• 4595 Citations
  • 36 Scopus h-Index
19992019

Research output per year

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Research Output

2011

G4 motifs correlate with promoter-proximal transcriptional pausing in human genes

Eddy, J., Vallur, A. C., Varma, S., Liu, H., Reinhold, W. C., Pommier, Y. & Maizels, N., Jul 1 2011, In : Nucleic acids research. 39, 12, p. 4975-4983 9 p.

Research output: Contribution to journalArticle

53 Scopus citations

Generality and reuse in a common type system for clinical natural language processing

Wu, S. T., Kaggal, V. C., Savova, G. K., Liu, H., Dligach, D., Zheng, J., Chapman, W. W. & Chute, C. G., Dec 15 2011, CIKM 2011 Glasgow: MIXHS'11 - Proceedings of the 1st International Workshop on Managing Interoperability and Complexity in Health Systems. p. 27-34 8 p. (International Conference on Information and Knowledge Management, Proceedings).

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

3 Scopus citations

Genome-wide depletion of replication initiation events in highly transcribed regions

Martin, M. M., Ryan, M., Kim, R. G., Zakas, A. L., Fu, H., Lin, C. M., Reinhold, W. C., Davis, S. R., Bilke, S., Liu, H., Doroshow, J. H., Reimers, M. A., Valenzuela, M. S., Pommier, Y., Meltzer, P. S. & Aladjem, M. I., Nov 1 2011, In : Genome Research. 21, 11, p. 1822-1832 11 p.

Research output: Contribution to journalArticle

83 Scopus citations

Human gene/protein synonym dictionary from WikiLinks

Wagholikar, K., Torii, M. & Liu, H., Dec 1 2011, 2011 ACM Conference on Bioinformatics, Computational Biology and Biomedicine, BCB 2011. p. 462-464 3 p. (2011 ACM Conference on Bioinformatics, Computational Biology and Biomedicine, BCB 2011).

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

Identification of a predominant co-regulation among kinetochore genes, prospective regulatory elements, and association with genomic instability

Reinhold, W. C., Erliandri, I., Liu, H., Zoppoli, G., Pommier, Y. & Larionov, V., Oct 10 2011, In : PloS one. 6, 10, e25991.

Research output: Contribution to journalArticle

13 Scopus citations

Learning from positive and unlabeled documents for automated detection of alternative splicing sentences in MEDLINE abstracts

Chen, Y., Torii, M., Lu, C. T. & Liu, H., Dec 1 2011, 2011 IEEE International Conference on Bioinformatics and Biomedicine Workshops, BIBMW 2011. p. 530-537 8 p. 6112425. (2011 IEEE International Conference on Bioinformatics and Biomedicine Workshops, BIBMW 2011).

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

3 Scopus citations

RedundancyMiner: De-replication of redundant GO categories in microarray and proteomics analysis

Zeeberg, B. R., Liu, H., Kahn, A. B., Ehler, M., Rajapakse, V. N., Bonner, R. F., Brown, J. D., Brooks, B. P., Larionov, V. L., Reinhold, W., Weinstein, J. N. & Pommier, Y. G., Feb 10 2011, In : BMC bioinformatics. 12, 52.

Research output: Contribution to journalArticle

14 Scopus citations
6 Scopus citations

The gene normalization task in BioCreative III

Lu, Z., Kao, H. Y., Wei, C. H., Huang, M., Liu, J., Kuo, C. J., Hsu, C. N., Tsai, R. T., Dai, H. J., Okazaki, N., Cho, H. C., Gerner, M., Solt, I., Agarwal, S., Liu, F., Vishnyakova, D., Ruch, P., Romacker, M., Rinaldi, F., Bhattacharya, S. & 8 others, Srinivasan, P., Liu, H., Torii, M., Matos, S., Campos, D., Verspoor, K., Livingston, K. M. & Wilbur, W. J., Oct 3 2011, In : BMC bioinformatics. 12, SUPPL. 8, S2.

Research output: Contribution to journalArticle

84 Scopus citations

Using machine learning for concept extraction on clinical documents from multiple data sources

Torii, M., Wagholikar, K. & Liu, H., Sep 1 2011, In : Journal of the American Medical Informatics Association. 18, 5, p. 580-587 8 p.

Research output: Contribution to journalArticle

72 Scopus citations
2010

An exploratory study of news article clustering for web-based bio-surveillance

Torii, M., Bayarsaikhan, B. U., Liu, H., Nguyen, T., Jones, K., Nelson, N. P. G. & Hartley, D. M., Dec 1 2010, IHI'10 - Proceedings of the 1st ACM International Health Informatics Symposium. p. 435-439 5 p. (IHI'10 - Proceedings of the 1st ACM International Health Informatics Symposium).

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

Document classification for mining host pathogen protein-protein interactions

Yin, L., Xu, G., Torii, M., Niu, Z., Maisog, J. M., Wu, C., Hu, Z. & Liu, H., Jul 1 2010, In : Artificial Intelligence in Medicine. 49, 3, p. 155-160 6 p.

Research output: Contribution to journalArticle

16 Scopus citations

Evaluating gene/protein name tagging and mapping for article retrieval

Lee, C. M., Torii, M., Shah, J., Tsai, Y. T., Hu, Z. Z. & Liu, H., Dec 1 2010, In : CEUR Workshop Proceedings. 714, p. 104-109 6 p.

Research output: Contribution to journalConference article

1 Scopus citations

Exon array analyses across the NCI-60 reveal potential regulation of TOP1 by transcription pausing at guanosine quartets in the first intron

Reinhold, W. C., Mergny, J. L., Liu, H., Ryan, M., Pfister, T. D., Kinders, R., Parchment, R., Doroshow, J., Weinstein, J. N. & Pommier, Y., Mar 15 2010, In : Cancer research. 70, 6, p. 2191-2203 13 p.

Research output: Contribution to journalArticle

52 Scopus citations

Imbalanced text classification on host pathogen protein-protein interaction documents

Xu, G., Niu, Z., Gao, X. & Liu, H., May 28 2010, 2010 The 2nd International Conference on Computer and Automation Engineering, ICCAE 2010. p. 418-422 5 p. 5451921. (2010 The 2nd International Conference on Computer and Automation Engineering, ICCAE 2010; vol. 1).

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

1 Scopus citations

Learning from positive and unlabeled documents for retrieval of bacterial protein-protein interaction literature

Liu, H., Torii, M., Xu, G., Hu, Z. & Goll, J., Jun 25 2010, Linking Literature, Information, and Knowledge for Biology - Workshop of the BioLink Special Interest Group, ISMB/ECCB 2009, Revised Selected Papers. p. 62-70 9 p. (Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics); vol. 6004 LNBI).

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

4 Scopus citations

LFXtractor: Text chunking for long form detection from biomedical text

Song, M. & Liu, H., Dec 1 2010, In : International Journal of Functional Informatics and Personalised Medicine. 3, 2, p. 89-102 14 p.

Research output: Contribution to journalArticle

Microarray probes and probe sets

Liu, H., Bebu, I. & Li, X., Jan 1 2010, In : Frontiers in Bioscience - Elite. 2 E, 1, p. 325-338 14 p.

Research output: Contribution to journalArticle

18 Scopus citations

mRNA and microRNA expression profiles of the NCI-60 integrated with drug activities

Liu, H., D'Andrade, P., Fulmer-Smentek, S., Lorenzi, P., Kohn, K. W., Weinstein, J. N., Pommier, Y. & Reinhold, W. C., May 1 2010, In : Molecular cancer therapeutics. 9, 5, p. 1080-1091 12 p.

Research output: Contribution to journalArticle

108 Scopus citations

Regulation of human skin pigmentation in situ by repetitive UV exposure: Molecular characterization of responses to UVA and/or UVB

Choi, W., Miyamura, Y., Wolber, R., Smuda, C., Reinhold, W., Liu, H., Kolbe, L. & Hearing, V. J., Jun 1 2010, In : Journal of Investigative Dermatology. 130, 6, p. 1685-1696 12 p.

Research output: Contribution to journalArticle

61 Scopus citations

Testing the theory of relative defect proneness for closed-source software

Koru, G., Liu, H., Zhang, D. & El Emam, K., Dec 1 2010, In : Empirical Software Engineering. 15, 6, p. 577-598 22 p.

Research output: Contribution to journalArticle

17 Scopus citations

The fibroblast-derived paracrine factor neuregulin-1 has a novel role in regulating the constitutive color and melanocyte function in human skin

Choi, W., Wolber, R., Gerwat, W., Mann, T., Batzer, J., Smuda, C., Liu, H., Kolbe, L. & Hearing, V. J., Sep 15 2010, In : Journal of cell science. 123, 18, p. 3102-3111 10 p.

Research output: Contribution to journalArticle

68 Scopus citations
2009

An investigation into the functional form of the size-defect relationship for software modules

Koru, A. G., Zhang, D., El Emam, K. & Liu, H., Mar 23 2009, In : IEEE Transactions on Software Engineering. 35, 2 SPEC. ISS., p. 293-304 12 p.

Research output: Contribution to journalArticle

90 Scopus citations

BioTagger-GM: A Gene/Protein Name Recognition System

Torii, M., Hu, Z., Wu, C. H. & Liu, H., Mar 1 2009, In : Journal of the American Medical Informatics Association. 16, 2, p. 247-255 9 p.

Research output: Contribution to journalArticle

42 Scopus citations

Development of dbOGAP: A bioinformatics resource of O-GlcNAcylated proteins and site prediction

Hu, Z. Z., Torii, M., Wang, J., Liu, H. & Hart, G. W., Dec 1 2009, Proceedings - 2009 IEEE International Conference on Bioinformatics and Biomedicine Workshops, BIBMW 2009. 1 p. 5332094. (Proceedings - 2009 IEEE International Conference on Bioinformatics and Biomedicine Workshops, BIBMW 2009).

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

North Central Cancer Treatment Group (NCCTG) N0432: Phase II trial of docetaxel with capecitabine and bevacizumab as first-line chemotherapy for patients with metastatic breast cancer

Perez, E. A., Hillman, D. W., Dentchev, T., Le-Lindqwister, N. A., Geeraerts, L. H., Fitch, T. R., Liu, H., Graham, D. L., Kahanic, S. P., Gross, H. M., Patel, T. A., Palmieri, F. M. & Dueck, A. C., Nov 9 2009, In : Annals of Oncology. 21, 2, p. 269-274 6 p., mdp512.

Research output: Contribution to journalArticle

25 Scopus citations

Semi-supervised learning of text classification on bacterial protein-protein interaction documents

Xu, G., Niu, Z., Uetz, P., Gao, X., Qin, X. & Liu, H., Nov 26 2009, Proceedings - 2009 International Joint Conference on Bioinformatics, Systems Biology and Intelligent Computing, IJCBS 2009. p. 263-270 8 p. 5260672. (Proceedings - 2009 International Joint Conference on Bioinformatics, Systems Biology and Intelligent Computing, IJCBS 2009).

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

5 Scopus citations

Software engineering education for bioinformatics

Umarji, M., Seaman, C., Koru, A. G. & Liu, H., Jan 1 2009, Proceedings - 22nd Conference on Software Engineering Education and Training, CSEET 2009. IEEE Computer Society, p. 216-223 8 p. 4812701. (Proceedings - 22nd Conference on Software Engineering Education and Training, CSEET 2009).

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

11 Scopus citations
7 Scopus citations

TGF-beta signaling proteins and the Protein Ontology

Arighi, C. N., Liu, H., Natale, D. A., Barker, W. C., Drabkin, H., Blake, J. A., Smith, B. & Wu, C. H., May 6 2009, In : BMC bioinformatics. 10, SUPPL. 5, S3.

Research output: Contribution to journalArticle

6 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

Teaching software engineering to end-users

Umarji, M., Pohl, M., Seaman, C., Koru, A. G. & Liu, H., Dec 8 2008, 30th International Conference on Software Engineering, ICSE 2008 Co-located Workshops - Proceedings of the 4th International Workshop on End-user Software Engineering, WEUSE IV. p. 40-42 3 p. 1370856. (Proceedings - International Conference on Software Engineering).

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

3 Scopus citations

Theory of relative defect proneness: Replicated studies on the functional form of the size-defect relationship

Koru, A. G., El Emam, K., Zhang, D., Liu, H. & Mathew, D., Oct 1 2008, In : Empirical Software Engineering. 13, 5, p. 473-498 26 p.

Research output: Contribution to journalArticle

45 Scopus citations

VennMaster: area-proportional Euler diagrams for functional GO analysis of microarrays.

Kestler, H. A., Müller, A., Kraus, J. M., Buchholz, M., Gress, T. M., Liu, H., Kane, D. W., Zeeberg, B. R. & Weinstein, J. N., 2008, In : BMC bioinformatics. 9, 1 p.

Research output: Contribution to journalArticle

75 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