• 4612 Citations
  • 36 Scopus h-Index
19992019

Research output per year

If you made any changes in Pure these will be visible here soon.

Research Output

2014

Study on hot topic discovery from Chinese texts

Xu, G., Qiu, L. & Liu, H., Aug 1 2014, In : Journal of Digital Information Management. 12, 4, p. 267-272 6 p.

Research output: Contribution to journalArticle

2 Scopus citations

Towards a multi-level framework for supporting systematic review - A pilot study

Li, D., Wang, Z., Shen, F., Murad, M. H. & Liu, H., Dec 29 2014, Proceedings - 2014 IEEE International Conference on Bioinformatics and Biomedicine, IEEE BIBM 2014. Zheng, H., Hu, X. T., Wang, Y., Hao, J-K., Gilbert, D., Berrar, D., Cho, K-H. & Dubitzky, W. (eds.). Institute of Electrical and Electronics Engineers Inc., p. 43-50 8 p. 6999266. (Proceedings - 2014 IEEE International Conference on Bioinformatics and Biomedicine, IEEE BIBM 2014).

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

4 Scopus citations

Towards pathway curation through literature mining - A case study using PharmGKB

Ravikumar, K. E., Wagholikar, K. B. & Liu, H., Jan 1 2014, In : Pacific Symposium on Biocomputing. p. 352-363 12 p.

Research output: Contribution to journalConference article

9 Scopus citations

Using large clinical corpora for query expansion in text-based cohort identification

Zhu, D., Wu, S., Carterette, B. & Liu, H., Jun 2014, In : Journal of Biomedical Informatics. 49, p. 275-281 7 p.

Research output: Contribution to journalArticle

20 Scopus citations

Using semantic web technologies for quality measure phenotyping algorithm representation and automatic execution on EHR data

Shen, F., Li, D., Liu, H., Lee, Y., Pathak, J., Chute, C. G. & Tao, C., Jan 1 2014, 2014 IEEE-EMBS International Conference on Biomedical and Health Informatics, BHI 2014. IEEE Computer Society, p. 531-534 4 p. 6864419. (2014 IEEE-EMBS International Conference on Biomedical and Health Informatics, BHI 2014).

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

2013

A common type system for clinical natural language processing

Wu, S. T., Kaggal, V. C., Dligach, D., Masanz, J. J., Chen, P., Becker, L., Chapman, W. W., Savova, G. K., Liu, H. & Chute, C. G., Jan 3 2013, In : Journal of Biomedical Semantics. 4, 1, 1.

Research output: Contribution to journalArticle

13 Scopus citations

Analysis of vaccine-related networks using semantic medline and the vaccine ontology

Zhang, Y., Tao, C., He, Y., Kanjamala, P. & Liu, H., Jan 1 2013, In : CEUR Workshop Proceedings. 1061

Research output: Contribution to journalConference article

An incremental approach to MEDLINE MeSH indexing

Zhu, D., Li, D., Carterette, B. & Liu, H., Jan 1 2013, In : CEUR Workshop Proceedings. 1094

Research output: Contribution to journalConference article

5 Scopus citations

An integrative computational approach to identify disease-specific networks from PubMed literature information

Zhang, Y., Li, D., Tao, C., Shen, F. & Liu, H., Dec 1 2013, Proceedings - 2013 IEEE International Conference on Bioinformatics and Biomedicine, IEEE BIBM 2013. p. 72-75 4 p. 6732738. (Proceedings - 2013 IEEE International Conference on Bioinformatics and Biomedicine, IEEE BIBM 2013).

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

7 Scopus citations

Automated chart review for asthma cohort identification using natural language processing: An exploratory study

Wu, S. T., Sohn, S., Ravikumar, K. E., Wagholikar, K., Jonnalagadda, S. R., Liu, H. & Juhn, Y. J., Nov 1 2013, In : Annals of Allergy, Asthma and Immunology. 111, 5, p. 364-369 6 p.

Research output: Contribution to journalArticle

32 Scopus citations

Automatically extracting sentences from medline citations to support clinicians' information needs

Jonnalagadda, S. R., Del Fiol, G., Medlin, R., Weir, C., Fiszman, M., Mostafa, J. & Liu, H., Aug 28 2013, In : Journal of the American Medical Informatics Association. 20, 5, p. 995-1000 6 p.

Research output: Contribution to journalArticle

23 Scopus citations

Automatic identification of comparative effectiveness research from medline citations to support clinicians' treatment information needs

Zhang, M., Del Fiol, G., Grout, R. W., Jonnalagadda, S., Medlin, R., Mishra, R., Weir, C., Liu, H., Mostafa, J. & Fiszman, M., Jan 1 2013, MEDINFO 2013 - Proceedings of the 14th World Congress on Medical and Health Informatics. 1-2 ed. IOS Press, p. 846-850 5 p. (Studies in Health Technology and Informatics; vol. 192, no. 1-2).

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

2 Scopus citations

Building a knowledge base of severe adverse drug events based on AERS reporting data using semantic Web technologies

Jiang, G., Wang, L., Liu, H., Solbrig, H. R. & Chute, C. G., Jan 1 2013, MEDINFO 2013 - Proceedings of the 14th World Congress on Medical and Health Informatics. 1-2 ed. IOS Press, p. 496-500 5 p. (Studies in Health Technology and Informatics; vol. 192, no. 1-2).

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

9 Scopus citations

Comprehensive temporal information detection from clinical text: Medical events, time, and TLINK identification

Sohn Dr., S., Wagholikar, K. B., Li, D., Jonnalagadda, S. R., Tao, C., Elayavilli, R. K. & Liu, H., Aug 28 2013, In : Journal of the American Medical Informatics Association. 20, 5, p. 836-842 7 p.

Research output: Contribution to journalArticle

27 Scopus citations

Formative evaluation of the accuracy of a clinical decision support system for cervical cancer screening

Wagholikar Dr., K. B., MacLaughlin, K. L., Kastner, T. M., Casey, P. M., Henry, M., Greenes, R. A., Liu, H. & Chaudhry, R., Sep 2 2013, In : Journal of the American Medical Informatics Association. 20, 4, p. 749-757 9 p.

Research output: Contribution to journalArticle

21 Scopus citations

Identifying protein complexes with fuzzy machine learning model

Xu, B., Lin, H., Wagholikar, K. B., Yang, Z. & Liu, H. D., Jan 1 2013, In : Proteome Science. 11, S21.

Research output: Contribution to journalArticle

1 Scopus citations

Integrated cTAKES for concept mention detection and normalization

Liu, H., Wagholikar, K., Jonnalagadda, S. & Sohn, S., Jan 1 2013, In : CEUR Workshop Proceedings. 1179

Research output: Contribution to journalConference article

1 Scopus citations

MayoClinicNLP–CORE: Semantic representations for textual similarity

Wu, S., Zhu, D., Carterette, B. & Liu, H. D., Jan 1 2013, *SEM 2013 - 2nd Joint Conference on Lexical and Computational Semantics. Association for Computational Linguistics (ACL), Vol. 1. p. 148-154 7 p.

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

4 Scopus citations

Network-based analysis of vaccine-related associations reveals consistent knowledge with the vaccine ontology

Zhang, Y., Tao, C., He, Y., Kanjamala, P. & Liu, H., Nov 11 2013, In : Journal of Biomedical Semantics. 4, 1, 33.

Research output: Contribution to journalArticle

16 Scopus citations

Normalization and standardization of electronic health records for high-throughput phenotyping: The sharpn consortium

Pathak, J., Bailey, K. R., Beebe, C. E., Bethard, S., Carrell, D. S., Chen, P. J., Dligach, D., Endle, C. M., Hart, L. A., Haug, P. J., Huff, S. M., Kaggal, V. C., Li, D., Liu, H., Marchant, K., Masanz, J., Miller, T., Oniki, T. A., Palmer, M., Peterson, K. J. & 12 others, Rea, S., Savova, G. K., Stancl, C. R., Sohn, S., Solbrig, H. R., Suesse, D. B., Tao, C., Taylor, D. P., Westberg, L., Wu, S., Zhuo, N. & Chute, C. G., Dec 23 2013, In : Journal of the American Medical Informatics Association. 20, E2, p. e341-e348

Research output: Contribution to journalArticle

59 Scopus citations

Phenotyping on EHR data using OWL and semantic web technologies

Tao, C., Li, D., Shen, F., Lian, Z., Pathak, J., Liu, H. & Chute, C. G., Aug 12 2013, Smart Health - International Conference, ICSH 2013, Proceedings. p. 31-32 2 p. (Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics); vol. 8040 LNCS).

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

1 Scopus citations

Pooling annotated corpora for clinical concept extraction

Wagholikar, K. B., Torii, M., Jonnalagadda, S. R. & Liu, H., Jan 8 2013, In : Journal of Biomedical Semantics. 4, 1, 3.

Research output: Contribution to journalArticle

6 Scopus citations

Prioritizing journals relevant to a topic for addressing clinicians' information needs

Jonnalagadda, S. R., Moosavinasab, S., Li, D., Abel, M. D., Chute, C. G. & Liu, H., Dec 1 2013, Proceedings - 2013 IEEE International Conference on Bioinformatics and Biomedicine, IEEE BIBM 2013. p. 5-6 2 p. 6732590. (Proceedings - 2013 IEEE International Conference on Bioinformatics and Biomedicine, IEEE BIBM 2013).

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

2 Scopus citations

Profiling adverse drug events of cancer drug ingredients using normalized AERS data

Wang, L. & Liu, H., Dec 1 2013, Proceedings - 2013 IEEE International Conference on Bioinformatics and Biomedicine, IEEE BIBM 2013. p. 46-52 7 p. 6732599. (Proceedings - 2013 IEEE International Conference on Bioinformatics and Biomedicine, IEEE BIBM 2013).

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

1 Scopus citations

Protein complex identification by integrating protein-protein interaction evidence from multiple sources

Xu, B., Lin, H., Chen, Y., Yang, Z. & Liu, H., Dec 27 2013, In : PloS one. 8, 12, e83841.

Research output: Contribution to journalArticle

6 Scopus citations

Standardizing drug adverse event reporting data

Wang, L., Jiang, G., Li, D. & Liu, H., Jan 1 2013, MEDINFO 2013 - Proceedings of the 14th World Congress on Medical and Health Informatics. 1-2 ed. IOS Press, 1 p. (Studies in Health Technology and Informatics; vol. 192, no. 1-2).

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

5 Scopus citations

Towards assigning references using semantic, journal and citation relevance

Li, D. C., Liu, H., Chute, C. G. & Jonnalagadda, S. R., Dec 1 2013, Proceedings - 2013 IEEE International Conference on Bioinformatics and Biomedicine, IEEE BIBM 2013. p. 499-503 5 p. 6732545. (Proceedings - 2013 IEEE International Conference on Bioinformatics and Biomedicine, IEEE BIBM 2013).

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

1 Scopus citations

Transcription poisoning by topoisomerase i is controlled by gene length, splice sites, and miR-142-3p

Solier, S., Ryan, M. C., Martin, S. E., Varma, S., Kohn, K. W., Liu, H., Zeeberg, B. R. & Pommier, Y., Aug 1 2013, In : Cancer research. 73, 15, p. 4830-4839 10 p.

Research output: Contribution to journalArticle

34 Scopus citations

Using discharge summaries to improve information retrieval in clinical domain

Zhu, D., Stephen, W., James, M., Carterette, B. & Liu, H., Jan 1 2013, In : CEUR Workshop Proceedings. 1179

Research output: Contribution to journalConference article

2012

A study of transportability of an existing smoking status detection module across institutions.

Liu, M., Shah, A., Jiang, M., Peterson, N. B., Dai, Q., Aldrich, M. C., Chen, Q., Bowton, E. A., Liu, H., Denny, J. C. & Xu, H., 2012, In : Unknown Journal. 2012, p. 577-586 10 p.

Research output: Contribution to journalArticle

23 Scopus citations

Automatically extracting sentences from medline citations to support clinicians' information needs

Jonnalagadda, S., Fiol, G. D., Medlin, R., Weir, C., Fiszman, M., Mostafa, J. & Liu, H., Dec 1 2012, Proceedings - 2012 IEEE 2nd Conference on Healthcare Informatics, Imaging and Systems Biology, HISB 2012. 1 p. 6366197. (Proceedings - 2012 IEEE 2nd Conference on Healthcare Informatics, Imaging and Systems Biology, HISB 2012).

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

2 Scopus citations

CellMiner: A web-based suite of genomic and pharmacologic tools to explore transcript and drug patterns in the NCI-60 cell line set

Reinhold, W. C., Sunshine, M., Liu, H., Varma, S., Kohn, K. W., Morris, J., Doroshow, J. & Pommier, Y., Jul 15 2012, In : Cancer research. 72, 14, p. 3499-3511 13 p.

Research output: Contribution to journalArticle

231 Scopus citations

CHEK2 genomic and proteomic analyses reveal genetic inactivation or endogenous activation across the 60 cell lines of the US National Cancer Institute

Zoppoli, G., Solier, S., Reinhold, W. C., Liu, H., Connelly, J. W., Monks, A., Shoemaker, R. H., Abaan, O. D., Davis, S. R., Meltzer, P. S., Doroshow, J. H. & Pommier, Y., Jan 26 2012, In : Oncogene. 31, 4, p. 403-418 16 p.

Research output: Contribution to journalArticle

14 Scopus citations

Classifying protein complexes from candidate subgraphs using fuzzy machine learning model

Xu, B., Lin, H., Yang, Z., Wagholikar, K. B. & Liu, H., Dec 1 2012, Proceedings - 2012 IEEE International Conference on Bioinformatics and Biomedicine Workshops, BIBMW 2012. p. 640-647 8 p. 6470213. (Proceedings - 2012 IEEE International Conference on Bioinformatics and Biomedicine Workshops, BIBMW 2012).

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

1 Scopus citations

Clinical decision support for colonoscopy surveillance using natural language processing

Wagholikar, K., Sohn, S., Wu, S., Kaggal, V., Buehler, S., Greenes, R., Wu, T. T., Larson, D., Liu, H., Chaudhry, R. & Boardman, L., Dec 1 2012, Proceedings - 2012 IEEE 2nd Conference on Healthcare Informatics, Imaging and Systems Biology, HISB 2012. p. 12-21 10 p. 6366186. (Proceedings - 2012 IEEE 2nd Conference on Healthcare Informatics, Imaging and Systems Biology, HISB 2012).

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

3 Scopus citations

Clinical decision support with automated text processing for cervical cancer screening

Wagholikar, K. B., MacLaughlin, K. L., Henry, M. R., Greenes, R. A., Hankey, R. A., Liu, H. & Chaudhry, R. C., Sep 1 2012, In : Journal of the American Medical Informatics Association. 19, 5, p. 833-839 7 p.

Research output: Contribution to journalArticle

40 Scopus citations

Coreference analysis in clinical notes: A multi-pass sieve with alternate anaphora resolution modules

Jonnalagadda, S. R., Li, D., Sohn, S., Wu, S. T. I., Wagholikar, K., Torii, M. & Liu, H., Sep 1 2012, In : Journal of the American Medical Informatics Association. 19, 5, p. 867-874 8 p.

Research output: Contribution to journalArticle

17 Scopus citations

Introductory remarks

Ananiadou, S., Salakoski, T., Pyysalo, S., Rebholz-Schuhmann, D., Rinaldi, F., Schneider, G., Clematide, S., Grigonyte, G., Shepherd, A., Burgun-Parenthoine, A., McClosky, D., Demner-Fushman, D., Ginter, F., Leitner, F., Nenadic, G., Yi, G. S., Liu, H., Su, J., Lee, H., Kim, J. D. & 24 others, Park, J. C., Kim, J. J., Verspoor, K., Cohen, K., Miwa, M., Krallinger, M., Romacker, M., Volk, M., Krauthammer, M., Conway, M., Okazaki, N., Collier, N., Ruch, P., Lambrix, P., Zweigenbaum, P., Ohta, T., Sætre, R., Hahn, U., Chapman, W., Tsuruoka, Y., Sasaki, Y., Mulkar-Mehta, R., Zhang, W. & Stenetorp, P., Dec 1 2012, In : SMBM 2012 - Proceedings of the 5th International Symposium on Semantic Mining in Biomedicine. p. iii-v

Research output: Contribution to journalEditorial

Mass homozygotes accumulation in the NCI-60 cancer cell lines as compared to HapMap trios, and relation to fragile site location

Ruan, X., Kocher, J. P. A., Pommier, Y., Liu, H. & Reinhold, W. C., Feb 9 2012, In : PloS one. 7, 2, e31628.

Research output: Contribution to journalArticle

12 Scopus citations

Modeling UIMA type system using web ontology language - Towards interoperability among UIMA-based NLP tools

Liu, H., Wu, S., Tao, C. & Chute, C., Dec 7 2012, MIX-HS'12 - Proceedings of the 2nd International Workshop on Managing Interoperability and Complexity in Health Systems, Co-located with CIKM 2012. p. 31-36 6 p. (International Conference on Information and Knowledge Management, Proceedings).

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

3 Scopus citations

Ontology-based temporal relation modeling with map-reduce latent dirichlet allocations for big EHR data

Li, D., Tao, C., Liu, H. & Chute, C., Dec 1 2012, Proceedings - 2nd International Conference on Cloud and Green Computing and 2nd International Conference on Social Computing and Its Applications, CGC/SCA 2012. p. 708-715 8 p. 6382894. (Proceedings - 2nd International Conference on Cloud and Green Computing and 2nd International Conference on Social Computing and Its Applications, CGC/SCA 2012).

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

1 Scopus citations

Primary Sjogren's syndrome: Cognitive symptoms, mood, and cognitive performance

Segal, B. M., Pogatchnik, B., Holker, E., Liu, H., Sloan, J., Rhodus, N. & Moser, K. L., Apr 1 2012, In : Acta neurologica Scandinavica. 125, 4, p. 272-278 7 p.

Research output: Contribution to journalArticle

35 Scopus citations

Systematic analysis of cross-institutional medication description patterns in clinical notes

Sohn, S., Murphy, S. P., Jonnalagadda, S. R., Wagholikar, K., Wu, S. T., Chute, C. G., Liu, H. & Halgrim, S., Dec 1 2012, Proceedings - 2012 IEEE 2nd Conference on Healthcare Informatics, Imaging and Systems Biology, HISB 2012. 1 p. 6366211. (Proceedings - 2012 IEEE 2nd Conference on Healthcare Informatics, Imaging and Systems Biology, HISB 2012).

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

Towards a semantic lexicon for clinical natural language processing.

Liu, H., Wu, S. T., Li, D., Jonnalagadda, S., Sohn, S., Wagholikar, K., Haug, P. J., Huff, S. M. & Chute, C. G., 2012, In : Unknown Journal. 2012, p. 568-576 9 p.

Research output: Contribution to journalArticle

13 Scopus citations

Unified medical Language System term occurrences in clinical notes: A large-scale corpus analysis

Wu, S. T., Liu, H., Li, D., Tao, C., Musen, M. A., Chute, C. G. & Shah, N. H., Jun 1 2012, In : Journal of the American Medical Informatics Association. 19, E1, p. e149-e156

Research output: Contribution to journalArticle

49 Scopus citations
2011

AMP kinase-related kinase NUAK2 affects tumor growth, migration, and clinical outcome of human melanoma

Namiki, T., Tanemura, A., Valencia, J. C., Coelho, S. G., Passeron, T., Kawaguchi, M., Vieira, W. D., Ishikawa, M., Nishijima, W., Izumo, T., Kaneko, Y., Katayama, I., Yamaguchi, Y., Yin, L., Polley, E. C., Liu, H., Kawakami, Y., Eishi, Y., Takahashi, E., Yokozeki, H. & 1 others, Hearing, V. J., Apr 19 2011, In : Proceedings of the National Academy of Sciences of the United States of America. 108, 16, p. 6597-6602 6 p.

Research output: Contribution to journalArticle

31 Scopus citations

An exploratory study of a text classification framework for Internet-based surveillance of emerging epidemics

Torii, M., Yin, L., Nguyen, T., Mazumdar, C. T., Liu, H., Hartley, D. M. & Nelson, N. P., Jan 1 2011, In : International Journal of Medical Informatics. 80, 1, p. 56-66 11 p.

Research output: Contribution to journalArticle

32 Scopus citations

Coordinated regulation of mitochondrial topoisomerase IB with mitochondrial nuclear encoded genes and MYC

Zoppoli, G., Douarre, C., Rosa, I. D., Liu, H., Reinhold, W. & Pommier, Y., Aug 1 2011, In : Nucleic acids research. 39, 15, p. 6620-6632 13 p.

Research output: Contribution to journalArticle

15 Scopus citations

dbOGAP - An Integrated Bioinformatics Resource for Protein O-GlcNAcylation

Wang, J., Torii, M., Liu, H., Hart, G. W. & Hu, Z. Z., Apr 6 2011, In : BMC bioinformatics. 12, 91.

Research output: Contribution to journalArticle

69 Scopus citations

Empirical ontologies for cohort identification

Wu, S., Wagholikar, K., Sohn, S., Kaggal, V. & Liu, H., Dec 1 2011, In : NIST Special Publication.

Research output: Contribution to journalConference article