Please note: The University of Texas Health Science Center at San Antonio will now be called "UT Health San Antonio."

Search Program Faculty/Research

Yufei Huang, Ph.D.

Yufei v2 cropped

RESEARCH

Dr. Yufei Huang received his Ph.D. degree in electrical engineering from the State University of New York at Stony Brook in 2001. Since 2002, he has been with the Department of Electrical and Computer Engineering at the University of Texas at San Antonio (UTSA), where he is now Professor. He is also an adjunct professor at the Dept. of Epidemiology and Biostatistics at the University of Texas Health Science Center at San Antonio. He has been a visiting professor at the Center of Bioinformatics, Harvard Center for Neurodegeneration & Repair.

Dr. Huang’s expertise is in the areas of computational biology, computationalneuroergonomics, brain computer interface, statistical modeling, and Bayesian methods. He is currently focusing on uncovering the functions of mRNA methylation using high throughput sequencing technologies, developing passive EEG-based brain-machine-interaction, and deep learning algorithms for EEG data analysis. He was a recipient of US National Science Foundation (NSF) Early CAREER Award in 2005, Best Paper Award of 2006 Artificial Neural Networks in Engineering Conference, and 2007 Best Paper Award of IEEE Signal Processing Magazine. His research has been supported by NSF, National Institute of Health, Air Force Office of Scientific Research, Army Research Lab, Department of Defense, and Qatar National Research Fund. He has been an organizer of workshops and several special sessions including the IEEE Workshop on Genomic Signal Processing and Statistics, and Workshop on Systems Biology and Medicine, and IEEE Bioinformatics and Biomedicine Conference. He is an Associate Editor of IEEE Transactions on Signal Processing, BMC Systems Biology, EURASIP Journal on Bioinformatics and Computational Biology, and International Journal Machine Leaning and Cybernetics.

Selected Publications

Zhou, Yi, Hung‐I. H. Chen, A. L. Lin, H. Dang, Karin Haack, Shelley A. Cole,Yufei Huang, Haiyang Yu, Yidong Chen, and Chih‐Ko Yeh. "Early Gene Expression in Salivary Gland After Isoproterenol Treatment."Journal of cellular biochemistry116, no. 3 (2015): 431-437. (IF: 3.368)

Liu H, Flores MA, Meng J, Zhang L, Zhao X, Rao MK, Chen Y, Huang Y*. MeT-DB: a database of transcriptome methylation in mammalian cells. Nucleic Acids Res. 2014 Nov 6. pii: gku1024. PubMed PMID: 25378335. (IF: 8.378)

Yao, Wan X., Jinqi Li, Zhiguo Jiang, Jia-Hong Gao, Crystal G. Franklin, Yufei Huang, Jack L. Lancaster, and Guang H. Yue. "Aging interferes central control mechanism for eccentric muscle contraction." Frontiers in aging neuroscience 6 (2014).

Liu, Lian, Shao-Wu Zhang, Yu-Chen Zhang, Hui Liu, Lin Zhang, RunshengChen, Yufei Huang, and Jia Meng. "Decomposition of RNA methylome reveals co-methylation patterns induced by latent enzymatic regulators of theepitranscriptome."Molecular BioSystems11, no. 1 (2015): 262-274. (IF:3.18)

M. Flores, Y. Chen, Y. Huang*. TraceRNA: A Web Application for Competing Endogenous RNA Exploration.Circ Cardiovasc. Genet, 2014, Aug; 7(4): 548-57. doi: 10.1161/CIRCGENETICS.113.000125 (IF: 6.728)

Rosalie Moody, Ying Zhu, Yufei Huang, Xiaodong Cui, Tiffany Jones, RobleBedolla, Xiufen Lei, Zhiqiang Bai, Shou-Jiang Gao. KSHV MicroRNAs Mediate Cellular Transformation and Tumorigenesis by Redundantly Targeting Cell Growth and Survival Pathways. PLoS Pathogens, 2014; 9 (12): e1003857 DOI: 10.1371/journal.ppat.1003857, PMID:24385912 (IF: 8.13)

Meng J, Lu Z, Liu H, Zhang L, Zhang S, Chen Y, Rao MK, Huang Y*. A protocol for RNA methylation differential analysis with MeRIP-Seq data and exomePeakR/Bioconductor package. Methods. 2014 Oct 1;69(3):274-81. doi: 10.1016/j.ymeth.2014.06.008. Epub 2014 Jun 27. PubMed PMID: 24979058; PubMed Central PMCID: PMC4194139. (IF:4.197)

Ma, Chifeng, Hung-I. H. Chen, Mario Flores, Yufei Huang*, and Yidong Chen. "BRCA-Monet: a breast cancer specific drug treatment mode-of-action network for treatment effective prediction using large scale microarray database." BMC Systems Biology 7, no. Suppl 5 (2013): S5. (IF:2.98)

J. Meng, L. M. Merino, K. Robbins, Y Huang*, “Classification of imperfectly time-locked image RSVP events with EEG device,” Neuroinformatics, Sept. 2013 DOI 10.1007/s12021-013-9203-4, PMID:24037139 (IF: 3.13)

Xuan, P., Han, K., Guo, M., Guo, Y., Li, J., Ding, J., & Huang, Y*. (2013). Prediction of microRNAs Associated with Human Diseases Based on Weighted k Most Similar Neighbors. PLoS one, 8(8), e70204. (IF:3.73)

J. Meng, X. Cui, M. Rao, Y. Chen, Y. Huang*,Exome-based Analysis for RNAEpigenome Sequencing DataBioinformatics, Apr. 2013; doi: 10.1093/bioinformatics/btt171, PMID:23589649 (IF:5.32)

M. Flores, T-H Hsiao, Y-C Chiu, E. Y. Chuang, Y. Huang*, Y. Chen, “Gene Regulation, Modulation and Their Applications in Gene Expression Data Analysis,” Advances in Bioinformatics, 2013: 360678, 2013 March 13. doi: 10.1155/2013/360678, PMID:23573084

Sanchez-Diaz PC, Hsiao TH, Chang JC, Yue D, Tan MC, Chen HI, Tomlinson GE, Huang Y, Chen Y, Hung JY. “De-Regulated MicroRNAs in Pediatric Cancer Stem Cells Target Pathways Involved in Cell Proliferation, Cell Cycle and Development.” PLoS One. 2013 Apr 17;8(4):e61622. PMID: 23613887, PMCID: PMC3629228 (IF: 4.09)

J. Meng, Y. Chen, Y. Huang*, “Uncover context-specific gene regulation by transcription factors and microRNAs using Bayesian sparse nonnegative factor regression analysis,” Journal of Biological Systems, Vol. 20, No. 4 (2012) 377–402 (IF: 0.57)

X. Lei, Y. Zhu, T. Jones, Z Bai, Y. Huang, and S-J Gao, “A KSHV microRNA targets TGF-β pathway to promote cell survival” Journal of Virology, 86:11698116711, Nov. 2012, doi: 10.1128/JVI.06855-11 (IF: 5.42)

J. Meng, L. M. Merino, N. B. Shamlo, S. Makeig, K. Robbins, Y Huang* “Characterization and robust classification of EEG signal from image RSVP events with independent time-frequency features,” PLoS ONE, in press (IF: 4.41)

L. Zhang, J. Meng, H. Liu, Y. Huang*, “Clustering DNA methylation expressions using nonparametric beta mixture model,” BMC Genomics, in press (IF: 4.21)

D. Yue, Y. Chen, Y. Huang*, “A Bayesian Decision Fusion Approach for microRNA Target Prediction,” BMC Genomics, in press (IF: 4.21)

Huang Y*, Zhao Z, Xu H, Shyr Y, Zhang B (2012) “Advances in Systems Biology: Computational Algorithms and Applications” BMC Systems Biology, in press (IF: 3.57)

Zhao Z, Zhang B, Shyr Y, Huang Y, Xu H, (2012) Genomics in 2012: challenges and opportunities in the next generation sequencing era. BMC Genomics, in press (IF: 4.21)

D. Yue, J. Meng, M. Lu, P. Chen, M. Guo, Y. Huang*, “Understanding microRNA regulation: A computational perspective,” IEEE Signal Process Magazine, 29:1, 77-88, 2012. (IF:6.0)

N. Nguyen, Y. Chiao, Y. Huang, S-J, Gao, M. Lindsey, Y. Chen, Y. Jin “Temporal clustering of gene expression patterns using short-time segments” Int. J. Functional Informatics and Personalised Medicine, Vol 4, No. 1, 2011

O. Ghasemi, M. Lindsey, T. Yang, N. Nguyen, Y. Huang, Y. Jin, “Bayesian parameter estimation for nonlinear modeling of biological pathways,” BMC Systems Biology, 2011, 5(Suppl 3):S9 doi:10.1186/1752-0509-5-S3-S9 (IF: 3.57)

Xuan, P; Guo, MZ; Huang, YC; Li, WB; Huang, Y*, “MaturePred: Efficient Identification of MicroRNAs within Novel Plant Pre-miRNAs”, PLOS ONE, 6 (11): - NOV 16 2011 (IF: 4.41)

J. Meng, J. Zhang, Y. Chen, Y. Huang*, “Bayesian non-negative factor analysis for reconstructing transcription factor mediated regulatory networks,” Proteome Science, Volume 9, Supplement 1, 2011 (IF: 2.49)

Boutz DR, Collins P, Suresh U, Lu M, Ramírez CM, Fernández-Hernando C,Huang Y, de Sousa Abreu R, Le SY, Shapiro BA, Liu AM, Luk JM, Aldred SF,Trinklein N, Marcotte EM, Penalva LO, A two-tiered approach identifies a network of cancer and liver diseases related genes regulated by miR-122,Journal of Biological Chemistry, 286: 18066-78, 2011 (IF:5.33)

P. Xuan, M. Guo, X. Liu, Y. Huang, W. Li, Y. Huang*, “PlantMiRNAPred: efficient classification of real and pseudo plant pre-miRNAs” (2011) Bioinformatics 27: 1368-1376 (IF:4.88)

Professor Department of Electrical and Computer Engineering 

University of Texas at San Antonio 

Adjunct Professor Department of Epidemiology and Biostatistics 

University of Texas Health Science Center at San Antonio

Education

Ph.D., State University of New York at Stony Brook, 2001.

Contact

Phone: (210) 458-6270

Fax: (210) 458-5947

Email: Yufei.Huang@utsa.edu