• Grausam, Katie B., Dooyema, Samuel D., Bihannic, Laure, Premathilake, Hasitha, Morrissy, Sorana, Forget, Antoine, Schaefer, Amanda M., Gundelach, Justin H., Macura, Slobodan, Maher, Diane M., Wang, Xin, Heglin, Alex H., Ge, Xijin, Zeng, Erliang, Puget, Stephanie, Chandrasekar, Indra, Surendran, Kameswaran, Bram, Richard J., Schüller, Ulrich, Taylor, Michael D., Ayrault, Olivier, and Zhao, Haotian. ATOH1 promotes leptomeningeal dissemination and metastasis of Sonic Hedgehog subgroup medulloblastomas. Cancer Research, 2017. (DOI:;10.1158/0008-5472.CAN-16-1836)

• Fernandez, Mitch, Aguiar-Pulido, Vanessa, Riveros, Juan, Huang, Wenrui, Segal, Jonathan, Zeng, Erliang, Campos, Michael, Mathee, Kalai, and Narasimhan, Giri. Microbiome analysis: state-of-the-art and future trends. In Computational Methods for Next Generation Sequencing Data Analysis, edited by Ion Mandoiu and Alexander Zelikovsky. Wiley, 2016. (DOI:;10.1002/9781119272182.ch18;)

• Rund, Samuel S., Yoo, Boyoung, Alam, Camille, Green, Taryn, Stephens, Melissa T., Zeng, Erliang, George, Gary F., Sheppard, Aaron D., Duffield, Giles E., Milenkovic, Tijana, and Pfrender, Michael E.. Genome-wide profiling of 24 hr diel rhythmicity in the water flea, Daphnia pulex: network analysis reveals rhythmic gene expression and enhances functional gene annotation. Vol. 17, Iss. 653. BMC Genomics, 2016. (DOI:;10.1186/s12864-016-2998-2)

• Vermeer, Daniel W., Coppock, Joseph D., Zeng, Erliang, Lee, Kimberly M., Spanos, William C., Onken, Michael D., Uppaluri, Ravindra, Lee, John H., and Vermeer, Paola D.. Metastatic model of HPV+ oropharyngeal squamous cell carcinoma demonstrates heterogeneity in tumor metastasis, 14. Oncotarget, 2016. (DOI:;10.18632/oncotarget.8254) Li, Li, Grausam, Katie B., Wang, Jun, Lun, Melody P., Ohli, Jasmin, Lidov, Hart G., Calicchio, Monica L., Zeng, Erliang, Salisbury, Jeffrey L., Wechsler-Reya, Robert J., Lehtinen, Maria K., Schu?ller, Ulrich, and Zhao, Haotian. Sonic Hedgehog promotes proliferation of Notch-dependent monociliated choroid plexus tumour cells. Nature Cell Biology, 2016. (DOI:;10.1038/ncb3327)

• Liu, Bingqiang, Zhou, Chuan, Li, Guojun, Zhang, Hanyuan, Zeng, Erliang, Liu, Qi, and Ma, Qin. Bacterial regulon modeling and prediction based on systematic cis regulatory motif analyses, 1-11. Vol. 6, Iss. 23030. Scientific Reports, 2016. (DOI:;10.1038/srep23030)

• Liang, Hanquan, and Zeng, Erliang. RNA-seq experiment and data analysis. In Methods in Molecular Biology, edited by Kathleen M. Eyster, 99-114. Vol. 1366. Springer, 2016. (DOI:;10.1007/978-1-4939-3127-9)

• Zeng, Erliang, Zhang, Wei, Emrich, Scott, Liu, Dan, Livermore, Josh, and Jones, Stuart. p Computational Framework for Integrative Analysis of Large Microbial Genomics Data, 1109 – 1116. Washington D.C.: IEEE International Conference on Bioinformatics and Biomedicine (BIBM)), 2015. (DOI:;10.1109/BIBM.2015.7359837)

• Patel, Sagar, Swaminathan, Padmapriya, Fennell, Anne, and Zeng, Erliang. De novo genome assembly tool comparison for highly heterozygous species Vitis vinifera cv. Sultanina, 1771-1773. Washington D.C.: IEEE International Conference on Bioinformatics and Biomedicine (BIBM)), 2015. (DOI:;10.1109/BIBM.2015.7359957)

• Hickner, Paul V., Mori, Akio, Zeng, Erliang, Tan, John C., and Severson, David W.. Whole transcriptome responses among females of the filariasis and arbovirus vector mosquito Culex pipiens implicate TGF-? signaling and chromatin modification as key drivers of diapause induction, 9. Functional & Integrative Genomics, 2015. (DOI:;10.1007/s10142-015-0432-5)

• Yampolsky, L Y., Zeng, Erliang, Lopez, J, Williams, P J., Dick, K B., Colbourne, J K., and Pfrender, M E.. Functional genomics of acclimation and adaptation in response to thermal stress in Daphnia, 859. Vol. 15, Iss. 1. BMC genomics, 2014. (DOI:;10.1186/1471-2164-15-859)

• Galvan, M D., Hulsebus, H, Heitker, T, Zeng, Erliang, and Bohlson, S S.. Complement Protein C1q and Adiponectin Stimulate Mer Tyrosine Kinase-Dependent Engulfment of Apoptotic Cells through p Shared Pathway. Journal of innate immunity, 2014. (DOI:;10.1159/000363295)

• Favila, M p., Geraci, N S., Zeng, Erliang, Harker, B, Condon, D, Cotton, R N., Jayakumar, p, Tripathi, V, and McDowell, M p.. Human dendritic cells exhibit p pronounced type I IFN signature following Leishmania major infection that is required for IL-12 induction, 5863-72. Vol. 192, Iss. 12. Journal of immunology, 2014. (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, Erliang, Tan, J C., Wu, G C., Emrich, S J., and Hellmann, J J.. Gene expression in closely related species mirrors local adaptation: consequences for responses to p warming world, 2686-98. Vol. 23, Iss. 11. Molecular ecology, 2014. (DOI:;10.1111/mec.12773)

• Zhang, W, Zeng, Erliang, Liu, D, Jones, S E., and Emrich, S. Mapping genomic features to functional traits through microbial whole genome sequences, 461-78. Vol. 10, Iss. 4. International journal of bioinformatics research and applications, 2014. (DOI:;10.1504/IJBRA.2014.062995)

• Zeng, Erliang, and Li, Tao. Applications of Data Mining in Bioinformatics and Health Informatics. p Book Chapter in Data Mining Where Theory Meets Practice, ISBN 978-7-5615-4294-1, 2013.

• Sarro, J, Andrews, E, Sun, L, Behura, S K., Tan, J C., Zeng, Erliang, Severson, D W., and Duman-Scheel, M. Requirement for commissureless2 function during dipteran insect nerve cord development, 1466-77. Vol. 242, Iss. 12. Developmental dynamics, 2013. (DOI:;10.1002/dvdy.24059)

• Zhang, Wei, Zeng, Erliang, Emrich, S.J., Livermore, J., Liu, Dan, and Jones, S.E.. Predicting bacterial functional traits from whole genome sequences using random forest, 1-2. Proceedings of Computational Advances in Bio and Medical Sciences (ICCABS), 2013 IEEE 3rd International Conference on, 2013. (DOI:;10.1109/ICCABS.2013.6629212)

• Zhang, Wei, Emrich, Scott J., and Zeng, Erliang. Assess genomic biomarkers of toxicity in drug development. Proceedings of CAMDA’13: the Critical Assessment of Massive Data Analysis,, 2013.

• Galvan, M D., Foreman, D B., Zeng, Erliang, Tan, J C., and Bohlson, S S.. Complement component C1q regulates macrophage expression of Mer tyrosine kinase to promote clearance of apoptotic cells, 3716-23. Vol. 188, Iss. 8. Journal of immunology, 2012. (DOI:;10.4049/jimmunol.1102920)

• Wang, T, Jiang, F, Oehrlein, S, Zeng, Erliang, Kershner, R, and Cerrina, F. Optical trapping force reduction and manipulation of nanoporous beads, 153702-1537023. Vol. 100, Iss. 15. Applied physics letters, 2012. (DOI:;10.1063/1.3703604)

• Zhang, Wei, Zeng, Erliang, Liu, Dan, Jones, Stuart, and Emrich, Scott J.. p machine learning framework for trait based genomics, 1-6. Proceedings of IEEE 2nd International Conference on Computational Advancesin Bio and Medical Sciences, ICCABS 2012, 2012.

• Wang, Dingding, Ogihara, Mitsunori, Zeng, Erliang, and Li, Tao. Combining Gene Expression Profiles and Protein-Protein Interactionsfor Identifying Functional Modules, 114-119. Proceedings of 11th International Conference on Machine Learning and Applications, ICMLA, Boca Raton, FL, USA, December 12-15, 2012, 2012. (DOI:;10.1109/ICMLA.2012.28)

• Zeng, Erliang, Ding, Chris, Mathee, Kalai, Schneper, Lisa, and Narasimhan, Giri. Gene Function Prediction and Functional Network: The Role of Gene Ontology. Edited by Holmes, Dawn E.; Jain, Lakhmi C, 123-162. Vol. 25. Data Mining: Foundations and Intelligent Paradigms, 2012. (DOI:;10.1007/978-3-642-23151-3_7)

• Singh, P P., LeMaire, C, Tan, J C., Zeng, Erliang, and Schorey, J S.. Exosomes released from M. tuberculosis infected cells can suppress IFN-? mediated activation of naïve macrophages, e18564. Vol. 6, Iss. 4. PloS one, 2011. (DOI:;10.1371/journal.pone.0018564)

• Zhang, Wei, Emrich, Scott J., and Zeng, Erliang. p two-stage machine learning approach for pathway analysis, 274-279. Proceedings of IEEE International Conference on Bioinformatics andBiomedicine, BIBM 2010, 2010.

• Zeng, Erliang, Yang, Chengyong, Li, Tao, and Narasimhan, Giri. Clustering Genes Using Heterogeneous Data Sources, 12-28. Vol. 1, Iss. 2. International Journal of Knowledge Discovery in Bioinformatics, 2010.

• Doud, Melissa, Zeng, Erliang, Schneper, Lisa, Narasimhan, Giri, and Mathee, Kalai. Approaches to analyse dynamic microbial communities such as those seen in cystic fibrosis lung, 246-256. Vol. 3, Iss. 3. Human Genomics, 2009. (DOI:;10.1186/1479-7364-3-3-246)

• Zeng, Erliang, and Ogihara, Mitsunori. Nonnegative Least Square – p New Look Into SAGE Data, 151-161. Proceedings of CSB’09: the LSS Computational Systems Bioinformatics Conference, 2009.

• Zhang, Yi, Zeng, Erliang, Li, Tao, and Narasimhan, Giri. Weighted Consensus Clustering for Identifying Functional Modules in Protein-Protein Interaction Networks. Edited by Wani, M. Arif; Kantardzic, Mehmed M.; Palade, Vasile; Kurgan, Lukasz p.; Qi, Yuan, 539-544. Proceedings of ICMLA’09: the International Conference on Machine Learning and Applications, 2009.

• Zeng, Erliang, Narasimhan, G., Schneper, L., and Mathee, K.. p Functional Network of Yeast Genes Using Gene Ontology Information, 343-346. Proceedings of IEEE International Conference on Bioinformatics and Biomedicine, BIBM ’08, 2008. (DOI:;10.1109/BIBM.2008.60)

• Mathee, K, Narasimhan, G, Valdes, C, Qiu, X, Matewish, J M., Koehrsen, M, Rokas, p, Yandava, C N., Engels, R, Zeng, Erliang, Olavarietta, R, Doud, M, Smith, R S., Montgomery, P, White, J R., Godfrey, P p., Kodira, C, Birren, B, Galagan, J E., and Lory, S. Dynamics of Pseudomonas aeruginosa genome evolution, 3100-5. Vol. 105, Iss. 8. Proceedings of the National Academy of Sciences of the United States of America, 2008. (DOI:;10.1073/pnas.0711982105)

• Zeng, Erliang, Ding, C, Narasimhan, G, and Holbrook, S R.. Estimating support for protein-protein interaction data with applications to function prediction, 73-84. Vol. 7. Proceedings of Life Sciences Society Computational Systems Bioinformatics, 2008.

• Zeng, Erliang, Yang, Chengyong, Li, Tao, and Narasimhan, G.. On the Effectiveness of Constraints Sets in Clustering Genes, 79-86. Proceedings of the 7th IEEE International Conference on Bioinformatics and Bioengineering, BIBE 2007, 2007. (DOI:;10.1109/BIBE.2007.4375548)

• Zeng, Erliang, and Narasimhan, Giri. Enhancing Motif Refinement by Incorporating Comparative Genomics Data. Edited by M?ndoiu, Ion; Zelikovsky, Alexander, 329-337. Vol. 4463. Lecture Notes in Computer Science: Bioinformatics Research and Applications, 2007. (DOI:;10.1007/978-3-540-72031-7_30)

• Yang, Chengyong, Zeng, Erliang, Mathee, Kalai, and Narasimhan, Giri. PlasmoTFBM: An Intelligent Queriable Database for Predicted Transcription Factor Binding Motifs in Plasmodium falciparum. Edited by McConnell, Patrick; Lin, SimonM.; Hurban, Patrick, 121-136. Methods of Microarray Data Analysis V, Springer US, 2007. (DOI:;10.1007/978-0-387-34569-7_9)

• Zeng, Erliang, Mathee, K, and Narasimhan, G. IEM: an algorithm for iterative enhancement of motifs using comparative genomics data., 227-35. Vol. 6. Proceedings of Life Sciences Society Computational Systems Bioinformatics, 2007.

• Yang, Chengyong, Zeng, Erliang, Li, Tao, and Narasimhan, Giri. p Knowledge-Driven Method to Evaluate Multi-source Clustering. Edited by Chen, Guihai; Pan, Yi; Guo, Minyi; Lu, Jian, 196-202. Vol. 3759. Parallel and Distributed Processing and Applications – ISPA 2005 Workshops, 2005. (DOI:;10.1007/11576259_22)

• Yang, C, Zeng, Erliang, Li, T, and Narasimhan, G. Clustering genes using gene expression and text literature data, 329-40. Proceedings of IEEE Computational Systems Bioinformatics Conference, CSB, 2005.

• Yang, Chengyong, Zeng, Erliang, Mathee, Kalai, and Narasimhan, Giri. Mining Regulatory Elements in the Plas- modium falciparum Genome Using Gene Expression Data. Proceedings of CAMDA’04: the Critical Assessment of Microarray Data Analysis,, 2004.

• Yang, Chengyong, Zeng, Erliang, Mathee, Kalai, and Narasimhan, Giri. Querying p database of regulatory elements. Proceedings of ICBA’04: the International Conference on Bioinformatics and its Applications, 2004.

• Yue, Jun, Zeng, Erliang, Xie, Jianping, Li, Yao, Liu, Lirong, and Wang, Honghai. Reliable detection of rifampin-resistance of Mycobacterium tuberculosis strains by using p specialized oligonucleotide microarray, 264—269. Vol. 20, Iss. 2. Chinese journal of biochemistry and molecular biology, 2004.

• Yue, J, Shi, W, Xie, J, Li, Y, Zeng, Erliang, Liang, L, and Wang, Hongmin. Detection of rifampin-resistant Mycobacterium tuberculosis strains by using p specialized oligonucleotide microarray, 47-54. Vol. 48, Iss. 1. Diagnostic microbiology and infectious disease, 2004. (DOI:;10.1016/j.diagmicrobio.2003.08.005)

• Gao, X, Fu, X, Li, T, Zi, J, Luo, Y, Wei, Q, Zeng, Erliang, Xie, Y, Li, Y, and Mao, Y. Determining p detectable threshold of signal intensity in cDNA microarray based on accumulated distribution, 558-64. Vol. 36, Iss. 6. Journal of biochemistry and molecular biology, 2003.

• Yue, J, Shi, W, Xie, J, Li, Y, Zeng, Erliang, and Wang, Hongmin. Mutations in the rpoB gene of multidrug-resistant Mycobacterium tuberculosis isolates from China, 2209-12. Vol. 41, Iss. 5. Journal of clinical microbiology, 2003.

• Zeng, Erliang, Liu, JH, and Lin, ZX. The nucleic acid analysis by DNA chip technique based on nuclease S1 protection, 89—92. Vol. 23, Iss. 1. Zhongguo yi xue ke xue yuan xue bao. Acta Academiae Medicinae Sinicae, 2001.