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Items: 1 to 50 of 165

1.

Ras Post-transcriptionally Enhances a Pre-malignantly Primed EMT to Promote Invasion.

Bisogno LS, Friedersdorf MB, Keene JD.

iScience. 2018 Jun 29;4:97-108. doi: 10.1016/j.isci.2018.05.011. Epub 2018 May 18.

2.

RNA Binding Proteins Control Transdifferentiation of Hepatic Stellate Cells into Myofibroblasts.

Wang S, Jung Y, Hyun J, Friedersdorf M, Oh SH, Kim J, Premont RT, Keene JD, Diehl AM.

Cell Physiol Biochem. 2018;48(3):1215-1229. doi: 10.1159/000491987. Epub 2018 Jul 25.

3.

RNA regulons in cancer and inflammation.

Bisogno LS, Keene JD.

Curr Opin Genet Dev. 2018 Feb;48:97-103. doi: 10.1016/j.gde.2017.11.004. Epub 2017 Nov 22. Review.

PMID:
29175729
4.

Analysis of post-transcriptional regulation during cancer progression using a donor-derived isogenic model of tumorigenesis.

Bisogno LS, Keene JD.

Methods. 2017 Aug 15;126:193-200. doi: 10.1016/j.ymeth.2017.05.012. Epub 2017 May 19.

PMID:
28529064
5.

DO-RIP-seq to quantify RNA binding sites transcriptome-wide.

Nicholson CO, Friedersdorf MB, Bisogno LS, Keene JD.

Methods. 2017 Apr 15;118-119:16-23. doi: 10.1016/j.ymeth.2016.11.004. Epub 2016 Nov 10.

6.

Quantifying RNA binding sites transcriptome-wide using DO-RIP-seq.

Nicholson CO, Friedersdorf M, Keene JD.

RNA. 2017 Jan;23(1):32-46. Epub 2016 Oct 14.

7.

Biomarkers Predictive of Exacerbations in the SPIROMICS and COPDGene Cohorts.

Keene JD, Jacobson S, Kechris K, Kinney GL, Foreman MG, Doerschuk CM, Make BJ, Curtis JL, Rennard SI, Barr RG, Bleecker ER, Kanner RE, Kleerup EC, Hansel NN, Woodruff PG, Han MK, Paine R 3rd, Martinez FJ, Bowler RP, O'Neal WK; COPDGene and SPIROMICS Investigators ‡.

Am J Respir Crit Care Med. 2017 Feb 15;195(4):473-481. doi: 10.1164/rccm.201607-1330OC.

8.

SHAPE reveals transcript-wide interactions, complex structural domains, and protein interactions across the Xist lncRNA in living cells.

Smola MJ, Christy TW, Inoue K, Nicholson CO, Friedersdorf M, Keene JD, Lee DM, Calabrese JM, Weeks KM.

Proc Natl Acad Sci U S A. 2016 Sep 13;113(37):10322-7. doi: 10.1073/pnas.1600008113. Epub 2016 Aug 30.

9.

Quantum Yield Heterogeneity among Single Nonblinking Quantum Dots Revealed by Atomic Structure-Quantum Optics Correlation.

Orfield NJ, McBride JR, Wang F, Buck MR, Keene JD, Reid KR, Htoon H, Hollingsworth JA, Rosenthal SJ.

ACS Nano. 2016 Feb 23;10(2):1960-8. doi: 10.1021/acsnano.5b05876. Epub 2016 Feb 5.

PMID:
26849531
10.

Functional coordination and HuR-mediated regulation of mRNA stability during T cell activation.

Blackinton JG, Keene JD.

Nucleic Acids Res. 2016 Jan 8;44(1):426-36. doi: 10.1093/nar/gkv1066. Epub 2015 Oct 20.

11.

XRN1 stalling in the 5' UTR of Hepatitis C virus and Bovine Viral Diarrhea virus is associated with dysregulated host mRNA stability.

Moon SL, Blackinton JG, Anderson JR, Dozier MK, Dodd BJ, Keene JD, Wilusz CJ, Bradrick SS, Wilusz J.

PLoS Pathog. 2015 Mar 6;11(3):e1004708. doi: 10.1371/journal.ppat.1004708. eCollection 2015 Mar.

12.

Correlation of atomic structure and photoluminescence of the same quantum dot: pinpointing surface and internal defects that inhibit photoluminescence.

Orfield NJ, McBride JR, Keene JD, Davis LM, Rosenthal SJ.

ACS Nano. 2015 Jan 27;9(1):831-9. doi: 10.1021/nn506420w. Epub 2014 Dec 23.

PMID:
25526260
13.

Elimination of hole-surface overlap in graded CdS(x)Se(1-x) nanocrystals revealed by ultrafast fluorescence upconversion spectroscopy.

Keene JD, McBride JR, Orfield NJ, Rosenthal SJ.

ACS Nano. 2014 Oct 28;8(10):10665-73. doi: 10.1021/nn504235w. Epub 2014 Sep 12.

PMID:
25203834
14.

Transcriptional and posttranscriptional regulation of cytokine gene expression in HIV-1 antigen-specific CD8+ T cells that mediate virus inhibition.

Payne TL, Blackinton J, Frisbee A, Pickeral J, Sawant S, Vandergrift NA, Freel SA, Ferrari G, Keene JD, Tomaras GD.

J Virol. 2014 Sep 1;88(17):9514-28. doi: 10.1128/JVI.00802-14. Epub 2014 Jun 4.

15.

Post-transcriptional RNA regulons affecting cell cycle and proliferation.

Blackinton JG, Keene JD.

Semin Cell Dev Biol. 2014 Oct;34:44-54. doi: 10.1016/j.semcdb.2014.05.014. Epub 2014 Jun 2. Review.

16.

The globalization of messenger RNA regulation.

Keene JD.

Natl Sci Rev. 2014 Jun;1(2):184-186. doi: 10.1093/nsr/nwu004. Epub 2014 May 14. No abstract available.

17.

Plasmonic Cu(x)In(y)S2 quantum dots make better photovoltaics than their nonplasmonic counterparts.

Niezgoda JS, Yap E, Keene JD, McBride JR, Rosenthal SJ.

Nano Lett. 2014 Jun 11;14(6):3262-9. doi: 10.1021/nl500645k. Epub 2014 May 8.

PMID:
24793489
18.

Advancing the functional utility of PAR-CLIP by quantifying background binding to mRNAs and lncRNAs.

Friedersdorf MB, Keene JD.

Genome Biol. 2014 Jan 7;15(1):R2. doi: 10.1186/gb-2014-15-1-r2.

19.

Mechanisms coordinating ELAV/Hu mRNA regulons.

Simone LE, Keene JD.

Curr Opin Genet Dev. 2013 Feb;23(1):35-43. doi: 10.1016/j.gde.2012.12.006. Epub 2013 Jan 9. Review.

20.

Neuron-specific ELAV/Hu proteins suppress HuR mRNA during neuronal differentiation by alternative polyadenylation.

Mansfield KD, Keene JD.

Nucleic Acids Res. 2012 Mar;40(6):2734-46. doi: 10.1093/nar/gkr1114. Epub 2011 Dec 1.

21.

PARalyzer: definition of RNA binding sites from PAR-CLIP short-read sequence data.

Corcoran DL, Georgiev S, Mukherjee N, Gottwein E, Skalsky RL, Keene JD, Ohler U.

Genome Biol. 2011 Aug 18;12(8):R79. doi: 10.1186/gb-2011-12-8-r79.

22.

Integrative regulatory mapping indicates that the RNA-binding protein HuR couples pre-mRNA processing and mRNA stability.

Mukherjee N, Corcoran DL, Nusbaum JD, Reid DW, Georgiev S, Hafner M, Ascano M Jr, Tuschl T, Ohler U, Keene JD.

Mol Cell. 2011 Aug 5;43(3):327-39. doi: 10.1016/j.molcel.2011.06.007. Epub 2011 Jun 30.

23.

Single-nanocrystal spectroscopy of white-light-emitting CdSe nanocrystals.

Dukes AD 3rd, Samson PC, Keene JD, Davis LM, Wikswo JP, Rosenthal SJ.

J Phys Chem A. 2011 Apr 28;115(16):4076-81. doi: 10.1021/jp1109509. Epub 2011 Feb 22.

PMID:
21338163
24.

ATM regulates a DNA damage response posttranscriptional RNA operon in lymphocytes.

Mazan-Mamczarz K, Hagner PR, Zhang Y, Dai B, Lehrmann E, Becker KG, Keene JD, Gorospe M, Liu Z, Gartenhaus RB.

Blood. 2011 Feb 24;117(8):2441-50. doi: 10.1182/blood-2010-09-310987. Epub 2011 Jan 5.

25.

Systematic analysis of posttranscriptional gene expression.

Morris AR, Mukherjee N, Keene JD.

Wiley Interdiscip Rev Syst Biol Med. 2010 Mar-Apr;2(2):162-180. doi: 10.1002/wsbm.54. Review.

PMID:
20836020
26.

Tissue type-specific expression of the dsRNA-binding protein 76 and genome-wide elucidation of its target mRNAs.

Neplioueva V, Dobrikova EY, Mukherjee N, Keene JD, Gromeier M.

PLoS One. 2010 Jul 23;5(7):e11710. doi: 10.1371/journal.pone.0011710.

27.

The global dynamics of RNA stability orchestrates responses to cellular activation.

Keene JD.

BMC Biol. 2010 Jul 8;8:95. doi: 10.1186/1741-7007-8-95.

28.

Minireview: global regulation and dynamics of ribonucleic Acid.

Keene JD.

Endocrinology. 2010 Apr;151(4):1391-7. doi: 10.1210/en.2009-1250. Review.

29.

Coordinated posttranscriptional mRNA population dynamics during T-cell activation.

Mukherjee N, Lager PJ, Friedersdorf MB, Thompson MA, Keene JD.

Mol Syst Biol. 2009;5:288. doi: 10.1038/msb.2009.44. Epub 2009 Jul 28.

30.

Control of thymic T cell maturation, deletion and egress by the RNA-binding protein HuR.

Papadaki O, Milatos S, Grammenoudi S, Mukherjee N, Keene JD, Kontoyiannis DL.

J Immunol. 2009 Jun 1;182(11):6779-88. doi: 10.4049/jimmunol.0900377.

31.

The ribonome: a dominant force in co-ordinating gene expression.

Mansfield KD, Keene JD.

Biol Cell. 2009 Mar;101(3):169-81. doi: 10.1042/BC20080055. Review.

32.

Proteomic and immunologic analyses of brain tumor exosomes.

Graner MW, Alzate O, Dechkovskaia AM, Keene JD, Sampson JH, Mitchell DA, Bigner DD.

FASEB J. 2009 May;23(5):1541-57. doi: 10.1096/fj.08-122184. Epub 2008 Dec 24.

33.

Activity-dependent expression of ELAV/Hu RBPs and neuronal mRNAs in seizure and cocaine brain.

Tiruchinapalli DM, Caron MG, Keene JD.

J Neurochem. 2008 Dec;107(6):1529-43. doi: 10.1111/j.1471-4159.2008.05718.x. Epub 2008 Nov 6.

34.

Activity-dependent expression of RNA binding protein HuD and its association with mRNAs in neurons.

Tiruchinapalli DM, Ehlers MD, Keene JD.

RNA Biol. 2008 Jul-Sep;5(3):157-68. Epub 2008 Jul 14.

PMID:
18769135
35.

Post-transcriptional gene regulation by HuR promotes a more tumorigenic phenotype.

Mazan-Mamczarz K, Hagner PR, Corl S, Srikantan S, Wood WH, Becker KG, Gorospe M, Keene JD, Levenson AS, Gartenhaus RB.

Oncogene. 2008 Oct 16;27(47):6151-63. doi: 10.1038/onc.2008.215. Epub 2008 Jul 21.

36.

Biological clocks and the coordination theory of RNA operons and regulons.

Keene JD.

Cold Spring Harb Symp Quant Biol. 2007;72:157-65. doi: 10.1101/sqb.2007.72.013. Review.

PMID:
18419273
37.

Ribonomic analysis of human Pum1 reveals cis-trans conservation across species despite evolution of diverse mRNA target sets.

Morris AR, Mukherjee N, Keene JD.

Mol Cell Biol. 2008 Jun;28(12):4093-103. doi: 10.1128/MCB.00155-08. Epub 2008 Apr 14.

38.
39.

A two-phase innate host response to alphavirus infection identified by mRNP-tagging in vivo.

Konopka JL, Penalva LO, Thompson JM, White LJ, Beard CW, Keene JD, Johnston RE.

PLoS Pathog. 2007 Dec;3(12):e199. doi: 10.1371/journal.ppat.0030199.

40.

Signal sequence- and translation-independent mRNA localization to the endoplasmic reticulum.

Pyhtila B, Zheng T, Lager PJ, Keene JD, Reedy MC, Nicchitta CV.

RNA. 2008 Mar;14(3):445-53. doi: 10.1261/rna.721108. Epub 2008 Jan 11.

41.

Caspase-mediated cleavage of HuR in the cytoplasm contributes to pp32/PHAP-I regulation of apoptosis.

Mazroui R, Di Marco S, Clair E, von Roretz C, Tenenbaum SA, Keene JD, Saleh M, Gallouzi IE.

J Cell Biol. 2008 Jan 14;180(1):113-27. doi: 10.1083/jcb.200709030. Epub 2008 Jan 7.

42.

RNA regulons: coordination of post-transcriptional events.

Keene JD.

Nat Rev Genet. 2007 Jul;8(7):533-43. Review.

PMID:
17572691
43.
44.

Search for organising principles: understanding in systems biology.

Mesarovic MD, Sreenath SN, Keene JD.

Syst Biol (Stevenage). 2004 Jun;1(1):19-27. Review.

PMID:
17052112
45.

Stable ribosome binding to the endoplasmic reticulum enables compartment-specific regulation of mRNA translation.

Stephens SB, Dodd RD, Brewer JW, Lager PJ, Keene JD, Nicchitta CV.

Mol Biol Cell. 2005 Dec;16(12):5819-31. Epub 2005 Oct 12.

46.

Post-transcriptional operons and regulons co-ordinating gene expression.

Keene JD, Lager PJ.

Chromosome Res. 2005;13(3):327-37. Review.

PMID:
15868425
47.

Biotinylated tags for recovery and characterization of ribonucleoprotein complexes.

Penalva LO, Keene JD.

Biotechniques. 2004 Oct;37(4):604, 606, 608-10.

48.

RNA-binding proteins to assess gene expression states of co-cultivated cells in response to tumor cells.

Penalva LO, Burdick MD, Lin SM, Sutterluety H, Keene JD.

Mol Cancer. 2004 Sep 7;3:24.

49.

La gets its wings.

Kenan DJ, Keene JD.

Nat Struct Mol Biol. 2004 Apr;11(4):303-5. No abstract available.

PMID:
15048103
50.

Gene expression analysis of messenger RNP complexes.

Penalva LO, Tenenbaum SA, Keene JD.

Methods Mol Biol. 2004;257:125-34.

PMID:
14770002

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