• 4928 Citations
  • 38 Scopus h-Index
19992020

Research output per year

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Research Output

2020

A corpus-driven standardization framework for encoding clinical problems with HL7 FHIR

Peterson, K. J., Jiang, G. & Liu, H., Oct 2020, In : Journal of Biomedical Informatics. 110, 103541.

Research output: Contribution to journalArticle

A deep profiling and visualization framework to audit clinical assessment variation

Wen, A., Shen, F., Moon, S., Liu, H. D. & Fan, J., Jul 2020, Proceedings - 2020 IEEE 33rd International Symposium on Computer-Based Medical Systems, CBMS 2020. de Herrera, A. G. S., Rodriguez Gonzalez, A., Santosh, KC., Temesgen, Z., Kane, B. & Soda, P. (eds.). Institute of Electrical and Electronics Engineers Inc., p. 546-551 6 p. 9183364. (Proceedings - IEEE Symposium on Computer-Based Medical Systems; vol. 2020-July).

Research output: Chapter in Book/Report/Conference proceedingConference contribution

A query taxonomy describes performance of patient-level retrieval from electronic health record data

Chamberlin, S. R., Bedrick, S. D., Cohen, A. M., Wang, Y., Wen, A., Liu, S., Liu, H. & Hersh, W. R., Jan 1 2020, In : CEUR Workshop Proceedings. 2551, p. 27-33 7 p.

Research output: Contribution to journalConference article

Open Access
4 Scopus citations

Assessment of the impact of EHR heterogeneity for clinical research through a case study of silent brain infarction

Fu, S., Leung, L. Y., Raulli, A. O., Kallmes, D. F., Kinsman, K. A., Nelson, K. B., Clark, M. S., Luetmer, P. H., Kingsbury, P. R., Kent, D. M. & Liu, H., Mar 30 2020, In : BMC Medical Informatics and Decision Making. 20, 1, 60.

Research output: Contribution to journalArticle

Open Access
1 Scopus citations

Clinical concept extraction: A methodology review

Fu, S., Chen, D., He, H., Liu, S., Moon, S., Peterson, K. J., Shen, F., Wang, L., Wang, Y., Wen, A., Zhao, Y., Sohn, S. & Liu, H. D., Sep 2020, In : Journal of Biomedical Informatics. 109, 103526.

Research output: Contribution to journalReview article

Cohort Profile: The Right Drug, Right Dose, Right Time: Using Genomic Data to Individualize Treatment Protocol (RIGHT Protocol)

Bielinski, S. J., St Sauver, J. L., Olson, J. E., Larson, N. B., Black, J. L., Scherer, S. E., Bernard, M. E., Boerwinkle, E., Borah, B. J., Caraballo, P. J., Curry, T. B., Doddapaneni, H. V., Formea, C. M., Freimuth, R. R., Gibbs, R. A., Giri, J., Hathcock, M. A., Hu, J., Jacobson, D. J., Jones, L. A. & 28 others, Kalla, S., Koep, T. H., Korchina, V., Kovar, C. L., Lee, S., Liu, H., Matey, E. T., McGree, M. E., McAllister, T. M., Moyer, A. M., Muzny, D. M., Nicholson, W. T., Oyen, L. J., Qin, X., Raj, R., Roger, V. L., Rohrer Vitek, C. R., Ross, J. L., Sharp, R. R., Takahashi, P. Y., Venner, E., Walker, K., Wang, L., Wang, Q., Wright, J. A., Wu, T. J., Wang, L. & Weinshilboum, R. M., Feb 1 2020, In : International journal of epidemiology. 49, 1, p. 23-24K

Research output: Contribution to journalArticle

6 Scopus citations
Open Access

Expert artificial intelligence-based natural language processing characterises childhood asthma

Seol, H. Y., Rolfes, M. C., Chung, W., Sohn, S., Ryu, E., Park, M. A., Kita, H., Ono, J., Croghan, I., Armasu, S. M., Castro-Rodriguez, J. A., Weston, J. D., Liu, H. & Juhn, Y., Feb 4 2020, In : BMJ Open Respiratory Research. 7, 1, e000524.

Research output: Contribution to journalArticle

Open Access
1 Scopus citations

Impact of Diverse Data Sources on Computational Phenotyping

Wang, L., Olson, J. E., Bielinski, S. J., St. Sauver, J. L., Fu, S., He, H., Cicek, M. S., Hathcock, M. A., Cerhan, J. R. & Liu, H., Jun 3 2020, In : Frontiers in Genetics. 11, 556.

Research output: Contribution to journalArticle

Open Access

Investigating the impact of disease and health record duration on the eMERGE algorithm for rheumatoid arthritis

Kronzer, V. L., Wang, L., Liu, H., Davis, J. M., Sparks, J. A. & Crowson, C. S., Apr 1 2020, In : Journal of the American Medical Informatics Association : JAMIA. 27, 4, p. 601-605 5 p.

Research output: Contribution to journalArticle

Time event ontology (TEO): to support semantic representation and reasoning of complex temporal relations of clinical events

Li, F., Du, J., He, Y., Song, H. Y., Madkour, M., Rao, G., Xiang, Y., Luo, Y., Chen, H. W., Liu, S., Wang, L., Liu, H., Xu, H. & Tao, C. D., Jul 1 2020, In : Journal of the American Medical Informatics Association : JAMIA. 27, 7, p. 1046-1056 11 p.

Research output: Contribution to journalArticle

Unsupervised machine learning for the discovery of latent disease clusters and patient subgroups using electronic health records

Wang, Y., Zhao, Y., Therneau, T. M., Atkinson, E. J., Tafti, A. P., Zhang, N., Amin, S., Limper, A. H., Khosla, S. & Liu, H., Feb 2020, In : Journal of Biomedical Informatics. 102, 103364.

Research output: Contribution to journalArticle

1 Scopus citations
2019

Achievability to Extract Specific Date Information for Cancer Research

Wang, L., Wampfler, J., Dispenzieri, A., Xu, H., Yang, P. & Liu, H., 2019, In : AMIA ... Annual Symposium proceedings. AMIA Symposium. 2019, p. 893-902 10 p.

Research output: Contribution to journalArticle

9 Scopus citations

Annotating Cohort Data Elements with OHDSI Common Data Model to Promote Research Reproducibility

Zhao, Y., Wang, Y., Wang, H., Yan, B., Shen, F., Peterson, K. J., Rocca, W. A., St. Sauver, J. & Liu, H. D., Jan 21 2019, Proceedings - 2018 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2018. Schmidt, H., Griol, D., Wang, H., Baumbach, J., Zheng, H., Callejas, Z., Hu, X., Dickerson, J. & Zhang, L. (eds.). Institute of Electrical and Electronics Engineers Inc., p. 1310-1317 8 p. 8621269. (Proceedings - 2018 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2018).

Research output: Chapter in Book/Report/Conference proceedingConference contribution

A privacy-preserving distributed filtering framework for NLP artifacts

Sadat, M. N., Aziz, M. M. A., Mohammed, N., Pakhomov, S., Liu, H. & Jiang, X., Sep 7 2019, In : BMC Medical Informatics and Decision Making. 19, 1, 183.

Research output: Contribution to journalArticle

Open Access
1 Scopus citations

Artificial intelligence to organize patient portal messages: A journey from an ensemble deep learning text classification to rule-based named entity recognition

Tafti, A. P., Fu, S., Khurana, A., Mastorakos, G. M., Poole, K. G., Traub, S. J., Yiannias, J. A. & Liu, H., Nov 2019, Proceedings - 2019 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2019. Yoo, I., Bi, J. & Hu, X. T. (eds.). Institute of Electrical and Electronics Engineers Inc., p. 1380-1387 8 p. 8982942. (Proceedings - 2019 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2019).

Research output: Chapter in Book/Report/Conference proceedingConference contribution

Automated extraction of sudden cardiac death risk factors in hypertrophic cardiomyopathy patients by natural language processing

Moon, S., Liu, S., Scott, C. G., Samudrala, S., Abidian, M. M., Geske, J. B., Noseworthy, P. A., Shellum, J. L., Chaudhry, R., Ommen, S. R., Nishimura, R. A., Liu, H. & Arruda-Olson, A. M., Aug 2019, In : International Journal of Medical Informatics. 128, p. 32-38 7 p.

Research output: Contribution to journalArticle

Open Access
4 Scopus citations
1 Scopus citations

Desiderata for delivering NLP to accelerate healthcare AI advancement and a Mayo Clinic NLP-as-a-service implementation

Wen, A., Fu, S., Moon, S., El Wazir, M., Rosenbaum, A., Kaggal, V. C., Liu, S., Sohn, S., Liu, H. D. & Fan, J., Dec 1 2019, In : npj Digital Medicine. 2, 1, 130.

Research output: Contribution to journalArticle

Open Access
1 Scopus citations

Detecting lifestyle risk factors for chronic kidney disease with comorbidities: Association rule mining analysis of web-based survey data

Peng, S., Shen, F., Wen, A., Wang, L., Fan, Y., Liu, X. & Liu, H., Dec 1 2019, In : Journal of medical Internet research. 21, 12, e14204.

Research output: Contribution to journalReview article

Open Access
1 Scopus citations
5 Scopus citations

Developing a FHIR-based EHR phenotyping framework: A case study for identification of patients with obesity and multiple comorbidities from discharge summaries

Hong, N., Wen, A., Stone, D. J., Tsuji, S., Kingsbury, P. R., Rasmussen, L. V., Pacheco, J. A., Adekkanattu, P., Wang, F., Luo, Y., Pathak, J., Liu, H. & Jiang, G., Nov 2019, In : Journal of Biomedical Informatics. 99, 103310.

Research output: Contribution to journalArticle

2 Scopus citations

Developing an FHIR-Based Computational Pipeline for Automatic Population of Case Report Forms for Colorectal Cancer Clinical Trials Using Electronic Health Records

Zong, N., Wen, A., Stone, D. J., Sharma, D. K., Wang, C., Yu, Y., Liu, H., Shi, Q. & Jiang, G., 2019, In : JCO Clinical Cancer Informatics. 3, p. 201-209 9 p.

Research output: Contribution to journalArticle

Open Access
1 Scopus citations

Developing customizable cancer information extraction modules for pathology reports using clamp

Soysal, E., Warner, J. L., Wang, J., Jiang, M., Harvey, K., Jain, S. K., Dong, X., Song, H. Y., Siddhanamatha, H., Wang, L., Dai, Q., Chen, Q., Du, X., Tao, C. D., Yang, P., Denny, J. C., Liu, H. & Xu, H., Aug 21 2019, MEDINFO 2019: Health and Wellbeing e-Networks for All - Proceedings of the 17th World Congress on Medical and Health Informatics. Seroussi, B., Ohno-Machado, L., Ohno-Machado, L. & Seroussi, B. (eds.). IOS Press, p. 1041-1045 5 p. (Studies in Health Technology and Informatics; vol. 264).

Research output: Chapter in Book/Report/Conference proceedingConference contribution

Discovering associations between problem list and practice setting

Wang, L., Wang, Y., Shen, F., Rastegar-Mojarad, M. & Liu, H., Apr 4 2019, In : BMC Medical Informatics and Decision Making. 19, 69.

Research output: Contribution to journalArticle

Open Access
2 Scopus citations

Discovery of noncancer drug effects on survival in electronic health records of patients with cancer: A new paradigm for drug repurposing

Wu, Y., Warner, J. L., Wang, L., Jiang, M., Xu, J., Chen, Q., Nian, H., Dai, Q., Du, X., Yang, P., Denny, J. C., Liu, H. & Xu, H., 2019, In : JCO Clinical Cancer Informatics. 3

Research output: Contribution to journalArticle

Open Access
2 Scopus citations

Early identification of childhood asthma: The role of informatics in an era of electronic health records

Seol, H. Y., Sohn, S., Liu, H., Wi, C. I., Ryu, E., Park, M. A. & Juhn, Y. J., 2019, In : Frontiers in Pediatrics. 7, APR, 113.

Research output: Contribution to journalReview article

Open Access
1 Scopus citations

Enhancing Clinical Information Retrieval through Context-Aware Queries and Indices

Wen, A., Wang, Y., Kaggal, V. C., Liu, S., Liu, H. & Fan, J., Dec 2019, Proceedings - 2019 IEEE International Conference on Big Data, Big Data 2019. Baru, C., Huan, J., Khan, L., Hu, X. T., Ak, R., Tian, Y., Barga, R., Zaniolo, C., Lee, K. & Ye, Y. F. (eds.). Institute of Electrical and Electronics Engineers Inc., p. 2800-2807 8 p. 9006241. (Proceedings - 2019 IEEE International Conference on Big Data, Big Data 2019).

Research output: Chapter in Book/Report/Conference proceedingConference contribution

Ensembles of natural language processing systems for portable phenotyping solutions

Liu, C., Ta, C. N., Rogers, J. R., Li, Z., Lee, J., Butler, A. M., Shang, N., Kury, F. S. P., Wang, L., Shen, F., Liu, H., Ena, L., Friedman, C. & Weng, C., Dec 2019, In : Journal of Biomedical Informatics. 100, 103318.

Research output: Contribution to journalArticle

1 Scopus citations

HPO2Vec+: Leveraging heterogeneous knowledge resources to enrich node embeddings for the Human Phenotype Ontology

Shen, F., Peng, S., Fan, Y., Wen, A., Liu, S., Wang, Y., Wang, L. & Liu, H., Aug 2019, In : Journal of Biomedical Informatics. 96, 103246.

Research output: Contribution to journalArticle

4 Scopus citations

Integrating word embedding neural networks with pubmed abstracts to extract keyword proximity of chronic diseases

Tafti, A. P., Wang, Y., Shen, F., Sagheb, E., Kingsbury, P. & Liu, H., May 2019, 2019 IEEE EMBS International Conference on Biomedical and Health Informatics, BHI 2019 - Proceedings. Institute of Electrical and Electronics Engineers Inc., 8834626. (2019 IEEE EMBS International Conference on Biomedical and Health Informatics, BHI 2019 - Proceedings).

Research output: Chapter in Book/Report/Conference proceedingConference contribution

1 Scopus citations

Leveraging Association Rule Mining to Detect Pathophysiological Mechanisms of Chronic Kidney Disease Complicated by Metabolic Syndrome

Peng, S., Fan, Y., Wang, L., Wen, A., Liu, X., Liu, H. & Shen, F., Jan 21 2019, Proceedings - 2018 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2018. Schmidt, H., Griol, D., Wang, H., Baumbach, J., Zheng, H., Callejas, Z., Hu, X., Dickerson, J. & Zhang, L. (eds.). Institute of Electrical and Electronics Engineers Inc., p. 1302-1309 8 p. 8621226. (Proceedings - 2018 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2018).

Research output: Chapter in Book/Report/Conference proceedingConference contribution

2 Scopus citations

Natural language processing for populating lung cancer clinical research data

Wang, L., Luo, L., Wang, Y., Wampfler, J., Yang, P. & Liu, H., Dec 5 2019, In : BMC Medical Informatics and Decision Making. 19, 239.

Research output: Contribution to journalArticle

Open Access
3 Scopus citations

Natural language processing for the identification of silent brain infarcts from neuroimaging reports

Fu, S., Leung, L. Y., Wang, Y., Raulli, A. O., Kallmes, D. F., Kinsman, K. A., Nelson, K. B., Clark, M. S., Luetmer, P. H., Kingsbury, P. R., Kent, D. M. & Liu, H., May 2019, In : Journal of medical Internet research. 21, 5, e12109.

Research output: Contribution to journalArticle

Open Access
2 Scopus citations

Natural language processing of radiology reports for identification of skeletal site-specific fractures

Wang, Y., Mehrabi, S., Sohn, S., Atkinson, E. J., Amin, S. & Liu, H., Apr 4 2019, In : BMC Medical Informatics and Decision Making. 19, 73.

Research output: Contribution to journalArticle

Open Access
3 Scopus citations

Overview of the BioCreative VI Precision Medicine Track: Mining protein interactions and mutations for precision medicine

Islamaj Doǧan, R., Kim, S., Chatr-Aryamontri, A., Wei, C. H., Comeau, D. C., Antunes, R., Matos, S., Chen, Q., Elangovan, A., Panyam, N. C., Verspoor, K., Liu, H., Wang, Y., Liu, Z., Altlnel, B., Hüsünbeyi, Z. M., Özgür, A., Fergadis, A., Wang, C. K., Dai, H. J. & 7 others, Tran, T., Kavuluru, R., Luo, L., Steppi, A., Zhang, J., Qu, J. & Lu, Z., Jan 28 2019, In : Database. 2019

Research output: Contribution to journalReview article

Open Access
5 Scopus citations

PSB 2019 workshop on text mining and visualization for precision medicine

Gonzalez-Hernandez, G., Lu, Z., Leaman, R., Weissenbacher, D., Boland, M. R., Chen, Y., Du, J., Fluck, J., Greene, C. S., Holmes, J., Kashyap, A., Nielsen, R. L., Ouyang, Z., Schaaf, S., Taroni, J. N., Tao, C., Zhang, Y. & Liu, H., 2019, In : Pacific Symposium on Biocomputing. 24, 2019, p. 449-454 6 p.

Research output: Contribution to journalConference article

Rare disease knowledge enrichment through a data-driven approach

Shen, F., Zhao, Y., Wang, L., Mojarad, M. R., Wang, Y., Liu, S. & Liu, H., Feb 14 2019, In : BMC Medical Informatics and Decision Making. 19, 1, 32.

Research output: Contribution to journalArticle

8 Scopus citations

Relationship between very cold outside weather and surgical outcome: Integrating shallow and deep artificial neural nets

Tafti, A. P., Dong, Y., Habermann, E. B., Liu, H. D. & Herasevich, V. D., Aug 21 2019, MEDINFO 2019: Health and Wellbeing e-Networks for All - Proceedings of the 17th World Congress on Medical and Health Informatics. Seroussi, B., Ohno-Machado, L., Ohno-Machado, L. & Seroussi, B. (eds.). IOS Press, p. 1783-1784 2 p. (Studies in Health Technology and Informatics; vol. 264).

Research output: Chapter in Book/Report/Conference proceedingConference contribution

Salience of Medical Concepts of Inside Clinical Texts and Outside Medical Records for Referred Cardiovascular Patients

Moon, S., Liu, S., Chen, D., Wang, Y., Wood, D. L., Chaudhry, R., Liu, H. & Kingsbury, P., Jun 15 2019, In : Journal of Healthcare Informatics Research. 3, 2, p. 200-219 20 p.

Research output: Contribution to journalArticle

Open Access

Selected articles from the BioCreative/OHNLP challenge 2018

Liu, S., Wang, Y. & Liu, H., Dec 27 2019, In : BMC Medical Informatics and Decision Making. 19, 262.

Research output: Contribution to journalEditorial

Open Access

Special Issue on Healthcare Knowledge Discovery and Management

Shen, F., Chaudhary, V., Liu, Y., Ngufor, C. & Liu, H., Jun 15 2019, In : Journal of Healthcare Informatics Research. 3, 2, p. 157-158 2 p.

Research output: Contribution to journalEditorial

Open Access

A Comparison of Lifestyle Interventions for Alzheimer's Disease Extracted from Clinical Notes and Literature

Zhou, X., Liu, H. & Wang, Y., Jul 16 2018, Proceedings - 2018 IEEE International Conference on Healthcare Informatics Workshops, ICHI-W 2018. Institute of Electrical and Electronics Engineers Inc., p. 74-75 2 p. 8411812. (Proceedings - 2018 IEEE International Conference on Healthcare Informatics Workshops, ICHI-W 2018).

Research output: Chapter in Book/Report/Conference proceedingConference contribution

A comparison of word embeddings for the biomedical natural language processing

Wang, Y., Liu, S., Afzal, N., Rastegar-Mojarad, M., Wang, L., Shen, F., Kingsbury, P. & Liu, H., Nov 2018, In : Journal of Biomedical Informatics. 87, p. 12-20 9 p.

Research output: Contribution to journalArticle

59 Scopus citations

Advances in text mining and visualization for precision medicine

Gonzalez-Hernandez, G., Sarker, A., O’Connor, K., Greene, C. & Liu, H. D., Jan 1 2018, PACIFIC SYMPOSIUM ON BIOCOMPUTING 2018. 212669 ed. World Scientific Publishing Co. Pte Ltd, p. 559-565 7 p.

Research output: Chapter in Book/Report/Conference proceedingConference contribution

1 Scopus citations

Ascertainment of asthma prognosis using natural language processing from electronic medical records

Sohn, S., Wi, C. I., Wu, S. T., Liu, H., Ryu, E., Krusemark, E., Seabright, A., Voge, G. A. & Juhn, Y. J., Jun 2018, In : Journal of Allergy and Clinical Immunology. 141, 6, p. 2292-2294.e3

Research output: Contribution to journalArticle

6 Scopus citations
6 Scopus citations