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Implementing the reuse of public DIA proteomics datasets: from the PRIDE database to Expression Atlas.
- Published in:
- Scientific Data, 2022, v. 9, n. 1, p. 1, doi. 10.1038/s41597-022-01380-9
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- Publication type:
- Article
An integrated landscape of protein expression in human cancer.
- Published in:
- Scientific Data, 2021, v. 8, n. 1, p. 1, doi. 10.1038/s41597-021-00890-2
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- Publication type:
- Article
The ProteomeXchange consortium in 2017: supporting the cultural change in proteomics public data deposition.
- Published in:
- Nucleic Acids Research, 2017, v. 45, n. D1, p. D1100, doi. 10.1093/nar/gkw936
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- Publication type:
- Article
2016 update of the PRIDE database and its related tools.
- Published in:
- Nucleic Acids Research, 2016, v. 44, n. 1, p. D447, doi. 10.1093/nar/gkv1145
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- Publication type:
- Article
Introducing the PRIDE Archive RESTful web services.
- Published in:
- Nucleic Acids Research, 2015, v. 43, n. W1, p. W599, doi. 10.1093/nar/gkv382
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- Publication type:
- Article
The Proteomics Identifications (PRIDE) database and associated tools: status in 2013.
- Published in:
- Nucleic Acids Research, 2013, v. 41, p. D1063, doi. 10.1093/nar/gks1262
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- Publication type:
- Article
The Proteomics Identifications database: 2010 update.
- Published in:
- Nucleic Acids Research, 2010, v. 38, p. D736, doi. 10.1093/nar/gkp964
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- Publication type:
- Article
The growing need for controlled data access models in clinical proteomics and metabolomics.
- Published in:
- Nature Communications, 2021, v. 12, n. 1, p. 1, doi. 10.1038/s41467-021-26110-4
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- Publication type:
- Article
PRIDE Inspector: a tool to visualize and validate MS proteomics data.
- Published in:
- 2012
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- Publication type:
- Letter
PRIDE Converter: making proteomics data-sharing easy.
- Published in:
- 2009
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- Publication type:
- Letter
PRIDE Cluster: building a consensus of proteomics data.
- Published in:
- Nature Methods, 2013, v. 10, n. 2, p. 95, doi. 10.1038/nmeth.2343
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- Publication type:
- Article
Generation, annotation, and analysis of ESTs from four different Trichoderma strains grown under conditions related to biocontrol.
- Published in:
- Applied Microbiology & Biotechnology, 2007, v. 75, n. 4, p. 853, doi. 10.1007/s00253-007-0885-0
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- Publication type:
- Article
lesSDRF is more: maximizing the value of proteomics data through streamlined metadata annotation.
- Published in:
- Nature Communications, 2023, v. 14, n. 1, p. 1, doi. 10.1038/s41467-023-42543-5
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- Publication type:
- Article
LipidHome: A Database of Theoretical Lipids Optimized for High Throughput Mass Spectrometry Lipidomics
- Published in:
- PLoS ONE, 2013, v. 8, n. 5, p. 1, doi. 10.1371/journal.pone.0061951
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- Publication type:
- Article
Open source libraries and frameworks for biological data visualisation: A guide for developers.
- Published in:
- Proteomics, 2015, v. 15, n. 8, p. 1356, doi. 10.1002/pmic.201400377
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- Publication type:
- Article
Proteomics Data Visualisation.
- Published in:
- 2015
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- Publication type:
- Editorial
Making proteomics data accessible and reusable: Current state of proteomics databases and repositories.
- Published in:
- Proteomics, 2015, v. 15, n. 5/6, p. 930, doi. 10.1002/pmic.201400302
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- Publication type:
- Article
Analysis of the tryptic search space in UniProt databases.
- Published in:
- Proteomics, 2015, v. 15, n. 1, p. 48, doi. 10.1002/pmic.201400227
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- Publication type:
- Article
A standardized framing for reporting protein identifications in mzIdentML 1.2.
- Published in:
- Proteomics, 2014, v. 14, n. 21/22, p. 2389, doi. 10.1002/pmic.201400080
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- Publication type:
- Article
How to submit MS proteomics data to ProteomeXchange via the PRIDE database.
- Published in:
- Proteomics, 2014, v. 14, n. 20, p. 2233, doi. 10.1002/pmic.201400120
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- Publication type:
- Article
jmzTab: A Java interface to the mzTab data standard.
- Published in:
- Proteomics, 2014, v. 14, n. 11, p. 1328, doi. 10.1002/pmic.201300560
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- Publication type:
- Article
From Peptidome to PRIDE: Public proteomics data migration at a large scale.
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- Proteomics, 2013, v. 13, n. 10/11, p. 1692, doi. 10.1002/pmic.201200514
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- Publication type:
- Article
jmzReader: A Java parser library to process and visualize multiple text and XML-based mass spectrometry data formats.
- Published in:
- Proteomics, 2012, v. 12, n. 6, p. 795, doi. 10.1002/pmic.201100578
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- Publication type:
- Article
jmz Ident ML API: A Java interface to the mz Ident ML standard for peptide and protein identification data.
- Published in:
- Proteomics, 2012, v. 12, n. 6, p. 790, doi. 10.1002/pmic.201100577
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- Publication type:
- Article
From Proteomics Data Representation to Public Data Flow: A Report on the HUPO-PSI Workshop September 2011, Geneva, Switzerland.
- Published in:
- Proteomics, 2012, v. 12, n. 3, p. 351, doi. 10.1002/pmic.201290016
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- Publication type:
- Article
Consequences of the discontinuation of the International Protein Index (IPI) database and its substitution by the UniProtKB 'complete proteome' sets.
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- Proteomics, 2011, v. 11, n. 22, p. 4434, doi. 10.1002/pmic.201100363
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- Publication type:
- Article
Organelle proteomics experimental designs and analysis.
- Published in:
- Proteomics, 2010, v. 10, n. 22, p. 3957, doi. 10.1002/pmic.201000244
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- Publication type:
- Article
A guide to the Proteomics Identifications Database proteomics data repository.
- Published in:
- Proteomics, 2009, v. 9, n. 18, p. 4276, doi. 10.1002/pmic.200900402
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- Publication type:
- Article
Analysis of the experimental detection of central nervous system-related genes in human brain and cerebrospinal fluid datasets.
- Published in:
- Proteomics, 2008, v. 8, n. 6, p. 1138, doi. 10.1002/pmic.200700761
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- Publication type:
- Article
High Performance Proteomics: 7<sup>th</sup> HUPO Brain Proteome Project Workshop March 7-9, 2007 Wellcome Trust Conference Centre, Hinxton, UK.
- Published in:
- Proteomics, 2007, v. 7, n. 15, p. 2490, doi. 10.1002/pmic.200700449
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- Publication type:
- Article
The PSI formal document process and its implementation on the PSI website.
- Published in:
- Proteomics, 2007, v. 7, n. 14, p. 2355, doi. 10.1002/pmic.200700064
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- Publication type:
- Article
Quantifying the impact of public omics data.
- Published in:
- Nature Communications, 2019, v. 10, n. 1, p. N.PAG, doi. 10.1038/s41467-019-11461-w
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- Publication type:
- Article
The HUPO proteomics standards initiativemass spectrometry controlled vocabulary.
- Published in:
- Database: The Journal of Biological Databases & Curation, 2013, v. 2013, p. 1, doi. 10.1093/database/bat009
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- Publication type:
- Article
PRIDE: Quality control in a proteomics data repository.
- Published in:
- Database: The Journal of Biological Databases & Curation, 2012, v. 2012, p. 1, doi. 10.1093/database/bas004
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- Publication type:
- Article
Embedding standards in metabolomics: the Metabolomics Society data standards task group.
- Published in:
- 2015
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- Publication type:
- Report
Integrated view and comparative analysis of baseline protein expression in mouse and rat tissues.
- Published in:
- PLoS Computational Biology, 2022, v. 18, n. 6, p. 1, doi. 10.1371/journal.pcbi.1010174
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- Publication type:
- Article
Development of data representation standards by the human proteome organization proteomics standards initiative.
- Published in:
- Journal of the American Medical Informatics Association, 2015, v. 22, n. 3, p. 495, doi. 10.1093/jamia/ocv001
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- Publication type:
- Article
Analysis of the Protein Domain and Domain Architecture Content in Fungi and Its Application in the Search of New Antifungal Targets.
- Published in:
- PLoS Computational Biology, 2014, v. 10, n. 7, p. 1, doi. 10.1371/journal.pcbi.1003733
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- Publication type:
- Article
mzIdentML 1.3.0 – Essential progress on the support of crosslinking and other identifications based on multiple spectra.
- Published in:
- Proteomics, 2024, v. 24, n. 17, p. 1, doi. 10.1002/pmic.202300385
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- Publication type:
- Article
TopDownApp: An open and modular platform for analysis and visualisation of top-down proteomics data.
- Published in:
- Proteomics, 2024, v. 24, n. 3/4, p. 1, doi. 10.1002/pmic.202200403
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- Publication type:
- Article
TopDownApp: An open and modular platform for analysis and visualisation of top‐down proteomics data.
- Published in:
- Proteomics, 2024, v. 24, n. 2, p. 1, doi. 10.1002/pmic.202200403
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- Publication type:
- Article
Is DIA proteomics data FAIR? Current data sharing practices, available bioinformatics infrastructure and recommendations for the future.
- Published in:
- Proteomics, 2023, v. 23, n. 7, p. 1, doi. 10.1002/pmic.202200014
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- Publication type:
- Article
Using Deep Learning to Extrapolate Protein Expression Measurements.
- Published in:
- Proteomics, 2020, v. 20, n. 21/22, p. 1, doi. 10.1002/pmic.202000009
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- Publication type:
- Article
Future Prospects of Spectral Clustering Approaches in Proteomics.
- Published in:
- Proteomics, 2018, v. 18, n. 14, p. 1, doi. 10.1002/pmic.201700454
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- Publication type:
- Article
Minimal Information About an Immuno‐Peptidomics Experiment (MIAIPE).
- Published in:
- Proteomics, 2018, v. 18, n. 12, p. 1, doi. 10.1002/pmic.201800110
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- Publication type:
- Article
OLS Client and OLS Dialog: Open Source Tools to Annotate Public Omics Datasets.
- Published in:
- Proteomics, 2017, v. 17, n. 19, p. n/a, doi. 10.1002/pmic.201700244
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- Publication type:
- Article
Does Asymmetric Hearing Loss Affect the Ability to Understand in Noisy Environments?
- Published in:
- Journal of International Advanced Otology, 2019, v. 15, n. 2, p. 267, doi. 10.5152/iao.2019.5765
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- Publication type:
- Article
Integrated meta-analysis of colorectal cancer public proteomic datasets for biomarker discovery and validation.
- Published in:
- PLoS Computational Biology, 2024, v. 20, n. 1, p. 1, doi. 10.1371/journal.pcbi.1011828
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- Publication type:
- Article
Ten Simple Rules for Taking Advantage of Git and GitHub.
- Published in:
- 2016
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- Publication type:
- Product Review
PRIDE database resources in 2022: a hub for mass spectrometry-based proteomics evidences.
- Published in:
- Nucleic Acids Research, 2022, v. 50, n. D1, p. D543, doi. 10.1093/nar/gkab1038
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- Publication type:
- Article