Relevant bibliographies by topics / RNA-protein interactions. Protein binding. RNA splicing

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  2. Dissertations / Theses
  3. Books
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  5. Conference papers

Academic literature on the topic 'RNA-protein interactions. Protein binding. RNA splicing'

Author: Grafiati
Published: 4 June 2021
Last updated: 11 February 2022

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Journal articles on the topic "RNA-protein interactions. Protein binding. RNA splicing"

1

Sawicka, Kirsty, Martin Bushell, Keith A. Spriggs, and Anne E. Willis. "Polypyrimidine-tract-binding protein: a multifunctional RNA-binding protein." Biochemical Society Transactions 36, no. 4 (2008): 641–47. http://dx.doi.org/10.1042/bst0360641.

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PTB (polypyrimidine-tract-binding protein) is a ubiquitous RNA-binding protein. It was originally identified as a protein with a role in splicing but it is now known to function in a large number of diverse cellular processes including polyadenylation, mRNA stability and translation initiation. Specificity of PTB function is achieved by a combination of changes in the cellular localization of this protein (its ability to shuttle from the nucleus to the cytoplasm is tightly controlled) and its interaction with additional proteins. These differences in location and trans-acting factor requiremen
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Das, Arundhati, Tanvi Sinha, Sharmishtha Shyamal, and Amaresh Chandra Panda. "Emerging Role of Circular RNA–Protein Interactions." Non-Coding RNA 7, no. 3 (2021): 48. http://dx.doi.org/10.3390/ncrna7030048.

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Circular RNAs (circRNAs) are emerging as novel regulators of gene expression in various biological processes. CircRNAs regulate gene expression by interacting with cellular regulators such as microRNAs and RNA binding proteins (RBPs) to regulate downstream gene expression. The accumulation of high-throughput RNA–protein interaction data revealed the interaction of RBPs with the coding and noncoding RNAs, including recently discovered circRNAs. RBPs are a large family of proteins known to play a critical role in gene expression by modulating RNA splicing, nuclear export, mRNA stability, localiz
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Lang, Benjamin, Jae-Seong Yang, Mireia Garriga-Canut, et al. "Matrix-screening reveals a vast potential for direct protein-protein interactions among RNA binding proteins." Nucleic Acids Research 49, no. 12 (2021): 6702–21. http://dx.doi.org/10.1093/nar/gkab490.

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Abstract RNA-binding proteins (RBPs) are crucial factors of post-transcriptional gene regulation and their modes of action are intensely investigated. At the center of attention are RNA motifs that guide where RBPs bind. However, sequence motifs are often poor predictors of RBP-RNA interactions in vivo. It is hence believed that many RBPs recognize RNAs as complexes, to increase specificity and regulatory possibilities. To probe the potential for complex formation among RBPs, we assembled a library of 978 mammalian RBPs and used rec-Y2H matrix screening to detect direct interactions between RB
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Shi, H., B. E. Hoffman, and J. T. Lis. "A specific RNA hairpin loop structure binds the RNA recognition motifs of the Drosophila SR protein B52." Molecular and Cellular Biology 17, no. 5 (1997): 2649–57. http://dx.doi.org/10.1128/mcb.17.5.2649.

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B52, also known as SRp55, is a member of the Drosophila melanogaster SR protein family, a group of nuclear proteins that are both essential splicing factors and specific splicing regulators. Like most SR proteins, B52 contains two RNA recognition motifs in the N terminus and a C-terminal domain rich in serine-arginine dipeptide repeats. Since B52 is an essential protein and is expected to play a role in splicing a subset of Drosophila pre-mRNAs, its function is likely to be mediated by specific interactions with RNA. To investigate the RNA-binding specificity of B52, we isolated B52-binding RN
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Soucek, Sharon, Yi Zeng, Deepti L. Bellur, et al. "Evolutionarily Conserved Polyadenosine RNA Binding Protein Nab2 Cooperates with Splicing Machinery To Regulate the Fate of Pre-mRNA." Molecular and Cellular Biology 36, no. 21 (2016): 2697–714. http://dx.doi.org/10.1128/mcb.00402-16.

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Numerous RNA binding proteins are deposited onto an mRNA transcript to modulate posttranscriptional processing events ensuring proper mRNA maturation. Defining the interplay between RNA binding proteins that couple mRNA biogenesis events is crucial for understanding how gene expression is regulated. To explore how RNA binding proteins control mRNA processing, we investigated a role for the evolutionarily conserved polyadenosine RNA binding protein, Nab2, in mRNA maturation within the nucleus. This study reveals thatnab2mutant cells accumulate intron-containing pre-mRNAin vivo. We extend this a
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Delgado Blanco, Javier, Leandro G. Radusky, Damiano Cianferoni, and Luis Serrano. "Protein-assisted RNA fragment docking (RnaX) for modeling RNA–protein interactions using ModelX." Proceedings of the National Academy of Sciences 116, no. 49 (2019): 24568–73. http://dx.doi.org/10.1073/pnas.1910999116.

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RNA–protein interactions are crucial for such key biological processes as regulation of transcription, splicing, translation, and gene silencing, among many others. Knowing where an RNA molecule interacts with a target protein and/or engineering an RNA molecule to specifically bind to a protein could allow for rational interference with these cellular processes and the design of novel therapies. Here we present a robust RNA–protein fragment pair-based method, termed RnaX, to predict RNA-binding sites. This methodology, which is integrated into the ModelX tool suite (http://modelx.crg.es), take
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Markovtsov, Vadim, Julia M. Nikolic, Joseph A. Goldman, Christoph W. Turck, Min-Yuan Chou, and Douglas L. Black. "Cooperative Assembly of an hnRNP Complex Induced by a Tissue-Specific Homolog of Polypyrimidine Tract Binding Protein." Molecular and Cellular Biology 20, no. 20 (2000): 7463–79. http://dx.doi.org/10.1128/mcb.20.20.7463-7479.2000.

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ABSTRACT Splicing of the c-src N1 exon in neuronal cells depends in part on an intronic cluster of RNA regulatory elements called the downstream control sequence (DCS). Using site-specific cross-linking, RNA gel shift, and DCS RNA affinity chromatography assays, we characterized the binding of several proteins to specific sites along the DCS RNA. Heterogeneous nuclear ribonucleoprotein (hnRNP) H, polypyrimidine tract binding protein (PTB), and KH-type splicing-regulatory protein (KSRP) each bind to distinct elements within this sequence. We also identified a new 60-kDa tissue-specific protein
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Burgute, Bhagyashri D., Vivek S. Peche, Anna-Lena Steckelberg, et al. "NKAP is a novel RS-related protein that interacts with RNA and RNA binding proteins." Nucleic Acids Research 42, no. 5 (2013): 3177–93. http://dx.doi.org/10.1093/nar/gkt1311.

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Abstract NKAP is a highly conserved protein with roles in transcriptional repression, T-cell development, maturation and acquisition of functional competency and maintenance and survival of adult hematopoietic stem cells. Here we report the novel role of NKAP in splicing. With NKAP-specific antibodies we found that NKAP localizes to nuclear speckles. NKAP has an RS motif at the N-terminus followed by a highly basic domain and a DUF 926 domain at the C-terminal region. Deletion analysis showed that the basic domain is important for speckle localization. In pull-down experiments, we identified R
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Mattaj, Iain W. "A binding consensus: RNA-protein interactions in splicing, snRNPs, and sex." Cell 57, no. 1 (1989): 1–3. http://dx.doi.org/10.1016/0092-8674(89)90164-5.

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Kafasla, Panagiota, Ian Mickleburgh, Miriam Llorian, et al. "Defining the roles and interactions of PTB." Biochemical Society Transactions 40, no. 4 (2012): 815–20. http://dx.doi.org/10.1042/bst20120044.

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PTB (polypyrimidine tract-binding protein) is an abundant and widely expressed RNA-binding protein with four RRM (RNA recognition motif) domains. PTB is involved in numerous post-transcriptional steps in gene expression in both the nucleus and cytoplasm, but has been best characterized as a regulatory repressor of some ASEs (alternative splicing events), and as an activator of translation driven by IRESs (internal ribosome entry segments). We have used a variety of approaches to characterize the activities of PTB and its molecular interactions with RNA substrates and protein partners. Using sp
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Dissertations / Theses on the topic "RNA-protein interactions. Protein binding. RNA splicing"

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Cass, Danielle Marie. "Role of two RNA binding properties in pre-mRNA splicing /." view abstract or download file of text, 2007. http://proquest.umi.com/pqdweb?did=1400950811&sid=2&Fmt=2&clientId=11238&RQT=309&VName=PQD.

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Thesis (Ph. D.)--University of Oregon, 2007.<br>Typescript. Includes vita and abstract. Includes bibliographical references (leaves 67-80). Also available for download via the World Wide Web; free to University of Oregon users.
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Henscheid, Kristy L. "Functional conservation and RNA binding of the pre-mRNA splicing factor U2AF65 /." view abstract or download file of text, 2007. http://proquest.umi.com/pqdweb?did=1400950821&sid=5&Fmt=2&clientId=11238&RQT=309&VName=PQD.

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Thesis (Ph. D.)--University of Oregon, 2007.<br>Typescript. Includes vita and abstract. Includes bibliographical references (leaves 129-141). Also available for download via the World Wide Web; free to University of Oregon users.
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Huang, Ching-jung. "The role of HnRNP proteins, PSF and nonO/p54[superscript nrb], in pre-mRNA binding and splicing /." Full text (PDF) from UMI/Dissertation Abstracts International, 2000. http://wwwlib.umi.com/cr/utexas/fullcit?p3004292.

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Garrey, Stephen M. "Characterization of the specificity and affinity of the splicing factor BBP/SF1 /." view abstract or download file of text, 2007. http://proquest.umi.com/pqdweb?did=1324375731&sid=2&Fmt=2&clientId=11238&RQT=309&VName=PQD.

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Thesis (Ph. D.)--University of Oregon, 2007.<br>Typescript. Includes vita and abstract. Includes bibliographical references (leaves 81-88). Also available for download via the World Wide Web; free to University of Oregon users.
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Joshi, Amar. "Investigating the protein and RNA interactions of the Polypyrimidine Tract Binding protein : high resolution structures with implications in the regulation of alternative splicing." Thesis, Imperial College London, 2012. http://hdl.handle.net/10044/1/9645.

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Alternative splicing produces multiple mRNAs from a single gene. It is a powerful mechanism used to amplify complexity of the metazoan proteome. The Polypyrimidine Tract Binding protein (PTB) is a key regulator of alternative splicing. In addition, it has roles in the localization and stability of mRNA and is involved in IRES mediated translation initiation. It has four RNA recognition motif domains (RRMs) which consist of two α‐helices which pack against a β‐sheet. The RRMs act in concert to direct splicing as each RRM binds pyrimidine rich RNA (UCUU or CUCUCU) across the β‐sheet. Solution st
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Meznad, Koceila. "Interaction entre l’oncoprotéine E6 d’HPV16 et le métabolisme des ARN messagers." Thesis, Bourgogne Franche-Comté, 2018. http://www.theses.fr/2018UBFCE012.

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Les papillomavirus humains (HPV) sont des virus à ADN double brin qui infectent la peau et les muqueuses. Les infections par les HPV, bien que majoritairement asymptomatique, provoquent des défauts de prolifération cellulaire pouvant parfois générer des cancers. Selon leur pouvoir carcinogène, on distingue les HPV à bas risque oncogène (HPV-BR) provoquant des lésions bénignes, et les HPV à haut risque (HPV-HR) responsables de l’apparition de nombreux cancers ano-génitaux et de certains cancers des voies aéro-digestives supérieures. Parmi les HPV-HR, HPV16 est le plus prévalent. La carcinogenès
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Hahn, Daniela. "Brr2 RNA helicase and its protein and RNA interactions." Thesis, University of Edinburgh, 2011. http://hdl.handle.net/1842/5775.

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The dynamic rearrangements of RNA and protein complexes and the fidelity of pre-mRNA splicing are governed by DExD/H-box ATPases. One of the spliceosomal ATPases, Brr2, is believed to facilitate conformational rearrangements during spliceosome activation and disassembly. It features an unusual architecture, with two consecutive helicase-cassettes, each comprising a helicase and a Sec63 domain. Only the N-terminal cassette exhibits catalytic activity. By contrast, the C-terminal half of Brr2 engages in protein interactions. Amongst interacting proteins are the Prp2 and Prp16 helicases. The work
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Öhrmalm, Christina. "Functional characterization of the cellular protein p32 : a protein regulating adenovirus transcription and splicing through targeting of phosphorylation /." Uppsala : Acta Universitatis Upsaliensis : Univ.-bibl. [distributör], 2006. http://urn.kb.se/resolve?urn=urn:nbn:se:uu:diva-6794.

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Wang, Weizhong. "Nuclear galectins and their role in pre-mRNA splicing." Diss., Connect to online resource - MSU authorized users, 2006.

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Thesis (Ph. D.)--Michigan State University. Dept. of Microbiology and Molecular Genetics, 2006.<br>Title from PDF t.p. (viewed on Nov. 20, 2008) Includes bibliographical references. Also issued in print.
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Murray, Jill Isobel. "Identification of motifs that function in the splicing of non-canonical introns /." Connect to title online (ProQuest), 2007. http://proquest.umi.com/pqdweb?did=1453227351&sid=1&Fmt=2&clientId=11238&RQT=309&VName=PQD.

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Thesis (Ph. D.)--University of Oregon, 2007.<br>Typescript. Includes vita and abstract. Includes bibliographical references (leaves 76-84). Also available online in ProQuest, free to University of Oregon users.
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Books on the topic "RNA-protein interactions. Protein binding. RNA splicing"

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Steitz, Thomas A. Structural studies of protein-nucleic acid interaction: Thesources of sequence-specific binding. Cambridge University Press, 1993.

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Steitz, Thomas A. Structural studies of protein-nucleic acid interaction: The sources of sequence-specific binding. Cambridge University Press, 1993.

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Travers, A. A. DNA-protein interactions. Chapman & Hall, 1993.

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Post-transcriptional regulation by STAR proteins : control of RNA metabolism in development and disease. Springer Science+Business Media, LLC, 2010.

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Ren-Jang, Lin, ed. RNA-protein interaction protocols. 2nd ed. Humana, 2008.

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Ren-Jang, Lin, ed. RNA-protein interaction protocols. 2nd ed. Humana, 2008.

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(Editor), Kathryn Sandberg, and Susan E. Mulroney (Editor), eds. RNA Binding Proteins: New Concepts in Gene Regulation (Endocrine Updates). Springer, 2001.

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Yeo, Gene W. Systems Biology of RNA Binding Proteins. Springer, 2014.

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Rna Protein Interaction Protocols: Preliminary Entry 2139 (Methods in Molecular Biology). 2nd ed. Humana Press, 2008.

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Kuhel, David Gerald. Mutation of 4f-rnp, an RNA-binding protein, through local hop P-element mutagenesis. 1999.

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Book chapters on the topic "RNA-protein interactions. Protein binding. RNA splicing"

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Marmier-Gourrier, Nathalie, Audrey Vautrin, Christiane Branlant, and Isabelle Behm-Ansmant. "Analysis of Site-Specific RNA-Protein Interactions." In Alternative pre-mRNA Splicing. Wiley-VCH Verlag GmbH & Co. KGaA, 2012. http://dx.doi.org/10.1002/9783527636778.ch32.

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Greulich, Karl Otto. "Intrinsic Fluorescence Techniques for Studies on Protein-Protein and Protein-RNA Interactions in RNP Particles." In RNP Particles, Splicing and Autoimmune Diseases. Springer Berlin Heidelberg, 1998. http://dx.doi.org/10.1007/978-3-642-80356-7_3.

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Schenckbecher, Emma, Guillaume Bec, Taiichi Sakamoto, Benoit Meyer, and Eric Ennifar. "Biophysical Studies of the Binding of Viral RNA with the 80S Using switchSENSE." In Protein-Ligand Interactions. Springer US, 2021. http://dx.doi.org/10.1007/978-1-0716-1197-5_15.

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Jens, Marvin. "Binding Site Occupancy with Competition Interactions in Equilibrium." In Dissecting Regulatory Interactions of RNA and Protein. Springer International Publishing, 2014. http://dx.doi.org/10.1007/978-3-319-07082-7_4.

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Ven Murthy, M. R., and Lise Carrier-Malhotra. "Progressive Unfolding of the Conformational States of Transfer RNA and Ribosomal 5S RNA by Methylene Blue Binding." In Protein-Dye Interactions: Developments and Applications. Springer Netherlands, 1989. http://dx.doi.org/10.1007/978-94-009-1107-9_32.

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Munschauer, Mathias. "Mapping Regulatory Interactions of the RNA-Binding Protein LIN28B." In High-Resolution Profiling of Protein-RNA Interactions. Springer International Publishing, 2015. http://dx.doi.org/10.1007/978-3-319-16253-9_2.

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Jens, Marvin. "Transcriptome-Wide Analysis of Regulatory Interactions of the RNA-Binding Protein HuR." In Dissecting Regulatory Interactions of RNA and Protein. Springer International Publishing, 2014. http://dx.doi.org/10.1007/978-3-319-07082-7_3.

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Munschauer, Mathias. "Exploring the Sequence Space Contacted by the Ensemble of RNA-Binding Proteins." In High-Resolution Profiling of Protein-RNA Interactions. Springer International Publishing, 2015. http://dx.doi.org/10.1007/978-3-319-16253-9_3.

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Tollervey, James, and Jernej Ule. "The CLIP Method to Study Protein-RNA Interactions in Intact Cells and Tissues." In Alternative pre-mRNA Splicing. Wiley-VCH Verlag GmbH & Co. KGaA, 2012. http://dx.doi.org/10.1002/9783527636778.ch25.

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Van Nostrand, Eric L., Stephanie C. Huelga, and Gene W. Yeo. "Experimental and Computational Considerations in the Study of RNA-Binding Protein-RNA Interactions." In Advances in Experimental Medicine and Biology. Springer International Publishing, 2016. http://dx.doi.org/10.1007/978-3-319-29073-7_1.

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Conference papers on the topic "RNA-protein interactions. Protein binding. RNA splicing"

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Shaw, Harry, Nagarajan Pattabiraman, Deborah Preston, et al. "Information theory and signal processing methodology to identify nucleic acid-protein binding sequences in RNA-protein interactions." In 2019 53rd Annual Conference on Information Sciences and Systems (CISS). IEEE, 2019. http://dx.doi.org/10.1109/ciss.2019.8692826.

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Venugopal, Anand, Satish Ramalingam, Dharmalingam Subramaniam, Zhiyun He, Roy Jensen, and Shrikant Anant. "Abstract 3080: Novel splicing activity for RNA binding protein CUGBP2 in radiation-induced mitotic catastrophe." In Proceedings: AACR 102nd Annual Meeting 2011‐‐ Apr 2‐6, 2011; Orlando, FL. American Association for Cancer Research, 2011. http://dx.doi.org/10.1158/1538-7445.am2011-3080.

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San, Avdar, Anjana Saxena, and Shaneen Singh. "Abstract 844: RNA binding domains of nucleolin exhibit specificity in driving nucleolin-miRNA interactions: Anin silicomodeling and RNA-protein docking study." In Proceedings: AACR Annual Meeting 2020; April 27-28, 2020 and June 22-24, 2020; Philadelphia, PA. American Association for Cancer Research, 2020. http://dx.doi.org/10.1158/1538-7445.am2020-844.

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Jacob, Aishwarya, Sanjay Sinha, and Chris Smith. "BS17 RNA binding protein multiple splicing (RBPMS) drives a contractile splicing network in human embryonic stem cell derived vascular smooth muscle cells." In British Cardiovascular Society Virtual Annual Conference, ‘Cardiology and the Environment’, 7–10 June 2021. BMJ Publishing Group Ltd and British Cardiovascular Society, 2021. http://dx.doi.org/10.1136/heartjnl-2021-bcs.215.

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