Hongfang Liu

Stephen Tze-Inn Wu, Vinod Kaggal, Dmitriy Dligach, James J. Masanz, Pei Chen, Lee Becker, Wendy Webber Chapman, Guergana K. Savova, Hongfang Liu, Christopher G. Chute: A common type system for clinical natural language processing. J. Biomedical Semantics 4: 1 (2013)

Kavishwar B. Wagholikar, Manabu Torii, Siddhartha Jonnalagadda, Hongfang Liu: Pooling annotated corpora for clinical concept extraction. J. Biomedical Semantics 4: 3 (2013)

Kavishwar B. Wagholikar, Kathy L. MacLaughlin, Michael R. Henry, Robert A. Greenes, Ronald A. Hankey, Hongfang Liu, Rajeev Chaudhry: Clinical decision support with automated text processing for cervical cancer screening. JAMIA 19(5): 833-839 (2012)

Siddhartha Jonnalagadda, Dingcheng Li, Sunghwan Sohn, Stephen Tze-Inn Wu, Kavishwar Wagholikar, Manabu Torii, Hongfang Liu: Coreference analysis in clinical notes: a multi-pass sieve with alternate anaphora resolution modules. JAMIA 19(5): 867-874 (2012)

Stephen Tze-Inn Wu, Hongfang Liu, Dingcheng Li, Cui Tao, Mark A. Musen, Christopher G. Chute, Nigam H. Shah: Unified Medical Language System term occurrences in clinical notes: a large-scale corpus analysis. JAMIA 19(e1) (2012)

Bo Xu, Hongfei Lin, Zhihao Yang, Kavishwar B. Wagholikar, Hongfang Liu: Classifying protein complexes from candidate subgraphs using fuzzy machine learning model. BIBM Workshops 2012: 640-647

Dingcheng Li, Cui Tao, Hongfang Liu, Christopher G. Chute: Ontology-Based Temporal Relation Modeling with MapReduce Latent Dirichlet Allocations for Big EHR Data. CGC 2012: 708-715

Hongfang Liu, Stephen Tze-Inn Wu, Cui Tao, Christopher G. Chute: Modeling UIMA type system using web ontology language: towards interoperability among UIMA-based NLP tools. MIX-HS 2012: 31-36

Kavishwar Wagholikar, Sunghwan Sohn, Stephen Tze-Inn Wu, Vinod Kaggal, Sheila Buehler, Robert A. Greenes, Tsung-Teh Wu, David Larson, Hongfang Liu, Rajeev Chaudhry, Lisa Boardman: Clinical Decision Support for Colonoscopy Surveillance Using Natural Language Processing. HISB 2012: 12-21

Siddhartha Jonnalagadda, Guilherme Del Fiol, Richard Medlin, Charlene R. Weir, Marcelo Fiszman, Javed Mostafa, Hongfang Liu: Automatically Extracting Sentences from Medline Citations to Support Clinicians' Information Needs. HISB 2012: 72

Sunghwan Sohn, Sean P. Murphy, Siddhartha Jonnalagadda, Kavishwar Wagholikar, Stephen Tze-Inn Wu, Christopher G. Chute, Hongfang Liu, Scott Halgrim: Systematic Analysis of Cross-Institutional Medication Description Patterns in Clinical Notes. HISB 2012: 118

Barry Zeeberg, Hongfang Liu, Ari B. Kahn, Martin Ehler, Vinodh N. Rajapakse, Robert F. Bonner, Jacob D. Brown, Brian P. Brooks, Vladimir L. Larionov, William C. Reinhold, John N. Weinstein, Yves Pommier: RedundancyMiner: De-replication of redundant GO categories in microarray and proteomics analysis. BMC Bioinformatics 12: 52 (2011)

Jinlian Wang, Manabu Torii, Hongfang Liu, Gerald W. Hart, Zhang-Zhi Hu: dbOGAP - An Integrated Bioinformatics Resource for Protein O-GlcNAcylation. BMC Bioinformatics 12: 91 (2011)

Zhiyong Lu, Hung-Yu Kao, Chih-Hsuan Wei, Minlie Huang, Jingchen Liu, Cheng-Ju Kuo, Chun-Nan Hsu, Richard Tzong-Han Tsai, Hong-Jie Dai, Naoaki Okazaki, Han-Cheol Cho, Martin Gerner, Illés Solt, Shashank Agarwal, Feifan Liu, Dina Vishnyakova, Patrick Ruch, Martin Romacker, Fabio Rinaldi, Sanmitra Bhattacharya, Padmini Srinivasan, Hongfang Liu, Manabu Torii, Sérgio Matos, David Campos, Karin Verspoor, Kevin M. Livingston, W. John Wilbur: The gene normalization task in BioCreative III. BMC Bioinformatics 12(S-8): S2 (2011)

Manabu Torii, Lanlan Yin, Thang Nguyen, Chand T. Mazumdar, Hongfang Liu, David M. Hartley, Noele P. Nelson: An exploratory study of a text classification framework for Internet-based surveillance of emerging epidemics. I. J. Medical Informatics 80(1): 56-66 (2011)

Manabu Torii, Kavishwar B. Wagholikar, Hongfang Liu: Using machine learning for concept extraction on clinical documents from multiple data sources. JAMIA 18(5): 580-587 (2011)

Kavishwar Wagholikar, Manabu Torii, Hongfang Liu: Human gene/protein synonym dictionary from WikiLinks. BCB 2011: 462-464

Yang Chen, Manabu Torii, Chang-Tien Lu, Hongfang Liu: Learning from positive and unlabeled documents for automated detection of alternative splicing sentences in medline abstracts. BIBM Workshops 2011: 530-537

Hongfang Liu, Ruijuan Li, Nana Li: Hamilton Non-holonomic Momentum Equation of the System and Conclusions. ICICA (1) 2011: 23-29

Stephen Tze-Inn Wu, Kavishwar Wagholikar, Sunghwan Sohn, Vinod Kaggal, Hongfang Liu: Empirical Ontologies for Cohort Identification. TREC 2011

Lanlan Yin, Guixian Xu, Manabu Torii, Zhendong Niu, José M. Maisog, Cathy H. Wu, Zhang-Zhi Hu, Hongfang Liu: Document classification for mining host pathogen protein-protein interactions. Artificial Intelligence in Medicine 49(3): 155-160 (2010)

Gunes Koru, Hongfang Liu, Dongsong Zhang, Khaled El Emam: Testing the theory of relative defect proneness for closed-source software. Empirical Software Engineering 15(6): 577-598 (2010)

Hongfang Liu, Manabu Torii, Guixian Xu, Johannes Goll: Classification Systems for Bacterial Protein-Protein Interaction Document Retrieval. IJCMAM 1(1): 34-44 (2010)

Min Song, Hongfang Liu: LFXtractor: Text chunking for long form detection from biomedical text. I. J. Functional Informatics and Personalised Medicine 3(2): 89-102 (2010)

Manabu Torii, Burt-Ujin Bayarsaikhan, Hongfang Liu, Thang Nguyen, Kevin Jones, Noele P. Nelson, David M. Hartley: An exploratory study of news article clustering for web-based bio-surveillance. IHI 2010: 435-439

Chong Min Lee, Manabu Torii, Zhang-Zhi Hu, Yi-Ting Tsai, Jinesh Shah, Hongfang Liu: Evaluating gene/protein name tagging and mapping for article retrieval. Semantic Mining in Biomedicine 2010

Cecilia N. Arighi, Hongfang Liu, Darren A. Natale, Winona C. Barker, Harold J. Drabkin, Judith A. Blake, Barry Smith, Cathy H. Wu: TGF-beta signaling proteins and the Protein Ontology. BMC Bioinformatics 10(S-5) (2009)

Manabu Torii, Zhang-Zhi Hu, Cathy H. Wu, Hongfang Liu: Research Paper: BioTagger-GM: A Gene/Protein Name Recognition System. JAMIA 16(2): 247-255 (2009)

Akif Günes Koru, Dongsong Zhang, Khaled El Emam, Hongfang Liu: An Investigation into the Functional Form of the Size-Defect Relationship for Software Modules. IEEE Trans. Software Eng. 35(2): 293-304 (2009)

Medha Umarji, Carolyn B. Seaman, Akif Günes Koru, Hongfang Liu: Software Engineering Education for Bioinformatics. CSEE&T 2009: 216-223

Hongyong Jin, Xiuping Zhao, Hongfang Liu: Testing of the Uniformity of Color Appearance Space. CSIE (6) 2009: 307-311

Guixian Xu, Zhendong Niu, Peter Uetz, Xu Gao, Xuping Qin, Hongfang Liu: Semi-supervised Learning of Text Classification on Bacterial Protein-Protein Interaction Documents. IJCBS 2009: 263-270

Hans A. Kestler, André Müller, Johann M. Kraus, Malte Buchholz, Thomas M. Gress, Hongfang Liu, David W. Kane, Barry Zeeberg, John N. Weinstein: VennMaster: Area-proportional Euler diagrams for functional GO analysis of microarrays. BMC Bioinformatics 9 (2008)

Michael C. Ryan, Barry Zeeberg, Natasha J. Caplen, James A. Cleland, Ari B. Kahn, Hongfang Liu, John N. Weinstein: SpliceCenter: A suite of web-based bioinformatic applications for evaluating the impact of alternative splicing on RT-PCR, RNAi, microarray, and peptide-based studies. BMC Bioinformatics 9 (2008)

Akif Günes Koru, Khaled El Emam, Dongsong Zhang, Hongfang Liu, Divya Mathew: Theory of relative defect proneness. Empirical Software Engineering 13(5): 473-498 (2008)

Guixian Xu, Lanlan Yin, Manabu Torii, Zhendong Niu, Cathy H. Wu, Zhang-Zhi Hu, Hongfang Liu: Document Classification for Mining Host Pathogen Protein-Protein Interactions. BIBM 2008: 461-466

Zhang-Zhi Hu, K. Bretonnel Cohen, Lynette Hirschman, Alfonso Valencia, Hongfang Liu, Michelle G. Giglio, Cathy H. Wu: iProLINK: A Framework for Linking Text Mining with Ontology and Systems Biology. BIBM 2008: 467-472

Ionut Bebu, Françoise Seillier-Moiseiwitsch, Hongfang Liu: Analysis of Microarray Titration Experiments. BIOCOMP 2008: 942-946

Hongfang Liu, Barry Zeeberg, Gang Qu, Akif Günes Koru, Alessandro Ferrucci, Ari B. Kahn, Michael C. Ryan, Antej Nuhanovic, Peter J. Munson, William C. Reinhold, David W. Kane, John N. Weinstein: AffyProbeMiner: a web resource for computing or retrieving accurately redefined Affymetrix probe sets. Bioinformatics 23(18): 2385-2390 (2007)

Ari B. Kahn, Michael C. Ryan, Hongfang Liu, Barry Zeeberg, D. Curtis Jamison, John N. Weinstein: SpliceMiner: a high-throughput database implementation of the NCBI Evidence Viewer for microarray splice variant analysis. BMC Bioinformatics 8 (2007)

Darren A. Natale, Cecilia N. Arighi, Winona C. Barker, Judith A. Blake, Ti-Cheng Chang, Zhang-Zhi Hu, Hongfang Liu, Barry Smith, Cathy H. Wu: Framework for a Protein Ontology. BMC Bioinformatics 8(S-9) (2007)

Manabu Torii, Zhang-Zhi Hu, Min Song, Cathy H. Wu, Hongfang Liu: A comparison study on algorithms of detecting long forms for short forms in biomedical text. BMC Bioinformatics 8(S-9) (2007)

Akif Günes Koru, Hongfang Liu: Identifying and characterizing change-prone classes in two large-scale open-source products. Journal of Systems and Software 80(1): 63-73 (2007)

Ionut Bebu, Françoise Seillier-Moiseiwitsch, Hongfang Liu: Semiparametric RMA Background-Correction for Oligonucleotide Arrays. BIBE 2007: 1404-1408

Hongfang Liu, Manabu Torii, Zhang-Zhi Hu, Cathy H. Wu: Mapping Gene/Protein Names in Free Text to Biomedical Databases. ICDM Workshops 2007: 101-106

Akif Günes Koru, Dongsong Zhang, Hongfang Liu: Modeling the Effect of Size on Defect Proneness for Open-Source Software. ICSE Companion 2007: 115-124

Manabu Torii, Hongfang Liu: Classifier Ensemble for Biomedical Document Retrieval. LBM (Short Papers) 2007

Akif Günes Koru, Dongsong Zhang, Hongfang Liu: Effect of Coupling on Defect Proneness in Evolutionary Open-Source Software Development. OSS 2007: 271-276

Miguel E. Ruiz, Ying Sun, Jianqiang Wang, Hongfang Liu: Exploring Traits of Adjectives to Predict Polarity Opinion in Blogs and Semantic Filters in Genomics. TREC 2007

Hongfang Liu, Zhang-Zhi Hu, Jian Zhang, Cathy H. Wu: BioThesaurus: a web-based thesaurus of protein and gene names. Bioinformatics 22(1): 103-105 (2006)

Hua Xu, Marianthi Markatou, Rositsa Dimova, Hongfang Liu, Carol Friedman: Machine learning and word sense disambiguation in the biomedical domain: design and evaluation issues. BMC Bioinformatics 7: 334 (2006)

Hongfang Liu, Zhang-Zhi Hu, Manabu Torii, Cathy H. Wu, Carol Friedman: Research Paper: Quantitative Assessment of Dictionary-based Protein Named Entity Tagging. JAMIA 13(5): 497-507 (2006)

Li Zhou, Ying Tao, James J. Cimino, Elizabeth S. Chen, Hongfang Liu, Yves A. Lussier, George Hripcsak, Carol Friedman: Terminology model discovery using natural language processing and visualization techniques. : 626-636 (2006)

Manabu Torii, Hongfang Liu: Headwords and Suffixes in Biomedical Names. KDLL 2006: 29-41

Lifeng Chen, Hongfang Liu, Carol Friedman: Gene name ambiguity of eukaryotic nomenclatures. Bioinformatics 21(2): 248-256 (2005)

Hongfang Liu, Zhang-Zhi Hu, Cathy H. Wu: DynGO: a tool for visualizing and mining of Gene Ontology and its associations. BMC Bioinformatics 6: 201 (2005)

Akif Günes Koru, Hongfang Liu: An investigation of the effect of module size on defect prediction using static measures. ACM SIGSOFT Software Engineering Notes 30(4): 1-5 (2005)

Akif Günes Koru, Hongfang Liu: Building Effective Defect-Prediction Models in Practice. IEEE Software 22(6): 23-29 (2005)

Hongfang Liu, Zhang-Zhi Hu, Cathy H. Wu: Dynamically Generating a Protein Entity Dictionary Using Online Resources. ACL 2005

Alan R. Aronson, Dina Demner-Fushman, Susanne M. Humphrey, Jimmy J. Lin, Patrick Ruch, Miguel E. Ruiz, Lawrence H. Smith, Lorraine K. Tanabe, W. John Wilbur, Hongfang Liu: Fusion of Knowledge-Intensive and Statistical Approaches for Retrieving and Annotating Textual Genomics Documents. TREC 2005

Zhang-Zhi Hu, Inderjeet Mani, Vincent Hermoso, Hongfang Liu, Cathy H. Wu: iProLINK: an integrated protein resource for literature mining. Computational Biology and Chemistry 28(5-6): 409-416 (2004)

Hongfang Liu, Virginia Teller, Carol Friedman: Research Paper: A Multi-aspect Comparison Study of Supervised Word Sense Disambiguation. JAMIA 11(4): 320-331 (2004)

Han-Yu Chuang, Hongfang Liu, Stuart M. Brown, Cameron McMunn-Coffran, Cheng-Yan Kao, D. Frank Hsu: Identifying Significant Genes from Microarray Data. BIBE 2004: 358-365

Han-Yu Chuang, Hongfang Liu, Fang-An Chen, Cheng-Yan Kao, D. Frank Hsu: Combination Methods in Microarray Analysis. ISPAN 2004: 625-630

Olivia Tuason, Lifeng Chen, Hongfang Liu, Judith A. Blake, Carol Friedman: Biological Nomenclatures: A Source of Lexical Knowledge and Ambiguity. Pacific Symposium on Biocomputing 2004: 238-249

Alan R. Aronson, Susanne M. Humphrey, Nicholas C. Ide, Won Kim, Russell R. Loane, James G. Mork, Lawrence H. Smith, Lorraine K. Tanabe, W. John Wilbur, Natalie Xie, Dina Demner-Fushman, Hongfang Liu: Knowledge-Intensive and Statistical Approaches to the Retrieval and Annotation of Genomics MEDLINE Citations. TREC 2004

Carol Friedman, Hongfang Liu, Lyudmila Shagina: A vocabulary development and visualization tool based on natural language processing and the mining of textual patient reports. Journal of Biomedical Informatics 36(3): 189-201 (2003)

Hongfang Liu, Carol Friedman: Mining Terminological Knowledge in Large Biomedical Corpora. Pacific Symposium on Biocomputing 2003: 415-426

Hongfang Liu, Stephen B. Johnson, Carol Friedman: Research Paper: Automatic Resolution of Ambiguous Terms Based on Machine Learning and Conceptual Relations in the UMLS. JAMIA 9(6): 621-636 (2002)

Hongfang Liu, Yves A. Lussier, Carol Friedman: Disambiguating Ambiguous Biomedical Terms in Biomedical Narrative Text: An Unsupervised Method. Journal of Biomedical Informatics 34(4): 249-261 (2001)

Carol Friedman, George Hripcsak, Lyudmila Shagina, Hongfang Liu: Research Paper: Representing Information in Patient Reports Using Natural Language Processing and the Extensible Markup Language. JAMIA 6(1): 76-87 (1999)

Hongfang Liu, D. Frank Hsu, S. Horiguchi: Generalized shuffle-exchange digraphs: Hamiltonian properties. ISCAS (6) 1999: 157-160