Haiyan (Nancy) Hu

Associate Professor

Computer Science Department

University of Central Florida

Office: HEC-233

Phone: 407-882-0134
Email: haihu at cs.ucf.edu
Mail: UCF, 4000 Central Florida Blvd, Harris Engineering Center, Bldg. 116, Room 233, Orlando, Fl. 32816-2005



Lab Page

Research Interests




         Bioinformatics/Computational Biology

        Data Mining; Machine Learning; Pattern Recognition

Grants & Projects




         Computational Analysis of microRNA Binding

         Epigenetic Regulation

         Discovery of Cis-Regulatory Modules

         Data mining, Machine Learning and Pattern Recognition

        <<<Graduate and Undergraduate Research Assisant Positions are available in areas including data mining, machine learning, pattern recognition, modeling and simulation, bioinformatics and computational biology. For interested students, please read here>>>





         CAP5510 Introduction to Bioinformatics (Fall 2017, Fall 2016, Fall 2015, 2013, 2012, 2011)

         CAP 6545 Machine Learning in Bioinformatics (Spring 2016, 2013, 2012, 2011, 2010)

         CAP 6938 Advanced Topics in Machine Learning (Fall 2014, 2013)

         COT3100H Introduction to Discrete Structures (Honors) (Spring 2012)

         CAP6938 Graphs and Networks in Computational Biology (Fall 2011)

         COT3100 Introduction to Discrete Structures (Spring 2011)

        CAP6938 Data Mining in Bioinformatics (Fall 2010, 2009)

        COP 3503 Computer Science II (CS2) (Fall 2008, Spring 2009)





         Wang Y, Hu H, Li X. rRNAFilter: a fast approach for ribosomal RNA read removal without a reference database. Journal of Computational Biology, doi: 10.1089/cmb.2016.0113. 2016.

         Zhao C, Li X, Hu H. PETModule: a motif module based approach for enhancer target gene prediction. Scientific Reports, doi: 10.1038/srep30043. 2016.

        Wang Y, Hu H, Li X. MBMC: An Effective Markov Chain Approach for Binning Metagenomic Reads from Environmental Shotgun Sequencing Projects. OMICS: A Journal of Integrative Biology, doi:10.1089/omi.2016.0081. 2016.

        Li X, Zheng Y, Hu H, Li X. Integrative analyses shed new light on human ribosomal protein gene regulation. Scientific Reports, doi: 10.1038/srep28619. 2016.

         Ding J, Li X, Hu H. TarPmiR: a new approach for microRNA target site prediction. Bioinformatics. doi: 10.1093/bioinformatics/btw318. 2016.

         Zheng Y, Li X, Hu H. PreDrem: a database of predicted DNA regulatory motifs from 349 human cell and tissue samples. DATABASE - The Journal of Biological Databases and Curation, doi: 10.1093/database/bav007. 2015.

         Wang Y, Hu H, Li X. MBBC: an efficient approach for metagenomic binning based on composition, BMC Bioinformatics, 2015.

         Ding J, Li X, Hu H. MicroRNA modules prefer to bind weak and unconventional target sites. Bioinformatics, 31 (9): 1366 - 1374. doi: 10.1093/bioinformatics/btu833. 2015.

         Ding J, Dhillon V, Li X, Hu H. Systematic Discovery of Cofactor Motifs from ChIP-seq Data by SIOMICS. Methods. doi: 10.1016/j.ymeth.2014.08.006. 2015.

         Zheng Y, Li X, Hu H. Comprehensive discovery of DNA motifs in 349 human cells and tissues reveals new features of motifs. Nucleic Acids Research. doi: 10.1093/nar/gku1261. 2014.

         Zheng Y, Li X, Hu H. Computational discovery of feature patterns in nucleosomal DNA sequences. Genomics, 104 (2). doi: 10.1016/j.ygeno.2014.07.002. 2014.

         Wang Y, Li X, Hu H. H3K4me2 reliably defines transcription factor binding regions.Genomics. doi: 10.1016/j.ygeno.2014.02.002, 2014.

         Ding J, Hu H, Li X. SIOMICS: a novel approach for systematic identification of motifs in ChIP-seq data, Nucleic Acids Research., 42 (5): e35, doi: 10.1093/nar/gkt1288, 2014.

         Ding J, Hu H, Li X. NIM, A novel computational method for predicting nuclear-encoded chloroplast proteins, Journal of Medical and Bioengineering, 2(2): 115-119. doi: 10.12720/jomb.2.2.115-119, 2013.

        Ding J, Cai X, Wang Y, Hu H, Li X. ChIPModule: Systematic discovery of transcription factors and their cofactors from ChIP-seq data, Pac Symp Biocomput. 2013.

        Ding J, Li X, Hu H. Systematic discovery of cis-regulatory elements in Chlamydomonas reinhardtii genome using comparative genomics, Plant Physiology, doi: http://dx.doi.org/10.1104/pp.112.200840, 2012.

         Ruppert SM , Chehtane M , Zhang G , Hu H , Li X , Khaled AR. JunD/AP-1-Mediated gene expression promotes lymphocyte growth dependent on Interleukin-7 signal transduction. PLoS ONE 7(2): e32262. doi:10.1371/journal.pone.0032262, 2012.

         Li W, Hu H, Huang Y, Li H, Mehan MR, Nunez-Iglesias J, Xu M, Yan X, Zhou XJ. Pattern mining across many massive networks. Book Chapter in Functional Coherence of Biological Networks. Springer, M. Koyuturk, S. Subramaniam, and A. Grama Eds., 137-170, 2012.

         Wang Y, Ding J, Daniell H, Hu H, Li X. Motif analysis unveils the possible co-regulation of chloroplast genes and nuclear genes encoding chloroplast proteins. Plant Mol Biol, 80(2): 177-187. doi:10.1007/s11103-012-9938-6, 2012.

        Ding J, Hu H, Li X. Thousands of cis-regulatory sequence combinations are shared by Arabidopsis and Poplar. Plant Physiology, doi: http://dx.doi.org/10.1104/pp.111.186080, 2011.

        Wang Y, Li X, Hu H. Transcriptional regulation of co-expressed microRNA target genes. Genomics. doi:10.1016/j.ygeno.2011.09.004, 2011.

        Li W, Hu H, Huang Y, Li H, Mehan MR, Nunez-Iglesias J, Xu M, Yan X, and Zhou XJ. Frequent pattern discovery in multiple biological networks: algorithms and applications. Statistics in Biosciences, p. 1-20. DOI: 10.1007/s12561-011-9047-0, 2011.

        Hu H. Mining patterns in disease classification forests. Journal of Biomedical Informatics, 43(5):820-7, 2010.

        Cai X, Hou L, Su N, Hu H, Deng M, Li X. Systematic identification of conserved motif modules in the human genome. BMC Genomics, 11:567, 2010.

        Hu H, Li X. Whole genome identification of target genes of transcription factors. The 2010 International Conference On Bioinformatics and Biomedical Technology, Chengdu, China. April 16-18, 2010.

        Hu H, Li X. Hierarchical order of gene expression levels. The 2010 International Conference On Bioinformatics and Biomedical Technology, Chengdu, China. April 16-18, 2010.

        Hu H, Li X. Transcription factor binding site identification by phylogenetic footprinting. Book Chapter in Frontiers in Computational and Systems Biology, 113-132, 2010.

        Cai X, Hu H, Li X. A new measurement of sequence conservation. BMC Genomics, 10:623, 2009.

        Hu H. An efficient method to identify conditionally activated transcription factors and their corresponding signal transduction pathway segments. Bioinformatics and Biology Insights, 3:179-187, 2009.

        Hu J, Hu H, Li X. MOPAT: a graph-based method to predict recurrent cis-regulatory modules from known motifs. Nucleic Acids Res, 36(13):4488-4497, 2008.

        Hu H, Li X. Networking Pathways unveils Association between Obesity and Non-Insulin Dependent Diabetes Mellitus. Pac Symp Biocomput.13: 255-66, 2008.

        Hu H, Li X. Transcriptional regulation in eukaryotic ribosomal protein genes, Genomics. 90(4):421-3, 2007.

        Cai X, Hu H, Li X. Tree Gibbs Sampler: Identifying Conserved Motifs without Aligning Orthologous Sequences. Bioinformatics. 23(15):2013-4, 2007.

        Huang Y, Li H, Hu H, Yan X, Waterman MS, Huang H, Zhou XJ. Systematic Discovery of Functional Modules and Context-Specific Functional Annotation of Human Genome. Bioinformatics, 23(13):i222-i229, 2007.

        Pan F, Kamath K, Zhang K, Pulapura S, Achar A, Nunez-Iglesias J, Huang Y, Yan X, Han J, Hu H, Xu M, Zhou XJ. Integrative Array Analyzer: a software package for analysis of cross-platform and cross-species microarray data. Bioinformatics. 22(13):1665-7, 2006.

        Hu H, Yan X, Huang Y, Han J, Zhou XJ. Mining coherent dense subgraphs across massive biological networks for functional discovery. Bioinformatics. 21 Suppl. 1, i213-i221, 2005.

        Pan F, Kamath Kiran, Hu H, Huang Y, Zhang K, Xu M, Yan X, Han J and Zhou XJ. BioArrayMiner: A software package for integrative analysis of cross-platform and cross-species microarray data. Bioinformatics (ISMB 2005).

        Xue L, Sun X, Yang L, Hu H, Li W. Study on the control system of casing-bag machine hand. New Technology & New Process 6: 11-13, 1999.

         Sun X, Hu H, Pang J, Xue L. Physical Realization of Palletizing Robot Computer Control System. Journal of Beijing Institute of Petro-Chemical Technology 2:1008-2565, 1999.

        Xue L, Sun X, Yang L, Zhang S, Hu H. Robot for sheathing bags and PLC control, Low Voltage Apparatus 5: 38-39+64, 1998.