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Items: 48

1.

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 Aug 13. doi: 10.1038/s41388-019-0947-7. [Epub ahead of print]

PMID:
31409897
2.

RNA Next-Generation Sequencing and a Bioinformatics Pipeline to Identify Expressed LINE-1s at the Locus-Specific Level.

Kaul T, Morales ME, Smither E, Baddoo M, Belancio VP, Deininger P.

J Vis Exp. 2019 May 19;(147). doi: 10.3791/59771.

PMID:
31157783
3.

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.

4.

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]

PMID:
31063017
5.

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.

6.

Screen technical noise in single cell RNA sequencing data.

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

Genomics. 2019 Feb 22. pii: S0888-7543(18)30580-9. doi: 10.1016/j.ygeno.2019.02.014. [Epub ahead of print]

PMID:
30802598
7.

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.

8.

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.

9.

Comparative analysis of miRNA profile in human dendritic cells infected with respiratory syncytial virus and human metapneumovirus.

Baños-Lara MDR, Zabaleta J, Garai J, Baddoo M, Guerrero-Plata A.

BMC Res Notes. 2018 Jul 3;11(1):432. doi: 10.1186/s13104-018-3541-0.

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.

11.

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.

12.

Ancestry as a potential modifier of gene expression in breast tumors from Colombian women.

Serrano-Gómez SJ, Sanabria-Salas MC, Garay J, Baddoo MC, Hernández-Suarez G, Mejía JC, García O, Miele L, Fejerman L, Zabaleta J.

PLoS One. 2017 Aug 23;12(8):e0183179. doi: 10.1371/journal.pone.0183179. eCollection 2017.

13.

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.

14.

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.

15.

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.

16.

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.

17.

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.

18.

Analysis of EBV Transcription Using High-Throughput RNA Sequencing.

O'Grady T, Baddoo M, Flemington EK.

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

19.

Aging is associated with impaired angiogenesis, but normal microvascular network structure, in the rat mesentery.

Sweat RS, Sloas DC, Stewart SA, Czarny-Ratajczak M, Baddoo M, Eastwood JR, Suarez-Martinez AD, Azimi MS, Burks HE, Chedister LO, Myers L, Murfee WL.

Am J Physiol Heart Circ Physiol. 2017 Feb 1;312(2):H275-H284. doi: 10.1152/ajpheart.00200.2016. Epub 2016 Nov 18.

20.

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.

21.

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.

22.

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.

23.

TAF4b Regulates Oocyte-Specific Genes Essential for Meiosis.

Grive KJ, Gustafson EA, Seymour KA, Baddoo M, Schorl C, Golnoski K, Rajkovic A, Brodsky AS, Freiman RN.

PLoS Genet. 2016 Jun 24;12(6):e1006128. doi: 10.1371/journal.pgen.1006128. eCollection 2016 Jun.

24.

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.

25.

The endonuclease domain of the LINE-1 ORF2 protein can tolerate multiple mutations.

Kines KJ, Sokolowski M, deHaro DL, Christian CM, Baddoo M, Smither ME, Belancio VP.

Mob DNA. 2016 Apr 19;7:8. doi: 10.1186/s13100-016-0064-x. eCollection 2016.

26.

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.

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.

28.

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.

29.

The impact of oil spill to lung health--Insights from an RNA-seq study of human airway epithelial cells.

Liu YZ, Roy-Engel AM, Baddoo MC, Flemington EK, Wang G, Wang H.

Gene. 2016 Mar 1;578(1):38-51. doi: 10.1016/j.gene.2015.12.016. Epub 2015 Dec 9.

30.

Latent Expression of the Epstein-Barr Virus (EBV)-Encoded Major Histocompatibility Complex Class I TAP Inhibitor, BNLF2a, in EBV-Positive Gastric Carcinomas.

Strong MJ, Laskow T, Nakhoul H, Blanchard E, Liu Y, Wang X, Baddoo M, Lin Z, Yin Q, Flemington EK.

J Virol. 2015 Oct;89(19):10110-4. doi: 10.1128/JVI.01110-15. Epub 2015 Jul 15.

31.

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.

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.

J Virol. 2015 Jul;89(14):7120-32. doi: 10.1128/JVI.00608-15. Epub 2015 Apr 29.

32.

p53 Enables metabolic fitness and self-renewal of nephron progenitor cells.

Li Y, Liu J, Li W, Brown A, Baddoo M, Li M, Carroll T, Oxburgh L, Feng Y, Saifudeen Z.

Development. 2015 Apr 1;142(7):1228-41. doi: 10.1242/dev.111617.

33.

Microbial contamination in next generation sequencing: implications for sequence-based analysis of clinical samples.

Strong MJ, Xu G, Morici L, Splinter Bon-Durant S, Baddoo M, Lin Z, Fewell C, Taylor CM, Flemington EK.

PLoS Pathog. 2014 Nov 20;10(11):e1004437. doi: 10.1371/journal.ppat.1004437. eCollection 2014 Nov.

34.

High-throughput RNA sequencing-based virome analysis of 50 lymphoma cell lines from the Cancer Cell Line Encyclopedia project.

Cao S, Strong MJ, Wang X, Moss WN, Concha M, Lin Z, O'Grady T, Baddoo M, Fewell C, Renne R, Flemington EK.

J Virol. 2015 Jan;89(1):713-29. doi: 10.1128/JVI.02570-14. Epub 2014 Oct 29.

35.

miR-155 induced transcriptome changes in the MCF-7 breast cancer cell line leads to enhanced mitogen activated protein kinase signaling.

Martin EC, Krebs AE, Burks HE, Elliott S, Baddoo M, Collins-Burow BM, Flemington EK, Burow ME.

Genes Cancer. 2014 Sep;5(9-10):353-64.

36.

Comprehensive high-throughput RNA sequencing analysis reveals contamination of multiple nasopharyngeal carcinoma cell lines with HeLa cell genomes.

Strong MJ, Baddoo M, Nanbo A, Xu M, Puetter A, Lin Z.

J Virol. 2014 Sep;88(18):10696-704. doi: 10.1128/JVI.01457-14. Epub 2014 Jul 2.

37.

The placental specific gene, PLAC1, is induced by the Epstein-Barr virus and is expressed in human tumor cells.

Wang X, Baddoo MC, Yin Q.

Virol J. 2014 Jun 9;11:107. doi: 10.1186/1743-422X-11-107.

38.

Global bidirectional transcription of the Epstein-Barr virus genome during reactivation.

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.

J Virol. 2014 Feb;88(3):1604-16. doi: 10.1128/JVI.02989-13. Epub 2013 Nov 20.

39.

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. 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.

40.

Differences in gastric carcinoma microenvironment stratify according to EBV infection intensity: implications for possible immune adjuvant therapy.

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.

PLoS Pathog. 2013;9(5):e1003341. doi: 10.1371/journal.ppat.1003341. Epub 2013 May 9.

41.

Whole-genome sequencing of the Akata and Mutu Epstein-Barr virus strains.

Lin Z, Wang X, Strong MJ, Concha M, Baddoo M, Xu G, Baribault C, Fewell C, Hulme W, Hedges D, Taylor CM, Flemington EK.

J Virol. 2013 Jan;87(2):1172-82. doi: 10.1128/JVI.02517-12. Epub 2012 Nov 14.

42.

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.

Lin Z, Puetter A, Coco J, Xu G, Strong MJ, Wang X, Fewell C, Baddoo M, Taylor C, Flemington EK.

J Virol. 2012 Mar;86(6):2970-7. doi: 10.1128/JVI.06717-11. Epub 2012 Jan 11.

43.

Identification of new viral genes and transcript isoforms during Epstein-Barr virus reactivation using RNA-Seq.

Concha M, Wang X, Cao S, Baddoo M, Fewell C, Lin Z, Hulme W, Hedges D, McBride J, Flemington EK.

J Virol. 2012 Feb;86(3):1458-67. doi: 10.1128/JVI.06537-11. Epub 2011 Nov 16.

44.

MicroRNA miR-155 inhibits bone morphogenetic protein (BMP) signaling and BMP-mediated Epstein-Barr virus reactivation.

Yin Q, Wang X, Fewell C, Cameron J, Zhu H, Baddoo M, Lin Z, Flemington EK.

J Virol. 2010 Jul;84(13):6318-27. doi: 10.1128/JVI.00635-10. Epub 2010 Apr 28.

46.

Biological activities encoded by the murine mesenchymal stem cell transcriptome provide a basis for their developmental potential and broad therapeutic efficacy.

Phinney DG, Hill K, Michelson C, DuTreil M, Hughes C, Humphries S, Wilkinson R, Baddoo M, Bayly E.

Stem Cells. 2006 Jan;24(1):186-98. Epub 2005 Aug 11.

47.

Characterization of mesenchymal stem cells isolated from murine bone marrow by negative selection.

Baddoo M, Hill K, Wilkinson R, Gaupp D, Hughes C, Kopen GC, Phinney DG.

J Cell Biochem. 2003 Aug 15;89(6):1235-49.

PMID:
12898521
48.

Mesenchymal stem cell engraftment in lung is enhanced in response to bleomycin exposure and ameliorates its fibrotic effects.

Ortiz LA, Gambelli F, McBride C, Gaupp D, Baddoo M, Kaminski N, Phinney DG.

Proc Natl Acad Sci U S A. 2003 Jul 8;100(14):8407-11. Epub 2003 Jun 18.

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