Brian D. Gregory, Ph.D. - Publications

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

59 high-probability publications. We are testing a new system for linking publications to authors. You can help! If you notice any innacuracies, 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
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  0.72
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  0.72
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. DOI: 10.1111/pbi.12548  0.72
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  0.72
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  0.72
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  0.72
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  0.72
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  0.72
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  0.72
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  0.72
2015 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, ... ... Gregory BD, et al. Functional Analysis and Transcriptomic Profiling of iPSC-Derived Macrophages and Their Application in Modeling Mendelian Disease. Circulation Research. 117: 17-28. PMID 25904599 DOI: 10.1161/CIRCRESAHA.117.305860  0.72
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  0.72
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  0.72
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  0.72
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  0.72
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  0.72
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  0.72
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  0.72
2014 Liu X, Zheng Q, Vrettos N, Maragkakis M, Alexiou P, Gregory BD, Mourelatos Z. A MicroRNA precursor surveillance system in quality control of MicroRNA synthesis. Molecular Cell. 55: 868-79. PMID 25175028 DOI: 10.1016/j.molcel.2014.07.017  0.72
2014 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, et al. Inactivation of yeast Isw2 chromatin remodeling enzyme mimics longevity effect of calorie restriction via induction of genotoxic stress response. Cell Metabolism. 19: 952-66. PMID 24814484 DOI: 10.1016/j.cmet.2014.04.004  0.72
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  0.72
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  0.72
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  0.72
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  0.72
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  0.72
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  0.72
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  0.72
2013 Elliott R, Li F, Dragomir I, Chua MM, Gregory BD, Weiss SR. Analysis of the host transcriptome from demyelinating spinal cord of murine coronavirus-infected mice. Plos One. 8: e75346. PMID 24058676 DOI: 10.1371/journal.pone.0075346  0.72
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  0.72
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  0.72
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  0.72
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  0.72
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  0.72
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  0.72
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  0.72
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  0.72
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  0.72
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  0.72
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  0.72
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  0.72
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  0.72
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  0.72
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  0.72
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  0.72
2009 Gregory BD, Belostotsky DA. Whole-genome microarrays: applications and technical issues. Methods in Molecular Biology (Clifton, N.J.). 553: 39-56. PMID 19588100 DOI: 10.1007/978-1-60327-563-7_3  0.72
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  0.72
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  0.72
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  0.72
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  0.72
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  0.72
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  0.72
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  0.72
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  0.72
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  0.72
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  0.72
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  0.72
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  0.72
1999 Choe S, Dilkes BP, Gregory BD, Ross AS, Yuan H, Noguchi T, Fujioka S, Takatsuto S, Tanaka A, Yoshida S, Tax FE, Feldmann KA. The Arabidopsis dwarf1 mutant is defective in the conversion of 24-methylenecholesterol to campesterol in brassinosteroid biosynthesis Plant Physiology. 119: 897-907. PMID 10069828  0.72
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  0.72
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