Review: Genomic era analyses of RNA secondary structure and RNA-binding proteins reveal their significance to post-transcriptional regulation in plants

by Silverman, Ian M., Li, Fan, Gregory, Brian D.
Published 2013

Cytoplasmic poly(A) binding protein-1 binds to genomically encoded sequences within mammalian mRNAs

by Kini, Hemant K., Silverman, Ian M., Ji, Xinjun, Gregory, Brian D., Liebhaber, Stephen A.
Published in RNA (2016)

Evaluating the Impact of Sequencing Depth on Transcriptome Profiling in Human Adipose

by Liu, Yichuan, Ferguson, Jane F., Xue, Chenyi, Silverman, Ian M., Gregory, Brian, Reilly, Muredach P., Li, Mingyao
Published 2013

RNase-mediated protein footprint sequencing reveals protein-binding sites throughout the human transcriptome

by Silverman, Ian M, Li, Fan, Alexander, Anissa, Goff, Loyal, Trapnell, Cole, Rinn, John L, Gregory, Brian D
Published 2014

Chemical Modifications Mark Alternatively Spliced and Uncapped Messenger RNAs in Arabidopsis

by Vandivier, Lee E., Campos, Rafael, Kuksa, Pavel P., Silverman, Ian M., Wang, Li-San, Gregory, Brian D.
Published in Plant Cell (2015)

A comprehensive database of high-throughput sequencing-based RNA secondary structure probing data (Structure Surfer)

by Berkowitz, Nathan D., Silverman, Ian M., Childress, Daniel M., Kazan, Hilal, Wang, Li-San, Gregory, Brian D.
Published in BMC Bioinformatics (2016)

Terpene metabolic engineering via nuclear or chloroplast genomes profoundly and globally impacts off‐target pathways through metabolite signalling

by Pasoreck, Elise K., Su, Jin, Silverman, Ian M., Gosai, Sager J., Gregory, Brian D., Yuan, Joshua S., Daniell, Henry
Published in Plant Biotechnol J (2016)

HAMR: high-throughput annotation of modified ribonucleotides

by Ryvkin, Paul, Leung, Yuk Yee, Silverman, Ian M., Childress, Micah, Valladares, Otto, Dragomir, Isabelle, Gregory, Brian D., Wang, Li-San
Published 2013

Dynamic changes in RNA–protein interactions and RNA secondary structure in mammalian erythropoiesis

by Shan, Mengge, Ji, Xinjun, Janssen, Kevin, Silverman, Ian M, Humenik, Jesse, Garcia, Ben A, Liebhaber, Stephen A, Gregory, Brian D
Published in Life Sci Alliance (2021)

Poly(C)-Binding Protein Pcbp2 Enables Differentiation of Definitive Erythropoiesis by Directing Functional Splicing of the Runx1 Transcript

by Ghanem, Louis R., Kromer, Andrew, Silverman, Ian M., Ji, Xinjun, Gazzara, Matthew, Nguyen, Nhu, Aguilar, Gabrielle, Martinelli, Massimo, Barash, Yoseph, Liebhaber, Stephen A.
Published in Mol Cell Biol (2018)

The Poly(C) Binding Protein Pcbp2 and Its Retrotransposed Derivative Pcbp1 Are Independently Essential to Mouse Development

by Ghanem, Louis R., Kromer, Andrew, Silverman, Ian M., Chatterji, Priya, Traxler, Elizabeth, Penzo-Mendez, Alfredo, Weiss, Mitchell J., Stanger, Ben Z., Liebhaber, Stephen A.
Published in Mol Cell Biol (2016)

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

by Zhao, Taolan, Huan, Qing, Sun, Jing, Liu, Chunyan, Hou, Xiuli, Yu, Xiang, Silverman, Ian M., Zhang, Yi, Gregory, Brian D., Liu, Chun-Ming, Qian, Wenfeng, Cao, Xiaofeng
Published in Genome Biol (2019)

Global Analysis of the RNA-Protein Interaction and RNA Secondary Structure Landscapes of the Arabidopsis Nucleus

by Gosai, Sager J., Foley, Shawn W., Wang, Dongxue, Silverman, Ian M., Selamoglu, Nur, Nelson, Andrew D.L., Beilstein, Mark A., Daldal, Fevzi, Deal, Roger B., Gregory, Brian D.
Published in Mol Cell (2014)

Tissue-specific RNA-Seq in Human Evoked Inflammation Identifies Blood and Adipose LincRNA Signatures of Cardio-metabolic Diseases

by Liu, Yichuan, Ferguson, Jane F., Xue, Chenyi, Ballantyne, Rachel L., Silverman, Ian M., Gosai, Sager J., Serfecz, Jacquelyn, Morley, Michael P., Gregory, Brian D., Li, Mingyao, Reilly, Muredach P.
Published 2014

Loss of NAD homeostasis leads to progressive and reversible degeneration of skeletal muscle

by Frederick, David W., Loro, Emanuele, Liu, Ling, Davila, Antonio, Chellappa, Karthikeyani, Silverman, Ian M., Quinn, William J., Gosai, Sager J., Tichy, Elisia D., Davis, James G., Mourkioti, Foteini, Gregory, Brian D., Dellinger, Ryan W., Redpath, Philip, Migaud, Marie E., Nakamaru-Ogiso, Eiko, Rabinowitz, Joshua D., Khurana, Tejvir S., Baur, Joseph A.
Published in Cell Metab (2016)

Genomic Analysis of Posterior Fossa Meningioma Demonstrates Frequent AKT1 E17K Mutations in Foramen Magnum Meningiomas

by Williams, Sally R., Juratli, Tareq A., Castro, Brandyn A., Lazaro, Tyler T., Gill, Corey M., Nayyar, Naema, Strickland, Matthew R., Babinski, Melanie, Johnstone, Sarah E., Frosch, Matthew P., Silverman, Ian M., Ely, Heather A., Kaplan, Alexander B., D'Andrea, Megan R., Bihun, Ivanna V., Hoang, Kaitlin, Batchelor, Emily, Christiansen, Jason, Cahill, Daniel P., Barker, Frederick G., Brastianos, Priscilla K.
Published in J Neurol Surg B Skull Base (2019)

Intratumoral heterogeneity and TERT promoter mutations in progressive/higher-grade meningiomas

by Juratli, Tareq A., Thiede, Christian, Koerner, Mara V.A., Tummala, Shilpa S., Daubner, Dirk, Shankar, Ganesh M., Williams, Erik A., Martinez-Lage, Maria, Soucek, Silke, Robel, Katja, Penson, Tristan, Krause, Mechthild, Appold, Steffen, Meinhardt, Matthias, Pinzer, Thomas, Miller, Julie J., Krex, Dietmar, Ely, Heather A., Silverman, Ian M., Christiansen, Jason, Schackert, Gabriele, Wakimoto, Hiroaki, Kirsch, Matthias, Brastianos, Priscilla K., Cahill, Daniel P.
Published in Oncotarget (2017)