• 4595 Citations
  • 36 Scopus h-Index
19992019

Research output per year

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Research Output

1999

Generalized shuffle-exchange digraphs: Hamiltonian properties

Liu, H., Hsu, D. F. & Horiguchi, S., Jan 1 1999, In : Proceedings - IEEE International Symposium on Circuits and Systems. 6, p. VI-157-VI-160

Research output: Contribution to journalConference article

1 Scopus citations
2000
7 Scopus citations
2001

A study of abbreviations in the UMLS.

Liu, H., Lussier, Y. A. & Friedman, C., 2001, In : Proceedings / AMIA ... Annual Symposium. AMIA Symposium. p. 393-397 5 p.

Research output: Contribution to journalArticle

36 Scopus citations

Disambiguating ambiguous biomedical terms in biomedical narrative text: An unsupervised method

Liu, H., Lussier, Y. A. & Friedman, C., Jan 1 2001, In : Journal of Biomedical Informatics. 34, 4, p. 249-261 13 p.

Research output: Contribution to journalArticle

55 Scopus citations

Evaluating the UMLS as a source of lexical knowledge for medical language processing.

Friedman, C., Liu, H., Shagina, L., Johnson, S. & Hripcsak, G., 2001, In : Proceedings / AMIA ... Annual Symposium. AMIA Symposium. p. 189-193 5 p.

Research output: Contribution to journalArticle

31 Scopus citations
2002

A study of abbreviations in MEDLINE abstracts.

Liu, H., Aronson, A. R. & Friedman, C., 2002, In : Proceedings / AMIA ... Annual Symposium. AMIA Symposium. p. 464-468 5 p.

Research output: Contribution to journalArticle

44 Scopus citations

Automatic resolution of ambiguous terms based on machine learning and conceptual relations in the UMLS

Liu, H., Johnson, S. B. & Friedman, C., Nov 1 2002, In : Journal of the American Medical Informatics Association. 9, 6, p. 621-636 16 p.

Research output: Contribution to journalArticle

70 Scopus citations
2003

A vocabulary development and visualization tool based on natural language processing and the mining of textual patient reports

Friedman, C., Liu, H. & Shagina, L., Jun 2003, In : Journal of Biomedical Informatics. 36, 3, p. 189-201 13 p.

Research output: Contribution to journalArticle

13 Scopus citations

Mining terminological knowledge in large biomedical corpora.

Liu, H. & Friedman, C., 2003, In : Pacific Symposium on Biocomputing. Pacific Symposium on Biocomputing. p. 415-426 12 p.

Research output: Contribution to journalArticle

38 Scopus citations
2004

A multi-aspect comparison study of supervised word sense disambiguation

Liu, H., Teller, V. & Friedman, C., Jul 1 2004, In : Journal of the American Medical Informatics Association. 11, 4, p. 320-331 12 p.

Research output: Contribution to journalArticle

51 Scopus citations

Biological nomenclatures: a source of lexical knowledge and ambiguity.

Tuason, O., Chen, L., Liu, H., Blake, J. A. & Friedman, C., 2004, In : Pacific Symposium on Biocomputing. Pacific Symposium on Biocomputing. p. 238-249 12 p.

Research output: Contribution to journalArticle

56 Scopus citations

CliniViewer: A tool for viewing electronic medical records based on natural language processing and XML

Liu, H. & Friedman, C., Jan 1 2004, In : Studies in health technology and informatics. 107, p. 639-643 5 p.

Research output: Contribution to journalArticle

7 Scopus citations

Combination methods in microarray analysis

Chuang, H. Y., Liu, H., Chen, F. A., Kao, C. Y. & Hsu, D. F., Aug 16 2004, p. 625-630. 6 p.

Research output: Contribution to conferencePaper

10 Scopus citations

Identifying significant genes from microarray data

Chuang, H. Y., Liu, H., Brown, S., McMunn-Coffran, C., Kao, C. Y. & Hsu, D. F., Sep 24 2004, Proceedings - Fourth IEEE Symposium on Bioinformatics and Bioengineering, BIBE 2004. p. 358-365 8 p. (Proceedings - Fourth IEEE Symposium on Bioinformatics and Bioengineering, BIBE 2004).

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

16 Scopus citations

IProLINK: An integrated protein resource for literature mining

Hu, Z. Z., Mani, I., Hermoso, V., Liu, H. & Wu, C. H., Dec 1 2004, In : Computational Biology and Chemistry. 28, 5-6, p. 409-416 8 p.

Research output: Contribution to journalArticle

32 Scopus citations
2005

An investigation of the effect of module size on defect prediction using static measures

Koru, A. G. & Liu, H. D., May 15 2005, Proceedings of the 2005 Workshop on Predictor Models in Software Engineering, PROMISE 2005. Association for Computing Machinery, Inc, a7

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

45 Scopus citations

Building effective defect-prediction models in practice

Koru, A. G. & Liu, H., Nov 1 2005, In : IEEE Software. 22, 6, p. 23-29 7 p.

Research output: Contribution to journalArticle

120 Scopus citations

Dynamically generating a protein entity dictionary using online resources

Liu, H., Hu, Z. & Wu, C., Dec 1 2005, ACL-05 - 43rd Annual Meeting of the Association for Computational Linguistics, Proceedings of the Conference. p. 17-20 4 p. (ACL-05 - 43rd Annual Meeting of the Association for Computational Linguistics, Proceedings of the Conference).

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

DynGO: A tool for visualizing and mining of Gene Ontology and its associations

Liu, H., Hu, Z. Z. & Wu, C. H., Aug 9 2005, In : BMC bioinformatics. 6, 201.

Research output: Contribution to journalArticle

28 Scopus citations

Fusion of knowledge-intensive and statistical approaches for retrieving and annotating textual genomics documents

Aronson, A. R., Demner-Fushman, D., Humphrey, S. M., Lin, J., Liu, H., Ruch, P., Ruiz, M. E., Smith, L. H., Tanabe, L. K. & John Wilbur, W., Dec 1 2005, In : NIST Special Publication.

Research output: Contribution to journalConference article

1 Scopus citations

Gene name ambiguity of eukaryotic nomenclatures

Chen, L., Liu, H. & Friedman, C., Jan 15 2005, In : Bioinformatics. 21, 2, p. 248-256 9 p.

Research output: Contribution to journalArticle

105 Scopus citations
2006

A comparison study of biomedical short form definition detection algorithms

Torii, M., Liu, H., Hu, Z. & Wu, C., Dec 1 2006, CIKM 2006 Workshop - Proceedings of TMBIO 2006: ACM First International Workshop on Text Mining in Bioinformatics. p. 52-59 8 p. (Proceedings of TMBIO 2006: ACM First International Workshop on Text Mining in Bioinformatics).

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

2 Scopus citations

BioThesaurus: A web-based thesaurus of protein and gene names

Liu, H., Hu, Z. Z., Zhang, J. & Wu, C., Jan 1 2006, In : Bioinformatics. 22, 1, p. 103-105 3 p.

Research output: Contribution to journalArticle

87 Scopus citations

Framework for a protein ontology

Natale, D. A., Arighi, C. N., Barker, W., Blake, J., Chang, T. C., Hu, Z., Liu, H., Smith, B. & Wu, C. H., Dec 1 2006, CIKM 2006 Workshop - Proceedings of TMBIO 2006: ACM First International Workshop on Text Mining in Bioinformatics. p. 29-36 8 p. (Proceedings of TMBIO 2006: ACM First International Workshop on Text Mining in Bioinformatics).

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

3 Scopus citations

Headwords and suffixes in biomedical names

Torii, M. & Liu, H., Jul 10 2006, Knowledge Discovery in Life Science Literature - PAKDD 2006 International Workshop, KDLL 2006, Proceedings. p. 29-41 13 p. (Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics); vol. 3886 LNBI).

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

1 Scopus citations

Machine learning and word sense disambiguation in the biomedical domain: Design and evaluation issues

Xu, H., Markatou, M., Dimova, R., Liu, H. & Friedman, C., Jul 5 2006, In : BMC bioinformatics. 7, 334.

Research output: Contribution to journalArticle

35 Scopus citations

Quantitative Assessment of Dictionary-based Protein Named Entity Tagging

Liu, H., Hu, Z. Z., Torii, M., Wu, C. & Friedman, C., Sep 1 2006, In : Journal of the American Medical Informatics Association. 13, 5, p. 497-507 11 p.

Research output: Contribution to journalArticle

25 Scopus citations

Terminology model discovery using natural language processing and visualization techniques

Zhou, L., Tao, Y., Cimino, J. J., Chen, E. S., Liu, H., Lussier, Y. A., Hripcsak, G. & Friedman, C., Dec 1 2006, In : Journal of Biomedical Informatics. 39, 6, p. 626-636 11 p.

Research output: Contribution to journalArticle

9 Scopus citations
2007

A comparison study on algorithms of detecting long forms for short forms in biomedical text

Torii, M., Hu, Z. Z., Song, M., Wu, C. H. & Liu, H., Nov 27 2007, In : BMC bioinformatics. 8, SUPPL. 9, S5.

Research output: Contribution to journalArticle

22 Scopus citations

AffyProbeMiner: A web resource for computing or retrieving accurately redefined Affymetrix probe sets

Liu, H., Zeeberg, B. R., Qu, G., Koru, A. G., Ferrucci, A., Kahn, A., Ryan, M. C., Nuhanovic, A., Munson, P. J., Reinhold, W. C., Kane, D. W. & Weinstein, J. N., Sep 15 2007, In : Bioinformatics. 23, 18, p. 2385-2390 6 p.

Research output: Contribution to journalArticle

57 Scopus citations

Classifier ensemble for biomedical document retrieval

Torii, M. & Liu, H., Dec 1 2007, In : CEUR Workshop Proceedings. 319, p. 5.1-5.17

Research output: Contribution to journalConference article

2 Scopus citations

Effect of coupling on defect proneness in evolutionary open-source software development

Koru, A. G., Zhang, D. & Liu, H., Aug 22 2007, Open Source Development, Adoption and Innovation: IFIP Working Group 2.13 on Open Source Software, June 11-14, 2007, Limerick, Ireland. Feller, J., Fitzgerald, B., Scacchi, W. & Sillitti, A. (eds.). p. 271-276 6 p. (IFIP International Federation for Information Processing; vol. 234).

Research output: Chapter in Book/Report/Conference proceedingChapter

2 Scopus citations

Exploring traits of adjectives to predict polarity opinion in BLOGS and semantic filters in Genomics

Ruiz, M. E., Sun, Y., Wang, J. & Liu, H., Dec 1 2007, In : NIST Special Publication.

Research output: Contribution to journalConference article

Framework for a protein ontology

Natale, D. A., Arighi, C. N., Barker, W. C., Blake, J., Chang, T. C., Hu, Z., Liu, H., Smith, B. & Wu, C. H., Nov 27 2007, In : BMC bioinformatics. 8, SUPPL. 9, S1.

Research output: Contribution to journalArticle

68 Scopus citations

Identifying and characterizing change-prone classes in two large-scale open-source products

Güneş Koru, A. & Liu, H., Jan 1 2007, In : Journal of Systems and Software. 80, 1, p. 63-73 11 p.

Research output: Contribution to journalArticle

58 Scopus citations

Mapping gene/protein names in free text to biomedical databases

Liu, H., Torii, M., Hu, Z. Z. & Wu, C., Dec 1 2007, ICDM Workshops 2007 - Proceedings of the 17th IEEE International Conference on Data Mining Workshops. p. 101-106 6 p. 4476653. (Proceedings - IEEE International Conference on Data Mining, ICDM).

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

2 Scopus citations

Modeling the effect of size on defect proneness for open-source software

Günes Koru, A., Dongsong, Z. & Liu, H., Dec 17 2007, Proceedings - ICSE 2007 Workshops: Third International Workshop on Predictor Models in Software Engineering, PROMISE'07. 4273266. (Proceedings - ICSE 2007 Workshops: Third International Workshop on Predictor Models in Software Engineering, PROMISE'07).

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

12 Scopus citations

Modeling the effect of size on defect proneness for open-source software

Koru, A. G., Zhang, D. & Liu, H., Sep 25 2007, Proceedings - 29th International Conference on Software Engineering, ICSE 2007; Companion Volume. p. 115-124 10 p. 4222706. (Proceedings - International Conference on Software Engineering).

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

9 Scopus citations

Semiparametric RMA background-correction for oligonucleotide arrays

Bebu, I., Seillier-Moiseiwitsch, F. & Liu, H., Dec 1 2007, Proceedings of the 7th IEEE International Conference on Bioinformatics and Bioengineering, BIBE. p. 1404-1408 5 p. 4375756. (Proceedings of the 7th IEEE International Conference on Bioinformatics and Bioengineering, BIBE).

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

1 Scopus citations

SpliceMiner: A high-throughput database implementation of the NCBI Evidence Viewer for microarray splice variant analysis

Kahn, A. B., Ryan, M. C., Liu, H., Zeeberg, B. R., Jamison, C. & Weinstein, J. N., Mar 5 2007, In : BMC bioinformatics. 8, 75.

Research output: Contribution to journalArticle

19 Scopus citations
2008

Analysis of microarray titration experiments

Bebu, I., Seillier-Moiseiwitsch, F. & Liu, H., Dec 1 2008, Proceedings of the 2008 International Conference on Bioinformatics and Computational Biology, BIOCOMP 2008. p. 942-946 5 p. (Proceedings of the 2008 International Conference on Bioinformatics and Computational Biology, BIOCOMP 2008).

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

Annotating breast cancer microarray samples using ontologies.

Liu, H., Li, X., Yoon, V. & Clarke, R., 2008, In : AMIA ... Annual Symposium proceedings / AMIA Symposium. AMIA Symposium. p. 414-418 5 p.

Research output: Contribution to journalArticle

1 Scopus citations

Comparison of classification methods on protein-protein interaction document classification

Xu, G., Niu, Z., Uetz, P., Gao, X. & Liu, H., Dec 1 2008, Proceedings - 2008 IEEE International Conference on Bioinformatics and Biomedicine Workshops, BIBMW. p. 83-90 8 p. 4686213. (Proceedings - 2008 IEEE International Conference on Bioinformatics and Biomedicine Workshops, BIBMW).

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

1 Scopus citations

Document classification for mining host pathogen protein-protein interactions

Xu, G., Yin, L., Torii, M., Niu, Z., Wu, C., Hu, Z. & Liu, H., Dec 1 2008, Proceedings - IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2008. p. 461-466 6 p. 4684940. (Proceedings - IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2008).

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

3 Scopus citations

iProLINK: A framework for linking text mining with ontology and systems biology

Hu, Z. Z., Cohen, K. B., Hirschman, L., Valencia, A., Liu, H., Giglio, M. G. & Wu, C. H., Dec 1 2008, Proceedings - IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2008. p. 467-472 6 p. 4684941. (Proceedings - IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2008).

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

2 Scopus citations

Overview of BioCreative II gene mention recognition

Smith, L., Tanabe, L. K., Ando, R., Kuo, C. J., Chung, I. F., Hsu, C. N., Lin, Y. S., Klinger, R., Friedrich, C. M., Ganchev, K., Torii, M., Liu, H., Haddow, B., Struble, C. A., Povinelli, R. J., Vlachos, A., Baumgartner, W. A., Hunter, L., Carpenter, B., Tsai, R. T. H. & 14 others, Dai, H. J., Liu, F., Chen, Y., Sun, C., Katrenko, S., Adriaans, P., Blaschke, C., Torres, R., Neves, M., Nakov, P., Divoli, A., Maña-López, M., Mata, J. & Wilbur, W. J., Sep 1 2008, In : Genome biology. 9, SUPPL. 2, S2.

Research output: Contribution to journalReview article

199 Scopus citations

Overview of BioCreative II gene normalization

Morgan, A. A., Lu, Z., Wang, X., Cohen, A. M., Fluck, J., Ruch, P., Divoli, A., Fundel, K., Leaman, R., Hakenberg, J., Sun, C., Liu, H. H., Torres, R., Krauthammer, M., Lau, W. W., Liu, H., Hsu, C. N., Schuemie, M., Cohen, K. B. & Hirschman, L., Sep 1 2008, In : Genome biology. 9, SUPPL. 2, S3.

Research output: Contribution to journalReview article

198 Scopus citations

SpliceCenter: A suite of web-based bioinformatic applications for evaluating the impact of alternative splicing on RT-PCR, RNAi, microarray, and peptide-based studies

Ryan, M. C., Zeeberg, B. R., Caplen, N. J., Cleland, J. A., Kahn, A. B., Liu, H. & Weinstein, J. N., Jul 18 2008, In : BMC bioinformatics. 9, 313.

Research output: Contribution to journalArticle

28 Scopus citations