Shan, M., Ji, X., Janssen, K., Silverman, I. M., Humenik, J., Garcia, B. A., Liebhaber, S. A., & Gregory, B. D. (2021). Dynamic changes in RNA-protein interactions and RNA secondary structure in mammalian erythropoiesis. Life science alliance4(9), e202000659.

Hua, X., Berkowitz, N. D., Willmann, M. R., Yu, X., Lyons, E., & Gregory, B. D. (2021). Global Analysis of RNA-Dependent RNA Polymerase-Dependent Small RNAs Reveals New Substrates and Functions for These Proteins and SGS3 in Arabidopsis. Non-coding RNA7(2), 28.

Yu, X., Vandivier, L.E., Willmann, M.R., Trefely, S., Kramer, M.C., Guo, R., Snyder, N.W., and Gregory, B.D. 2021. Messenger RNA 5’ NAD+ capping is a dynamic regulatory epitranscriptome mark that is required for proper response to abscisic acid in Arabidopsis. Dev. Cell doi: 10.1016/j.devcel.2020.11.009.

Yu, X., Sharma, B., and Gregory, B.D. 2020. The impact of epitranscriptomic marks on post-transcriptional regulation in plants. Brief. Funct. Genomics doi: 10.1093/bfgp/elaa021.


Bhat, S.S., Bielewicz, D., Gulanicz, T., Bodi, Z., Yu, X., Anderson, S.J., Szewc, L., Bajczyk, M., Dolata, J., Grzelak, N., Smolinski, D.J., Gregory, B.D., Fray, R.G., Jarmolowski, A., and Szweykowska-Kulinska, Z. 2020. mRNA adenosine methylase (MTA) deposits m6A on pri-miRNAs to modulate miRNA biogenesis in Arabidopsis thaliana. Proc. Natl. Acad. Sci. U.S.A. 117: 21785-21795.

Kramer, M.C., Janssen, K.A., Palos, K.R., Nelson, A.D.L., Vandivier, L.E., Garcia, B.A., Lyons, E., Beilstein, M.A., and Gregory, B.D. 2020. N6-methyladenosine and RNA secondary structure affect transcript stability and protein abundance during systemic salt stress in Arabidopsis. Plant Direct 4: e00239.

Shan, M. and Gregory, B.D. 2020. Using RNA Affinity Purification Followed by Mass Spectrometry to Identify RNA-Binding Proteins (RBPs). Methods Mol. Biol. 2166: 241-253. Invited book chapter.

Tan, F., Tian, T., Hou, X., Yu, X., Gu, L., Mafra, F., Gregory, B.D., Wei, Z., and Hakonarson, H. 2020. Elucidation of DNA methylation on N6-adenine with deep learning. Nat. Mach. Intell. 2: 466-475.

Kuksa, P.P., Li, F., Kannan, S., Gregory, B.D., Leung, Y.Y, and Wang, L.S. 2020. HiPR: high-throughput probabilistic RNA structure inference. Comput. Struct. Biotechnol. J. 18: 1539-1547.

Kuksa, P.P., Amlie-Wolf, A., Hwang, Y.C., Valladares, O., Gregory, B.D., and Wang, L.S. 2020. HIPPIE2: a method for fine-scale identification of physically interacting chromatin regions. NAR Genom. Bioinform. 2: lqaa022.

Heldt, N.A., Seliga, A., Winfield, M., Gajghate, S., Reichenbach, N., Yu, X., Rom, S., Tenneti, A., May, D., Gregory, B.D., and Persidsky, Y. 2020. Electronic cigarette exposure disrupts blood-brain barrier integrity and promotes neuroinflammation. Brain Behav. Immun. 88: 363-380.

Peri, S., Roberts, S., Kreko, I.R., McHan, L.B., Naron, A., Ram, A., Murphy, R.L., Lyons, E., Gregory, B.D., Devisetty, U.K., and Nelson, A.D.L. 2020. RMTA: A scalable and high-throughput workflow for the processing and analysis of RNA-seq data. Front. Genet. 10: 1361.


Zhao, T., Huan, Q., Sun, J., Liu, C., Hou, X., Yu, X., Silverman, I.M., Zhang, Y., Gregory, B.D., Liu, C.M., Qian, W., and Cao, X. 2019. Impact of poly(A)-tail G-content on Arabidopsis PAB binding and their role in enhancing translational efficiency. Genome Biol. 20: 189.

International Arabidopsis Informatics Consortium 2019. Arabidopsis bioinformatics resources: The current state, challenges, and priorities for the future. Plant Direct 3: e00109. B.D.G. was a primary contributor to this article.

Prall, W., Sharma, B., and Gregory, B.D. 2019. Transcription is just the beginning of gene expression regulation: The functional significance of RNA-binding proteins to post-transcriptional processes in plants. Plant Cell Physiol. 60: 1939-1952. Invited review.

Shan, M., Anderson, Z.D., and Gregory, B.D. 2019. Computationally characterizing protein bound long non-coding RNAs and their secondary structure using protein interaction profile sequencing (PIP-seq) in plants. Methods Mol. Biol. 1933: 363-380. Invited book chapter.

Kramer, M.C. and Gregory, B.D. 2019. Using protein interaction profile sequencing (PIP-seq) to identify RNA secondary structure and RNA-protein interaction sites of long non-coding RNAs in plants. Methods Mol. Biol. 1933: 343-361. Invited book chapter.

Vandivier, L.E., Anderson, Z.D., and Gregory, B.D. 2019. HAMR: High-throughput annotation of modified ribonucleotides. Methods Mol. Biol. 1870: 51-67. Invited book chapter


Anderson, S.J., Kramer, M.C., Gosai, S.J., Yu, X., Vandivier, L.E., Nelson, A.D.L., Anderson, Z.D., Beilstein, M.A., Fray, R.G., Lyons, E., and Gregory, B.D. 2018. N6-methyladenosine inhibits local ribonucleolytic cleavage to stabilize messenger RNAs in Arabidopsis. Cell Rep. 25: 1146-1157.

Kramer, M.C. and Gregory, B.D. 2018. Does RNA secondary structure drive translation or vice versa? Nat. Struct. Mol. Biol. 25: 641-643. Invited News & Views.

Chatterji, P., Hamilton, K.E., Liang, S., Andres, S.F., Sagara Wijeratne, H.R., Mizuno, R., Simon, L.A., Hicks, P.D., Foley, S.W., Pitarresi, J.R., Klein-Szanto, A.J., Mah, A.T., Van Landeghem, L., Gregory, B.D., Lengner, C.J., Madison, B.B., Shah, P., and Rustgi, A.K. 2018. The LIN28B-IMP1 post-transcriptional regulon has opposing effects on oncogenic signaling in the intestine. Genes Dev. 32: 1020-1034.

Shimada, E., Ahsan, F.M., Nili, M., Huang, D., Atamdede, S., TeSlaa, T., Case, D., Yu, X., Gregory, B.D., Perrin, B.J., Koehler, C.M., Teitell, M.A. 2018. PNPase knockout results in mtDNA loss and an altered metabolic gene expression program. PLoS One 13: e0200925.

Vandivier, L.E. and Gregory B.D. 2018. New insights into the plant epitranscriptome. J. Exp. Bot. 69: 4659-4665. Invited Expert View.

Kakrana, A., Mathioni, S.M., Huang, K., Hammond, R., Vandivier, L., Patel, P., Arikit, S., Shevchenko, O., Harkess, A.E., Kingham, B., Gregory, B.D., Leebens-Mack, J.H., and Meyers, B.C. 2018. Plant 24-nt reproductive phasiRNAs from intramolecular duplex mRNAs in diverse monocots. Genome Res. 28: 1333-1344.

Gregory, B.D. 2018. Shedding some blue light on alternative promoter usage in plants. Proc. Natl. Acad. Sci. U.S.A. 115: 7654-7656. Invited Commentary.

Bao, Y., Pu, Y., Yu, X., Gregory, B.D., Srivastava, R., Howell, S.H., and Bassham, D.C. 2018. IRE1B degrades RNAs encoding proteins that interfere with the induction of autophagy by ER stress in Arabidopsis thaliana. Autophagy 14: 1562-1573.

Zhang, X., Xue, C., Lin, J., Ferguson, J.F., Weiner, A., Liu, W., Han, Y., Hinkle, C., Li, W., Jiang, H., Gosai, S., Hachet, M., Garcia, B.A., Gregory, B.D., Soccio, R.E., Hogenesch, J.B., Seale, P., Li, M., and Reilly, M.P. 2018. Interrogation of nonconserved human adipose lincRNAs identifies a regulatory role of linc-ADAL in adipocyte metabolism. Sci. Transl. Med. 10: eaar5987.

Kramer, M.C., Anderson, S.J., and Gregory, B.D. 2018. The nucleotides they are a-changin’: function of RNA binding proteins in post-transcriptional messenger RNA editing and modification in Arabidopsis. Curr. Opin. Plant Biol. 45: 88-95. Invited review.

Kasowitz, S.D., Ma, J., Anderson, S.J., Leu, N.A., Xu, Y., Gregory, B.D., Schultz, R.M., and Wang, P.J. 2018. Nuclear m6A reader YTHDC1 regulates alternative polyadenylation and splicing during mouse oocyte development. PLoS Genet. 14: e1007412.

Silverman, I.M., Gosai, S.J., Vrettos, N., Foley, S.W., Berkowitz, N.D., Mourelatos, Z., and Gregory, B.D. 2018. Isolation and sequencing of AGO-bound small RNA precursors reveals processing efficiency in vivo. bioRxiv 294488. doi: 10.1101/294488.

Nativio, R., Donahue, G., Berson, A., Lan, Y., Amlie-Wolf, A., Tuzer, F., Toledo, J.B., Gosai, S.J., Gregory, B.D., Torres, C., Trojanowski, J.Q., Wang, L.S., Johnson, F.B., Bonini, N.M., and Berger, S.L. 2018. Dysregulation of the epigenetic landscape of normal aging in Alzheimer’s disease. Nat. Neurosci. 21: 497-505.

Nelson, A.D.L., Haug-Baltzell, A.K., Davey, S., Gregory, B.D., and Lyons, E. 2018. EPIC-CoGe: Managing and analyzing genomic data. Bioinformatics 34: 2651-2653.

Mizuno, R., Chatterji, P., Andres, S.F., Hamilton, K.E., Simon, L., Foley, S.W., Jeganathan, A.N., Gregory, B.D., Madison, B.B., Rustgi, A.K. 2018. Differential regulation of LET-7 by LIN28B isoform-specific functions. Mol. Cancer Res. 16: 403-416.


Bazin, J., Baerenfaller, K., Gosai, S.J., Gregory, B.D., Crespi, M., and Bailey-Serres, J. 2017. Global analysis of ribosome-associated noncoding RNAs unveils new modes of translational regulation. Proc. Natl. Acad. Sci. U.S.A. 114: E10018-E10027.

Grover, J.W., Bomhoff, M., Davey, S., Gregory, B.D., Mosher, R.A., and Lyons, E. 2017. CoGe LoadExp+: A web-based suite that integrates next-gen sequencing data analysis workflows and visualization. Plant Direct 1: 1-7.

Foley, S.W., Kramer, M.C., and Gregory, B.D. 2017. RNA structure, binding, and coordination in Arabidopsis. Wiley Interdiscip. Rev. RNA e1426.

Yu, X., Wu, W., Bhavanasi, D., Wang, H., Gregory, B.D.*, and Huang, J.* 2017. Genome-wide chromatin dynamics during the differentiation of long-term hematopoietic stem cells to multipotent progenitors. Blood Adv. 1: 887-898. * denotes co-correspondents.

Foley, S.W., Gosai, S.J., Wang, D., Selamoglu, N., Solitti, A.C., Koster, T., Steffen, A., Lyons, E., Daldal, F., Garcia, B.A., Staiger, D., Deal, R.B., and Gregory, B.D. 2017. A global view of RNA-protein interactions identifies post-transcriptional regulators of root hair cell fate. Dev. Cell 41: 204-220.

Developmental Cell Cover Article

Yu, X., Davenport, J.W., Urtishak, K.A., Carillo, M.L., Gosai, S.J., Kolaris, C.P., Byl, J.A.W., Rappaport, E.F., Osheroff, N., Gregory, B.D.*, and Felix, C.A.* 2017. Landscape of TOP2A-mediated DNA cleavage across the human genome. Genome Res. 27: 1238-1249. * denotes co-correspondents.

Vandivier, L.E. and Gregory, B.D. 2017. Reading the epitranscriptome: new techniques and perspectives. Enzymes 41: 269-298.

Kuksa, P.P., Leung, Y.Y., Vandivier, L.E., Anderson, Z., Gregory, B.D., and Wang, L.S. 2017. In silico identification of RNA modifications from high-throughput sequencing data using HAMR. Methods Mol. Biol. 1562: 211-229.

Slabodnick, M.M., Ruby, J.G., Reiff, S.B., Swart, E.C., Gosai, S., Prabakaran, S., Witkowska, E., Larue, G.E., Fisher, S., Freeman, R.M. Jr., Gunawardena, J., Chu, W., Stover, N.A., Gregory, B.D., Nowacki, M., Derisi, J., Roy, S.W., Marshall, W.F., Sood, P. 2017. The macronuclear genome of Stentor coeruleus reveals tiny introns in a giant cell. Curr. Biol. 27: 569-575.


Yu, X., Willmann, M.R., Anderson, S.J., and Gregory, B.D. 2016. Genome-wide mapping of uncapped and cleaved transcripts reveals a role for the nuclear messenger RNA cap-binding complex in plant co-translational RNA decay. Plant Cell 28: 2385-2397.

Foley, S.W. and Gregory, B.D. 2016. Protein Interaction Profile Sequencing (PIP-seq). Curr. Protoc. Mol. Biol. 116: 27.5.1-27.5.15.

Anderson, S.J., Willmann, M.R., and Gregory, B.D. 2016. Protein interaction profile sequencing (PIP-seq) in plants. Curr. Protoc. Plant Biol. 1: 163-183.

Crowe, E.P., Tuzer, F., Gregory, B.D., Donahue, G., Gosai, S.J., Cohen, J., Leung, Y.Y., Yetkin, E., Nativio, R., Wang, L.S., Sell, C., Bonini, N.M., Berger, S.L., Johnson, F.B., and Torres, C. 2016. Changes in the transcriptome of human astrocytes accompanying oxidative stress-induced senescence. Front. Aging Neurosci. 8: 208.

Frederick, D.W., Loro, E., Liu, L., Davila, A. Jr., Chellappa, K., Silverman, I.M., Quinn, W.J. 3rd, Gosai, S.J., Tichy, E.D., Davis, J.G., Mourkioti, F., Gregory, B.D., Dellinger, R.W., Redpath, P., Migaud, M.E., Nakamaru-Ogiso, E., Rabinowitz, J.D., Khurana, T.S., and Baur, J.A. 2016. Loss of NAD homeostasis leads to progressive and reversible degeneration of skeletal muscle. Cell Metab. 24: 269-282.

Silverman I.M., Berkowitz, N.D., Gosai, S.J., and Gregory B.D. 2016. Genome-wide approaches for RNA structure probing. Adv. Exp. Med. Biol. 907: 29-59.

Berkowitz, N.D., Silverman, I.M., Childress, D.M., Wang, L.S., and Gregory, B.D. 2016. A comprehensive database of high-throughout sequencing-based RNA secondary structure probing data (Structure Surfer). BMC Bioinformatics 17: 215.

Pasoreck, E., Su, J., Silverman, I., Gosai, S., Gregory, B.D., Yuan, J., and Daniell, H. 2016.  Terpene metabolic engineering via nuclear or chloroplast genomes profoundly and globally impacts off-target pathways through metabolite signaling. Plant Biotechnol. J. 14: 1862-1875.

Vandivier, L.E., Anderson, S.J., Foley, S.W., and Gregory B.D. 2016. The conservation and function of RNAsecondary structure in plants. Annu. Rev. Plant Biol. 67: 463-488.

Lorenzi, H., Khan, A., Behnke, M.S., Namasivayam, S., Swapna, L.S., Hadjithomas, M., Karamycheva, S., Pinney, D., Brunk, B.P., Ajioka, J.W., Ajzenberg, D., Boothroyd, J.C., Boyle, J.P., Dardé, M.L., Diaz-Miranda, M.A., Dubey, J.P., Fritz, H.M., Gennari, S.M., Gregory, B.D., Kim, K., Saeij, J.P., Su, C., White, M.W., Zhu, X.Q., Howe, D.K., Rosenthal, B.M., Grigg, M.E., Parkinson, J., Liu, L., Kissinger, J.C., Roos, D.S., and Sibley, D.L. 2016. Local admixture of amplified and diversified secreted pathogenesis determinants shapes mosaicToxoplasma gondii genomes. Nat. Commun. 7: 10147.

Zhao, X., Bergland, A.O., Behrman, E.L., Gregory, B.D., Petrov, D.A., and Schmidt, P.S. 2016. Global transcriptional profiling of diapause and climatic adaptation in Drosophila melanogaster. Mol. Biol. Evol. 33: 707-720.

Kini, H.K., Silverman, I.M., Ji, X., Gregory, B.D., and Liebhaber, S.A. 2015. Cytoplasmic poly(A) bidning protein-1 binds to genomically encoded sequences within mammalian mRNAs. RNA 22: 61-74.

Leung, Y.Y., Kuksa, P.P., Amlie-Wolf, A., Valladares, O., Ungar, L.H., Kannan, S.K., Gregory, B.D.*, and Wang, L.S.* 2016. DASHR: Database of small human noncoding RNAs. Nucleic Acids Res. 44: D216-D222. *denotes co-correspondents.


Vandivier, L.E., Campos, R., Kuksa, P.P., Silverman, I.M., Wang, L.S., and Gregory B.D. 2015. Chemical modifications mark alternatively spliced and uncapped messenger RNAs in Arabidopsis. Plant Cell 27: 3024-3037.

Yu, Z., Li, N., Parada, K., Li, F., Naqvi, A.S., Wang, S., Nakauka-Ddamba, A., Rao, S., Valvezan, A., Shankar, S., Deering, R.P., Klein, P.S., Kharas, M.G., Gregory, B.D., and Lengner, C.J. 2015. The Msi family of RNA binding proteins function redundantly as intestinal oncoproteins. Cell Rep. 13: 2440-2455.

Amlie-Wolf, A., Ryvkin, P., Tong, R., Dragomir, I., Suh, E., Xu, Y., Van Deerlin, V.M., Gregory, B.D., Kwong, L.K., Trojanowski, J.Q., Lee, V.M., Wang, L.S., and Lee, E.B. 2015. Transcriptomic changes due to cytoplasmic TDP-43 expression reveal dysregulation of histone transcripts and nuclear chromatin. PLoS ONE 10: e0141836.

Lin, J.J., Zhang, X., Xue, C., Zhang, H., Shashaty, M.G., Gosai, S., Grazioli, A., Hinkle, C., Caughey, J., Li., W., Susztak, K., Gregory, B.D., Li, M., and Reilly, M.P. 2015 The long noncoding RNA landscape in hypoxic and inflammatory renal epithelial injury. Am. J. Physiol. Renal Physiol. 309: F901-F913.

Foley, S.W., Vandivier, L.E., Kuksa, P.P., and Gregory, B.D. 2015. Transcriptome-wide measurement of plant RNA secondary structure. Curr. Opin. Plant Biol. 27: 36-43.

Payel, S., Dang, W., Donahue, G., Dai, J., Dorsey, J., Cao, X., Liu, W., Cao, K., Perry, R., Lee, J.Y., Wasko, B.M., Carr, D.T., He, C., Robison, B., Wagner, J., Gregory, B.D., Kaeberlein, M., Kennedy, B.K., Boeke, J.D., and Berger, S.L. 2015. H3K36 methylation promotes longevity by enhancing transcriptional fidelity. Genes Dev. 29: 1362-1376.

Zhang, H., Xue, C., Shah, R., Bermingham, K., Hinkle, C.C., Li, W., Rodrigues, A., Tabita-Martinez, J., Millar, J.S., Cuchel, M., Pashos, E.E., Liu, Y., Yan, R., Yang, W., Gosai, S.J., VanDorn, D., Chou, S.T., Gregory, B.D., Morrisey, E.E., Li, M., Rader, D.J., and Reilly, M.P. Functional analysis and transcriptomic profiling of iPSC-derived macrophages and their application in modeling mendelian disease. Circ. Res. 117: 17-28.

Wang, S., Li, N., Yousefi, M., Nakauka-Ddamba, A., Li, F., Parada, K., Rao, S., Minuesa, G., Katz, Y., Gregory, B.D., Kharas, M.G., Yu, Z., and Lengner, C.J. 2015. Transformation of the intestinal epithelium by the MSI2 RNA binding protein. Nat. Commun. 6: 6517.

Vandivier, L.E., Li, F., and Gregory B.D. 2015. High-throughput nuclease-mediated probing of RNA secondary structure in plant transcriptomes. Methods Mol. Biol. 1284: 41-70.

Stein, P., Rozhkov, N.V., Li, F., Cardenas, F.L., Davydenko, O., Vandivier, L.E., Gregory, B.D., Hannon, G.J., and Schultz, R.M. 2015. Essential role for endogenous siRNAs during meiosis in mouse oocytes. PLoS Genet. 11: e1005013.

Gosai, S.J., Foley, S.W., Wang, D., Silverman, I.M., Selamoglu, N., Nelson, A.D.L., Beilstein, M.A., Daldal, F., Deal, R.B., and Gregory, B.D. 2015. Global analysis of the RNA-protein interaction and RNA secondary structure landscapes of the Arabidopsis nucleus. Mol. Cell 57: 376-388.

Hwang, Y.C., Lin, C.F., Valladares, O., Malamon, J., Kuksa, P., Zheng, Q., Gregory, B.D.*, and Wang, L.S.* 2015. HIPPIE: A high-throughput identification pipeline for promoter-interacting enhancer elements. Bioinformatics 31: 1290-1292. * denotes co-correspondents.

Silverman, I.M. and Gregory, B.D. 2015. Transcriptome-wide ribonuclease-mediated protein footprinting to identify RNA-protein interaction sites. Methods 72: 76-85.

Li, S., Vandivier, L.E., Tu, B., Gao, L., Won, S.Y., Li, S., Zheng, B., Gregory, B.D., and Chen, X. 2015. Detection of PolIV/RDR2-dependent transcripts at the genomic scale in Arabidopsis reveals features and regulation of siRNA biogenesis. Genome Res. 25: 235-245.


Liu, X., Zheng, Q., Vrettos, N., Maragkakis, M., Alexiou, P., Gregory, B.D., and Mourelatos, Z. 2014. A microRNA surveillance system in quality control of microRNA synthesis. Mol. Cell 55: 868-879.

Dang, W., Sutphin, G.L., Dorsey, J.A., Otte G.L., Cao, K., Perry, R.M., Wanat, J.J., Saviolaki, D., Murakami, C.J., Tsuchiyama, S., Robison, B., Gregory, B.D., Vermeulen, M., Shiekhattar, R., Johnson, F.B., Kennedy, B.K., Kaeberlein, M., and Berger, S.L. 2014. Repression of yeast Isw2 chromatin remodeling mimics the longevity effect of calorie restriction by potentiating genotoxic stress response. Cell Metab. 19: 952-966.

Ihara, M., Meyer-Ficca, M.L., Leu, N.A., Rao, S., Li, F., Gregory, B.D., Zalenskaya, I.A., Schultz R.M., and Meyer, R.G. 2014. Paternal poly(ADP-ribose) metabolism modulates retention of inheritable sperm histones and early embryonic gene expression. PLoS Genet. 10: e1004317.

Gregory, B.D.* and Meyers, B.C.* 2014. Genomic approaches for transcriptional and post-transcriptional processes. Methods 67: 1-2. * denotes co-correspondents.

Willmann, M.R., Berkowitz, N.D., and Gregory, B.D. Improved genome-wide mapping of uncapped and cleaved transcripts in eukaryotes-GMUCT2.0. Methods 67: 64-73.

Ryvkin, P., Leung, Y,Y., Ungar, L., Gregory, B.D.*, and Wang, L.S.* 2014. Using machine learning and high-throughput RNA sequencing to characterize small non-coding RNAs. Methods 67: 28-35. * denotes co-correspondents.

Liu, Y., Ferguson, J.F., Xue, C., Ballantyne, R., Silverman, I.M., Gosai, S.J., Serfecz, J., Morley, M.P., Gregory, B.D., Li, M., and Reilly, M.P. 2014. Tissue-specific RNA-seq in human evoked inflammation identifies blood and adipose lincRNA signatures of cardio-metabolic diseases. Arterioscler. Thromb. Vasc. Biol. 34: 902-912.

Silverman, I.M., Li, F., Alexander, A., Goff, L., Trapnell, C., Rinn, J.L., and Gregory, B.D. 2014. RNase-mediated protein footprint sequencing reveals protein-binding sites throughout the human transcriptome.Genome Biol. 15: R3.


Ryvkin, P., Leung, Y,Y., Silverman, I., Childress, M., Valladares, O., Dragomir, I., Gregory, B.D.*, and Wang, L.S.* 2013. HAMR: High throughput Annotation of Modified Ribonucleotides. RNA 19: 1684-1692. * denotes co-correspondents.

Elliot, R., Li, F., Dragomir, I., Chua, M.M.W., Gregory, B.D., and Weiss, S.R. 2013. Analysis of the host transcriptome from demyelinating spinal cord of murine coronavirus-infected mice. PLoS ONE 8: e75346.

Shah, P.P., Donahue, G., Otte, G.L., Capell, B.C., Nelson, D.M., Cao, K., Aggarwala, V., Cruickshanks, H.A., Rai, T.S., McBryan, T., Gregory, B.D., Adams, P.D., and Berger, S.L. 2013. Lamin B1 depletion in senescent cells triggers large-scale changes in gene expression and the chromatin landscape. Genes Dev. 27: 1787-1799.

Liu, Y., Ferguson, J.F., Xue, C., Silverman, I.M., Gregory, B., Reilly, M.P., and Li, M. 2013. Evaluating the impact of sequencing depth on transcriptome profiling in human adipose. PLoS ONE 8: e66883.

Leung, Y,Y., Ryvkin, P., Ungar, L., Gregory, B.D.*, and Wang, L.S.* 2013. CoRAL: predicting non-coding RNAs from small RNA-sequencing data. Nucleic Acids Res. 41: e137. * denotes co-correspondents.

Vandivier, L.E., Li, F., Zheng, Q., Willmann, M.R., Chen, Y., and Gregory, B.D. 2013. Arabidopsis mRNA secondary structure correlates with protein function and domains. Plant Signal. Behav. 8: e24301.

Hwang, Y-C., Zheng, Q., Gregory, B.D.*, and Wang, L.S.* 2013. High-throughput identification of long-range regulatory elements and their target promoters in the human genome. Nucleic Acids Res. 41: 4835-4846. * denotes co-correspondents.

Sabin, L.R., Zheng, Q., Thekkat, P., Yang, J., Hannon, G.J., Gregory, B.D.*, Tudor, M.*, and Cherry, S.* 2013. Dicer-2 processes diverse viral RNAs. PLoS ONE 8: e55458. * denotes co-correspondents.

Silverman, I.M., Li, F., and Gregory, B.D. 2013. Genomic era analyses of RNA secondary structure and RNA-binding proteins reveal their significance to post-transcriptional regulation in plants. Plant Sci. 205-206: 55-62.

Zheng, Q., Rowley, M.J., Bohmdorfer, G., Sandhu, D., Gregory, B.D.*, and Wierzbicki, A.T.* 2013. RNA Polymerase V targets transcriptional silencing components to promoters of protein-coding genes. Plant J. 73: 179-189.§
* denotes co-correspondents.
§. Plant J. cover article.


Li, F., Zheng, Q., Vandivier, L.E., Willmann, M.R., Chen, Y., and Gregory, B.D. 2012. Regulatory impact of RNA secondary structure across the Arabidopsis transcriptome. Plant Cell 24: 4346-4359.

Wierzbicki, A.T., Cocklin, R., Mayampurath, A., Lister, R., Rowley, M.J., Gregory, B.D., Ecker, J.R., Tang, H., and Pikaard, C.S. 2012. Spatial and functional relationships among Pol V-associated loci, Pol IV-dependent siRNAs, and cytosine methylation in the Arabidopsis epigenome. Genes Dev. 26: 1825-1836.

Vourekas, A., Zheng, Q., Alexiou, P., Maragkakis, M., Kirino, Y., Gregory, B.D., and Mourelatos, Z. 2012. Mili and Miwi target RNA repertoire reveals piRNA biogenesis and function of Miwi in spermiogenesis. Nat. Struct. Mol. Biol. 19: 773-781.

Li, F., Ryvkin, P., Childress, D.M., Valladares, O., Gregory, B.D.*, and Wang, L.S.* 2012. SAVoR: a server for sequencing annotation and visualization of RNA structures. Nucleic Acids Res. 40: W59-W64. * denotes co-correspondents.

Li, F., Zheng, Q., Ryvkin, P., Dragomir, I., Desai, Y., Aiyer, S., Valladares, O., Yang, J., Bambina, S., Sabin, L.R., Murray, J.I., Lamitina, T., Raj, A., Cherry, S., Wang, L.S., and Gregory, B.D. 2012. Global analysis of RNA secondary structure in two metazoans. Cell Rep. 1: 69-82.


Willmann, M.R., Endres, M.W., Cook R.T., and Gregory, B.D. 2011. The functions of RNA-dependent RNA Polymerases in Arabidopsis. The Arabidopsis Book 9: e0146.

Endres, M.W., Cook R.T., and Gregory, B.D. 2011. A High-Throughput Sequencing-Based Methodology to Identify All Uncapped and Cleaved RNA Molecules in Eukaryotic Genomes. Methods Mol. Biol. 732: 209-223.


Zheng, Q., Ryvkin, P., Li, F., Dragomir, I., Valladares, O., Yang, J., Cao, K., Wang, L.S., and Gregory, B.D.2010. Genome-wide double-stranded RNA sequencing reveals the functional significance of base-paired RNAs in Arabidopsis. PLoS Genet. 6: e1001141.

Earley, K., Smith, M., Weber, R., Gregory, B.D., and Poethig, R. 2010. An endogenous F-box protein regulates ARGONAUTE1 in Arabidopsis thaliana. Silence 1: 15.

Selected Postdoctoral Publications

Gregory, B.D., O’ Malley, R.C., Lister, R., Urich, M.A., Tonti-Filippini, J., Chen, H., Millar, A.H., and Ecker, J.R. 2008. A link between RNA metabolism and silencing affecting Arabidopsis development. Dev. Cell 14: 854-866.

Lister, R., O’ Malley, R.C., Tonti-Filippini, J., Gregory, B.D., Berry, C.C., Millar, A.H., and Ecker, J.R. 2008. Highly integrated single-base resolution maps of the epigenome in Arabidopsis. Cell 133: 523-536.

Chekanova, J.A.*, Gregory, B.D.*, Reverdatto, S.V., Chen, H., Kumar, R., Hooker, T., Yazaki, J., Li, P., Skiba, N., Peng, Q., Alonso, J., Brukhin, V., Grossniklaus, U., Ecker, J.R., and Belostotsky, D.A. 2007. Genome-wide high-resolution mapping of exosome substrates reveals hidden features in the Arabidopsis transcriptome. Cell 131: 1340-1353. *These authors contributed equally to this work.

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