Year 2008

1. H. Liu, X. Li, V. Yoon, and Robert Clarke (2008) Annotating breast cancer microarray samples using ontologies (AMIA 2008, in press)
2. I. Bebu, F. Seillier-Moiseiwitsch, H. Liu (2008) Analysis of microarray titration experiments (Biocomp'2008, in press)
3. M. Torii, H. Liu (2008) At-least-N voting over biomedical named entity recognition systems (BioLink 2008, in press)
4. C. Arighi, H. Liu, D. Natale, W. Barker, H. Drabkin, ZZ Hu, J. Blake, B. Smith, and C. Wu (2008) TGF-beta Signaling Proteins and the Protein Ontology (Bio-Ontologies 2008, in press)
5. A.G. Koru, K El Emam, D. Zhang, H Liu, and D Mathew (2008) The Size-Defect Relationship for Software Modules: Replicated Studies on Open-Source Office Applications (Empirical Software Engineering, in press)
6. M Umarji, M Pohl, C Seaman, AG Koru, and H Liu (2008) Teaching Software Engineering to End-users (Fourth Workshop on End-User Software Engineering (WEUSE IV))
7. A A. Morgan, Z Lu, X Wang, A M. Cohen, J Fluck, P Ruch, A Divoli, K Fundel, R Leaman, J. Hakenberg, C Sun, HH Liu, R Torres, M Krauthammer, W W. Lau, H Liu, C Hsu, M Schuemie, and L Hirschman (2008) Overview of BioCreative II gene normalization (Genome Biology. In press)
8. L Smith, L K. Tanabe, R Johnson, C Kuo, I Chung, Y Lin, R Klinger, C M. Friedrich, K Ganchev, M Torii, H Liu, B Haddow, C A. Struble, R J. Povinelli, A Vlachos, W A. Baumgartner Jr., L Hunter, B Carpenter, R Tsai, H Dai, F Liu, Y Chen, C Sun, S Katrenko, P Adriaans, C Blaschke, R Torres, M Neves, P Nakov, A Divoli, M Lopez, J Mata-Vazquez, and W. John Wilbur (2008) Overview of BioCreative II gene mention recognition (Genome Biology. In press)

Year 2007

1. H. Liu, M. Torii (2007) Entity Names in Biomedical Databases and in Free Text (ICDM 2007, in press)
2. I. Bebu, F. Seillier-Moiseiwitsch, H. Liu (2007) Semiparametric RMA Background-Correction for Oligonucleotide Arrays (BIBE 2007, in press)
3. H. Liu, Zeeberg, B.R., Qu, G., Koru, A.G., Ferrucci, A., Kahn, A., Ryan, C., Nuhanovic, A, Munson, R., Reinhold, W.C. and Weinstein, J.N. (2007) AffyProbeMiner: a web resource for computing or retrieving accurately redefined Affymetrix probe sets (Bioinformatics 2007, in press)
4. H. Liu, I. Bebu, Xin Li, Microarray probes and probe sets (Frontier of Science 2007, in press)
5. M. Torii, H. Liu Semantic Category Assignment for Long Forms Extracted from Text (Proceeding of AMIA 2007, in press)
6. M. Torii, ZZ Hu, C. Wu, H. Liu A Comparison Study of Algorithms on Biomedical Short Form Definition Detection (BMC Bioinformatics, 2007, in press)
7. D. Natale, C. Arighi, W. Barker, J. Blake, Ti-Cheng Chang, Zhangzhi Hu, H. Liu, B. Smith, and C. Wu (2007) Conceptual Framework for a Protein Ontology (BMC Bioinformatics, 2007, in press)
8. A.G. Koru, D. Zhang, and H. Liu Modeling the Effect of Size on Defect Proneness for Open-Source Software (Proceeding of Predictor Models in Software Engineering (PROMISE) 2007)
9. A.G.Koru, D. Zhang, and H. Liu Effect of Coupling on Defect Proneness in Evolutionary Open-Source Software Development (Proceedings of Open Source Software (OSS) 2007)
10. H. Liu, M. Torii, ZZ Hu, and C. Wu Gene Mention and Gene Normalization Based on Machine Learning and Online Resources, Proceeding of the Second BioCreative Challenge Evaluation Workshop 2007, 135-140
11. Kahn, M. Ryan, H. Liu, BR Zeeberg, DC Jamison and J Weinstein SpliceMiner: A High-Throughput Database Implementation of the NCBI Evidence Viewer for Microarray Splice Variant Analysis BMC Bioinformatics 2007 (online at http://www.biomedcentral.com/1471-2105/8/75).
12. H. Liu. Application of Programming Languages in Biology (2007). In Bioinformatics: A practical approach by Shui Qing Ye, Chapman & Hall/Crc Mathematical & Computational Biology, 455-510

Year 2006

1. H. Liu, Z. Hu, M. Torii, C. Wu, and C. Friedman (2006, in press) Quantitative Assessment of Dictionary-based Protein Named Entity Tagging JAMIA.
2. H. Xu, M. Markatou, R Dimova, H. Liu, and C. Friedman (2006, in press) Machine Learning and Word Sense Disambiguation in the Biomedical Domain: Design and Evaluation Issues. BMC Bioinformatics.
3. G. Koru and H. Liu (2006, in press) Characterizing Change-Prone Modules in two large-scale open source products. Journal of Software and Systems.
4. H. Liu, D. F. Hsu (2006, in press) Generalized Shuffle-Exchange Networks: Combinatorial and Fault-Tolerant Properties. Journal of Dynamics of Continuous, Discrete and Impulsive Systems.
5. H. Liu, Z. Hu, and C Wu (2006) BioThesaurus: a thesaurus of gene and protein names. BioInformatics, Jan 1;22(1):103-5.
6. M. Torii, H. Liu (2006) Headwords and Suffixes in Biomedical Names, Proceedings of KDLL 2006. Lecture Notes in Bioinformatics, Eds. Bremer, E.G.; Hakenberg, J.; Han, E.-H.S.; Berrar, D.; Dubitzky, W.Vol. 3886.