Format
Sort by
Items per page

Send to

Choose Destination

Search results

Items: 1 to 50 of 82

1.

Interrogation of nonconserved human adipose lincRNAs identifies a regulatory role of linc-ADAL in adipocyte metabolism.

Zhang X, Xue C, Lin J, Ferguson JF, Weiner A, Liu W, Han Y, Hinkle C, Li W, Jiang H, Gosai S, Hachet M, Garcia BA, Gregory BD, Soccio RE, Hogenesch JB, Seale P, Li M, Reilly MP.

Sci Transl Med. 2018 Jun 20;10(446). pii: eaar5987. doi: 10.1126/scitranslmed.aar5987.

PMID:
29925637
2.

The nucleotides they are a-changin': function of RNA binding proteins in post-transcriptional messenger RNA editing and modification in Arabidopsis.

Kramer MC, Anderson SJ, Gregory BD.

Curr Opin Plant Biol. 2018 Jun 5;45(Pt A):88-95. doi: 10.1016/j.pbi.2018.05.010. [Epub ahead of print] Review.

PMID:
29883934
3.

Nuclear m6A reader YTHDC1 regulates alternative polyadenylation and splicing during mouse oocyte development.

Kasowitz SD, Ma J, Anderson SJ, Leu NA, Xu Y, Gregory BD, Schultz RM, Wang PJ.

PLoS Genet. 2018 May 25;14(5):e1007412. doi: 10.1371/journal.pgen.1007412. eCollection 2018 May.

4.

Publisher Correction: Dysregulation of the epigenetic landscape of normal aging in Alzheimer's disease.

Nativio R, Donahue G, Berson A, Lan Y, Amlie-Wolf A, Tuzer F, Toledo JB, Gosai SJ, Gregory BD, Torres C, Trojanowski JQ, Wang LS, Johnson FB, Bonini NM, Berger SL.

Nat Neurosci. 2018 Mar 19. doi: 10.1038/s41593-018-0124-2. [Epub ahead of print]

PMID:
29556027
5.

Dysregulation of the epigenetic landscape of normal aging in Alzheimer's disease.

Nativio R, Donahue G, Berson A, Lan Y, Amlie-Wolf A, Tuzer F, Toledo JB, Gosai SJ, Gregory BD, Torres C, Trojanowski JQ, Wang LS, Johnson FB, Bonini NM, Berger SL.

Nat Neurosci. 2018 Apr;21(4):497-505. doi: 10.1038/s41593-018-0101-9. Epub 2018 Mar 5. Erratum in: Nat Neurosci. 2018 Mar 19;:.

PMID:
29507413
6.

EPIC-CoGe: Managing and Analyzing Genomic Data.

Nelson ADL, Haug-Baltzell AK, Davey S, Gregory BD, Lyons E.

Bioinformatics. 2018 Feb 20. doi: 10.1093/bioinformatics/bty106. [Epub ahead of print]

PMID:
29474529
7.

Differential Regulation of LET-7 by LIN28B Isoform-Specific Functions.

Mizuno R, Chatterji P, Andres S, Hamilton K, Simon L, Foley SW, Jeganathan A, Gregory BD, Madison B, Rustgi AK.

Mol Cancer Res. 2018 Mar;16(3):403-416. doi: 10.1158/1541-7786.MCR-17-0514. Epub 2018 Jan 12.

PMID:
29330293
8.

Chromatin dynamics during the differentiation of long-term hematopoietic stem cells to multipotent progenitors.

Yu X, Wu C, Bhavanasi D, Wang H, Gregory BD, Huang J.

Blood Adv. 2017 May 30;1(14):887-898. doi: 10.1182/bloodadvances.2016003384. eCollection 2017 Jun 13.

9.

Global analysis of ribosome-associated noncoding RNAs unveils new modes of translational regulation.

Bazin J, Baerenfaller K, Gosai SJ, Gregory BD, Crespi M, Bailey-Serres J.

Proc Natl Acad Sci U S A. 2017 Nov 14;114(46):E10018-E10027. doi: 10.1073/pnas.1708433114. Epub 2017 Oct 30.

10.

RNA structure, binding, and coordination in Arabidopsis.

Foley SW, Kramer MC, Gregory BD.

Wiley Interdiscip Rev RNA. 2017 Sep;8(5). doi: 10.1002/wrna.1426. Epub 2017 Jun 28. Review.

PMID:
28660659
11.

Reading the Epitranscriptome: New Techniques and Perspectives.

Vandivier LE, Gregory BD.

Enzymes. 2017;41:269-298. doi: 10.1016/bs.enz.2017.03.004. Epub 2017 Apr 14.

PMID:
28601224
12.

A Global View of RNA-Protein Interactions Identifies Post-transcriptional Regulators of Root Hair Cell Fate.

Foley SW, Gosai SJ, Wang D, Selamoglu N, Sollitti AC, Köster T, Steffen A, Lyons E, Daldal F, Garcia BA, Staiger D, Deal RB, Gregory BD.

Dev Cell. 2017 Apr 24;41(2):204-220.e5. doi: 10.1016/j.devcel.2017.03.018.

13.

Genome-wide TOP2A DNA cleavage is biased toward translocated and highly transcribed loci.

Yu X, Davenport JW, Urtishak KA, Carillo ML, Gosai SJ, Kolaris CP, Byl JAW, Rappaport EF, Osheroff N, Gregory BD, Felix CA.

Genome Res. 2017 Jul;27(7):1238-1249. doi: 10.1101/gr.211615.116. Epub 2017 Apr 6.

14.

In Silico Identification of RNA Modifications from High-Throughput Sequencing Data Using HAMR.

Kuksa PP, Leung YY, Vandivier LE, Anderson Z, Gregory BD, Wang LS.

Methods Mol Biol. 2017;1562:211-229. doi: 10.1007/978-1-4939-6807-7_14.

PMID:
28349463
15.

The Macronuclear Genome of Stentor coeruleus Reveals Tiny Introns in a Giant Cell.

Slabodnick MM, Ruby JG, Reiff SB, Swart EC, Gosai S, Prabakaran S, Witkowska E, Larue GE, Fisher S, Freeman RM Jr, Gunawardena J, Chu W, Stover NA, Gregory BD, Nowacki M, Derisi J, Roy SW, Marshall WF, Sood P.

Curr Biol. 2017 Feb 20;27(4):569-575. doi: 10.1016/j.cub.2016.12.057. Epub 2017 Feb 9.

16.
17.

Protein Interaction Profile Sequencing (PIP-seq).

Foley SW, Gregory BD.

Curr Protoc Mol Biol. 2016 Oct 10;116:27.5.1-27.5.15. doi: 10.1002/cpmb.21.

18.

Changes in the Transcriptome of Human Astrocytes Accompanying Oxidative Stress-Induced Senescence.

Crowe EP, Tuzer F, Gregory BD, Donahue G, Gosai SJ, Cohen J, Leung YY, Yetkin E, Nativio R, Wang LS, Sell C, Bonini NM, Berger SL, Johnson FB, Torres C.

Front Aging Neurosci. 2016 Aug 31;8:208. doi: 10.3389/fnagi.2016.00208. eCollection 2016.

19.

Loss of NAD Homeostasis Leads to Progressive and Reversible Degeneration of Skeletal Muscle.

Frederick DW, Loro E, Liu L, Davila A Jr, Chellappa K, Silverman IM, Quinn WJ 3rd, Gosai SJ, Tichy ED, Davis JG, Mourkioti F, Gregory BD, Dellinger RW, Redpath P, Migaud ME, Nakamaru-Ogiso E, Rabinowitz JD, Khurana TS, Baur JA.

Cell Metab. 2016 Aug 9;24(2):269-82. doi: 10.1016/j.cmet.2016.07.005.

20.

Terpene metabolic engineering via nuclear or chloroplast genomes profoundly and globally impacts off-target pathways through metabolite signalling.

Pasoreck EK, Su J, Silverman IM, Gosai SJ, Gregory BD, Yuan JS, Daniell H.

Plant Biotechnol J. 2016 Sep;14(9):1862-75. doi: 10.1111/pbi.12548. Epub 2016 Mar 8.

21.

Genome-Wide Approaches for RNA Structure Probing.

Silverman IM, Berkowitz ND, Gosai SJ, Gregory BD.

Adv Exp Med Biol. 2016;907:29-59. doi: 10.1007/978-3-319-29073-7_2.

PMID:
27256381
22.

A comprehensive database of high-throughput sequencing-based RNA secondary structure probing data (Structure Surfer).

Berkowitz ND, Silverman IM, Childress DM, Kazan H, Wang LS, Gregory BD.

BMC Bioinformatics. 2016 May 17;17(1):215. doi: 10.1186/s12859-016-1071-0.

23.

The Conservation and Function of RNA Secondary Structure in Plants.

Vandivier LE, Anderson SJ, Foley SW, Gregory BD.

Annu Rev Plant Biol. 2016 Apr 29;67:463-88. doi: 10.1146/annurev-arplant-043015-111754. Epub 2016 Feb 8. Review.

24.

Local admixture of amplified and diversified secreted pathogenesis determinants shapes mosaic Toxoplasma gondii genomes.

Lorenzi H, Khan A, Behnke MS, Namasivayam S, Swapna LS, Hadjithomas M, Karamycheva S, Pinney D, Brunk BP, Ajioka JW, Ajzenberg D, Boothroyd JC, Boyle JP, Dardé ML, Diaz-Miranda MA, Dubey JP, Fritz HM, Gennari SM, Gregory BD, Kim K, Saeij JP, Su C, White MW, Zhu XQ, Howe DK, Rosenthal BM, Grigg ME, Parkinson J, Liu L, Kissinger JC, Roos DS, Sibley LD.

Nat Commun. 2016 Jan 7;7:10147. doi: 10.1038/ncomms10147.

25.

The Msi Family of RNA-Binding Proteins Function Redundantly as Intestinal Oncoproteins.

Li N, Yousefi M, Nakauka-Ddamba A, Li F, Vandivier L, Parada K, Woo DH, Wang S, Naqvi AS, Rao S, Tobias J, Cedeno RJ, Minuesa G, Y K, Barlowe TS, Valvezan A, Shankar S, Deering RP, Klein PS, Jensen ST, Kharas MG, Gregory BD, Yu Z, Lengner CJ.

Cell Rep. 2015 Dec 22;13(11):2440-2455. doi: 10.1016/j.celrep.2015.11.022. Epub 2015 Dec 8.

26.

Global Transcriptional Profiling of Diapause and Climatic Adaptation in Drosophila melanogaster.

Zhao X, Bergland AO, Behrman EL, Gregory BD, Petrov DA, Schmidt PS.

Mol Biol Evol. 2016 Mar;33(3):707-20. doi: 10.1093/molbev/msv263. Epub 2015 Nov 13.

27.

Chemical Modifications Mark Alternatively Spliced and Uncapped Messenger RNAs in Arabidopsis.

Vandivier LE, Campos R, Kuksa PP, Silverman IM, Wang LS, Gregory BD.

Plant Cell. 2015 Nov;27(11):3024-37. doi: 10.1105/tpc.15.00591. Epub 2015 Nov 11.

28.

Cytoplasmic poly(A) binding protein-1 binds to genomically encoded sequences within mammalian mRNAs.

Kini HK, Silverman IM, Ji X, Gregory BD, Liebhaber SA.

RNA. 2016 Jan;22(1):61-74. doi: 10.1261/rna.053447.115. Epub 2015 Nov 9.

29.

DASHR: database of small human noncoding RNAs.

Leung YY, Kuksa PP, Amlie-Wolf A, Valladares O, Ungar LH, Kannan S, Gregory BD, Wang LS.

Nucleic Acids Res. 2016 Jan 4;44(D1):D216-22. doi: 10.1093/nar/gkv1188. Epub 2015 Nov 8.

30.

Transcriptomic Changes Due to Cytoplasmic TDP-43 Expression Reveal Dysregulation of Histone Transcripts and Nuclear Chromatin.

Amlie-Wolf A, Ryvkin P, Tong R, Dragomir I, Suh E, Xu Y, Van Deerlin VM, Gregory BD, Kwong LK, Trojanowski JQ, Lee VM, Wang LS, Lee EB.

PLoS One. 2015 Oct 28;10(10):e0141836. doi: 10.1371/journal.pone.0141836. eCollection 2015.

31.

The long noncoding RNA landscape in hypoxic and inflammatory renal epithelial injury.

Lin J, Zhang X, Xue C, Zhang H, Shashaty MG, Gosai SJ, Meyer N, Grazioli A, Hinkle C, Caughey J, Li W, Susztak K, Gregory BD, Li M, Reilly MP.

Am J Physiol Renal Physiol. 2015 Dec 1;309(11):F901-13. doi: 10.1152/ajprenal.00290.2015. Epub 2015 Sep 23.

32.

H3K36 methylation promotes longevity by enhancing transcriptional fidelity.

Sen P, Dang W, Donahue G, Dai J, Dorsey J, Cao X, Liu W, Cao K, Perry R, Lee JY, Wasko BM, Carr DT, He C, Robison B, Wagner J, Gregory BD, Kaeberlein M, Kennedy BK, Boeke JD, Berger SL.

Genes Dev. 2015 Jul 1;29(13):1362-76. doi: 10.1101/gad.263707.115.

33.

Transcriptome-wide measurement of plant RNA secondary structure.

Foley SW, Vandivier LE, Kuksa PP, Gregory BD.

Curr Opin Plant Biol. 2015 Oct;27:36-43. doi: 10.1016/j.pbi.2015.05.021. Epub 2015 Jun 26. Review.

34.

Functional analysis and transcriptomic profiling of iPSC-derived macrophages and their application in modeling Mendelian disease.

Zhang H, Xue C, Shah R, Bermingham K, Hinkle CC, Li W, Rodrigues A, Tabita-Martinez J, Millar JS, Cuchel M, Pashos EE, Liu Y, Yan R, Yang W, Gosai SJ, VanDorn D, Chou ST, Gregory BD, Morrisey EE, Li M, Rader DJ, Reilly MP.

Circ Res. 2015 Jun 19;117(1):17-28. doi: 10.1161/CIRCRESAHA.117.305860. Epub 2015 Apr 22.

35.

Transformation of the intestinal epithelium by the MSI2 RNA-binding protein.

Wang S, Li N, Yousefi M, Nakauka-Ddamba A, Li F, Parada K, Rao S, Minuesa G, Katz Y, Gregory BD, Kharas MG, Yu Z, Lengner CJ.

Nat Commun. 2015 Mar 16;6:6517. doi: 10.1038/ncomms7517.

36.

High-throughput nuclease-mediated probing of RNA secondary structure in plant transcriptomes.

Vandivier LE, Li F, Gregory BD.

Methods Mol Biol. 2015;1284:41-70. doi: 10.1007/978-1-4939-2444-8_3.

PMID:
25757767
37.

Essential Role for endogenous siRNAs during meiosis in mouse oocytes.

Stein P, Rozhkov NV, Li F, Cárdenas FL, Davydenko O, Vandivier LE, Gregory BD, Hannon GJ, Schultz RM.

PLoS Genet. 2015 Feb 19;11(2):e1005013. doi: 10.1371/journal.pgen.1005013. eCollection 2015 Feb. Erratum in: PLoS Genet. 2015 Apr;11(4):e1005129.

38.

Global analysis of the RNA-protein interaction and RNA secondary structure landscapes of the Arabidopsis nucleus.

Gosai SJ, Foley SW, Wang D, Silverman IM, Selamoglu N, Nelson AD, Beilstein MA, Daldal F, Deal RB, Gregory BD.

Mol Cell. 2015 Jan 22;57(2):376-88. doi: 10.1016/j.molcel.2014.12.004. Epub 2014 Dec 31.

39.

HIPPIE: a high-throughput identification pipeline for promoter interacting enhancer elements.

Hwang YC, Lin CF, Valladares O, Malamon J, Kuksa PP, Zheng Q, Gregory BD, Wang LS.

Bioinformatics. 2015 Apr 15;31(8):1290-2. doi: 10.1093/bioinformatics/btu801. Epub 2014 Dec 4.

40.

Transcriptome-wide ribonuclease-mediated protein footprinting to identify RNA-protein interaction sites.

Silverman IM, Gregory BD.

Methods. 2015 Jan 15;72:76-85. doi: 10.1016/j.ymeth.2014.10.021. Epub 2014 Oct 28.

PMID:
25448484
41.

Detection of Pol IV/RDR2-dependent transcripts at the genomic scale in Arabidopsis reveals features and regulation of siRNA biogenesis.

Li S, Vandivier LE, Tu B, Gao L, Won SY, Li S, Zheng B, Gregory BD, Chen X.

Genome Res. 2015 Feb;25(2):235-45. doi: 10.1101/gr.182238.114. Epub 2014 Nov 20.

42.

A MicroRNA precursor surveillance system in quality control of MicroRNA synthesis.

Liu X, Zheng Q, Vrettos N, Maragkakis M, Alexiou P, Gregory BD, Mourelatos Z.

Mol Cell. 2014 Sep 18;55(6):868-879. doi: 10.1016/j.molcel.2014.07.017. Epub 2014 Aug 28.

43.

Inactivation of yeast Isw2 chromatin remodeling enzyme mimics longevity effect of calorie restriction via induction of genotoxic stress response.

Dang W, Sutphin GL, Dorsey JA, Otte GL, Cao K, Perry RM, Wanat JJ, Saviolaki D, Murakami CJ, Tsuchiyama S, Robison B, Gregory BD, Vermeulen M, Shiekhattar R, Johnson FB, Kennedy BK, Kaeberlein M, Berger SL.

Cell Metab. 2014 Jun 3;19(6):952-66. doi: 10.1016/j.cmet.2014.04.004. Epub 2014 May 8.

44.

Paternal poly (ADP-ribose) metabolism modulates retention of inheritable sperm histones and early embryonic gene expression.

Ihara M, Meyer-Ficca ML, Leu NA, Rao S, Li F, Gregory BD, Zalenskaya IA, Schultz RM, Meyer RG.

PLoS Genet. 2014 May 8;10(5):e1004317. doi: 10.1371/journal.pgen.1004317. eCollection 2014 May.

45.

Genomic approaches for studying transcriptional and post-transcriptional processes.

Gregory BD, Meyers BC.

Methods. 2014 May 1;67(1):1-2. doi: 10.1016/j.ymeth.2014.03.025. No abstract available.

PMID:
24766879
46.

Tissue-specific RNA-Seq in human evoked inflammation identifies blood and adipose LincRNA signatures of cardiometabolic diseases.

Liu Y, Ferguson JF, Xue C, Ballantyne RL, Silverman IM, Gosai SJ, Serfecz J, Morley MP, Gregory BD, Li M, Reilly MP.

Arterioscler Thromb Vasc Biol. 2014 Apr;34(4):902-12. doi: 10.1161/ATVBAHA.113.303123. Epub 2014 Feb 6.

47.

RNase-mediated protein footprint sequencing reveals protein-binding sites throughout the human transcriptome.

Silverman IM, Li F, Alexander A, Goff L, Trapnell C, Rinn JL, Gregory BD.

Genome Biol. 2014 Jan 7;15(1):R3. doi: 10.1186/gb-2014-15-1-r3.

48.

HAMR: high-throughput annotation of modified ribonucleotides.

Ryvkin P, Leung YY, Silverman IM, Childress M, Valladares O, Dragomir I, Gregory BD, Wang LS.

RNA. 2013 Dec;19(12):1684-92. doi: 10.1261/rna.036806.112. Epub 2013 Oct 22.

49.

Using machine learning and high-throughput RNA sequencing to classify the precursors of small non-coding RNAs.

Ryvkin P, Leung YY, Ungar LH, Gregory BD, Wang LS.

Methods. 2014 May 1;67(1):28-35. doi: 10.1016/j.ymeth.2013.10.002. Epub 2013 Oct 18.

50.

Analysis of the host transcriptome from demyelinating spinal cord of murine coronavirus-infected mice.

Elliott R, Li F, Dragomir I, Chua MM, Gregory BD, Weiss SR.

PLoS One. 2013 Sep 18;8(9):e75346. doi: 10.1371/journal.pone.0075346. eCollection 2013.

Supplemental Content

Loading ...
Support Center