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Items: 1 to 20 of 36

1.

Loose ends: almost one in five human genes still have unresolved coding status.

Abascal F, Juan D, Jungreis I, Martinez L, Rigau M, Rodriguez JM, Vazquez J, Tress ML.

Nucleic Acids Res. 2018 Jun 30. doi: 10.1093/nar/gky587. [Epub ahead of print]

PMID:
29982784
2.

APPRIS 2017: principal isoforms for multiple gene sets.

Rodriguez JM, Rodriguez-Rivas J, Di Domenico T, Vázquez J, Valencia A, Tress ML.

Nucleic Acids Res. 2018 Jan 4;46(D1):D213-D217. doi: 10.1093/nar/gkx997.

3.

Most Alternative Isoforms Are Not Functionally Important.

Tress ML, Abascal F, Valencia A.

Trends Biochem Sci. 2017 Jun;42(6):408-410. doi: 10.1016/j.tibs.2017.04.002. Epub 2017 May 5. No abstract available.

4.

Extreme genomic erosion after recurrent demographic bottlenecks in the highly endangered Iberian lynx.

Abascal F, Corvelo A, Cruz F, Villanueva-Cañas JL, Vlasova A, Marcet-Houben M, Martínez-Cruz B, Cheng JY, Prieto P, Quesada V, Quilez J, Li G, García F, Rubio-Camarillo M, Frias L, Ribeca P, Capella-Gutiérrez S, Rodríguez JM, Câmara F, Lowy E, Cozzuto L, Erb I, Tress ML, Rodriguez-Ales JL, Ruiz-Orera J, Reverter F, Casas-Marce M, Soriano L, Arango JR, Derdak S, Galán B, Blanc J, Gut M, Lorente-Galdos B, Andrés-Nieto M, López-Otín C, Valencia A, Gut I, García JL, Guigó R, Murphy WJ, Ruiz-Herrera A, Marques-Bonet T, Roma G, Notredame C, Mailund T, Albà MM, Gabaldón T, Alioto T, Godoy JA.

Genome Biol. 2016 Dec 14;17(1):251.

5.

Alternative Splicing May Not Be the Key to Proteome Complexity.

Tress ML, Abascal F, Valencia A.

Trends Biochem Sci. 2017 Feb;42(2):98-110. doi: 10.1016/j.tibs.2016.08.008. Epub 2016 Oct 3. Review.

6.

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, Rehman HU, Re M, Mesiti M, Valentini G, Bargsten JW, van Dijk AD, Gemovic B, Glisic S, Perovic V, Veljkovic V, Veljkovic N, Almeida-E-Silva DC, Vencio RZ, Sharan M, Vogel J, Kansakar L, Zhang S, Vucetic S, Wang Z, Sternberg MJ, Wass MN, Huntley RP, Martin MJ, O'Donovan C, Robinson PN, Moreau Y, Tramontano A, Babbitt PC, Brenner SE, Linial M, Orengo CA, Rost B, Greene CS, Mooney SD, Friedberg I, Radivojac P.

Genome Biol. 2016 Sep 7;17(1):184. doi: 10.1186/s13059-016-1037-6.

7.

The potential clinical impact of the release of two drafts of the human proteome.

Ezkurdia I, Calvo E, Del Pozo A, Vázquez J, Valencia A, Tress ML.

Expert Rev Proteomics. 2015;12(6):579-93. doi: 10.1586/14789450.2015.1103186. Epub 2015 Oct 23.

8.

Alternatively Spliced Homologous Exons Have Ancient Origins and Are Highly Expressed at the Protein Level.

Abascal F, Ezkurdia I, Rodriguez-Rivas J, Rodriguez JM, del Pozo A, Vázquez J, Valencia A, Tress ML.

PLoS Comput Biol. 2015 Jun 10;11(6):e1004325. doi: 10.1371/journal.pcbi.1004325. eCollection 2015 Jun.

9.

APPRIS WebServer and WebServices.

Rodriguez JM, Carro A, Valencia A, Tress ML.

Nucleic Acids Res. 2015 Jul 1;43(W1):W455-9. doi: 10.1093/nar/gkv512. Epub 2015 May 18.

10.

The evolutionary fate of alternatively spliced homologous exons after gene duplication.

Abascal F, Tress ML, Valencia A.

Genome Biol Evol. 2015 Apr 29;7(6):1392-403. doi: 10.1093/gbe/evv076.

11.

Alternative splicing and co-option of transposable elements: the case of TMPO/LAP2α and ZNF451 in mammals.

Abascal F, Tress ML, Valencia A.

Bioinformatics. 2015 Jul 15;31(14):2257-61. doi: 10.1093/bioinformatics/btv132. Epub 2015 Mar 2.

12.

Most highly expressed protein-coding genes have a single dominant isoform.

Ezkurdia I, Rodriguez JM, Carrillo-de Santa Pau E, Vázquez J, Valencia A, Tress ML.

J Proteome Res. 2015 Apr 3;14(4):1880-7. doi: 10.1021/pr501286b. Epub 2015 Mar 11.

13.

Multiple evidence strands suggest that there may be as few as 19,000 human protein-coding genes.

Ezkurdia I, Juan D, Rodriguez JM, Frankish A, Diekhans M, Harrow J, Vazquez J, Valencia A, Tress ML.

Hum Mol Genet. 2014 Nov 15;23(22):5866-78. doi: 10.1093/hmg/ddu309. Epub 2014 Jun 16.

14.

FireDB: a compendium of biological and pharmacologically relevant ligands.

Maietta P, Lopez G, Carro A, Pingilley BJ, Leon LG, Valencia A, Tress ML.

Nucleic Acids Res. 2014 Jan;42(Database issue):D267-72. doi: 10.1093/nar/gkt1127. Epub 2013 Nov 15.

15.

APPRIS: annotation of principal and alternative splice isoforms.

Rodriguez JM, Maietta P, Ezkurdia I, Pietrelli A, Wesselink JJ, Lopez G, Valencia A, Tress ML.

Nucleic Acids Res. 2013 Jan;41(Database issue):D110-7. doi: 10.1093/nar/gks1058. Epub 2012 Nov 17.

16.

Comparative proteomics reveals a significant bias toward alternative protein isoforms with conserved structure and function.

Ezkurdia I, del Pozo A, Frankish A, Rodriguez JM, Harrow J, Ashman K, Valencia A, Tress ML.

Mol Biol Evol. 2012 Sep;29(9):2265-83. doi: 10.1093/molbev/mss100. Epub 2012 Mar 22.

17.

Evidence for transcript networks composed of chimeric RNAs in human cells.

Djebali S, Lagarde J, Kapranov P, Lacroix V, Borel C, Mudge JM, Howald C, Foissac S, Ucla C, Chrast J, Ribeca P, Martin D, Murray RR, Yang X, Ghamsari L, Lin C, Bell I, Dumais E, Drenkow J, Tress ML, Gelpí JL, Orozco M, Valencia A, van Berkum NL, Lajoie BR, Vidal M, Stamatoyannopoulos J, Batut P, Dobin A, Harrow J, Hubbard T, Dekker J, Frankish A, Salehi-Ashtiani K, Reymond A, Antonarakis SE, Guigó R, Gingeras TR.

PLoS One. 2012;7(1):e28213. doi: 10.1371/journal.pone.0028213. Epub 2012 Jan 4.

18.

Protein structural domains: definition and prediction.

Ezkurdia I, Tress ML.

Curr Protoc Protein Sci. 2011 Nov;Chapter 2:Unit2.14. doi: 10.1002/0471140864.ps0214s66.

PMID:
22045561
19.

firestar--advances in the prediction of functionally important residues.

Lopez G, Maietta P, Rodriguez JM, Valencia A, Tress ML.

Nucleic Acids Res. 2011 Jul;39(Web Server issue):W235-41. doi: 10.1093/nar/gkr437. Epub 2011 Jun 14.

20.

Predicted residue-residue contacts can help the scoring of 3D models.

Tress ML, Valencia A.

Proteins. 2010 Jun;78(8):1980-91. doi: 10.1002/prot.22714.

PMID:
20408174

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