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2003 Biocomputing 2004  
To support the development of this approach, we have developed the Manually Annotated Alternatively Spliced Events (MAASE) database system, which is a unique alternative splicing information resource designed  ...  A unique microarray approach has been developed to profile alternative splicing in the cell.  ...  We therefore decided to build such a database in order to efficiently facilitate this experimental approach.  ... 
doi:10.1142/9789812704856_0008 fatcat:zm2rxl6clvblzf3ijz6uezvi6i

MAASE: An alternative splicing database designed for supporting splicing microarray applications

2005 RNA: A publication of the RNA Society  
offer adequate information in an appropriate format to aid in splicing array design.  ...  database of annotated events that allows convenient export of information to aid in microarray design and data analysis.  ...  ACKNOWLEDGMENTS This work was supported by a grant from the National Cancer Institute (CA888351) to X-D.F. and M.G., and by the facilities of the National Biomedical Computational Resource (RR-08605) at  ... 
doi:10.1261/rna.2650905 pmid:16251387 pmcid:PMC1370865 fatcat:l3q6syhygnhvbpm7keeeau4jbi

Review: Alternative Splicing (AS) of Genes As An Approach for Generating Protein Complexity

Bishakha Roy, Larisa M. Haupt, Lyn R. Griffiths
2013 Current Genomics  
Microarrays and deep sequencing approaches also aid in the detection of splicing events.  ...  The inequality in the ratio of gene to protein formation gave rise to the theory of alternative splicing (AS). AS is a mechanism by which one gene gives rise to multiple protein products.  ...  The largest part of ASD is AltSplice, a database of computationally defined AS events.  ... 
doi:10.2174/1389202911314030004 pmid:24179441 pmcid:PMC3664468 fatcat:h7pkjfvxezauznlx3dthpyf2ce

A proteogenomic approach to understand splice isoform functions through sequence and expression-based computational modeling

Hong-Dong Li, Gilbert S. Omenn, Yuanfang Guan
2016 Briefings in Bioinformatics  
Computational approaches provide an efficient complement to expensive and time-consuming experimental studies.  ...  The products of multi-exon genes are a mixture of alternatively spliced isoforms, from which the translated proteins can have similar, different or even opposing functions.  ...  Based on RSPR, Lu et al. proposed an approach for predicting functional alternative splicing with the aid of multi-genome alignment [37] .  ... 
doi:10.1093/bib/bbv109 pmid:26740460 pmcid:PMC5142014 fatcat:fn3irxjnnra5rbui47q2iqck6q

Bioinformatics of alternative splicing and its regulation

Liliana Florea
2006 Briefings in Bioinformatics  
This article is a survey of these methods. Alternative splicing has important implications for biology and medicine.  ...  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.  ... 
doi:10.1093/bib/bbk005 pmid:16761365 fatcat:m3y6dxczujblnasvypznhww72i

News section

D. S. Gonzalez
2003 Briefings in Bioinformatics  
The Alternative Splice Database 19 was created by an algorithm that defines a possible alternative splice form by comparing high-scoring ESTs to mRNA sequences using BLAST.  ...  EXProt combine protein sequences, which are stated to have an experimentally verified function, from different databases in order to provide a non-redundant database with proteins having an experimentally  ... 
doi:10.1093/bib/4.1.91 pmid:12715837 fatcat:nyzdvbct45h6ngxkumzaoraife

Human cytosolic sulfotransferase database mining: identification of seven novel genes and pseudogenes

R R Freimuth, M Wiepert, C G Chute, E D Wieben, R M Weinshilboum
2003 The Pharmacogenomics Journal  
We performed a comprehensive genome-wide search for novel SULT genes using two different but complementary approaches, and developed a novel graphical display to aid in the annotation of the hits.  ...  Expression-profiling studies were conducted for one novel gene, SULT6B1, and a series of alternatively spliced transcripts were identified in the human testis.  ...  All fees and honoraria for these services and/or seminars were paid to Mayo Foundation. In addition, Drs. Wieben and Weinshilboum currently hold a peer-reviewed grant from Eli Lilly.  ... 
doi:10.1038/sj.tpj.6500223 pmid:14676822 fatcat:j6di7jdctvdkdog72vwvzkcmxq

Large-scale RACE approach for proactive experimental definition of C. elegans ORFeome

K. Salehi-Ashtiani, C. Lin, T. Hao, Y. Shen, D. Szeto, X. Yang, L. Ghamsari, H. Lee, C. Fan, R. R. Murray, S. Milstein, N. Svrzikapa (+4 others)
2009 Genome Research  
Approximately two-thirds of the ORFeome has been verified reactively by amplifying and cloning computationally predicted transcript models; still a full third of the ORFeome remains experimentally unverified  ...  To fully identify the protein-coding potential of the worm genome including transcripts that may not satisfy existing heuristics for gene prediction, we developed a computational and experimental platform  ...  of AceDB (''A C. elegans DataBase'').  ... 
doi:10.1101/gr.098640.109 pmid:19801531 pmcid:PMC2792173 fatcat:62wfcmywgfg4hfl2rei4z7uruu

Identifying alternative splicing isoforms in the human proteome with small proteotranscriptomic databases [article]

Edward Lau, Maggie Pui Yu Lam
2018 bioRxiv   pre-print
The proteotranscriptomics approach using restricted sequence databases described here may help reveal previously unidentified alternative protein isoforms, and aid in the study of alternative splicing  ...  We further limit in silico sequence translation strictly to a single phase to reduce false positives in splice junction identification at the protein level.  ...  and The University of Colorado Consortium for Fibrosis Research and Translation Pilot Grant to M.P.L.  ... 
doi:10.1101/372995 fatcat:gmvhz536mrbqtdr4irc53uzxbq

Discovery and Mass Spectrometric Analysis of Novel Splice-junction Peptides Using RNA-Seq

Gloria M. Sheynkman, Michael R. Shortreed, Brian L. Frey, Lloyd M. Smith
2013 Molecular & Cellular Proteomics  
To our knowledge this is the first example of using sample-specific RNA-Seq data to create a splice-junction database and discover new peptides resulting from alternative splicing.  ...  In particular, alternative splicing has been shown to be a major source of this cell-specific proteomic variation.  ...  Acknowledgments-We would like to thank Dr. Mark Scalf for assistance with the mass spectrometric data collection. We would like to thank Dr. Victor Ruotti and Dr.  ... 
doi:10.1074/mcp.o113.028142 pmid:23629695 pmcid:PMC3734590 fatcat:ocig4na66ffzrinzxqme2gel7e

A detailed transcript-level probe annotation reveals alternative splicing based microarray platform differences

Joseph C Lee, David Stiles, Jun Lu, Margaret C Cam
2007 BMC Genomics  
to alternative splicing differences.  ...  The presence of alternative splicing within a given sample can affect gene expression measurements and is a contributing factor to overall technical differences across platforms.  ...  Acknowledgements The authors would like to thank Danielle Thierry-Mieg and Jean Thierry-Mieg for their helpful feedback, and Tom Downey (Partek Incorporated) for helpful advice with the data analysis.  ... 
doi:10.1186/1471-2164-8-284 pmid:17708771 pmcid:PMC2000902 fatcat:qvpfhymg75g6djlc6jwfnsfcja

Function of alternative splicing

Stefan Stamm, Shani Ben-Ari, Ilona Rafalska, Yesheng Tang, Zhaiyi Zhang, Debra Toiber, T.A. Thanaraj, Hermona Soreq
2005 Gene  
Alternative splicing is one of the most important mechanisms to generate a large number of mRNA and protein isoforms from the surprisingly low number of human genes.  ...  Therefore, evidence is now accumulating that alternative splicing coordinates physiologically meaningful changes in protein isoform expression and is a key mechanism to generate the complex proteome of  ...  Data on splice events are derived through three approaches: (i) manual collection of experimentally reported alternative exons from peer-reviewed journals; (ii) computational delineation of alternative  ... 
doi:10.1016/j.gene.2004.10.022 pmid:15656968 fatcat:b6fmscsft5gsxbzdpu7oghgqwy

Proteogenomic analysis of pathogenic yeast Cryptococcus neoformans using high resolution mass spectrometry

Lakshmi Nagarajha Selvan, Jyothi Kaviyil, Raja Nirujogi, Babylakshmi Muthusamy, Vinuth N Puttamallesh, Tejaswini Subbannayya, Nazia Syed, Aneesha Radhakrishnan, Dhanashree S Kelkar, Sartaj Ahmad, Sneha M Pinto, Praveen Kumar (+7 others)
2014 Clinical Proteomics  
In addition, our studies led to the correction of translational start site, splice junctions and reading frame used for translation in a number of proteins.  ...  Owing to an increase in the number of immunosuppressed individuals along with emergence of drug-resistant strains, C. neoformans is gaining importance as a pathogen.  ...  The study was supported by a research grant "DBT Programme Support on Neuroproteomics of Neurological Disorders" to IOB and NIMHANS by DBT, Government of India  ... 
doi:10.1186/1559-0275-11-5 pmid:24484775 pmcid:PMC3915034 fatcat:5b5u4xghurauveyrs3pzghvs5a

Quantitative model of R-loop forming structures reveals a novel level of RNA-DNA interactome complexity

T. Wongsurawat, P. Jenjaroenpun, C. K. Kwoh, V. Kuznetsov
2011 Nucleic Acids Research  
alternative splicing, DNA-editing and epigenetic modifications.  ...  We created R-loopDB ( .sg/), the database that collects all RLFS identified within over half of the human genes and links to the UCSC Genome Browser for information integration  ...  ACKNOWLEDGEMENTS The authors are grateful to Dr Micheal R.  ... 
doi:10.1093/nar/gkr1075 pmid:22121227 pmcid:PMC3258121 fatcat:drweemz65bgkhhv62sbgqsdzoq

Exon Size and Sequence Conservation Improves Identification of Splice Altering Nucleotides

Maliheh Movassat, Elmira Forouzmand, Fairlie Reese, Klemens J. Hertel
2019 RNA: A publication of the RNA Society  
To test this hypothesis, an exon size database was created, filtering 76 vertebrate sequence alignments based on exon size conservation.  ...  Our analysis identified evolutionarily young exons and demonstrated that length conservation is a strong predictor of alternative splicing.  ...  and R01 GM110244 to K.J.H.).  ... 
doi:10.1261/rna.070987.119 pmid:31554659 pmcid:PMC6859846 fatcat:nahl3ted7rg2tisucyim7atl3q
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