Haiyan (Nancy) Hu

Professor, Computer Science

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

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Research Interests

·         Bioinformatics/Computational Biology

·        Data Mining; Machine Learning; 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>>>

 

Teaching  

·         CAP5510 Introduction to Bioinformatics

·         CAP 6545 Machine Learning in Bioinformatics

·         CAP 6938 Advanced Topics in Machine Learning

·         COT3100H Introduction to Discrete Structures (Honors)

·         CAP6938 Graphs and Networks in Computational Biology

·        COT3100 Introduction to Discrete Structures

·        CAP6938 Data Mining in Bioinformatics

·        COP 3503 Computer Science II (CS2)

 

Publications  

·        Zheng H, Wang S, Li X, Hu H. A computational modeling of pri-miRNA expression, PLOS ONE, https://doi.org/10.1371/journal.pone.0290768. 2024.

·       Athaya T, Li X, Hu H. A deep learning method to integrate extracellular miRNA with mRNA for cancer studies, Bioinformatics, https://doi.org/10.1093/bioinformatics/btae653. 2024.

·       Weston M, Hu H, Li X. A deep learning approach for prokaryotic small protein identification, Frontiers in Genetics, https://doi.org/10.3389/fgene.2024.1439423. 2024.

·       Beals J, Hu H, Li X. A survey of experimental and computational identification of small proteins, Briefings in Bioinformatics, https://doi.org/10.1093/bib/bbae345. 2024.

·       Athaya T, Ripan CR, Li X, Hu H. Multimodal deep learning approaches for single cell multi-omics data integration, Briefings in Bioinformatics, https://doi.org/10.1093/bib/bbad313. 2023.

·       Ventolero M, Wang, S, Hu H, Li X. Are the predicted known bacterial strains in a smple really present? A case study, Plos one, https://doi.org/10.1371/journal.pone.0291964. 2023.

·       Wang S, Ventolero M, Hu H, Li X. A novel approach for bacterial strain analysis in multiple samples, Journal of Bioinformatics and Systems Biology, https://doi.org/10.26502/jbsb.5107065. 2023.

·       Ventolero M, Wang, S, Hu H, Li X. Computational analyses of bacterial strains from shotgun reads, Briefings in Bioinformatics, https://doi.org/10.1093/bib/bbac013. 2022.

·       Zhang Y, Wang S, Hu H, Li X. A systematic study of HIF1A cofactors in hypoxic cancer cells, Scientific Reports, https://doi.org/10.1038/s41598-022-23060-9. 2022.

·       Ghuathakurta S, Adams L, Jeong I, Sivakumar A, Cha M, Fiadeiro MB, Hu H, Kim Y. Precise epigenomic editing with a SunTag-based modular epigenetic toolkit, Epigenetics, https://doi.org/10.1080/15592294.2022.2106646. 2022.

·       Wang S, Ventolero M, Hu H, Li X. A revisit to universal single-copy genes in bacterial genomes, Scientific Reports, https://doi.org/10.1038/s41598-022-18762-z. 2022.

·       Zheng H, Wang S, Li X, Hu H. INSISTC: Incorporating network structure information for single-cell type classification, Genomics, 114(5), https://doi.org/10.1016/j.ygeno. 2022.

·       Wang S, Zheng H, Choi JS, Lee JK, Li X, Hu H. A systematic evaluation of the computational tools for ligand-receptor-based cell-cell interaction inference, Briefings in Functional Genomics, https://doi.org/10.1093/bfgp/elac019. 2022.

·       Wang S, Hu H, Li X. A systematic study of motif pairs that may facilitate enhancer-promoter interactions, Journal of Integrative Bioinformatics, https://doi.org/10.1515/jib-2021-0038. 2022.

·      Talukder A, Zhang W, Li X, Hu H. A deep learning method for miRNA/IsomiR target detection, Scientific Reports, https://doi.org/10.1038/s41598-022-14890-8. 2022.·       

·        Wang S, Talukder A, Cha M, Li X, Hu H. Computational annotation of miRNA transcription start sites, Briefings in Bioinformatics, https://doi.org/10.1093/bib/bbz178. 2021.

·       Talukder A, Hu H, Li X. An intriguing characteristic of enhancer-promoter interactions, BMC Genomics, https://doi.org/10.1186/s12864-021-07440-5. 2021.

·        Zheng H, Talukder A, Li X, Hu H. A systematic evaluation of the computational tools for lncRNA identification, Briefings in Bioinformatics, https://doi.org/10.1093/bib/bbab285. 2021.

·        Cha M, Zheng H, Talukder A, Barham C, Li X, Hu H. A two-stream convolutional neural network for microRNA transcription start site feature integration and identification, Scientific Reports, https://doi.org/10.1038/s41598-021-85173-x. 2021.

·        Zheng H, Li X, Hu H. Deep learning to identify transcription start sites from CAGE data, IEEE International Conference on Bioinformatics and Biomedicine (BIBM). 2020.

·        Li X, Hu H, Li X. mixtureS: a novel tool for bacterial strain reconstruction from reads, Bioinformatics, https://doi.org/10.1093/bioinformatics/btaa728. 2020.

·        Talukder A, Barham C, Li X, Hu H. Interpretation of deep learning in genomics and epigenomics, Briefing in Bioinformatics, https://doi.org/10.1093/bib/bbaa177. 2020.

·        Talukder A, Li X, Hu H. Position-wise binding preference is important for miRNA target prediction, Bioinformatics, https://doi.org/10.1093/bioinformatics/btaa195. 2020.

·        Wang S, Hu H, Li X.Shared distal regulatory regions may contribute to the coordinated expression of human ribosomal protein genes, Genomics, https://doi.org/10.1016/j.ygeno.2020.03.028. 2020.

·        Talukder A, Saadat S, Li X, Hu H. EPIP: A novel approach for condition-specific enhancer-promoter interaction prediction. Bioinformatics, https://doi.org/10.1093/bioinformatics/btz664. 2019.

·        Li X, Saadat S, Hu H, Li X. BHap: a novel approach for bacterial haplotype reconstruction. Bioinformatics, DOI:10.1093/bioinformatics/btz280. 2019.

·        Li X, Hu H. Improving miRNA target prediction using CLASH data. in A. Lagana (Ed): microRNA Target Identification, Springer Nature, New York: NY, pp. 75-83. DOI: 10.1007/978-1-4939-9207-2_6. 2019.

·         Barham C, Cha M, Li X, Hu H, Application of deep learning models to microRNA transcription start site identification. IEEE 7th International Conference on Bioinformatics and Computational Biology (ICBCB), 2019.

·         Li X, Naser SA, Khaled A, Hu H, Li X. When old metagenomic data meet newly sequenced genomes, a case study. PLoS One, DOI:10.1371/journal.pone.0198773. 2018.

·         Li X, Ge P, Hu H. FlexSLiM: a novel approach for short linear motif discovery in protein sequences. The 6th International Conference on Bioinformatics and Computational Biology, DOI: 10.1145/3194480.3194501. 2018.

·         Ding J, Li X, Hu H. CCmiR: a computational approach for competitive and cooperative microRNA binding prediction. Bioinformatics, DOI:10.1093/bioinformatics/btx606. 2018.

·         Wang Y, Goodison S, Li X, Hu H. Prognostic cancer gene signatures share common regulatory motifs. Scientific Reports, DOI:10.1038/s41598-017-05035-3. 2017.

·         Zheng Y, Li X, Hu H, Discover the semantic structure of Human reference epigenome by differential latent Dirichlet allocation. IEEE International Conference on Bioinformatics and Biomedicine (BIBM 2017).

·         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. DOI:10.1186/s12859-015-0473-8

·         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: 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. DOI:10.1016/j.jbi.2010.06.004

·        Hu H. An efficient algorithm to identify coordinately activated transcription factors. Genomics, 95(3):143-50, 2010. DOI: 10.1016/j.ygeno.2009.12.006.

·        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. doi:10.1186/1471-2164-11-567

·        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. DOI: 10.1109/ICBBT.2010.5479016

·        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. DOI: 10.1109/ICBBT.2010.5479017

·        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.