PUBLICATIONS

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  1. Tobacco use and age are associated with different morphologic features of anterior communicating artery aneurysms. Sci Rep. 2021 Feb 26; 11(1):4791. View abstract
  2. Clinical Natural Language Processing for Radiation Oncology: A Review and Practical Primer. Int J Radiat Oncol Biol Phys. 2021 07 01; 110(3):641-655. View abstract
  3. Morphological variables associated with ruptured basilar tip aneurysms. Sci Rep. 2021 01 28; 11(1):2526. View abstract
  4. Geometric variations associated with posterior communicating artery aneurysms. J Neurointerv Surg. 2021 Jan 21. View abstract
  5. Vascular Geometry Associated with Anterior Communicating Artery Aneurysm Formation. World Neurosurg. 2021 02; 146:e1318-e1325. View abstract
  6. Surrounding vascular geometry associated with basilar tip aneurysm formation. Sci Rep. 2020 10 21; 10(1):17928. View abstract
  7. Adverse drug event presentation and tracking (ADEPT): semiautomated, high throughput pharmacovigilance using real-world data. JAMIA Open. 2020 Oct; 3(3):413-421. View abstract
  8. Age and morphology of posterior communicating artery aneurysms. Sci Rep. 2020 07 14; 10(1):11545. View abstract
  9. Mining Misdiagnosis Patterns from Biomedical Literature. AMIA Jt Summits Transl Sci Proc. 2020; 2020:360-366. View abstract
  10. Interactive Exploration of Longitudinal Cancer Patient Histories Extracted From Clinical Text. JCO Clin Cancer Inform. 2020 05; 4:412-420. View abstract
  11. Does BERT need domain adaptation for clinical negation detection? J Am Med Inform Assoc. 2020 04 01; 27(4):584-591. View abstract
  12. Adverse drug event rates in pediatric pulmonary hypertension: a comparison of real-world data sources. J Am Med Inform Assoc. 2020 02 01; 27(2):294-300. View abstract
  13. High-throughput phenotyping with electronic medical record data using a common semi-supervised approach (PheCAP). Nat Protoc. 2019 12; 14(12):3426-3444. View abstract
  14. Use of Narrative Concepts in Electronic Health Records to Validate Associations Between Genetic Factors and Response to Treatment of Inflammatory Bowel Diseases. Clin Gastroenterol Hepatol. 2020 07; 18(8):1890-1892. View abstract
  15. Use of Natural Language Processing to Extract Clinical Cancer Phenotypes from Electronic Medical Records. Cancer Res. 2019 11 01; 79(21):5463-5470. View abstract
  16. Morphological Variables Associated With Ruptured Middle Cerebral Artery Aneurysms. Neurosurgery. 2019 07 01; 85(1):75-83. View abstract
  17. Supervised methods to extract clinical events from cardiology reports in Italian. J Biomed Inform. 2019 07; 95:103219. View abstract
  18. Decreased Total Iron Binding Capacity May Correlate with Ruptured Intracranial Aneurysms. Sci Rep. 2019 04 15; 9(1):6054. View abstract
  19. Potential Impact of Initial Clinical Data on Adjustment of Pediatric Readmission Rates. Acad Pediatr. 2019 07; 19(5):589-598. View abstract
  20. Elevated International Normalized Ratio Is Associated With Ruptured Aneurysms. Stroke. 2018 09; 49(9):2046-2052. View abstract
  21. Association between aspirin dose and subarachnoid hemorrhage from saccular aneurysms: A case-control study. Neurology. 2018 09 18; 91(12):e1175-e1181. View abstract
  22. Low Serum Calcium and Magnesium Levels and Rupture of Intracranial Aneurysms. Stroke. 2018 07; 49(7):1747-1750. View abstract
  23. Lipid-Lowering Agents and High HDL (High-Density Lipoprotein) Are Inversely Associated With Intracranial Aneurysm Rupture. Stroke. 2018 05; 49(5):1148-1154. View abstract
  24. Clinical Natural Language Processing in languages other than English: opportunities and challenges. J Biomed Semantics. 2018 03 30; 9(1):12. View abstract
  25. Antihyperglycemic Agents Are Inversely Associated With Intracranial Aneurysm Rupture. Stroke. 2018 01; 49(1):34-39. View abstract
  26. Heroin Use Is Associated with Ruptured Saccular Aneurysms. Transl Stroke Res. 2018 08; 9(4):340-346. View abstract
  27. DeepPhe: A Natural Language Processing System for Extracting Cancer Phenotypes from Clinical Records. Cancer Res. 2017 11 01; 77(21):e115-e118. View abstract
  28. Capturing the Patient's Perspective: a Review of Advances in Natural Language Processing of Health-Related Text. Yearb Med Inform. 2017 Aug; 26(1):214-227. View abstract
  29. Phelan-McDermid syndrome data network: Integrating patient reported outcomes with clinical notes and curated genetic reports. Am J Med Genet B Neuropsychiatr Genet. 2018 10; 177(7):613-624. View abstract
  30. Association of intracranial aneurysm rupture with smoking duration, intensity, and cessation. Neurology. 2017 Sep 26; 89(13):1408-1415. View abstract
  31. Alcohol Consumption and Aneurysmal Subarachnoid Hemorrhage. Transl Stroke Res. 2018 02; 9(1):13-19. View abstract
  32. Towards generalizable entity-centric clinical coreference resolution. J Biomed Inform. 2017 05; 69:251-258. View abstract
  33. Large-scale identification of patients with cerebral aneurysms using natural language processing. Neurology. 2017 Jan 10; 88(2):164-168. View abstract
  34. An information model for computable cancer phenotypes. BMC Med Inform Decis Mak. 2016 09 15; 16(1):121. View abstract
  35. Suboptimal Clinical Documentation in Young Children with Severe Obesity at Tertiary Care Centers. Int J Pediatr. 2016; 2016:4068582. View abstract
  36. Electronic Health Record Based Algorithm to Identify Patients with Autism Spectrum Disorder. PLoS One. 2016; 11(7):e0159621. View abstract
  37. Developing an Algorithm to Detect Early Childhood Obesity in Two Tertiary Pediatric Medical Centers. Appl Clin Inform. 2016 07 20; 7(3):693-706. View abstract
  38. Normalizing acronyms and abbreviations to aid patient understanding of clinical texts: ShARe/CLEF eHealth Challenge 2013, Task 2. J Biomed Semantics. 2016 Jul 01; 7:43. View abstract
  39. Comparative Effectiveness of Infliximab and Adalimumab in Crohn's Disease and Ulcerative Colitis. Inflamm Bowel Dis. 2016 Apr; 22(4):880-5. View abstract
  40. PheKB: a catalog and workflow for creating electronic phenotype algorithms for transportability. J Am Med Inform Assoc. 2016 11; 23(6):1046-1052. View abstract
  41. Identification of Nonresponse to Treatment Using Narrative Data in an Electronic Health Record Inflammatory Bowel Disease Cohort. Inflamm Bowel Dis. 2016 Jan; 22(1):151-8. View abstract
  42. Semi-supervised Learning for Phenotyping Tasks. AMIA Annu Symp Proc. 2015; 2015:502-11. View abstract
  43. Multilayered temporal modeling for the clinical domain. J Am Med Inform Assoc. 2016 Mar; 23(2):387-95. View abstract
  44. Identification of subjects with polycystic ovary syndrome using electronic health records. Reprod Biol Endocrinol. 2015 Oct 29; 13:116. View abstract
  45. 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. View abstract
  46. An Introduction to Natural Language Processing: How You Can Get More From Those Electronic Notes You Are Generating. Pediatr Emerg Care. 2015 Jul; 31(7):536-41. View abstract
  47. Development of phenotype algorithms using electronic medical records and incorporating natural language processing. BMJ. 2015 Apr 24; 350:h1885. View abstract
  48. Developing a section labeler for clinical documents. AMIA Annu Symp Proc. 2014; 2014:636-44. View abstract
  49. Automatic identification of methotrexate-induced liver toxicity in patients with rheumatoid arthritis from the electronic medical record. J Am Med Inform Assoc. 2015 Apr; 22(e1):e151-61. View abstract
  50. Evaluating the state of the art in disorder recognition and normalization of the clinical narrative. J Am Med Inform Assoc. 2015 Jan; 22(1):143-54. View abstract
  51. Temporal Annotation in the Clinical Domain. Trans Assoc Comput Linguist. 2014 Apr; 2:143-154. View abstract
  52. Carrell et al. respond to "Observational research and the EHR". Am J Epidemiol. 2014 Mar 15; 179(6):762-3. View abstract
  53. Using natural language processing to improve efficiency of manual chart abstraction in research: the case of breast cancer recurrence. Am J Epidemiol. 2014 Mar 15; 179(6):749-58. View abstract
  54. Modeling disease severity in multiple sclerosis using electronic health records. PLoS One. 2013; 8(11):e78927. View abstract
  55. Normalization and standardization of electronic health records for high-throughput phenotyping: the SHARPn consortium. J Am Med Inform Assoc. 2013 Dec; 20(e2):e341-8. View abstract
  56. Discovering body site and severity modifiers in clinical texts. J Am Med Inform Assoc. 2014 May-Jun; 21(3):448-54. View abstract
  57. Improved de-identification of physician notes through integrative modeling of both public and private medical text. BMC Med Inform Decis Mak. 2013 Oct 02; 13:112. View abstract
  58. Automatic prediction of rheumatoid arthritis disease activity from the electronic medical records. PLoS One. 2013; 8(8):e69932. View abstract
  59. 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. View abstract
  60. 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. View abstract
  61. Formative evaluation of ontology learning methods for entity discovery by using existing ontologies as reference standards. Methods Inf Med. 2013; 52(4):308-16. View abstract
  62. Towards comprehensive syntactic and semantic annotations of the clinical narrative. J Am Med Inform Assoc. 2013 Sep-Oct; 20(5):922-30. View abstract
  63. 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. View abstract
  64. Psychiatric co-morbidity is associated with increased risk of surgery in Crohn's disease. Aliment Pharmacol Ther. 2013 Feb; 37(4):445-54. View abstract
  65. A common type system for clinical natural language processing. J Biomed Semantics. 2013 Jan 03; 4(1):1. View abstract
  66. Large-scale evaluation of automated clinical note de-identification and its impact on information extraction. J Am Med Inform Assoc. 2013 Jan 01; 20(1):84-94. View abstract
  67. Anaphoric reference in clinical reports: characteristics of an annotated corpus. J Biomed Inform. 2012 Jun; 45(3):507-21. View abstract
  68. Building a robust, scalable and standards-driven infrastructure for secondary use of EHR data: the SHARPn project. J Biomed Inform. 2012 Aug; 45(4):763-71. View abstract
  69. A system for coreference resolution for the clinical narrative. J Am Med Inform Assoc. 2012 Jul-Aug; 19(4):660-7. View abstract
  70. Automated discovery of drug treatment patterns for endocrine therapy of breast cancer within an electronic medical record. J Am Med Inform Assoc. 2012 Jun; 19(e1):e83-9. View abstract
  71. The MiPACQ clinical question answering system. AMIA Annu Symp Proc. 2011; 2011:171-80. View abstract
  72. The SHARPn project on secondary use of Electronic Medical Record data: progress, plans, and possibilities. AMIA Annu Symp Proc. 2011; 2011:248-56. View abstract
  73. Drug side effect extraction from clinical narratives of psychiatry and psychology patients. J Am Med Inform Assoc. 2011 Dec; 18 Suppl 1:i144-9. View abstract
  74. Overcoming barriers to NLP for clinical text: the role of shared tasks and the need for additional creative solutions. J Am Med Inform Assoc. 2011 Sep-Oct; 18(5):540-3. View abstract
  75. Coreference resolution: a review of general methodologies and applications in the clinical domain. J Biomed Inform. 2011 Dec; 44(6):1113-22. View abstract
  76. Anaphoric relations in the clinical narrative: corpus creation. J Am Med Inform Assoc. 2011 Jul-Aug; 18(4):459-65. View abstract
  77. The emerging role of electronic medical records in pharmacogenomics. Clin Pharmacol Ther. 2011 Mar; 89(3):379-86. View abstract
  78. CNTRO: A Semantic Web Ontology for Temporal Relation Inferencing in Clinical Narratives. AMIA Annu Symp Proc. 2010 Nov 13; 2010:787-91. View abstract
  79. Classification of medication status change in clinical narratives. AMIA Annu Symp Proc. 2010 Nov 13; 2010:762-6. View abstract
  80. Discovering peripheral arterial disease cases from radiology notes using natural language processing. AMIA Annu Symp Proc. 2010 Nov 13; 2010:722-6. View abstract
  81. Effectiveness of lexico-syntactic pattern matching for ontology enrichment with clinical documents. Methods Inf Med. 2011; 50(5):397-407. View abstract
  82. Leveraging informatics for genetic studies: use of the electronic medical record to enable a genome-wide association study of peripheral arterial disease. J Am Med Inform Assoc. 2010 Sep-Oct; 17(5):568-74. View abstract
  83. Mayo clinical Text Analysis and Knowledge Extraction System (cTAKES): architecture, component evaluation and applications. J Am Med Inform Assoc. 2010 Sep-Oct; 17(5):507-13. View abstract
  84. The Rochester Epidemiology Project: exploiting the capabilities for population-based research in rheumatic diseases. Rheumatology (Oxford). 2011 Jan; 50(1):6-15. View abstract
  85. Mayo clinic smoking status classification system: extensions and improvements. AMIA Annu Symp Proc. 2009 Nov 14; 2009:619-23. View abstract
  86. Towards temporal relation discovery from the clinical narrative. AMIA Annu Symp Proc. 2009 Nov 14; 2009:568-72. View abstract
  87. Discerning tumor status from unstructured MRI reports--completeness of information in existing reports and utility of automated natural language processing. J Digit Imaging. 2010 Apr; 23(2):119-32. View abstract
  88. Automatically extracting cancer disease characteristics from pathology reports into a Disease Knowledge Representation Model. J Biomed Inform. 2009 Oct; 42(5):937-49. View abstract
  89. The first step toward data reuse: disambiguating concept representation of the locally developed ICU nursing flowsheets. Comput Inform Nurs. 2008 Sep-Oct; 26(5):282-9. View abstract
  90. Word sense disambiguation across two domains: biomedical literature and clinical notes. J Biomed Inform. 2008 Dec; 41(6):1088-100. View abstract
  91. Extracting information from textual documents in the electronic health record: a review of recent research. Yearb Med Inform. 2008; 128-44. View abstract
  92. Mayo clinic NLP system for patient smoking status identification. J Am Med Inform Assoc. 2008 Jan-Feb; 15(1):25-8. View abstract
  93. Formalizing the International Classification of Functioning, Disability, and Health (ICF) using Formal Concept Analysis (FCA). AMIA Annu Symp Proc. 2007 Oct 11; 994. View abstract
  94. Toward near real-time acuity estimation: a feasibility study. Nurs Res. 2007 Jul-Aug; 56(4):288-94. View abstract
  95. Building and evaluating annotated corpora for medical NLP systems. AMIA Annu Symp Proc. 2006; 1050. View abstract
  96. Content coverage of SNOMED-CT toward the ICU nursing flowsheets and the acuity indicators. Stud Health Technol Inform. 2006; 122:722-6. View abstract
  97. Frame semantics and the domain of functioning, disability and health. AMIA Annu Symp Proc. 2005; 1106. View abstract
  98. A term extraction tool for expanding content in the domain of functioning, disability, and health: proof of concept. J Biomed Inform. 2003 Aug-Oct; 36(4-5):250-9. View abstract
  99. Testing the generalizability of the ISO model for nursing diagnoses. AMIA Annu Symp Proc. 2003; 274-8. View abstract
  100. A data-driven approach for extracting "the most specific term" for ontology development. AMIA Annu Symp Proc. 2003; 579-83. View abstract