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Bioinformatics of alternative splicing and its regulation

Liliana Florea
<span title="2006-03-01">2006</span> <i title="Oxford University Press (OUP)"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/op7ztx4fhvairowgqifu7dnvsi" style="color: black;">Briefings in Bioinformatics</a> </i> &nbsp;
Identifying all splice variations and the signals that regulate splicing are core problems in genomics and bioinformatics.  ...  The sequencing of the human genome and ensuing wave of data generation have brought new light upon the extent and importance of alternative splicing as an RNA regulatory mechanism.  ...  Acknowledgment Thanks to Rosane Charlab for her careful review of the manuscript.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1093/bib/bbk005">doi:10.1093/bib/bbk005</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/16761365">pmid:16761365</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/m3y6dxczujblnasvypznhww72i">fatcat:m3y6dxczujblnasvypznhww72i</a> </span>
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Genome-wide analysis of SRSF10-regulated alternative splicing by deep sequencing of chicken transcriptome

Xuexia Zhou, Wenwu Wu, Ning Wei, Yuanming Cheng, Zhiqin Xie, Ying Feng
<span title="">2014</span> <i title="Elsevier BV"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/g4t2znz3wvgvpcxwreg22y77va" style="color: black;">Genomics Data</a> </i> &nbsp;
Splicing factor SRSF10 is known to function as a sequence-specific splicing activator that is capable of regulating alternative splicing both in vitro and in vivo.  ...  Our data thus provide a resource for studying regulation of alternative splicing in vivo that underlines biological functions of splicing regulatory proteins in cells.  ...  Experimental design, materials and methods Sample preparation and RNA-seq analysis It is known that phosphorylated SRSF10 functions as a sequencespecific splicing activator that is capable of regulating  ... 
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Bioinformatics challenges and perspectives when studying the effect of epigenetic modifications on alternative splicing

Clare Pacini, Magdalena J. Koziol
<span title="2018-04-23">2018</span> <i title="The Royal Society"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/p7stgfom7rbkheuw5cc6avanwu" style="color: black;">Philosophical Transactions of the Royal Society of London. Biological Sciences</a> </i> &nbsp;
We then discuss the bioinformatics methods that can be used to model interactions between epigenetic marks and regulators of splicing.  ...  Here, we give a brief overview of the role of epigenetics in alternative splicing and disease.  ...  The authors are grateful to John Gurdon, Charles Bradshaw and Jerome Jullien for reading the manuscript, useful comments and discussions on the topic.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1098/rstb.2017.0073">doi:10.1098/rstb.2017.0073</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/29685977">pmid:29685977</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC5915717/">pmcid:PMC5915717</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/nkiaoku5rjhivdgbaurwrlqzm4">fatcat:nkiaoku5rjhivdgbaurwrlqzm4</a> </span>
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Alternative splicing in humans [chapter]

John G. Conboy, Inna Dubchak
<span title="2005-04-15">2005</span> <i title="John Wiley &amp; Sons, Ltd"> Encyclopedia of Genetics, Genomics, Proteomics and Bioinformatics </i> &nbsp;
The phenomenon of multiple alternative splicing pathways in the human genome, and the opportunity to regulate these pathways during development, allows a relatively small number of genes to encode a complex  ...  Recent advances in genome sequencing, gene expression profiling, bioinformatics, and biochemical analysis of the splicing machinery give hope that the rules by which splicing regulatory networks govern  ...  of the mechanisms by which alternative splicing is regulated.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1002/047001153x.g402305">doi:10.1002/047001153x.g402305</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/eojm3eakyfaodig4vfmczn6d3e">fatcat:eojm3eakyfaodig4vfmczn6d3e</a> </span>
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Bioinformatics analysis of alternative splicing

C. Lee
<span title="2005-01-01">2005</span> <i title="Oxford University Press (OUP)"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/op7ztx4fhvairowgqifu7dnvsi" style="color: black;">Briefings in Bioinformatics</a> </i> &nbsp;
regulate alternative splicing, and propose a new mechanism for regulation based on the interaction of alternative splicing and nonsense-mediated decay.  ...  Over the past few years, the analysis of alternative splicing using bioinformatics has emerged as an important new field, and has significantly changed our view of genome function.  ...  Bioinformatics studies were the first to show that alternative splicing, long considered to be a relatively unusual form of regulation, is actually ubiquitous throughout the human genome and other genomes  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1093/bib/6.1.23">doi:10.1093/bib/6.1.23</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/15826354">pmid:15826354</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/6abvovvbwvdgfnn374o2glirju">fatcat:6abvovvbwvdgfnn374o2glirju</a> </span>
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RNA processing and its regulation: global insights into biological networks

Donny D. Licatalosi, Robert B. Darnell
<span title="">2010</span> <i title="Springer Nature"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/wg7vnqrxzveutlxxgtyxqydvjy" style="color: black;">Nature reviews genetics</a> </i> &nbsp;
Advances in technologies for characterizing RNA populations are revealing increasingly complete descriptions of RNA regulation and complexity-for example through alternative splicing, alternative polyadenylation  ...  These advances, combined with bioinformatics and genetic validation, are leading to the generation of functional RNA maps that reveal rules underlying RNA regulation and networks of biologically coherent  ...  The combinatorial actions of both core and auxiliary splicing factors participate in the regulation of alternative splicing.  ... 
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Alternative Splicing for Diseases, Cancers, Drugs, and Databases

Jen-Yang Tang, Jin-Ching Lee, Ming-Feng Hou, Chun-Lin Wang, Chien-Chi Chen, Hurng-Wern Huang, Hsueh-Wei Chang
<span title="">2013</span> <i title="Hindawi Limited"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/nxzqpsogkbe55mjq33syzghf2e" style="color: black;">The Scientific World Journal</a> </i> &nbsp;
Other agents known to have modulating effects on alternative splicing during therapeutic treatment of cancer are also discussed. Several commonly used bioinformatics resources are also summarized.  ...  Several diseases, including cancers, have been associated with dysregulation of alternative splicing.  ...  Alternative Splicing-Related Bioinformatics Resources Several bioinformatics analyses for the detection and regulation of alternative splicing have been well reviewed [101] [102] [103] .  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1155/2013/703568">doi:10.1155/2013/703568</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/23766705">pmid:23766705</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC3674688/">pmcid:PMC3674688</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/fo7g3fhoubefjmyt53wepw2bdi">fatcat:fo7g3fhoubefjmyt53wepw2bdi</a> </span>
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HITS-CLIP yields genome-wide insights into brain alternative RNA processing

Donny D. Licatalosi, Aldo Mele, John J. Fak, Jernej Ule, Melis Kayikci, Sung Wook Chi, Tyson A. Clark, Anthony C. Schweitzer, John E. Blume, Xuning Wang, Jennifer C. Darnell, Robert B. Darnell
<span title="">2008</span> <i title="Springer Nature"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/drfdii35rzaibj3aml5uhvr5xm" style="color: black;">Nature</a> </i> &nbsp;
Efforts to develop comprehensive understanding of protein-RNA interactions in vivo have combined genetics, bioinformatics, microarray-profiling, and biochemical approaches.  ...  HITS-CLIP revealed a large number of Nova-RNA interactions in 3′ UTRs, leading to the discovery that Nova regulates alternative polyadenylation in the brain.  ...  Acknowledgments The authors are grateful to members of the Darnell and Ule laboratories and Joel Richter for critical discussions and review of the manuscript, Brad Friedman for suggesting the use of Exon  ... 
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Regulation of alternative pre-mRNA splicing

L. Woodley
<span title="2002-01-01">2002</span> <i title="Oxford University Press (OUP)"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/db7gv4nqurbrhk7jywtr3wbcme" style="color: black;">Briefings in Functional Genomics &amp; Proteomics</a> </i> &nbsp;
Together with the realisation of the impact of the process on cell differentiation, development and disease, these studies portray alternative splicing as a fundamental component of gene regulation.  ...  The first wave of bioinformatic studies that followed genome and complementary DNA sequencing projects revealed that alternative splicing of messenger RNA precursors (pre-mRNAs) contributes substantially  ...  Acknowledgments We thank Richard Copley, Roderic Guigó, Nuno Morais, colleagues at the EMBL Gene Expression Programme and an anonymous reviewer for useful comments on the manuscript.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1093/bfgp/1.3.266">doi:10.1093/bfgp/1.3.266</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/15239893">pmid:15239893</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/uiycdtc7xbedxkszr2p4w7rnnq">fatcat:uiycdtc7xbedxkszr2p4w7rnnq</a> </span>
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Identification and comparative analysis of novel alternatively spliced transcripts of RhoGEF domain encoding gene in C. elegans and C. briggsae

Luv Kashyap, Mohammad Tabish, Subramaniam Ganesh, Deepti Dubey
<span title="2007-08-16">2007</span> <i title="Biomedical Informatics"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/iztfdaqh6bclfpgb2mitxtn5sm" style="color: black;">Bioinformation</a> </i> &nbsp;
Alternative splicing increases transcriptome and proteome diversification. Y95B8A.12 gene has two reported alternatively spliced transcripts by the C. elegans genome sequencing consortium.  ...  Our methodology involved the use of various gene or exon finding programmes and several other bioinformatics tools followed by experimental validation.  ...  grants to the Department in the form of DRS and FIST for developing infrastructure facilities.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.6026/97320630002043">doi:10.6026/97320630002043</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/18188419">pmid:18188419</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC2174416/">pmcid:PMC2174416</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/yvfrc36tprgzzorl3w3ma5wi4q">fatcat:yvfrc36tprgzzorl3w3ma5wi4q</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20180721215745/http://www.bioinformation.net/002/001200022007.pdf" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/51/3b/513bdf1a857a01f4c0aea08d59e4ac527f834b15.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.6026/97320630002043"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="unlock alternate icon" style="background-color: #fb971f;"></i> Publisher / doi.org </button> </a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2174416" title="pubmed link"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> pubmed.gov </button> </a>

Widespread predicted nonsense-mediated mRNA decay of alternatively-spliced transcripts of human normal and disease genes

R. E. Green, B. P. Lewis, R. T. Hillman, M. Blanchette, L. F. Lareau, A. T. Garnett, D. C. Rio, S. E. Brenner
<span title="2003-07-03">2003</span> <i title="Oxford University Press (OUP)"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/wmo54ba2jnemdingjj4fl3736a" style="color: black;">Bioinformatics</a> </i> &nbsp;
Rather than being translated to yield protein, these transcripts are expected to be degraded and may be subject to regulated unproductive splicing and translation (RUST).  ...  We have recently shown that a third of reliably-inferred alternative mRNA isoforms are candidates for nonsensemediated mRNA decay (NMD), an mRNA surveillance system (Lewis et al., 2003, Proc.  ...  ACKNOWLEDGEMENTS This work was supported by National Institutes of Health Grants K22 HG00056 and T32 HG0047, the Searle Scholars' Program (01-L-116) and an IBM Shared University Research grant.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1093/bioinformatics/btg1015">doi:10.1093/bioinformatics/btg1015</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/12855447">pmid:12855447</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/hxbm6hjwcrfldfke6vy5zqooyq">fatcat:hxbm6hjwcrfldfke6vy5zqooyq</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20170812073330/http://bioinformatics.berkeley.edu/people/brenner/pubs/green-2003-bioi-ismb2003-rust.pdf" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/e7/c4/e7c48a85570f9ccb1d9e89db88ca7af9a469d778.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1093/bioinformatics/btg1015"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="external alternate icon"></i> oup.com </button> </a>

Identification of novel alternative splicing biomarkers for breast cancer with LC/MS/MS and RNA-Seq

Fan Zhang, Chris K. Deng, Mu Wang, Bin Deng, Robert Barber, Gang Huang
<span title="2020-12-03">2020</span> <i title="Springer Science and Business Media LLC"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/n5zrklrhlzhtdorf4rk4rmeo3i" style="color: black;">BMC Bioinformatics</a> </i> &nbsp;
Background Alternative splicing isoforms have been reported as a new and robust class of diagnostic biomarkers.  ...  Results We developed a bioinformatics workflow to discover alternative splicing biomarkers from LC–MS/MS using RNA-Seq.  ...  About this supplement This article has been published as part of BMC Bioinformatics Volume 21 Supplement 9, 2020: Selected Articles from the 20th International Conference on Bioinformatics & Computational  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1186/s12859-020-03824-8">doi:10.1186/s12859-020-03824-8</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/33272210">pmid:33272210</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/4l73kuftxjcrlohg3x3yi7chf4">fatcat:4l73kuftxjcrlohg3x3yi7chf4</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20201205230230/https://bmcbioinformatics.biomedcentral.com/track/pdf/10.1186/s12859-020-03824-8.pdf" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/61/3e/613e42953f7be8903d275c960e61718d31f254d5.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1186/s12859-020-03824-8"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="unlock alternate icon" style="background-color: #fb971f;"></i> springer.com </button> </a>

Computational and molecular characterization of multiple isoforms of lfe-2 gene in nematode C. elegans

Luv Kashyap, Mohammad Tabish, Subramaniam Ganesh, Deepti Dubey
<span title="2007-05-20">2007</span> <i title="Biomedical Informatics"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/iztfdaqh6bclfpgb2mitxtn5sm" style="color: black;">Bioinformation</a> </i> &nbsp;
These novel un-reported spliced variants not only point towards the extent of alternative splicing in C. elegans genes but also hint towards the complex nature of alternative splicing.  ...  C. elegans genome sequencing consortium has reported three alternatively spliced transcripts of C46H11.4 gene which encodes for three hypothetical proteins namely, C46H11.4a, C46H11.4b and C46H11.4c.  ...  Authors are also grateful to UGC and DST, New Delhi, India for providing special grants to the Department in the form of DRS and FIST for developing infrastructure facilities.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.6026/97320630002017">doi:10.6026/97320630002017</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/18084645">pmid:18084645</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC2139989/">pmcid:PMC2139989</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/crdqcyshyfg6pk2ws5ms4ww6c4">fatcat:crdqcyshyfg6pk2ws5ms4ww6c4</a> </span>
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Understanding splicing regulation through RNA splicing maps

Joshua T. Witten, Jernej Ule
<span title="">2011</span> <i title="Elsevier BV"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/alw4ab5u3vdqlgfh3smvbfnjqu" style="color: black;">Trends in Genetics</a> </i> &nbsp;
Genome-wide studies play a key role in understanding the regulation of alternative splicing in disease and normal physiology.  ...  Bioinformatic studies have also directly evaluated the importance of protein-RNA interactions in regulating splicing choices.  ...  This work was funded by the Medical Research Council and European Research Council grant 206726-CLIP.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1016/j.tig.2010.12.001">doi:10.1016/j.tig.2010.12.001</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/21232811">pmid:21232811</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC3165201/">pmcid:PMC3165201</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/oyctecxtozcazfto2bmkqfn34u">fatcat:oyctecxtozcazfto2bmkqfn34u</a> </span>
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Genome-wide Analysis of Alternative Pre-mRNA Splicing

Claudia Ben-Dov, Britta Hartmann, Josefin Lundgren, Juan Valcárcel
<span title="2007-11-16">2007</span> <i title="American Society for Biochemistry &amp; Molecular Biology (ASBMB)"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/mryncoafc5cxdicldzfm4vlsze" style="color: black;">Journal of Biological Chemistry</a> </i> &nbsp;
3 The abbreviations used are: AS, alternative pre-mRNA splicing; SR protein, serine/arginine-rich protein; hnRNP, hnRNP, heterogeneous nuclear ribonucleoprotein.  ...  Acknowledgments-We thank Ben Blencowe and Chris Smith for comments on the manuscript.  ...  Pre-mRNA splicing and its regulation play important roles in human pathologies, and genome-wide analyses in this area are paving the way for improved diagnostic tools and for the identification of novel  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1074/jbc.r700033200">doi:10.1074/jbc.r700033200</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/18024428">pmid:18024428</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/i6vqklpqf5f2tdc4zcc5m5krny">fatcat:i6vqklpqf5f2tdc4zcc5m5krny</a> </span>
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