Publications by authors named "Yasset Pérez-Riverol"

71Publications

Toward a Sample Metadata Standard in Public Proteomics Repositories.

J Proteome Res 2020 Oct 22;19(10):3906-3909. Epub 2020 Sep 22.

European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, U.K.

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http://dx.doi.org/10.1021/acs.jproteome.0c00376DOI Listing
October 2020

The omics discovery REST interface.

Nucleic Acids Res 2020 07;48(W1):W380-W384

European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Cambridge CB10 1SD, UK.

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http://dx.doi.org/10.1093/nar/gkaa326DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7319562PMC
July 2020

ThermoRawFileParser: Modular, Scalable, and Cross-Platform RAW File Conversion.

J Proteome Res 2020 01 6;19(1):537-542. Epub 2019 Dec 6.

European Molecular Biology Laboratory , European Bioinformatics Institute (EMBL-EBI) , Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD , United Kingdom.

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http://dx.doi.org/10.1021/acs.jproteome.9b00328DOI Listing
January 2020

Scalable Data Analysis in Proteomics and Metabolomics Using BioContainers and Workflows Engines.

Proteomics 2020 05 18;20(9):e1900147. Epub 2019 Dec 18.

European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD, UK.

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http://dx.doi.org/10.1002/pmic.201900147DOI Listing
May 2020

Sodium dodecyl sulfate free gel electrophoresis/electroelution sorting for peptide fractionation.

J Sep Sci 2019 Dec 10;42(24):3712-3717. Epub 2019 Nov 10.

Department of Proteomics, Center for Genetic Engineering and Biotechnology, La Habana, Cuba.

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http://dx.doi.org/10.1002/jssc.201900495DOI Listing
December 2019

Quantifying the impact of public omics data.

Nat Commun 2019 08 5;10(1):3512. Epub 2019 Aug 5.

European Molecular Biology Laboratory, EMBL-European Bioinformatics Institute (EMBL-EBI), Cambridge, CB10 1SD, UK.

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http://dx.doi.org/10.1038/s41467-019-11461-wDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6683138PMC
August 2019

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

J Proteome Res 2019 04 22;18(4):1477-1485. Epub 2019 Mar 22.

Research Institute of Molecular Pathology (IMP) , Vienna Biocenter (VBC) , Campus-Vienna-Biocenter 1 , 1030 Vienna , Austria.

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http://pubs.acs.org/doi/10.1021/acs.jproteome.8b00377
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http://dx.doi.org/10.1021/acs.jproteome.8b00377DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6456873PMC
April 2019

Protein Inference Using PIA Workflows and PSI Standard File Formats.

J Proteome Res 2019 02 5;18(2):741-747. Epub 2018 Dec 5.

Ruhr University Bochum , Medical Faculty, Medizinisches Proteom-Center , Universitaetsstrasse 150 , D-44801 Bochum , Germany.

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http://pubs.acs.org/doi/10.1021/acs.jproteome.8b00723
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http://dx.doi.org/10.1021/acs.jproteome.8b00723DOI Listing
February 2019

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

Anal Biochem 2018 10 23;559:51-54. Epub 2018 Aug 23.

Proteomics Unit, Chemistry Institute, Federal University of Rio de Janeiro, 21941-909, Rio de Janeiro, Brazil. Electronic address:

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http://dx.doi.org/10.1016/j.ab.2018.08.013DOI Listing
October 2018

Future Prospects of Spectral Clustering Approaches in Proteomics.

Proteomics 2018 07;18(14):e1700454

European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD, UK.

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http://dx.doi.org/10.1002/pmic.201700454DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6099476PMC
July 2018

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

J Proteome Res 2018 05 25;17(5):1993-1996. Epub 2018 Apr 25.

European Molecular Biology Laboratory , European Bioinformatics Institute (EMBL-EBI) , Wellcome Trust Genome Campus , Hinxton, Cambridge CB10 1SD , United Kingdom.

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http://dx.doi.org/10.1021/acs.jproteome.7b00824DOI Listing
May 2018

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

J Proteome Res 2018 05 16;17(5):1879-1886. Epub 2018 Apr 16.

Science for Life Laboratory, School of Engineering Sciences in Chemistry, Biotechnology and Health , KTH - Royal Institute of Technology , Box 1031 , 17121 Solna , Sweden.

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http://dx.doi.org/10.1021/acs.jproteome.7b00899DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6474350PMC
May 2018

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

PLoS One 2017 20;12(12):e0189875. Epub 2017 Dec 20.

Department of Congenital Heart Disease and Pediatric Cardiology, Universitätsklinikum Schleswig-Holstein Kiel, Kiel, Germany.

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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0189875PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5738110PMC
January 2018

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

Proteomics 2017 Oct;17(19)

European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge, UK.

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http://dx.doi.org/10.1002/pmic.201700244DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5707441PMC
October 2017

Synthetic human proteomes for accelerating protein research.

Nat Methods 2017 02;14(3):240-242

European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton, UK.

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http://dx.doi.org/10.1038/nmeth.4191DOI Listing
February 2017

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

J Proteomics 2017 01 4;150:170-182. Epub 2016 Aug 4.

European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL- EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK. Electronic address:

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http://dx.doi.org/10.1016/j.jprot.2016.08.002DOI Listing
January 2017

2016 update of the PRIDE database and its related tools.

Nucleic Acids Res 2016 12 28;44(22):11033. Epub 2016 Sep 28.

European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD, UK.

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http://dx.doi.org/10.1093/nar/gkw880DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5159556PMC
December 2016

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

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

European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge, United Kingdom.

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http://dx.doi.org/10.1038/nmeth.3902DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4968634PMC
August 2016

Ten Simple Rules for Taking Advantage of Git and GitHub.

PLoS Comput Biol 2016 07 14;12(7):e1004947. Epub 2016 Jul 14.

European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge, United Kingdom.

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http://dx.doi.org/10.1371/journal.pcbi.1004947DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4945047PMC
July 2016

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

Bioinformatics 2016 03 14;32(6):821-7. Epub 2015 Nov 14.

Department European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD, UK and.

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http://dx.doi.org/10.1093/bioinformatics/btv674DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5939969PMC
March 2016

2016 update of the PRIDE database and its related tools.

Nucleic Acids Res 2016 Jan 2;44(D1):D447-56. Epub 2015 Nov 2.

European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD, UK National Center for Protein Sciences, Beijing, China.

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http://nar.oxfordjournals.org/content/44/D1/D447.full.pdf
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https://academic.oup.com/nar/article-lookup/doi/10.1093/nar/
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http://dx.doi.org/10.1093/nar/gkv1145DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4702828PMC
January 2016

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

J Proteomics 2015 Nov;129:1-2

European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK. Electronic address:

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http://dx.doi.org/10.1016/j.jprot.2015.10.013DOI Listing
November 2015

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

J Proteome Res 2015 Jul 10;14(7):2988-97. Epub 2015 Jun 10.

Medizinisches Proteom-Center, Ruhr-Universität Bochum, 44801 Bochum, Germany.

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http://pubs.acs.org/doi/10.1021/acs.jproteome.5b00121
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http://dx.doi.org/10.1021/acs.jproteome.5b00121DOI Listing
July 2015

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

Bioinformatics 2015 Sep 24;31(17):2903-5. Epub 2015 Apr 24.

European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD, UK.

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http://dx.doi.org/10.1093/bioinformatics/btv250DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4547611PMC
September 2015

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

Proteomics 2015 Apr 5;15(8):1356-74. Epub 2015 Feb 5.

European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge, UK.

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http://dx.doi.org/10.1002/pmic.201400377DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4409855PMC
April 2015

Identifying novel biomarkers through data mining-a realistic scenario?

Proteomics Clin Appl 2015 Apr 12;9(3-4):437-43. Epub 2015 Jan 12.

European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge, UK; Division of Immunology, Allergy and Infectious Diseases, Department of Dermatology, Medical University of Vienna, Austria.

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http://doi.wiley.com/10.1002/prca.201400107
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http://dx.doi.org/10.1002/prca.201400107DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4833187PMC
April 2015

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

Proteomics 2015 Mar;15(5-6):930-49

European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge, UK.

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http://dx.doi.org/10.1002/pmic.201400302DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4409848PMC
March 2015

On best practices in the development of bioinformatics software.

Front Genet 2014 2;5:199. Epub 2014 Jul 2.

Laboratory for Proteomics and Protein Engineering, Carlos Chagas Institute - Fiocruz Curitiba, Brazil.

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http://dx.doi.org/10.3389/fgene.2014.00199DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4078907PMC
July 2014

Editorial: Genomics and proteomics behind drug design.

Curr Top Med Chem 2014 ;14(3):343

Laboratory for Proteomics and Protein Engineering Carlos Chagas Institute Fiocruz - Parana Brazil.

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http://dx.doi.org/10.2174/1568026613666131204101110DOI Listing
October 2014

Bioinformatics tools for the functional interpretation of quantitative proteomics results.

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

Department of Bioinformatics, Center for Genetic Engineering and Biotechnology, Ciudad de la Habana, Cuba.

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http://dx.doi.org/10.2174/1568026613666131204105110DOI Listing
October 2014

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

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

Department of Proteomics, Center for Genetic Engineering and Biotechnology, Ciudad de la Habana. Cuba.

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http://dx.doi.org/10.2174/1568026613666131204113537DOI Listing
October 2014

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

J Proteomics 2013 Oct 11;91:164-71. Epub 2013 Jul 11.

Department of Proteomics, Center for Genetic Engineering and Biotechnology, Ave. 31 e/158 y 190, Cubanacán, Playa, P.O. Box 6162, 10600 Havana, Cuba. Electronic address:

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http://dx.doi.org/10.1016/j.jprot.2013.06.033DOI Listing
October 2013

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

Database (Oxford) 2013 11;2013:bat051. Epub 2013 Jul 11.

Department of Physics, Polytechnic University Jose E. Echeverria, Havana, Cuba.

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http://dx.doi.org/10.1093/database/bat051DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3708619PMC
October 2013

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

Biochim Biophys Acta 2014 Jan 1;1844(1 Pt A):63-76. Epub 2013 Mar 1.

EMBL Outstation, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD, UK; Department of Proteomics, Center for Genetic Engineering and Biotechnology, Ciudad de la Habana, Cuba.

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http://dx.doi.org/10.1016/j.bbapap.2013.02.032DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3898926PMC
January 2014

Effectively addressing complex proteomic search spaces with peptide spectrum matching.

Bioinformatics 2013 May 27;29(10):1343-4. Epub 2013 Feb 27.

Systems Engineering and Computer Science Program, Federal University of Rio de Janeiro, 21941-972 Rio de Janeiro, Brazil.

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http://dx.doi.org/10.1093/bioinformatics/btt106DOI Listing
May 2013

A parallel systematic-Monte Carlo algorithm for exploring conformational space.

Curr Top Med Chem 2012 ;12(16):1790-6

Department of Proteomics and Bioinformatics, Center for Genetic Engineering and Biotechnology, Havana, Cuba.

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June 2013

Isoelectric point optimization using peptide descriptors and support vector machines.

J Proteomics 2012 Apr 3;75(7):2269-74. Epub 2012 Feb 3.

Department of Proteomics, Center for Genetic Engineering and Biotechnology, Ave 31 e/ 158 y 190, Cubanacán, Playa, Ciudad de la Habana, Cuba.

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http://dx.doi.org/10.1016/j.jprot.2012.01.029DOI Listing
April 2012

Selective isolation of multiply charged peptides: a confident strategy for protein identification using a linear trap quadrupole mass spectrometer.

Eur J Mass Spectrom (Chichester) 2012 ;18(6):505-8

Department of Proteomics and Bioinformatics. Center for Genetic Engineering and Biotechnotogy, Havana, Cuba.

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http://dx.doi.org/10.1255/ejms.1204DOI Listing
June 2013

In silico analysis of accurate proteomics, complemented by selective isolation of peptides.

J Proteomics 2011 Sep 27;74(10):2071-82. Epub 2011 May 27.

Department of Proteomics, Center for Genetic Engineering and Biotechnology, Cubanacán, Playa, Ciudad de la Habana, Cuba.

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http://dx.doi.org/10.1016/j.jprot.2011.05.034DOI Listing
September 2011

Peptide fractionation by acid pH SDS-free electrophoresis.

Electrophoresis 2011 Jun 2;32(11):1323-6. Epub 2011 May 2.

Center for Genetic Engineering and Biotechnology, La Habana, Cuba.

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http://dx.doi.org/10.1002/elps.201000677DOI Listing
June 2011