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Items: 1 to 50 of 62

1.

Proteomics Standards Initiative Extended FASTA Format.

Binz PA, Shofstahl J, Vizcaíno JA, Barsnes H, Chalkley RJ, Menschaert G, Alpi E, Clauser K, Eng JK, Lane L, Seymour SL, Sánchez LFH, Mayer G, Eisenacher M, Perez-Riverol Y, Kapp EA, Mendoza L, Baker PR, Collins A, Van Den Bossche T, Deutsch EW.

J Proteome Res. 2019 Jun 7;18(6):2686-2692. doi: 10.1021/acs.jproteome.9b00064. Epub 2019 May 23.

PMID:
31081335
2.

Spectral Clustering Improves Label-Free Quantification of Low-Abundant Proteins.

Griss J, Stanek F, Hudecz O, Dürnberger G, Perez-Riverol Y, Vizcaíno JA, Mechtler K.

J Proteome Res. 2019 Apr 5;18(4):1477-1485. doi: 10.1021/acs.jproteome.8b00377. Epub 2019 Mar 22.

3.

mzTab-M: A Data Standard for Sharing Quantitative Results in Mass Spectrometry Metabolomics.

Hoffmann N, Rein J, Sachsenberg T, Hartler J, Haug K, Mayer G, Alka O, Dayalan S, Pearce JTM, Rocca-Serra P, Qi D, Eisenacher M, Perez-Riverol Y, Vizcaíno JA, Salek RM, Neumann S, Jones AR.

Anal Chem. 2019 Mar 5;91(5):3302-3310. doi: 10.1021/acs.analchem.8b04310. Epub 2019 Feb 13.

PMID:
30688441
4.

Protein Inference Using PIA Workflows and PSI Standard File Formats.

Uszkoreit J, Perez-Riverol Y, Eggers B, Marcus K, Eisenacher M.

J Proteome Res. 2019 Feb 1;18(2):741-747. doi: 10.1021/acs.jproteome.8b00723. Epub 2018 Dec 5.

PMID:
30474983
5.

The PRIDE database and related tools and resources in 2019: improving support for quantification data.

Perez-Riverol Y, Csordas A, Bai J, Bernal-Llinares M, Hewapathirana S, Kundu DJ, Inuganti A, Griss J, Mayer G, Eisenacher M, Pérez E, Uszkoreit J, Pfeuffer J, Sachsenberg T, Yilmaz S, Tiwary S, Cox J, Audain E, Walzer M, Jarnuczak AF, Ternent T, Brazma A, Vizcaíno JA.

Nucleic Acids Res. 2019 Jan 8;47(D1):D442-D450. doi: 10.1093/nar/gky1106.

6.

Expanding the Use of Spectral Libraries in Proteomics.

Deutsch EW, Perez-Riverol Y, Chalkley RJ, Wilhelm M, Tate S, Sachsenberg T, Walzer M, Käll L, Delanghe B, Böcker S, Schymanski EL, Wilmes P, Dorfer V, Kuster B, Volders PJ, Jehmlich N, Vissers JPC, Wolan DW, Wang AY, Mendoza L, Shofstahl J, Dowsey AW, Griss J, Salek RM, Neumann S, Binz PA, Lam H, Vizcaíno JA, Bandeira N, Röst H.

J Proteome Res. 2018 Dec 7;17(12):4051-4060. doi: 10.1021/acs.jproteome.8b00485. Epub 2018 Oct 11.

7.

Mass spectrometry evaluation of a neuroblastoma SH-SY5Y cell culture protocol.

Murillo JR, Pla I, Goto-Silva L, Nogueira FCS, Domont GB, Perez-Riverol Y, Sánchez A, Junqueira M.

Anal Biochem. 2018 Oct 15;559:51-54. doi: 10.1016/j.ab.2018.08.013. Epub 2018 Aug 23.

PMID:
30145218
8.

ABRF Proteome Informatics Research Group (iPRG) 2016 Study: Inferring Proteoforms from Bottom-up Proteomics Data.

Lee JY, Choi H, Colangelo CM, Davis D, Hoopmann MR, Käll L, Lam H, Payne SH, Perez-Riverol Y, The M, Wilson R, Weintraub ST, Palmblad M.

J Biomol Tech. 2018 Jul;29(2):39-45. doi: 10.7171/jbt.18-2902-003. Epub 2018 Jun 21.

9.

Future Prospects of Spectral Clustering Approaches in Proteomics.

Perez-Riverol Y, Vizcaíno JA, Griss J.

Proteomics. 2018 Jul;18(14):e1700454. doi: 10.1002/pmic.201700454.

10.

Response to "Comparison and Evaluation of Clustering Algorithms for Tandem Mass Spectra".

Griss J, Perez-Riverol Y, The M, Käll L, Vizcaíno JA.

J Proteome Res. 2018 May 4;17(5):1993-1996. doi: 10.1021/acs.jproteome.7b00824. Epub 2018 Apr 25.

PMID:
29682973
11.

A Protein Standard That Emulates Homology for the Characterization of Protein Inference Algorithms.

The M, Edfors F, Perez-Riverol Y, Payne SH, Hoopmann MR, Palmblad M, Forsström B, Käll L.

J Proteome Res. 2018 May 4;17(5):1879-1886. doi: 10.1021/acs.jproteome.7b00899. Epub 2018 Apr 16.

12.

Accurate and fast feature selection workflow for high-dimensional omics data.

Perez-Riverol Y, Kuhn M, Vizcaíno JA, Hitz MP, Audain E.

PLoS One. 2017 Dec 20;12(12):e0189875. doi: 10.1371/journal.pone.0189875. eCollection 2017.

13.

Enhanced Missing Proteins Detection in NCI60 Cell Lines Using an Integrative Search Engine Approach.

Guruceaga E, Garin-Muga A, Prieto G, Bejarano B, Marcilla M, Marín-Vicente C, Perez-Riverol Y, Casal JI, Vizcaíno JA, Corrales FJ, Segura V.

J Proteome Res. 2017 Dec 1;16(12):4374-4390. doi: 10.1021/acs.jproteome.7b00388. Epub 2017 Oct 11.

14.

Proteomics Standards Initiative: Fifteen Years of Progress and Future Work.

Deutsch EW, Orchard S, Binz PA, Bittremieux W, Eisenacher M, Hermjakob H, Kawano S, Lam H, Mayer G, Menschaert G, Perez-Riverol Y, Salek RM, Tabb DL, Tenzer S, Vizcaíno JA, Walzer M, Jones AR.

J Proteome Res. 2017 Dec 1;16(12):4288-4298. doi: 10.1021/acs.jproteome.7b00370. Epub 2017 Sep 15.

15.

OLS Client and OLS Dialog: Open Source Tools to Annotate Public Omics Datasets.

Perez-Riverol Y, Ternent T, Koch M, Barsnes H, Vrousgou O, Jupp S, Vizcaíno JA.

Proteomics. 2017 Oct;17(19). doi: 10.1002/pmic.201700244.

16.

Four simple recommendations to encourage best practices in research software.

Jiménez RC, Kuzak M, Alhamdoosh M, Barker M, Batut B, Borg M, Capella-Gutierrez S, Chue Hong N, Cook M, Corpas M, Flannery M, Garcia L, Gelpí JL, Gladman S, Goble C, González Ferreiro M, Gonzalez-Beltran A, Griffin PC, Grüning B, Hagberg J, Holub P, Hooft R, Ison J, Katz DS, Leskošek B, López Gómez F, Oliveira LJ, Mellor D, Mosbergen R, Mulder N, Perez-Riverol Y, Pergl R, Pichler H, Pope B, Sanz F, Schneider MV, Stodden V, Suchecki R, Svobodová Vařeková R, Talvik HA, Todorov I, Treloar A, Tyagi S, van Gompel M, Vaughan D, Via A, Wang X, Watson-Haigh NS, Crouch S.

F1000Res. 2017 Jun 13;6. pii: ELIXIR-876. doi: 10.12688/f1000research.11407.1. eCollection 2017.

17.

An "on-matrix" digestion procedure for AP-MS experiments dissects the interplay between complex-conserved and serotype-specific reactivities in Dengue virus-human plasma interactome.

Ramos Y, Huerta V, Martín D, Palomares S, Yero A, Pupo D, Gallien S, Martín AM, Pérez-Riverol Y, Sarría M, Guirola O, Chinea G, Domon B, González LJ.

J Proteomics. 2019 Feb 20;193:71-84. doi: 10.1016/j.jprot.2017.07.004. Epub 2017 Jul 13.

PMID:
28713027
18.

The mzIdentML Data Standard Version 1.2, Supporting Advances in Proteome Informatics.

Vizcaíno JA, Mayer G, Perkins S, Barsnes H, Vaudel M, Perez-Riverol Y, Ternent T, Uszkoreit J, Eisenacher M, Fischer L, Rappsilber J, Netz E, Walzer M, Kohlbacher O, Leitner A, Chalkley RJ, Ghali F, Martínez-Bartolomé S, Deutsch EW, Jones AR.

Mol Cell Proteomics. 2017 Jul;16(7):1275-1285. doi: 10.1074/mcp.M117.068429. Epub 2017 May 17.

19.

Discovering and linking public omics data sets using the Omics Discovery Index.

Perez-Riverol Y, Bai M, da Veiga Leprevost F, Squizzato S, Park YM, Haug K, Carroll AJ, Spalding D, Paschall J, Wang M, Del-Toro N, Ternent T, Zhang P, Buso N, Bandeira N, Deutsch EW, Campbell DS, Beavis RC, Salek RM, Sarkans U, Petryszak R, Keays M, Fahy E, Sud M, Subramaniam S, Barbera A, Jiménez RC, Nesvizhskii AI, Sansone SA, Steinbeck C, Lopez R, Vizcaíno JA, Ping P, Hermjakob H.

Nat Biotechnol. 2017 May 9;35(5):406-409. doi: 10.1038/nbt.3790. No abstract available.

20.

BioContainers: an open-source and community-driven framework for software standardization.

da Veiga Leprevost F, Grüning BA, Alves Aflitos S, Röst HL, Uszkoreit J, Barsnes H, Vaudel M, Moreno P, Gatto L, Weber J, Bai M, Jimenez RC, Sachsenberg T, Pfeuffer J, Vera Alvarez R, Griss J, Nesvizhskii AI, Perez-Riverol Y.

Bioinformatics. 2017 Aug 15;33(16):2580-2582. doi: 10.1093/bioinformatics/btx192.

21.

Synthetic human proteomes for accelerating protein research.

Perez-Riverol Y, Vizcaíno JA.

Nat Methods. 2017 Feb 28;14(3):240-242. doi: 10.1038/nmeth.4191. No abstract available.

PMID:
28245213
22.

The ProteomeXchange consortium in 2017: supporting the cultural change in proteomics public data deposition.

Deutsch EW, Csordas A, Sun Z, Jarnuczak A, Perez-Riverol Y, Ternent T, Campbell DS, Bernal-Llinares M, Okuda S, Kawano S, Moritz RL, Carver JJ, Wang M, Ishihama Y, Bandeira N, Hermjakob H, Vizcaíno JA.

Nucleic Acids Res. 2017 Jan 4;45(D1):D1100-D1106. doi: 10.1093/nar/gkw936. Epub 2016 Oct 18.

23.

A multicenter study benchmarks software tools for label-free proteome quantification.

Navarro P, Kuharev J, Gillet LC, Bernhardt OM, MacLean B, Röst HL, Tate SA, Tsou CC, Reiter L, Distler U, Rosenberger G, Perez-Riverol Y, Nesvizhskii AI, Aebersold R, Tenzer S.

Nat Biotechnol. 2016 Nov;34(11):1130-1136. doi: 10.1038/nbt.3685. Epub 2016 Oct 3.

24.

In-depth analysis of protein inference algorithms using multiple search engines and well-defined metrics.

Audain E, Uszkoreit J, Sachsenberg T, Pfeuffer J, Liang X, Hermjakob H, Sanchez A, Eisenacher M, Reinert K, Tabb DL, Kohlbacher O, Perez-Riverol Y.

J Proteomics. 2017 Jan 6;150:170-182. doi: 10.1016/j.jprot.2016.08.002. Epub 2016 Aug 4.

PMID:
27498275
25.

2016 update of the PRIDE database and its related tools.

Vizcaíno JA, Csordas A, Del-Toro N, Dianes JA, Griss J, Lavidas I, Mayer G, Perez-Riverol Y, Reisinger F, Ternent T, Xu QW, Wang R, Hermjakob H.

Nucleic Acids Res. 2016 Dec 15;44(22):11033. Epub 2016 Sep 28. No abstract available.

26.

Recognizing millions of consistently unidentified spectra across hundreds of shotgun proteomics datasets.

Griss J, Perez-Riverol Y, Lewis S, Tabb DL, Dianes JA, Del-Toro N, Rurik M, Walzer MW, Kohlbacher O, Hermjakob H, Wang R, Vizcaíno JA.

Nat Methods. 2016 Aug;13(8):651-656. Epub 2016 Jun 27.

27.

Ten Simple Rules for Taking Advantage of Git and GitHub.

Perez-Riverol Y, Gatto L, Wang R, Sachsenberg T, Uszkoreit J, Leprevost Fda V, Fufezan C, Ternent T, Eglen SJ, Katz DS, Pollard TJ, Konovalov A, Flight RM, Blin K, Vizcaíno JA.

PLoS Comput Biol. 2016 Jul 14;12(7):e1004947. doi: 10.1371/journal.pcbi.1004947. eCollection 2016 Jul. No abstract available. Erratum in: PLoS Comput Biol. 2019 Jun 14;15(6):e1007142.

28.

Accurate estimation of isoelectric point of protein and peptide based on amino acid sequences.

Audain E, Ramos Y, Hermjakob H, Flower DR, Perez-Riverol Y.

Bioinformatics. 2016 Mar 15;32(6):821-7. doi: 10.1093/bioinformatics/btv674. Epub 2015 Nov 14.

29.

Novel interactions of domain III from the envelope glycoprotein of dengue 2 virus with human plasma proteins.

Huerta V, Ramos Y, Yero A, Pupo D, Martín D, Toledo P, Fleitas N, Gallien S, Martín AM, Márquez GJ, Pérez-Riverol Y, Sarría M, Guirola O, González LJ, Domon B, Chinea G.

J Proteomics. 2016 Jan 10;131:205-213. doi: 10.1016/j.jprot.2015.11.003. Epub 2015 Nov 3.

PMID:
26546555
30.

PRIDE Inspector Toolsuite: Moving Toward a Universal Visualization Tool for Proteomics Data Standard Formats and Quality Assessment of ProteomeXchange Datasets.

Perez-Riverol Y, Xu QW, Wang R, Uszkoreit J, Griss J, Sanchez A, Reisinger F, Csordas A, Ternent T, Del-Toro N, Dianes JA, Eisenacher M, Hermjakob H, Vizcaíno JA.

Mol Cell Proteomics. 2016 Jan;15(1):305-17. doi: 10.1074/mcp.O115.050229. Epub 2015 Nov 6.

31.

2016 update of the PRIDE database and its related tools.

Vizcaíno JA, Csordas A, del-Toro N, Dianes JA, Griss J, Lavidas I, Mayer G, Perez-Riverol Y, Reisinger F, Ternent T, Xu QW, Wang R, Hermjakob H.

Nucleic Acids Res. 2016 Jan 4;44(D1):D447-56. doi: 10.1093/nar/gkv1145. Epub 2015 Nov 2. Erratum in: Nucleic Acids Res. 2016 Dec 15;44(22):11033.

32.

Computational proteomics: Integrating mass spectral data into a biological context.

Carvalho PC, Padron G, Calvete JJ, Perez-Riverol Y.

J Proteomics. 2015 Nov 3;129:1-2. doi: 10.1016/j.jprot.2015.10.013. No abstract available.

PMID:
26521030
33.

Data for comparative proteomics analysis of the antitumor effect of CIGB-552 peptide in HT-29 colon adenocarcinoma cells.

Núñez de Villavicencio-Díaz T, Ramos Gómez Y, Oliva Argüelles B, Fernández Masso JR, Rodríguez-Ulloa A, Cruz García Y, Guirola-Cruz O, Perez-Riverol Y, Javier González L, Tiscornia I, Victoria S, Bollati-Fogolín M, Besada Pérez V, Guerra Vallespi M.

Data Brief. 2015 Jul 8;4:468-73. doi: 10.1016/j.dib.2015.06.024. eCollection 2015 Sep.

34.

Comparative proteomics analysis of the antitumor effect of CIGB-552 peptide in HT-29 colon adenocarcinoma cells.

Núñez de Villavicencio-Díaz T, Ramos Gómez Y, Oliva Argüelles B, Fernández Masso JR, Rodríguez-Ulloa A, Cruz García Y, Guirola-Cruz O, Perez-Riverol Y, Javier González L, Tiscornia I, Victoria S, Bollati-Fogolín M, Besada Pérez V, Guerra Vallespi M.

J Proteomics. 2015 Aug 3;126:163-71. doi: 10.1016/j.jprot.2015.05.024. Epub 2015 May 24.

PMID:
26013411
35.

PIA: An Intuitive Protein Inference Engine with a Web-Based User Interface.

Uszkoreit J, Maerkens A, Perez-Riverol Y, Meyer HE, Marcus K, Stephan C, Kohlbacher O, Eisenacher M.

J Proteome Res. 2015 Jul 2;14(7):2988-97. doi: 10.1021/acs.jproteome.5b00121. Epub 2015 Jun 10.

PMID:
25938255
36.

ms-data-core-api: an open-source, metadata-oriented library for computational proteomics.

Perez-Riverol Y, Uszkoreit J, Sanchez A, Ternent T, Del Toro N, Hermjakob H, Vizcaíno JA, Wang R.

Bioinformatics. 2015 Sep 1;31(17):2903-5. doi: 10.1093/bioinformatics/btv250. Epub 2015 Apr 24.

37.

Open source libraries and frameworks for biological data visualisation: a guide for developers.

Wang R, Perez-Riverol Y, Hermjakob H, Vizcaíno JA.

Proteomics. 2015 Apr;15(8):1356-74. doi: 10.1002/pmic.201400377. Epub 2015 Feb 5. Review.

38.

Identifying novel biomarkers through data mining-a realistic scenario?

Griss J, Perez-Riverol Y, Hermjakob H, Vizcaíno JA.

Proteomics Clin Appl. 2015 Apr;9(3-4):437-43. doi: 10.1002/prca.201400107. Epub 2015 Jan 12. Review.

39.

Making proteomics data accessible and reusable: current state of proteomics databases and repositories.

Perez-Riverol Y, Alpi E, Wang R, Hermjakob H, Vizcaíno JA.

Proteomics. 2015 Mar;15(5-6):930-49. doi: 10.1002/pmic.201400302. Review.

40.

On best practices in the development of bioinformatics software.

Leprevost Fda V, Barbosa VC, Francisco EL, Perez-Riverol Y, Carvalho PC.

Front Genet. 2014 Jul 2;5:199. doi: 10.3389/fgene.2014.00199. eCollection 2014. No abstract available.

41.

The mzTab data exchange format: communicating mass-spectrometry-based proteomics and metabolomics experimental results to a wider audience.

Griss J, Jones AR, Sachsenberg T, Walzer M, Gatto L, Hartler J, Thallinger GG, Salek RM, Steinbeck C, Neuhauser N, Cox J, Neumann S, Fan J, Reisinger F, Xu QW, Del Toro N, Pérez-Riverol Y, Ghali F, Bandeira N, Xenarios I, Kohlbacher O, Vizcaíno JA, Hermjakob H.

Mol Cell Proteomics. 2014 Oct;13(10):2765-75. doi: 10.1074/mcp.O113.036681. Epub 2014 Jun 30.

42.

Editorial: Genomics and proteomics behind drug design.

Perez-Riverol Y, Carvalho PC.

Curr Top Med Chem. 2014;14(3):343. No abstract available.

PMID:
24304322
43.

Bioinformatics tools for the functional interpretation of quantitative proteomics results.

Villavicencio-Diaz TN, Rodriguez-Ulloa A, Guirola-Cruz O, Perez-Riverol Y.

Curr Top Med Chem. 2014;14(3):435-49. Review.

PMID:
24304321
44.

A survey of molecular descriptors used in mass spectrometry based proteomics.

Audain E, Sanchez A, Vizcaíno JA, Perez-Riverol Y.

Curr Top Med Chem. 2014;14(3):388-97. Review.

PMID:
24304317
45.

SCX charge state selective separation of tryptic peptides combined with 2D-RP-HPLC allows for detailed proteome mapping.

Betancourt LH, De Bock PJ, Staes A, Timmerman E, Perez-Riverol Y, Sanchez A, Besada V, Gonzalez LJ, Vandekerckhove J, Gevaert K.

J Proteomics. 2013 Oct 8;91:164-71. doi: 10.1016/j.jprot.2013.06.033. Epub 2013 Jul 11.

PMID:
23851314
46.

JBioWH: an open-source Java framework for bioinformatics data integration.

Vera R, Perez-Riverol Y, Perez S, Ligeti B, Kertész-Farkas A, Pongor S.

Database (Oxford). 2013 Jul 11;2013:bat051. doi: 10.1093/database/bat051. Print 2013.

47.

Pinpointing differentially expressed domains in complex protein mixtures with the cloud service of PatternLab for Proteomics.

Leprevost FV, Lima DB, Crestani J, Perez-Riverol Y, Zanchin N, Barbosa VC, Carvalho PC.

J Proteomics. 2013 Aug 26;89:179-82. doi: 10.1016/j.jprot.2013.06.013. Epub 2013 Jun 21.

PMID:
23796493
48.

Open source libraries and frameworks for mass spectrometry based proteomics: a developer's perspective.

Perez-Riverol Y, Wang R, Hermjakob H, Müller M, Vesada V, Vizcaíno JA.

Biochim Biophys Acta. 2014 Jan;1844(1 Pt A):63-76. doi: 10.1016/j.bbapap.2013.02.032. Epub 2013 Mar 1. Review.

49.

HI-bone: a scoring system for identifying phenylisothiocyanate-derivatized peptides based on precursor mass and high intensity fragment ions.

Perez-Riverol Y, Sánchez A, Noda J, Borges D, Carvalho PC, Wang R, Vizcaíno JA, Betancourt L, Ramos Y, Duarte G, Nogueira FC, González LJ, Padrón G, Tabb DL, Hermjakob H, Domont GB, Besada V.

Anal Chem. 2013 Apr 2;85(7):3515-20. doi: 10.1021/ac303239g. Epub 2013 Mar 20.

PMID:
23448308
50.

Effectively addressing complex proteomic search spaces with peptide spectrum matching.

Borges D, Perez-Riverol Y, Nogueira FC, Domont GB, Noda J, da Veiga Leprevost F, Besada V, França FM, Barbosa VC, Sánchez A, Carvalho PC.

Bioinformatics. 2013 May 15;29(10):1343-4. doi: 10.1093/bioinformatics/btt106. Epub 2013 Feb 27.

PMID:
23446294

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