Wang C, Jiang S, Ke L, Teng M, Chen C, Zhang L, Li D, Liang J, Narita Y, Hou I, Wang L, Zhong Q, Lv X, Xiang Y, Tsao SW, Guo X, Gewurz BE, Zeng MS, Zhao B. Super-enhancer driven MYST histone lysine acetyltransferases family members are critical for nasopharyngeal carcinoma cell growth and survival. (submitted)

Jiang C, Trudeau SJ, Cheong TC, Teng M,Wang LW, Pighi C, Gautier-Courteille C, Ma Y, Jiang S, Wang C, Zhao B, Paillard L, Doench J, Chiarle R, Gewurz BE. CRISPR/Cas9 screens reveal multiple layers of B-cell CD40 regulation. (submitted)

Korthauer K, Kimes PK, Duvallet C, Reyes A, Subramanian A, Teng M, Shukla C, Alm EJ, Hicks SC. A practical guide to methods controlling false discoveries in computational biology. (submitted)

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 revision)


Published

Chu Y#, Teng M#, Wang Y. Modeling and correct the GC bias of tumor and normal WGS data for SCNA based tumor subclonal population inferring. BMC Bioinformatics, 2018;19(Suppl 5):112.

Hicks SC, Townes FW, Teng M, Irizarry RA. Missing data and technical variability in single-cell RNA-sequencing experiments. Biostatistics, 2018;19(4):562-578.

Teng M, Irizarry RA. Accounting for GC-content bias reduces systematic errors and batch effects in ChIP-seq data. Genome Research, 2017;27(11):1930-1938.

Nakayama RT, Pulice JL, Valencia AM, McBride MJ, McKenzie ZM, Gillespie MA, Ku WL, Teng M, Cui K, Williams RT, Cassel SH, Qing H, Widmer CJ, Demetri GD, Irizarry RA, Zhao K, Ranish JA, Kadoch C. SMARCB1 is required for widespread BAF complex-mediated activation of enhancers and bivalent promoters. Nature Genetics, 2017;49(11):1613-1623.

Chu Y, Wang Z, Wang R, Zhang N, Li J, Hu Y, Teng M, Wang Y. 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.

Teng M, Love MI, Davis CA, Djebali S, Dobin A, Graveley BR, Li S, Mason CE, Olson S, Pervouchine D, Sloan CA, Wei X, Zhan L, Irizarry RA. A benchmark for RNA-seq quantification pipelines. Genome Biology, 2016;17:74.

Liu B, Guan D, Teng M, Wang Y. rHAT: fast alignment of noisy long reads with regional hashing. Bioinformatics, 2016;32(11):1625-1631.

Juan L, Liu Y, Wang Y, Teng M, Zang T, Wang Y. Family genome browser: visualizing genomes with pedigree information. Bioinformatics, 2015;31(14):2262-2268.

Juan L, Teng M, Zang T, Hao Y, Wang Z, Yan C, Liu Y, Li J, Zhang T, Wang Y. The personal genome browser: visualizing functions of genetic variants. Nucleic Acids Research, 2014;42(W1):W192-W197.

Wang G, Qi K, Zhao Y, Li Y, Juan L, Teng M, Li L, Liu Y, Wang Y. Identification of regulatory regions of bidirectional genes in cervical cancer. BMC Medical Genomics, 2013;6(Suppl 1):S5.

Teng M, Wang Y, Kim S, Li L, Shen C, Wang G, Liu Y, Huang THM, Nephew KP, Balch C. Empirical bayes model comparisons for differential methylation analysis. Comparative and Functional Genomics, 2012;2012:376706.

Teng M#, Ichikawa S#, Padgett LR, Wang Y, Mort M, Cooper DN, Koller DL, Foroud T, Edenberg HJ, Econs MJ, Liu Y. regSNPs: a strategy for prioritizing regulatory single nucleotide substitutions. Bioinformatics, 2012;28(14):1879-1886.

Teng M#, Balch C#, Liu Y, Li M, Huang THM, Wang Y, Nephew KP, Li L. The influence of cis-regulatory elements on DNA methylation fidelity. PLoS ONE, 2012;7(3):e32928.

Zhu S, Jiang Q, Wang G, Liu B, Teng M, Wang Y. Chromatin structure characteristics of pre-miRNA genomic sequences. BMC Genomics, 2011;12:329.

Teng M, Wang Y, Wang G, Jung J, Edenberg HJ, Sanford JR, Liu Y. Prioritizing single-nucleotide variations that potentially regulate alternative splicing. BMC Proceedings, 2011;5(Suppl 9):S40.

Shen C, Huang Y, Liu Y, Wang G, Zhao Y, Wang Z, Teng M, Wang Y, Flockhart DA, Skaar TC, Yan P, Nephew KP, Huang THM, Li L. A modulated empirical Bayes model for identifying topological and temporal estrogen receptor α regulatory networks in breast cancer. BMC Systems Biology, 2011;5:67.

Zhou FC, Balaraman Y, Teng M, Liu Y, Singh RP, Nephew KP. Alcohol alters DNA methylation patterns and inhibits neural stem cell differentiation. Alcoholism: Clinical and Experimental Research, 2011;35(4):735-746.

Wang G, Wang Y, Teng M, Zhang D, Li L, Liu Y. Signal transducers and activators of transcription-1 (STAT1) regulates microRNA transcription in interferon γ-stimulated HeLa cells. PLoS ONE, 2010;5(7):e11794.

Jiang Q, Hao Y, Wang G, Juan L, Zhang T, Teng M, Liu Y, Wang Y. Prioritization of disease microRNAs through a human phenome-microRNAome network. BMC Systems Biology, 2010;4(Suppl 1):S2.

Jiang Q, Wang Y, Hao Y, Juan L, Teng M, Zhang X, Li M, Wang G, Liu Y. miR2Disease: a manually curated database for microRNA deregulation in human disease. Nucleic Acids Research, 2009;37(suppl 1):D98-D104.