A copy of this work was available on the public web and has been preserved in the Wayback Machine. The capture dates from 2015; you can also visit the original URL.
The file type is application/pdf.
Filters
A DATABASE DESIGNED TO COMPUTATIONALLY AID AN EXPERIMENTAL APPROACH TO ALTERNATIVE SPLICING
2003
Biocomputing 2004
Preserved Fulltext
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
Preserved Fulltext
A copy of this work was available on the public web and has been preserved in the Wayback Machine. The capture dates from 2018; you can also visit the original URL.
The file type is application/pdf.
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
2013
Current Genomics
Preserved Fulltext
A copy of this work was available on the public web and has been preserved in the Wayback Machine. The capture dates from 2018; you can also visit the original URL.
The file type is application/pdf.
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
2016
Briefings in Bioinformatics
Preserved Fulltext
A copy of this work was available on the public web and has been preserved in the Wayback Machine. The capture dates from 2020; you can also visit the original URL.
The file type is application/pdf.
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
2006
Briefings in Bioinformatics
Preserved Fulltext
A copy of this work was available on the public web and has been preserved in the Wayback Machine. The capture dates from 2017; you can also visit the original URL.
The file type is application/pdf.
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
2003
Briefings in Bioinformatics
Preserved Fulltext
A copy of this work was available on the public web and has been preserved in the Wayback Machine. The capture dates from 2018; you can also visit the original URL.
The file type is application/pdf.
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
2003
The Pharmacogenomics Journal
Preserved Fulltext
A copy of this work was available on the public web and has been preserved in the Wayback Machine. The capture dates from 2020; you can also visit the original URL.
The file type is application/pdf.
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
2009
Genome Research
Preserved Fulltext
A copy of this work was available on the public web and has been preserved in the Wayback Machine. The capture dates from 2019; you can also visit the original URL.
The file type is application/pdf.
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]
2018
bioRxiv
pre-print
Preserved Fulltext
A copy of this work was available on the public web and has been preserved in the Wayback Machine. The capture dates from 2019; you can also visit the original URL.
The file type is application/pdf.
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
2013
Molecular & Cellular Proteomics
Preserved Fulltext
A copy of this work was available on the public web and has been preserved in the Wayback Machine. The capture dates from 2018; you can also visit the original URL.
The file type is application/pdf.
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
2007
BMC Genomics
Preserved Fulltext
A copy of this work was available on the public web and has been preserved in the Wayback Machine. The capture dates from 2017; you can also visit the original URL.
The file type is application/pdf.
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
2005
Gene
Preserved Fulltext
A copy of this work was available on the public web and has been preserved in the Wayback Machine. The capture dates from 2017; you can also visit the original URL.
The file type is application/pdf.
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
2014
Clinical Proteomics
Preserved Fulltext
The Internet Archive has a preservation copy of this work in our general collections.
The file type is application/pdf.
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
2011
Nucleic Acids Research
Preserved Fulltext
A copy of this work was available on the public web and has been preserved in the Wayback Machine. The capture dates from 2017; you can also visit the original URL.
The file type is application/pdf.
alternative splicing, DNA-editing and epigenetic modifications. ...
We created R-loopDB (http://rloop.bii.a-star.edu .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
2019
RNA: A publication of the RNA Society
Preserved Fulltext
A copy of this work was available on the public web and has been preserved in the Wayback Machine. The capture dates from 2021; you can also visit the original URL.
The file type is application/pdf.
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
« Previous
Showing results 1 — 15 out of 1,892 results