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Items: 1 to 50 of 139


Circular RNAs add diversity to androgen receptor isoform repertoire in castration-resistant prostate cancer.

Cao S, Ma T, Ungerleider N, Roberts C, Kobelski M, Jin L, Concha M, Wang X, Baddoo M, Nguyen HM, Corey E, Fazli L, Ledet E, Zhang R, Silberstein JL, Zhang W, Zhang K, Sartor O, Dong X, Flemington EK, Dong Y.

Oncogene. 2019 Nov;38(45):7060-7072. doi: 10.1038/s41388-019-0947-7. Epub 2019 Aug 13.


High-Throughput Sequence Analysis of Peripheral T-Cell Lymphomas Indicates Subtype-Specific Viral Gene Expression Patterns and Immune Cell Microenvironments.

Nakhoul H, Lin Z, Wang X, Roberts C, Dong Y, Flemington E.

mSphere. 2019 Jul 10;4(4). pii: e00248-19. doi: 10.1128/mSphere.00248-19.


Genome-wide Transcript Structure Resolution Reveals Abundant Alternate Isoform Usage from Murine Gammaherpesvirus 68.

O'Grady T, Feswick A, Hoffman BA, Wang Y, Medina EM, Kara M, van Dyk LF, Flemington EK, Tibbetts SA.

Cell Rep. 2019 Jun 25;27(13):3988-4002.e5. doi: 10.1016/j.celrep.2019.05.086.


Detection of Epstein-Barr Virus Infection in Non-Small Cell Lung Cancer.

Kheir F, Zhao M, Strong MJ, Yu Y, Nanbo A, Flemington EK, Morris GF, Reiss K, Li L, Lin Z.

Cancers (Basel). 2019 May 31;11(6). pii: E759. doi: 10.3390/cancers11060759.


SpliceV: analysis and publication quality printing of linear and circular RNA splicing, expression and regulation.

Ungerleider N, Flemington E.

BMC Bioinformatics. 2019 May 8;20(1):231. doi: 10.1186/s12859-019-2865-7.


Defining the dynamic chromatin landscape of mouse nephron progenitors.

Hilliard S, Song R, Liu H, Chen CH, Li Y, Baddoo M, Flemington E, Wanek A, Kolls J, Saifudeen Z, El-Dahr SS.

Biol Open. 2019 May 20;8(5). pii: bio042754. doi: 10.1242/bio.042754.


Bacterial TLR4 and NOD2 signaling linked to reduced mitochondrial energy function in active inflammatory bowel disease.

Ruiz E, Penrose HM, Heller S, Nakhoul H, Baddoo M, Flemington EF, Kandil E, Savkovic SD.

Gut Microbes. 2019 May 7:1-14. doi: 10.1080/19490976.2019.1611152. [Epub ahead of print]


Gammaherpesvirus RNAs Come Full Circle.

Ungerleider NA, Tibbetts SA, Renne R, Flemington EK.

mBio. 2019 Apr 2;10(2). pii: e00071-19. doi: 10.1128/mBio.00071-19. Review.


A positive role of c-Myc in regulating androgen receptor and its splice variants in prostate cancer.

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.

Oncogene. 2019 Jun;38(25):4977-4989. doi: 10.1038/s41388-019-0768-8. Epub 2019 Feb 28.


Screen technical noise in single cell RNA sequencing data.

Bai YL, Baddoo M, Flemington EK, Nakhoul HN, Liu YZ.

Genomics. 2020 Jan;112(1):346-355. doi: 10.1016/j.ygeno.2019.02.014. Epub 2019 Feb 22.


Loss of Forkhead Box O3 Facilitates Inflammatory Colon Cancer: Transcriptome Profiling of the Immune Landscape and Novel Targets.

Penrose HM, Cable C, Heller S, Ungerleider N, Nakhoul H, Baddoo M, Hartono AB, Lee SB, Burow ME, Flemington EF, Crawford SE, Savkovic SD.

Cell Mol Gastroenterol Hepatol. 2019;7(2):391-408. doi: 10.1016/j.jcmgh.2018.10.003. Epub 2018 Oct 13.


Gammaherpesvirus Readthrough Transcription Generates a Long Non-Coding RNA That Is Regulated by Antisense miRNAs and Correlates with Enhanced Lytic Replication In Vivo.

Kara M, O'Grady T, Feldman ER, Feswick A, Wang Y, Flemington EK, Tibbetts SA.

Noncoding RNA. 2019 Jan 10;5(1). pii: E6. doi: 10.3390/ncrna5010006.


Comparative Analysis of Gammaherpesvirus Circular RNA Repertoires: Conserved and Unique Viral Circular RNAs.

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.

J Virol. 2019 Mar 5;93(6). pii: e01952-18. doi: 10.1128/JVI.01952-18. Print 2019 Mar 15.


Connivance, Complicity, or Collusion? The Role of Noncoding RNAs in Promoting Gammaherpesvirus Tumorigenesis.

Bullard WL, Flemington EK, Renne R, Tibbetts SA.

Trends Cancer. 2018 Nov;4(11):729-740. doi: 10.1016/j.trecan.2018.09.005. Epub 2018 Oct 10. Review.


Epigenetically Silenced Candidate Tumor Suppressor Genes in Prostate Cancer: Identified by Modeling Methylation Stratification and Applied to Progression Prediction.

Zhang W, Flemington EK, Deng HW, Zhang K.

Cancer Epidemiol Biomarkers Prev. 2019 Jan;28(1):198-207. doi: 10.1158/1055-9965.EPI-18-0491. Epub 2018 Sep 27.


The Epstein Barr virus circRNAome.

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.

PLoS Pathog. 2018 Aug 6;14(8):e1007206. doi: 10.1371/journal.ppat.1007206. eCollection 2018 Aug.


Driver gene mutations based clustering of tumors: methods and applications.

Zhang W, Flemington EK, Zhang K.

Bioinformatics. 2018 Jul 1;34(13):i404-i411. doi: 10.1093/bioinformatics/bty232.


Transactivation of human endogenous retrovirus K (HERV-K) by KSHV promotes Kaposi's sarcoma development.

Dai L, Del Valle L, Miley W, Whitby D, Ochoa AC, Flemington EK, Qin Z.

Oncogene. 2018 Aug;37(33):4534-4545. doi: 10.1038/s41388-018-0282-4. Epub 2018 May 10.


In colonic ρ0 (rho0) cells reduced mitochondrial function mediates transcriptomic alterations associated with cancer.

Penrose HM, Heller S, Cable C, Nakhoul H, Ungerleider N, Baddoo M, Pursell ZF, Flemington EK, Crawford SE, Savkovic SD.

Oncoscience. 2017 Dec 27;4(11-12):189-198. doi: 10.18632/oncoscience.386. eCollection 2017 Nov.


Maintenance of AP-2-Dependent Functional Activities of Nef Restricts Pathways of Immune Escape from CD8 T Lymphocyte Responses.

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.

J Virol. 2018 Feb 12;92(5). pii: e01822-17. doi: 10.1128/JVI.01822-17. Print 2018 Mar 1.


Racial disparities in patient survival and tumor mutation burden, and the association between tumor mutation burden and cancer incidence rate.

Zhang W, Edwards A, Flemington EK, Zhang K.

Sci Rep. 2017 Oct 20;7(1):13639. doi: 10.1038/s41598-017-13091-y.


Lipids, lipid metabolism and Kaposi's sarcoma-associated herpesvirus pathogenesis.

Dai L, Lin Z, Jiang W, Flemington EK, Qin Z.

Virol Sin. 2017 Oct;32(5):369-375. doi: 10.1007/s12250-017-4027-2. Epub 2017 Oct 10. Review.


MALT1 Inhibition Is Efficacious in Both Naïve and Ibrutinib-Resistant Chronic Lymphocytic Leukemia.

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.

Cancer Res. 2017 Dec 15;77(24):7038-7048. doi: 10.1158/0008-5472.CAN-17-2485. Epub 2017 Oct 9.


Induction of a novel isoform of the lncRNA HOTAIR in Claudin-low breast cancer cells attached to extracellular matrix.

Li M, Li X, Zhuang Y, Flemington EK, Lin Z, Shan B.

Mol Oncol. 2017 Dec;11(12):1698-1710. doi: 10.1002/1878-0261.12133. Epub 2017 Oct 30.


Exposure of Mycobacterium marinum to low-shear modeled microgravity: effect on growth, the transcriptome and survival under stress.

Abshire CF, Prasai K, Soto I, Shi R, Concha M, Baddoo M, Flemington EK, Ennis DG, Scott RS, Harrison L.

NPJ Microgravity. 2016 Dec 1;2:16038. doi: 10.1038/npjmgrav.2016.38. eCollection 2016.


Arsenic trioxide inhibits EBV reactivation and promotes cell death in EBV-positive lymphoma cells.

Yin Q, Sides M, Parsons CH, Flemington EK, Lasky JA.

Virol J. 2017 Jun 21;14(1):121. doi: 10.1186/s12985-017-0784-7.


A computational framework for distinguishing direct versus indirect interactions in human functional protein-protein interaction networks.

Mei S, Flemington EK, Zhang K.

Integr Biol (Camb). 2017 Jul 17;9(7):595-606. doi: 10.1039/c7ib00013h.


Significant Prognostic Features and Patterns of Somatic TP53 Mutations in Human Cancers.

Zhang W, Edwards A, Flemington EK, Zhang K.

Cancer Inform. 2017 Feb 20;16:1176935117691267. doi: 10.1177/1176935117691267. eCollection 2017.


Ribonucleotide reductase represents a novel therapeutic target in primary effusion lymphoma.

Dai L, Lin Z, Qiao J, Chen Y, Flemington EK, Qin Z.

Oncogene. 2017 Aug 31;36(35):5068-5074. doi: 10.1038/onc.2017.122. Epub 2017 May 1.


High-fat diet induced leptin and Wnt expression: RNA-sequencing and pathway analysis of mouse colonic tissue and tumors.

Penrose HM, Heller S, Cable C, Nakhoul H, Baddoo M, Flemington E, Crawford SE, Savkovic SD.

Carcinogenesis. 2017 Mar 1;38(3):302-311. doi: 10.1093/carcin/bgx001.


Interaction of Epstein-Barr virus genes with human gastric carcinoma transcriptome.

Zhang R, Strong MJ, Baddoo M, Lin Z, Wang YP, Flemington EK, Liu YZ.

Oncotarget. 2017 Jun 13;8(24):38399-38412. doi: 10.18632/oncotarget.16417.


Reduced mitochondrial activity in colonocytes facilitates AMPKα2-dependent inflammation.

Heller S, Penrose HM, Cable C, Biswas D, Nakhoul H, Baddoo M, Flemington E, Crawford SE, Savkovic SD.

FASEB J. 2017 May;31(5):2013-2025. doi: 10.1096/fj.201600976R. Epub 2017 Feb 9.


A comprehensive approach to expression of L1 loci.

Deininger P, Morales ME, White TB, Baddoo M, Hedges DJ, Servant G, Srivastav S, Smither ME, Concha M, DeHaro DL, Flemington EK, Belancio VP.

Nucleic Acids Res. 2017 Mar 17;45(5):e31. doi: 10.1093/nar/gkw1067.


Analysis of EBV Transcription Using High-Throughput RNA Sequencing.

O'Grady T, Baddoo M, Flemington EK.

Methods Mol Biol. 2017;1532:105-121.


Mutant TP53 disrupts age-related accumulation patterns of somatic mutations in multiple cancer types.

Zhang W, Flemington EK, Zhang K.

Cancer Genet. 2016 Sep;209(9):376-380. doi: 10.1016/j.cancergen.2016.07.001. Epub 2016 Jul 9.


Interplay between Cytoplasmic and Nuclear Androgen Receptor Splice Variants Mediates Castration Resistance.

Zhan Y, Zhang G, Wang X, Qi Y, Bai S, Li D, Ma T, Sartor O, Flemington EK, Zhang H, Lee P, Dong Y.

Mol Cancer Res. 2017 Jan;15(1):59-68. doi: 10.1158/1541-7786.MCR-16-0236. Epub 2016 Sep 26.


Global transcript structure resolution of high gene density genomes through multi-platform data integration.

O'Grady T, Wang X, Höner Zu Bentrup K, Baddoo M, Concha M, Flemington EK.

Nucleic Acids Res. 2016 Oct 14;44(18):e145. Epub 2016 Jul 12.


A comprehensive next generation sequencing-based virome assessment in brain tissue suggests no major virus - tumor association.

Strong MJ, Blanchard E 4th, Lin Z, Morris CA, Baddoo M, Taylor CM, Ware ML, Flemington EK.

Acta Neuropathol Commun. 2016 Jul 11;4(1):71. doi: 10.1186/s40478-016-0338-z.


Gene network analysis reveals a novel 22-gene signature of carbon metabolism in hepatocellular carcinoma.

Zhang J, Baddoo M, Han C, Strong MJ, Cvitanovic J, Moroz K, Dash S, Flemington EK, Wu T.

Oncotarget. 2016 Aug 2;7(31):49232-49245. doi: 10.18632/oncotarget.10249.


Transcriptomic analysis of KSHV-infected primary oral fibroblasts: The role of interferon-induced genes in the latency of oncogenic virus.

Dai L, Bai L, Lin Z, Qiao J, Yang L, Flemington EK, Zabaleta J, Qin Z.

Oncotarget. 2016 Jul 26;7(30):47052-47060. doi: 10.18632/oncotarget.9720.


Nerve growth factor receptor negates the tumor suppressor p53 as a feedback regulator.

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.

Elife. 2016 Jun 10;5. pii: e15099. doi: 10.7554/eLife.15099.


Methylation status and AP1 elements are involved in EBV-mediated miR-155 expression in EBV positive lymphoma cells.

Yin Q, Wang X, Roberts C, Flemington EK, Lasky JA.

Virology. 2016 Jul;494:158-67. doi: 10.1016/j.virol.2016.04.005. Epub 2016 Apr 26.


TFIIS.h, a new target of p53, regulates transcription efficiency of pro-apoptotic bax gene.

Liao JM, Cao B, Deng J, Zhou X, Strong M, Zeng S, Xiong J, Flemington E, Lu H.

Sci Rep. 2016 Mar 23;6:23542. doi: 10.1038/srep23542.


SON and Its Alternatively Spliced Isoforms Control MLL Complex-Mediated H3K4me3 and Transcription of Leukemia-Associated Genes.

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.

Mol Cell. 2016 Mar 17;61(6):859-73. doi: 10.1016/j.molcel.2016.02.024.


The modularity and dynamicity of miRNA-mRNA interactions in high-grade serous ovarian carcinomas and the prognostic implication.

Zhang W, Edwards A, Fan W, Flemington EK, Zhang K.

Comput Biol Chem. 2016 Aug;63:3-14. doi: 10.1016/j.compbiolchem.2016.02.005. Epub 2016 Feb 27.


RNA-sequencing study of peripheral blood monocytes in chronic periodontitis.

Liu YZ, Maney P, Puri J, Zhou Y, Baddoo M, Strong M, Wang YP, Flemington E, Deng HW.

Gene. 2016 May 1;581(2):152-60. doi: 10.1016/j.gene.2016.01.036. Epub 2016 Jan 23.


Secreted Oral Epithelial Cell Membrane Vesicles Induce Epstein-Barr Virus Reactivation in Latently Infected B Cells.

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.

J Virol. 2016 Jan 13;90(7):3469-79. doi: 10.1128/JVI.02830-15.


Correction for Strong et al., Epstein-Barr Virus and Human Herpesvirus 6 Detection in a Non-Hodgkin's Diffuse Large B-Cell Lymphoma Cohort by Using RNA Sequencing.

Strong MJ, O'Grady T, Lin Z, Xu G, Baddoo M, Parsons C, Zhang K, Taylor CM, Flemington EK.

J Virol. 2015 Dec 30;90(2):1152. doi: 10.1128/JVI.02772-15. Print 2016 Jan 15. No abstract available.

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