I am an assistant professor at USD with joint appointment to the Department of Biology and the Department of Computer Science. I received advanced degrees in both biological and computer sciences. After a post-doc at the University of Miami, I joined the research faculty of the University of Notre Dame (ND). Prior to taking the tenure track position at USD in 2014, I was a research assistant professor in the Department of Computer Science and Engineering at ND, and the managing director of ND bioinformatics core facility.
Bioinformatics, Computational Systems Biology, Biostatistics, Algorithm, Data Mining, Data Structure, Programing Language.
I am recruiting post-doctoral associates, graduate (both PhD and Master levels) and undergraduate students. If you are interested in doing research in bioinformatics, computational systems biology, and biological data mining, and are interested in joining my group, please email me. If you are already on USD campus, welcome to stop by. The research interests of my group are in the general areas of bioinformatics, computational systems biology, and biological big data mining. My lab is a dry lab, and we collaborate with several web labs. Currently, work of my group focuses on developing and applying algorithms and computational tools for analyzing high-throughput biological data including next-generation sequencing data, metagenomics data, SNPs data, and many more. The research projects of my group are related to functional genomic data analysis, comparative genomics analysis, biological big data mining, gene expression data analysis, promoter sequence data analysis, protein-protein interaction data mining, functional gene network analysis, and biological ontology data mining.
- Ph D, Computer Science, Florida International University, 2008
- MS, Biochemistry and Molecular Biology, Shanghai Jiao Tong University, 2001
- BS, Biotechnology, Shanghai Jiao Tong University, 1998
- Bioinformatic Development for Mining Genomic Patterns Corresponding for Ecological Adapting through Massive Microbial Whole Genome Sequences, Office of Research, University of Notre Dame, (2013)
- Zhang, W., Emrich, S., Zeng, E., (2014), Comparative study of machine learning approaches for pathway analysis, International Journal of Data Mining and Bioinformatics.
- Yampolsky, L. Y., Zeng, E., Lopez, J., Williams, P. J., Dick, K. B., Colbourne, J. K., Pfrender, M. E., (2014), Functional genomics of acclimation and adaptation in response to thermal stress in Daphnia, BMC genomics, vol. 15, iss. 1, p. 859. (DOI: 10.1186/1471-2164-15-859)
- Galvan, M. D., Hulsebus, H., Heitker, T., Zeng, E., Bohlson, S. S., (2014), Complement Protein C1q and Adiponectin Stimulate Mer Tyrosine Kinase-Dependent Engulfment of Apoptotic Cells through a Shared Pathway, Journal of innate immunity. (DOI: 10.1159/000363295)
- Favila, M. A., Geraci, N. S., Zeng, E., Harker, B., Condon, D., Cotton, R. N., Jayakumar, A., Tripathi, V., McDowell, M. A., (2014), Human dendritic cells exhibit a pronounced type I IFN signature following Leishmania major infection that is required for IL-12 induction, Journal of immunology, vol. 192, iss. 12, pp. 5863-72. (DOI: 10.4049/jimmunol.1203230)
- O'Neil, S. T., Dzurisin, J. D., Williams, C. M., Lobo, N. F., Higgins, J. K., Deines, J. M., Carmichael, R. D., Zeng, E., Tan, J. C., Wu, G. C., Emrich, S. J., Hellmann, J. J., (2014), Gene expression in closely related species mirrors local adaptation: consequences for responses to a warming world, Molecular ecology, vol. 23, iss. 11, pp. 2686-98. (DOI: 10.1111/mec.12773)
- Zhang, W., Zeng, E., Liu, D., Jones, S. E., Emrich, S., (2014), Mapping genomic features to functional traits through microbial whole genome sequences, International journal of bioinformatics research and applications, vol. 10, iss. 4, pp. 461-78. (DOI: 10.1504/IJBRA.2014.062995)
- Zeng, E., Li, T., (2013), Applications of Data Mining in Bioinformatics and Health Informatics, a Book Chapter in Data Mining Where Theory Meets Practice, ISBN 978-7-5615-4294-1.
- Zhang, W., Emrich, S. J., Zeng, E., (2013), Assess genomic biomarkers of toxicity in drug development, Proceedings of CAMDA’13: the Critical Assessment of Massive Data Analysis,.
- Sarro, J., Andrews, E., Sun, L., Behura, S. K., Tan, J. C., Zeng, E., Severson, D. W., Duman-Scheel, M., (2013), Requirement for commissureless2 function during dipteran insect nerve cord development, Developmental dynamics, vol. 242, iss. 12, pp. 1466-77. (DOI: 10.1002/dvdy.24059)
- Zhang, W., Zeng, E., Emrich, S., Livermore, J., Liu, D., Jones, S., (2013), Predicting bacterial functional traits from whole genome sequences using random forest, Proceedings of Computational Advances in Bio and Medical Sciences (ICCABS), 2013 IEEE 3rd International Conference on, pp. 1-2. (DOI: 10.1109/ICCABS.2013.6629212)
- Zhang, W., Zeng, E., Liu, D., Jones, S., Emrich, S. J., (2012), A machine learning framework for trait based genomics, Proceedings of IEEE 2nd International Conference on Computational Advancesin Bio and Medical Sciences, ICCABS 2012, pp. 1-6.
- Wang, D., Ogihara, M., Zeng, E., Li, T., (2012), Combining Gene Expression Profiles and Protein-Protein Interactionsfor Identifying Functional Modules, Proceedings of 11th International Conference on Machine Learning and Applications, ICMLA, Boca Raton, FL, USA, December 12-15, 2012, p. 114–119. (DOI: 10.1109/ICMLA.2012.28)
- Zeng, E., Ding, C., Mathee, K., Schneper, L., Narasimhan, G., (2012), Gene Function Prediction and Functional Network: The Role of Gene Ontology, Data Mining: Foundations and Intelligent Paradigms, vol. 25, pp. 123-162. (DOI: 10.1007/978-3-642-23151-3_7)
- Galvan, M. D., Foreman, D. B., Zeng, E., Tan, J. C., Bohlson, S. S., (2012), Complement component C1q regulates macrophage expression of Mer tyrosine kinase to promote clearance of apoptotic cells, Journal of immunology, vol. 188, iss. 8, pp. 3716-23. (DOI: 10.4049/jimmunol.1102920)
- Wang, T., Jiang, F., Oehrlein, S., Zeng, E., Kershner, R., Cerrina, F., (2012), Optical trapping force reduction and manipulation of nanoporous beads, Applied physics letters, vol. 100, iss. 15, pp. 153702-1537023. (DOI: 10.1063/1.3703604)
- Singh, P. P., LeMaire, C., Tan, J. C., Zeng, E., Schorey, J. S., (2011), Exosomes released from M. tuberculosis infected cells can suppress IFN-? mediated activation of naïve macrophages, PloS one, vol. 6, iss. 4, p. e18564. (DOI: 10.1371/journal.pone.0018564)
- Zhang, W., Emrich, S. J., Zeng, E., (2010), A two-stage machine learning approach for pathway analysis, Proceedings of IEEE International Conference on Bioinformatics andBiomedicine, BIBM 2010, pp. 274-279.
- Zeng, E., Yang, C., Li, T., Narasimhan, G., (2010), Clustering Genes Using Heterogeneous Data Sources, International Journal of Knowledge Discovery in Bioinformatics, vol. 1, iss. 2, pp. 12-28.
- Doud, M., Zeng, E., Schneper, L., Narasimhan, G., Mathee, K., (2009), Approaches to analyse dynamic microbial communities such as those seen in cystic fibrosis lung, Human Genomics, vol. 3, iss. 3, pp. 246-256. (DOI: 10.1186/1479-7364-3-3-246)
- Zeng, E., Ogihara, M., (2009), Nonnegative Least Square - A New Look Into SAGE Data, Proceedings of CSB’09: the LSS Computational Systems Bioinformatics Conference, pp. 151-161.
- Zhang, Y., Zeng, E., Li, T., Narasimhan, G., (2009), Weighted Consensus Clustering for Identifying Functional Modules in Protein-Protein Interaction Networks, Proceedings of ICMLA’09: the International Conference on Machine Learning and Applications, pp. 539-544.
- Zeng, E., Ding, C., Narasimhan, G., Holbrook, S. R., (2008), Estimating support for protein-protein interaction data with applications to function prediction, Proceedings of Life Sciences Society Computational Systems Bioinformatics, vol. 7, pp. 73-84.
- Zeng, E., Narasimhan, G., Schneper, L., Mathee, K., (2008), A Functional Network of Yeast Genes Using Gene Ontology Information, Proceedings of IEEE International Conference on Bioinformatics and Biomedicine, BIBM ’08, pp. 343-346. (DOI: 10.1109/BIBM.2008.60)
- Mathee, K., Narasimhan, G., Valdes, C., Qiu, X., Matewish, J. M., Koehrsen, M., Rokas, A., Yandava, C. N., Engels, R., Zeng, E., Olavarietta, R., Doud, M., Smith, R. S., Montgomery, P., White, J. R., Godfrey, P. A., Kodira, C., Birren, B., Galagan, J. E., Lory, S., (2008), Dynamics of Pseudomonas aeruginosa genome evolution, Proceedings of the National Academy of Sciences of the United States of America, vol. 105, iss. 8, pp. 3100-5. (DOI: 10.1073/pnas.0711982105)
- Zeng, E., Narasimhan, G., (2007), Enhancing Motif Refinement by Incorporating Comparative Genomics Data, Lecture Notes in Computer Science: Bioinformatics Research and Applications, vol. 4463, pp. 329-337. (DOI: 10.1007/978-3-540-72031-7_30)
- Yang, C., Zeng, E., Mathee, K., Narasimhan, G., (2007), PlasmoTFBM: An Intelligent Queriable Database for Predicted Transcription Factor Binding Motifs in Plasmodium falciparum, Methods of Microarray Data Analysis V, Springer US, pp. 121-136. (DOI: 10.1007/978-0-387-34569-7_9)
- Zeng, E., Yang, C., Li, T., Narasimhan, G., (2007), On the Effectiveness of Constraints Sets in Clustering Genes, Proceedings of the 7th IEEE International Conference on Bioinformatics and Bioengineering, BIBE 2007, pp. 79-86. (DOI: 10.1109/BIBE.2007.4375548)
- Zeng, E., Mathee, K., Narasimhan, G., (2007), IEM: an algorithm for iterative enhancement of motifs using comparative genomics data., Proceedings of Life Sciences Society Computational Systems Bioinformatics, vol. 6, pp. 227-35.
- Yang, C., Zeng, E., Li, T., Narasimhan, G., (2005), A Knowledge-Driven Method to Evaluate Multi-source Clustering, Parallel and Distributed Processing and Applications - ISPA 2005 Workshops, vol. 3759, pp. 196-202. (DOI: 10.1007/11576259_22)
- Yang, C., Zeng, E., Li , T., Narasimhan, G., (2005), Clustering genes using gene expression and text literature data, Proceedings of IEEE Computational Systems Bioinformatics Conference, CSB, pp. 329-40.
- Yang, C., Zeng, E., Mathee, K., Narasimhan, G., (2004), Mining Regulatory Elements in the Plas- modium falciparum Genome Using Gene Expression Data, Proceedings of CAMDA’04: the Critical Assessment of Microarray Data Analysis,.
- Yang, C., Zeng, E., Mathee, K., Narasimhan, G., (2004), Querying a database of regulatory elements, Proceedings of ICBA’04: the International Conference on Bioinformatics and its Applications.
- Yue, J., Zeng, E., Xie, J., Li, Y., Liu, L., Wang, H., (2004), Reliable detection of rifampin–resistance of Mycobacterium tuberculosis strains by using a specialized oligonucleotide microarray, Chinese journal of biochemistry and molecular biology, vol. 20, iss. 2, p. 264—269.
- Yue, J., Shi, W., Xie, J., Li , Y., Zeng, E., Liang, L., Wang, H., (2004), Detection of rifampin-resistant Mycobacterium tuberculosis strains by using a specialized oligonucleotide microarray, Diagnostic microbiology and infectious disease, vol. 48, iss. 1, pp. 47-54. (DOI: 10.1016/j.diagmicrobio.2003.08.005)
- Gao, X., Fu, X., Li , T., Zi, J., Luo, Y., Wei, Q., Zeng, E., Xie, Y., Li , Y., Mao, Y., (2003), Determining a detectable threshold of signal intensity in cDNA microarray based on accumulated distribution, Journal of biochemistry and molecular biology, vol. 36, iss. 6, pp. 558-64.
- Yue, J., Shi, W., Xie, J., Li , Y., Zeng, E., Wang, H., (2003), Mutations in the rpoB gene of multidrug-resistant Mycobacterium tuberculosis isolates from China, Journal of clinical microbiology, vol. 41, iss. 5, pp. 2209-12.
- Zeng, E., Liu, J., Lin, Z., (2001), The nucleic acid analysis by DNA chip technique based on nuclease S1 protection, Zhongguo yi xue ke xue yuan xue bao. Acta Academiae Medicinae Sinicae, vol. 23, iss. 1, p. 89—92.
Awards and Honors:
- Faculty Research Support Program Award, University of Notre Dame, 2013
- Dissertation Year Fellowship, Florida International University, 2008
- Excellence Award, Florida International University, 2007
- Presidential Fellowship, Florida International University, 2003
- Zeng, E. (2014, September). Mining Massive Genomic Data to Understand Microbial Functions. Presented at the Fall Seminar Series - Invited Speaker, SDSU Department of Plant Science, USDA-ARS North Central Agricultural Research Laboratory, Brookings, SD.
- Zeng, E. (2014, March). Challenges and opportunities: when biology meets big data. Presented at the TSRI Research Seminar Series, Saban Research Institute, Children's Hospital Los Angeles, CA.
- Zeng, E., Zhang, W., Liu, D., Jones, S., Emrich, S. (2012, December). Gene content based functional trait analysis through comparative microbial whole genome sequences. Presented at the 10th Annual Rocky Mountain Bioinformatics Conference, Snowmass, CO.