000196538 001__ 196538
000196538 005__ 20190316235838.0
000196538 0247_ $$2doi$$a10.1109/TCBB.2012.145
000196538 037__ $$aARTICLE
000196538 245__ $$aA transcript perspective on evolution
000196538 269__ $$a2013
000196538 260__ $$bIeee Computer Soc$$c2013$$aLos Alamitos
000196538 300__ $$a9
000196538 336__ $$aJournal Articles
000196538 520__ $$aAlternative splicing is now recognized as a major mechanism for transcriptome and proteome diversity in higher eukaryotes, yet its evolution is poorly understood. Most studies focus on the evolution of exons and introns at the gene level, while only few consider the evolution of transcripts. In this paper, we present a framework for transcript phylogenies where ancestral transcripts evolve along the gene tree by gains, losses, and mutation. We demonstrate the usefulness of our method on a set of 805 genes and two different topics. First, we improve a method for transcriptome reconstruction from ESTs (ASPic), then we study the evolution of function in transcripts. The use of transcript phylogenies allows us to double the precision of ASPic, whereas results on the functional study reveal that conserved transcripts are more likely to share protein domains than functional sites. These studies validate our framework for the study of evolution in large collections of organisms from the perspective of transcripts; for this purpose, we developed and provide a new tool, TrEvoR.
000196538 6531_ $$aAlternative splicing
000196538 6531_ $$atranscript
000196538 6531_ $$aevolution
000196538 6531_ $$aphylogeny
000196538 6531_ $$aprotein domain
000196538 6531_ $$atranscriptome reconstruction
000196538 700__ $$0242191$$g146870$$uEcole Polytech Fed Lausanne, Lab Computat Biol & Bioinformat, CH-1015 Lausanne, Switzerland$$aChristinat, Yann
000196538 700__ $$aMoret, Bernard M. E.$$0241987$$g172233
000196538 773__ $$j10$$tIEEE-ACM Transactions On Computational Biology And Bioinformatics$$k6$$q1403-1411
000196538 8564_ $$uhttp://doi.ieeecomputersociety.org/10.1109/TCBB.2012.145$$zURL
000196538 909C0 $$xU11274$$0252020$$pLCBB
000196538 909CO $$ooai:infoscience.tind.io:196538$$qGLOBAL_SET$$pIC$$particle
000196538 917Z8 $$x172233
000196538 937__ $$aEPFL-ARTICLE-196538
000196538 973__ $$rREVIEWED$$sPUBLISHED$$aEPFL
000196538 980__ $$aARTICLE