Computational Omics
We focus on computational challenges in processing, integrating and interpreting cancer omics data.
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Mingxiang Teng, PhD
Assistant Member |
Selected Publications
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Wang H, Mou Z, Yeo YY, Ge Q, Liu X, Narita Y, Li Z, Wang C, Li W, Zhao KRS, Li J, Bu W, Gewurz B, Cohen JI, Teng M, Dai X, Liu X, Jiang S, Bo Zhao. Epstein-Barr virus exploits Desmocollin 2 as the principal epithelial cell entry receptor. Nature Microbiology. 2025. (accepted)
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Liu X†, Tang Y†, Blachly J, Edge S, Jakubek YA, McCarter M, Naqash AR, Nepple KG, Osman A, Reilley MJ, Riedlinger G, Salhia B, Schneider BP, Shriver C, Churchman ML, Rounbehler RJ, Teer JK, Gillis N*, Teng M*. qcCHIP: An R package to identify clonal hematopoiesis variants using cohort-specific data characteristics. Bioinformatics. 2025;btaf522.
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Shepard A, Lester DK, Troutman S, Hoxha S, Khaled WT, Smith ESJ, Park TJ, Buffenstein R, Du D, Teng M, Dengler-Crish CM, Tsai KY, Flores ER, Ventura A, Kissil JL. An Autochthonous Model of Lung Cancer Identifies Requirements for Cellular Transformation in the Naked Mole-Rat. Cancer Discovery. 2025.
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Wang C*, Leong MM, Ding W, Narita Y, Liu X, Wang H, Yiu SPT, Lee J, Zhao KRS, Cui A, Gewurz B, Hammerschmidt W, Teng M*, Zhao B*. Viral oncogene EBNALP regulates YY1 DNA binding and alters host 3D genome organization. EMBO Reports. 2025;26(3):810-835.
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Liu X, Gillis N, Jiang C, McCofie A, Shaw TI, Tan AC, Zhao B, Wan L, Duckett DR, Teng M. An epigenomic fingerprint of human cancers by landscape interrogation of super enhancers at the constituent level. PLoS Computational Biology. 2024;20(2):e1011873.
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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. Nature Communications. 2023;14(1):1598.
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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 Biology. 2022;54:102358.
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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 Research. 2022;50(6):3115-3127.
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Teng M*, Du D, Chen D, Irizarry RA. Characterizing batch effects and binding site-specific variability in ChIP-seq data. NAR Genomics and Bioinformatics. 2021;3(4):lqab098.
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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. Nature Microbiology. 2020;5(8):1051-1063.
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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. Nature Communications. 2020;11(1):6318.
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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. Molecular Cell. 2020;78(4):653-669.e8.
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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.
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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.