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Items: 30

1.

SanXoT: a modular and versatile package for the quantitative analysis of high-throughput proteomics experiments.

Trevisan-Herraz M, Bagwan N, García-Marqués F, Rodriguez JM, Jorge I, Ezkurdia I, Bonzon-Kulichenko E, Vázquez J.

Bioinformatics. 2019 May 1;35(9):1594-1596. doi: 10.1093/bioinformatics/bty815.

2.

Corrigendum: SQANTI: extensive characterization of long-read transcript sequences for quality control in full-length transcriptome identification and quantification.

Tardaguila M, de la Fuente L, Marti C, Pereira C, Pardo-Palacios FJ, Del Risco H, Ferrell M, Mellado M, Macchietto M, Verheggen K, Edelmann M, Ezkurdia I, Vazquez J, Tress M, Mortazavi A, Martens L, Rodriguez-Navarro S, Moreno-Manzano V, Conesa A.

Genome Res. 2018 Jul;28(7):1096. doi: 10.1101/gr.239137.118. No abstract available.

3.

Comprehensive Quantification of the Modified Proteome Reveals Oxidative Heart Damage in Mitochondrial Heteroplasmy.

Bagwan N, Bonzon-Kulichenko E, Calvo E, Lechuga-Vieco AV, Michalakopoulos S, Trevisan-Herraz M, Ezkurdia I, Rodríguez JM, Magni R, Latorre-Pellicer A, Enríquez JA, Vázquez J.

Cell Rep. 2018 Jun 19;23(12):3685-3697.e4. doi: 10.1016/j.celrep.2018.05.080.

4.

SQANTI: extensive characterization of long-read transcript sequences for quality control in full-length transcriptome identification and quantification.

Tardaguila M, de la Fuente L, Marti C, Pereira C, Pardo-Palacios FJ, Del Risco H, Ferrell M, Mellado M, Macchietto M, Verheggen K, Edelmann M, Ezkurdia I, Vazquez J, Tress M, Mortazavi A, Martens L, Rodriguez-Navarro S, Moreno-Manzano V, Conesa A.

Genome Res. 2018 Feb 9. doi: 10.1101/gr.222976.117. [Epub ahead of print] Erratum in: Genome Res. 2018 Jul;28(7):1096.

5.

Quantitative HDL Proteomics Identifies Peroxiredoxin-6 as a Biomarker of Human Abdominal Aortic Aneurysm.

Burillo E, Jorge I, Martínez-López D, Camafeita E, Blanco-Colio LM, Trevisan-Herraz M, Ezkurdia I, Egido J, Michel JB, Meilhac O, Vázquez J, Martin-Ventura JL.

Sci Rep. 2016 Dec 9;6:38477. doi: 10.1038/srep38477.

6.

Mechanism of super-assembly of respiratory complexes III and IV.

Cogliati S, Calvo E, Loureiro M, Guaras AM, Nieto-Arellano R, Garcia-Poyatos C, Ezkurdia I, Mercader N, Vázquez J, Enriquez JA.

Nature. 2016 Nov 24;539(7630):579-582. doi: 10.1038/nature20157. Epub 2016 Oct 24.

PMID:
27775717
7.

A novel high-content analysis tool reveals Rab8-driven cytoskeletal reorganization through Rho GTPases, calpain and MT1-MMP.

Bravo-Cordero JJ, Cordani M, Soriano SF, Díez B, Muñoz-Agudo C, Casanova-Acebes M, Boullosa C, Guadamillas MC, Ezkurdia I, González-Pisano D, Del Pozo MA, Montoya MC.

J Cell Sci. 2016 Apr 15;129(8):1734-49. doi: 10.1242/jcs.174920. Epub 2016 Mar 3.

8.

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.

9.

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.

10.

Correction to "Analyzing the first drafts of the human proteome".

Ezkurdia I, Vázquez J, Valencia A, Tress M.

J Proteome Res. 2015 Apr 3;14(4):1991. doi: 10.1021/acs.jproteome.5b00186. Epub 2015 Mar 10. No abstract available.

11.

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.

12.

Analyzing the first drafts of the human proteome.

Ezkurdia I, Vázquez J, Valencia A, Tress M.

J Proteome Res. 2014 Aug 1;13(8):3854-5. doi: 10.1021/pr500572z. Epub 2014 Jul 16. Erratum in: J Proteome Res. 2015 Apr 3;14(4):1991.

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.

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.

15.

GENCODE: the reference human genome annotation for The ENCODE Project.

Harrow J, Frankish A, Gonzalez JM, Tapanari E, Diekhans M, Kokocinski F, Aken BL, Barrell D, Zadissa A, Searle S, Barnes I, Bignell A, Boychenko V, Hunt T, Kay M, Mukherjee G, Rajan J, Despacio-Reyes G, Saunders G, Steward C, Harte R, Lin M, Howald C, Tanzer A, Derrien T, Chrast J, Walters N, Balasubramanian S, Pei B, Tress M, Rodriguez JM, Ezkurdia I, van Baren J, Brent M, Haussler D, Kellis M, Valencia A, Reymond A, Gerstein M, Guigó R, Hubbard TJ.

Genome Res. 2012 Sep;22(9):1760-74. doi: 10.1101/gr.135350.111.

16.

Chimeras taking shape: potential functions of proteins encoded by chimeric RNA transcripts.

Frenkel-Morgenstern M, Lacroix V, Ezkurdia I, Levin Y, Gabashvili A, Prilusky J, Del Pozo A, Tress M, Johnson R, Guigo R, Valencia A.

Genome Res. 2012 Jul;22(7):1231-42. doi: 10.1101/gr.130062.111. Epub 2012 May 15.

17.

Targeted proteome investigation via selected reaction monitoring mass spectrometry.

Maiolica A, Jünger MA, Ezkurdia I, Aebersold R.

J Proteomics. 2012 Jun 27;75(12):3495-513. doi: 10.1016/j.jprot.2012.04.048. Epub 2012 May 8. Review.

PMID:
22579752
18.

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.

19.

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
20.

Inference of functional relations in predicted protein networks with a machine learning approach.

García-Jiménez B, Juan D, Ezkurdia I, Andrés-León E, Valencia A.

PLoS One. 2010 Apr 1;5(4):e9969. doi: 10.1371/journal.pone.0009969.

21.

Assessment of ligand binding residue predictions in CASP8.

López G, Ezkurdia I, Tress ML.

Proteins. 2009;77 Suppl 9:138-46. doi: 10.1002/prot.22557.

22.

Assessment of domain boundary predictions and the prediction of intramolecular contacts in CASP8.

Ezkurdia I, Graña O, Izarzugaza JM, Tress ML.

Proteins. 2009;77 Suppl 9:196-209. doi: 10.1002/prot.22554.

PMID:
19714769
23.

Target domain definition and classification in CASP8.

Tress ML, Ezkurdia I, Richardson JS.

Proteins. 2009;77 Suppl 9:10-7. doi: 10.1002/prot.22497.

24.

Progress and challenges in predicting protein-protein interaction sites.

Ezkurdia I, Bartoli L, Fariselli P, Casadio R, Valencia A, Tress ML.

Brief Bioinform. 2009 May;10(3):233-46. doi: 10.1093/bib/bbp021. Epub 2009 Apr 3.

PMID:
19346321
25.

EcID. A database for the inference of functional interactions in E. coli.

Andres Leon E, Ezkurdia I, García B, Valencia A, Juan D.

Nucleic Acids Res. 2009 Jan;37(Database issue):D629-35. doi: 10.1093/nar/gkn853. Epub 2008 Nov 12.

26.

Assessment of predictions submitted for the CASP7 domain prediction category.

Tress M, Cheng J, Baldi P, Joo K, Lee J, Seo JH, Lee J, Baker D, Chivian D, Kim D, Ezkurdia I.

Proteins. 2007;69 Suppl 8:137-51.

PMID:
17680686
27.

Domain definition and target classification for CASP7.

Clarke ND, Ezkurdia I, Kopp J, Read RJ, Schwede T, Tress M.

Proteins. 2007;69 Suppl 8:10-8.

PMID:
17654725
28.

Assessment of predictions submitted for the CASP6 comparative modeling category.

Tress M, Ezkurdia I, Graña O, López G, Valencia A.

Proteins. 2005;61 Suppl 7:27-45.

PMID:
16187345
29.

Domain definition and target classification for CASP6.

Tress M, Tai CH, Wang G, Ezkurdia I, López G, Valencia A, Lee B, Dunbrack RL Jr.

Proteins. 2005;61 Suppl 7:8-18.

PMID:
16187342
30.

Empirical limits for template-based protein structure prediction: the CASP5 example.

Contreras-Moreira B, Ezkurdia I, Tress ML, Valencia A.

FEBS Lett. 2005 Feb 14;579(5):1203-7.

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