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How to talk about protein-level false discovery rates in shotgun proteomics.
- Published in:
- Proteomics, 2016, v. 16, n. 18, p. 2461, doi. 10.1002/pmic.201500431
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- Article
IPeak: An open source tool to combine results from multiple MS/MS search engines.
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- Proteomics, 2015, v. 15, n. 17, p. 2916, doi. 10.1002/pmic.201400208
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- Article
GradientOptimizer: An open-source graphical environment for calculating optimized gradients in reversed-phase liquid chromatography.
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- Proteomics, 2014, v. 14, n. 12, p. 1464, doi. 10.1002/pmic.201400036
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- Article
Membrane protein shaving with thermolysin can be used to evaluate topology predictors.
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- Proteomics, 2013, v. 13, n. 9, p. 1467, doi. 10.1002/pmic.201200517
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- Article
A guideline to proteome-wide α-helical membrane protein topology predictions.
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- Proteomics, 2012, v. 12, n. 14, p. 2282, doi. 10.1002/pmic.201100495
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- Article
Chromatographic retention time prediction for posttranslationally modified peptides.
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- Proteomics, 2012, v. 12, n. 8, p. 1151, doi. 10.1002/pmic.201100386
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- Article
Quality assessments of peptide-spectrum matches in shotgun proteomics.
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- Proteomics, 2011, v. 11, n. 6, p. 1086, doi. 10.1002/pmic.201000432
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- Article
The TOPCONS web server for consensus prediction of membrane protein topology and signal peptides.
- Published in:
- Nucleic Acids Research, 2015, v. 43, n. W1, p. W401, doi. 10.1093/nar/gkv485
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- Article
Focus on the spectra that matter by clustering of quantification data in shotgun proteomics.
- Published in:
- Nature Communications, 2020, v. 11, n. 1, p. 1, doi. 10.1038/s41467-020-17037-3
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- Article
Survival analysis of pathway activity as a prognostic determinant in breast cancer.
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- PLoS Computational Biology, 2022, v. 18, n. 3, p. 1, doi. 10.1371/journal.pcbi.1010020
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- Article
Transmembrane Topology and Signal Peptide Prediction Using Dynamic Bayesian Networks.
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- PLoS Computational Biology, 2008, v. 4, n. 11, p. 1, doi. 10.1371/journal.pcbi.1000213
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- Article
ECCB2024: The 23rd European Conference on Computational Biology.
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- Bioinformatics, 2024, v. 40, p. ii1, doi. 10.1093/bioinformatics/btae422
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- Article
Pathway analysis through mutual information.
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- Bioinformatics, 2024, v. 40, n. 1, p. 1, doi. 10.1093/bioinformatics/btad776
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- Article
Parallelized calculation of permutation tests.
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- Bioinformatics, 2020, v. 36, n. 22/23, p. 5392, doi. 10.1093/bioinformatics/btaa1007
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- Article
Uncertainty estimation of predictions of peptides' chromatographic retention times in shotgun proteomics.
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- Bioinformatics, 2017, v. 33, n. 4, p. 508, doi. 10.1093/bioinformatics/btw619
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- Article
qvality: non-parametric estimation of q-values and posterior error probabilities.
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- Bioinformatics, 2009, v. 25, n. 7, p. 964, doi. 10.1093/bioinformatics/btp021
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- Article
Non-parametric estimation of posterior error probabilities associated with peptides identified by tandem mass spectrometry.
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- Bioinformatics, 2008, v. 24, n. 16, p. i42, doi. 10.1093/bioinformatics/btn294
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- Article
An HMM posterior decoder for sequence feature prediction that includes homology information.
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- Bioinformatics, 2005, v. 21, p. i251, doi. 10.1093/bioinformatics/bti1014
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- Article
An HMM posterior decoder for sequence feature prediction that includes homology information.
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- Bioinformatics, 2005, v. 21, n. 1, p. i251, doi. 10.1093/bioinformatics/bti1014
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- Article
A cross-validation scheme for machine learning algorithms in shotgun proteomics.
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- BMC Bioinformatics, 2012, v. 13, n. Suppl 16, p. 1, doi. 10.1186/1471-2105-13-S16-S3
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- Article
Finding haplotypic signatures in proteins.
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- GigaScience, 2023, v. 12, n. 1, p. 1, doi. 10.1093/gigascience/giad093
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- Article
Spatial multimodal analysis of transcriptomes and metabolomes in tissues.
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- Nature Biotechnology, 2024, v. 42, n. 7, p. 1046, doi. 10.1038/s41587-023-01937-y
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- Article
HiRIEF LC-MS enables deep proteome coverage and unbiased proteogenomics.
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- Nature Methods, 2014, v. 11, n. 1, p. 59, doi. 10.1038/nmeth.2732
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- Article
Semi-supervised learning for peptide identification from shotgun proteomics datasets.
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- Nature Methods, 2007, v. 4, n. 11, p. 923, doi. 10.1038/nmeth1113
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- Article
A novel transmembrane topology of presenilin based on reconciling experimental and computational evidence.
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- FEBS Journal, 2005, v. 272, n. 11, p. 2727, doi. 10.1111/j.1742-4658.2005.04691.x
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- Article
The Association of Biomolecular Resource Facilities Proteome Informatics Research Group Study on Metaproteomics (iPRG-2020).
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- Journal of Biomolecular Techniques, 2023, v. 34, n. 3, p. 1, doi. 10.7171/3fc1f5fe.a058bad4
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- Article
ABRF Proteome Informatics Research Group (iPRG) 2016 Study: Inferring Proteoforms from Bottom-up Proteomics Data.
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- Journal of Biomolecular Techniques, 2018, v. 29, n. 2, p. 39, doi. 10.7171/jbt.18-2902-003
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- Article
Peptide retention time prediction.
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- Mass Spectrometry Reviews, 2017, v. 36, n. 5, p. 615, doi. 10.1002/mas.21488
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- Article
A general model of G protein-coupled receptor sequences and its application to detect remote homologs.
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- Protein Science: A Publication of the Protein Society, 2006, v. 15, n. 3, p. 509, doi. 10.1110/ps.051745906
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- Article
Advantages of combined transmembrane topology and signal peptide prediction—the Phobius web server.
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- Nucleic Acids Research, 2007, v. 35, n. suppl_2, p. W429, doi. 10.1093/nar/gkm256
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- Article
A simple null model for inferences from network enrichment analysis.
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- PLoS ONE, 2018, v. 13, n. 11, p. 1, doi. 10.1371/journal.pone.0206864
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- Article
Multi-omic data analysis using Galaxy.
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- Nature Biotechnology, 2015, v. 33, n. 2, p. 137, doi. 10.1038/nbt.3134
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- Article
Membrane topology of the Drosophila OR83b odorant receptor
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- FEBS Letters, 2007, v. 581, n. 29, p. 5601, doi. 10.1016/j.febslet.2007.11.007
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- Article
Reliability of transmembrane predictions in whole-genome data
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- FEBS Letters, 2002, v. 532, n. 3, p. 415, doi. 10.1016/S0014-5793(02)03730-4
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- Article
CoExpresso: assess the quantitative behavior of protein complexes in human cells.
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- BMC Bioinformatics, 2019, v. 20, n. 1, p. 1, doi. 10.1186/s12859-018-2573-8
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- Article
Gene-specific correlation of RNA and protein levels in human cells and tissues.
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- Molecular Systems Biology, 2016, v. 12, n. 10, p. n/a, doi. 10.15252/msb.20167144
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- Article