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Mingxiang Teng, PhD

Program: Biostatistics and Bioinformatics

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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.


Associations

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

Education & Training

Graduate:

  • Harbin Institute of Technology, M.Eng - Computer Science
  • Harbin Institute of Technology, Ph.D. - Computational Biology

Fellowship:

  • 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, Liu X, Liang J, Narita Y, Ding W, Li D, Zhang L, Wang H, Leong MML, Hou I, Gerdt C, Jiang C, Zhong Q, Tang Z, Forney C, Kottyan L, Weirauch MT, Gewurz BE, Zeng MS, Jiang S, Teng M, Zhao B. A DNA tumor virus globally reprograms host 3D genome architecture to achieve immortal growth. Nat Commun. 2023 Mar.14(1):1598. Pubmedid: 36949074. Pmcid: PMC10033825.
  • Obermayer A, Chang D, Nobles G, Teng M, Tan AC, Wang X, Eschrich S, Rodriguez P, Grass GD, Meshinchi S, Tarhini A, Chen DT, Shaw T. DRPPM-PATH-SURVEIOR: Plug-and-Play Survival Analysis of Pathway-level Signatures and Immune Components. Res Sq. 2023 Mar. Pubmedid: 36993526. Pmcid: PMC10055629.
  • Ding W, Wang C, Narita Y, Wang H, Leong MML, Huang A, Liao Y, Liu X, Okuno Y, Kimura H, Gewurz B, Teng M, Jin S, Sato Y, Zhao B. The Epstein-Barr Virus Enhancer Interaction Landscapes in Virus-Associated Cancer Cell Lines. J Virol. 2022 Sep.96(18):e0073922. Pubmedid: 36094314. Pmcid: PMC9517713.
  • Peres LC, Colin-Leitzinger C, Teng M, Dutil J, Alugubelli RR, DeAvila G, Teer JK, Du D, Mo Q, Siegel EM, Hampton O, Alsina M, Brayer J, Blue B, Baz R, Siqueira Silva A, Nishihori T, Shain KH, Gillis N. Racial and ethnic differences in clonal hematopoiesis, tumor markers, and outcomes of patients with multiple myeloma. Blood Adv. 2022 Jun.6(12):3767-3778. Pubmedid: 35500227. Pmcid: PMC9631567.
  • Guo R, Zhang Y, Teng M, Jiang C, Schineller M, Zhao B, Doench JG, O'Reilly RJ, Cesarman E, Giulino-Roth L, Gewurz BE. Author Correction: DNA methylation enzymes and PRC1 restrict B-cell Epstein-Barr virus oncoprotein expression. Nat Microbiol. 2022 Jun.7(6):928. Pubmedid: 35505195.
  • Wei G, Teng M, Rosa M, Wang X. Unique ER PR expression pattern in breast cancers with CHEK2 mutation: a hormone receptor and HER2 analysis based on germline cancer predisposition genes. Breast Cancer Res. 2022 Feb.24(1):11. Pubmedid: 35135604. Pmcid: PMC8822747.
  • Obermayer A, Dong L, Hu Q, Golden M, Noble JD, Rodriguez P, Robinson TJ, Teng M, Tan AC, Shaw TI. DRPPM-EASY: A Web-Based Framework for Integrative Analysis of Multi-Omics Cancer Datasets. Biology (Basel). 2022 Feb.11(2). Pubmedid: 35205126. Pmcid: PMC8869715.
  • Jiang C, Ward NP, Prieto-Farigua N, Kang YP, Thalakola A, Teng M, DeNicola GM. A CRISPR screen identifies redox vulnerabilities for KEAP1/NRF2 mutant non-small cell lung cancer. Redox Biol. 2022 Aug.54:102358. Pubmedid: 35667246. Pmcid: PMC9168196.
  • Jiang C, Ward NP, Prieto-Farigua N, Kang YP, Thalakola A, Teng M, DeNicola GM. Corrigendum to "A CRISPR screen identifies redox vulnerabilities for KEAP1/NRF2 mutant non-small cell lung cancer" [Redox Biol. 54 (2022) 102358]. Redox Biol. 2022 Aug.54:102393. Pubmedid: 35794066. Pmcid: PMC9287741.
  • Liu X, Zhao B, Shaw TI, Fridley BL, Duckett DR, Tan AC, Teng M. Summarizing internal dynamics boosts differential analysis and functional interpretation of super enhancers. Nucleic Acids Res. 2022 Apr.50(6):3115-3127. Pubmedid: 35234924. Pmcid: PMC8989535.
  • Huang J, Soupir AC, Schlick BD, Teng M, Sahin IH, Permuth JB, Siegel EM, Manley BJ, Pellini B, Wang L. Cancer Detection and Classification by CpG Island Hypermethylation Signatures in Plasma Cell-Free DNA. Cancers (Basel). 2021 Nov.13(22). Pubmedid: 34830765. Pmcid: PMC8616264.
  • Wang Z, Guo R, Trudeau SJ, Wolinsky E, Ast T, Liang JH, Jiang C, Ma Y, Teng M, Mootha V, Gewurz B. CYB561A3 is the key lysosomal iron reductase required for Burkitt B-cell growth and survival. Blood. 2021 Dec.138(22):2216-2230. Pubmedid: 34232987. Pmcid: PMC8641094.
  • Teng M, Du D, Chen D, Irizarry RA. Characterizing batch effects and binding site-specific variability in ChIP-seq data. NAR Genom Bioinform. 2021 Dec.3(4):lqab098. Pubmedid: 34661103. Pmcid: PMC8515842.
  • Xie M, Lee K, Lockhart JH, Cukras SD, Carvajal R, Beg AA, Flores ER, Teng M, Chung CH, Tan AC. TIMEx: tumor-immune microenvironment deconvolution web-portal for bulk transcriptomics using pan-cancer scRNA-seq signatures. Bioinformatics. 2021 Apr. Pubmedid: 33901274.
  • Zhang Y, Jiang C, Trudeau SJ, Narita Y, Zhao B, Teng M, Guo R, Gewurz BE. Histone Loaders CAF1 and HIRA Restrict Epstein-Barr Virus B-Cell Lytic Reactivation. MBio. 2020 Oct.11(5). Pubmedid: 33109754. Pmcid: PMC7593962.
  • Cheng L, Deng L, Teng M. Editorial: System Biology Methods and Tools for Integrating Omics Data. Front Genet. 2020 Nov.11:563108. Pubmedid: 33281868. Pmcid: PMC7689002.
  • Guo R, Jiang C, Zhang Y, Govande A, Trudeau SJ, Chen F, Fry CJ, Puri R, Wolinsky E, Schineller M, Frost TC, Gebre M, Zhao B, Giulino-Roth L, Doench JG, Teng M, Gewurz BE. MYC Controls the Epstein-Barr Virus Lytic Switch. Mol Cell. 2020 May.78(4):653-669.e8. Pubmedid: 32315601. Pmcid: PMC7245572.
  • Vander Velde R, Yoon N, Marusyk V, Durmaz A, Dhawan A, Miroshnychenko D, Lozano-Peral D, Desai B, Balynska O, Poleszhuk J, Kenian L, Teng M, Abazeed M, Mian O, Tan AC, Haura E, Scott J, Marusyk A. Resistance to targeted therapies as a multifactorial, gradual adaptation to inhibitor specific selective pressures. Nat Commun. 2020 May.11(1):2393. Pubmedid: 32409712. Pmcid: PMC7224215.
  • Wang C, Zhang L, Ke L, Ding W, Jiang S, Li D, Narita Y, Hou I, Liang J, Li S, Xiao H, Gottwein E, Kaye KM, Teng M, Zhao B. Primary effusion lymphoma enhancer connectome links super-enhancers to dependency factors. Nat Commun. 2020 Dec.11(1):6318. Pubmedid: 33298918. Pmcid: PMC7726151.
  • Guo R, Zhang Y, Teng M, Jiang C, Schineller M, Zhao B, Doench JG, O'Reilly RJ, Cesarman E, Giulino-Roth L, Gewurz BE. DNA methylation enzymes and PRC1 restrict B-cell Epstein-Barr virus oncoprotein expression. Nat Microbiol. 2020 Aug.5(8):1051-1063. Pubmedid: 32424339. Pmcid: PMC7462085.
  • Vena F, Bayle S, Nieto A, Quereda V, Aceti M, Frydman SM, Sansil SS, Grant W, Monastyrskyi A, McDonald P, Roush WR, Teng M, Duckett D. Targeting Casein Kinase 1 Delta Sensitizes Pancreatic and Bladder Cancer Cells to Gemcitabine Treatment by Upregulating Deoxycytidine Kinase. Mol Cancer Ther. 2020 Aug.19(8):1623-1635. Pubmedid: 32430484. Pmcid: PMC7415672.
  • 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 Jun.93(13). Pubmedid: 31019051. Pmcid: PMC6580941.
  • 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 Jul.93(16). Pubmedid: 31167905. Pmcid: PMC6675876.
  • 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.
  • Teng M, Irizarry RA. Accounting for GC-content bias reduces systematic errors and batch effects in ChIP-seq data. Genome Res. 2017 Nov.27(11):1930-1938. Pubmedid: 29025895. Pmcid: PMC5668949.
  • 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, 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 Sep.17(1):203. Pubmedid: 27716375. Pmcid: PMC5045616.
  • 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.

Grants

  • Title: Integrative Analysis to Identify Genomic Biomarkers in HPV Positive Oral Cancer
    Sponsor: Nat Institutes of Health
    PI: Teng, M.