Dostęp publiczny

Integrated analysis of shotgun proteomic data with PatternLab for proteomics 4.0

PC Carvalho, DB Lima, FV Leprevost, MDM Santos, JSG Fischer, ...

Nature protocols 11 (1), 102-117, 2016

Upoważnienia: US National Institutes of Health

PatternLab: from mass spectra to label‐free differential shotgun proteomics

PC Carvalho, JSG Fischer, T Xu, JR Yates III, VC Barbosa

Current Protocols in Bioinformatics 40 (1), 13.19. 1-13.19. 18, 2012

Upoważnienia: US National Institutes of Health

A quantitation module for isotope-labeled peptides integrated into PatternLab for proteomics

MDM Santos, DB Lima, ARF Silva, LU Kurt, MA Clasen, AFM Pinto, ...

Journal of Proteomics 202, 103371, 2019

Upoważnienia: US National Institutes of Health

Leveraging the partition selection bias to achieve a high-quality clustering of mass spectra

ARF Silva, DB Lima, LU Kurt, M Dupré, J Chamot-Rooke, MDM Santos, ...

Journal of Proteomics 245, 104282, 2021

Upoważnienia: European Commission, Agence Nationale de la Recherche

Dostępne w jakimś miejscu: 24

[HTML] springer.com

PatternLab for proteomics: a tool for differential shotgun proteomics

PC Carvalho, JSG Fischer, EI Chen, JR Yates, VC Barbosa

BMC bioinformatics 9, 1-14, 2008

Upoważnienia: US National Institutes of Health

Search engine processor: filtering and organizing peptide spectrum matches

PC Carvalho, JSG Fischer, T Xu, D Cociorva, TS Balbuena, RH Valente, ...

Proteomics 12 (7), 944-949, 2012

Upoważnienia: US National Institutes of Health

XDIA: improving on the label-free data-independent analysis

PC Carvalho, X Han, T Xu, D Cociorva, MG Carvalho, VC Barbosa, ...

Bioinformatics 26 (6), 847-848, 2010

Upoważnienia: US National Institutes of Health

[PDF] geneticsmr.com

Identifying differences in protein expression levels by spectral counting and feature selection

PC Carvalho, J Hewel, VC Barbosa, JR Yates III

Genetics and molecular research: GMR 7 (2), 342, 2008

Upoważnienia: US National Institutes of Health

YADA: a tool for taking the most out of high-resolution spectra

PC Carvalho, T Xu, X Han, D Cociorva, VC Barbosa, JR Yates III

Bioinformatics 25 (20), 2734-2736, 2009

Upoważnienia: US National Institutes of Health

Improving the TFold test for differential shotgun proteomics

PC Carvalho, JR Yates III, VC Barbosa

Bioinformatics 28 (12), 1652-1654, 2012

Upoważnienia: US National Institutes of Health

[PDF] frontiersin.org

On best practices in the development of bioinformatics software

FV Leprevost, VC Barbosa, EL Francisco, Y Perez-Riverol, PC Carvalho

Frontiers in genetics 5, 199, 2014

Upoważnienia: UK Biotechnology and Biological Sciences Research Council

[PDF] researchgate.net

Characterization of homodimer interfaces with cross-linking mass spectrometry and isotopically labeled proteins

DB Lima, JT Melchior, J Morris, VC Barbosa, J Chamot-Rooke, ...

Nature protocols 13 (3), 431-458, 2018

Upoważnienia: US National Institutes of Health, American Heart Association

[PDF] google.com

Simple, efficient and thorough shotgun proteomic analysis with PatternLab V

MDM Santos, DB Lima, JSG Fischer, MA Clasen, LU Kurt, ...

Nature protocols 17 (7), 1553-1578, 2022

Upoważnienia: US National Institutes of Health

[HTML] sciencedirect.com

PepExplorer: a similarity-driven tool for analyzing de novo sequencing results

FV Leprevost, RH Valente, DB Lima, J Perales, R Melani, JR Yates III, ...

Molecular & Cellular Proteomics 13 (9), 2480-2489, 2014

Upoważnienia: US National Institutes of Health

Can the false‐discovery rate be misleading?

R Barboza, D Cociorva, T Xu, VC Barbosa, J Perales, RH Valente, ...

Proteomics 11 (20), 4105-4108, 2011

Upoważnienia: US National Institutes of Health

[PDF] springer.com

GO Explorer: a gene-ontology tool to aid in the interpretation of shotgun proteomics data

PC Carvalho, JSG Fischer, EI Chen, GB Domont, MGC Carvalho, ...

Proteome Science 7, 1-11, 2009

Upoważnienia: US National Institutes of Health

Analyzing shotgun proteomic data with PatternLab for proteomics

PC Carvalho, JR Yates III, VC Barbosa

Current protocols in bioinformatics 30 (1), 13.13. 1-13.13. 15, 2010

Upoważnienia: US National Institutes of Health

Dynamic proteomic overview of glioblastoma cells (A172) exposed to perillyl alcohol

JS da Gama Fischer, L Liao, PC Carvalho, VC Barbosa, GB Domont, ...

Journal of proteomics 73 (5), 1018-1027, 2010

Upoważnienia: US National Institutes of Health

[HTML] nature.com

A multi-protease, multi-dissociation, bottom-up-to-top-down proteomic view of the Loxosceles intermedia venom

D Trevisan-Silva, AV Bednaski, JSG Fischer, SS Veiga, N Bandeira, ...

Scientific data 4 (1), 1-7, 2017

Upoważnienia: US National Institutes of Health