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Expert Review of Proteomics Volume 12, 2015 - Issue 6

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

Iakes EzkurdiaUnidad de Proteómica, Centro Nacional de Investigaciones Cardiovasculares, CNIC, Madrid, Spain

Enrique CalvoUnidad de Proteómica, Centro Nacional de Investigaciones Cardiovasculares, CNIC, Madrid, Spain

Angela Del PozoInstituto de Genetica Medica y Molecular, Hospital Universitario La Paz, Madrid, Spain

Jesús VázquezLaboratorio de Proteómica Cardiovascular, Centro Nacional de Investigaciones Cardiovasculares, CNIC, Madrid, Spain

Alfonso ValenciaStructural Biology and Bioinformatics Programme, Spanish National Cancer Research Centre (CNIO), Madrid, Spain;National Bioinformatics Institute (INB), Spanish National Cancer Research Centre (CNIO), Madrid, Spain

Michael L. TressStructural Biology and Bioinformatics Programme, Spanish National Cancer Research Centre (CNIO), Madrid, SpainCorrespondence[email protected]

Pages 579-593 | Published online: 23 Oct 2015

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https://doi.org/10.1586/14789450.2015.1103186
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Laura Martinez-Gomez, Daniel Cerdán-Vélez, Federico Abascal & Michael L Tress. (2022) Origins and Evolution of Human Tandem Duplicated Exon Substitution Events. Genome Biology and Evolution 14:12.
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Fernando Pozo, José Manuel Rodriguez, Laura Martínez Gómez, Jesús Vázquez & Michael L Tress. (2022) APPRIS principal isoforms and MANE Select transcripts define reference splice variants. Bioinformatics 38:Supplement_2, pages ii89-ii94.
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Wen-Jing Zhou, Zhuo-Hong Wei, Si-Min He & Hao Chi. (2022) pValid 2: A deep learning based validation method for peptide identification in shotgun proteomics with increased discriminating power. Journal of Proteomics 251, pages 104414.
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Laura Martinez Gomez, Fernando Pozo, Thomas A Walsh, Federico Abascal & Michael L Tress. (2021) The clinical importance of tandem exon duplication-derived substitutions. Nucleic Acids Research 49:14, pages 8232-8246.
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Fernando Pozo, Laura Martinez-Gomez, Thomas A Walsh, José Manuel Rodriguez, Tomas Di Domenico, Federico Abascal, Jesús Vazquez & Michael L Tress. (2021) Assessing the functional relevance of splice isoforms. NAR Genomics and Bioinformatics 3:2.
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Sara L. Banerjee, Ugo Dionne, Ana I. Osornio-Hernandez & Nicolas Bisson. 2020. Detection Methods in Precision Medicine. Detection Methods in Precision Medicine 191 222 .

Yohann Couté, Christophe Bruley & Thomas Burger. (2020) Beyond Target–Decoy Competition: Stable Validation of Peptide and Protein Identifications in Mass Spectrometry-Based Discovery Proteomics. Analytical Chemistry 92:22, pages 14898-14906.
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Mailys De Sousa Mendes, Alexandra L. Orton, Helen E. Humphries, Barry Jones, Iain Gardner, Sibylle Neuhoff & Venkatesh Pilla Reddy. (2020) A Laboratory-Specific Scaling Factor to Predict the In Vivo Human Clearance of Aldehyde Oxidase Substrates. Drug Metabolism and Disposition 48:11, pages 1231-1238.
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Gorka Prieto & Jesús Vázquez. (2020) Protein Probability Model for High-Throughput Protein Identification by Mass Spectrometry-Based Proteomics. Journal of Proteome Research 19:3, pages 1285-1297.
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Laura Martinez-Gomez, Federico Abascal, Irwin Jungreis, Fernando Pozo, Manolis Kellis, Jonathan M Mudge & Michael L Tress. (2020) Few SINEs of life: Alu elements have little evidence for biological relevance despite elevated translation. NAR Genomics and Bioinformatics 2:1.
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Gorka Prieto & Jesús Vázquez. 2020. Mass Spectrometry Data Analysis in Proteomics. Mass Spectrometry Data Analysis in Proteomics 145 159 .

Hao Chi, Chao Liu, Hao Yang, Wen-Feng Zeng, Long Wu, Wen-Jing Zhou, Rui-Min Wang, Xiu-Nan Niu, Yue-He Ding, Yao Zhang, Zhao-Wei Wang, Zhen-Lin Chen, Rui-Xiang Sun, Tao Liu, Guang-Ming Tan, Meng-Qiu Dong, Ping Xu, Pei-Heng Zhang & Si-Min He. (2018) Comprehensive identification of peptides in tandem mass spectra using an efficient open search engine. Nature Biotechnology 36:11, pages 1059-1061.
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Markus M. Rinschen, Kavee LimbutaraMark A. KnepperD. Michael PayneTrairak Pisitkun. (2018) From Molecules to Mechanisms: Functional Proteomics and Its Application to Renal Tubule Physiology. Physiological Reviews 98:4, pages 2571-2606.
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Barbara Uszczynska-Ratajczak, Julien Lagarde, Adam Frankish, Roderic Guigó & Rory Johnson. (2018) Towards a complete map of the human long non-coding RNA transcriptome. Nature Reviews Genetics 19:9, pages 535-548.
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Wout Bittremieux, David L. Tabb, Francis Impens, An Staes, Evy Timmerman, Lennart Martens & Kris Laukens. (2018) Quality control in mass spectrometry-based proteomics. Mass Spectrometry Reviews 37:5, pages 697-711.
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Rui Yan, Ju Zhang, Lucas Zellmer, Lichan Chen, Di Wu, Siqi Liu, Ningzhi Xu & Joshua D. Liao. (2017) Probably less than one-tenth of the genes produce only the wild type protein without at least one additional protein isoform in some human cancer cell lines. Oncotarget 8:47, pages 82714-82727.
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José Eduardo Kroll, Vandeclécio Lira da Silva, Sandro José de Souza & Gustavo Antonio de Souza. (2017) A tool for integrating genetic and mass spectrometry-based peptide data: Proteogenomics Viewer. BioEssays 39:7, pages 1700015.
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Michael L. Tress, Federico Abascal & Alfonso Valencia. (2017) Alternative Splicing May Not Be the Key to Proteome Complexity. Trends in Biochemical Sciences 42:2, pages 98-110.
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Wout Bittremieux, Dirk Valkenborg, Lennart Martens & Kris Laukens. (2017) Computational quality control tools for mass spectrometry proteomics. PROTEOMICS 17:3-4, pages 1600159.
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