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Identification of protein features encoded by alternative exons using Exon Ontology.
Tranchevent LC, Aubé F, Dulaurier L, Benoit-Pilven C, Rey A, Poret A, Chautard E, Mortada H, Desmet FO, Chakrama FZ, Moreno-Garcia MA, Goillot E, Janczarski S, Mortreux F, Bourgeois CF, Auboeuf D. Tranchevent LC, et al. Genome Res. 2017 Jun;27(6):1087-1097. doi: 10.1101/gr.212696.116. Epub 2017 Apr 18. Genome Res. 2017. PMID: 28420690 Free PMC article.
Interplay between coding and exonic splicing regulatory sequences.
Fontrodona N, Aubé F, Claude JB, Polvèche H, Lemaire S, Tranchevent LC, Modolo L, Mortreux F, Bourgeois CF, Auboeuf D. Fontrodona N, et al. Among authors: tranchevent lc. Genome Res. 2019 May;29(5):711-722. doi: 10.1101/gr.241315.118. Epub 2019 Apr 8. Genome Res. 2019. PMID: 30962178 Free PMC article.
RNA helicases DDX5 and DDX17 dynamically orchestrate transcription, miRNA, and splicing programs in cell differentiation.
Dardenne E, Polay Espinoza M, Fattet L, Germann S, Lambert MP, Neil H, Zonta E, Mortada H, Gratadou L, Deygas M, Chakrama FZ, Samaan S, Desmet FO, Tranchevent LC, Dutertre M, Rimokh R, Bourgeois CF, Auboeuf D. Dardenne E, et al. Among authors: tranchevent lc. Cell Rep. 2014 Jun 26;7(6):1900-13. doi: 10.1016/j.celrep.2014.05.010. Epub 2014 Jun 6. Cell Rep. 2014. PMID: 24910439 Free article.
Candidate gene prioritization with Endeavour.
Tranchevent LC, Ardeshirdavani A, ElShal S, Alcaide D, Aerts J, Auboeuf D, Moreau Y. Tranchevent LC, et al. Nucleic Acids Res. 2016 Jul 8;44(W1):W117-21. doi: 10.1093/nar/gkw365. Epub 2016 Apr 30. Nucleic Acids Res. 2016. PMID: 27131783 Free PMC article.
An expanded evaluation of protein function prediction methods shows an improvement in accuracy.
Jiang Y, Oron TR, Clark WT, Bankapur AR, D'Andrea D, Lepore R, Funk CS, Kahanda I, Verspoor KM, Ben-Hur A, Koo da CE, Penfold-Brown D, Shasha D, Youngs N, Bonneau R, Lin A, Sahraeian SM, Martelli PL, Profiti G, Casadio R, Cao R, Zhong Z, Cheng J, Altenhoff A, Skunca N, Dessimoz C, Dogan T, Hakala K, Kaewphan S, Mehryary F, Salakoski T, Ginter F, Fang H, Smithers B, Oates M, Gough J, Törönen P, Koskinen P, Holm L, Chen CT, Hsu WL, Bryson K, Cozzetto D, Minneci F, Jones DT, Chapman S, Bkc D, Khan IK, Kihara D, Ofer D, Rappoport N, Stern A, Cibrian-Uhalte E, Denny P, Foulger RE, Hieta R, Legge D, Lovering RC, Magrane M, Melidoni AN, Mutowo-Meullenet P, Pichler K, Shypitsyna A, Li B, Zakeri P, ElShal S, Tranchevent LC, Das S, Dawson NL, Lee D, Lees JG, Sillitoe I, Bhat P, Nepusz T, Romero AE, Sasidharan R, Yang H, Paccanaro A, Gillis J, Sedeño-Cortés AE, Pavlidis P, Feng S, Cejuela JM, Goldberg T, Hamp T, Richter L, Salamov A, Gabaldon T, Marcet-Houben M, Supek F, Gong Q, Ning W, Zhou Y, Tian W, Falda M, Fontana P, Lavezzo E, Toppo S, Ferrari C, Giollo M, Piovesan D, Tosatto SC, Del Pozo A, Fernández JM, Maietta P, Valencia A, Tress ML, Benso A, Di Carlo S, Politano G, Savino A… See abstract for full author list ➔ Jiang Y, et al. Among authors: tranchevent lc. Genome Biol. 2016 Sep 7;17(1):184. doi: 10.1186/s13059-016-1037-6. Genome Biol. 2016. PMID: 27604469 Free PMC article.
Beegle: from literature mining to disease-gene discovery.
ElShal S, Tranchevent LC, Sifrim A, Ardeshirdavani A, Davis J, Moreau Y. ElShal S, et al. Among authors: tranchevent lc. Nucleic Acids Res. 2016 Jan 29;44(2):e18. doi: 10.1093/nar/gkv905. Epub 2015 Sep 17. Nucleic Acids Res. 2016. PMID: 26384564 Free PMC article.
41 results