Home | Publications | Teaching

Publications:

Book Chapters

E. Zeng, C. Ding, K. Mathee, L. Schneper, G. Narasimhan, Gene function prediction and functional network: the role of gene ontology, DATA MINING: Foundations and Intelligent Paradigms, Dawan E. Holmes and Lakhmi C. Jain (Eds.), Springer, p123-162, 2012, ISBN 978-3-642-23150-6.
C. Yang^*, E. Zeng^*, K. Mathee, G. Narasimhan, PlasmoTFBM: an intelligent queriable database for predicted transcription factor binding motifs in Plasmodium falciparum, Methods of Microarray Data Analysis V , McConnell, Lin, Hurban (Eds.), Springer, p121-136, 2007. ^*contributed equally. [pdf]

Journals

W. Zhang, E. Zeng, D. Liu, S. Jones, S. Emrich, Mapping genomic features to functional traits through microbial whole genome sequences, to appear in the BMC Genomics.
M. Galvan, D. Foreman, E. Zeng, J. Tan, S. Bohlson, Complement component C1q regulates macrophage expression of Mer tyrosine kinase to promote clearance of apoptotic cells, The Journal of Immunology, March 14, 2012; 1102920.
W. Zhang, S. Emrich, E. Zeng, Comparative study of machine learning approaches for pathway analysis, to appear in the International Journal of Data Mining and Bioinformatics.
T. Wang, F. Jiang, S. Oehrlein, E. Zeng, R. Kershner, F. Cerrina, Optical trapping torce reduction and manipulation of nanoporous beads, Appl. Phys. Lett. 100, 153702 (2012); doi: 10.1063/1.3703604.
P. Singh, C. LeMaire, J. Tan, E. Zeng, J. Schorey, Exosomes released from M.tuberculosis infected cells can suppress IFN-γ mediated activation of Naļve macrophages, PLoS ONE. 2011; 6(4): e18564. doi:10.1371/journal.pone.0018564.
E. Zeng, C. Yang, T. Li, G. Narasimhan, Clustering genes using heterogeneous data sources, International Journal of Knowledge Discovery in Bioinformatics. 2010; 1(2):12-28. [pdf]
M. Doud, E. Zeng, L. Schneper, G. Narasimhan, K. Mathee, Approaches to analyze dynamic microbial communities such as those seen in cystic fibrosis lung, Human Genomics. 2009; 3(3):246-256.
K. Mathee, G. Narasimhan, C. Valdes, X. Qiu, J. Matewish, M. Koehrsen, A. Rokas, C. Yandava, R. Engels, E. Zeng, R. Olavarietta, M. Doud, R. Smith, P. Montgomery, J. White, P. Godfrey, C. Kodira, B. Birren, J. Galagan, S. Lory, Dynamics of Pseudomonas aeruginosa genome evolution, Proceedings of the National Academy of Sciences (PNAS). 2008; 105(8):3100-05.
J. Yue, W. Shi, J. Xie, Y. Li, E. Zeng, L. Liang, H. Wang, Detection of rifampin-resistant Mycobacterium tuberculosis strains by using a specialized oligonucleotide microarray, Diagn Microbiol Infect Dis. 2004 Jan;48(1):47-54. [pdf]
X. Gao, X. Fu, T. Li, J. Zi, Y. Luo, Q. Wei, E. Zeng, Y. Xie, Y. Li, Y. Mao, Determining a detectable threshold of signal intensity in cDNA microarray based on accumulated distribution, J Biochem Mol Biol. 2003 Nov 30;36(6):558-64. [pdf]
J. Yue, W. Shi, J. Xie, Y. Li, E. Zeng, H. Wang, Mutations in the rpoB gene of multidrug-resistant Mycobacterium tuberculosis isolates from China, J Clin Microbiol. 2003 May;41(5):2209-12. [pdf]
J. Yue, E. Zeng, J. Xie, Y. Li, L. Liang, H. Wang, Reliable detection of Rifampin-resistance of Mycobacterium tuberculosis strains by using a specialized oligonucleotide microarray (in Chinese), Chinese Journal of Biochemistry and Molecular Biology. 2004 ;20(2):264-9.
J. Yue, E. Zeng, J. Xie, Y. Li, L. Liu, H. Wang, Molecular mutations of rpoB gene of multidrug resistant Mycobacterium tuberculosis isolates from China (in Chinese), Journal of Genetics and Genomics. 2004 Dec;31(12):1332-6.
M. He, E. Zeng, Y. Zheng, Z. Tang, X. Lu, B. Sun, D. Xu, Z. Zhang, L. Yang, Identification of Mycobacterium tuberculosis and rifampin-resistant strains by gene-chips (in Chinese), Chinese Journal of Epidemiology. 2003 May; 24(5):385-8.
L. Li, Y. Lin, Y. Liu, E. Zeng, C. Li, The use of shareware for mtDNA sequence comparison (in Chinese), Chinese Journal of Forensic Sciences. 2003;(1):29-31.
E. Zeng, J. Liu, Z. Lin, The nucleic acid analysis by DNA chip technique based on nuclease S1 protection (in Chinese), Acta Academiae Medicinae Sinicae. 2001 Feb;23(1):89-92.
D. Wang, M. Li, E. Zeng, W. Zhang, X. Wu, Cloning of secondary lymphoid-tissue chemokine (SLC) and its expression in prokaryotic system (in Chinese), Chinese Journal of Biotechnology. 2001; 17(4):392-395.

Conference Proceedings

W. Zhang, E. Zeng, J. Livermore, D. Liu, S. Jones, S. Emrich, Predicting bacterial functional traits from whole genome sequences using random forest, Proceedings of ICCABS'13: the IEEE International Conference on Computational Advances in Bio and Medical Sciences, to appear, New Orleans, June 12-14, 2013.
D. Wang, M. Ogihara, E. Zeng, T. Li, Combining gene expression profiles and protein-protein interactions for identifying functional modules, Proceedings of ICMLA'12: the 11th International Conference on Machine Learning and Applications ICMLA (2012).
W. Zhang, E. Zeng, D. Liu, S. Jones, S. Emrich, A machine learning framework for trait based genomics, Proceedings of ICCABS'12: the IEEE International Conference on Computational Advances in Bio and Medical Sciences, Las Vegas, February, 2012.
W. Zhang, S. Emrich, E. Zeng, A two-stage machine learning approach for pathway analysis, Proceedings of BIBM'10: the IEEE International Conference on Bioinformatics and Biomedicine, p274-279, Hong Kong, December, 2010.
Y. Zhang, E. Zeng, T. Li, G. Narasimhan, Weighted consensus clustering for identifying functional modules in protein-protein interaction networks, Proceedings of ICMLA'09: the International Conference on Machine Learning and Applications, Miami, December, 2009.
E. Zeng, M. Ogihara, Nonnegative least square - a new look into SAGE data, Proceedings of CSB'09: the LSS Computational Systems Bioinformatics Conference, p151-161, Stanford, CA, August, 2009.
E. Zeng, K. Mathee, L. Schneper, G. Narasimhan, A functional network of yeast genes using gene ontology information, Proceedings of BIBM'08: the IEEE International Conference on Bioinformatics and Biomedicine, p343-346, Philadelphia, PA, November, 2008. [pdf]
E. Zeng, C. Ding, G. Narasimhan, S. R. Holbrook, Estimating support for protein-protein interaction data with applications to function prediction, Proceedings of CSB'08: the LSS Computational Systems Bioinformatics Conference, p73-84, Stanford, CA, August, 2008. [pdf]
E. Zeng, C. Yang, T. Li, G. Narasimhan, On the effectiveness of constraints sets in clustering genes, Proceedings of BIBE'07: the 7th IEEE International Symposium on Bioinformatics & Bioengineering (Full Regular Research Paper), p79-86, Boston, MA, October, 2007. [pdf]
E. Zeng, K. Mathee, G. Narasimhan, IEM: an algorithm for iterative enhancement of motifs using comparative genomics data, Proceedings of CSB'07: the LSS Computational Systems Bioinformatics Conference, p227-235, UCSD, CA, August, 2007. [pdf]
E. Zeng, G. Narasimhan, Enhancing motif refinement by incorporating comparative genomics data, Proceedings of ISBRA'07: the International Symposium on Bioinformatics Research and Applications, Lecture Notes in Computer Science, Vol. 4463, Springer Verlag, p329-337, 2007. [pdf]
C. Yang, E. Zeng, T. Li, G. Narasimhan, Clustering genes using gene expression and text literature data, Proceedings of CSB'05: the IEEE Computer Society Bioinformatics Conference, p329-340, Stanford, CA, August 2005. [pdf]
C. Yang, E. Zeng, T. Li, G. Narasimhan, A knowledge-driven method to evaluate multi-source clustering, Proceedings of BIOS'05: the International Workshop on Bioinformatics, Lecture Notes in Computer Science, Vol. 3759, Springer Verlag, 2005. [pdf]
C. Yang^*, E. Zeng^*, K. Mathee, G. Narasimhan, Querying a database of regulatory elements, Proceedings of ICBA'04: the International Conference on Bioinformatics and its Applications, Fort Lauderdale, Florida, December 2004. ^*contributed equally. [pdf]
C. Yang^*, E. Zeng^*, K. Mathee, G. Narasimhan, Mining regulatory elements in the Plasmodium falciparum genome using gene expression data, Proceedings of CAMDA'04: the Critical Assessment of Microarray Data Analysis, Durham, NC, November 2004. ^*contributed equally. [pdf]

Conference Abstracts and Posters

E. Zeng, W. Zhang, D. Liu, S. Jones, S. Emrich, Gene content based functional trait analysis through comparative microbial whole genome sequences, ISCB 10th Annual Rocky Mountain Bioinformatics Conference (Rocky 2012), Aspen/Snowmass, CO, December 6-8, 2012.
J. Livermore, J. Lennon, S. Emrich, W. Zhang, E. Zeng, D. Liu, S. Jones, Genomic predictors of the bacterial soil moisture niche, The 4th Annual Argonne Soil Metagenomics, Chicago, IL, October 3–5, 2012.
M. Champion, E. Zeng, Proteogenomic methods for small and orphan polypeptide discovery in pathogenic Mycobacteria using non-biased translation, Great Lakes Bioinformatics Conference (GLBIO) 2011, Ohio University, Athens, OH, May 2011.
P. McHenry, S. Peddibhotla, M. Hwang, P. Chang, J. Sears, K. Park, C. Mohar, E. Zeng, J. Rosen, and T. Vargo-Gogola1, P190B RhoGAP regulates mitotic spindle function in breast cancer cells and spindle orientation in primary mammary epithelial cells, Cancer Research Day, Indiana University Melvin and Bren Simon Cancer Center, 2011.
E. Zeng, S. Chaterjee, K. Mathee, G. Narasimhan, Iterative enhancement of motifs using comparative genomics data, Fourth Annual RECOMB Satellite on Regulatory Genomics, Boston, October 2007.
G. Narasimhan, K. Mathee, C. Valdes, E. Zeng, R. Olavarietta, M. Doud, P. Godfrey, M. Koehrsen, A. Rokas, C. Yandava, R. Engels, C. Kodira, Bruce Birren, J. Galagan, S. Lory, Comparative genomics of the pathogen Pseudomonas aeruginosa, Fifth Annual RECOMB Satellite on Comparative Genomics, San Diego, September 2007.
P. Godfrey, K. Mathee, G. Narasimhan, C. Valdes, E. Zeng, R. Olavarietta, M. Doud, C. Yandava, M. Koehrsen, R. Engels, P. Montgomery, J. White, C. Kodira, S. Lory , B. Birren, J. Galagan, Comparative genomics of P. aeruginosa, CSHL workshop on Genome Informatics, Cold Spring Harbor Laboratory, November 2007.
C. Yang, E. Zeng, G. Narasimhan, A Knowledge-driven method to evaluate multi-source clustering, The ISMB BioLINK Special Interest Group, Detroit, June 2005.
G. Zheng, E. Zeng, E.O. George, G. Narasimhan, Integrating information from different microarray data sets, In Silico Conference, Atlanta, November 2003.

Patents:

E. Zeng, J. Liu, Z. Lin, Number: 00119541.7 (Chinese), 2001.