| Year |
Citation |
Score |
| 2023 |
Guo R, Gregory BD. PELOTA and HBS1 suppress co-translational messenger RNA decay in Arabidopsis. Plant Direct. 7: e553. PMID 38149303 DOI: 10.1002/pld3.553 |
0.317 |
|
| 2023 |
Baumer ZT, Erber L, Jolley E, Lawrence S, Lin C, Murakami S, Perez V, Prall W, Schaening-Burgos C, Sylvia M, Chen S, Gregory BD. Defining the commonalities between post-transcriptional and post-translational modification communities. Trends in Biochemical Sciences. PMID 37884411 DOI: 10.1016/j.tibs.2023.09.011 |
0.315 |
|
| 2023 |
Eckardt NA, Axtell MJ, Barta A, Chen X, Gregory BD, Guo H, Manavella PA, Mosher RA, Meyers BC. Focus on RNA biology. The Plant Cell. PMID 36943779 DOI: 10.1093/plcell/koad082 |
0.42 |
|
| 2023 |
Sharma B, Prall W, Bhatia G, Gregory BD. The Diversity and Functions of Plant RNA Modifications: What We Know and Where We Go from Here. Annual Review of Plant Biology. PMID 36917824 DOI: 10.1146/annurev-arplant-071122-085813 |
0.453 |
|
| 2023 |
Prall W, Ganguly DR, Gregory BD. The covalent nucleotide modifications within plant mRNAs: What we know, how we find them, and what should be done in the future. The Plant Cell. PMID 36794718 DOI: 10.1093/plcell/koad044 |
0.391 |
|
| 2023 |
Guo R, Yu X, Gregory BD. The identification of conserved sequence features of co-translationally decayed mRNAs and upstream open reading frames in angiosperm transcriptomes. Plant Direct. 7: e479. PMID 36643787 DOI: 10.1002/pld3.479 |
0.301 |
|
| 2022 |
Prall W, Gregory BD. The fold makes all the difference in COOLAIR-mediated regulation of plant flowering time. Developmental Cell. 57: 2254-2256. PMID 36220080 DOI: 10.1016/j.devcel.2022.09.008 |
0.412 |
|
| 2022 |
Bhatia G, Prall W, Sharma B, Gregory BD. Covalent RNA modifications and their budding crosstalk with plant epigenetic processes. Current Opinion in Plant Biology. 69: 102287. PMID 35988352 DOI: 10.1016/j.pbi.2022.102287 |
0.327 |
|
| 2022 |
Kramer MC, Kim HJ, Palos KR, Garcia BA, Lyons E, Beilstein MA, Nelson ADL, Gregory BD. A Conserved Long Intergenic Non-coding RNA Containing snoRNA Sequences, , Affects Arabidopsis Germination and Development. Frontiers in Plant Science. 13: 906603. PMID 35693169 DOI: 10.3389/fpls.2022.906603 |
0.396 |
|
| 2022 |
Palos K, Nelson Dittrich AC, Yu L, Brock JR, Railey CE, Wu HL, Sokolowska E, Skirycz A, Hsu PY, Gregory BD, Lyons E, Beilstein MA, Nelson ADL. Identification and functional annotation of long intergenic non-coding RNAs in Brassicaceae. The Plant Cell. PMID 35666179 DOI: 10.1093/plcell/koac166 |
0.466 |
|
| 2022 |
Janssen KA, Xie Y, Kramer MC, Gregory BD, Garcia BA. Data-Independent Acquisition for the Detection of Mononucleoside RNA Modifications by Mass Spectrometry. Journal of the American Society For Mass Spectrometry. PMID 35357823 DOI: 10.1021/jasms.2c00065 |
0.382 |
|
| 2021 |
Yu X, Vandivier LE, Gregory BD. NAD-seq for profiling the NAD capped transcriptome of . Star Protocols. 2: 100901. PMID 34816126 DOI: 10.1016/j.xpro.2021.100901 |
0.442 |
|
| 2021 |
Shan M, Ji X, Janssen K, Silverman IM, Humenik J, Garcia BA, Liebhaber SA, Gregory BD. Dynamic changes in RNA-protein interactions and RNA secondary structure in mammalian erythropoiesis. Life Science Alliance. 4. PMID 34315813 DOI: 10.26508/lsa.202000659 |
0.48 |
|
| 2021 |
Hua X, Berkowitz ND, Willmann MR, Yu X, Lyons E, Gregory BD. Global Analysis of RNA-Dependent RNA Polymerase-Dependent Small RNAs Reveals New Substrates and Functions for These Proteins and SGS3 in Arabidopsis. Non-Coding Rna. 7. PMID 33925339 DOI: 10.3390/ncrna7020028 |
0.765 |
|
| 2020 |
Yu X, Willmann MR, Vandivier LE, Trefely S, Kramer MC, Shapiro J, Guo R, Lyons E, Snyder NW, Gregory BD. Messenger RNA 5' NAD Capping Is a Dynamic Regulatory Epitranscriptome Mark That Is Required for Proper Response to Abscisic Acid in Arabidopsis. Developmental Cell. PMID 33290723 DOI: 10.1016/j.devcel.2020.11.009 |
0.755 |
|
| 2020 |
Yu X, Sharma B, Gregory BD. The impact of epitranscriptomic marks on post-transcriptional regulation in plants. Briefings in Functional Genomics. PMID 33274735 DOI: 10.1093/bfgp/elaa021 |
0.483 |
|
| 2020 |
Bhat SS, Bielewicz D, Gulanicz T, Bodi Z, Yu X, Anderson SJ, Szewc L, Bajczyk M, Dolata J, Grzelak N, Smolinski DJ, Gregory BD, Fray RG, Jarmolowski A, Szweykowska-Kulinska Z. mRNA adenosine methylase (MTA) deposits mA on pri-miRNAs to modulate miRNA biogenesis in . Proceedings of the National Academy of Sciences of the United States of America. PMID 32817553 DOI: 10.1073/Pnas.2003733117 |
0.35 |
|
| 2020 |
Kramer MC, Janssen KA, Palos K, Nelson ADL, Vandivier LE, Garcia BA, Lyons E, Beilstein MA, Gregory BD. N-methyladenosine and RNA secondary structure affect transcript stability and protein abundance during systemic salt stress in Arabidopsis. Plant Direct. 4: e00239. PMID 32724893 DOI: 10.1002/pld3.239 |
0.465 |
|
| 2020 |
Shan M, Gregory BD. Using RNA Affinity Purification Followed by Mass Spectrometry to Identify RNA-Binding Proteins (RBPs). Methods in Molecular Biology (Clifton, N.J.). 2166: 241-253. PMID 32710413 DOI: 10.1007/978-1-0716-0712-1_14 |
0.543 |
|
| 2020 |
Kuksa PP, Li F, Kannan S, Gregory BD, Leung YY, Wang LS. HiPR: High-throughput probabilistic RNA structure inference. Computational and Structural Biotechnology Journal. 18: 1539-1547. PMID 32637050 DOI: 10.1016/J.Csbj.2020.06.004 |
0.498 |
|
| 2019 |
Peri S, Roberts S, Kreko IR, McHan LB, Naron A, Ram A, Murphy RL, Lyons E, Gregory BD, Devisetty UK, Nelson ADL. Read Mapping and Transcript Assembly: A Scalable and High-Throughput Workflow for the Processing and Analysis of Ribonucleic Acid Sequencing Data. Frontiers in Genetics. 10: 1361. PMID 32038716 DOI: 10.3389/Fgene.2019.01361 |
0.502 |
|
| 2019 |
Zhao T, Huan Q, Sun J, Liu C, Hou X, Yu X, Silverman IM, Zhang Y, Gregory BD, Liu CM, Qian W, Cao X. Impact of poly(A)-tail G-content on Arabidopsis PAB binding and their role in enhancing translational efficiency. Genome Biology. 20: 189. PMID 31481099 DOI: 10.1186/S13059-019-1799-8 |
0.342 |
|
| 2019 |
Prall W, Sharma B, Gregory BD. Transcription Is Just the Beginning of Gene Expression Regulation: The Functional Significance of RNA-Binding Proteins to Post-transcriptional Processes in Plants. Plant & Cell Physiology. PMID 31155676 DOI: 10.1093/Pcp/Pcz067 |
0.47 |
|
| 2019 |
Shan M, Anderson ZD, Gregory BD. Computationally Characterizing Protein-Bound Long Noncoding RNAs and Their Secondary Structure Using Protein Interaction Profile Sequencing (PIP-Seq) in Plants. Methods in Molecular Biology (Clifton, N.J.). 1933: 363-380. PMID 30945197 DOI: 10.1007/978-1-4939-9045-0_22 |
0.572 |
|
| 2019 |
Kramer MC, Gregory BD. Using Protein Interaction Profile Sequencing (PIP-seq) to Identify RNA Secondary Structure and RNA-Protein Interaction Sites of Long Noncoding RNAs in Plants. Methods in Molecular Biology (Clifton, N.J.). 1933: 343-361. PMID 30945196 DOI: 10.1007/978-1-4939-9045-0_21 |
0.581 |
|
| 2019 |
Vandivier LE, Anderson ZD, Gregory BD. HAMR: High-Throughput Annotation of Modified Ribonucleotides. Methods in Molecular Biology (Clifton, N.J.). 1870: 51-67. PMID 30539546 DOI: 10.1007/978-1-4939-8808-2_4 |
0.529 |
|
| 2018 |
Anderson SJ, Kramer MC, Gosai SJ, Yu X, Vandivier LE, Nelson ADL, Anderson ZD, Beilstein MA, Fray RG, Lyons E, Gregory BD. N-Methyladenosine Inhibits Local Ribonucleolytic Cleavage to Stabilize mRNAs in Arabidopsis. Cell Reports. 25: 1146-1157.e3. PMID 30380407 DOI: 10.1016/J.Celrep.2018.10.020 |
0.449 |
|
| 2018 |
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, et al. The LIN28B-IMP1 post-transcriptional regulon has opposing effects on oncogenic signaling in the intestine. Genes & Development. 32: 1020-1034. PMID 30068703 DOI: 10.1101/Gad.314369.118 |
0.471 |
|
| 2018 |
Kramer MC, Gregory BD. Does RNA secondary structure drive translation or vice versa? Nature Structural & Molecular Biology. PMID 30061597 DOI: 10.1038/S41594-018-0100-2 |
0.524 |
|
| 2018 |
Vandivier LE, Gregory BD. New insights into the plant epitranscriptome. Journal of Experimental Botany. PMID 30020491 DOI: 10.1093/Jxb/Ery262 |
0.396 |
|
| 2018 |
Gregory BD. Shedding some blue light on alternative promoter usage in plants. Proceedings of the National Academy of Sciences of the United States of America. PMID 29970421 DOI: 10.1073/Pnas.1809312115 |
0.399 |
|
| 2018 |
Bao Y, Pu Y, Yu X, Gregory BD, Srivastava R, Howell SH, Bassham DC. IRE1B degrades RNAs encoding proteins that interfere with the induction of autophagy by ER stress in Arabidopsis thaliana. Autophagy. 1-12. PMID 29940799 DOI: 10.1080/15548627.2018.1462426 |
0.399 |
|
| 2018 |
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, et al. Interrogation of nonconserved human adipose lincRNAs identifies a regulatory role of in adipocyte metabolism. Science Translational Medicine. 10. PMID 29925637 DOI: 10.1126/Scitranslmed.Aar5987 |
0.414 |
|
| 2018 |
Kramer MC, Anderson SJ, Gregory BD. The nucleotides they are a-changin': function of RNA binding proteins in post-transcriptional messenger RNA editing and modification in Arabidopsis. Current Opinion in Plant Biology. 45: 88-95. PMID 29883934 DOI: 10.1016/J.Pbi.2018.05.010 |
0.578 |
|
| 2018 |
Kasowitz SD, Ma J, Anderson SJ, Leu NA, Xu Y, Gregory BD, Schultz RM, Wang PJ. Nuclear m6A reader YTHDC1 regulates alternative polyadenylation and splicing during mouse oocyte development. Plos Genetics. 14: e1007412. PMID 29799838 DOI: 10.1371/Journal.Pgen.1007412 |
0.414 |
|
| 2018 |
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. Publisher Correction: Dysregulation of the epigenetic landscape of normal aging in Alzheimer's disease. Nature Neuroscience. PMID 29556027 DOI: 10.1038/S41593-018-0124-2 |
0.466 |
|
| 2018 |
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. Dysregulation of the epigenetic landscape of normal aging in Alzheimer's disease. Nature Neuroscience. PMID 29507413 DOI: 10.1038/S41593-018-0101-9 |
0.503 |
|
| 2018 |
Mizuno R, Chatterji P, Andres SF, Hamilton KE, Simon L, Foley SW, Jeganathan AN, Gregory BD, Madison BB, Rustgi AK. Differential Regulation of LET-7 by LIN28B Isoform-specific Functions. Molecular Cancer Research : McR. PMID 29330293 DOI: 10.1158/1541-7786.Mcr-17-0514 |
0.352 |
|
| 2018 |
Chatterji P, Hamilton KE, Liang S, Andres SF, Wijeratne HS, Mizuno R, Simon L, Hicks PD, Foley S, Pitarresi J, Klein-Szanto A, Mah A, Van Landeghem L, Gregory B, Lengner C, et al. Sa1664 - The Lin28B-Imp1 Axis Directs a Post-Transcriptional Regulon of Oncogenic Signaling in the Intestine Gastroenterology. 154: S-346. DOI: 10.1016/S0016-5085(18)31488-4 |
0.318 |
|
| 2017 |
Bazin J, Baerenfaller K, Gosai SJ, Gregory BD, Crespi M, Bailey-Serres J. Global analysis of ribosome-associated noncoding RNAs unveils new modes of translational regulation. Proceedings of the National Academy of Sciences of the United States of America. PMID 29087317 DOI: 10.1073/Pnas.1708433114 |
0.529 |
|
| 2017 |
Foley SW, Kramer MC, Gregory BD. RNA structure, binding, and coordination in Arabidopsis. Wiley Interdisciplinary Reviews. Rna. PMID 28660659 DOI: 10.1002/Wrna.1426 |
0.58 |
|
| 2017 |
Vandivier LE, Gregory BD. Reading the Epitranscriptome: New Techniques and Perspectives. The Enzymes. 41: 269-298. PMID 28601224 DOI: 10.1016/Bs.Enz.2017.03.004 |
0.546 |
|
| 2017 |
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. A Global View of RNA-Protein Interactions Identifies Post-transcriptional Regulators of Root Hair Cell Fate. Developmental Cell. 41: 204-220.e5. PMID 28441533 DOI: 10.1016/J.Devcel.2017.03.018 |
0.526 |
|
| 2017 |
Yu X, Davenport JW, Urtishak KA, Carillo ML, Gosai SJ, Kolaris CP, Byl JA, Rappaport EF, Osheroff N, Gregory BD, Felix CA. Genome-wide TOP2A DNA cleavage is biased towards translocated and highly transcribed loci. Genome Research. PMID 28385713 DOI: 10.1101/Gr.211615.116 |
0.397 |
|
| 2017 |
Kuksa PP, Leung YY, Vandivier LE, Anderson Z, Gregory BD, Wang LS. In Silico Identification of RNA Modifications from High-Throughput Sequencing Data Using HAMR. Methods in Molecular Biology (Clifton, N.J.). 1562: 211-229. PMID 28349463 DOI: 10.1007/978-1-4939-6807-7_14 |
0.542 |
|
| 2016 |
Anderson SJ, Willmann MR, Gregory BD. Protein Interaction Profile Sequencing (PIP-seq) in Plants. Current Protocols in Plant Biology. 1: 163-183. PMID 31725981 DOI: 10.1002/cppb.20001 |
0.761 |
|
| 2016 |
Yu X, Willmann MR, Anderson SJ, Gregory BD. Genome-Wide Mapping of Uncapped and Cleaved Transcripts Reveals a Role for the Nuclear mRNA Cap-Binding Complex in Co-translational RNA Decay in Arabidopsis. The Plant Cell. PMID 27758893 DOI: 10.1105/Tpc.16.00456 |
0.765 |
|
| 2016 |
Foley SW, Gregory BD. Protein Interaction Profile Sequencing (PIP-seq). Current Protocols in Molecular Biology. 116: 27.5.1-27.5.15. PMID 27723083 DOI: 10.1002/cpmb.21 |
0.493 |
|
| 2016 |
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. Changes in the Transcriptome of Human Astrocytes Accompanying Oxidative Stress-Induced Senescence. Frontiers in Aging Neuroscience. 8: 208. PMID 27630559 DOI: 10.3389/Fnagi.2016.00208 |
0.549 |
|
| 2016 |
Pasoreck EK, Su J, Silverman IM, Gosai SJ, Gregory BD, Yuan JS, Daniell H. Terpene metabolic engineering via nuclear or chloroplast genomes profoundly and globally impacts off-target pathways through metabolite signalling. Plant Biotechnology Journal. 14: 1862-75. PMID 27507797 DOI: 10.1111/Pbi.12548 |
0.33 |
|
| 2016 |
Silverman IM, Berkowitz ND, Gosai SJ, Gregory BD. Genome-Wide Approaches for RNA Structure Probing. Advances in Experimental Medicine and Biology. 907: 29-59. PMID 27256381 DOI: 10.1007/978-3-319-29073-7_2 |
0.54 |
|
| 2016 |
Berkowitz ND, Silverman IM, Childress DM, Kazan H, Wang LS, Gregory BD. A comprehensive database of high-throughput sequencing-based RNA secondary structure probing data (Structure Surfer). Bmc Bioinformatics. 17: 215. PMID 27188311 DOI: 10.1186/S12859-016-1071-0 |
0.497 |
|
| 2016 |
Vandivier LE, Anderson SJ, Foley SW, Gregory BD. The Conservation and Function of RNA Secondary Structure in Plants. Annual Review of Plant Biology. PMID 26865341 DOI: 10.1146/Annurev-Arplant-043015-111754 |
0.544 |
|
| 2016 |
Kini HK, Silverman IM, Ji X, Gregory BD, Liebhaber SA. Cytoplasmic poly(A) binding protein-1 binds to genomically encoded sequences within mammalian mRNAs. Rna (New York, N.Y.). 22: 61-74. PMID 26554031 DOI: 10.1261/Rna.053447.115 |
0.425 |
|
| 2015 |
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, ... ... Gregory BD, et al. The Msi Family of RNA-Binding Proteins Function Redundantly as Intestinal Oncoproteins. Cell Reports. PMID 26673327 DOI: 10.1016/J.Celrep.2015.11.022 |
0.75 |
|
| 2015 |
Zhao X, Bergland AO, Behrman EL, Gregory BD, Petrov DA, Schmidt PS. Global transcriptional profiling of diapause and climatic adaptation in Drosophila melanogaster. Molecular Biology and Evolution. PMID 26568616 DOI: 10.1093/Molbev/Msv263 |
0.327 |
|
| 2015 |
Vandivier LE, Campos R, Kuksa PP, Silverman IM, Wang LS, Gregory BD. Chemical Modifications Mark Alternatively Spliced and Uncapped Messenger RNAs in Arabidopsis. The Plant Cell. PMID 26561561 DOI: 10.1105/Tpc.15.00591 |
0.559 |
|
| 2015 |
Leung YY, Kuksa PP, Amlie-Wolf A, Valladares O, Ungar LH, Kannan S, Gregory BD, Wang LS. DASHR: database of small human noncoding RNAs. Nucleic Acids Research. PMID 26553799 DOI: 10.1093/Nar/Gkv1188 |
0.527 |
|
| 2015 |
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. Transcriptomic Changes Due to Cytoplasmic TDP-43 Expression Reveal Dysregulation of Histone Transcripts and Nuclear Chromatin. Plos One. 10: e0141836. PMID 26510133 DOI: 10.1371/Journal.Pone.0141836 |
0.534 |
|
| 2015 |
Lin JJ, Zhang X, Xue C, Zhang H, Shashaty MG, Gosai S, Meyer NJ, Grazioli A, Hinkle C, Caughey J, Li W, Susztak K, Gregory BD, Li M, Reilly MP. The Long Noncoding RNA Landscape in Hypoxic and Inflammatory Renal Epithelial Injury. American Journal of Physiology. Renal Physiology. ajprenal.00290.2015. PMID 26400545 DOI: 10.1152/Ajprenal.00290.2015 |
0.403 |
|
| 2015 |
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, et al. H3K36 methylation promotes longevity by enhancing transcriptional fidelity. Genes & Development. 29: 1362-1376. PMID 26159996 DOI: 10.1101/Gad.263707.115 |
0.364 |
|
| 2015 |
Foley SW, Vandivier LE, Kuksa PP, Gregory BD. Transcriptome-wide measurement of plant RNA secondary structure. Current Opinion in Plant Biology. 27: 36-43. PMID 26119389 DOI: 10.1016/J.Pbi.2015.05.021 |
0.548 |
|
| 2015 |
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. Transformation of the intestinal epithelium by the MSI2 RNA-binding protein. Nature Communications. 6: 6517. PMID 25774828 DOI: 10.1038/Ncomms7517 |
0.425 |
|
| 2015 |
Vandivier LE, Li F, Gregory BD. High-throughput nuclease-mediated probing of RNA secondary structure in plant transcriptomes. Methods in Molecular Biology (Clifton, N.J.). 1284: 41-70. PMID 25757767 DOI: 10.1007/978-1-4939-2444-8_3 |
0.531 |
|
| 2015 |
Stein P, Rozhkov NV, Li F, Cárdenas FL, Davydenk O, Vandivier LE, Gregory BD, Hannon GJ, Schultz RM. Essential Role for endogenous siRNAs during meiosis in mouse oocytes. Plos Genetics. 11: e1005013. PMID 25695507 DOI: 10.1371/Journal.Pgen.1005013 |
0.423 |
|
| 2015 |
Gosai SJ, Foley SW, Wang D, Silverman IM, Selamoglu N, Nelson AD, Beilstein MA, Daldal F, Deal RB, Gregory BD. Global analysis of the RNA-protein interaction and RNA secondary structure landscapes of the Arabidopsis nucleus. Molecular Cell. 57: 376-88. PMID 25557549 DOI: 10.1016/J.Molcel.2014.12.004 |
0.568 |
|
| 2015 |
Hwang YC, Lin CF, Valladares O, Malamon J, Kuksa PP, Zheng Q, Gregory BD, Wang LS. HIPPIE: a high-throughput identification pipeline for promoter interacting enhancer elements. Bioinformatics (Oxford, England). 31: 1290-2. PMID 25480377 DOI: 10.1093/Bioinformatics/Btu801 |
0.312 |
|
| 2015 |
Silverman IM, Gregory BD. Transcriptome-wide ribonuclease-mediated protein footprinting to identify RNA-protein interaction sites. Methods (San Diego, Calif.). 72: 76-85. PMID 25448484 DOI: 10.1016/J.Ymeth.2014.10.021 |
0.554 |
|
| 2015 |
Li S, Vandivier LE, Tu B, Gao L, Won SY, Li S, Zheng B, Gregory BD, Chen X. Detection of Pol IV/RDR2-dependent transcripts at the genomic scale in Arabidopsis reveals features and regulation of siRNA biogenesis. Genome Research. 25: 235-45. PMID 25414514 DOI: 10.1101/Gr.182238.114 |
0.537 |
|
| 2015 |
Chen Q, Crowe EP, Kuhn T, Johnson JE, Gregory BD, Donahue G, Bonini NM, Berger SL, Sell C, Torres C, Brad Johnson F. Connections between cell senescence, chromatin, and neurodegeneration Experimental Gerontology. 68: 93-94. DOI: 10.1016/J.Exger.2015.01.011 |
0.495 |
|
| 2014 |
Ihara M, Meyer-Ficca ML, Leu NA, Rao S, Li F, Gregory BD, Zalenskaya IA, Schultz RM, Meyer RG. Paternal poly (ADP-ribose) metabolism modulates retention of inheritable sperm histones and early embryonic gene expression. Plos Genetics. 10: e1004317. PMID 24810616 DOI: 10.1371/Journal.Pgen.1004317 |
0.322 |
|
| 2014 |
Gregory BD, Meyers BC. Genomic approaches for studying transcriptional and post-transcriptional processes. Methods (San Diego, Calif.). 67: 1-2. PMID 24766879 DOI: 10.1016/J.Ymeth.2014.03.025 |
0.377 |
|
| 2014 |
Liu Y, Ferguson JF, Xue C, Ballantyne RL, Silverman IM, Gosai SJ, Serfecz J, Morley MP, Gregory BD, Li M, Reilly MP. Tissue-specific RNA-Seq in human evoked inflammation identifies blood and adipose LincRNA signatures of cardiometabolic diseases. Arteriosclerosis, Thrombosis, and Vascular Biology. 34: 902-12. PMID 24504737 DOI: 10.1161/Atvbaha.113.303123 |
0.405 |
|
| 2014 |
Silverman IM, Li F, Alexander A, Goff L, Trapnell C, Rinn JL, Gregory BD. RNase-mediated protein footprint sequencing reveals protein-binding sites throughout the human transcriptome. Genome Biology. 15: R3. PMID 24393486 DOI: 10.1186/Gb-2014-15-1-R3 |
0.486 |
|
| 2014 |
Ryvkin P, Leung YY, Ungar LH, Gregory BD, Wang LS. Using machine learning and high-throughput RNA sequencing to classify the precursors of small non-coding RNAs. Methods (San Diego, Calif.). 67: 28-35. PMID 24145223 DOI: 10.1016/J.Ymeth.2013.10.002 |
0.53 |
|
| 2014 |
Willmann MR, Berkowitz ND, Gregory BD. Improved genome-wide mapping of uncapped and cleaved transcripts in eukaryotes--GMUCT 2.0. Methods (San Diego, Calif.). 67: 64-73. PMID 23867340 DOI: 10.1016/J.Ymeth.2013.07.003 |
0.769 |
|
| 2013 |
Ryvkin P, Leung YY, Silverman IM, Childress M, Valladares O, Dragomir I, Gregory BD, Wang LS. HAMR: high-throughput annotation of modified ribonucleotides. Rna (New York, N.Y.). 19: 1684-92. PMID 24149843 DOI: 10.1261/Rna.036806.112 |
0.534 |
|
| 2013 |
Shah PP, Donahue G, Otte GL, Capell BC, Nelson DM, Cao K, Aggarwala V, Cruickshanks HA, Rai TS, McBryan T, Gregory BD, Adams PD, Berger SL. Lamin B1 depletion in senescent cells triggers large-scale changes in gene expression and the chromatin landscape. Genes & Development. 27: 1787-99. PMID 23934658 DOI: 10.1101/Gad.223834.113 |
0.342 |
|
| 2013 |
Liu Y, Ferguson JF, Xue C, Silverman IM, Gregory B, Reilly MP, Li M. Evaluating the impact of sequencing depth on transcriptome profiling in human adipose. Plos One. 8: e66883. PMID 23826166 DOI: 10.1371/Journal.Pone.0066883 |
0.416 |
|
| 2013 |
Leung YY, Ryvkin P, Ungar LH, Gregory BD, Wang LS. CoRAL: predicting non-coding RNAs from small RNA-sequencing data. Nucleic Acids Research. 41: e137. PMID 23700308 DOI: 10.1093/Nar/Gkt426 |
0.527 |
|
| 2013 |
Vandivier L, Li F, Zheng Q, Willmann M, Chen Y, Gregory B. Arabidopsis mRNA secondary structure correlates with protein function and domains. Plant Signaling & Behavior. 8: e24301. PMID 23603972 DOI: 10.4161/Psb.24301 |
0.745 |
|
| 2013 |
Hwang YC, Zheng Q, Gregory BD, Wang LS. High-throughput identification of long-range regulatory elements and their target promoters in the human genome. Nucleic Acids Research. 41: 4835-46. PMID 23525463 DOI: 10.1093/Nar/Gkt188 |
0.43 |
|
| 2013 |
Silverman IM, Li F, Gregory BD. Genomic era analyses of RNA secondary structure and RNA-binding proteins reveal their significance to post-transcriptional regulation in plants. Plant Science : An International Journal of Experimental Plant Biology. 205: 55-62. PMID 23498863 DOI: 10.1016/J.Plantsci.2013.01.009 |
0.594 |
|
| 2013 |
Sabin LR, Zheng Q, Thekkat P, Yang J, Hannon GJ, Gregory BD, Tudor M, Cherry S. Dicer-2 processes diverse viral RNA species. Plos One. 8: e55458. PMID 23424633 DOI: 10.1371/Journal.Pone.0055458 |
0.509 |
|
| 2013 |
Zheng Q, Rowley MJ, Böhmdorfer G, Sandhu D, Gregory BD, Wierzbicki AT. RNA polymerase V targets transcriptional silencing components to promoters of protein-coding genes. The Plant Journal : For Cell and Molecular Biology. 73: 179-89. PMID 23013441 DOI: 10.1111/Tpj.12034 |
0.508 |
|
| 2013 |
Ryvkin P, Leung YY, Dragomir I, Schuck T, Schellenberg G, Arnold S, Chen-Plotkin A, Van Deerlin V, Lee V, Trojanowski J, Gregory B, Wang L. P3-064: Characterizing the Alzheimer's disease prefrontal cortex transcriptome by multiple RNA-sequencing Alzheimer's & Dementia. 9: P574-P574. DOI: 10.1016/J.Jalz.2013.05.1134 |
0.386 |
|
| 2012 |
Li F, Zheng Q, Vandivier LE, Willmann MR, Chen Y, Gregory BD. Regulatory impact of RNA secondary structure across the Arabidopsis transcriptome. The Plant Cell. 24: 4346-59. PMID 23150631 DOI: 10.1105/Tpc.112.104232 |
0.785 |
|
| 2012 |
Wierzbicki AT, Cocklin R, Mayampurath A, Lister R, Jordan Rowley M, Gregory BD, Ecker JR, Tang H, Pikaard CS. Spatial and functional relationships among Pol V-associated loci, Pol IV-dependent siRNAs, and cytosine methylation in the Arabidopsis epigenome Genes and Development. 26: 1825-1836. PMID 22855789 DOI: 10.1101/Gad.197772.112 |
0.395 |
|
| 2012 |
Vourekas A, Zheng Q, Alexiou P, Maragkakis M, Kirino Y, Gregory BD, Mourelatos Z. Mili and Miwi target RNA repertoire reveals piRNA biogenesis and function of Miwi in spermiogenesis. Nature Structural & Molecular Biology. 19: 773-81. PMID 22842725 DOI: 10.1038/Nsmb.2347 |
0.592 |
|
| 2012 |
Li F, Zheng Q, Ryvkin P, Dragomir I, Desai Y, Aiyer S, Valladares O, Yang J, Bambina S, Sabin LR, Murray JI, Lamitina T, Raj A, Cherry S, Wang LS, Gregory BD, et al. Global analysis of RNA secondary structure in two metazoans. Cell Reports. 1: 69-82. PMID 22832108 DOI: 10.1016/J.Celrep.2011.10.002 |
0.57 |
|
| 2012 |
Li F, Ryvkin P, Childress DM, Valladares O, Gregory BD, Wang LS. SAVoR: a server for sequencing annotation and visualization of RNA structures. Nucleic Acids Research. 40: W59-64. PMID 22492627 DOI: 10.1093/Nar/Gks310 |
0.509 |
|
| 2011 |
Willmann MR, Endres MW, Cook RT, Gregory BD. The Functions of RNA-Dependent RNA Polymerases in Arabidopsis. The Arabidopsis Book / American Society of Plant Biologists. 9: e0146. PMID 22303271 DOI: 10.1199/Tab.0146 |
0.783 |
|
| 2011 |
Endres MW, Cook RT, Gregory BD. A high-throughput sequencing-based methodology to identify all uncapped and cleaved RNA molecules in eukaryotic genomes. Methods in Molecular Biology (Clifton, N.J.). 732: 209-23. PMID 21431715 DOI: 10.1007/978-1-61779-083-6_15 |
0.531 |
|
| 2011 |
Ryvkin P, Leung YY, Wang LS, Gregory BD. Invited: Multiclass RNA function classification using next-generation sequencing 2011 Ieee 1st International Conference On Computational Advances in Bio and Medical Sciences, Iccabs 2011. 10. DOI: 10.1109/ICCABS.2011.5729859 |
0.409 |
|
| 2010 |
Zheng Q, Ryvkin P, Li F, Dragomir I, Valladares O, Yang J, Cao K, Wang LS, Gregory BD. Genome-wide double-stranded RNA sequencing reveals the functional significance of base-paired RNAs in Arabidopsis. Plos Genetics. 6: e1001141. PMID 20941385 DOI: 10.1371/Journal.Pgen.1001141 |
0.566 |
|
| 2010 |
Endres MW, Gregory BD, Gao Z, Foreman AW, Mlotshwa S, Ge X, Pruss GJ, Ecker JR, Bowman LH, Vance V. Two plant viral suppressors of silencing require the ethylene-inducible host transcription factor RAV2 to block RNA silencing Plos Pathogens. 6. PMID 20084269 DOI: 10.1371/Journal.Ppat.1000729 |
0.496 |
|
| 2010 |
Earley K, Smith MR, Weber R, Gregory BD, Poethig RS. An endogenous F-box protein regulates ARGONAUTE1 in Arabidopsis thaliana Silence. 1. DOI: 10.1186/1758-907X-1-15 |
0.324 |
|
| 2009 |
Lister R, Gregory BD, Ecker JR. Next is now: new technologies for sequencing of genomes, transcriptomes, and beyond Current Opinion in Plant Biology. 12: 107-118. PMID 19157957 DOI: 10.1016/J.Pbi.2008.11.004 |
0.381 |
|
| 2008 |
Yuan AH, Gregory BD, Sharp JS, McCleary KD, Dove SL, Hochschild A. Rsd family proteins make simultaneous interactions with regions 2 and 4 of the primary sigma factor. Molecular Microbiology. 70: 1136-51. PMID 18826409 DOI: 10.1111/J.1365-2958.2008.06462.X |
0.749 |
|
| 2008 |
Gregory BD, O'Malley RC, Lister R, Urich MA, Tonti-Filippini J, Chen H, Millar AH, Ecker JR. A link between RNA metabolism and silencing affecting Arabidopsis development. Developmental Cell. 14: 854-66. PMID 18486559 DOI: 10.1016/J.Devcel.2008.04.005 |
0.536 |
|
| 2008 |
Lister R, O'Malley RC, Tonti-Filippini J, Gregory BD, Berry CC, Millar AH, Ecker JR. Highly integrated single-base resolution maps of the epigenome in Arabidopsis. Cell. 133: 523-36. PMID 18423832 DOI: 10.1016/J.Cell.2008.03.029 |
0.411 |
|
| 2008 |
Gregory BD, Yazaki J, Ecker JR. Utilizing tiling microarrays for whole-genome analysis in plants Plant Journal. 53: 636-644. PMID 18269573 DOI: 10.1111/J.1365-313X.2007.03320.X |
0.337 |
|
| 2007 |
Chekanova JA, Gregory BD, Reverdatto SV, Chen H, Kumar R, Hooker T, Yazaki J, Li P, Skiba N, Peng Q, Alonso J, Brukhin V, Grossniklaus U, Ecker JR, Belostotsky DA. Genome-Wide High-Resolution Mapping of Exosome Substrates Reveals Hidden Features in the Arabidopsis Transcriptome Cell. 131: 1340-1353. PMID 18160042 DOI: 10.1016/J.Cell.2007.10.056 |
0.503 |
|
| 2007 |
Yazaki J, Gregory BD, Ecker JR. Mapping the genome landscape using tiling array technology Current Opinion in Plant Biology. 10: 534-542. PMID 17703988 DOI: 10.1016/J.Pbi.2007.07.006 |
0.364 |
|
| 2006 |
Olmedo G, Guo H, Gregory BD, Nourizadeh SD, Aguilar-Henonin L, Li H, An F, Guzman P, Ecker JR. ETHYLENE-INSENSITIVE5 encodes a 5′→3′ exoribonuclease required for regulation of the EIN3-targeting F-box proteins EBF1/2 Proceedings of the National Academy of Sciences of the United States of America. 103: 13286-13293. PMID 16920797 DOI: 10.1073/Pnas.0605528103 |
0.376 |
|
| 2005 |
Gregory BD, Deighan P, Hochschild A. An artificial activator that contacts a normally occluded surface of the RNA polymerase holoenzyme. Journal of Molecular Biology. 353: 497-506. PMID 16185714 DOI: 10.1016/J.Jmb.2005.08.047 |
0.639 |
|
| 2005 |
Gregory BD, Nickels BE, Darst SA, Hochschild A. An altered-specificity DNA-binding mutant of Escherichia coli sigma70 facilitates the analysis of sigma70 function in vivo. Molecular Microbiology. 56: 1208-19. PMID 15882415 DOI: 10.1111/J.1365-2958.2005.04624.X |
0.752 |
|
| 2004 |
Pineda M, Gregory BD, Szczypinski B, Baxter KR, Hochschild A, Miller ES, Hinton DM. A family of anti-sigma70 proteins in T4-type phages and bacteria that are similar to AsiA, a Transcription inhibitor and co-activator of bacteriophage T4. Journal of Molecular Biology. 344: 1183-97. PMID 15561138 DOI: 10.1016/J.Jmb.2004.10.003 |
0.618 |
|
| 2004 |
Gregory BD, Nickels BE, Garrity SJ, Severinova E, Minakhin L, Urbauer RJ, Urbauer JL, Heyduk T, Severinov K, Hochschild A. A regulator that inhibits transcription by targeting an intersubunit interaction of the RNA polymerase holoenzyme. Proceedings of the National Academy of Sciences of the United States of America. 101: 4554-9. PMID 15070756 DOI: 10.1073/Pnas.0400923101 |
0.752 |
|
| 1999 |
Choe S, Noguchi T, Fujioka S, Takatsuto S, Tissier CP, Gregory BD, Ross AS, Tanaka A, Yoshida S, Tax FE, Feldmann KA. The Arabidopsis dwf7/ste1 mutant is defective in the Δ7 sterol C-5 desaturation step leading to brassinosteroid biosynthesis Plant Cell. 11: 207-221. PMID 9927639 DOI: 10.1105/Tpc.11.2.207 |
0.305 |
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