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Mingxiang Teng, PhD

Academic Rank: Assistant Member

Overview

Dr. Teng’s research focuses on statistical/computational methods to address data challenges in cancer genomics studies, such as data quality, data bias, pre-processing and functional annotation of high-throughput sequencing data. Areas of his ongoing works include:  1) Integrating large sequencing datasets in regulatory genomics to improve the estimation of gene regulation patterns, particularly under cancer settings; 2) Comparative learning on the effects of technical sequencing parameters to optimize the nomination of somatic mutations; 3) Integrative analysis with multidimensional genomic data to uncover virus effects on tumorigenesis. Besides, Dr. Teng’s expertise in data science is extensively engaged in collaborative researches for cancer discoveries.


Discipline

    • Biostatistics and Bioinformatics
    • Cancer Biology and Evolution Program
    • Melanoma Research Center of Excellence

Education & Training

Fellowship:

  • Harbin Institute of Technology, M.Eng - Computer Science
  • Harbin Institute of Technology, Ph.D. - Computational Biology
  • Dana-Farber Cancer Institute, Fellow - Biostatistics/Computational Biology
Research

Dr. Teng’s research focuses on statistical/computational methods to address data challenges in cancer genomics studies, such as data quality, data bias, pre-processing and functional annotation of high-throughput sequencing data. Areas of his ongoing works include:  1) Integrating large sequencing datasets in regulatory genomics to improve the estimation of gene regulation patterns, particularly under cancer settings; 2) Comparative learning on the effects of technical sequencing parameters to optimize the nomination of somatic mutations; 3) Integrative analysis with multidimensional genomic data to uncover virus effects on tumorigenesis. Besides, Dr. Teng’s expertise in data science is extensively engaged in collaborative researches for cancer discoveries.

Publications

  • Wang C, Jiang S, Ke L, Zhang L, Li D, Liang J, Narita Y, Hou I, Chen CH, Wang LW, Zhong Q, Ling Y, Lv X, Xiang Y, Guo X, Teng M, Tsao SW, Gewurz BE, Zeng MS, Zhao B. Genome-wide CRISPR-based gene knockout screens reveal cellular factors and pathways essential for nasopharyngeal carcinoma. J Biol Chem. 2019 Jun;294(25):9734-9745. Pubmedid: 31073033. Pmcid: PMC6597810.
  • 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. Genome Biol. 2019 Jun;20(1):118. Pubmedid: 31164141. Pmcid: PMC6547503.
  • Wang C, Jiang S, Zhang L, Li D, Liang J, Narita Y, Hou I, Zhong Q, Gewurz BE, Teng M, Zhao B. TAF Family Proteins and MEF2C Are Essential for Epstein-Barr Virus Super-Enhancer Activity. J Virol. 2019 Jun;93(16). Pubmedid: 31167905. Pmcid: PMC6675876.
  • Wang C, Li D, Zhang L, Jiang S, Liang J, Narita Y, Hou I, Zhong Q, Zheng Z, Xiao H, Gewurz BE, Teng M, Zhao B. RNA Sequencing Analyses of Gene Expression during Epstein-Barr Virus Infection of Primary B Lymphocytes. J Virol. 2019 Jul;93(13). Pubmedid: 31019051. Pmcid: PMC6580941.
  • Jiang C, Trudeau SJ, Cheong TC, Guo R, Teng M, Wang LW, Wang Z, Pighi C, Gautier-Courteille C, Ma Y, Jiang S, Wang C, Zhao B, Paillard L, Doench JG, Chiarle R, Gewurz BE. CRISPR/Cas9 Screens Reveal Multiple Layers of B cell CD40 Regulation. Cell Rep. 2019 Jul;28(5):1307-1322.e8. Pubmedid: 31365872. Pmcid: PMC6684324.
  • Hicks SC, Townes FW, Teng M, Irizarry RA. Missing data and technical variability in single-cell RNA-sequencing experiments. Biostatistics. 2018 Oct;19(4):562-578. Pubmedid: 29121214. Pmcid: PMC6215955.
  • 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 Apr;19(Suppl 5):112. Pubmedid: 29671389. Pmcid: PMC5907144.
  • 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. J Bioinform Comput Biol. 2017 Oct;15(5):1750021. Pubmedid: 28918707.
  • 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. Nat Genetics. 2017 Nov;49(11):1613-1623. Pubmedid: 28945250. Pmcid: PMC5803080.
  • Teng M, Irizarry RA. Accounting for GC-content bias reduces systematic errors and batch effects in ChIP-seq data. Genome Res. 2017 11;27(11):1930-1938. Pubmedid: 29025895. Pmcid: PMC5668949.
  • 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. Erratum to: A benchmark for RNA-seq quantification pipelines. Genome Biol. 2016 May.17(1):107. Pubmedid: 27215799. Pmcid: PMC4877800.
  • 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 Biol. 2016 Apr;17:74. Pubmedid: 27107712. Pmcid: PMC4842274.
  • Liu B, Guan D, Teng M, Wang Y. rHAT: fast alignment of noisy long reads with regional hashing. Bioinformatics. 2016 06;32(11):1625-1631. Pubmedid: 26568628.
  • Juan L, Liu Y, Wang Y, Teng M, Zang T, Wang Y. Family genome browser: visualizing genomes with pedigree information. Bioinformatics. 2015 Jul;31(14):2262-2268. Pubmedid: 25788626.
  • 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 Res. 2014 Jul;42(Web):W192-W197. Pubmedid: 24799434. Pmcid: PMC4086072.
  • 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 Med Genomics. 2013 Aug;6 Suppl 1:S5. Pubmedid: 23369456. Pmcid: PMC3552671.
  • Teng M, Wang Y, Kim S, Li L, Shen C, Wang G, Liu Y, Huang TH, Nephew KP, Balch C. Empirical bayes model comparisons for differential methylation analysis. Comp Funct Genomics. 2012 Sep;2012:376706. Pubmedid: 22956892. Pmcid: PMC3432337.
  • 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 Jul;28(14):1879-1886. Pubmedid: 22611130. Pmcid: PMC3389767.
  • Teng M, Balch C, Liu Y, Li M, Huang TH, Wang Y, Nephew KP, Li L. The influence of cis-regulatory elements on DNA methylation fidelity. PLoS One. 2012 Aug;7(3):e32928. Pubmedid: 22412954. Pmcid: PMC3295790.
  • Teng M, Wang Y, Wang G, Jung J, Edenberg HJ, Sanford JR, Liu Y. Prioritizing single-nucleotide variations that potentially regulate alternative splicing. BMC Proc. 2011 Nov;5 Suppl 9:S40. Pubmedid: 22373210. Pmcid: PMC3287877.
  • 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 TH, Li L. A modulated empirical Bayes model for identifying topological and temporal estrogen receptor α regulatory networks in breast cancer. BMC Syst Biol. 2011 May;5:67. Pubmedid: 21554733. Pmcid: PMC3117732.
  • Zhu S, Jiang Q, Wang G, Liu B, Teng M, Wang Y. Chromatin structure characteristics of pre-miRNA genomic sequences. BMC Genomics. 2011 Jun;12:329. Pubmedid: 21702984. Pmcid: PMC3135579.
  • Zhou FC, Balaraman Y, Teng M, Liu Y, Singh RP, Nephew KP. Alcohol alters DNA methylation patterns and inhibits neural stem cell differentiation. Alcohol Clin Exp Res. 2011 Apr;35(4):735-746. Pubmedid: 21223309. Pmcid: PMC3076804.
  • 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 Syst Biol. 2010 May;4 Suppl 1:S2. Pubmedid: 20522252. Pmcid: PMC2880408.
  • 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 gamma-stimulated HeLa cells. PLoS One. 2010 Jul;5(7):e11794. Pubmedid: 20668688. Pmcid: PMC2909916.
  • Camerlengo T, Ozer HG, Yan P, Parvin J, Huang T, Huang K, Perez F, Teng M, Li L, Liu Y, Kurc T. 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. Proceedings (IEEE Int Conf Bioinformatics Biomed). 2009 Nov.1-4(Nov 2009):392-395. Pubmedid: 21151835. Pmcid: PMC2998767.
  • 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 Res. 2009 Jan;37(Database):D98-104. Pubmedid: 18927107. Pmcid: PMC2686559.