Brian D. Gregory, Ph.D. - Publications

Affiliations: 
2005 Harvard University, Cambridge, MA, United States 
Area:
Microbiology Biology

103 high-probability publications. We are testing a new system for linking publications to authors. You can help! If you notice any inaccuracies, please sign in and mark papers as correct or incorrect matches. If you identify any major omissions or other inaccuracies in the publication list, please let us know.

Year Citation  Score
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  0.329
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  0.397
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  0.47
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  0.384
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  0.446
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  0.483
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  0.769
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  0.758
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  0.486
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  0.351
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  0.468
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  0.546
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  0.501
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  0.505
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  0.344
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  0.574
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  0.583
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  0.533
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  0.45
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  0.472
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  0.526
2018 Vandivier LE, Gregory BD. New insights into the plant epitranscriptome. Journal of Experimental Botany. PMID 30020491 DOI: 10.1093/Jxb/Ery262  0.398
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  0.4
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  0.415
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  0.581
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  0.469
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  0.506
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  0.353
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  0.531
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  0.583
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  0.55
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  0.546
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  0.764
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  0.768
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  0.496
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  0.552
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  0.543
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  0.5
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  0.546
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  0.426
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  0.757
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  0.326
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  0.562
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  0.53
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  0.536
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  0.405
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  0.363
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  0.551
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  0.427
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  0.535
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  0.425
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  0.569
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  0.31
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  0.555
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  0.538
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  0.497
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  0.376
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  0.406
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  0.488
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  0.534
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  0.773
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  0.537
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  0.341
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  0.419
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  0.53
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  0.748
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  0.428
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  0.596
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  0.512
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  0.509
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  0.389
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  0.787
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  0.396
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  0.595
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  0.573
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  0.513
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  0.786
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  0.534
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  0.413
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  0.568
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  0.497
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  0.325
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  0.382
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  0.76
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  0.539
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  0.413
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  0.338
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  0.506
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  0.365
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  0.375
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  0.64
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  0.751
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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