2026

• Treatment with the Nox1/4 inhibitor Setanaxib ameliorates cardiac function in mouse models of Duchenne muscular dystrophy.
  Deng R, De Oliveira Silva T, Liu X, Fan C, Seok HY, Wu J, Wickramage I, Guo H, Lin T, Zhang S, Semerci N, Taheri S, Lu YW, Huang ZP, Mably JD, Teng M, Chen H, Diniz GP, Wang DZ.
  PubMed | Mol Ther

• Evolution of clonal hematopoiesis during cancer treatment and its impact on outcomes.
  Arabzadeh M, Tang YH, Colin-Leitzinger C, Marzban S, Walgenbach D, Morganti S, Mahaganapathy V, Harper E, Teng M, Kresovich JK, Washington I, Parsons HA, Garber JE, West J, Ganesan S, Khiabanian H, Gillis N.
  PubMed | J Clin Invest

• Abundance and balance of circulating leukocyte subsets and colorectal cancer survival.
  Richards AR, Gomez MF, Dowling BI, Bulka CM, Gigic B, Figueiredo JC, Li CI, Shibata D, Toriola AT, Byrd DA, Ulrich CM, Teng M, Stewart PA, Siegel EM, Kresovich JK.
  PubMed | Br J Cancer

• Integrated Genomic and Epigenomic Analysis Reveals Epigenetic Plasticity in Disease Progression and Multidrug Resistance in Multiple Myeloma.
  Canevarolo RR, Sudalagunta PR, Meads MB, Silva M, Zhao X, Magaletti D, Alugubelli RR, DeAvila G, DeAvila D, Persi E, Maura F, Bell ET, Bishop RT, Cubitt CL, Sansil SS, Zhang W, Teer JK, Teng M, Yoder SJ, Siegel EM, Shah BD, Nishihori T, Hazlehurst L, Lynch CC, Landgren O, Hampton O, Gatenby RA, Sullivan DM, Brayer J, Dalton W, Cleveland JL, Alsina M, Baz R, Shain KH, Silva AS.
  PubMed | Cancer Res

• Genome-wide variation in cell-free DNA end-motif entropy predicts immunotherapy response in head and neck cancer.
  Bandaru R, Fu H, Zheng H, Liang J, Wang L, Gulati S, Hinrichs BH, Teng M, Zhang B, Kocherginsky M, Lin DC, Hildeman DA, Worden FP, Old M, Dunlap NE, Kaczmar JM, Gillison ML, El-Gamal D, Wise Draper T, Liu Y.
  PubMed | J Clin Invest

• ShinyEvents: harmonizing longitudinal data for real-world survival estimation.
  Obermayer A, Davis J, Talada DP, Teng M, Eschrich S, Yin V, Spakowicz D, Chatterjee D, Rounbehler RJ, Churchman ML, Tarhini AA, Wang X, Gupta S, Markowitz J, Goecks J, Li R, Rodrigues Pessoa R, Manley BJ, Tan AC, Grass GD, Chen DT, Shaw TI.
  PubMed | NPJ Precis Oncol

2025

• Ancestry-dependent patterns of somatic mosaicism and clonal hematopoiesis mutations in over 125,000 individuals reveal distinct cancer associations.
  Colin-Leitzinger C^†, Tang YH^†, Teng M^$, Gillis N^$.
  PubMed | Hum Genomics

• Epstein-Barr virus exploits desmocollin 2 as the principal epithelial cell entry receptor.
  Wang H, Mou Z, Yeo YY, Ge Q, Liu X, Narita Y, Li Z, Wang C, Li W, Zhao KR, Li J, Bu W, Gewurz B, Cohen JI, Teng M, Dai X, Liu X, Jiang S, Zhao B.
  PubMed | Nat Microbiol

• qcCHIP: An R package to identify clonal hematopoiesis variants using cohort-specific data characteristics.
  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^$, Teng M^$.
  PubMed | Bioinformatics

• An Autochthonous Model of Lung Cancer Identifies Requirements for Cellular Transformation in the Naked Mole-Rat.
  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.
  PubMed | Cancer Discov

• PROTAC-Mediated Degradation of TAF1 Induces Apoptosis in AML Cells and Inhibits Tumor Growth In Vivo.
  Chen L, Shultz ZP, Sansone M, Fang B, Liu X, Teng M, Schonbrunn E, Lopchuk JM, Chen J.
  PubMed | Mol Cancer Ther

• Viral oncogene EBNALP regulates YY1 DNA binding and alters host 3D genome organization.
  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^$.
  PubMed | EMBO Rep

2024

• BatchFLEX: feature-level equalization of X-batch.
  Davis JT, Obermayer AN, Soupir AC, Hesterberg RS, Duong T, Yang CY, Dao KP, Manley BJ, Grass GD, Avram D, Rodriguez PC, Fridley BL, Yu X, Teng M, Wang X, Shaw TI.
  PubMed | Bioinformatics

• Clonal hematopoiesis in patients With human immunodeficiency virus and cancer.
  Gillis N, Dickey BL, Colin-Leitzinger C, Tang YH, Putney RM, Mesa TE, Yoder SJ, Suneja G, Spivak AM, Patel AB, Extermann M, Giuliano AR, Teng M, Kresovich J, Berglund A, Coghill AE.
  PubMed | J Infect Dis

• The DNA loop release factor WAPL suppresses Epstein-Barr virus latent membrane protein expression to maintain the highly restricted latency I program.
  Murray-Nerger LA, Maestri D^†, Liu X^†, Li Z^†, Auld NR, Tempera I, Teng M, Gewurz BE.
  PubMed | PLoS Pathog

• An epigenomic fingerprint of human cancers by landscape interrogation of super enhancers at the constituent level.
  Liu X, Gillis N, Jiang C, McCofie A, Shaw TI, Tan AC, Zhao B, Wan L, Duckett DR, Teng M.
  PubMed | PLoS Comput Biol

2023

• Differences in epigenetic age by HIV status among patients with a non-AIDS defining cancer.
  Dickey BL, Putney RM, Suneja G, Kresovich JK, Spivak AM, Patel AB, Teng M, Extermann M, Giuliano AR, Gillis N, Berglund A, Coghill AE.
  PubMed | AIDS

• Pilot Study of Donor-Engrafted Clonal Hematopoiesis Evolution and Clinical Outcomes in Allogeneic Hematopoietic Cell Transplantation Recipients Using a National Registry.
  Gillis N, Padron E, Wang T, Chen K, DeVos JD, Spellman SR, Lee SJ, Kitko CL, MacMillan ML, West J, Tang YH, Teng M, McNulty S, Druley TE, Pidala JA, Lazaryan A.
  PubMed | Transplant Cell Ther

• Clonal Hematopoiesis as a Molecular Risk Factor for Doxorubicin-Induced Cardiotoxicity: A Proof-of-Concept Study.
  Mammadova J, Colin-Leitzinger C, Nguyen D, Mhaskar R, Ganesan S, Tang YH, Teng M, Ismail-Khan R, Gillis N.
  PubMed | JCO Precis Oncol

• PATH-SURVEYOR: pathway level survival enquiry for immuno-oncology and drug repurposing.
  Obermayer AN, Chang D, Nobles G, Teng M, Tan AC, Wang X, Chen YA, Eschrich S, Rodriguez PC, Grass GD, Meshinchi S, Tarhini A, Chen DT, Shaw TI.
  PubMed | BMC Bioinformatics

• A DNA tumor virus globally reprograms host 3D genome architecture to achieve immortal growth.
  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^$.
  PubMed | Nat Commun

• Statistical analysis in ChIP-seq-related applications.
  Teng M.
  PubMed | Methods Mol Biol (Book Chapter)

2022

• The Epstein-Barr virus enhancer interaction landscapes in virus-associated cancer cell lines.
  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.
  PubMed | J Virol

• A CRISPR screen identifies redox vulnerabilities for KEAP1/NRF2 mutant non-small cell lung cancer.
  Jiang C, Ward NP, Prieto-Farigua N, Kang YP, Thalakola A, Teng M, DeNicola GM.
  PubMed | Redox Biol

• Racial and ethnic differences in clonal hematopoiesis, tumor markers, and outcomes of patients with multiple myeloma.
  Peres LC, Colin-Leitzinger CM, Teng M, Dutil J, Alugubelli RR, DeAvila G, Teer JK, Du D, Mo Q, Siegel EM, Hampton OA, Alsina M, Brayer J, Blue B, Baz R, Silva AS, Nishihori T, Shain KH, Gillis N.
  PubMed | Blood Adv

• Summarizing internal dynamics boosts differential analysis and functional interpretation of super enhancers.
  Liu X, Zhao B, Shaw TI, Fridley BL, Duckett DR, Tan AC, Teng M.
  PubMed | Nucleic Acids Res

• Unique ER PR expression pattern in breast cancers with CHEK2 mutation: a hormone receptor and HER2 analysis based on germline cancer predisposition genes.
  Wei G, Teng M, Rosa M, Wang X.
  PubMed | Breast Cancer Res

• DRPPM-EASY: a web-based framework for integrative analysis of multi-omics cancer datasets.
  Obermayer A, Dong L, Hu Q, Golden M, Noble JD, Rodriguez P, Robinson TJ, Teng M, Tan AC, Shaw TI.
  PubMed | Biology

2021

• Cancer detection and classification by CpG island hypermethylation signatures in plasma cell-free DNA.
  Huang J, Soupir AC, Schlick BD, Teng M, Sahin IH, Permuth JB, Siegel EM, Manley BJ, Pellini B, Wang L.
  PubMed | Cancers

• Characterizing batch effects and binding site-specific variability in ChIP-seq data.
  Teng M^$, Du D, Chen D, Irizarry RA.
  PubMed | NAR Genom Bioinform

• CYB561A3 is the key lysosomal iron reductase required for Burkitt B-cell growth and survival.
  Wang Z, Guo R, Trudeau SJ, Wolinsky E, Ast T, Liang JH, Jiang C, Ma Y, Teng M, Mootha VK, Gewurz BE.
  PubMed | Blood

• TIMEx: tumor-immune microenvironment deconvolution web-portal for bulk transcriptomics using pan-cancer scRNA-seq signatures.
  Xie M, Lee K, Lockhart JH, Cukras SD, Carvajal R, Beg AA, Flores ER, Teng M, Chung CH, Tan AC.
  PubMed | Bioinformatics

2020

• Primary effusion lymphoma enhancer connectome links super-enhancers to dependency factors.
  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^$, Zhao B^$.
  PubMed | Nat Commun

• Histone loaders CAF1 and HIRA restrict Epstein-Barr virus B-cell lytic reactivation.
  Zhang Y, Jiang C, Trudeau SJ, Narita Y, Zhao B, Teng M, Guo R, Gewurz BE.
  PubMed | mBio

• DNA methylation enzymes and PRC1 restrict B-cell Epstein–Barr virus oncoprotein expression.
  Guo R, Zhang Y, Teng M, Jiang C, Schineller M, Zhao B, Doench JG, O’Reilly RJ, Cesarman E, Giulino-Roth L, Gewurz BE.
  PubMed | Nat Microbiol

• Targeting casein kinase 1 delta sensitizes pancreatic and bladder cancer cells to gemcitabine treatment by upregulating deoxycytidine kinase.
  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.
  PubMed | Mol Cancer Ther

• Expanded encyclopaedias of DNA elements in the human and mouse genomes.
  The ENCODE Project Consortium.
  PubMed | Nature

• MYC controls the Epstein-Barr Virus lytic switch.
  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^$, Gewurz BE^$.
  PubMed | Mol Cell

• Resistance to targeted therapies as a multifactorial, gradual adaptation to inhibitor specific selective pressures.
  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.
  PubMed | Nat Commun

2019

• CRISPR/Cas9 Screens Reveal Multiple Layers of B cell CD40 Regulation.
  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.
  PubMed | Cell Rep

• A practical guide to methods controlling false discoveries in computational biology.
  Korthauer K, Kimes PK, Duvallet C, Reyes A, Subramanian A, Teng M, Shukla C, Alm EJ, Hicks SC.
  PubMed | Genome Biol

• TAF family proteins and MEF2C are essential for Epstein-Barr virus MYC super-enhancer activity.
  Wang C, Jiang S, Zhang L, Li D, Liang J, Narita Y, Hou I, Zhong Q, Gewurz BE, Teng M^$, Zhao B^$.
  PubMed | J Virol

• RNA sequencing analyses of gene expression during Epstein-Barr virus infection of primary B lymphocytes.
  Wang C, Li D, Zhang L, Jiang S, Liang J, Narita Y, Hou I, Zhong Q, Zheng Z, Xiao H, Gewurz BE, Teng M^$, Zhao B^$.
  PubMed | J Virol

• Genome-wide CRISPR-based gene knockout screens reveal cellular factors and pathways essential for nasopharyngeal carcinoma.
  Wang C, Jiang S, Ke L, Zhang L, Li D, Liang J, Narita Y, Hou I, Chen CH, Wang L, Zhong Q, Ling Y, Lv X, Xiang Y, Guo X, Teng M, Tsao SW, Gewurz BE, Zeng MS, Zhao B.
  PubMed | J Biol Chem

Earlier

• Missing data and technical variability in single-cell RNA-sequencing experiments.
  Hicks SC, Townes FW, Teng M, Irizarry RA.
  PubMed | Biostatistics

• Modeling and correct the GC bias of tumor and normal WGS data for SCNA based tumor subclonal population inferring.
  Chu Y^†, Teng M^†, Wang Y.
  PubMed | BMC Bioinformatics

• Accounting for GC-content bias reduces systematic errors and batch effects in ChIP-seq data.
  Teng M, Irizarry RA.
  PubMed | Genome Res

• SMARCB1 is required for widespread BAF complex-mediated activation of enhancers and bivalent promoters.
  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.
  PubMed | Nat Genet

• WDNfinder: a method for minimum driver node set detection and analysis in directed and weighted biological network.
  Chu Y, Wang Z, Wang R, Zhang N, Li J, Hu Y, Teng M, Wang Y.
  PubMed | J Bioinform Comput Biol

• A benchmark for RNA-seq quantification pipelines.
  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.
  PubMed | Genome Biol

• rHAT: fast alignment of noisy long reads with regional hashing.
  Liu B, Guan D, Teng M, Wang Y.
  PubMed | Bioinformatics

• Family genome browser: visualizing genomes with pedigree information.
  Juan L, Liu Y, Wang Y, Teng M, Zang T, Wang Y.
  PubMed | Bioinformatics

• The personal genome browser: visualizing functions of genetic variants.
  Juan L, Teng M, Zang T, Hao Y, Wang Z, Yan C, Liu Y, Li J, Zhang T, Wang Y.
  PubMed | Nucleic Acids Res

• Identification of regulatory regions of bidirectional genes in cervical cancer.
  Wang G, Qi K, Zhao Y, Li Y, Juan L, Teng M, Li L, Liu Y, Wang Y.
  PubMed | BMC Med Genomics

• Empirical bayes model comparisons for differential methylation analysis.
  Teng M, Wang Y, Kim S, Li L, Shen C, Wang G, Liu Y, Huang TH, Nephew KP, Balch C.
  PubMed | Comp Funct Genomics

• regSNPs: a strategy for prioritizing regulatory single nucleotide substitutions.
  Teng M^†, Ichikawa S^†, Padgett LR, Wang Y, Mort M, Cooper DN, Koller DL, Foroud T, Edenberg HJ, Econs MJ, Liu Y.
  PubMed | Bioinformatics

• The influence of cis-regulatory elements on DNA methylation fidelity.
  Teng M^†, Balch C^†, Liu Y, Li M, Huang TH, Wang Y^$, Nephew KP^$, Li L^$.
  PubMed | PLoS ONE

• Chromatin structure characteristics of pre-miRNA genomic sequences.
  Zhu S, Jiang Q, Wang G, Liu B, Teng M, Wang Y.
  PubMed | BMC Genomics

• Prioritizing single-nucleotide variations that potentially regulate alternative splicing.
  Teng M, Wang Y, Wang G, Jung J, Edenberg HJ, Sanford JR, Liu Y.
  PubMed | BMC Proc

• A modulated empirical Bayes model for identifying topological and temporal estrogen receptor α regulatory networks in breast cancer.
  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.
  PubMed | BMC Syst Biol

• Alcohol alters DNA methylation patterns and inhibits neural stem cell differentiation.
  Zhou FC, Balaraman Y, Teng M, Liu Y, Singh RP, Nephew KP.
  PubMed | Alcohol Clin Exp Res

• Signal transducers and activators of transcription-1 (STAT1) regulates microRNA transcription in interferon γ-stimulated HeLa cells.
  Wang G, Wang Y, Teng M, Zhang D, Li L, Liu Y.
  PubMed | PLoS ONE

• Prioritization of disease microRNAs through a human phenome-microRNAome network.
  Jiang Q, Hao Y, Wang G, Juan L, Zhang T, Teng M, Liu Y, Wang Y.
  PubMed | BMC Syst Biol

• miR2Disease: a manually curated database for microRNA deregulation in human disease.
  Jiang Q, Wang Y, Hao Y, Juan L, Teng M, Zhang X, Li M, Wang G, Liu Y.
  PubMed | Nucleic Acids Res