Publications
Access the publications and learn how to cite TIES in your manuscripts.- Tseytlin E, Mitchell K, Legowski E, Corrigan J, Chavan G, Jacobson RS. NOBLE – Flexible concept recognition for large-scale biomedical natural language processing. BMC Bioinformatics 2016 17:32. PMID: 26763894 PMCID: PMC4712516
- Jacobson RS, Becich MJ, Bollag RJ, Chavan G, Corrigan J, Dhir R, et al. A federated network for translational cancer research using clinical data and biospecimens. Cancer Res. 2015 December 15;75(24):5194-201.
- Crowley RS, Castine M, Mitchell KJ, Chavan G, McSherry T, Feldman M. caTIES
A Grid Based System for Coding and Retrieval of Surgical Pathology Reports and Tissue Specimens In Support Of Translational Research.
J Am Med Inform Assoc. 2010 May 1;17(3):253-64. PMID: 20442142
- Mitchell KJ, Becich MJ, Berman, JJ, Chapman WW, Gilbertson J, Gupta D, Harrison J, Legowski E, and Crowley RS.
Implementation and Evaluation of a Negation Tagger in a Pipeline-based System for Information Extraction from Pathology Reports.
Proc MEDINFO 2004; 11(Pt 1): 663-67.
- Liu K, Mitchell KJ, Chapman WW, and Crowley RS.
Automating tissue bank annotation from pathology reports – comparison to a gold standard expert annotation set.
Proc AMIA Symp, 2005 460-464, PMCID: PMC1560700
- Tobias J, Chilukuri R, Komatsoulis GA, Mohanty S, Sioutos N, Warzel DB, Wright LW, Crowley RS.
The CAP cancer protocols – a case study of caCORE based data standards implementation to integrate with the Cancer Biomedical Informatics Grid.
BMC Med Inform Decis Mak. 2006 Jun 20; 6:25, PMCID: PMC1524939
- Drake TA, Braun J, Marchevsky A, Kohane IS, Fletcher C, Chueh H, Beckwith B, Berkowicz D, Kuo F, Zeng QT, Balis U, Holzbach A, McMurry A, Gee CE, McDonald CJ, Schadow G, Davis M, Hattab EM, Blevins L, Hook J, Becich M, Crowley RS, Taube SE, Berman J;
A system for sharing routine surgical pathology specimens across institutions: the Shared Pathology Informatics Network.
Hum Pathol. 2007 Aug; 38(8): 1212-25
- Liu K, Chapman W, Hwa R, Crowley RS.
Heuristic sample selection to minimize reference standard training set for a part-of-speech tagger.
J Am Med Inform Assoc. 2007 Sep-Oct; 14 (5):641-50.
- Mohanty SK, Parwani AV, Crowley RS, Winters S, Becich MJ.
The Importance of Pathology Informatics in Translational Research.
Adv Anat Pathol. 2007 Sep;14(5):320-22
- Piwowar H, Becich MJ, Bilofsky H, Crowley RS.
Towards a data sharing culture: Recommendations for leadership from Academic Health Centers.
PLoS Med. 2008 Sep 2;5(9):e183, PMCID: PMC2528049
- Manion FJ, Robbins RJ, Weems WA, Crowley RS.
Security and privacy requirements for a multi-institutional cancer research data grid: an interview-based study.
BMC Med Inform Decis Mak. 2009 Jun 15;9(1):31. PMCID: PMC270961
- Lui K, Hogan WR, Crowley RS.
Natural Language Processing Methods and Systems for Biomedical Ontology Learning.
J Biomed Inform. 2011 Feb;44(1):163-79. PMCID: PMC2990796
- Liu K, Chapman WW, Savova G, Chute CG, Sioutos N, Crowley RS.
Effectiveness of Lexico-syntactic Pattern Matching for Ontology Enrichment with Clinical Documents.
Methods Inf Med. Oct 17, 2011;50(5):397-407. PMCID: PMC3125434
- Savova GK, Chapman WW, Zheng J, Crowley RS.
Anaphoric relations in the clinical narrative: corpus creation.
J Am Med Inform Assoc. 2011 Jul 1;18(4):459-65. PMCID:PMC3128403
- Chapman WW, Savova GK, Zheng J, Tharp M, Crowley R.
Anaphoric Reference in Clinical Reports: Characteristics of an Annotated Corpus.
J Biomed Inform. 2012 Jun;45(3):507-21. doi: 10.1016/j.jbi.2012.01.010. Epub 2012 Feb 9. PMID: 22343015
- Liu K, Mitchell KJ, Chapman WW, Savova GK, Sioutos N, Ruben DL, Crowley RS.
Formative Evaluation of Ontology Learning Methods by Using Existing Ontologies as Reference Standards.
Methods of Information in Medicine, 2013 May 13;52(4). PMID: 23666409
For manuscripts that make use of the TIES system to access clinical data or biospecimens, we request that you add the following comment to your acknowledgments section: