Collaborative Research

  1. A Geva, M Liu, VA Panickan, P Avillach, T Cai, KD Mandl. A high-throughput phenotyping algorithm is portable from adult to pediatric populations. Journal of the American Medical Informatics Association 2021.
  2. IS Kohane, BJ Aronow, P Avillach, BK Beaulieu-Jones, R Bellazzi, RL Bradford, GA Brat, M Cannataro, JJ Cimino, N Garc{'{}}a-Barrio, N Gehlenborg, M Ghassemi, A Guti{'{e}}rrez-Sacrist{'{a}}n, DA Hanauer, JH Holmes, C Hong, JG Klann, NH Loh, Y Luo, KD Mandl, M Daniar, JH Moore, SN Murphy, A Neuraz, KY Ngiam, GS Omenn, N Palmer, LP Patel, M Pedrera-Jim{'{e}}nez, P Sliz, AM South, AL Tan, DM Taylor, BW Taylor, C Torti, AK Vallejos, KB Wagholikar, GM Weber, T Cai. What Every Reader Should Know About Studies Using Electronic Health Record Data but May Be Afraid to Ask. Journal of Medical Internet Research 2021;23(3):e22219.
  3. J Zhang, A Can, PM Lai, JS Mukundan, VM Castro, D Dligach, S Finan, V Gainer, N Shadick, G Savova, SN Murphy, T Cai, ST Weiss, R Du. Geometric variations associated with posterior communicating artery aneurysms. Journal of {NeuroInterventional} Surgery 2021;neurintsurg–2020–017062.
  4. J Zhang, A Can, PM Lai, S Mukundan, VM Castro, D Dligach, S Finan, VS Gainer, NA Shadick, G Savova, SN Murphy, T Cai, ST Weiss, R Du. Morphological variables associated with ruptured basilar tip aneurysms. Scientific Reports 2021;11(1).
  5. J Zhang, A Can, PM Lai, S Mukundan, VM Castro, D Dligach, S Finan, VS Gainer, NA Shadick, G Savova, SN Murphy, T Cai, ST Weiss, R Du. Vascular Geometry Associated with Anterior Communicating Artery Aneurysm Formation. World Neurosurgery 2021;146:e1318–e1325.
  6. J Zhang, PM Lai, A Can, S Mukundan, VM Castro, D Dligach, S Finan, VS Gainer, NA Shadick, G Savova, SN Murphy, T Cai, ST Weiss, R Du. Tobacco use and age are associated with different morphologic features of anterior communicating artery aneurysms. Scientific Reports 2021;11(1).
  7. LL Chepelev, X Wang, B Gold, C Bonzel, F Rybicki, JW Uyeda, A Sheikh, D Anderson, J Lindaman, G Mogel, D Mitsouras, MC Mahoney, T Cai, FJ Rybicki. Improved Appropriateness of Advanced Diagnostic Imaging After Implementation of Clinical Decision Support Mechanism. Journal of Digital Imaging 2021.
  8. SK Tedeschi, T Cai, Z He, Y Ahuja, C Hong, KA Yates, K Dahal, C Xu, H Lyu, K Yoshida, DH Solomon, T Cai, KP Liao. Classifying Pseudogout Using Machine Learning Approaches With Electronic Health Record Data. Arthritis Care {&} Research 2021;73(3):442–448.
  9. TT Le, A Guti{'{e}}rrez-Sacrist{'{a}}n, J Son, C Hong, AM South, BK Beaulieu-Jones, NH Loh, Y Luo, M Morris, KY Ngiam, LP Patel, MJ Samayamuthu, E Schriver, AL Tan, J Moore, T Cai, GS Omenn, P Avillach, IS Kohane, S Visweswaran, DL Mowery, Z Xia. Multinational Prevalence of Neurological Phenotypes in Patients Hospitalized with {COVID}-19. __ 2021.
  10. W Yuan, BK Beaulieu-Jones, K Yu, SL Lipnick, N Palmer, J Loscalzo, T Cai, IS Kohane. Temporal bias in case-control design: preventing reliable predictions of the future. Nature Communications 2021;12(1).
  11. Y Ahuja, N Kim, L Liang, T Cai, K Dahal, T Seyok, C Lin, S Finan, K Liao, G Savovoa, T Chitnis, T Cai, Z Xia. Leveraging electronic health records data to predict multiple sclerosis disease activity. Annals of Clinical and Translational Neurology 2021.
  12. AL Beam, B Kompa, A Schmaltz, I Fried, G Weber, N Palmer, X Shi, T Cai, IS Kohane. Clinical Concept Embeddings Learned from Massive Sources of Multimodal Medical Data. Pac Symp Biocomput 2020;25:295–306.
  13. AN Ananthakrishnan, A Cagan, T Cai, VS Gainer, G Savova, SY Shaw, S Churchill, KE Burke, EW Karlson, SN Murphy, I Kohane, KP Liao, RJ Xavier. Use of Narrative Concepts in Electronic Health Records to Validate Associations Between Genetic Factors and Response to Treatment of Inflammatory Bowel Diseases. Clinical Gastroenterology and Hepatology 2020;18(8):1890–1892.
  14. AW Sonabend, AM Pellegrini, S Chan, HE Brown, JN Rosenquist, PJ Vuijk, AE Doyle, RH Perlis, T Cai. Integrating questionnaire measures for transdiagnostic psychiatric phenotyping using word2vec. PLOS} {ONE} 2020;15(4):e0230663.
  15. D Cheng, KC Cushing, T Cai, AN Ananthakrishnan. Safety and Efficacy of Tumor Necrosis Factor Antagonists in Older Patients With Ulcerative Colitis: Patient-Level Pooled Analysis of Data From Randomized Trials. Clinical Gastroenterology and Hepatology 2020.
  16. FM Sacks, L Liang, JD Furtado, T Cai, WS Davidson, Z He, RL McClelland, EB Rimm, MK Jensen. Protein-Defined Subspecies of {HDLs} (High-Density Lipoproteins) and Differential Risk of Coronary Heart Disease in 4 Prospective Studies. Arteriosclerosis, Thrombosis, and Vascular Biology 2020;40(11):2714–2727.
  17. GA Brat, GM Weber, N Gehlenborg, P Avillach, NP Palmer, L Chiovato, J Cimino, LR Waitman, GS Omenn, A Malovini, JH Moore, BK Beaulieu-Jones, V Tibollo, SN Murphy, SL Yi, MS Keller, R Bellazzi, DA Hanauer, A Serret-Larmande, A Gutierrez-Sacristan, JJ Holmes, DS Bell, KD Mandl, RW Follett, JG Klann, DA Murad, L Scudeller, M Bucalo, K Kirchoff, J Craig, J Obeid, V Jouhet, R Griffier, S Cossin, B Moal, LP Patel, A Bellasi, HU Prokosch, D Kraska, P Sliz, AL Tan, KY Ngiam, A Zambelli, DL Mowery, E Schiver, B Devkota, RL Bradford, M Daniar, C Daniel, V Benoit, R Bey, N Paris, P Serre, N Orlova, J Dubiel, M Hilka, AS Jannot, S Breant, J Leblanc, N Griffon, A Burgun, M Bernaux, A Sandrin, E Salamanca, S Cormont, T Ganslandt, T Gradinger, J Champ, M Boeker, P Martel, L Esteve, A Gramfort, O Grisel, D Leprovost, T Moreau, G Varoquaux, J Vie, D Wassermann, A Mensch, C Caucheteux, C Haverkamp, G Lemaitre, S Bosari, ID Krantz, A South, T Cai, IS Kohane. International electronic health record-derived {COVID}-19 clinical course profiles: the 4CE consortium. npj Digital Medicine 2020;3(1).
  18. GM Weber, C Hong, NP Palmer, P Avillach, SN Murphy, A Guti{'{e}}rrez-Sacrist{'{a}}n, Z Xia, A Serret-Larmande, A Neuraz, GS Omenn, S Visweswaran, JG Klann, AM South, NH Loh, M Cannataro, BK Beaulieu-Jones, R Bellazzi, G Agapito, M Alessiani, BJ Aronow, DS Bell, A Bellasi, V Benoit, M Beraghi, M Boeker, J Booth, S Bosari, FT Bourgeois, NW Brown, M Bucalo, L Chiovato, L Chiudinelli, A Dagliati, B Devkota, SL DuVall, RW Follett, T Ganslandt, NG Barrio, T Gradinger, R Griffier, DA Hanauer, JH Holmes, P Horki, KM Huling, RW Issitt, V Jouhet, MS Keller, D Kraska, M Liu, Y Luo, KE Lynch, A Malovini, KD Mandl, C Mao, A Maram, ME Matheny, T Maulhardt, M Mazzitelli, M Milano, JH Moore, JS Morris, M Morris, DL Mowery, TP Naughton, KY Ngiam, JB Norman, LP Patel, MP Jimenez, RB Ramoni, ER Schriver, L Scudeller, NJ Sebire, PS Balazote, A Spiridou, AL Tan, BW Tan, V Tibollo, C Torti, EM Trecarichi, M Vitacca, A Zambelli, C Zucco, IS Kohane, T Cai, GA Brat. International Comparisons of Harmonized Laboratory Value Trajectories to Predict Severe {COVID}-19: Leveraging the 4CE Collaborative Across 342 Hospitals and 6 Countries: A Retrospective Cohort Study. __ 2020.
  19. IS Beam. Clinical Concept Embeddings Learned from Massive Sources of Multimodal Medical Data. Pac Symp Biocomput 2020;25:295–306.
  20. J Zhang, A Can, PM Lai, S Mukundan, VM Castro, D Dligach, S Finan, S Yu, VS Gainer, NA Shadick, G Savova, SN Murphy, T Cai, ST Weiss, R Du. Age and morphology of posterior communicating artery aneurysms. Scientific Reports 2020;10(1).
  21. J Zhang, A Can, PM Lai, S Mukundan, VM Castro, D Dligach, S Finan, VS Gainer, NA Shadick, G Savova, SN Murphy, T Cai, ST Weiss, R Du. Surrounding vascular geometry associated with basilar tip aneurysm formation. Scientific Reports 2020;10(1).
  22. M Koch, ST DeKosky, M Goodman, J Sun, JD Furtado, AL Fitzpatrick, RH Mackey, T Cai, OL Lopez, LH Kuller, KJ Mukamal, MK Jensen. Association of Apolipoprotein E in Lipoprotein Subspecies With Risk of Dementia. JAMA} Network Open 2020;3(7):e209250.
  23. M Koch, ST DeKosky, M Goodman, J Sun, JD Furtado, AL Fitzpatrick, RH Mackey, T Cai, OL Lopez, LH Kuller, KJ Mukamal, MK Jensen. High density lipoprotein and its apolipoprotein-defined subspecies and risk of dementia. Journal of Lipid Research 2020;61(3):445–454.
  24. S Huang, J Huang, T Cai, KP Dahal, A Cagan, Z He, J Stratton, I Gorelik, C Hong, T Cai, KP Liao. Impact of {ICD}10 and secular changes on electronic medical record rheumatoid arthritis algorithms. Rheumatology 2020;59(12):3759–3766.
  25. SK Tedeschi, T Cai, Z He, Y Ahuja, C Hong, KA Yates, K Dahal, C Xu, H Lyu, K Yoshida, DH Solomon, T Cai, KP Liao. Classifying Pseudogout using Machine Learning Approaches with Electronic Health Record Data. Arthritis Care & Research 2020.
  26. T Zhang, M Goodman, F Zhu, B Healy, R Carruthers, T Chitnis, H Weiner, T Cai, P De Jager, H Tremlett, Z Xia. Phenome-wide examination of comorbidity burden and multiple sclerosis disease severity. Neurology - Neuroimmunology Neuroinflammation 2020;7(6):e864.
  27. Y Wang, J Zhu, S Aroner, K Overvad, T Cai, M Yang, A Tjønneland, A Handberg, MK Jensen. Plasma CD36 and Incident Diabetes: A Case-Cohort Study in Danish Men and Women. Diabetes & Metabolism Journal 2020;44(1):134.
  28. A Can, PM Lai, VM Castro, S Yu, D Dligach, S Finan, V Gainer, NA Shadick, G Savova, S Murphy, T Cai, ST Weiss, R Du. Decreased Total Iron Binding Capacity May Correlate with Ruptured Intracranial Aneurysms. Scientific Reports 2019;9(1):6054.
  29. A Jorge, VM Castro, A Barnado, V Gainer, C Hong, T Cai, T Cai, R Carroll, JC Denny, L Crofford, KH Costenbader, KP Liao, EW Karlson, CH Feldman. Identifying lupus patients in electronic health records: Development and validation of machine learning algorithms and application of rule-based algorithms. Seminars in Arthritis and Rheumatism 2019;49(1):84–90.
  30. M Koch, ST DeKosky, M Goodman, J Sun, JD Furtado, AL Fitzpatrick, RH Mackey, T Cai, OL Lopez, LH Kuller, KJ Mukamal, MK Jensen. High density lipoprotein and its apolipoprotein-defined subspecies and risk of dementia. Journal of Lipid Research 2019;61(3):445–454.
  31. Q Zhong, B Gelaye, EW Karlson, P Avillach, JW Smoller, T Cai, MA Williams. Associations of antepartum suicidal behaviour with adverse infant and obstetric outcomes. Paediatric and Perinatal Epidemiology 2019;33(2):137–144.
  32. SS Zhao, C Hong, T Cai, C Xu, J Huang, J Ermann, NJ Goodson, DH Solomon, T Cai, KP Liao. Incorporating natural language processing to improve classification of axial spondyloarthritis using electronic health records. Rheumatology 2019;59(5):1059–1065.
  33. SS Zhao, C Hong, T Cai, C Xu, J Huang, J Ermann, NJ Goodson, DH Solomon, T Cai, KP Liao. Incorporating natural language processing to improve classification of axial spondyloarthritis using electronic health records. Rheumatology 2019;59(5):1059–1065.
  34. T Cai, L Zhang, N Yang, KK Kumamaru, FJ Rybicki, T Cai, KP Liao. EXTraction of EMR numerical data: an efficient and generalizable tool to EXTEND clinical research. BMC Medical Informatics and Decision Making 2019;19(1):226.
  35. A Aghayev, AA Giannopoulos, J Gronsbell, E George, T Cai, ML Steigner, D Mitsouras, FJ Rybicki. Common First-Pass CT Angiography Findings Associated With Rapid Growth Rate in Abdominal Aorta Aneurysms Between 3 and 5 cm in Largest Diameter. American Journal of Roentgenology 2018;210(2):431–437.
  36. A Can, RF Rudy, VM Castro, S Yu, D Dligach, S Finan, V Gainer, NA Shadick, G Savova, S Murphy, T Cai, ST Weiss, R Du. Association between aspirin dose and subarachnoid hemorrhage from saccular aneurysms. Neurology 2018;91(12):e1175–e1181.
  37. A Can, VM Castro, S Yu, D Dligach, S Finan, VS Gainer, NA Shadick, G Savova, S Murphy, T Cai, ST Weiss, R Du. Antihyperglycemic Agents Are Inversely Associated With Intracranial Aneurysm Rupture. Stroke 2018;49(1):34–39.
  38. B Qian, RF Rudy, T Cai, R Du. Cerebral Artery Diameter in Inbred Mice Varies as a Function of Strain. Frontiers in Neuroanatomy 2018;12.
  39. BP Hejblum, J Cui, LJ Lahey, A Cagan, JA Sparks, J Sokolove, T Cai, KP Liao. Association Between Anti-Citrullinated Fibrinogen Antibodies and Coronary Artery Disease in Rheumatoid Arthritis. Arthritis Care & Research 2018;70(7):1113–1117.
  40. J Zhang, A Can, S Mukundan, M Steigner, VM Castro, D Dligach, S Finan, S Yu, V Gainer, NA Shadick, G Savova, S Murphy, T Cai, Z Wang, ST Weiss, R Du. Morphological Variables Associated With Ruptured Middle Cerebral Artery Aneurysms. Neurosurgery 2018;85(1):75–83.
  41. JD Furtado, R Yamamoto, JT Melchior, AB Andraski, M Gamez-Guerrero, P Mulcahy, Z He, T Cai, WS Davidson, FM Sacks. Distinct Proteomic Signatures in 16 HDL (High-Density Lipoprotein) Subspecies. Arteriosclerosis, Thrombosis, and Vascular Biology 2018;38(12):2827–2842.
  42. Q Zhong, B Gelaye, JW Smoller, P Avillach, T Cai, MA Williams. Adverse obstetric outcomes during delivery hospitalizations complicated by suicidal behavior among US pregnant women. PLOS ONE 2018;13(2):e0192943.
  43. Q Zhong, LP Mittal, MD Nathan, KM Brown, DK González, T Cai, S Finan, B Gelaye, P Avillach, JW Smoller, EW Karlson, T Cai, MA Williams. Use of natural language processing in electronic medical records to identify pregnant women with suicidal behavior: towards a solution to the complex classification problem. European Journal of Epidemiology 2018;34(2):153–162.
  44. T Cai, Y Zhang, Y Ho, N Link, J Sun, J Huang, TA Cai, S Damrauer, Y Ahuja, J Honerlaw, J Huang, L Costa, P Schubert, C Hong, D Gagnon, YV Sun, JM Gaziano, P Wilson, K Cho, P Tsao, CJ O’Donnell, KP and. Association of Interleukin 6 Receptor Variant With Cardiovascular Disease Effects of Interleukin 6 Receptor Blocking Therapy. JAMA Cardiology 2018;3(9):849–857.
  45. TF Imran, D Posner, J Honerlaw, J Vassy, R Song, Y Ho, S Kittner, K Liao, T Cai, CJ O’Donnell, L Djousse, DR Gagnon, JM Gaziano, PW Wilson, K Cho. A phenotyping algorithm to identify acute ischemic stroke accurately from a national biobank: the Million Veteran Program. Clinical Epidemiology 2018;10:1509–1521.
  46. TH McCoy, S Yu, KL Hart, VM Castro, HE Brown, JN Rosenquist, AE Doyle, PJ Vuijk, T Cai, RH Perlis. High Throughput Phenotyping for Dimensional Psychopathology in Electronic Health Records. Biological Psychiatry 2018;83(12):997–1004.
  47. TH McCoy, VM Castro, KL Hart, AM Pellegrini, S Yu, T Cai, RH Perlis. Genome-wide Association Study of Dimensional Psychopathology Using Electronic Health Records. Biological Psychiatry 2018;83(12):1005–1011.
  48. V Gamerman, T Cai, A Elsäßer. Pragmatic randomized clinical trials: best practices and statistical guidance. Health Services and Outcomes Research Methodology 2018;19(1):23–35.
  49. A Can, VM Castro, YH Ozdemir, S Dagen, D Dligach, S Finan, S Yu, V Gainer, NA Shadick, G Savova, S Murphy, T Cai, ST Weiss, R Du. Alcohol Consumption and Aneurysmal Subarachnoid Hemorrhage. Translational Stroke Research 2017;9(1):13–19.
  50. A Can, VM Castro, YH Ozdemir, S Dagen, S Yu, D Dligach, S Finan, V Gainer, NA Shadick, S Murphy, T Cai, G Savova, R Dammers, ST Weiss, R Du. Association of intracranial aneurysm rupture with smoking duration, intensity, and cessation. Neurology 2017;89(13):1408–1415.
  51. A Geva, JL Gronsbell, T Cai, T Cai, SN Murphy, JC Lyons, MM Heinz, MD Natter, N Patibandla, J Bickel, MP Mullen, KD Mandl, S Abman, I Adatia, ED Austin, J Feinstein, J Fineman, B Hanna, R Hopper, D Ivy, R Keller, U Krishnan, T Kulik, M Mullen, U Raj, EB Rosenzweig. A Computable Phenotype Improves Cohort Ascertainment in a Pediatric Pulmonary Hypertension Registry. The Journal of Pediatrics 2017;188:224–231.e5.
  52. C Chen, M Stein, R Ursano, T Cai, J Gelernter, S Heeringa, S Jain, K Jensen, A Maihofer, C Mitchell, C Nievergelt, M Nock, B Neale, R Polimanti, S Ripke, M Thomas, Q Wang, E Ware, S Borja, R Kessler, J Smoller. Genome-Wide Association Study Of Posttraumatic Stress Disorder Symptoms In Two Cohorts Of United States Army Soldiers. European Neuropsychopharmacology 2017;27:S472.
  53. K Naxerova, JG Reiter, E Brachtel, JK Lennerz, M van de Wetering, A Rowan, T Cai, H Clevers, C Swanton, MA Nowak, SJ Elledge, RK Jain. Origins of lymphatic and distant metastases in human colorectal cancer. Science 2017;357(6346):55–60.
  54. KP Liao, JA Sparks, BP Hejblum, I Kuo, J Cui, LJ Lahey, A Cagan, VS Gainer, W Liu, TT Cai, J Sokolove, T Cai. Phenome-Wide Association Study of Autoantibodies to Citrullinated and Noncitrullinated Epitopes in Rheumatoid Arthritis. Arthritis & Rheumatology 2017;69(4):742–749.
  55. M Koch, JD Furtado, GZ Jiang, BE Gray, T Cai, F Sacks, A Tjønneland, K Overvad, MK Jensen. Associations of anthropometry and lifestyle factors with HDL subspecies according to apolipoprotein C-III. Journal of Lipid Research 2017;58(6):1196–1203.
  56. M Ong, MP Mullen, ED Austin, P Szolovits, MD Natter, A Geva, T Cai, SW Kong, KD Mandl. Learning a Comorbidity-Driven Taxonomy of Pediatric Pulmonary Hypertension. Circulation Research 2017;121(4):341–353.
  57. MB Stein, EB Ware, C Mitchell, C Chen, S Borja, T Cai, CL Dempsey, CS Fullerton, J Gelernter, SG Heeringa, S Jain, RC Kessler, JA Naifeh, MK Nock, S Ripke, X Sun, JC Beckham, NA Kimbrel, RJ Ursano, JW and. Genomewide association studies of suicide attempts in US soldiers. American Journal of Medical Genetics Part B: Neuropsychiatric Genetics 2017;174(8):786–797.
  58. SA Aroner, M Yang, J Li, JD Furtado, FM Sacks, A Tjønneland, K Overvad, T Cai, MK Jensen. Apolipoprotein C-III and High-Density Lipoprotein Subspecies Defined by Apolipoprotein C-III in Relation to Diabetes Risk. American Journal of Epidemiology 2017;186(6):736–744.
  59. W Xie, D Agniel, A Shevchenko, SV Malov, A Svitin, N Cherkasov, MK Baum, A Campa, S Gaseitsiwe, H Bussmann, J Makhema, R Marlink, V Novitsky, T Lee, T Cai, SJ O’Brien, M Essex. Genome-Wide Analyses Reveal Gene Influence on HIV Disease Progression and HIV-1C Acquisition in Southern Africa. AIDS Research and Human Retroviruses 2017;33(6):597–609.
  60. AN Ananthakrishnan, A Cagan, T Cai, VS Gainer, SY Shaw, G Savova, S Churchill, EW Karlson, I Kohane, KP Liao, SN Murphy. Comparative Effectiveness of Infliximab and Adalimumab in Crohn’s Disease and Ulcerative Colitis. Inflammatory Bowel Diseases 2016;22(4):880–885.
  61. AN Ananthakrishnan, A Cagan, T Cai, VS Gainer, SY Shaw, G Savova, S Churchill, EW Karlson, SN Murphy, KP Liao, I Kohane. Identification of Nonresponse to Treatment Using Narrative Data in an Electronic Health Record Inflammatory Bowel Disease Cohort. Inflammatory Bowel Diseases 2016;22(1):151–158.
  62. AN Ananthakrishnan, A Cagan, T Cai, VS Gainer, SY Shaw, S Churchill, EW Karlson, SN Murphy, KP Liao, I Kohane. Statin Use Is Associated With Reduced Risk of Colorectal Cancer in Patients With Inflammatory Bowel Diseases. Clinical Gastroenterology and Hepatology 2016;14(7):973–979.
  63. VM Castro, D Dligach, S Finan, S Yu, A Can, M Abd-El-Barr, V Gainer, NA Shadick, S Murphy, T Cai, G Savova, ST Weiss, R Du. Large-scale identification of patients with cerebral aneurysms using natural language processing. Neurology 2016;88(2):164–168.
  64. AN Ananthakrishnan, A Cagan, T Cai, VS Gainer, SY Shaw, S Churchill, EW Karlson, SN Murphy, I Kohane, KP Liao. Diabetes and the risk of infections with immunomodulator therapy in inflammatory bowel diseases. Alimentary Pharmacology & Therapeutics 2015;41(11):1141–1148.
  65. AN Ananthakrishnan, A Cagan, T Cai, VS Gainer, SY Shaw, S Churchill, EW Karlson, SN Murphy, I Kohane, KP Liao. Colonoscopy Is Associated With a Reduced Risk for Colon Cancer and Mortality in Patients With Inflammatory Bowel Diseases. Clinical Gastroenterology and Hepatology 2015;13(2):322–329.e1.
  66. AN Ananthakrishnan, A Cagan, T Cai, VS Gainer, SY Shaw, S Churchill, EW Karlson, SN Murphy, I Kohane, KP Liao, RJ Xavier. Common Genetic Variants Influence Circulating Vitamin D Levels in Inflammatory Bowel Diseases. Inflammatory Bowel Diseases 2015;21(11):2507–2514.
  67. H Uno, J Wittes, H Fu, SD Solomon, B Claggett, L Tian, T Cai, MA Pfeffer, SR Evans, L Wei. Alternatives to Hazard Ratios for Comparing the Efficacy or Safety of Therapies in Noninferiority Studies. Annals of Internal Medicine 2015;163(2):127.
  68. KP Liao, T Cai, GK Savova, SN Murphy, EW Karlson, AN Ananthakrishnan, VS Gainer, SY Shaw, Z Xia, P Szolovits, S Churchill, I Kohane. Development of phenotype algorithms using electronic medical records and incorporating natural language processing. BMJ 2015;350:h1885–h1885.
  69. Q Zhong, B Gelaye, M Miller, GL Fricchione, T Cai, PA Johnson, DC Henderson, MA Williams. Suicidal behavior-related hospitalizations among pregnant women in the USA, 2006-2012. Archives of Women’s Mental Health 2015;19(3):463–472.
  70. RC Kessler, CH Warner, C Ivany, MV Petukhova, S Rose, EJ Bromet, M Brown, T Cai, LJ Colpe, KL Cox, CS Fullerton, SE Gilman, MJ Gruber, SG Heeringa, L Lewandowski-Romps, J Li, AM Millikan-Bell, JA Naifeh, MK Nock, AJ Rosellini, NA Sampson, M Schoenbaum, MB Stein, S Wessely, AM Zaslavsky, RJ Ursano. Predicting Suicides After Psychiatric Hospitalization in US Army Soldiers. JAMA Psychiatry 2015;72(1):49–57.
  71. VM Castro, J Minnier, SN Murphy, I Kohane, SE Churchill, V Gainer, T Cai, AG Hoffnagle, Y Dai, S Block, SR Weill, M Nadal-Vicens, AR Pollastri, JN Rosenquist, S Goryachev, D Ongur, P Sklar, RH Perlis, JW Smoller, JW Smoller, RH Perlis, PH Lee, VM Castro, AG Hoffnagle, P Sklar, EA Stahl, SM Purcell, DM Ruderfer, AW Charney, P Roussos, C Pato, M Pato, H Medeiros, J Sobel, N Craddock, I Jones, L Forty, A DiFlorio, E Green, L Jones, K Dunjewski, M Landén, C Hultman, A Juréus, S Bergen, O Svantesson, S McCarroll, J Moran, JW Smoller, K Chambert, RA and. Validation of Electronic Health Record Phenotyping of Bipolar Disorder Cases and Controls. American Journal of Psychiatry 2015;172(4):363–372.
  72. AN Ananthakrishnan, A Cagan, VS Gainer, S Cheng, T Cai, E Scoville, GG Konijeti, P Szolovits, SY Shaw, S Churchill, EW Karlson, SN Murphy, I Kohane, KP Liao. Thromboprophylaxis Is Associated With Reduced Post-hospitalization Venous Thromboembolic Events in Patients With Inflammatory Bowel Diseases. Clinical Gastroenterology and Hepatology 2014;12(11):1905–1910.
  73. AN Ananthakrishnan, A Cagan, VS Gainer, S Cheng, T Cai, P Szolovits, SY Shaw, S Churchill, EW Karlson, SN Murphy, I Kohane, KP Liao. Mortality and extraintestinal cancers in patients with primary sclerosing cholangitis and inflammatory bowel disease. Journal of Crohn’s and Colitis 2014;8(9):956–963.
  74. AN Ananthakrishnan, A Cagan, VS Gainer, SC Cheng, T Cai, P Szolovits, SY Shaw, S Churchill, EW Karlson, SN Murphy, I Kohane, KP Liao. Higher plasma vitamin D is associated with reduced risk of Clostridium difficileinfection in patients with inflammatory bowel diseases. Alimentary Pharmacology & Therapeutics 2014;39(10):1136–1142.
  75. AN Ananthakrishnan, A Cheng, A Cagan, T Cai, VS Gainer, SY Shaw, S Churchill, EW Karlson, SN Murphy, I Kohane, KP Liao. Mode of Childbirth and Long-Term Outcomes in Women with Inflammatory Bowel Diseases. Digestive Diseases and Sciences 2014;60(2):471–477.
  76. AN Ananthakrishnan, S Cheng, T Cai, A Cagan, VS Gainer, P Szolovits, SY Shaw, S Churchill, EW Karlson, SN Murphy, I Kohane, KP Liao. Serum Inflammatory Markers and Risk of Colorectal Cancer in Patients With Inflammatory Bowel Diseases. Clinical Gastroenterology and Hepatology 2014;12(8):1342–1348.e1.
  77. AN Ananthakrishnan, S Cheng, T Cai, A Cagan, VS Gainer, P Szolovits, SY Shaw, S Churchill, EW Karlson, SN Murphy, I Kohane, KP Liao. Association Between Reduced Plasma 25-Hydroxy Vitamin D and Increased Risk of Cancer in Patients With Inflammatory Bowel Diseases. Clinical Gastroenterology and Hepatology 2014;12(5):821–827.
  78. HM van Loo, T Cai, MJ Gruber, J Li, P de Jonge, M Petukhova, S Rose, NA Sampson, RA Schoevers, KJ Wardenaar, MA Wilcox, AO Al-Hamzawi, LH Andrade, EJ Bromet, B Bunting, J Fayyad, SE Florescu, O Gureje, C Hu, Y Huang, D Levinson, ME Medina-Mora, Y Nakane, J Posada-Villa, KM Scott, M Xavier, Z Zarkov, RC Kessler. Major depressive disorder subtypes to predict long-term course. Depression and Anxiety 2014;31(9):765–777.
  79. KJ Wardenaar, HM van Loo, T Cai, M Fava, MJ Gruber, J Li, P de Jonge, AA Nierenberg, MV Petukhova, S Rose, NA Sampson, RA Schoevers, MA Wilcox, J Alonso, EJ Bromet, B Bunting, SE Florescu, A Fukao, O Gureje, C Hu, YQ Huang, AN Karam, D Levinson, ME Mora, J Posada-Villa, KM Scott, NI Taib, MC Viana, M Xavier, Z Zarkov, RC Kessler. The effects of co-morbidity in defining major depression subtypes associated with long-term course and severity. Psychological Medicine 2014;44(15):3289–3302.
  80. M Ong, IS Kohane, T Cai, MP Gorman, KD Mandl. Population-Level Evidence for an Autoimmune Etiology of Epilepsy. JAMA Neurology 2014;71(5):569–574.
  81. S Yu, KK Kumamaru, E George, RM Dunne, A Bedayat, M Neykov, AR Hunsaker, KE Dill, T Cai, FJ Rybicki. Classification of CT pulmonary angiography reports by presence, chronicity, and location of pulmonary embolism with natural language processing. Journal of Biomedical Informatics 2014;52:386–393.
  82. AN Ananthakrishnan, T Cai, G Savova, S Cheng, P Chen, RG Perez, VS Gainer, SN Murphy, P Szolovits, Z Xia, S Shaw, S Churchill, EW Karlson, I Kohane, RM Plenge, KP Liao. Improving Case Definition of Crohn’s Disease and Ulcerative Colitis in Electronic Medical Records Using Natural Language Processing. Inflammatory Bowel Diseases 2013;19(7):1411–1420.
  83. AN Ananthakrishnan, VS Gainer, RG Perez, T Cai, SC Cheng, G Savova, P Chen, P Szolovits, Z Xia, PL De Jager, SY Shaw, S Churchill, EW Karlson, I Kohane, RH Perlis, RM Plenge, SN Murphy, KP Liao. Psychiatric co-morbidity is associated with increased risk of surgery in Crohn’s disease. Alimentary Pharmacology & Therapeutics 2013;37(4):445–454.
  84. AN Ananthakrishnan, VS Gainer, T Cai, RG Perez, S Cheng, G Savova, P Chen, P Szolovits, Z Xia, PL De Jager, S Shaw, S Churchill, EW Karlson, I Kohane, RH Perlis, RM Plenge, SN Murphy, KP Liao. Similar Risk of Depression and Anxiety Following Surgery or Hospitalization for Crohn’s Disease and Ulcerative Colitis. American Journal of Gastroenterology 2013;108(4):594–601.
  85. GM Altschuler, O Hofmann, I Kalatskaya, R Payne, SJ Sui, U Saxena, AV Krivtsov, SA Armstrong, T Cai, L Stein, WA Hide. Pathprinting: An integrative approach to understand the functional basis of disease. Genome Medicine 2013;5(7):68.
  86. KP Liao, D Diogo, J Cui, T Cai, Y Okada, VS Gainer, SN Murphy, N Gupta, D Mirel, AN Ananthakrishnan, P Szolovits, SY Shaw, S Raychaudhuri, S Churchill, I Kohane, EW Karlson, RM Plenge. Association between low density lipoprotein and rheumatoid arthritis genetic factors with low density lipoprotein levels in rheumatoid arthritis and non-rheumatoid arthritis controls. Annals of the Rheumatic Diseases 2013;73(6):1170–1175.
  87. KP Liao, F Kurreeman, G Li, G Duclos, S Murphy, R Guzman, T Cai, N Gupta, V Gainer, P Schur, J Cui, JC Denny, P Szolovits, S Churchill, I Kohane, EW Karlson, RM Plenge. Associations of autoantibodies, autoimmune risk alleles, and clinical diagnoses from the electronic medical records in rheumatoid arthritis cases and non-rheumatoid arthritis controls. Arthritis & Rheumatism 2013;65(3):571–581.
  88. KP Liao, T Cai, VS Gainer, A Cagan, SN Murphy, C Liu, S Churchill, SY Shaw, I Kohane, DH Solomon, RM Plenge, EW Karlson. Lipid and Lipoprotein Levels and Trend in Rheumatoid Arthritis Compared to the General Population. Arthritis Care & Research 2013;65(12):2046–2050.
  89. PS Lai, JQ Hang, FY Zhang, X Lin, BY Zheng, HL Dai, L Su, T Cai, DC Christiani. Gender differences in the effect of occupational endotoxin exposure on impaired lung function and death: the Shanghai Textile Worker Study. Occupational and Environmental Medicine 2013;71(2):118–125.
  90. RT Gandhi, .. , RJ Bosch, E Aga, MA Bedison, B Bastow, JL Schmitz, JD Siliciano, RF Siliciano, JJ Eron, JW Mellors. Residual plasma viremia and infectious HIV-1 recovery from resting memory CD4 cells in patients on antiretroviral therapy: results from ACTG A5173. Antiviral Therapy 2013.
  91. Z Xia, E Secor, LB Chibnik, RM Bove, S Cheng, T Chitnis, A Cagan, VS Gainer, PJ Chen, KP Liao, SY Shaw, AN Ananthakrishnan, P Szolovits, HL Weiner, EW Karlson, SN Murphy, GK Savova, T Cai, SE Churchill, RM Plenge, IS Kohane, PL De Jager. Modeling Disease Severity in Multiple Sclerosis Using Electronic Health Records. PLoS ONE 2013;8(11):e78927.
  92. AN Ananthakrishnan, R Guzman-Perez, V Gainer, T Cai, S Churchill, I Kohane, RM Plenge, S Murphy. Predictors of severe outcomes associated with Clostridium difficile infection in patients with inflammatory bowel disease. Alimentary Pharmacology & Therapeutics 2012;35(7):789–795.
  93. MT Lu, S Demehri, T Cai, L Parast, AR Hunsaker, SZ Goldhaber, FJ Rybicki. Axial and Reformatted Four-Chamber Right Ventricle-to-Left Ventricle Diameter Ratios on Pulmonary CT Angiography as Predictors of Death After Acute Pulmonary Embolism. American Journal of Roentgenology 2012;198(6):1353–1360.
  94. RJ Carroll, WK Thompson, AE Eyler, AM Mandelin, T Cai, RM Zink, JA Pacheco, CS Boomershine, TA Lasko, H Xu, EW Karlson, RG Perez, VS Gainer, SN Murphy, EM Ruderman, RM Pope, RM Plenge, AN Kho, KP Liao, JC Denny. Portability of an algorithm to identify rheumatoid arthritis in electronic health records. Journal of the American Medical Informatics Association 2012;19(e1):e162–e169.
  95. S Wassertheil-Smoller, A McGinn, M Allison, T Cai, D Curb, C Eaton, S Hendrix, R Kaplan, M Ko, LW Martin, X Xue. Improvement in Stroke Risk Prediction: Role of C-Reactive Protein and Lipoprotein-Associated Phospholipase A2 in the Women’s Health Initiative. International Journal of Stroke 2012;9(7):902–909.
  96. F Kurreeman, K Liao, L Chibnik, B Hickey, E Stahl, V Gainer, G Li, L Bry, S Mahan, K Ardlie, B Thomson, P Szolovits, S Churchill, SN Murphy, T Cai, S Raychaudhuri, I Kohane, E Karlson, RM Plenge. Genetic Basis of Autoantibody Positive and Negative Rheumatoid Arthritis Risk in a Multi-ethnic Cohort Derived from Electronic Health Records. The American Journal of Human Genetics 2011;88(1):57–69.
  97. L Qi, L Parast, T Cai, C Powers, EV Gervino, TH Hauser, FB Hu, A Doria. Genetic Susceptibility to Coronary Heart Disease in Type 2 Diabetes. Journal of the American College of Cardiology 2011;58(25):2675–2682.
  98. RH Perlis, DV Iosifescu, VM Castro, SN Murphy, VS Gainer, J Minnier, T Cai, S Goryachev, Q Zeng, PJ Gallagher, M Fava, JB Weilburg, SE Churchill, IS Kohane, JW Smoller. Using electronic medical records to enable large-scale studies in psychiatry: treatment resistant depression as a model. Psychological Medicine 2011;42(1):41–50.
  99. TJ Love, T Cai, EW Karlson. Validation of Psoriatic Arthritis Diagnoses in Electronic Medical Records Using Natural Language Processing. Seminars in Arthritis and Rheumatism 2011;40(5):413–420.
  100. AR Hunsaker, IB Oliva, T Cai, B Trotman-Dickenson, RR Gill, H Hatabu, FJ Rybicki. Contrast Opacification Using a Reduced Volume of Iodinated Contrast Material and Low Peak Kilovoltage in Pulmonary CT Angiography: Objective and Subjective Evaluation. American Journal of Roentgenology 2010;195(2):W118–W124.
  101. C Wu, A Sodickson, T Cai, NA Levit, ML Steigner, FJ Rybicki, SM Ledbetter. Comparison of Respiratory Motion Artifact From Craniocaudal Versus Caudocranial Scanning With 64-MDCT Pulmonary Angiography. American Journal of Roentgenology 2010;195(1):155–159.
  102. FJ Rybicki, D Mitsouras, CD Owens, A Whitmore, M Gerhard-Herman, N Wake, T Cai, Q Zhou, MS Conte, MA Creager, RV Mulkern. Multi-contrast high spatial resolution black blood inner volume three-dimensional fast spin echo MR imaging in peripheral vein bypass grafts. The International Journal of Cardiovascular Imaging 2010;26(6):683–691.
  103. KP Liao, T Cai, V Gainer, S Goryachev, Q Zeng-treitler, S Raychaudhuri, P Szolovits, S Churchill, S Murphy, I Kohane, EW Karlson, RM Plenge. Electronic medical records for discovery research in rheumatoid arthritis. Arthritis Care & Research 2010;62(8):1120–1127.
  104. ML Steigner, D Mitsouras, AG Whitmore, HJ Otero, C Wang, O Buckley, NA Levit, AZ Hussain, T Cai, RT Mather, O Smedby, MF DiCarli, FJ Rybicki. Iodinated Contrast Opacification Gradients in Normal Coronary Arteries Imaged With Prospectively ECG-Gated Single Heart Beat 320-Detector Row Computed Tomography. Circulation: Cardiovascular Imaging 2010;3(2):179–186.
  105. X Gao, CQ Lai, T Scott, J Shen, T Cai, JM Ordovas, KL Tucker. Urinary 8-Hydroxy-2-deoxyguanosine and Cognitive Function in Puerto Rican Adults. American Journal of Epidemiology 2010;172(3):271–278.
  106. C Wu, T Cai, K Rikova, D Merberg, S Kasif, M Steffen. A Predictive Phosphorylation Signature of Lung Cancer. PLoS ONE 2009;4(11):e7994.
  107. MC Cornelis, L Qi, C Zhang, P Kraft, J Manson, T Cai, DJ Hunter, FB Hu. Joint Effects of Common Genetic Variants on the Risk for Type 2 Diabetes in U.S. Men and Women of European Ancestry. Annals of Internal Medicine 2009;150(8):541–550.
  108. FJ Rybicki, HJ Otero, ML Steigner, G Vorobiof, L Nallamshetty, D Mitsouras, H Ersoy, RT Mather, PF Judy, T Cai, K Coyner, K Schultz, AG Whitmore, MF Di Carli. Initial evaluation of coronary images from 320-detector row computed tomography. The International Journal of Cardiovascular Imaging 2008;24(5):535–546.
  109. K Chien, T Cai, H Hsu, T Su, W Chang, M Chen, Y Lee, FB Hu. A prediction model for type 2 diabetes risk among Chinese people. Diabetologia 2008;52(3):443–450.
  110. ML Steigner, HJ Otero, T Cai, D Mitsouras, L Nallamshetty, AG Whitmore, H Ersoy, NA Levit, MF Di Carli, FJ Rybicki. Narrowing the phase window width in prospectively ECG-gated single heart beat 320-detector row coronary CT angiography. The International Journal of Cardiovascular Imaging 2008;25(1):85–90.
  111. MT Lu, T Cai, H Ersoy, AG Whitmore, NA Levit, SZ Goldhaber, FJ Rybicki. Comparison of ECG-gated versus non-gated CT ventricular measurements in thirty patients with acute pulmonary embolism. The International Journal of Cardiovascular Imaging 2008;25(1):101–107.
  112. MT Lu, T Cai, H Ersoy, AG Whitmore, R Quiroz, SZ Goldhaber, FJ Rybicki. Interval Increase in Right-Left Ventricular Diameter Ratios at CT as a Predictor of 30-day Mortality after Acute Pulmonary Embolism: Initial Experience. Radiology 2008;246(1):281–287.
  113. H Ersoy, SZ Goldhaber, T Cai, T Luu, J Rosebrook, R Mulkern, F Rybicki. Time-Resolved MR Angiography: A Primary Screening Examination of Patients with Suspected Pulmonary Embolism and Contraindications to Administration of Iodinated Contrast Material. American Journal of Roentgenology 2007;188(5):1246–1254.
  114. JD MacKenzie, J Nazario-Larrieu, T Cai, MS Ledbetter, MA Duran-Mendicuti, PF Judy, FJ Rybicki. Reduced-Dose CT: Effect on Reader Evaluation in Detection of Pulmonary Embolism. American Journal of Roentgenology 2007;189(6):1371–1379.
  115. SK Chuang, T Cai. Predicting Clustered Dental Implant Survival Using Frailty Methods. Journal of Dental Research 2006;85(12):1147–1151.
  116. SK Chuang, T Cai, CW Douglass, LJ Wei, TB Dodson. Frailty Approach for the Analysis of Clustered Failure Time Observations in Dental Research. Journal of Dental Research 2005;84(1):54–58.
  117. JJ Rogus, T Cai, L Wei. Issues in genomic screening: Critical values, sample sizes, and the ability to detect linkage. Genetic Epidemiology 1999;17(S1):S697–S701.

© Tianxi Cai, Harvard University