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Impact of poly(A)-tail G-content on Arabidopsis PAB binding and their role in enhancing translational efficiency.

Zhao T, Huan Q, Sun J, Liu C, Hou X, Yu X, Silverman IM, Zhang Y, Gregory BD, Liu CM, Qian W, Cao X.

Genome Biol. 2019 Sep 3;20(1):189. doi: 10.1186/s13059-019-1799-8.


Transcription Is Just the Beginning of Gene Expression Regulation: The Functional Significance of RNA-Binding Proteins to Post-transcriptional Processes in Plants.

Prall W, Sharma B, Gregory BD.

Plant Cell Physiol. 2019 Sep 1;60(9):1939-1952. doi: 10.1093/pcp/pcz067. Review.


Computationally Characterizing Protein-Bound Long Noncoding RNAs and Their Secondary Structure Using Protein Interaction Profile Sequencing (PIP-Seq) in Plants.

Shan M, Anderson ZD, Gregory BD.

Methods Mol Biol. 2019;1933:363-380. doi: 10.1007/978-1-4939-9045-0_22.


HAMR: High-Throughput Annotation of Modified Ribonucleotides.

Vandivier LE, Anderson ZD, Gregory BD.

Methods Mol Biol. 2019;1870:51-67. doi: 10.1007/978-1-4939-8808-2_4.


N6-Methyladenosine Inhibits Local Ribonucleolytic Cleavage to Stabilize mRNAs in Arabidopsis.

Anderson SJ, Kramer MC, Gosai SJ, Yu X, Vandivier LE, Nelson ADL, Anderson ZD, Beilstein MA, Fray RG, Lyons E, Gregory BD.

Cell Rep. 2018 Oct 30;25(5):1146-1157.e3. doi: 10.1016/j.celrep.2018.10.020.


The LIN28B-IMP1 post-transcriptional regulon has opposing effects on oncogenic signaling in the intestine.

Chatterji P, Hamilton KE, Liang S, Andres SF, Wijeratne HRS, Mizuno R, Simon LA, Hicks PD, Foley SW, Pitarresi JR, Klein-Szanto AJ, Mah AT, Van Landeghem L, Gregory BD, Lengner CJ, Madison BB, Shah P, Rustgi AK.

Genes Dev. 2018 Aug 1;32(15-16):1020-1034. doi: 10.1101/gad.314369.118.


Does RNA secondary structure drive translation or vice versa?

Kramer MC, Gregory BD.

Nat Struct Mol Biol. 2018 Aug;25(8):641-643. doi: 10.1038/s41594-018-0100-2. No abstract available.


PNPase knockout results in mtDNA loss and an altered metabolic gene expression program.

Shimada E, Ahsan FM, Nili M, Huang D, Atamdede S, TeSlaa T, Case D, Yu X, Gregory BD, Perrin BJ, Koehler CM, Teitell MA.

PLoS One. 2018 Jul 19;13(7):e0200925. doi: 10.1371/journal.pone.0200925. eCollection 2018.


New insights into the plant epitranscriptome.

Vandivier LE, Gregory BD.

J Exp Bot. 2018 Sep 14;69(20):4659-4665. doi: 10.1093/jxb/ery262. Review.


Plant 24-nt reproductive phasiRNAs from intramolecular duplex mRNAs in diverse monocots.

Kakrana A, Mathioni SM, Huang K, Hammond R, Vandivier L, Patel P, Arikit S, Shevchenko O, Harkess AE, Kingham B, Gregory BD, Leebens-Mack JH, Meyers BC.

Genome Res. 2018 Sep;28(9):1333-1344. doi: 10.1101/gr.228163.117. Epub 2018 Jul 12.


Shedding some blue light on alternative promoter usage in plants.

Gregory BD.

Proc Natl Acad Sci U S A. 2018 Jul 24;115(30):7654-7656. doi: 10.1073/pnas.1809312115. Epub 2018 Jul 3. No abstract available.


IRE1B degrades RNAs encoding proteins that interfere with the induction of autophagy by ER stress in Arabidopsis thaliana.

Bao Y, Pu Y, Yu X, Gregory BD, Srivastava R, Howell SH, Bassham DC.

Autophagy. 2018;14(9):1562-1573. doi: 10.1080/15548627.2018.1462426. Epub 2018 Aug 17.


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.


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 Oct;45(Pt A):88-95. doi: 10.1016/j.pbi.2018.05.010. Epub 2018 Jun 5. Review.


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.


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 Jul;21(7):1018. doi: 10.1038/s41593-018-0124-2.


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;:.


EPIC-CoGe: managing and analyzing genomic data.

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

Bioinformatics. 2018 Aug 1;34(15):2651-2653. doi: 10.1093/bioinformatics/bty106.


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.


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.


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.


CoGe LoadExp+: A web-based suite that integrates next-generation sequencing data analysis workflows and visualization.

Grover JW, Bomhoff M, Davey S, Gregory BD, Mosher RA, Lyons E.

Plant Direct. 2017 Jul 20;1(2). doi: 10.1002/pld3.8. eCollection 2017 Jul.


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.


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. Review.


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.


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.


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.


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.


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.


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.


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.


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.


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.


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.


Protein Interaction Profile Sequencing (PIP-seq) in Plants.

Anderson SJ, Willmann MR, Gregory BD.

Curr Protoc Plant Biol. 2016 May;1(1):163-183. doi: 10.1002/cppb.20001.


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.


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.


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.


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.


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.


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.


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.


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.


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.


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.


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.


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.


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.

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