2021
Gajurel, K., Zhong, C., and Wang, G. (2021) A Fine-Grained Visual Attention Approach for Fingerspelling Recognition in the Wild, 2021 IEEE International Conference on Systems, Man, and Cybernetics (SMC) [Link]
Li, K., Fathan, M., Patel, K., Zhang, T., Zhong, C., Bansal, A., Rastogi, A., Wang, J., and Wang, G. (2021) Colonoscopy Polyp Detection and Classification: Dataset Creation and Comparative Evaluations, PLoS ONE [Link]
Chau, J., Yadav, M., Liu, B., Furqan, M., Dai, Q., Gupta, A., Mercer, K., Eastman, E., Abu-Hejleh, T., Chan, C., Weiner, G., Cherwin, C., Lee, S., Zhong, C., Mangalam, A., and Zhang, J. (2021) Analysis of patient microbiome and its correlation to the response and immune related adverse effects from immunotherapy in lung cancer, BMC Cancer [Link]
Liu, B., Thippabhotla, S., Zhang, J., and Zhong, C., (2021) DRAGoM: Classification and Quantification of Noncoding RNA in Metagenomic Data, Frontiers in Genetics [Link]
Zhang, J., Huang, C., Li, M., Liu, B., Zhu, H., Dai, Q., Fan, X., Mehta, K., Huang, C., Neupane, P., Wang, F., Sun, W., Umar, S., and Zhong, C. (2021) Relating gut microbiome and its modulating factors to immunotherapy in solid tumors: a systematic review, Frontiers in Oncology [Link]
Katsushima, K., Lee, B., Kunhiraman, H., Zhong, C., Murath, R., Ying, J., Liu, B., Garancher, A., Gonzalez-Gomez, I., Monforte, H., Stapleton, S., Vibhakar, R., Bettegowda, C., Wechsler-Reya, R., Jallo, G., Raabe, E., Eberhart, C., and Perara, P., (2021) The long non-coding RNA lnc-HLX-2-7 is oncogenic in group 3 medulloblastomas, Neuro-Oncology [Link]
2020
McClannahan, B., Patel, K., Sajid, U., Zhong, C., and Wang, G. (2020) Classification of Noncoding RNA Elements Using Deep Convolutional Neural Networks, In IEEE International Conference on Systems, Man, and Cybernetics (SMC2020), Toronto, Ontario, Canada [link]
Wu, X., Gardashova, G., Lan, L., Han, S., Zhong, C., Marquez, R., Wei, L., Wood, S., Roy, S., Gowthaman, R., Karanicolas, J., Gao, F., Dixon, D., Welch, D., Li, L., Ji, M., AubeĢ, J., and Xu, L. (2020) Targeting the interaction between RNA-binding protein HuR and FOXQ1 suppresses breast cancer invasion and metastasis, Communications Biology [Link]
2019
Aleti, G., Baker, J., Tang, X., Alvarez, R., Dinis, M., Tran, N., Melnik, A., Zhong, C., Ernst, M., Dorrestein, P., & Edlund, A. (2019). Identification of the bacterial biosynthetic gene clusters of the oral microbiome illuminates the unexplored social language of bacteria during health and disease. mBio [Link]
Thippabhotla, S., Wei, L., Zhu, Q., Zhong, C., and He, M. (2019) 3D cell culture stimulates the secretion of in vivo like exosomes, Scientific Reports [Link]
Zhong, C. and Zhang, S. (2019) Accurate and Efficient Mapping of the Crosslinked microRNA-mRNA Hybrid Reads, iScience [Link]
Zhong, C. , Yang, Y., and Yooseph, S. (2019) GRASP2: Fast and Memory-efficient Gene-centric Assembly and Homolog Search for Metagenomic Sequencing Data, BMC Bioinformatics [Link]
2018
Zou A, Magee N, Deng F, Lehn S, Zhong C , Zhang Y. (2018) Hepatocyte nuclear receptor SHP suppresses inflammation and fibrosis in a mouse model of nonalcoholic steatohepatitis. Journal of Biological Chemistry [Link]
Ge, P., Islam, S., Zhong, C. , and Zhang, S. (2018) De novo discovery of structural motifs in RNA 3D structures through clustering. Nucleic Acids Research [Link]
2016
Zhong, C., Yang, Y., Edlund, A., McLean, J., and Yooseph, S. (2016) Metagenome and metatranscriptome analyses using protein family profiles. PLOS Computational Biology [Link]
Zhong, C., Yang, Y., and Yooseph, S. (2016) GRASPx: an efficient reference-guided short peptide assembler. BMC Bioinformatics [Link]
2015
Yang, Y., Zhong, C., and Yooseph, S. (2015) SFA-SPA: a suffix array based short peptide assembler for metagenomic data. Bioinformatics [Link]
Zhong, C., Yang, Y., and Yooseph, S. (2015) GRASPx: an efficient reference-guided short peptide assembler. In 11th International Symposium on Bioinformatics Research and Applications (ISBRA), Norfolk, VA, USA
Zhong, C. and Zhang, S. (2015) RNAMotifScanX: a graph alignment approach for RNA structural motif identification. RNA [Link]
2014
Zhong, C., Yang, Y., and Yooseph, S. (2014) GRASP: Guided Reference-based Assembly of Short Peptides. Nucleic Acids Research [Link]
Ge, P., Zhong, C., and Zhang, S. (2014) ProbeAlign: incorporating high-throughput sequencing based structure probing information into ncRNA homology search. In BMC Bioinformatics [Link]
Ge, P., Zhong, C., and Zhang, S. (2014) ProbeAlign: incorporating high-throughput sequencing based structure probing information into ncRNA homology search. In 4th Annual RECOMB Satellite Workshop on Massively Parallel Sequencing
Zhong, C. and Zhang, S. (2014) Simultaneous folding of alternative RNA structures with mutual constraints: an application to next-generation sequencing-based RNA structure probing. Journal of Computational Biology doi:10.1089/cmb.2013.0044 [Link]
Li, Y., Zhong, C., and Zhang, S. (2014) Finding consensus stable local optimal structures for aligned RNA sequences and its application to discovering riboswitch elements. International Journal of Bioinformatics Research and Applications [Link]
Zhong, C., Andrews. J, and Zhang, S. (2014) Discovering non-coding RNA elements in drosophila 3' untranslated regions. International Journal of Bioinformatics Research and Applications [Link]
2013
Li, J., Mazar, J., Zhong, C., Faulkner, G., Govindarajan, S., Zhang, Z., E.Dinger M., Meredith, G., Adams, C., Zhang, S., Mattick, J., Ray, A., and Perera, R. (2013) Genome-wide methylated CpG island profiles of melanoma cells reveal a melanoma coregulation network. Scientific Reports 2013, 3:2962 [Link]
Zhong, C. and Zhang, S. (2013) Efficient alignment of RNA secondary structures using sparse dynamic programming. BMC Bioinformatics 2013, 14:269 [Link]
2012
Zhong, C., Andrews. J, and Zhang, S. (2012) Discovering non-coding RNA elements in drosophila 3' untranslated regions. In Proceedings of the 2nd IEEE International Conference on Computational Advances in Bio and Medical Sciences (ICCABS) , Las Vegas, Nevada, USA (Best paper award)
Zhong, C. and Zhang, S. (2012) Clustering RNA structural motifs in ribosomal RNAs using secondary structural alignment. Nucleic Acids Res. 40, 1307-1317 (Cover page story) [Link]
Mazar, J., Khaitan, D., DeBlasio, D., Zhong, C., Govindarajan, S., Kopanathi, S., Zhang, S., Ray, A. and Perera, R. (2012) Epigenetic Regulation of MicroRNA Genes and the Role of miR-34b in Cell Invasion and Motility in Human Melanoma. PLoS ONE, 6(9): e24922 [Link]
2010
Zhang, S and Zhong, C.. (2010) Computational tools for RNA structural motif identification. Biotech International, Vol 22, page 6-9 (invited review) [Link]
Zhong, C., Tang, H. and Zhang, S. (2010) RNAMotifScan: automatic identification of RNA structural motifs using secondary structural alignment. Nucleic Acids Res., 38(18): e176 [Link]