Relevant bibliographies by topics / RNA-protein interactions

Contents

  1. Journal articles
  2. Dissertations / Theses
  3. Books
  4. Book chapters
  5. Conference papers
  6. Reports

Academic literature on the topic 'RNA-protein interactions'

Author: Grafiati
Published: 4 June 2021
Last updated: 25 July 2025

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Journal articles on the topic "RNA-protein interactions"

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Hall, Kathleen B. "RNA–protein interactions." Current Opinion in Structural Biology 12, no. 3 (2002): 283–88. http://dx.doi.org/10.1016/s0959-440x(02)00323-8.

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Wickens, Marvin P., and James E. Dahlberg. "RNA-protein interactions." Cell 51, no. 3 (1987): 339–42. http://dx.doi.org/10.1016/0092-8674(87)90629-5.

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Frankel, Alan D., Iain W. Mattaj, and Donald C. Rio. "RNA-protein interactions." Cell 67, no. 6 (1991): 1041–46. http://dx.doi.org/10.1016/0092-8674(91)90282-4.

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Nagai, Kiyoshi. "RNA-protein interactions." Current Opinion in Structural Biology 2, no. 1 (1992): 131–37. http://dx.doi.org/10.1016/0959-440x(92)90188-d.

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Puglisi, Joseph D. "RNA-protein interactions." Chemistry & Biology 2, no. 9 (1995): 581. http://dx.doi.org/10.1016/1074-5521(95)90121-3.

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Struhl, Kevin. "RNA-Protein Interactions." Current Protocols in Molecular Biology 73, no. 1 (2006): 27.0.1. http://dx.doi.org/10.1002/0471142727.mb2700s73.

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Garrett, Roger A. "RNA-protein interactions." FEBS Letters 375, no. 3 (1995): 313. http://dx.doi.org/10.1016/0014-5793(95)90104-3.

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Doetsch, Martina, Renée Schroeder, and Boris Fürtig. "Transient RNA-protein interactions in RNA folding." FEBS Journal 278, no. 10 (2011): 1634–42. http://dx.doi.org/10.1111/j.1742-4658.2011.08094.x.

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Osório, Joana. "Exploring protein–RNA interactions with RNA Tagging." Nature Reviews Genetics 17, no. 1 (2015): 7. http://dx.doi.org/10.1038/nrg.2015.6.

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Wilson, Katie A., Ryan W. Kung, Simmone D’souza та Stacey D. Wetmore. "Anatomy of noncovalent interactions between the nucleobases or ribose and π-containing amino acids in RNA–protein complexes". Nucleic Acids Research 49, № 4 (2021): 2213–25. http://dx.doi.org/10.1093/nar/gkab008.

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Abstract A set of >300 nonredundant high-resolution RNA–protein complexes were rigorously searched for π-contacts between an amino acid side chain (W, H, F, Y, R, E and D) and an RNA nucleobase (denoted π–π interaction) or ribose moiety (denoted sugar–π). The resulting dataset of >1500 RNA–protein π-contacts were visually inspected and classified based on the interaction type, and amino acids and RNA components involved. More than 80% of structures searched contained at least one RNA–protein π-interaction, with π–π contacts making up 59% of the identified interactions. RNA–protei
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Dissertations / Theses on the topic "RNA-protein interactions"

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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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Chandran, V. "Structural and functional characterisation of the protein-protein and protein-RNA interactions in the RNA degradosome." Thesis, University of Cambridge, 2006. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.597437.

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The C-terminal domain of RNase E is intrinsically unstructured, but small segments of 13 to 80 residues are predicted to have propensity for defined conformation and evidence presented here indicates that they function in nucleic acid binding and protein-protein interactions in the degradosome. Binding of two of these ordered regions to their predicted partners, enolase and PNPase, has been demonstrated using non-dissociating nano-flow mass spectrometry (MS). Binding of helicase to an arginine rich domain of RNase E (residues 628-843) has also been shown by MS and other approaches. The binding
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Batal, Rami. "RNA and protein interactions of the measles virus nucleocapsid protein." Thesis, McGill University, 1994. http://digitool.Library.McGill.CA:80/R/?func=dbin-jump-full&object_id=55437.

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We are interested in studying the RNA and protein binding activities of the measles virus (MV) NP. MV is one of the members of Paramyxoviridae, a family of non-segmented negative-stranded RNA viruses family. We have expressed the MV NP in procaryotic systems and by in vitro translation. We have created a number of carboxy-terminal deletions of NP to use in mapping the domains involved in RNA and protein binding. We have transcribed the 5$ sp prime$ end antigenome sequences (positive leader) in vitro. We have metabolically labeled viral and MV-infected cellular proteins. We have applied differe
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Xu, Deming. "RNA and protein interactions in the yeast spliceosome." Thesis, National Library of Canada = Bibliothèque nationale du Canada, 1998. http://www.collectionscanada.ca/obj/s4/f2/dsk1/tape10/PQDD_0005/NQ41534.pdf.

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Turner, David Richard. "Protein-RNA interactions in tobacco mosaic virus assembly." Thesis, University of Cambridge, 1987. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.328799.

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Singh, Jagjit. "RNA-Protein Interactions in the U12-Dependent Spliceosome." Cleveland State University / OhioLINK, 2016. http://rave.ohiolink.edu/etdc/view?acc_num=csu1484307043050366.

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Terribilini, Michael Joseph. "Computational analysis and prediction of protein-RNA interactions." [Ames, Iowa : Iowa State University], 2008.

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Peters, Daniel. "Structural and biochemical investigation of protein-RNA interactions." Thesis, University of York, 2014. http://etheses.whiterose.ac.uk/6784/.

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Non-coding RNAs (ncRNAs) are nucleic acids that do not code for protein. Rather, they have evolved highly specialised secondary structures and catalytic mechanisms that place them at the heart of regulating gene expression. The function of ncRNAs is often mediated or dependent on their interactions with RNA binding proteins. The study of both the structure and function of these proteins is crucial for understanding the biological role of the protein-RNA complexes. In this thesis, the structure and function of two RNA binding proteins: Lin28 and dihydrouridine synthase C (DusC) were investigate
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Ellis, Jonathan James. "Towards the prediction of protein-RNA interactions through protein structure analysis." Thesis, University of Sussex, 2008. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.444117.

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Ribeiro, Diogo. "Discovery of the role of protein-RNA interactions in protein multifunctionality and cellular complexity." Thesis, Aix-Marseille, 2018. http://www.theses.fr/2018AIXM0449/document.

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Au fil du temps, la vie a évolué pour produire des organismes remarquablement complexes. Pour faire face à cette complexité, les organismes ont développé une pléthore de mécanismes régulateurs. Par exemple, les mammifères transcrivent des milliers d'ARN longs non codants (ARNlnc), accroissant ainsi la capacité régulatrice de leurs cellules. Un concept émergent est que les ARNlnc peuvent servir d'échafaudages aux complexes protéiques, mais la prévalence de ce mécanisme n'a pas encore été démontrée. De plus, pour chaque ARN messager, plusieurs régions 3’ non traduites (3’UTRs) sont souvent prése
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Books on the topic "RNA-protein interactions"

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Kiyoshi, Nagai, and Mattaj Iain W, eds. RNA-protein interactions. IRL Press at Oxford University Press, 1994.

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Lin, Ren-Jang, ed. RNA-Protein Complexes and Interactions. Springer New York, 2016. http://dx.doi.org/10.1007/978-1-4939-3591-8.

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Joo, Chirlmin, and David Rueda, eds. Biophysics of RNA-Protein Interactions. Springer New York, 2019. http://dx.doi.org/10.1007/978-1-4939-9726-8.

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Lin, Ren-Jang, ed. RNA-Protein Complexes and Interactions. Springer US, 2023. http://dx.doi.org/10.1007/978-1-0716-3191-1.

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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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J, Smith Christopher W., ed. RNA-protein interactions: A practical approach. Oxford University Press, 1998.

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

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Koloteva, Nadejda. Regulation of eukaryotic gene expression via RNA-RNA and RNA-protein interactions. UMIST, 1997.

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Book chapters on the topic "RNA-protein interactions"

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Manoharan, Vijayalaxmi, Jose Manuel Pérez-Cañadillas, and Andres Ramos. "Protein-RNA Interactions." In NMR of Biomolecules. Wiley-VCH Verlag GmbH & Co. KGaA, 2012. http://dx.doi.org/10.1002/9783527644506.ch12.

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Turnbull, Andrew P., and Xiaoqiu Wu. "Studying RNA–Protein Complexes Using." In Protein-Ligand Interactions. Springer US, 2021. http://dx.doi.org/10.1007/978-1-0716-1197-5_20.

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Martin, Stephen R., Andres Ramos, and Laura Masino. "Biolayer Interferometry: Protein–RNA Interactions." In Protein-Ligand Interactions. Springer US, 2021. http://dx.doi.org/10.1007/978-1-0716-1197-5_16.

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Lamichhane, Rajan. "How Proteins Recognize RNA." In Biophysics of RNA-Protein Interactions. Springer New York, 2019. http://dx.doi.org/10.1007/978-1-4939-9726-8_1.

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Sprinzl, M., H. P. Hoffmann, S. Brock, M. Nanninga, and V. Hornung. "RNA-Aptamers for Studying RNA Protein Interactions." In RNA Biochemistry and Biotechnology. Springer Netherlands, 1999. http://dx.doi.org/10.1007/978-94-011-4485-8_16.

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Lang, Matti A., and Françoise Raffalli-Mathieu. "Cytochrome P450 RNA—Protein Interactions." In Endocrine Updates. Springer US, 2002. http://dx.doi.org/10.1007/978-1-4757-6446-8_13.

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Kumarevel, Thirumananseri. "Barium and Protein–RNA Interactions." In Encyclopedia of Metalloproteins. Springer New York, 2013. http://dx.doi.org/10.1007/978-1-4614-1533-6_169.

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Re, Angela, Tejal Joshi, Eleonora Kulberkyte, Quaid Morris, and Christopher T. Workman. "RNA–Protein Interactions: An Overview." In Methods in Molecular Biology. Humana Press, 2013. http://dx.doi.org/10.1007/978-1-62703-709-9_23.

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Fareh, Mohamed. "Dynamics of MicroRNA Biogenesis." In Biophysics of RNA-Protein Interactions. Springer New York, 2019. http://dx.doi.org/10.1007/978-1-4939-9726-8_10.

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Huang, Lin, and David M. J. Lilley. "The Interaction Between L7Ae Family of Proteins and RNA Kink Turns." In Biophysics of RNA-Protein Interactions. Springer New York, 2019. http://dx.doi.org/10.1007/978-1-4939-9726-8_2.

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Conference papers on the topic "RNA-protein interactions"

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Li, Danyu, Jiedong Xie, Jiyuan Chen, and Yunci Ma. "Heterogeneous Graph Representation Combined with LSTM for Predicting RNA–Protein Interactions." In 2024 6th International Conference on Electronics and Communication, Network and Computer Technology (ECNCT). IEEE, 2024. http://dx.doi.org/10.1109/ecnct63103.2024.10704550.

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Li, Danyu, Yunci Ma, Jinhuang Chen, and Jiedong Xie. "Using Bipartite Graph Embedding and Deep Learning Method Predicting RNA Protein Interactions." In 2024 7th International Conference on Computer Information Science and Application Technology (CISAT). IEEE, 2024. http://dx.doi.org/10.1109/cisat62382.2024.10695327.

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Orenstein, Yaron. "Computational Modeling of Protein-RNA Interactions." In BCB '17: 8th ACM International Conference on Bioinformatics, Computational Biology, and Health Informatics. ACM, 2017. http://dx.doi.org/10.1145/3107411.3107495.

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Bastos, Luana Luiza, Rafael P. Lemos, Diego Mariano, and Raquel C. de Melo-Minardi. "A strategy for refining the calculation of contacts in protein-RNA complexes." In Simpósio Brasileiro de Bioinformática. Sociedade Brasileira de Computação, 2024. https://doi.org/10.5753/bsb.2024.245555.

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Protein-RNA interactions are essential for several biological processes, including gene expression. However, traditional methods for studying these interactions use superficial criteria to perform this analysis, which can lead to false positives. This study presents a new strategy for modeling protein-RNA contacts. We classify RNA atoms and integrate methods previously used for protein contacts, developing the proposed approach that detects a broader range of interactions. We compare our proposal to an existing benchmark and observe that this method identifies more contacts and provides detail
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Wang, Tong, Hongmei Li, Xiaoming Hu, and Xiaoxia Cao. "Predicting RNA-protein interactions using a novel method." In 2012 5th International Conference on Biomedical Engineering and Informatics (BMEI). IEEE, 2012. http://dx.doi.org/10.1109/bmei.2012.6513097.

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Tong Wang, Zhizhen Yang, Wenan Tan, and Xiaoming Hu. "Identifying RNA-protein interactions using feature dimension reduction method." In 2013 8th International Conference on Computer Science & Education (ICCSE). IEEE, 2013. http://dx.doi.org/10.1109/iccse.2013.6554053.

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BLENCOWE, BENJAMIN, STEVEN BRENNER, TIMOTHY HUGHES, and QUAID MORRIS. "POST-TRANSCRIPTIONAL GENE REGULATION: RNA-PROTEIN INTERACTIONS, RNA PROCESSING, MRNA STABILITY AND LOCALIZATION." In Proceedings of the Pacific Symposium. WORLD SCIENTIFIC, 2008. http://dx.doi.org/10.1142/9789812836939_0052.

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Kralj, Sebastjan, Milan Hodošček, Marko Jukić, and Urban Bren. "A comprehensive in silico protocol for fast automated mutagenesis and binding affinity scoring of protein-ligand complexes." In 2nd International Conference on Chemo and Bioinformatics. Institute for Information Technologies, University of Kragujevac, 2023. http://dx.doi.org/10.46793/iccbi23.674k.

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Protein-protein interactions (PPI) are critical for cellular functions, host-pathogen dynamics and are crucial with drug design efforts. The interaction of proteins is dependent on the amino acid sequence of a protein as it determines its binding affinity to various molecules, including drugs, DNA, RNA, and proteins. Polymorphisms, natural DNA variations, affect PPIs by altering protein structure and stability. Computational chemistry is vital for the prediction of ligand-protein interactions through techniques such as docking and molecular dynamics and can elucidate the changes in energy asso
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Adamek, Maksimiljan. "Molecular Grammar of RNA-binding Protein Interactions in Formation and Function of Ribonucleoprotein Complexes." In Socratic Lectures 8. University of Lubljana Press, 2023. http://dx.doi.org/10.55295/psl.2023.ii15.

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Ribonucleoproteins (RNPs) are macromolecular assemblies of proteins along RNA molecules to carry out specialized cellular processes. Understanding how RNA binding proteins (RBPs) and RNA sequences determine the interactions to form RNPs and ultimately steer biomolecular processes remains poorly understood. There is a mounting evidence that RNP assembly de-pends on the formation of a network of transient, multivalent RBP RNA and RBP RBP interac-tions, particularly between tyrosine residues from intrinsically disordered domains and argi-nine residues from RNA-binding domains of RBPs. Furthermore
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Ram, A. K., A. Mahajan, A. Kumar, and N. K. Dhillon. "Lnc RNA T-536 and RNA Binding Protein RBM25 Interactions in the Development of Pulmonary Arterial Hypertension." In American Thoracic Society 2024 International Conference, May 17-22, 2024 - San Diego, CA. American Thoracic Society, 2024. http://dx.doi.org/10.1164/ajrccm-conference.2024.209.1_meetingabstracts.a2582.

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Reports on the topic "RNA-protein interactions"

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Lee, Jae-Hyung. Analysis of Protein-RNA and Protein-Peptide Interactions in Equine Infectious Anemia. Office of Scientific and Technical Information (OSTI), 2007. http://dx.doi.org/10.2172/933138.

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Citovsky, Vitaly, and Yedidya Gafni. Suppression of RNA Silencing by TYLCV During Viral Infection. United States Department of Agriculture, 2009. http://dx.doi.org/10.32747/2009.7592126.bard.

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The Israeli isolate of Tomato yellow leaf curl geminivirus (TYLCV-Is) is a major tomato pathogen, causing extensive (up to 100%) crop losses in Israel and in the south-eastern U.S. (e.g., Georgia, Florida). Surprisingly, however, little is known about the molecular mechanisms of TYLCV-Is interactions with tomato cells. In the current BARD project, we have identified a TYLCV-Is protein, V2, which acts as a suppressor of RNA silencing, and showed that V2 interacts with the tomato (L. esculentum) member of the SGS3 (LeSGS3) protein family known to be involved in RNA silencing. This proposal will
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Gafni, Yedidya, and Vitaly Citovsky. Inactivation of SGS3 as Molecular Basis for RNA Silencing Suppression by TYLCV V2. United States Department of Agriculture, 2013. http://dx.doi.org/10.32747/2013.7593402.bard.

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The Israeli isolate of Tomato yellow leaf curl geminivirus(TYLCV-Is) is a major tomato pathogen, causing extensive crop losses in Israel and in the south-eastern U.S. Yet, little is known about the molecular mechanisms of its interaction with tomato cells. One of the most interesting aspects of such interaction is how the invading virus counteracts the RNA silencing response of the plant. In the former BARD project, we have shown that TYLCV-Is V2 protein is an RNA silencing suppressor, and that this suppression is carried out via the interaction of V2 with the SGS3 component of the plant RNA s
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Gafni, Yedidya, Moshe Lapidot, and Vitaly Citovsky. Dual role of the TYLCV protein V2 in suppressing the host plant defense. United States Department of Agriculture, 2013. http://dx.doi.org/10.32747/2013.7597935.bard.

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TYLCV-Is is a major tomato pathogen, causing extensive crop losses in Israel and the U.S. We have identified a TYLCV-Is protein, V2, which acts as a suppressor of RNA silencing. Intriguingly, the counter-defense function of V2 may not be limited to silencing suppression. Our recent data suggest that V2 interacts with the tomato CYP1 protease. CYP1 belongs to the family of papain-like cysteine proteases which participate in programmed cell death (PCD) involved in plant defense against pathogens. Based on these data we proposed a model for dual action of V2 in suppressing the host antiviral defe
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Wang, X. F., and M. Schuldiner. Systems biology approaches to dissect virus-host interactions to develop crops with broad-spectrum virus resistance. United States-Israel Binational Agricultural Research and Development Fund, 2020. http://dx.doi.org/10.32747/2020.8134163.bard.

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More than 60% of plant viruses are positive-strand RNA viruses that cause billion-dollar losses annually and pose a major threat to stable agricultural production, including cucumber mosaic virus (CMV) that infects numerous vegetables and ornamental trees. A highly conserved feature among these viruses is that they form viral replication complexes (VRCs) to multiply their genomes by hijacking host proteins and remodeling host intracellular membranes. As a conserved and indispensable process, VRC assembly also represents an excellent target for the development of antiviral strategies that can b
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Stern, David, and Gadi Schuster. Manipulation of Gene Expression in the Chloroplast. United States Department of Agriculture, 2000. http://dx.doi.org/10.32747/2000.7575289.bard.

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The steady-state level of a given mRNA is determined by its rates of transcription and degradation. The stabilities of chloroplast mRNAs vary during plant development, in part regulating gene expression. Furthermore, the fitness of the organelle depends on its ability to destroy non-functional transcripts. In addition, there is a resurgent interest by the biotechnology community in chloroplast transformation due to the public concerns over pollen transmission of introduced traits or foreign proteins. Therefore, studies into basic gene expression mechanisms in the chloroplast will open the door
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Rodriguez Muxica, Natalia. Open configuration options Bioinformatics for Researchers in Life Sciences: Tools and Learning Resources. Inter-American Development Bank, 2022. http://dx.doi.org/10.18235/0003982.

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The COVID-19 pandemic has shown that bioinformatics--a multidisciplinary field that combines biological knowledge with computer programming concerned with the acquisition, storage, analysis, and dissemination of biological data--has a fundamental role in scientific research strategies in all disciplines involved in fighting the virus and its variants. It aids in sequencing and annotating genomes and their observed mutations; analyzing gene and protein expression; simulation and modeling of DNA, RNA, proteins and biomolecular interactions; and mining of biological literature, among many other c
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Dickman, Martin B., and Oded Yarden. Genetic and chemical intervention in ROS signaling pathways affecting development and pathogenicity of Sclerotinia sclerotiorum. United States Department of Agriculture, 2015. http://dx.doi.org/10.32747/2015.7699866.bard.

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Abstract: The long-term goals of our research are to understand the regulation of sclerotial development and pathogenicity in S. sclerotior11111. The focus in this project was on the elucidation of the signaling events and environmental cues involved in the regulation of these processes, utilizing and continuously developing tools our research groups have established and/or adapted for analysis of S. sclerotiorum, Our stated objectives: To take advantage of the recent conceptual (ROS/PPs signaling) and technical (amenability of S. sclerotiorumto manipulations coupled with chemical genomics and
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Liao, Jianhua, Jingting Liu, Baoqing Liu, Chunyan Meng, and Peiwen Yuan. Effect of OIP5-AS1 on clinicopathological characteristics and prognosis of cancer patients: a meta-analysis. INPLASY - International Platform of Registered Systematic Review and Meta-analysis Protocols, 2022. http://dx.doi.org/10.37766/inplasy2022.10.0118.

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Review question / Objective: According to recent studies, long non-coding RNA (lncRNAs) i.e., OPA-interacting protein 5 antisense RNA 1 (OIP5-AS1) has an important role in various carcinomas. However, its role in the cancer is contradictory. Therefore, we aimed to evaluate the link between OIP5-AS1 and cancer patients' clinicopathological characteristics and prognosis to better understand OIP5-AS1's role in cancer. Condition being studied: Reported studies have revealed that long non-coding RNA (lncRNAs) are considerably involved in crucial physiological events in several carcinomas, it can in
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Elroy-Stein, Orna, and Dmitry Belostotsky. Mechanism of Internal Initiation of Translation in Plants. United States Department of Agriculture, 2010. http://dx.doi.org/10.32747/2010.7696518.bard.

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Original objectives Elucidation of PABP's role in crTMV148 IRES function in-vitro using wheat germ extract and krebs-2 cells extract. Fully achieved. Elucidation of PABP's role in crTMV148 IRES function in-vivo in Arabidopsis. Characterization of the physical interactions of PABP and other potential ITAFs with crTMV148 IRES. Partly achieved. To conduct search for additional ITAFs using different approaches and evaluate the candidates. Partly achieved. Background of the topic The power of internal translation via the activity of internal ribosomal entry site (IRES) elements allow coordinated sy
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