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Items: 1 to 50 of 53

1.

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

Santos MDM, Lima DB, Silva ARF, Kurt LU, Clasen MA, Pinto AFM, Moresco JJ, Yates JR 3rd, Aquino P, Barbosa VC, Fischer JSG, Carvalho PC.

J Proteomics. 2019 Jun 30;202:103371. doi: 10.1016/j.jprot.2019.04.021. Epub 2019 Apr 26.

PMID:
31034900
2.

Differential proteomic comparison of breast cancer secretome using a quantitative paired analysis workflow.

Brunoro GVF, Carvalho PC, Barbosa VC, Pagnoncelli D, De Moura Gallo CV, Perales J, Zahedi RP, Valente RH, Neves-Ferreira AGDC.

BMC Cancer. 2019 Apr 18;19(1):365. doi: 10.1186/s12885-019-5547-y.

3.

Top-Down Garbage Collector: a tool for selecting high-quality top-down proteomics mass spectra.

Lima DB, Silva ARF, Dupré M, Santos MDM, Clasen MA, Kurt LU, Aquino PF, Barbosa VC, Carvalho PC, Chamot-Rooke J.

Bioinformatics. 2019 Feb 4. doi: 10.1093/bioinformatics/btz085. [Epub ahead of print]

PMID:
30715205
4.

Information-theoretic signatures of biodiversity in the barcoding gene.

Barbosa VC.

J Theor Biol. 2018 Aug 14;451:111-116. doi: 10.1016/j.jtbi.2018.05.008. Epub 2018 May 8.

PMID:
29750998
5.

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

Lima DB, Melchior JT, Morris J, Barbosa VC, Chamot-Rooke J, Fioramonte M, Souza TACB, Fischer JSG, Gozzo FC, Carvalho PC, Davidson WS.

Nat Protoc. 2018 Mar;13(3):431-458. doi: 10.1038/nprot.2017.113. Epub 2018 Feb 1.

PMID:
29388937
6.

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

Trevisan-Silva D, Bednaski AV, Fischer JSG, Veiga SS, Bandeira N, Guthals A, Marchini FK, Leprevost FV, Barbosa VC, Senff-Ribeiro A, Carvalho PC.

Sci Data. 2017 Jul 11;4:170090. doi: 10.1038/sdata.2017.90.

7.

DiagnoProt: a tool for discovery of new molecules by mass spectrometry.

Silva ARF, Lima DB, Leyva A, Duran R, Batthyany C, Aquino PF, Leal JC, Rodriguez JE, Domont GB, Santos MDM, Chamot-Rooke J, Barbosa VC, Carvalho PC.

Bioinformatics. 2017 Jun 15;33(12):1883-1885. doi: 10.1093/bioinformatics/btx093.

PMID:
28186229
8.

Early detection of epilepsy seizures based on a weightless neural network.

de Aguiar K, Franca FM, Barbosa VC, Teixeira CA.

Conf Proc IEEE Eng Med Biol Soc. 2015 Aug;2015:4470-4. doi: 10.1109/EMBC.2015.7319387.

PMID:
26737287
9.

Integrated analysis of shotgun proteomic data with PatternLab for proteomics 4.0.

Carvalho PC, Lima DB, Leprevost FV, Santos MD, Fischer JS, Aquino PF, Moresco JJ, Yates JR 3rd, Barbosa VC.

Nat Protoc. 2016 Jan;11(1):102-17. doi: 10.1038/nprot.2015.133. Epub 2015 Dec 10.

10.

Using PepExplorer to Filter and Organize De Novo Peptide Sequencing Results.

da Veiga Leprevost F, Barbosa VC, Carvalho PC.

Curr Protoc Bioinformatics. 2015 Sep 3;51:13.27.1-9. doi: 10.1002/0471250953.bi1327s51.

PMID:
26334921
11.

SIM-XL: A powerful and user-friendly tool for peptide cross-linking analysis.

Lima DB, de Lima TB, Balbuena TS, Neves-Ferreira AGC, Barbosa VC, Gozzo FC, Carvalho PC.

J Proteomics. 2015 Nov 3;129:51-55. doi: 10.1016/j.jprot.2015.01.013. Epub 2015 Jan 29.

PMID:
25638023
12.

A scoring model for phosphopeptide site localization and its impact on the question of whether to use MSA.

Fischer JSDG, Dos Santos MDM, Marchini FK, Barbosa VC, Carvalho PC, Zanchin NIT.

J Proteomics. 2015 Nov 3;129:42-50. doi: 10.1016/j.jprot.2015.01.008. Epub 2015 Jan 23.

PMID:
25623781
13.

On best practices in the development of bioinformatics software.

Leprevost Fda V, Barbosa VC, Francisco EL, Perez-Riverol Y, Carvalho PC.

Front Genet. 2014 Jul 2;5:199. doi: 10.3389/fgene.2014.00199. eCollection 2014. No abstract available.

14.

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

Leprevost FV, Valente RH, Lima DB, Perales J, Melani R, Yates JR 3rd, Barbosa VC, Junqueira M, Carvalho PC.

Mol Cell Proteomics. 2014 Sep;13(9):2480-9. doi: 10.1074/mcp.M113.037002. Epub 2014 May 30.

15.

Exploring the proteomic landscape of a gastric cancer biopsy with the shotgun imaging analyzer.

Aquino PF, Lima DB, de Saldanha da Gama Fischer J, Melani RD, Nogueira FC, Chalub SR, Soares ER, Barbosa VC, Domont GB, Carvalho PC.

J Proteome Res. 2014 Jan 3;13(1):314-20. doi: 10.1021/pr400919k. Epub 2013 Nov 27.

PMID:
24283986
16.

Pinpointing differentially expressed domains in complex protein mixtures with the cloud service of PatternLab for Proteomics.

Leprevost FV, Lima DB, Crestani J, Perez-Riverol Y, Zanchin N, Barbosa VC, Carvalho PC.

J Proteomics. 2013 Aug 26;89:179-82. doi: 10.1016/j.jprot.2013.06.013. Epub 2013 Jun 21.

PMID:
23796493
17.

The conduciveness of CA-rule graphs.

Barbosa VC.

Artif Life. 2013 Spring;19(2):255-66. doi: 10.1162/ARTL_a_00107. Epub 2013 Mar 20.

PMID:
23514240
18.

Effectively addressing complex proteomic search spaces with peptide spectrum matching.

Borges D, Perez-Riverol Y, Nogueira FC, Domont GB, Noda J, da Veiga Leprevost F, Besada V, França FM, Barbosa VC, Sánchez A, Carvalho PC.

Bioinformatics. 2013 May 15;29(10):1343-4. doi: 10.1093/bioinformatics/btt106. Epub 2013 Feb 27.

PMID:
23446294
19.

PatternLab: from mass spectra to label-free differential shotgun proteomics.

Carvalho PC, Fischer JS, Xu T, Yates JR 3rd, Barbosa VC.

Curr Protoc Bioinformatics. 2012 Dec;Chapter 13:Unit13.19. doi: 10.1002/0471250953.bi1319s40.

PMID:
23255152
20.

Are gastric cancer resection margin proteomic profiles more similar to those from controls or tumors?

Aquino PF, Fischer JS, Neves-Ferreira AG, Perales J, Domont GB, Araujo GD, Barbosa VC, Viana J, Chalub SR, Lima de Souza AQ, Carvalho MG, Leão de Souza AD, Carvalho PC.

J Proteome Res. 2012 Dec 7;11(12):5836-42. doi: 10.1021/pr300612x. Epub 2012 Nov 13.

PMID:
23145836
21.

Quasispecies dynamics with network constraints.

Barbosa VC, Donangelo R, Souza SR.

J Theor Biol. 2012 Nov 7;312:114-9. doi: 10.1016/j.jtbi.2012.07.032. Epub 2012 Aug 9.

22.

Improving the TFold test for differential shotgun proteomics.

Carvalho PC, Yates JR 3rd, Barbosa VC.

Bioinformatics. 2012 Jun 15;28(12):1652-4. doi: 10.1093/bioinformatics/bts247. Epub 2012 Apr 26.

23.

Search engine processor: Filtering and organizing peptide spectrum matches.

Carvalho PC, Fischer JS, Xu T, Cociorva D, Balbuena TS, Valente RH, Perales J, Yates JR 3rd, Barbosa VC.

Proteomics. 2012 Apr;12(7):944-9. doi: 10.1002/pmic.201100529.

24.

Experimental analysis of lateral impact on planar brittle material: spatial properties of cracks.

dos Santos FP, Barbosa VC, Donangelo R, Souza SR.

Phys Rev E Stat Nonlin Soft Matter Phys. 2011 Aug;84(2 Pt 2):026115. Epub 2011 Aug 18.

PMID:
21929072
25.

Network algorithmics and the emergence of information integration in cortical models.

Nathan A, Barbosa VC.

Phys Rev E Stat Nonlin Soft Matter Phys. 2011 Jul;84(1 Pt 1):011904. Epub 2011 Jul 8.

PMID:
21867210
26.

Can the false-discovery rate be misleading?

Barboza R, Cociorva D, Xu T, Barbosa VC, Perales J, Valente RH, França FM, Yates JR 3rd, Carvalho PC.

Proteomics. 2011 Oct;11(20):4105-8. doi: 10.1002/pmic.201100297. Epub 2011 Sep 6.

27.

Early appraisal of the fixation probability in directed networks.

Barbosa VC, Donangelo R, Souza SR.

Phys Rev E Stat Nonlin Soft Matter Phys. 2010 Oct;82(4 Pt 2):046114. Epub 2010 Oct 22.

PMID:
21230352
28.

Analyzing marginal cases in differential shotgun proteomics.

Carvalho PC, Fischer JS, Perales J, Yates JR, Barbosa VC, Bareinboim E.

Bioinformatics. 2011 Jan 15;27(2):275-6. doi: 10.1093/bioinformatics/btq632. Epub 2010 Nov 11.

29.

Network conduciveness with application to the graph-coloring and independent-set optimization transitions.

Barbosa VC.

PLoS One. 2010 Jul 8;5(7):e11232. doi: 10.1371/journal.pone.0011232.

30.

Analyzing shotgun proteomic data with PatternLab for proteomics.

Carvalho PC, Yates Iii JR, Barbosa VC.

Curr Protoc Bioinformatics. 2010 Jun;Chapter 13:Unit 13.13.1-15. doi: 10.1002/0471250953.bi1313s30.

31.

Experimental analysis of lateral impact on planar brittle material.

dos Santos FP, Barbosa VC, Donangelo R, Souza SR.

Phys Rev E Stat Nonlin Soft Matter Phys. 2010 Apr;81(4 Pt 2):046108. Epub 2010 Apr 20.

PMID:
20481787
32.

Network algorithmics and the emergence of the cortical synaptic-weight distribution.

Nathan A, Barbosa VC.

Phys Rev E Stat Nonlin Soft Matter Phys. 2010 Feb;81(2 Pt 1):021916. Epub 2010 Feb 19.

PMID:
20365604
33.

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

Carvalho PC, Han X, Xu T, Cociorva D, Carvalho Mda G, Barbosa VC, Yates JR 3rd.

Bioinformatics. 2010 Mar 15;26(6):847-8. doi: 10.1093/bioinformatics/btq031. Epub 2010 Jan 26.

34.

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

Fischer Jde S, Liao L, Carvalho PC, Barbosa VC, Domont GB, Carvalho Mda G, Yates JR 3rd.

J Proteomics. 2010 Mar 10;73(5):1018-27. doi: 10.1016/j.jprot.2010.01.003. Epub 2010 Jan 18.

35.

Network growth for enhanced natural selection.

Barbosa VC, Donangelo R, Souza SR.

Phys Rev E Stat Nonlin Soft Matter Phys. 2009 Aug;80(2 Pt 2):026115. Epub 2009 Aug 14.

PMID:
19792208
36.

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

Carvalho PC, Xu T, Han X, Cociorva D, Barbosa VC, Yates JR 3rd.

Bioinformatics. 2009 Oct 15;25(20):2734-6. doi: 10.1093/bioinformatics/btp489. Epub 2009 Aug 14.

37.

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

Carvalho PC, Fischer JS, Chen EI, Domont GB, Carvalho MG, Degrave WM, Yates JR 3rd, Barbosa VC.

Proteome Sci. 2009 Feb 24;7:6. doi: 10.1186/1477-5956-7-6.

38.

Charge prediction machine: tool for inferring precursor charge states of electron transfer dissociation tandem mass spectra.

Carvalho PC, Cociorva D, Wong CC, Carvalho Mda G, Barbosa VC, Yates JR 3rd.

Anal Chem. 2009 Mar 1;81(5):1996-2003. doi: 10.1021/ac8025288.

39.

PatternLab for proteomics: a tool for differential shotgun proteomics.

Carvalho PC, Fischer JS, Chen EI, Yates JR 3rd, Barbosa VC.

BMC Bioinformatics. 2008 Jul 21;9:316. doi: 10.1186/1471-2105-9-316.

40.

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

Carvalho PC, Hewel J, Barbosa VC, Yates JR 3rd.

Genet Mol Res. 2008 Apr 15;7(2):342-56.

41.

Descents and nodal load in scale-free networks.

Bareinboim E, Barbosa VC.

Phys Rev E Stat Nonlin Soft Matter Phys. 2008 Apr;77(4 Pt 2):046111. Epub 2008 Apr 17.

PMID:
18517694
42.

V-like formations in flocks of artificial birds.

Nathan A, Barbosa VC.

Artif Life. 2008 Spring;14(2):179-88. doi: 10.1162/artl.2008.14.2.179.

PMID:
18331189
43.

Learning in the combinatorial neural model.

Machado RJ, Barbosa VC, Neves PA.

IEEE Trans Neural Netw. 1998;9(5):831-47. doi: 10.1109/72.712156.

PMID:
18255770
44.

Osteoma of the middle ear.

Barbosa VC, Santos MA, Becker HM, Diniz RF.

Braz J Otorhinolaryngol. 2007 Sep-Oct;73(5):719. No abstract available.

45.

Dissemination strategy for immunizing scale-free networks.

Stauffer AO, Barbosa VC.

Phys Rev E Stat Nonlin Soft Matter Phys. 2006 Nov;74(5 Pt 2):056105. Epub 2006 Nov 6.

PMID:
17279966
46.

Emergence of scale-free networks from local connectivity and communication trade-offs.

Barbosa VC, Donangelo R, Souza SR.

Phys Rev E Stat Nonlin Soft Matter Phys. 2006 Jul;74(1 Pt 2):016113. Epub 2006 Jul 20.

PMID:
16907157
47.

[Cavernous hemangioma of the internal auditory canal encasing the VII and VIII cranial nerve complex: case report].

Silveira RL, Andrade GC, Pinheiro Júnior N, Pittella JE, Barbosa VC.

Arq Neuropsiquiatr. 2005 Mar;63(1):163-5. Epub 2005 Apr 13. Portuguese.

48.

A graph model for the evolution of specificity in humoral immunity.

Flores LE, Aguilar EJ, Barbosa VC, de Carvalho LA.

J Theor Biol. 2004 Aug 7;229(3):311-25.

PMID:
15234199
49.

Application of semiclassical and geometrical optics theories to resonant modes of a coated sphere.

Bambino TM, Breitschaft AM, Barbosa VC, Guimarães LG.

J Opt Soc Am A Opt Image Sci Vis. 2003 Mar;20(3):489-98.

PMID:
12630834
50.

Reply to "Comment on 'Macroscopic models for the fusion of very heavy ions' "

Aguiar CE, Barbosa VC, Souza SR, de Oliveira EC.

Phys Rev C Nucl Phys. 1994 Apr;49(4):2253. No abstract available.

PMID:
9969462

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