Flemington EK, Flemington SA, O'Grady TM, Baddoo M, Nguyen T, Dong Y, Ungerleider NA. SpliceTools, a suite of downstream RNA splicing analysis tools to investigate mechanisms and impact of alternative splicing. Nucleic Acids Res. 2023 Mar 2:gkad111. doi: 10.1093/nar/gkad111. Epub ahead of print. PMID: 36864749.


O’Grady TM, Baddoo, M, Flemington, SA, Ishaq, EY, Ungerleider, NA, Flemington, EK. Reversal of splicing infidelity is a pre-activation step in B cell differentiation. Front. Immunol. 2022 Dec 19; DOI 10.3389/fimmu.2022.1060114  PMID: 36601126; PMCID: PMC9806119.

Safa F, Rasmussen T, Lobelle-Rich P, Collier S, Milligan N, Schmeig J, Schmid J, Wiewiorowski C, Totaro D, Brown TC, Satyavarapu I, Badoo M, Ungerleider N, Flemington EK, Safah H, Saba NS. Establishment and characterization of a new mantle cell lymphoma cell line with a NOTCH2 mutation, Arbo EJHaem. 2022 Sep 20;3(4):1326-1329. doi: 10.1002/jha2.580 PMID: 36467812; PMCID: PMC9713070.

Wang Y, Ungerleider N, Hoffman BA, Kara M, Farrell PJ, Flemington EK, Lee N, Tibbetts SA. A Polymorphism in the Epstein-Barr Virus EBER2 Noncoding RNA Drives In Vivo Expansion of Latently Infected B Cells. mBio. 2022 Jun 28;13(3):e0083622. Epub 2022 Jun 1. doi: 10.1128/mbio.00836-22. PMID: 35642944; PMCID: PMC9239156.

Hartono AB, Kang HJ, Shi L, Phipps W, Ungerleider N, Giardina A, Chen W, Spraggon L, Somwar R, Moroz K, Drewry DH, Burow ME, Flemington E, Ladanyi M, Lee SB. Salt-Inducible Kinase 1 is a potential therapeutic target in Desmoplastic Small Round Cell Tumor Oncogenesis. 2022 Apr 20;11(1):18. doi: 10.1038/s41389-022-00395-6.

Melnik LI, Guha S, Ghimire J, Smither AR, Beddingfield BJ, Hoffmann AR, Sun L, Ungerleider NA, Baddoo MC, Flemington EK, Gallaher WR, Wimley WC, Garry RF. Ebola virus delta peptide is an enterotoxin. Cell Rep. 2022 Jan 4;38(1):110172. doi: 10.1016/j.celrep.2021.110172. PMID: 34986351.


Kim JH, Jeong K, Li J, Murphy JM, Vukadin L, Stone JK, Richard A, Tran J, Gillespie GY, Flemington EK, Sobol RW, Lim SS, Ahn EE. SON drives oncogenic RNA splicing in glioblastoma by regulating PTBP1/PTBP2 switching and RBFOX2 activity. Nat Commun. 2021 Sep 21;12(1):5551. doi: 10.1038/s41467-021-25892-x. PMID: 34548489; PMCID: PMC8455679.

Ungerleider, N, Bullard, W, Kara, M, Wang, X, Roberts, C, Renne, R, Tibbetts, S, and Flemington, EK. EBV microRNAs are potent effectors of tumor cell transcriptome remodeling in promoting immune escape. PLoS Pathog. 2021 May 6;17(5):e1009217.
doi: 10.1371/journal.ppat.1009217. PMID: 33956915; PMCID: PMC8130916.

Penrose HM, Iftikhar R, Collins ME, Toraih E, Ruiz E, Ungerleider N, Nakhoul H, Flemington EF, Kandil E, Shah SB, Savkovic SD. Ulcerative colitis immune cell landscapes and differentially expressed gene signatures determine novel regulators and predict clinical response to biologic therapy. Sci Rep. 2021 Apr 27;11(1):9010. doi:  10.1038/s41598-021-88489-w. PMID: 33907256; PMCID: PMC8079702.

Chandra P, Cikic S, Baddoo M, Rutkai I, Guidry J, Flemington E, Katakam P, Busija D. Transcriptome Analysis Reveals Sexual Disparities in Gene Expression in Rat Brain Microvessels. J Cereb Blood Flow Metab. 2021 Mar 9:271678X21999553. doi: 10.1177/0271678X21999553. Epub 2021 Mar 9. PMID: 33715494; PMCID: PMC8392780.

Ma T, Bai S, Qi Y, Zhan Y, Ungerleider N, Zhang DY, Neklesa T, Corey E, Dehm SM, Zhang K, *Flemington EK, *Dong Y. Increased transcription and high translation efficiency lead to accumulation of androgen receptor splice variant after androgen deprivation therapy. Cancer Lett. 2021 Feb 6;504:37-48. doi: 10.1016/j.canlet.2020.12.037. Epub ahead of print. PMID: 33556543; PMCID:PMC7940584.
     *Co-corresponding authors

Ma T, Ungerleider N, Zhang DY, Corey E, *Flemington EK, *Dong Y. Data of relative mRNA and protein abundances of androgen receptor splice variants in castration-resistant prostate cancer. Data Brief. 2021 Jan 18;34:106774. doi: 10.1016/j.dib.2021.106774. PMID: 33537376; PMCID: PMC7843390.
     *Co-corresponding authors

Schouest B, Peterson TA, Szeltner DM, Scheef EA, Baddoo M, Ungerleider N, Flemington EK, MacLean AG, Maness NJ. Transcriptional signatures of Zika virus infection in astrocytes. J Neurovirol. 2021 Feb;27(1):116-125. doi:10.1007/s13365-020-00931-3. Epub 2021 Jan 6. PMID: 33405202; PMCID: PMC7921019.


Vukadin L, Kim JH, Park EY, Stone JK, Ungerleider N, Baddoo MC, Kong HK, Richard A, Tran J, Giannini H, Flemington EK, Lim SS, Ahn EE. SON inhibits megakaryocytic differentiation via repressing RUNX1 and the megakaryocytic gene expression program in acute megakaryoblastic leukemia. Cancer Gene Ther. 2021 Sep;28(9):1000-1015. doi: 10.1038/s41417-020-00262-9. Epub 2020 Nov 27. PMID: 33247227; PMCID: PMC8155101.

Zhang W, Dong Y, Sartor O, Flemington EK, Zhang K. SEER and Gene Expression Data Analysis Deciphers Racial Disparity Patterns in Prostate Cancer Mortality and the Public Health Implication. Sci Rep. 2020 Apr 22;10(1):6820. doi: 10.1038/s41598-020-63764-4. PMID: 32321981; PMCID: PMC7176737.

Yadav S, Anbalagan M, Baddoo M, Chellamuthu VK, Mukhopadhyay S, Woods C, Jiang W, Moroz K, Flemington EK, Makridakis N. Somatic mutations in the DNA repairome in prostate cancers in African Americans and Caucasians. Oncogene. 2020 May;39(21):4299-4311. doi: 10.1038/s41388-020-1280-x. Epub 2020 Apr 16. PMID: 32300177; PMCID: PMC7239769.

Yin Q, Strong MJ, Zhuang Y, Flemington EK, Kaminski N, de Andrade JA, Lasky JA. Assessment of viral RNA in idiopathic pulmonary fibrosis using RNA-seq. BMC Pulm Med. 2020 Apr 3;20(1):81. doi: 10.1186/s12890-020-1114-1. PMID: 32245461; PMCID: PMC7119082.


Cao S, Ma T, Ungerleider N, Roberts C, Kobelski M, Jin L, Concha M, Wang X, Baddoo M, Fazli L, Corey E, Ledet E, Zhang R, Silberstein JL, Zhang W, Zhang K, Sartor O, Dong X, *Flemington EK, * Dong Y. Circular RNAs add diversity to androgen receptor isoform repertoire in castration-resistant prostate cancer. Oncogene. 2019 Nov;38(45):7060-7072. doi: 10.1038/s41388-019-0947-7. Epub 2019 Aug 13. PMID: 31409897; PMCID: PMC6842090
     *Co-corresponding authors

Nakhoul H, Lin Z, Wang X, Roberts C, Dong Y, Flemington E. High-Throughput Sequence Analysis of Peripheral T-Cell Lymphomas Indicates Subtype-Specific Viral Gene Expression Patterns and Immune Cell Microenvironments. mSphere. 2019 Jul 10;4(4). pii: e00248-19. doi: 10.1128/mSphere.00248-19.

O'Grady T, Feswick A, Hoffman BA, Wang  Y, Medina EM, Kara M, van Dyk LF, *Flemington EK, *Tibbetts SA. Genome-wide Transcript Structure Resolution Reveals Abundant Alternate Isoform Usage from Murine Gammaherpesvirus 68. Cell Rep. 2019 Jun 25;27(13):3988-4002.e5. doi: 10.1016/j.celrep.2019.05.086
     *Co-corresponding authors

Kheir F, Zhao M, Strong MJ, Yu Y, Nanbo A, Flemington EK, Morris GF, Reiss K, Li L, Lin Z. Detection of Epstein--Barr Virus Infection in Non-Small Cell Lung Cancer. Cancers (Basel).  2019 May 31;11(6). pii: E759. doi: 10.3390/cancers11060759

Hilliard S, Song R, Liu H, Chen CH, Li Y, Baddoo M, Flemington E, Wanek A, Kolls J, Saifudeen Z, El-Dahr SS. Defining the dynamic chromatin landscape of mouse nephron progenitors.  Biol Open. 2019 May 20;8(5). pii: bio042754. doi: 10.1242/bio.042754

Ungerleider N and Flemington EK. SpliceV: Analysis and publication quality printing of linear and circular RNA splicing, expression and regulation. BMC Bioinformatics. 2019 May 8;20(1):231. doi: 10.1186/s12859-019-2865-7

Ruiz E, Penrose HM, Heller S, Nakhoul H, Baddoo M, Flemington EF, Kandil E, Savkovic SD. Bacterial TLR4 and NOD2 signalling linked to reduced mictochondrial energy function in active inflammatory bowel disease. Gut Microbes. 2019 May 7:1-14. doi: 10.1080/19490976.2019.1611152. [Epub ahead of print]

Ungerleider N, Tibbetts S, Renne R, Flemington EK. Gammaherpesvirus RNAs come full circle. MBio 2018 2019 Apr 2;10(2). pii: e00071-19. doi: 10.1128/mBio.00071-19. Review.

Ungerleider N, Jain V, Wang Y, Maness N, Blair R, Alvarez X, Midkiff C, Kolson D, Bai S, Roberts C, Moss WN, Wang X, Serfecz J, Seddon M, Lehman T, Ma T, Dong Y, Renne R, Tibbetts S, and Flemington EK. Comparative analysis of gammaherpesvirus circRNA repertoires: conserved and unique viral circRNAs. J Virol 2019 93(6) pii: e01952-18

Ungerleider NA, Jain V, Wang Y, Maness NJ, Blair RV, Alvarez X, Midkiff C, Kolson D, Bai S, Roberts C, Moss WN, Wang X, Serfecz J, Seddon M, Lehman T, Ma T, Dong Y, Renne R, Tibbetts SA, Flemington EK. Comparative Analysis of Gammaherpesvirus Circular RNA Repertoires: Conserved and Unique Viral Circular RNAs.  J Virol. 2019 Mar5;93(6). pii: e01952-18. doi: 10.1128/JVI.01952-18. Print 2019 Mar 15.

Bai S, Cao S, Jin L, Kobelski M, Schouest B, Wang X, Ungerleider N, Baddoo M, Zhang W, Corey E, Vessella RL, Dong X, Zhang K, Yu X, *Flemington EK, *Dong Y. A positive role of c-Myc in regulating androgen receptor and its splice variants in prostate cancer. Oncogene. 2019 Jun;38(25):4977-4989. doi: 10.1038/s41388-019-0768-8. Epub 2019 Feb 28.
     *Co-corresponding authors

Bai YL, Baddoo M, Flemington EK, Nakhoul HN, Liu YZ. Screen technical noice in single cell RNA sequencing data. Genomics. 2019 Feb 22. pii: S0888-7543(18)30580-9. doi: 10.1016/j.ygeno.2019.02.014. [Epub ahead of print]

Kara M, O'Grady T, Feldman ER, Feswick A, Wang Y, Flemginton EK, Tibbetts SA. Gammaherpesvirus Readthrough Transcription Generates a Long Non-Coding RNA That is Regulated by Antisense miRNAs and Correlates with Enhanced Lytic Replication In Vivo. Noncoding RNA. 2019 Jan 10;5(1). pii E6. doi: 10.3390/ncrna5010006


Bullard WL, Flemington EK, Renne R, Tibbetts SA. Connivance, Complicity, or Collusion? The Role of Noncoding RNAs in Promoting Gammaherpesvirus Tumorigenesis. Trends Cancer. 2018 Nov;4(11):729-740. doi: 10.1016/j.trecan.2018.09.005. Epub 2018 Oct 10. Review. PubMed PMID: 30352676.

Penrose HM, Cable C, Heller S, Ungerleider N, Nakhoul H, Baddoo M,  Hartono AB, Lee SB, Burow ME, Flemington EF, Crawford SE, Savkovic SD. Loss of Forkhead Box O3 Facilitates Inflammatory Colon Cancer:  Transcriptome Profiling of the Immune Landscape and Novel Targets. Cell Mol Gastroenterol Hepatol. 2019;7(2):391-408. doi: 10.1016/j.jcmgh. 2018.10.003. Epub 2018 Oct 13.

Zhang W, Flemington EK, Deng HW, Zhang K. Epigenetically silenced candidate tumor suppressor genes in prostate cancer: identified by modelling methylation stratification and applied to progression prediction. Cancer Epidemiol Biomarkers Prev. 2018 Sep 27. pii: cebp.0491.2018. doi: 10.1158/1055-9965.EPI-18-0491. [Epub ahead of print] PubMed PMID: 30262601.

Ungerleider N, Concha M, Lin Z, Roberts C, Wang X, Cao S, Baddoo M, Moss WN, Yu Y, Seddon M, Lehman T, Tibbetts S, Renne R, Dong Y, Flemington EK. The Epstein Barr virus circRNAome. PLoS Pathog. 2018 Aug 6;14(8):e1007206. doi: 10.1371/journal.ppat.1007206. eCollection 2018 Aug. PubMed PMID: 30080890; PubMed Central PMCID: PMC6095625.

Dai L, Del Valle L, Miley W, Whitby D, Ochoa AC, Flemington EK, Qin Z. Transactivation of human endogenous retrovirus K (HERV-K) by KSHV promotes Kaposi's sarcoma development. Oncogene. 2018 Aug;37(33):4534-4545. doi: 10.1038/s41388-018-0282-4. Epub 2018 May 10. PubMed PMID: 29743595; PubMed Central PMCID: PMC6195842.

Zhang W, Flemington EK, Zhang K. Driver gene mutations based clustering of tumors: methods and applications. Bioinformatics. 2018 Jul 1;34(13):i404-i411. doi: 10.1093/bioinformatics/bty232. PubMed PMID: 29950003; PubMed Central PMCID: PMC6022677.

Mei S, Flemington EK, Zhang K. Transferring knowledge of bacterial protein interaction networks to predict pathogen targeted human genes and immune signaling pathways: a case study on M. tuberculosis. BMC Genomics. 2018 Jun 28;19(1):505. doi: 10.1186/s12864-018-4873-9. PubMed PMID: 29954330; PubMed Central PMCID: PMC6027805.

Lin Z, Nguyen C, Xu B, Flemington EK, Morris GF. Interleukin-17A in the Pathogenesis of Lung Adenocarcinoma. Ann Am Thorac Soc. 2018 Apr;15(Supplement_2):S125. doi: 10.1513/AnnalsATS.201707-583MG. PubMed PMID: 29676621.

Schouest B, Weiler AM, Janaka SK, Myers TA, Das A, Wilder SC, Furlott J, Baddoo M, Flemington EK, Rakasz EG, Evans DT, Friedrich TC, Maness NJ. Maintenance of AP-2-Dependent Functional Activities of Nef Restricts Pathways of Immune Escape from CD8 T Lymphocyte Responses. J Virol. 2018 Feb 12;92(5). pii: e01822-17. doi: 10.1128/JVI.01822-17. Print 2018 Mar 1. PubMed PMID: 29237831; PubMed Central PMCID: PMC5809740.


Penrose HM, Heller S, Cable C, Nakhoul H, Ungerleider N, Baddoo M, Pursell ZF, Flemington EK, Crawford SE, Savkovic SD. In colonic ρ0 (rho0) cells reduced mitochondrial function mediates transcriptomic alterations associated with cancer. Oncoscience. 2017 Dec 27;4(11-12):189-198. doi: 10.18632/oncoscience.386. eCollection 2017 Nov. PubMed PMID: 29344557; PubMed Central PMCID: PMC5769983.

Saba NS, Wong DH, Tanios G, Iyer JR, Lobelle-Rich P, Dadashian EL, Liu D, Fontan L, Flemington EK, Nichols CM, Underbayev C, Safah H, Melnick A, Wiestner A, Herman SEM. MALT1 Inhibition Is Efficacious in Both Naïve and Ibrutinib-Resistant Chronic Lymphocytic Leukemia. Cancer Res. 2017 Dec 15;77(24):7038- 7048. doi: 10.1158/0008-5472.CAN-17-2485. Epub 2017 Oct 9. PubMed PMID: 28993409; PubMed Central PMCID: PMC5732856.

Li M, Li X, Zhuang Y, Flemington EK, Lin Z, Shan B. Induction of a novel isoform of the lncRNA HOTAIR in Claudin-low breast cancer cells attached to extracellular matrix. Mol Oncol. 2017 Dec;11(12):1698-1710. doi: 10.1002/1878-0261.12133. Epub 2017 Oct 30. PubMed PMID: 28846832; PubMed Central PMCID: PMC5709615.

Zhang W, Edwards A, Flemington EK, Zhang K. Racial disparities in patient survival and tumor mutation burden, and the association between tumor mutation burden and cancer incidence rate. Sci Rep. 2017 Oct 20;7(1):13639. doi: 10.1038/s41598-017-13091-y. PubMed PMID: 29057889; PubMed Central PMCID: PMC5651797.

Dai L, Lin Z, Jiang W, Flemington EK, Qin Z. Lipids, lipid metabolism and Kaposi's sarcoma-associated herpesvirus pathogenesis. Virol Sin. 2017 Oct;32(5):369-375. doi: 10.1007/s12250-017-4027-2. Epub 2017 Oct 10. Review. PubMed PMID: 29019168; PubMed Central PMCID: PMC5869022.

Dai L, Lin Z, Qiao J, Chen Y, Flemington EK, Qin Z. Ribonucleotide reductase represents a novel therapeutic target in primary effusion lymphoma. Oncogene. 2017 Aug 31;36(35):5068-5074. doi: 10.1038/onc.2017.122. Epub 2017 May 1. PubMed PMID: 28459467; PubMed Central PMCID: PMC5578886.

Yin Q, Sides M, Parsons CH, Flemington EK, Lasky JA. Arsenic trioxide inhibits EBV reactivation and promotes cell death in EBV- positive lymphoma cells. Virol J. 2017 Jun 21;14(1):121. doi: 10.1186/s12985-017-0784-7. PubMed PMID: 28637474; PubMed Central PMCID: PMC5480106.

Zhang R, Strong MJ, Baddoo M, Lin Z, Wang YP, Flemington EK, Liu YZ. Interaction of Epstein-Barr virus genes with human gastric carcinoma transcriptome. Oncotarget. 2017 Jun 13;8(24):38399- 38412. doi: 10.18632/oncotarget.16417. PubMed PMID: 28415594; PubMed Central PMCID: PMC5503541.

Heller S, Penrose HM, Cable C, Biswas D, Nakhoul H, Baddoo M, Flemington E, Crawford SE, Savkovic SD. Reduced mitochondrial activity in colonocytes facilitates AMPKα2-dependent inflammation. FASEB J. 2017 May;31(5):2013-2025. doi: 10.1096/fj.201600976R. Epub 2017 Feb 9. PubMed PMID: 28183804; PubMed Central PMCID: PMC5388551.

Deininger P, Morales ME, White TB, Baddoo M, Hedges DJ, Servant G, Srivastav S, Smither ME, Concha M, DeHaro DL, Flemington EK, Belancio VP. A comprehensive approach to expression of L1 loci. Nucleic Acids Res. 2017 Mar 17;45(5):e31. doi: 10.1093/nar/gkw1067. PubMed PMID: 27899577; PubMed Central PMCID: PMC5389711.

Penrose HM, Heller S, Cable C, Nakhoul H, Baddoo M, Flemington E, Crawford SE, Savkovic SD. High-fat diet induced leptin and Wnt expression: RNA-sequencing and pathway analysis of mouse colonic tissue and tumors. Carcinogenesis. 2017 Mar 1;38(3):302-311. doi: 10.1093/carcin/bgx001. PubMed PMID: 28426873; PubMed Central PMCID: PMC5862315.

Zhang W, Edwards A, Flemington EK, Zhang K. Significant Prognostic Features and Patterns of Somatic TP53 Mutations in Human Cancers. Cancer Inform. 2017 Feb 20;16:1176935117691267. doi: 10.1177/1176935117691267. eCollection 2017. PubMed PMID: 28469388; PubMed Central PMCID: PMC5392013.

Zhan Y, Zhang G, Wang X, Qi Y, Bai S, Li D, Ma T, Sartor O, Flemington EK, Zhang H, Lee P, Dong Y. Interplay between Cytoplasmic and Nuclear Androgen Receptor Splice Variants Mediates Castration Resistance. Mol Cancer Res. 2017 Jan;15(1):59-68. doi: 10.1158/1541-7786.MCR-16-0236. Epub 2016 Sep 26. PubMed PMID: 27671337; PubMed Central PMCID: PMC5215946.


Abshire CF, Prasai K, Soto I, Shi R, Concha M, Baddoo M, Flemington EK, Ennis DG, Scott RS, Harrison L. Exposure of Mycobacterium marinum to low-shear modeled microgravity: effect on growth, the transcriptome and survival under stress. NPJ Microgravity. 2016 Dec 1;2:16038. doi: 10.1038/npjmgrav.2016.38. eCollection 2016. PubMed PMID: 28725743; PubMed Central PMCID: PMC5515531.

O'Grady T, Wang X, Höner Zu Bentrup K, Baddoo M, Concha M, Flemington EK. Global transcript structure resolution of high gene density genomes through multi-platform data integration. Nucleic Acids Res. 2016 Oct 14;44(18):e145. Epub 2016 Jul 12. PubMed PMID: 27407110; PubMed Central PMCID: PMC5062983.

Zhang W, Flemington EK, Zhang K. Mutant TP53 disrupts age-related accumulation patterns of somatic mutations in multiple cancer types. Cancer Genet. 2016 Sep;209(9):376-380. doi: 10.1016/j.cancergen.2016.07.001. Epub 2016 Jul 9. PubMed PMID: 27751354; PubMed Central PMCID: PMC5466170.

Zhang J, Baddoo M, Han C, Strong MJ, Cvitanovic J, Moroz K, Dash S, Flemington EK, Wu T. Gene network analysis reveals a novel 22-gene signature of carbon metabolism in hepatocellular carcinoma. Oncotarget. 2016 Aug 2;7(31):49232-49245. doi: 10.18632/oncotarget.10249. PubMed PMID: 27363021; PubMed Central PMCID: PMC5226503.

Zhang W, Edwards A, Fan W, Flemington EK, Zhang K. The modularity and dynamicity of miRNA-mRNA interactions in high- grade serous ovarian carcinomas and the prognostic implication. Comput Biol Chem. 2016 Aug;63:3-14. doi: 10.1016/j.compbiolchem.2016.02.005. Epub 2016 Feb 27. PubMed PMID: 26949157; PubMed Central PMCID: PMC4976019.

Dai L, Bai L, Lin Z, Qiao J, Yang L, Flemington EK, Zabaleta J, Qin Z. Transcriptomic analysis of KSHV-infected primary oral fibroblasts: The role of interferon-induced genes in the latency of oncogenic virus. Oncotarget. 2016 Jul 26;7(30):47052-47060. doi: 10.18632/oncotarget.9720. PubMed PMID: 27363016; PubMed Central PMCID: PMC5216923.

Strong MJ, Blanchard E 4th, Lin Z, Morris CA, Baddoo M, Taylor CM, Ware ML, Flemington EK. A comprehensive next generation sequencing-based virome assessment in brain tissue suggests no major virus - tumor association. Acta Neuropathol Commun. 2016 Jul 11;4(1):71. doi: 10.1186/s40478-016-0338-z. PubMed PMID: 27402152; PubMed Central PMCID: PMC4940872.

Yin Q, Wang X, Roberts C, Flemington EK, Lasky JA. Methylation status and AP1 elements are involved in EBV-mediated miR-155 expression in EBV positive lymphoma cells. Virology. 2016 Jul;494:158-67. doi: 10.1016/j.virol.2016.04.005. Epub 2016 Apr 26. PubMed PMID: 27110708; PubMed Central PMCID: PMC4884481.

Zhou X, Hao Q, Liao P, Luo S, Zhang M, Hu G, Liu H, Zhang Y, Cao B, Baddoo M, Flemington EK, Zeng SX, Lu H. Nerve growth factor receptor negates the tumor suppressor p53 as a feedback regulator. Elife. 2016 Jun 10;5. pii: e15099. doi: 10.7554/eLife.15099. PubMed PMID: 27282385; PubMed Central PMCID: PMC4943851.

Liu YZ, Maney P, Puri J, Zhou Y, Baddoo M, Strong M, Wang YP, Flemington E, Deng HW. RNA-sequencing study of peripheral blood monocytes in chronic periodontitis. Gene. 2016 May 1;581(2):152- 60. doi: 10.1016/j.gene.2016.01.036. Epub 2016 Jan 23. PubMed PMID: 26812355; PubMed Central PMCID: PMC4767619.

Zhang W, Edwards A, Fang Z, Flemington EK, Zhang K. Integrative Genomics and Transcriptomics Analysis Reveals Potential Mechanisms for Favorable Prognosis of Patients with HPV-Positive Head and Neck Carcinomas. Sci Rep. 2016 Apr 25;6:24927. doi: 10.1038/srep24927. PubMed PMID: 27108969; PubMed Central PMCID: PMC4842993.

Liao JM, Cao B, Deng J, Zhou X, Strong M, Zeng S, Xiong J, Flemington E, Lu H. TFIIS.h, a new target of p53, regulates transcription efficiency of pro-apoptotic bax gene. Sci Rep. 2016 Mar 23;6:23542. doi: 10.1038/srep23542. PubMed PMID: 27005522; PubMed Central PMCID: PMC4804275.

Kim JH, Baddoo MC, Park EY, Stone JK, Park H, Butler TW, Huang G, Yan X, Pauli-Behn F, Myers RM, Tan M, Flemington EK, Lim ST, Ahn EY. SON and Its Alternatively Spliced Isoforms Control MLL Complex-Mediated H3K4me3 and Transcription of Leukemia- Associated Genes. Mol Cell. 2016 Mar 17;61(6):859-73. doi: 10.1016/j.molcel.2016.02.024. PubMed PMID: 26990989; PubMed Central PMCID: PMC4799497.

Liu YZ, Roy-Engel AM, Baddoo MC, Flemington EK, Wang G, Wang H. The impact of oil spill to lung health--Insights from an RNA- seq study of human airway epithelial cells. Gene. 2016 Mar 1;578(1):38-51. doi: 10.1016/j.gene.2015.12.016. Epub 2015 Dec 9. PubMed PMID: 26692141; PubMed Central PMCID: PMC5072127.

Lin Z, Swan K, Zhang X, Cao S, Brett Z, Drury S, Strong MJ, Fewell C, Puetter A, Wang X, Ferris M, Sullivan DE, Li L, Flemington EK. Secreted Oral Epithelial Cell Membrane Vesicles Induce Epstein- Barr Virus Reactivation in Latently Infected B Cells. J Virol. 2016 Jan 13;90(7):3469-79. doi: 10.1128/JVI.02830-15. PubMed PMID: 26764001; PubMed Central PMCID: PMC4794692.


Zhuang Y, Nguyen HT, Burow ME, Zhuo Y, El-Dahr SS, Yao X, Cao S, Flemington EK, Nephew KP, Fang F, Collins-Burow B, Rhodes LV, Yu Q, Jayawickramarajah J, Shan B. Elevated expression of long intergenic non-coding RNA HOTAIR in a basal-like variant of MCF-7 breast cancer cells. Mol Carcinog. 2015 Dec;54(12):1656- 67. doi: 10.1002/mc.22237. Epub 2014 Oct 18. PubMed PMID: 25328122; PubMed Central PMCID: PMC4402121.

Strong MJ, Laskow T, Nakhoul H, Blanchard E, Liu Y, Wang X, Baddoo M, Lin Z, Yin Q, Flemington EK. Latent Expression of the Epstein-Barr Virus (EBV)-Encoded Major Histocompatibility Complex Class I TAP Inhibitor, BNLF2a, in EBV-Positive Gastric Carcinomas. J Virol. 2015 Oct;89(19):10110-4. doi: 10.1128/JVI.01110-15. Epub 2015 Jul 15. PubMed PMID: 26178981; PubMed Central PMCID: PMC4577887.

Xu D, Zhan Y, Qi Y, Cao B, Bai S, Xu W, Gambhir SS, Lee P, Sartor O, Flemington EK, Zhang H, Hu CD, Dong Y. Androgen Receptor Splice Variants Dimerize to Transactivate Target Genes. Cancer Res. 2015 Sep 1;75(17):3663-71. doi: 10.1158/0008-5472.CAN-15-0381. Epub 2015 Jun 9. PubMed PMID: 26060018; PubMed Central PMCID: PMC4558376.

Cao S, Moss W, O'Grady T, Concha M, Strong MJ, Wang X, Yu Y, Baddoo M, Zhang K, Fewell C, Lin Z, Dong Y, Flemington EK. New Noncoding Lytic Transcripts Derived from the Epstein-Barr Virus Latency Origin of Replication, oriP, Are Hyperedited, Bind the Paraspeckle Protein, NONO/p54nrb, and Support Viral Lytic Transcription. J Virol. 2015 Jul;89(14):7120-32. doi: 10.1128/JVI.00608-15. Epub 2015 Apr 29. PubMed PMID: 25926645; PubMed Central PMCID: PMC4473578.

Strong AL, Shi Z, Strong MJ, Miller DF, Rusch DB, Buechlein AM, Flemington EK, McLachlan JA, Nephew KP, Burow ME, Bunnell BA. Effects of the endocrine-disrupting chemical DDT on self-renewal and differentiation of human mesenchymal stem cells. Environ Health Perspect. 2015 Jan;123(1):42-8. doi: 10.1289/ehp.1408188. Epub 2014 Jul 11. PubMed PMID: 25014179; PubMed Central PMCID: PMC4286277.

Cao S, Strong MJ, Wang X, Moss WN, Concha M, Lin Z, O'Grady T, Baddoo M, Fewell C, Renne R, Flemington EK. High-throughput RNA sequencing-based virome analysis of 50 lymphoma cell lines from the Cancer Cell Line Encyclopedia project. J Virol. 2015 Jan;89(1):713-29. doi: 10.1128/JVI.02570-14. Epub 2014 Oct 29. PubMed PMID: 25355872; PubMed Central PMCID: PMC4301145.


Strong MJ, Xu G, Morici L, Splinter Bon-Durant S, Baddoo M, Lin Z, Fewell C, Taylor CM, Flemington EK. Microbial contamination in next generation sequencing: implications for sequence-based analysis of clinical samples. PLoS Pathog. 2014 Nov 20;10(11):e1004437. doi: 10.1371/journal.ppat.1004437. eCollection 2014 Nov. PubMed PMID: 25412476; PubMed Central PMCID: PMC4239086.

Zhang W, Edwards A, Flemington E, Zhang K. Somatic mutations favorable to patient survival are predominant in ovarian carcinomas. PLoS One. 2014 Nov 12;9(11):e112561. doi: 10.1371/journal.pone.0112561. eCollection 2014. PubMed PMID: 25390899; PubMed Central PMCID: PMC4229214.

Strong MJ, Lin Z, Flemington EK. Expanding the conversation on high-throughput virome sequencing standards to include consideration of microbial contamination sources. MBio. 2014 Oct 28;5(6):e01989. doi: 10.1128/mBio.01989-14. PubMed PMID: 25352620; PubMed Central PMCID: PMC4217176.

Martin EC, Rhodes LV, Elliott S, Krebs AE, Nephew KP, Flemington EK, Collins-Burow BM, Burow ME. microRNA regulation of mammalian target of rapamycin expression and activity controls estrogen receptor function and RAD001 sensitivity. Mol Cancer. 2014 Oct 6;13:229. doi: 10.1186/1476-4598-13-229. PubMed PMID: 25283550; PubMed Central PMCID: PMC4203920.

Martin EC, Krebs AE, Burks HE, Elliott S, Baddoo M, Collins-Burow BM, Flemington EK, Burow ME. miR-155 induced transcriptome changes in the MCF-7 breast cancer cell line leads to enhanced mitogen activated protein kinase signaling. Genes Cancer. 2014 Sep;5(9-10):353-64. PubMed PMID: 25352952; PubMed Central PMCID: PMC4209600.

Xu G, Strong MJ, Lacey MR, Baribault C, Flemington EK, Taylor CM. RNA CoMPASS: a dual approach for pathogen and host transcriptome analysis of RNA-seq datasets. PLoS One. 2014 Feb 25;9(2):e89445. doi: 10.1371/journal.pone.0089445. eCollection 2014. PubMed PMID: 24586784; PubMed Central PMCID: PMC3934900.

O'Grady T, Cao S, Strong MJ, Concha M, Wang X, Splinter Bondurant S, Adams M, Baddoo M, Srivastav SK, Lin Z, Fewell C, Yin Q, Flemington EK. Global bidirectional transcription of the Epstein-Barr virus genome during reactivation. J Virol. 2014 Feb;88(3):1604-16. doi: 10.1128/JVI.02989-13. Epub 2013 Nov 20. PubMed PMID: 24257595; PubMed Central PMCID: PMC3911580.

Qin Z, Dai L, Trillo-Tinoco J, Senkal C, Wang W, Reske T, Bonstaff K, Del Valle L, Rodriguez P, Flemington E, Voelkel-Johnson C, Smith CD, Ogretmen B, Parsons C. Targeting sphingosine kinase induces apoptosis and tumor regression for KSHV-associated primary effusion lymphoma. Mol Cancer Ther. 2014 Jan;13(1):154- 64. doi: 10.1158/1535-7163.MCT-13-0466. Epub 2013 Oct 18. PubMed PMID: 24140934; PubMed Central PMCID: PMC3918494.

Martin EC, Elliott S, Rhodes LV, Antoon JW, Fewell C, Zhu Y, Driver JL, Jodari-Karimi M, Taylor CW, Flemington EK, Beckman BS, Collins-Burow BM, Burow ME. Preferential star strand biogenesis of pre-miR-24-2 targets PKC-alpha and suppresses cell survival in MCF-7 breast cancer cells. Mol Carcinog. 2014 Jan;53(1):38-48. doi: 10.1002/mc.21946. Epub 2012 Aug 21. PubMed PMID: 22911661; PubMed Central PMCID: PMC4030540.


Strong MJ, O'Grady T, Lin Z, Xu G, Baddoo M, Parsons C, Zhang K, Taylor CM, Flemington EK. Epstein-Barr virus and human herpesvirus 6 detection in a non-Hodgkin's diffuse large B-cell lymphoma cohort by using RNA sequencing. J Virol. 2013 Dec;87(23):13059-62. doi: 10.1128/JVI.02380-13. Epub 2013 Sep 18. Erratum in: J Virol. 2016 Jan 15;90(2):1152. PubMed PMID: 24049168; PubMed Central PMCID: PMC3838131.

Zhang W, Edwards A, Flemington EK, Zhang K. Inferring polymorphism-induced regulatory gene networks active in human lymphocyte cell lines by weighted linear mixed model analysis of multiple RNA-Seq datasets. PLoS One. 2013 Oct 30;8(10):e78868. doi: 10.1371/journal.pone.0078868. eCollection 2013. PubMed PMID: 24205334; PubMed Central PMCID: PMC3813575.

Onyeagucha BC, Mercado-Pimentel ME, Hutchison J, Flemington EK, Nelson MA. S100P/RAGE signaling regulates microRNA-155 expression via AP-1 activation in colon cancer. Exp Cell Res. 2013 Aug 1;319(13):2081-90. doi: 10.1016/j.yexcr.2013.05.009. Epub 2013 May 18. PubMed PMID: 23693020; PubMed Central PMCID: PMC3726211.

Sides MD, Sosulski ML, Luo F, Lin Z, Flemington EK, Lasky JA. Co-treatment with arsenic trioxide and ganciclovir reduces tumor volume in a murine xenograft model of nasopharyngeal carcinoma. Virol J. 2013 May 16;10:152. doi: 10.1186/1743-422X-10-152. PubMed PMID: 23680002; PubMed Central PMCID: PMC3666899.

Zhuang Y, Wang X, Nguyen HT, Zhuo Y, Cui X, Fewell C, Flemington EK, Shan B. Induction of long intergenic non-coding RNA HOTAIR in lung cancer cells by type I collagen. J Hematol Oncol. 2013 May 13;6:35. doi: 10.1186/1756-8722-6-35. PubMed PMID: 23668363; PubMed Central PMCID: PMC3655931.

Strong MJ, Xu G, Coco J, Baribault C, Vinay DS, Lacey MR, Strong AL, Lehman TA, Seddon MB, Lin Z, Concha M, Baddoo M, Ferris M, Swan KF, Sullivan DE, Burow ME, Taylor CM, Flemington EK. Differences in gastric carcinoma microenvironment stratify according to EBV infection intensity: implications for possible immune adjuvant therapy. PLoS Pathog. 2013;9(5):e1003341. doi: 10.1371/journal.ppat.1003341. Epub 2013 May 9. PubMed PMID: 23671415; PubMed Central PMCID: PMC3649992.

Marsolier J, Pineau S, Medjkane S, Perichon M, Yin Q, Flemington E, Weitzman MD, Weitzman JB. OncomiR addiction is generated by a miR-155 feedback loop in Theileria-transformed leukocytes. PLoS Pathog. 2013;9(4):e1003222. doi: 10.1371/journal.ppat.1003222. Epub 2013 Apr 18. PubMed PMID: 23637592; PubMed Central PMCID: PMC3630095.

Kutty RK, Nagineni CN, Samuel W, Vijayasarathy C, Jaworski C, Duncan T, Cameron JE, Flemington EK, Hooks JJ, Redmond TM. Differential regulation of microRNA-146a and microRNA-146b-5p in human retinal pigment epithelial cells by interleukin-1β, tumor necrosis factor-α, and interferon-γ. Mol Vis. 2013 Apr 3;19:737-50. Print 2013. PubMed PMID: 23592910; PubMed Central PMCID: PMC3626297.

Fang Z, Du R, Edwards A, Flemington EK, Zhang K. The sequence structures of human microRNA molecules and their implications. PLoS One. 2013;8(1):e54215. doi: 10.1371/journal.pone.0054215. Epub 2013 Jan 18. PubMed PMID: 23349828; PubMed Central PMCID: PMC3548844.

Lin Z, Wang X, Strong MJ, Concha M, Baddoo M, Xu G, Baribault C, Fewell C, Hulme W, Hedges D, Taylor CM, Flemington EK. Whole-genome sequencing of the Akata and Mutu Epstein-Barr virus strains. J Virol. 2013 Jan;87(2):1172-82. doi: 10.1128/JVI.02517-12. Epub 2012 Nov 14. PubMed PMID: 23152513; PubMed Central PMCID: PMC3554088.


Li C, Nguyen HT, Zhuang Y, Lin Z, Flemington EK, Zhuo Y, Kantrow SP, Morris GF, Sullivan DE, Shan B. Comparative profiling of miRNA expression of lung adenocarcinoma cells in two-dimensional and three-dimensional cultures. Gene. 2012 Dec 15;511(2):143-50. doi: 10.1016/j.gene.2012.09.093. Epub 2012 Oct 2. PubMed PMID: 23036707; PubMed Central PMCID: PMC3969815.

Nguyen HT, Li C, Lin Z, Zhuang Y, Flemington EK, Burow ME, Lin YI, Shan B. The microRNA expression associated with morphogenesis of breast cancer cells in three-dimensional organotypic culture. Oncol Rep. 2012 Jul;28(1):117-126. doi: 10.3892/or.2012.1764. Epub 2012 Apr 19. PubMed PMID: 22576799; PubMed Central PMCID: PMC3991116.

Zhang W, Edwards A, Fan W, Flemington EK, Zhang K. miRNA- mRNA correlation-network modules in human prostate cancer and the differences between primary and metastatic tumor subtypes. PLoS One. 2012;7(6):e40130. doi: 10.1371/journal.pone.0040130. Epub 2012 Jun 29. PubMed PMID: 22768240; PubMed Central PMCID: PMC3387006.

Lin Z, Puetter A, Coco J, Xu G, Strong MJ, Wang X, Fewell C, Baddoo M, Taylor C, Flemington EK. Detection of murine leukemia virus in the Epstein-Barr virus-positive human B-cell line JY, using a computational RNA-Seq-based exogenous agent detection pipeline, PARSES. J Virol. 2012 Mar;86(6):2970-7. doi: 10.1128/JVI.06717-11. Epub 2012 Jan 11. PubMed PMID: 22238296; PubMed Central PMCID: PMC3302299.

Zhang W, Edwards A, Zhu D, Flemington EK, Deininger P, Zhang K. miRNA-mediated relationships between Cis-SNP genotypes and transcript intensities in lymphocyte cell lines. PLoS One. 2012;7(2):e31429. doi: 10.1371/journal.pone.0031429. Epub 2012 Feb 14. PubMed PMID: 22348086; PubMed Central PMCID: PMC3279374.


Concha M, Wang X, Cao S, Baddoo M, Fewell C, Lin Z, Hulme W, Hedges D, McBride J, Flemington EK. Identification of new viral genes and transcript isoforms during Epstein-Barr virus reactivation using RNA-Seq. J Virol. 2012 Feb;86(3):1458-67. doi: 10.1128/JVI.06537-11. Epub 2011 Nov 16. PubMed PMID: 22090128; PubMed Central PMCID: PMC3264377.

Sides MD, Block GJ, Chadwick RW, Shan B, Flemington EK, Lasky JA. Epstein - Barr virus Latent Membrane Protein 1 suppresses reporter activity through modulation of promyelocytic leukemia protein-nuclear bodies. Virol J. 2011 Oct 5;8:461. doi: 10.1186/1743-422X-8-461. PubMed PMID: 21975125; PubMed Central PMCID: PMC3204298.

Lin Z, Flemington EK. miRNAs in the pathogenesis of oncogenic human viruses. Cancer Lett. 2011 Jun 28;305(2):186-99. doi: 10.1016/j.canlet.2010.08.018. Epub 2010 Oct 12. Review. PubMed PMID: 20943311; PubMed Central PMCID: PMC3023823.

Sides MD, Klingsberg RC, Shan B, Gordon KA, Nguyen HT, Lin Z, Takahashi T, Flemington EK, Lasky JA. The Epstein-Barr virus latent membrane protein 1 and transforming growth factor--β1 synergistically induce epithelial--mesenchymal transition in lung epithelial cells. Am J Respir Cell Mol Biol. 2011 Jun;44(6):852-62. doi: 10.1165/rcmb.2009-0232OC. Epub 2010 Aug 6. PubMed PMID: 20693406; PubMed Central PMCID: PMC3135845.

Deng N, Puetter A, Zhang K, Johnson K, Zhao Z, Taylor C, Flemington EK, Zhu D. Isoform-level microRNA-155 target prediction using RNA-seq. Nucleic Acids Res. 2011 May;39(9):e61. doi: 10.1093/nar/gkr042. Epub 2011 Feb 11. PubMed PMID: 21317189; PubMed Central PMCID: PMC3089486.


Guenther JF, Cameron JE, Nguyen HT, Wang Y, Sullivan DE, Shan B, Lasky JA, Flemington EK, Morris GF. Modulation of lung inflammation by the Epstein-Barr virus protein Zta. Am J Physiol Lung Cell Mol Physiol. 2010 Dec;299(6):L771-84. doi: 10.1152/ajplung.00408.2009. Epub 2010 Sep 3. PubMed PMID: 20817778; PubMed Central PMCID: PMC3006272.

Lin Z, Xu G, Deng N, Taylor C, Zhu D, Flemington EK. Quantitative and qualitative RNA-Seq-based evaluation of Epstein-Barr virus transcription in type I latency Burkitt's lymphoma cells. J Virol. 2010 Dec;84(24):13053-8. doi: 10.1128/JVI.01521-10. Epub 2010 Oct 13. PubMed PMID: 20943983; PubMed Central PMCID: PMC3004295.

Lin Z, Wang X, Fewell C, Cameron J, Yin Q, Flemington EK. Differential expression of the miR-200 family microRNAs in epithelial and B cells and regulation of Epstein-Barr virus reactivation by the miR-200 family member miR-429. J Virol. 2010 Aug;84(15):7892-7. doi: 10.1128/JVI.00379-10. Epub 2010 May 19. PubMed PMID: 20484493; PubMed Central PMCID: PMC2897641.

Xu G, Fewell C, Taylor C, Deng N, Hedges D, Wang X, Zhang K, Lacey M, Zhang H, Yin Q, Cameron J, Lin Z, Zhu D, Flemington EK. Transcriptome and targetome analysis in MIR155 expressing cells using RNA-seq. RNA. 2010 Aug;16(8):1610-22. doi: 10.1261/rna.2194910. Epub 2010 Jun 28. PubMed PMID: 20584899; PubMed Central PMCID: PMC2905759.

Yin Q, Wang X, Fewell C, Cameron J, Zhu H, Baddoo M, Lin Z, Flemington EK. MicroRNA miR-155 inhibits bone morphogenetic protein (BMP) signaling and BMP-mediated Epstein-Barr virus reactivation. J Virol. 2010 Jul;84(13):6318-27. doi: 10.1128/JVI.00635-10. Epub 2010 Apr 28. PubMed PMID: 20427544; PubMed Central PMCID: PMC2903268.


Molina-Privado I, Rodríguez-Martínez M, Rebollo P, Martín-Pérez D, Artiga MJ, Menárguez J, Flemington EK, Piris MA, Campanero MR. E2F1 expression is deregulated and plays an oncogenic role in sporadic Burkitt's lymphoma. Cancer Res. 2009 May 1;69(9):4052- 8. doi: 10.1158/0008-5472.CAN-08-4617. PubMed PMID: 19406837; PubMed Central PMCID: PMC2704059.


Cameron JE, Fewell C, Yin Q, McBride J, Wang X, Lin Z, Flemington EK. Epstein-Barr virus growth/latency I program alters cellular microRNA expression. Virology. 2008 Dec 20;382(2):257- 66. doi: 10.1016/j.virol.2008.09.018. Epub 2008 Oct 31. PubMed PMID: 18950829; PubMed Central PMCID: PMC2640950.

Yin Q, McBride J, Fewell C, Lacey M, Wang X, Lin Z, Cameron J, Flemington EK. MicroRNA-155 is an Epstein-Barr virus-induced gene that modulates Epstein-Barr virus-regulated gene expression pathways. J Virol. 2008 Jun;82(11):5295-306. doi: 10.1128/JVI.02380-07. Epub 2008 Mar 26. PubMed PMID: 18367535; PubMed Central PMCID: PMC2395216.

Cameron JE, Yin Q, Fewell C, Lacey M, McBride J, Wang X, Lin Z, Schaefer BC, Flemington EK. Epstein-Barr virus latent membrane protein 1 induces cellular MicroRNA miR-146a, a modulator of lymphocyte signaling pathways. J Virol. 2008 Feb;82(4):1946-58. Epub 2007 Dec 5. PubMed PMID: 18057241; PubMed Central PMCID: PMC2258704.

Yin Q, Wang X, McBride J, Fewell C, Flemington E. B-cell receptor activation induces BIC/miR-155 expression through a conserved AP-1 element. J Biol Chem. 2008 Feb 1;283(5):2654-62. Epub 2007 Nov 28. PubMed PMID: 18048365; PubMed Central PMCID: PMC2810639.