G. W., Kurian, A. W., Clinical cancer research : an official journal of the American Association for Cancer Research 2018, doi: 10.1158/1078-0432.CCR-17-1323. (link)
  2. Utilization and effectiveness of multimodal discharge analgesia for postoperative pain management, Desai, K., Carroll, I., Asch, S., Seto, T., McDonald, K. M., Curtin, C., Hernandez-Boussard, T., Journal of Surgical Research 2018; 228.
  3. Architecture and implementation of a clinical research data warehouse for prostate cancer, Seneviratne, M., Seto, T., Blayney, D. W., Brooks, J. D., Hernandez-Boussard, T., EGEMS, 2018.
  4. Changes in Prostate Specific Antigen Screening and Prostate Cancer Diagnosis After Guideline Changes The Journal of Urology, Magnani, C. J., Li, K., Seto, T., McDonald, K. M., Blayney, D. W., Brooks, J. D., Hernandez-Boussard, T., 2018; 199 (4)

2016-2017

  1. Regional right ventricular dysfunction in acute pulmonary embolism: relationship with clot burden and biomarker profile, Tuzovic M, Adigopula S, Amsallem M, Kobayashi Y, Kadoch M, Boulate D, Krishnan G, Liang D, Schnittger I, Fleischmann D, McConnell MV, Haddad F, Int J Cardiovasc Imaging. 2016 Mar;32(3):389-98. (link)
  2.  Secure cloud computing for genomic data, Datta S, Bettinger K, Snyder M, Nature Biotechnology, 2016; 34 (6): 588-91. (link
  3. Patient Outcomes when Housestaff Exceed 80 Hours per Week, Ouyang D, Chen JH, Krishnan G, Hom J, Witteles R, Chi J, Am J Med. 2016 Sep;129(9):993-999. (link)
  4. Use of Gene Expression Profiling and Chemotherapy in Early-Stage Breast Cancer: A Study of Linked Electronic Medical Records, Cancer Registry Data, and Genomic Data Across Two Health Care Systems., Afghahi A, Mathur M, Thompson CA, Mitani A, Rigdon J, Desai M, Yu PP, de Bruin MA, Seto T, Olson C, Kenkare P, Gomez SL, Das AK, Luft HS, Sledge GW Jr, Sing AP, Kurian AW, J Oncol Pract. 2016 Jun;12(6):e697-709. (link)
  5. Digital Health: Tracking Physiomes and Activity Using Wearable Biosensors Reveals Useful Health-Related Information, Li X, Dunn J, Salins D, Zhou G, Zhou W, Schüssler-Fiorenza Rose SM, Perelman D, Colbert E, Runge R, Rego S, Sonecha R, Datta S, McLaughlin T, Snyder MP, PLoS Biology, January 12, 2017, https://doi.org/10.1371/journal.pbio.2001402. (link)
  6. Ethnic disparities in progression to advanced liver disease and overall survival in patients with chronic hepatitis C: impact of a sustained virological response, Le AK, Zhao C, Hoang JK, Tran SA, Chang CY, Jin M, Nguyen NH, Yasukawa LA, Zhang JQ, Weber SC, Garcia G, Nguyen MH, Aliment Pharmacol Ther. 2017 Sep;46(6):605-616. (link)
  7. HCV HBV Co-Infection Disproportionately Worsens Cirrhosis, Hepatic Decompensation, and Hepatocellular Carcinoma Incidence in Non-Asians as Compared to Asians, Mairin Joseph-Talreja, Nguyen P, Zhao C, Le AK, Hoang J, Yasukawa LA, Weber SC, Nguyen MH, Gastroenterology, April 2017 Volume 152, Issue 5, Supplement 1, Pages S1163–S1164. (link)
  8. Cloud-based interactive analytics for terabytes of genomic variants data, Pan C., McInnes G, Deflaux N, Snyder MP, Bingham J,  Datta S,  Tsao PS, Bioinformatics, btx468, Jul 2017,  https://doi.org/10.1093/bioinformatics/btx468. (link)
  9. A natural language processing algorithm to measure quality prostate cancer care. Hernandez-Boussard T, Kourdis P, Dulal R, Ferrari M, Henry S, Seto T, McDonald K, Blayney DW, Brooks JD, Journal of Clinical Oncology 35, no. 8_suppl (March 2017) 232-232. (link)
  10. Synergistic drug combinations from electronic health records and gene expression, Low YS, Daugherty AC, Schroeder EA, Chen W, Seto T, Weber S, Lim M, Hastie T, Mathur M, Desai M, Farrington C, Radin AA, Sirota M, Kenkare P, Thompson CA, Yu PP, Gomez SL, Sledge GW Jr, Kurian AW, Shah NH, J Am Med Inform Assoc. 2017 May 1;24(3):565-576. doi: 10.1093/jamia/ocw161. (Link)
  11. Validation of the Alliance Sleep Questionnaire (ASQ) Obstructive Sleep Apnea (OSA) Module in Sleep Disordered Patients. Leary EB, Malunjkar S, Ruoff CM, Cheung J, Schneider L, Walsh JK, Mignot E. Sleep, June 2016, Vol. 39 (Abstract suppl.) 

2014-2015

  1. Cohort Discovery Query Optimization via Computable Controlled Vocabulary Versioning, Ferris TA, Podchiyska T, Stud Health Technol Inform. 2015;216:1084. (link)
  2. Sequence to Medical Phenotypes: A Framework for Interpretation of Human Whole Genome DNA Sequence Data, Dewey FE, Grove ME, Priest JR, Waggott D, Batra P, Miller CL, Wheeler, M, Zia A, Pan C, Karzcewski KJ, Miyake C, Whirl-Carrillo M, Klein TE, Datta S, Altman RB, Snyder MP, Quertermous T, Ashley EA, PLOS GENETICS, 2015; 11 (10). (link)
  3. Chromosomal copy number alterations for associations of ductal carcinoma in situ with invasive breast cancer., Afghahi A, Forgó E, Mitani AA, Desai M, Varma S, Seto T, Rigdon J, Jensen KC, Troxell ML, Gomez SL, Das AK, Beck AH, Kurian AW, West RB, Breast Cancer Res. 2015 Aug 13;17:108. doi: 10.1186/s13058-015-0623-y. (Link)
  4. Validation of the Alliance Sleep Questionnaire (ASQ) Narcolepsy Module in Sleep Disordered Patients. Leary EB, Einen M, Malunjkar S, Ruoff CM, Walsh JK, Mignot E, Sleep, June 2014, Vol. 37 (Abstract suppl.) p. A360, #1026.
  5. Validation of the Alliance Sleep Questionnaire (ASQ) Restless Legs Syndrome Module in Sleep Disordered Patients, Leary EB, Malunjkar S, Ruoff CM, Walsh JK, Mignot E, Sleep, June 2015, Vol. 38 (Abstract suppl.) A432, #1219

2012-2013

  1. A simple heuristic for blindfolded record linkage., Weber SC, Lowe HJ, Das A, Ferris TA, J Am Med Inform Assoc. 2012 Jun;19(e1):e157-61. (link)
  2. Discordant aPTT and anti-Xa values and outcomes in hospitalized patients treated with intravenous unfractionated heparin, Price EA, Jin J, Nguyen HM, Krishnan G, Bowen R, Zehnder JL, Ann Pharmacother. 2013 Feb;47(2):151-8. (link)
  3. A social network of hospital acquired infection built from electronic medical record data, Cusumano-Towner M, Li DY, Tuo S, Krishnan G, Maslove DM, J Am Med Inform Assoc. 2013 May 1;20(3):427-34. (link)
  4. Oncoshare: lessons learned from building an integrated multi-institutional database for comparative effectiveness research, Weber SC, Seto T, Olson C, Kenkare P, Kurian AW, Das AK, AMIA Annu Symp Proc. 2012;2012:970-8. Epub 2012 Nov 3. (Link)
  5. Breast cancer treatment across health care systems: Linking electronic medical records and state registry data to enable outcomes research, 10.1002/cncr.28395. (Link)
  6. Alliance Sleep Questionnaire (ASQ) Feasibility Pilot Study. Leary EB, Griffin KS, Malunjkar S, Qadri S, Ruoff CM, Sullivan SS, Walsh JK, Mignot E, Sleep, June 2012, Vol. 35 (Abstract suppl.), p.A432; #1282.
  7. Deployment of the Alliance Sleep Questionnaire (ASQ) at the Stanford Sleep Disorders Clinic (SSDC) as Standard of Care. Leary EB, Malunjkar S, Qadri S. Ruoff CM, Sullivan SS, Walsh JK, Mignot E, Sleep, June 2013, Vol. 36 (Abstract suppl.), p. A413, #1209.

2010-2011

  1. STRIDE--An integrated standards-based translational research informatics platform., Lowe HJ, Ferris TA, Hernandez PM, Weber SC, AMIA Annu Symp Proc. 2009 Nov 14;2009:391-5. (link)
  2. Implementing a Real-time Complex Event Stream Processing System to Help Identify Potential Participants in Clinical and Translational Research Studies., Weber SC, Lowe HJ, Malunjkar S, Quinn J, AMIA Annu Symp Proc. 2010 Nov 13;2010:472-6. (link)
  3. Detecting drug interactions from adverse-event reports: interaction between paroxetine and pravastatin increases blood glucose levels., Tatonetti NP, Denny JC, Murphy SN, Fernald GH, Krishnan G, Castro V, Yue P, Tsao PS, Kohane I, Roden DM, Altman RB, Clin Pharmacol Ther. 2011 Jul;90(1):133-42. (link)
  4. Prolonged aPTT Relative to Anti-Xa Is Associated with Increased 30-Day Mortality in Hospitalized Patients Treated with Unfractionated Heparin, Jin J, Price E, Nguyen H, Krishnan G, Balise R, Bowen R AR, Zehnder JL, Blood 2011 118:1248. (link)
  5. Managing Medical Vocabulary Updates in a Clinical Data Warehouse: An RxNorm Case Study, Podchiyska T, Hernandez P, Ferris TA, Weber SC, Lowe HJ, AMIA Annu Symp Proc. 2010; 2010: 477–481. (link)

2008-2009

  1. Novel integration of hospital electronic medical records and gene expression measurements to identify genetic markers of maturation. Chen DP, Weber SC, Constantinou PS, Ferris TA, Lowe HJ, Butte AJ., Pac Symp Biocomput. 2008:243-54. (link)
  2. Clinical arrays of laboratory measures, or "clinarrays", built from an electronic health record enable disease subtyping by severity, Chen DP, Weber SC, Constantinou PS, Ferris TA, Lowe HJ, Butte AJ., AMIA Annu Symp Proc. 2007 Oct 11:115-9. (link)
  3. Automated Mapping of Pharmacy Orders from Two Electronic Health Record Systems to RxNorm within the STRIDE Clinical Data Warehouse, Hernandez P, Podchiyska T, Weber SC, Ferris TA, Lowe HJ, AMIA Annu Symp Proc. 2009; 2009: 244–248. (link)
  4. Using a statistical natural language Parser augmented with the UMLS specialist lexicon to assign SNOMED CT codes to anatomic sites and pathologic diagnoses in full text pathology reports., Lowe HJ, Huang Y, Regula DP, AMIA Annu Symp Proc. 2009 Nov 14;2009:386-90. (link)
  5. Managing Medical Vocabulary Updates in a Clinical Data Warehouse: An RxNorm Case Study., Podchiyska T, Hernandez P, Ferris T, Weber S, Lowe HJ, AMIA Annu Symp Proc. 2010 Nov 13;2010:477-81. (link)