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Items: 41

1.

Use of Natural Language Processing to Extract Clinical Cancer Phenotypes from Electronic Medical Records.

Savova GK, Danciu I, Alamudun F, Miller T, Lin C, Bitterman DS, Tourassi G, Warner JL.

Cancer Res. 2019 Nov 1;79(21):5463-5470. doi: 10.1158/0008-5472.CAN-19-0579. Epub 2019 Aug 8. Review.

PMID:
31395609
2.

Supervised methods to extract clinical events from cardiology reports in Italian.

Viani N, Miller TA, Napolitano C, Priori SG, Savova GK, Bellazzi R, Sacchi L.

J Biomed Inform. 2019 Jul;95:103219. doi: 10.1016/j.jbi.2019.103219. Epub 2019 May 28.

PMID:
31150777
3.

Potential Impact of Initial Clinical Data on Adjustment of Pediatric Readmission Rates.

Nakamura MM, Toomey SL, Zaslavsky AM, Petty CR, Lin C, Savova GK, Rose S, Brittan MS, Lin JL, Bryant MC, Ashrafzadeh S, Schuster MA.

Acad Pediatr. 2019 Jul;19(5):589-598. doi: 10.1016/j.acap.2018.09.006. Epub 2018 Nov 20.

PMID:
30470563
4.

DeepPhe: A Natural Language Processing System for Extracting Cancer Phenotypes from Clinical Records.

Savova GK, Tseytlin E, Finan S, Castine M, Miller T, Medvedeva O, Harris D, Hochheiser H, Lin C, Chavan G, Jacobson RS.

Cancer Res. 2017 Nov 1;77(21):e115-e118. doi: 10.1158/0008-5472.CAN-17-0615.

5.

Suboptimal Clinical Documentation in Young Children with Severe Obesity at Tertiary Care Centers.

Brady CC, Thaker VV, Lingren T, Woo JG, Kennebeck SS, Namjou-Khales B, Roach A, Bickel JP, Patibandla N, Savova GK, Solti I, Holm IA, Harley JB, Kohane IS, Crimmins NA.

Int J Pediatr. 2016;2016:4068582. Epub 2016 Sep 6.

6.

Multilayered temporal modeling for the clinical domain.

Lin C, Dligach D, Miller TA, Bethard S, Savova GK.

J Am Med Inform Assoc. 2016 Mar;23(2):387-95. doi: 10.1093/jamia/ocv113. Epub 2015 Oct 31.

7.

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

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

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

8.

Development of phenotype algorithms using electronic medical records and incorporating natural language processing.

Liao KP, Cai T, Savova GK, Murphy SN, Karlson EW, Ananthakrishnan AN, Gainer VS, Shaw SY, Xia Z, Szolovits P, Churchill S, Kohane I.

BMJ. 2015 Apr 24;350:h1885. doi: 10.1136/bmj.h1885. No abstract available.

9.

Semi-supervised Learning for Phenotyping Tasks.

Dligach D, Miller T, Savova GK.

AMIA Annu Symp Proc. 2015 Nov 5;2015:502-11. eCollection 2015.

10.

Automatic identification of methotrexate-induced liver toxicity in patients with rheumatoid arthritis from the electronic medical record.

Lin C, Karlson EW, Dligach D, Ramirez MP, Miller TA, Mo H, Braggs NS, Cagan A, Gainer V, Denny JC, Savova GK.

J Am Med Inform Assoc. 2015 Apr;22(e1):e151-61. doi: 10.1136/amiajnl-2014-002642. Epub 2014 Oct 25.

11.

Developing a section labeler for clinical documents.

Haug PJ, Wu X, Ferraro JP, Savova GK, Huff SM, Chute CG.

AMIA Annu Symp Proc. 2014 Nov 14;2014:636-44. eCollection 2014.

12.

Modeling disease severity in multiple sclerosis using electronic health records.

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.

PLoS One. 2013 Nov 11;8(11):e78927. doi: 10.1371/journal.pone.0078927. eCollection 2013.

13.

Normalization and standardization of electronic health records for high-throughput phenotyping: the SHARPn consortium.

Pathak J, Bailey KR, Beebe CE, Bethard S, Carrell DC, Chen PJ, Dligach D, Endle CM, Hart LA, Haug PJ, Huff SM, Kaggal VC, Li D, Liu H, Marchant K, Masanz J, Miller T, Oniki TA, Palmer M, Peterson KJ, Rea S, Savova GK, Stancl CR, Sohn S, Solbrig HR, Suesse DB, Tao C, Taylor DP, Westberg L, Wu S, Zhuo N, Chute CG.

J Am Med Inform Assoc. 2013 Dec;20(e2):e341-8. doi: 10.1136/amiajnl-2013-001939. Epub 2013 Nov 4.

14.

Discovering body site and severity modifiers in clinical texts.

Dligach D, Bethard S, Becker L, Miller T, Savova GK.

J Am Med Inform Assoc. 2014 May-Jun;21(3):448-54. doi: 10.1136/amiajnl-2013-001766. Epub 2013 Oct 3.

15.

Automatic prediction of rheumatoid arthritis disease activity from the electronic medical records.

Lin C, Karlson EW, Canhao H, Miller TA, Dligach D, Chen PJ, Perez RN, Shen Y, Weinblatt ME, Shadick NA, Plenge RM, Savova GK.

PLoS One. 2013 Aug 16;8(8):e69932. doi: 10.1371/journal.pone.0069932. eCollection 2013.

16.

Formative evaluation of ontology learning methods for entity discovery by using existing ontologies as reference standards.

Liu K, Mitchell KJ, Chapman WW, Savova GK, Sioutos N, Rubin DL, Crowley RS.

Methods Inf Med. 2013;52(4):308-16. doi: 10.3414/ME12-01-0029. Epub 2013 May 13.

PMID:
23666409
17.

Towards comprehensive syntactic and semantic annotations of the clinical narrative.

Albright D, Lanfranchi A, Fredriksen A, Styler WF 4th, Warner C, Hwang JD, Choi JD, Dligach D, Nielsen RD, Martin J, Ward W, Palmer M, Savova GK.

J Am Med Inform Assoc. 2013 Sep-Oct;20(5):922-30. doi: 10.1136/amiajnl-2012-001317. Epub 2013 Jan 25.

18.

A common type system for clinical natural language processing.

Wu ST, Kaggal VC, Dligach D, Masanz JJ, Chen P, Becker L, Chapman WW, Savova GK, Liu H, Chute CG.

J Biomed Semantics. 2013 Jan 3;4(1):1. doi: 10.1186/2041-1480-4-1.

19.

Anaphoric reference in clinical reports: characteristics of an annotated corpus.

Chapman WW, Savova GK, Zheng J, Tharp M, Crowley R.

J Biomed Inform. 2012 Jun;45(3):507-21. doi: 10.1016/j.jbi.2012.01.010. Epub 2012 Feb 9.

20.

A system for coreference resolution for the clinical narrative.

Zheng J, Chapman WW, Miller TA, Lin C, Crowley RS, Savova GK.

J Am Med Inform Assoc. 2012 Jul-Aug;19(4):660-7. doi: 10.1136/amiajnl-2011-000599. Epub 2012 Jan 31.

21.

The SHARPn project on secondary use of Electronic Medical Record data: progress, plans, and possibilities.

Chute CG, Pathak J, Savova GK, Bailey KR, Schor MI, Hart LA, Beebe CE, Huff SM.

AMIA Annu Symp Proc. 2011;2011:248-56. Epub 2011 Oct 22.

22.

The MiPACQ clinical question answering system.

Cairns BL, Nielsen RD, Masanz JJ, Martin JH, Palmer MS, Ward WH, Savova GK.

AMIA Annu Symp Proc. 2011;2011:171-80. Epub 2011 Oct 22.

23.

Automated discovery of drug treatment patterns for endocrine therapy of breast cancer within an electronic medical record.

Savova GK, Olson JE, Murphy SP, Cafourek VL, Couch FJ, Goetz MP, Ingle JN, Suman VJ, Chute CG, Weinshilboum RM.

J Am Med Inform Assoc. 2012 Jun;19(e1):e83-9. Epub 2011 Dec 1.

24.

Drug side effect extraction from clinical narratives of psychiatry and psychology patients.

Sohn S, Kocher JP, Chute CG, Savova GK.

J Am Med Inform Assoc. 2011 Dec;18 Suppl 1:i144-9. doi: 10.1136/amiajnl-2011-000351. Epub 2011 Sep 21.

25.

Coreference resolution: a review of general methodologies and applications in the clinical domain.

Zheng J, Chapman WW, Crowley RS, Savova GK.

J Biomed Inform. 2011 Dec;44(6):1113-22. doi: 10.1016/j.jbi.2011.08.006. Epub 2011 Aug 12. Review.

26.

Overcoming barriers to NLP for clinical text: the role of shared tasks and the need for additional creative solutions.

Chapman WW, Nadkarni PM, Hirschman L, D'Avolio LW, Savova GK, Uzuner O.

J Am Med Inform Assoc. 2011 Sep-Oct;18(5):540-3. doi: 10.1136/amiajnl-2011-000465. No abstract available.

27.

Anaphoric relations in the clinical narrative: corpus creation.

Savova GK, Chapman WW, Zheng J, Crowley RS.

J Am Med Inform Assoc. 2011 Jul-Aug;18(4):459-65. doi: 10.1136/amiajnl-2011-000108. Epub 2011 Apr 1.

28.

Classification of medication status change in clinical narratives.

Sohn S, Murphy SP, Masanz JJ, Kocher JP, Savova GK.

AMIA Annu Symp Proc. 2010 Nov 13;2010:762-6.

29.

Discovering peripheral arterial disease cases from radiology notes using natural language processing.

Savova GK, Fan J, Ye Z, Murphy SP, Zheng J, Chute CG, Kullo IJ.

AMIA Annu Symp Proc. 2010 Nov 13;2010:722-6.

30.

Leveraging informatics for genetic studies: use of the electronic medical record to enable a genome-wide association study of peripheral arterial disease.

Kullo IJ, Fan J, Pathak J, Savova GK, Ali Z, Chute CG.

J Am Med Inform Assoc. 2010 Sep-Oct;17(5):568-74. doi: 10.1136/jamia.2010.004366.

31.

Mayo clinical Text Analysis and Knowledge Extraction System (cTAKES): architecture, component evaluation and applications.

Savova GK, Masanz JJ, Ogren PV, Zheng J, Sohn S, Kipper-Schuler KC, Chute CG.

J Am Med Inform Assoc. 2010 Sep-Oct;17(5):507-13. doi: 10.1136/jamia.2009.001560.

32.

Discerning tumor status from unstructured MRI reports--completeness of information in existing reports and utility of automated natural language processing.

Cheng LT, Zheng J, Savova GK, Erickson BJ.

J Digit Imaging. 2010 Apr;23(2):119-32. doi: 10.1007/s10278-009-9215-7. Epub 2009 May 30. Review.

33.

Mayo clinic smoking status classification system: extensions and improvements.

Sohn S, Savova GK.

AMIA Annu Symp Proc. 2009 Nov 14;2009:619-23.

34.

The first step toward data reuse: disambiguating concept representation of the locally developed ICU nursing flowsheets.

Kim H, Harris MR, Savova GK, Chute CG.

Comput Inform Nurs. 2008 Sep-Oct;26(5):282-9. doi: 10.1097/01.NCN.0000304839.59831.28.

35.
36.

Extracting information from textual documents in the electronic health record: a review of recent research.

Meystre SM, Savova GK, Kipper-Schuler KC, Hurdle JF.

Yearb Med Inform. 2008:128-44. Review.

PMID:
18660887
37.

Word sense disambiguation across two domains: biomedical literature and clinical notes.

Savova GK, Coden AR, Sominsky IL, Johnson R, Ogren PV, de Groen PC, Chute CG.

J Biomed Inform. 2008 Dec;41(6):1088-100. doi: 10.1016/j.jbi.2008.02.003. Epub 2008 Mar 4.

38.

Mayo clinic NLP system for patient smoking status identification.

Savova GK, Ogren PV, Duffy PH, Buntrock JD, Chute CG.

J Am Med Inform Assoc. 2008 Jan-Feb;15(1):25-8. Epub 2007 Oct 18.

39.

Toward near real-time acuity estimation: a feasibility study.

Kim H, Harris MR, Savova GK, Speedie SM, Chute CG.

Nurs Res. 2007 Jul-Aug;56(4):288-94.

PMID:
17625469
40.

A data-driven approach for extracting "the most specific term" for ontology development.

Savova GK, Harris M, Johnson T, Pakhomov SV, Chute CG.

AMIA Annu Symp Proc. 2003:579-83.

41.

A term extraction tool for expanding content in the domain of functioning, disability, and health: proof of concept.

Harris MR, Savova GK, Johnson TM, Chute CG.

J Biomed Inform. 2003 Aug-Oct;36(4-5):250-9.

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