About Me


Personal Information

Name: PhD. Yasset Perez-Riverol

twitter: @ypriverol

github: ypriverol







Academics

March 2014 - Present: Bionformatian, PRIDE Group, Proteomics Services, European Bioinformatics Institute (EBI), UK.

September 2006 - March 2014: Research Scientist, Proteomics Department, Center for Genetic Engineering and Biotechnology, Havana, Cuba.

2010 - 2013:   PhD student in Biochemistry,  Biology Faculty, Havana University, Cuba. Development of new algorithms for Peptide/ Protein identifications. Thesis (Spanish)

July 2011 - December 2013:  Research Visitor at PRIDE Group, Proteomic Services, European Bioinformatics Institute (EBI), Cambridge, UK.


2001 - 2006:      Bachelors: Software Engineering: Superior Polytechnic Institute “José Antonio Echeverría” (ISPJAE), Habana, Cuba. Thesis: Parallel Conformational Search of small compounds. Thesis (Spanish) 


Editorial Board

- 2013 - Present:  Associate Editor of Frontiers in Bioinformatics and Computational Biology.

- 2014 - Present:  Executive Editor of Current Topics in Medicinal Chemistry.
  • Editorial: Genomics and proteomics behind drug design. Perez-Riverol Y, Carvalho PC. Curr Top Med Chem. 2014;14(3):343. (Special Issue).

Journal Referee (select list): 



Programming skills

- Java, Swing, JAXB, jsp
- R
- perl

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Current Projects

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PRIDE Inspector is an integrated desktop application for MS Proteomics data analysis and visualization. The current version of PRIDE Inspector is a suite of tools and libraries that support different peptide/protein identification standards such as PRIDE XML, mzTab and mzIdentML; as well as providing direct access to PRIDE resources. It also allows PRIDE submitters and journal reviewers to download private PRIDE experiments and perform quality checks. The present version also allow to check an visualize the quality of MS/MS files such mzML, mzxml, mgf, pkl, ms2. Some of the publications related with PRIDE Inspector toolsuite:

The PRIDE PRoteomics IDEntifications database is a centralized, standards compliant, public data repository for proteomics data, including protein and peptide identifications, post-translational modifications and supporting spectral evidence. PRIDE is currently part of proteomeXchange consortium with PeptideAtlas and MassIVE. PRIDE database is based on proteomics standards such as mzIdentML, PRIDE XML and mzTab files, ontologies and controlled vocabularies.


- Vizcaíno JA, Côté RG, Csordas A, Dianes JA, Fabregat A, Foster JM, Griss J, Alpi E, Birim M, Contell J, O'Kelly G, Schoenegger A, Ovelleiro D, Pérez-Riverol Y, Reisinger F, Ríos D, Wang R, Hermjakob H. The PRoteomics IDEntifications (PRIDE) database and associated tools: status in 2013. Nucleic Acids Res. 2013 Jan;41(Database issue):D1063-9. doi: 10.1093/nar/gks1262. Epub 2012 Nov 29.

- Perez-Riverol Y, Alpi E, Wang R, Hermjakob H, Vizcaíno JA. Making proteomics data accessible and reusable: Current state of proteomics databases and repositories. Proteomics. 2014 Aug 26. doi: 10.1002/pmic.201400302. 

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Development of new algorithms for proteins/peptide identification and validation. I developed new algorithms based on support vector machines and graph algorithms for isoelectric point prediction and protein identification based on sequence tag and spectrum patterns.

- Perez-Riverol Y, Audain E, Millan A, Ramos Y, Sanchez A, Vizcaíno JA, Wang R, Müller M, Machado YJ, Betancourt LH, González LJ, Padrón G, Besada V. Isoelectric point optimization using peptide descriptors and support vector machines. J Proteomics. 2012 Apr 3;75(7):2269-74. doi: 10.1016/j.jprot.2012.01.029. Epub 2012 Feb 3.

- 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. HI-bone: a scoring system for identifying phenylisothiocyanate-derivatized peptides based on precursor mass and high intensity fragment ions. Anal Chem. 2013 Apr 2;85(7):3515-20. doi: 10.1021/ac303239g. Epub 2013 Mar 20.

- Perez-Riverol Y, Sánchez A, Ramos Y, Schmidt A, Müller M, Betancourt L, González LJ, Vera R, Padron G, Besada V. In silico analysis of accurate proteomics, complemented by selective isolation of peptides. J Proteomics. 2011 Sep 6;74(10):2071-82. doi: 10.1016/j.jprot.2011.05.034. Epub 2011 May 27.

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Java Biological Warehouse (JBioWH) is a complete computational platform which provides a framework for biological data integration and management. The system is based in a relational schema (MySql) to integrate the most important public biological data sources (UNIPROT, GO, GENE, INTACT, BIOGRID, PFAM) into a DBMS and a Java API and  support rapid bioinformatics application development. Also, we developed a desktop application which contains an extended search interface and a SQL Editor to interact with the database. JBioWH provides a framework for biological data integration and management which contains a relational schema for biological data integration, a java Application Programming Interface (API) and a powerful Desktop tool. 


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List of Papers:

22- The PRoteomics IDEntification (PRIDE) Converter 2 framework: an improved suite of tools to facilitate data submission to the PRIDE database and the ProteomeXchange consortium. Côté RG1, Griss J, Dianes JA, Wang R, Wright JC, van den Toorn HW, van Breukelen B, Heck AJ, Hulstaert N, Martens L, Reisinger F, Csordas A, Ovelleiro D, Perez-Rivevol Y, Barsnes H, Hermjakob H, Vizcaíno JA. Mol Cell Proteomics. 2012 Dec;11(12):1682-9. doi: 10.1074/mcp.O112.021543. Epub 2012 Sep 4.

21- Charge state-selective separation of peptides by reversible modification of amino groups and strong cation-exchange chromatography: evaluation in proteomic studies using peptide-centric database searches. Betancourt LH1, Sánchez A, Pérez Y, Fernandez de Cossio J, Gil J, Toledo P, Iguchi S, Aimoto S, González LJ, Padrón G, Takao T, Besada V. J Proteomics. 2011 Sep 6;74(10):2210-3. doi: 10.1016/j.jprot.2011.04.029. Epub 2011 May 9.

20- Identifying novel biomarkers through data mining - a realistic scenario? Griss J, Perez-Riverol Y, Hermjakob H, Vizcaíno JA. Proteomics Clin Appl. 2014 Oct 28. doi: 10.1002/prca.201400107. [Epub ahead of print]

19- 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. 2014 Aug 26. doi: 10.1002/pmic.201400302.

18- 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.

17- 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.

16- Editorial: Genomics and proteomics behind drug design. Perez-Riverol Y, Carvalho PC. Curr Top Med Chem. 2014;14(3):343.

15- 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.

14- 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.

13- 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.

12- 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.

11- 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.

10- 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

9- 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.

8- 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.

7- Computational proteomics pitfalls and challenges: HavanaBioinfo 2012 workshop report. Perez-Riverol Y, Hermjakob H, Kohlbacher O, Martens L, Creasy D, Cox J, Leprevost F, Shan BP, Pérez-Nueno VI, Blazejczyk M, Punta M, Vierlinger K, Valiente PA, Leon K, Chinea G, Guirola O, Bringas R, Cabrera G, Guillen G, Padron G, Gonzalez LJ, Besada V. J Proteomics. 2013 Jul 11;87:134-8. doi: 10.1016/j.jprot.2013.01.019. Epub 2013 Jan 29.

6 - The PRoteomics IDEntifications (PRIDE) database and associated tools: status in 2013. Vizcaíno JA, Côté RG, Csordas A, Dianes JA, Fabregat A, Foster JM, Griss J, Alpi E, Birim M, Contell J, O'Kelly G, Schoenegger A, Ovelleiro D, Pérez-Riverol Y, Reisinger F, Ríos D, Wang R, Hermjakob H. Nucleic Acids Res. 2013 Jan;41(Database issue):D1063-9. doi: 10.1093/nar/gks1262. Epub 2012 Nov 29.

5- A parallel systematic-Monte Carlo algorithm for exploring conformational space. Perez-Riverol Y, Vera R, Mazola Y, Musacchio A. Curr Top Med Chem. 2012;12(16):1790-6.

4 - Isoelectric point optimization using peptide descriptors and support vector machines. Perez-Riverol Y, Audain E, Millan A, Ramos Y, Sanchez A, Vizcaíno JA, Wang R, Müller M, Machado YJ, Betancourt LH, González LJ, Padrón G, Besada V. J Proteomics. 2012 Apr 3;75(7):2269-74. doi: 10.1016/j.jprot.2012.01.029. Epub 2012 Feb 3.

3- PRIDE Inspector: a tool to visualize and validate MS proteomics data. Wang R, Fabregat A, Ríos D, Ovelleiro D, Foster JM, Côté RG, Griss J, Csordas A, Perez-Riverol Y, Reisinger F, Hermjakob H, Martens L, Vizcaíno JA. Nat Biotechnol. 2012 Feb 8;30(2):135-7. doi: 10.1038/nbt.2112.

2- Introducing an Asp-Pro linker in the synthesis of random one-bead-one-compound hexapeptide libraries compatible with ESI-MS analysis. Masforrol Y, Gil J, González LJ, Pérez-Riverol Y, Fernández-de-Cossío J, Sánchez A, Betancourt LH, Garay HE, Cabrales A, Albericio F, Yang H, Zubarev RA, Besada V, Acosta OR. ACS Comb Sci. 2012 Mar 12;14(3):145-9. doi: 10.1021/co200159r. Epub 2012 Feb 28.

1- Selective isolation of multiply charged peptides: a confident strategy for protein identification using a linear trap quadrupole mass spectrometer. Sanchez A, Sun W, Ma J, Betancourt L, Perez-Riverol Y, de-Cossio JF, Padron G, Jiang Y, He F, Gonzalez LJ, Besada V. Eur J Mass Spectrom (Chichester, Eng). 2012;18(6):505-8.