Uncovering a mammalian neural-specific poly(A) binding protein with unique properties

Authors: Sharma, Sahil, Kajjo, Sam, Harra, Zineb, Hasaj, Benedeta, Delisle, Victoria, Ray, Debashish, Gutierrez, Rodrigo L., Carrier, Isabelle, Kleinman, Claudia, Morris, Quaid

Source: GENES AND DEVELOPMENT. 37(15/16):760-777

Availability: http://explore.bl.uk/primo_library/libweb/action/display.do?tabs=detailsTab&gathStatTab=true&ct=display&fn=search&doc=ETOCRN632586033&indx=1&recIds=ETOCRN632586033

Regulation of alternative polyadenylation by the C2H2-zinc-finger protein Sp1

Authors: Song, Jingwen, Nabeel-Shah, Syed, Pu, Shuye, Lee, Hyunmin, Braunschweig, Ulrich, Ni, Zuyao, Ahmed, Nujhat, Marcon, Edyta, Zhong, Guoqing, Ray, Debashish, Ha, Kevin C.H., Guo, Xinghua, Zhang, Zhaolei, Hughes, Timothy R., Blencowe, Benjamin J., Greenblatt, Jack F.

Source: In Molecular Cell 1 September 2022 82(17):3135-3150

RNA-binding proteins that lack canonical RNA-binding domains are rarely sequence-specific.

Authors: Ray, Debashish¹ (AUTHOR), Laverty, Kaitlin U.^1,2 (AUTHOR), Jolma, Arttu¹ (AUTHOR), Nie, Kate^1,2 (AUTHOR), Samson, Reuben^1,2 (AUTHOR), Pour, Sara E.^1,2 (AUTHOR), Tam, Cyrus L.^3,4 (AUTHOR), von Krosigk, Niklas^1,2 (AUTHOR), Nabeel-Shah, Syed^1,2 (AUTHOR), Albu, Mihai¹ (AUTHOR), Zheng, Hong¹ (AUTHOR), Perron, Gabrielle^5,6 (AUTHOR), Lee, Hyunmin¹ (AUTHOR), Najafabadi, Hamed^5,6 (AUTHOR), Blencowe, Benjamin^1,2 (AUTHOR), Greenblatt, Jack^1,2 (AUTHOR), Morris, Quaid^1,2,3,4 (AUTHOR) morrisq@mskcc.org, Hughes, Timothy R.^1,2 (AUTHOR) t.hughes@utoronto.ca

Source: Scientific Reports. 3/31/2023, Vol. 13 Issue 1, p1-15. 15p.

Subject Terms: *RNA-binding proteins, *NUCLEOTIDE sequence, *PROTEOMICS, *RNA, *RIBOSOMAL proteins, *PROTEINS

RNAcompete-S: Combined RNA sequence/structure preferences for RNA binding proteins derived from a single-step in vitro selection

Authors: Cook, Kate B., Vembu, Shankar, Ha, Kevin C.H., Zheng, Hong, Laverty, Kaitlin U., Hughes, Timothy R., Ray, Debashish, Morris, Quaid D.

Source: In Methods 15 August 2017 126:18-28

Oncogenic Activation of the RNA Binding Protein NELFE and MYC Signaling in Hepatocellular Carcinoma

Authors: Dang, Hien, Takai, Atsushi, Forgues, Marshonna, Pomyen, Yotsowat, Mou, Haiwei, Xue, Wen, Ray, Debashish, Ha, Kevin C.H., Morris, Quaid D., Hughes, Timothy R., Wang, Xin Wei

Source: In Cancer Cell 10 July 2017 32(1):101-114

RNAcompete methodology and application to determine sequence preferences of unconventional RNA-binding proteins

Authors: Ray, Debashish, Ha, Kevin C.H., Nie, Kate, Zheng, Hong, Hughes, Timothy R., Morris, Quaid D.

Source: In Methods 15 April 2017 118-119:3-15

Development of a Mobile Robot for Remote Radiation Measurement
Advancements in Automation, Robotics and Sensing (International conference)

Authors: Sarkar, Ushnish, Saini, Surendra Singh, Swaroop, Tumapala Teja, Sreejith, P., Kumar, Ravinder, Ray, Debashish Datta

Source: Communications in computer and information science. 627:65-73

Availability: http://explore.bl.uk/primo_library/libweb/action/display.do?tabs=detailsTab&gathStatTab=true&ct=display&fn=search&doc=ETOCCN601860003&indx=1&recIds=ETOCCN601860003

Multilayered Control of Alternative Splicing Regulatory Networks by Transcription Factors

Authors: Han, Hong, Braunschweig, Ulrich, Gonatopoulos-Pournatzis, Thomas, Weatheritt, Robert J., Hirsch, Calley L., Ha, Kevin C.H., Radovani, Ernest, Nabeel-Shah, Syed, Sterne-Weiler, Tim, Wang, Juli, O’Hanlon, Dave, Pan, Qun, Ray, Debashish, Zheng, Hong, Vizeacoumar, Frederick, Datti, Alessandro, Magomedova, Lilia, Cummins, Carolyn L., Hughes, Timothy R., Greenblatt, Jack F., Wrana, Jeffrey L., Moffat, Jason, Blencowe, Benjamin J.

Source: In Molecular Cell 2 February 2017 65(3):539-553

A Chemical Biology Approach to Model Pontocerebellar Hypoplasia Type 1B (PCH1B)

Authors: François-Moutal, Liberty, Jahanbakhsh, Shahriyar, Nelson, Andrew D. L., Ray, Debashish, Scott, David D., Hennefarth, Matthew R., Moutal, Aubin, Perez-Miller, Samantha, Ambrose, Andrew J., Al-Shamari, Ahmed

Source: ACS chemical biology. 13(10):3000-3010

Availability: http://explore.bl.uk/primo_library/libweb/action/display.do?tabs=detailsTab&gathStatTab=true&ct=display&fn=search&doc=ETOCRN617901017&indx=1&recIds=ETOCRN617901017

The Crystal Structure of the NHL Domain in Complex with RNA Reveals the Molecular Basis of Drosophila Brain-Tumor-Mediated Gene Regulation

Authors: Loedige, Inga, Jakob, Leonhard, Treiber, Thomas, Ray, Debashish, Stotz, Mathias, Treiber, Nora, Hennig, Janosch, Cook, Kate B., Morris, Quaid, Hughes, Timothy R., Engelmann, Julia C., Krahn, Michael P., Meister, Gunter

Source: In Cell Reports 10 November 2015 13(6):1206-1220

A Pair of RNA-Binding Proteins Controls Networks of Splicing Events Contributing to Specialization of Neural Cell Types

Authors: Norris, Adam D., Gao, Shangbang, Norris, Megan L., Ray, Debashish, Ramani, Arun K., Fraser, Andrew G., Morris, Quaid, Hughes, Timothy R., Zhen, Mei, Calarco, John A.

Source: In Molecular Cell 19 June 2014 54(6):946-959

The X-linked splicing regulator MBNL3 has been co-opted to restrict placental growth in eutherians.

Authors: Spruce, Thomas¹, thomas.spruce@crg.eu, Plass, Mireya^1,2,3, Gohr, André¹, Ray, Debashish⁴, Martínez de Lagrán, María¹, Rot, Gregor⁵, Nóvoa, Ana⁶, Burguera, Demian¹, Permanyer, Jon¹, Miret, Marta¹, Zheng, Hong⁴, Swanson, Maurice S.⁷, Morris, Quaid⁴, Mallo, Moises⁶, Dierssen, Mara^1,8,9, Hughes, Timothy R.⁴, Pernaute, Barbara¹, thomas.spruce@crg.eu, Irimia, Manuel^1,8,10, thomas.spruce@crg.eu

Source: PLoS Biology; 4/27/2022, Vol. 20 Issue 4, p1-30, 30p, 5 Graphs

The RNA-binding protein SERBP1 functions as a novel oncogenic factor in glioblastoma by bridging cancer metabolism and epigenetic regulation

Authors: Kosti, Adam, de Araujo, Patricia Rosa, Li, Wei-Qing, Guardia, Gabriela D. A., Chiou, Jennifer, Yi, Caihong, Ray, Debashish, Meliso, Fabiana, Li, Yi-Ming, Delambre, Talia, Qiao, Mei, Burns, Suzanne S., Lorbeer, Franziska K., Georgi, Fanny, Flosbach, Markus, Klinnert, Sarah, Jenseit, Anne, Lei, Xiufen, Sandoval, Carolina Romero, Ha, Kevin, Zheng, Hong, Pandey, Renu, Gruslova, Aleksandra, Gupta, Yogesh K., Brenner, Andrew, Kokovay, Erzsebet, Hughes, Timothy R., Morris, Quaid D., Galante, Pedro A. F., Tiziani, Stefano, Penalva, Luiz O. F.

Source: Genome biology. 21(1)

Availability: http://explore.bl.uk/primo_library/libweb/action/display.do?tabs=detailsTab&gathStatTab=true&ct=display&fn=search&doc=ETOCvdc_100171988624.0x000001&indx=1&recIds=ETOCvdc_100171988624.0x000001

Large-scale interaction profiling of PDZ domains through proteomic peptide-phage display using human and viral phage peptidomes

Authors: Ivarsson, Ylva, Arnold, Roland, McLaughlin, Megan, Nim, Satra, Joshi, Rakesh, Ray, Debashish, Liu, Bernard, Teyra, Joan, Pawson, Tony, Moffat, Jason, Li, Shawn Shun-Cheng, Sidhu, Sachdev S., Kim, Philip M.

Source: Proceedings of the National Academy of Sciences of the United States of America, 2014 Feb . 111(7), 2542-2547.

Access URL: https://www.jstor.org/stable/23768924

3′-Terminal RNA secondary structures are important for accumulation of tomato bushy stunt virus DI RNAs.

Authors: Fabian, Marc R., Na, Hong, Ray, Debashish

Source: Virology; September 1 2003, Vol. 313 Issue 2, p567-580, 14p

A compendium of RNA-binding motifs for decoding gene regulation.

Authors: Ray, Debashish¹, Kazan, Hilal², Cook, Kate B.³, Weirauch, Matthew T.⁴, Najafabadi, Hamed S.⁵, Li, Xiao⁶, Gueroussov, Serge⁶, Albu, Mihai⁷, Zheng, Hong⁷, Yang, Ally⁷, Na, Hong⁷, Irimia, Manuel⁷, Matzat, Leah H.⁸, Dale, Ryan K.⁸, Smith, Sarah A.⁹, Yarosh, Christopher A.⁹, Kelly, Seth M.¹⁰, Nabet, Behnam⁹, Mecenas, Desirea¹¹, Li, Weimin¹²

Source: Nature. 7/11/2013, Vol. 499 Issue 7457, p172-177. 6p. 5 Graphs.

Subject Terms: *RIBONUCLEASES, *GENES, *EUKARYOTES, *PHYSIOLOGY, *DISEASES, *PROTEINS

RNAcontext: A New Method for Learning the Sequence and Structure Binding Preferences of RNA-Binding Proteins.

Authors: Kazan, Hilal¹, Ray, Debashish², Chan, Esther T.³, Hughes, Timothy R.^2,3,4, Morris, Quaid^1,2,3,4 quaid.morris@utoronto.ca

Source: PLoS Computational Biology. Jul2010, Vol. 6 Issue 7, p1-10. 10p. 2 Diagrams, 1 Chart, 3 Graphs.

Subject Terms: *CARRIER proteins, *NUCLEOTIDE sequence, *GENOMICS, *BIOMOLECULES, *RNA

Rapid and systematic analysis of the RNA recognition specificities of RNA-binding proteins.

Authors: Ray, Debashish, Kazan, Hilal, Chan, Esther T.

Source: Nature Biotechnology; July 2009, Vol. 27 Issue 7, p667-670, 4p

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Enhancer-like Properties of an RNA Element That Modulates Tombusvirus RNA Accumulation

Authors: Ray, Debashish, White, K.Andrew

Source: In Virology 30 March 1999 256(1):162-171