Manuscripts under consideration

Chong Wang, Mingxiang Teng, Bo Zhao. Genome-wide identification of super enhancers regulated by EBV and KSHV co-infection. In preparation.

Mingxiang Teng, Robert T Nakayama, Stephanie C Hicks, Cigall Kadoch, Rafael A Irizarry. ComplexDiff: differential binding estimation for protein complexes. In preparation.

Moore J, Purcaro MJ, Pratt HE, Epstein CB, Shoresh N, Adrian J, Kawli T, Davis CA, Dobin A, Kaul R, Halow J, Van Nostrand EL, Freese P, Gorkin DU, He Y, Mackiewicz M, The ENCODE Consortium, Cherry JM, Myers RM, Ren B, Graveley BR, Stamatoyannopoulos JA, Gerstein MB, Pennacchio LA, Gingeras T, Snyder MP, Bernstein BE, Wold B, Hardison RC, Weng Z. ENCODE phase III: building an encyclopaedia of candidate regulatory elements for human and mouse. In submission.


Stephanie C Hicks, F William Townes, Mingxiang Teng, Rafael A Irizarry. Missing data and technical variability in single-cell RNA-sequencing experiments. Biostatistics. (In press)

Mingxiang Teng, Rafael A Irizarry. Accounting for GC-content bias reduces systematic errors and batch effects in ChIP-seq data. Genome Research. (In press)

Robert T Nakayama, John L Pulice, Alfredo M Valencia, Matthew J McBride, Zachary M McKenzie, Mark A Gillespie, Wai Lim Ku, Mingxiang Teng, Kairong Cui, Robert T Williams, Seth H Cassel, He Qing, Christian J Widmer, George D Demetri, Rafael A Irizarry, Keji Zhao, Jeff Ranish, Cigall Kadoch. SMARCB1 is required for widespread BAF complex-mediated activation of enhancers and bivalent promoters. Nature Genetics, 2017. (Epub)

Yanshuo Chu, Zhenxing Wang, Rongjie Wang, Ningyi Zhang, Jie Li, Yang Hu, Mingxiang Teng, Yadong Wang. WDNfinder: a method for minimum driver node set detection and analysis in directed and weighted biological network. Journal of Bioinformatics and Computational Biology, 2017;15(5):1750021.

Rongjie Wang, Mingxiang Teng, Yang Bai, Tianyi Zang, Yadong Wang. DMcompress: dynamic Markov models for bacterial genome compression. BIBM16, 2016:776-779.

Mingxiang Teng, Michael I Love, Carrie A Davis, Sarah Djebali, Alexander Dobin, Brenton R Graveley, Sheng Li, Christopher E Mason, Sara Olson, Dmitri Pervouchine, Cricket A Sloan, Xintao Wei, Lijun Zhan and Rafael A Irizarry. A benchmark for RNA-seq quantification pipelines. Genome Biology, 2016;17:74.

Bo Liu, Dengfeng Guan, Mingxiang Teng, Yadong Wang. rHAT: fast alignment of noisy long reads with regional hashing. Bioinformatics, 2016;32(11):1625-1631.

Liran Juan, Yongzhuang Liu, Yongtian Wang, Mingxiang Teng, Tianyi Zang, Yadong Wang. Family genome browser: visualizing genomes with pedigree information. Bioinformatics, 2015;31(14):2262-2268.

Liran Juan, Mingxiang Teng, Tianyi Zang, Yafeng Hao, Zhenxing Wang, Chengwu Yan, Yongzhuang Liu, Jie Li, Tianjiao Zhang, Yadong Wang. The personal genome browser: visualizing functions of genetic variants. Nucleic Acids Research, 2014;42(W1):W192-W197.

Guohua Wang, Ke Qi, Yuming Zhao, Yu Li, Liran Juan, Mingxiang Teng, Lang Li, Yunlong Liu, Yadong Wang. Identification of regulatory regions of bidirectional genes in cervical cancer. BMC Medical Genomics, 2013;6(Suppl 1):S5.

Mingxiang Teng, Yadong Wang, Seongho Kim, Lang Li, Changyu Shen, Guohua Wang, Yunlong Liu, Tim HM Huang, Kenneth P Nephew, Curt Balch. Empirical bayes model comparisons for differential methylation analysis. Comparative and Functional Genomics, 2012;2012:376706.

Mingxiang Teng, Shoji Ichikawa, Leah R Padgett, Yadong Wang, Matthew Mort, David N Cooper, Daniel L Koller, Tatiana Foroud, Howard J Edenberg, Michael J Econs, Yunlong Liu. regSNPs: a strategy for prioritizing regulatory single nucleotide substitutions. Bioinformatics, 2012;28(14):1879-1886.

Mingxiang Teng, Curt Balch, Yunlong Liu, Meng Li, Tim HM Huang, Yadong Wang, Kenneth P Nephew, Lang Li. The influence of cis-regulatory elements on DNA methylation fidelity. PLoS ONE, 2012;7(3):e32928.

Shijia Zhu, Qinghua Jiang, Guohua Wang, Bo Liu, Mingxiang Teng, Yadong Wang. Chromatin structure characteristics of pre-miRNA genomic sequences. BMC Genomics, 2011;12:329.

Mingxiang Teng, Yadong Wang, Guohua Wang, Jeesun Jung, Howard J Edenberg, Jeremy R Sanford, Yunlong Liu. Prioritizing single-nucleotide variations that potentially regulate alternative splicing. BMC Proceedings, 2011;5(Suppl 9):S40.

Changyu Shen, Yiwen Huang, Yunlong Liu, Guohua Wang, Yuming Zhao, Zhiping Wang, Mingxiang Teng, Yadong Wang, David A Flockhart, Todd C Skaar, Pearlly Yan, Kenneth P Nephew, Tim HM Huang, Lang Li. A modulated empirical Bayes model for identifying topological and temporal estrogen receptor α regulatory networks in breast cancer. BMC Systems Biology, 2011;5:67.

Feng C Zhou, Yokesh Balaraman, Mingxiang Teng, Yunlong Liu, Rabindra P Singh, Kenneth P Nephew. Alcohol alters DNA methylation patterns and inhibits neural stem cell differentiation. Alcoholism: Clinical and Experimental Research, 2011;35(4):735-746.

Guohua Wang, Yadong Wang, Mingxiang Teng, Denan Zhang, Lang Li, Yunlong Liu. Signal transducers and activators of transcription-1 (STAT1) regulates microRNA transcription in interferon γ-stimulated HeLa cells. PLoS ONE, 2010;5(7):e11794.

Qinghua Jiang, Yangyang Hao, Guohua Wang, Liran Juan, Tianjiao Zhang, Mingxiang Teng, Yunlong Liu, Yadong Wang. Prioritization of disease microRNAs through a human phenome-microRNAome network. BMC Systems Biology, 2010;4(Suppl 1):S2.

Terry Camerlengo, Hatice Gulcin Ozer, Pearlly Yan, Jeffrey Parvin, Tim Huang, Kun Huang, Francisco Perez, Mingxiang Teng, Lang Li, Yunlong Liu, Tahsin Kurc. Enabling data analysis on high-throughput data in large data depository using web-based analysis platform – a case study on integrating QUEST with GenePattern in epigenetics research. BIBM09, 2009:392–395.

Xin Wang, Mingxiang Teng, Guohua Wang, Yuming Zhao, Xu Han, Weixing Feng, Lang Li, Jeremy Sanford, Yunlong Liu. xIP-seq platform: an integrative framework for high-throughput sequencing data analysis. OCCBIO09, 2009:26-31.

Qinghua Jiang, Yadong Wang, Yangyang Hao, Liran Juan, Mingxiang Teng, Xinjun Zhang, Meimei Li, Guohua Wang, Yunlong Liu. miR2Disease: a manually curated database for microRNA deregulation in human disease. Nucleic Acids Research, 2009;37(suppl 1):D98-D104.