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Valmir C. Barbosa · Papers
[2023]

[doi]
[acs]
Milan A. Clasen, Marlon D. M. Santos, Louise Ulrich Kurt, Juliana Fischer,
Amanda C. CamilloAndrade, Lucas Albuquerque Sales,
Tatiana de Arruda Campos Brasil de Souza, Diogo Borges Lima, Fabio C. Gozzo,
Richard Hemmi Valente, Rosario Duran, Valmir C. Barbosa, and Paulo C. Carvalho,
“PatternLab V handles multiplex spectra in shotgun proteomic searches and
increases identification,”
Journal of the American Society for Mass Spectrometry, to appear.

[doi]
Marlon D. M. Santos, Amanda C. CamilloAndrade, Diogo B. Lima,
Tatiana A. C. B. Souza, Juliana de S. da G. Fischer, Richard H. Valente,
Fabio C. Gozzo, Valmir C. Barbosa, Carlos Batthyany, Julia ChamotRooke,
Rosario Duran, and Paulo C. Carvalho,
“DiagnoMass: a proteomics hub for pinpointing discriminative spectral
clusters,”
Journal of Proteomics
277 (2023), 104853.

[doi]
Valmir C. Barbosa and Josina O. do Nascimento,
“A simple linear model to aid in analyses of the β Pictoris moving
group,”
Monthly Notices of the Royal Astronomical Society: Letters
519 (2023), L57–L61.
[2022]

[doi]
[pdf]
Milan A. Clasen, Louise U. Kurt, Marlon D. M. Santos, Diogo B. Lima, Fan Liu,
Fabio C. Gozzo, Valmir C. Barbosa, and Paulo C. Carvalho,
“Increasing confidence in proteomic spectral deconvolution through mass
defect,”
Bioinformatics
38 (2022), 5119–5120.

[arxiv]
Eduardo J. Aguilar and Valmir C. Barbosa,
“Shape complexity in cluster analysis,”
May 2022.

[doi]
[rdcu]
Marlon D. M. Santos, Diogo B. Lima, Juliana S. G. Fischer,
Milan A. Clasen, Louise U. Kurt, Amanda Caroline CamilloAndrade,
Leandro C. Monteiro, Priscila F. de Aquino, Ana G. C. NevesFerreira,
Richard H. Valente, Monique R. O. Trugilho, Giselle V. F. Brunoro,
Tatiana A. C. B. Souza, Renata M. Santos, Michel Batista, Fabio C. Gozzo,
Rosario Durán, John R. Yates III, Valmir C. Barbosa, and
Paulo C. Carvalho,
“Simple, efficient and thorough shotgun proteomic analysis with
PatternLab V,”
Nature Protocols
17 (2022), 1553–1578.
[2021]

[doi]
[pdf]
Raphael M. Guedes, José F. de Rezende, and Valmir C. Barbosa,
“Integrated optimization of heterogeneousnetwork management and the
elusive role of macrocells,”
IEEE Access
9 (2021), 149552–149559.

[doi]
André R. F. Silva, Diogo B. Lima, Louise U. Kurt, Mathieu Dupré,
Julia ChamotRooke, Marlon D. M. Santos, Carolina Alves Nicolau,
Richard Hemmi Valente, Valmir C. Barbosa, and Paulo C. Carvalho,
“Leveraging the partition selection bias to achieve a highquality
clustering of mass spectra,”
Journal of Proteomics
245 (2021), 104282.

[doi]
[pdf]
Eduardo J. Aguilar, Valmir C. Barbosa, Raul Donangelo, and Sergio R. Souza,
“Interspecies evolutionary dynamics mediated by public goods in bacterial
quorum sensing,”
Physical Review E
103 (2021), 012403.
[2020]

[doi]
Jefferson Elbert Simões, Daniel R. Figueiredo, and Valmir C. Barbosa,
“Local symmetry in random graphs,”
IEEE Transactions on Network Science and Engineering
7 (2020), 1913–1924.

[doi]
Marlon D. M. Santos, Amanda Caroline CamilloAndrade, Louise U. Kurt,
Milan A. Clasen, Eduardo Lyra, Fabio C. Gozzo, Michel Batista,
Richard H. Valente, Giselle V. F. Brunoro, Valmir C. Barbosa,
Juliana S. G. Fischer, and Paulo C. Carvalho,
“Mixeddata acquisition: nextgeneration quantitative proteomics data
acquisition,”
Journal of Proteomics
222 (2020), 103803.

[doi]
Guilherme I. Ricardo, José F. de Rezende, and Valmir C. Barbosa,
“Scheduling wireless links in the physical interference model by
fractional edge coloring,”
IEEE Wireless Communications Letters
9 (2020), 528–532.
[2019]

[doi]
[pdf]
Diogo B. Lima, André R. F. Silva, Mathieu Dupré,
Marlon D. M. Santos, Milan A. Clasen, Louise U. Kurt, Priscila F. Aquino,
Valmir C. Barbosa, Paulo C. Carvalho, and Julia ChamotRooke,
“TopDown Garbage Collector: a tool for selecting highquality topdown
proteomics mass spectra,”
Bioinformatics
35 (2019), 3489–3490.

[doi]
Giulio Iacobelli, Daniel R. Figueiredo, and Valmir C. Barbosa,
“Counting trees with random walks,”
Expositiones Mathematicae
37 (2019), 96–102.

[doi]
Marlon D. M. Santos, Diogo B. Lima, André R. F. Silva,
Louise U. Kurt, Milan A. Clasen, Antônio F. M. Pinto, James J. Moresco,
John R. Yates III, Priscila Aquino, Valmir C. Barbosa, Juliana S. G. Fischer,
and Paulo C. Carvalho,
“A quantitation module for isotopelabeled peptides integrated into
PatternLab for proteomics,”
Journal of Proteomics
202 (2019), 103371.

[doi]
[pdf]
Giselle Villa Flor Brunoro, Paulo Costa Carvalho, Valmir C. Barbosa,
Dante Pagnoncelli, Claudia Vitória de Moura Gallo, Jonas Perales,
René Peiman Zahedi, Richard Hemmi Valente, and
Ana Gisele da Costa NevesFerreira,
“Differential proteomic comparison of breast cancer secretome using a
quantitative paired analysis workflow,”
BMC Cancer
19 (2019), 365.

[doi]
[rdcu]
Juan P. A. Lopes, Fabiano S. Oliveira, Paulo E. D. Pinto, and Valmir C. Barbosa,
“Sketching data structures for massive graph problems,”
Heterogeneous Data Management, Polystores, and Analytics for Healthcare
(V. Gadepally et al., Eds.), 57–67,
Lecture Notes in Computer Science 11470,
Springer Nature, Cham, Switzerland, 2019.
[2018]

[doi]
[pdf]
Valmir C. Barbosa, Raul Donangelo, and Sergio R. Souza,
“Coevolution of the mitotic and meiotic modes of eukaryotic cellular
division,”
Physical Review E
98 (2018), 032409.

[pdf]
[pdf, erratum]
Ricardo M. Oliveira, Flavio B. Gonzaga, Valmir C. Barbosa, and
Geraldo B. Xexéo,
“A distributed system for SearchOnMath based on the Microsoft BizSpark
program,”
Proceedings of the 33rd Brazilian Symposium on Databases,
289–294, 2018.

[doi]
Carlos V. G. C. Lima, Leonardo I. L. Oliveira, Valmir C. Barbosa,
Mitre C. Dourado, Fábio Protti, and Jayme L. Szwarcfiter,
“A computational study of freversible processes on graphs,”
Discrete Applied Mathematics
245 (2018), 77–93.

[doi]
[pdf]
Valmir C. Barbosa,
“Informationtheoretic signatures of biodiversity in the barcoding
gene,”
Journal of Theoretical Biology
451 (2018), 111–116.

[doi]
[rdcu]
Diogo B. Lima, John T. Melchior, Jamie Morris, Valmir C. Barbosa,
Julia ChamotRooke, Mariana Fioramonte, Tatiana A. C. B. Souza,
Juliana S. G. Fischer, Fabio C. Gozzo, Paulo C. Carvalho, and W. Sean Davidson,
“Characterization of homodimer interfaces with crosslinking mass
spectrometry and isotopically labeled proteins,”
Nature Protocols
13 (2018), 431–458.
[2017]

[doi]
[pdf]
Jefferson Elbert Simões, Daniel R. Figueiredo, and Valmir C. Barbosa,
“Powerlaw decay of the degreesequence probabilities of multiple random
graphs with application to graph isomorphism,”
ESAIM: Probability and Statistics
21 (2017), 235–250.

[doi]
[rdcu]
Fabiano de S. Oliveira and Valmir C. Barbosa,
“A note on counting independent terms in asymptotic expressions of
computational complexity,”
Optimization Letters
11 (2017), 1757–1765.

[doi]
[pdf]
Dilza TrevisanSilva, Aline V. Bednaski, Juliana S. G. Fischer, Silvio S. Veiga,
Nuno Bandeira, Adrian Guthals, Fabricio K. Marchini, Felipe V. Leprevost,
Valmir C. Barbosa, Andrea SenffRibeiro, and Paulo C. Carvalho,
“A multiprotease, multidissociation, bottomuptotopdown proteomic
view of the Loxosceles intermedia venom,”
Scientific Data
4 (2017), 170090.

[doi]
[pdf]
André R. F. Silva, Diogo B. Lima, Alejandro Leyva, Rosario Duran,
Carlos Batthyany, Priscila F. Aquino, Juliana C. Leal, Jimmy E. Rodriguez,
Gilberto B. Domont, Marlon D. M. Santos, Julia ChamotRooke, Valmir C. Barbosa,
and Paulo C. Carvalho,
“DiagnoProt: a tool for discovery of new molecules by mass
spectrometry,”
Bioinformatics
33 (2017), 1883–1885.

[doi]
[pdf]
Valmir C. Barbosa,
“Information integration from distributed thresholdbased
interactions,”
Complexity
(2017), 7046359.
[2016]

[doi]
Rodrigo R. Esch, Fábio Protti, and Valmir C. Barbosa,
“Adaptive event sensing in networks of autonomous mobile agents,”
Journal of Network and Computer Applications
71 (2016), 118–129.

[doi]
Valmir C. Barbosa, Raul Donangelo, and Sergio R. Souza,
“Quasispecies dynamics on a network of interacting genotypes and
idiotypes: applications to autoimmunity and immunodeficiency,”
Journal of Statistical Mechanics
(2016), 063501.

[arxiv]
Fabiano de S. Oliveira and Valmir C. Barbosa,
“On the mediation of program allocation in highdemand
environments,”
April 2016.

[doi]
[acm]
Valmir C. Barbosa, Alan Diêgo A. Carneiro, Fábio Protti, and
Uéverton S. Souza,
“Deadlock models in distributed computation: foundations, design, and
computational complexity,”
Proceedings of the 31st Annual ACM Symposium on Applied Computing,
538–541, 2016.

[doi]
Fabio R. J. Vieira, José F. de Rezende, and Valmir C. Barbosa,
“Scheduling wireless links by vertex multicoloring in the physical
interference model,”
Computer Networks
99 (2016), 125–133.

[doi]
[rdcu]
Paulo C. Carvalho, Diogo B. Lima, Felipe V. Leprevost, Marlon D. M. Santos,
Juliana S. G. Fischer, Priscila F. Aquino, James J. Moresco, John R. Yates III,
and Valmir C. Barbosa,
“Integrated analysis of shotgun proteomic data with PatternLab for
proteomics 4.0,”
Nature Protocols
11 (2016), 102–117.
[2015]

[doi]
[pdf]
Luciano Dyballa and Valmir C. Barbosa,
“Further insights into the interareal connectivity of a cortical
network,”
Network Science
3 (2015), 526–550.

[doi]
Diogo B. Lima, Tatiani B. de Lima, Tiago S. Balbuena, Ana Gisele C.
NevesFerreira, Valmir C. Barbosa, Fábio C. Gozzo, and Paulo C.
Carvalho,
“SIMXL: a powerful and userfriendly tool for peptide crosslinking
analysis,”
Journal of Proteomics
129 (2015), 51–55.

[doi]
Juliana de S. da G. Fischer, Marlon D. M. dos Santos, Fabricio K. Marchini,
Valmir C. Barbosa, Paulo C. Carvalho, and Nilson I. T. Zanchin,
“A scoring model for phosphopeptide site localization and its impact on
the question of whether to use MSA,”
Journal of Proteomics
129 (2015), 42–50.

[doi]
Kleber de Aguiar, Felipe M. G. França, Valmir C. Barbosa, and
César A. D. Teixeira,
“Early detection of epilepsy seizures based on a weightless neural
network,”
Proceedings of the 37th Annual International Conference of the IEEE
Engineering in Medicine and Biology Society,
4470–4474, 2015.

[doi]
Felipe da Veiga Leprevost, Valmir C. Barbosa, and Paulo Costa Carvalho,
“Using PepExplorer to filter and organize de novo peptide
sequencing results,”
Current Protocols in Bioinformatics
51 (2015), 13.27.1–13.27.9.

[doi]
[pdf]
Kátia K. Cassiano and Valmir C. Barbosa,
“Errorprone cellular automata as metaphors of immunity as
computation,”
Complex Systems
24 (2015), 93–111.

[oldcitypublishing]
[pdf]
Kátia K. Cassiano and Valmir C. Barbosa,
“Information integration in elementary cellular automata,”
Journal of Cellular Automata
10 (2015), 235–260.

[doi]
[acm]
Ubiratam de Paula Junior, Lúcia M. A. Drummond, Daniel de Oliveira,
Yuri Frota, and Valmir C. Barbosa,
“Handling flashcrowd events to improve the performance of web
applications,”
Proceedings of the 30th Annual ACM Symposium on Applied Computing,
769–774, 2015.

[doi]
Diogo B. Lima, Tatiani B. de Lima, Tiago S. Balbuena, Ana Gisele C.
NevesFerreira, Valmir C. Barbosa, Fabio C. Gozzo, and Paulo C. Carvalho,
“Using SIMXL to identify and annotate crosslinked peptides analyzed by
mass spectrometry,”
Protocol Exchange
(2015).

[doi]
[doi, erratum]
Valmir C. Barbosa, Raul Donangelo, and Sergio R. Souza,
“Quasispecies dynamics on a network of interacting genotypes and
idiotypes: formulation of the model,”
Journal of Statistical Mechanics
(2015), P01022.

[doi]
[pdf]
Leonardo I. L. Oliveira, Valmir C. Barbosa, and Fábio Protti,
“The predecessorexistence problem for kreversible
processes,”
Theoretical Computer Science
562 (2015), 406–418.
[2014]

[doi]
[pdf]
Flavio B. Gonzaga, Valmir C. Barbosa, and Geraldo B. Xexéo,
“The network structure of mathematical knowledge according to the
Wikipedia, MathWorld, and DLMF online libraries,”
Network Science
2 (2014), 367–386.

[doi]
[pdf]
Felipe V. Leprevost, Richard H. Valente, Diogo B. Lima, Jonas Perales,
Rafael Melani, John R. Yates III, Valmir C. Barbosa, Magno Junqueira, and
Paulo C. Carvalho,
“PepExplorer: a similaritydriven tool for analyzing de novo
sequencing results,”
Molecular & Cellular Proteomics
13 (2014), 2480–2489.

[doi]
[pdf]
Felipe V. Leprevost, Valmir C. Barbosa, Eduardo L. Francisco,
Yasset PerezRiverol, and Paulo C. Carvalho,
“On best practices in the development of bioinformatics software,”
Frontiers in Genetics
5 (2014), 199.

[doi]
[wiley]
Fabiano de S. Oliveira and Valmir C. Barbosa,
“Revisiting deadlock prevention: a probabilistic approach,”
Networks
63 (2014), 203–210.

[doi]
[acs]
Priscila F. Aquino, Diogo B. Lima, Juliana S. G. Fischer, Rafael D. Melani,
Fabio C. S. Nogueira, Sidney R. S. Chalub, Elzalina R. Soares,
Valmir C. Barbosa, Gilberto B. Domont, and Paulo C. Carvalho,
“Exploring the proteomic landscape of a gastric cancer biopsy with the
Shotgun Imaging Analyzer,”
Journal of Proteome Research
13 (2014), 314–320.
[2013]

[doi]
Felipe V. Leprevost, Diogo B. Lima, Juliana Crestani, Yasset PerezRiverol,
Nilson Zanchin, Valmir C. Barbosa, and Paulo C. Carvalho,
“Pinpointing differentially expressed domains in complex protein mixtures
with the cloud service of PatternLab for Proteomics,”
Journal of Proteomics
89 (2013), 179–182.

[doi]
[pdf]
Valmir C. Barbosa,
“The conduciveness of CArule graphs,”
Artificial Life
19 (2013), 255–266.

[doi]
[pdf]
Diogo Borges, Yasset PerezRiverol, Fabio C. S. Nogueira, Gilberto B. Domont,
Jesus Noda, Felipe da Veiga Leprevost, Vladimir Besada, Felipe M. G.
França, Valmir C. Barbosa, Aniel Sánchez, and Paulo C. Carvalho,
“Effectively addressing complex proteomic search spaces with peptide
spectrum matching,”
Bioinformatics
29 (2013), 1343–1344.

[doi]
Fabio R. J. Vieira, José F. de Rezende, Valmir C. Barbosa, and Serge
Fdida,
“Local heuristic for the refinement of multipath routing in wireless mesh
networks,”
Computer Networks
57 (2013), 273–285.
[2012]

[doi]
Paulo C. Carvalho, Juliana S. G. Fischer, Tao Xu, John R. Yates III, and
Valmir C. Barbosa,
“PatternLab: from mass spectra to labelfree differential shotgun
proteomics,”
Current Protocols in Bioinformatics
40 (2012), 13.19.1–13.19.18.

[doi]
[acs]
Priscila F. Aquino, Juliana S. G. Fischer, Ana G. C. NevesFerreira, Jonas
Perales, Gilberto B. Domont, Gabriel D. T. Araujo, Valmir C. Barbosa, Jucilana
Viana, Sidney R. S. Chalub, Antonia Q. Lima de Souza, Maria G. C. Carvalho,
Afonso D. Leão de Souza, and Paulo C. Carvalho,
“Are gastric cancer resection margin proteomic profiles more similar to
those from controls or tumors?”
Journal of Proteome Research
11 (2012), 5836–5842.

[doi]
Alexandre Sardinha, Tiago A. O. Alves, Leandro A. J. Marzulo, Felipe M. G.
França, Valmir C. Barbosa, and Vítor Santos Costa,
“Scheduling cyclic task graphs with SCCMap,”
Proceedings of the Third Workshop on Applications for MultiCore
Architecture,
54–59, 2012.

[doi]
[pdf]
Valmir C. Barbosa, Raul Donangelo, and Sergio R. Souza,
“Quasispecies dynamics with network constraints,”
Journal of Theoretical Biology
312 (2012), 114–119.

[doi]
[pdf]
Paulo C. Carvalho, John R. Yates III, and Valmir C. Barbosa,
“Improving the TFold test for differential shotgun proteomics,”
Bioinformatics
28 (2012), 1652–1654.

[doi]
[wiley]
Paulo C. Carvalho, Juliana S. G. Fischer, Tao Xu, Daniel Cociorva, Tiago S.
Balbuena, Richard H. Valente, Jonas Perales, John R. Yates III, and Valmir C.
Barbosa,
“Search engine processor: filtering and organizing peptide spectrum
matches,”
Proteomics
12 (2012), 944–949.

[doi]
Fabio R. J. Vieira, José F. de Rezende, Valmir C. Barbosa, and Serge
Fdida,
“Scheduling links for heavy traffic on interfering routes in wireless mesh
networks,”
Computer Networks
56 (2012), 1584–1598.
[2011]

[doi]
[pdf]
Luís O. Rigo Jr. and Valmir C. Barbosa,
“Evolved preambles for MAXSAT heuristics,”
Proceedings of the International Conference on Evolutionary Computation
Theory and Applications,
23–31, 2011.

[doi]
[wiley]
Rodrigo Barboza, Daniel Cociorva, Tao Xu, Valmir C. Barbosa, Jonas Perales,
Richard H. Valente, Felipe M. G. França, John R. Yates III, and Paulo C.
Carvalho,
“Can the falsediscovery rate be misleading?”
Proteomics
11 (2011), 4105–4108.

[arxiv]
Andre Nathan and Valmir C. Barbosa,
“Network algorithmics and the emergence of synchronization in cortical
models,”
July 2011.

[doi]
[pdf]
Andre Nathan and Valmir C. Barbosa,
“Network algorithmics and the emergence of information integration in
cortical models,”
Physical Review E
84 (2011), 011904.

[doi]
[rdcu]
Fabio R. J. Vieira and Valmir C. Barbosa,
“Optimization of supply diversity for the selfassembly of simple objects
in two and three dimensions,”
Natural Computing
10 (2011), 551–581.

[doi]
[pdf]
Paulo C. Carvalho, Juliana S. G. Fischer, Jonas Perales, John R. Yates III,
Valmir C. Barbosa, and Elias Bareinboim,
“Analyzing marginal cases in differential shotgun proteomics,”
Bioinformatics
27 (2011), 275–276.
[2010]

[doi]
[pdf]
Valmir C. Barbosa, Raul Donangelo, and Sergio R. Souza,
“Early appraisal of the fixation probability in directed networks,”
Physical Review E
82 (2010), 046114.

[doi]
[acm]
Rodrigo S. C. Leão and Valmir C. Barbosa,
“Exploiting the distribution of distances between nodes to efficiently
solve the localization problem in wireless sensor networks,”
Proceedings of the 5th ACM International Workshop on Performance
Monitoring, Measurement and Evaluation of Heterogeneous Wireless and Wired
Networks,
9–16, 2010.

[doi]
[pdf]
Valmir C. Barbosa,
“Network conduciveness with application to the graphcoloring and
independentset optimization transitions,”
PLOS ONE
5 (2010), e11232.

[doi]
Paulo C. Carvalho, John R. Yates III, and Valmir C. Barbosa,
“Analyzing shotgun proteomic data with PatternLab for proteomics,”
Current Protocols in Bioinformatics
30 (2010), 13.13.1–13.13.15.

[doi]
Juliana S. G. Fischer, Lujian Liao, Paulo C. Carvalho, Valmir C. Barbosa,
Gilberto B. Domont, Maria G. C. Carvalho, and John R. Yates III,
“Dynamic proteomic overview of glioblastoma cells (A172) exposed to
perillyl alcohol,”
Journal of Proteomics
73 (2010), 1018–1027.

[doi]
[pdf]
Paulo C. Carvalho, Xuemei Han, Tao Xu, Daniel Cociorva, Maria G. C. Carvalho,
Valmir C. Barbosa, and John R. Yates III,
“XDIA: improving on the labelfree dataindependent analysis,”
Bioinformatics
26 (2010), 847–848.

[doi]
[pdf]
Andre Nathan and Valmir C. Barbosa,
“Network algorithmics and the emergence of the cortical synapticweight
distribution,”
Physical Review E
81 (2010), 021916.
[2009]

[doi]
[pdf]
Paulo C. Carvalho, Tao Xu, Xuemei Han, Daniel Cociorva, Valmir C. Barbosa, and
John R. Yates III,
“YADA: a tool for taking the most out of highresolution spectra,”
Bioinformatics
25 (2009), 2734–2736.

[doi]
[pdf]
Valmir C. Barbosa, Raul Donangelo, and Sergio R. Souza,
“Network growth for enhanced natural selection,”
Physical Review E
80 (2009), 026115.

[doi]
[rdcu]
Rodrigo S. C. Leão and Valmir C. Barbosa,
“Approximate conditional distributions of distances between nodes in a
twodimensional sensor network,”
Analytical and Stochastic Modeling Techniques and Applications
(K. AlBegain, D. Fiems, and G. Horváth, Eds.), 324–338,
Lecture Notes in Computer Science 5513,
SpringerVerlag, Berlin, Germany, 2009.

[doi]
Valmir C. Barbosa, Fernando M. L. Ferreira, Daniel V. Kling, Eduardo Lopes,
Fábio Protti, and Eber A. Schmitz,
“Structured construction and simulation of nondeterministic stochastic
activity networks,”
European Journal of Operational Research
198 (2009), 266–274.

[doi]
[acs]
Paulo C. Carvalho, Daniel Cociorva, Catherine C. L. Wong, Maria da Gloria da C.
Carvalho, Valmir C. Barbosa, and John R. Yates III,
“Charge prediction machine: tool for inferring precursor charge states of
electron transfer dissociation tandem mass spectra,”
Analytical Chemistry
81 (2009), 1996–2003.

[doi]
[pdf]
Paulo C. Carvalho, Juliana S. G. Fischer, Emily I. Chen, Gilberto B. Domont,
Maria G. C. Carvalho, Wim M. Degrave, John R. Yates III, and Valmir C. Barbosa,
“GO Explorer: a geneontology tool to aid in the interpretation of shotgun
proteomics data,”
Proteome Science
7 (2009), 6.

[doi]
Rodolfo M. Pussente and Valmir C. Barbosa,
“An algorithm for clock synchronization with the gradient property in
sensor networks,”
Journal of Parallel and Distributed Computing
69 (2009), 261–265.

[doi]
Ricardo C. Corrêa and Valmir C. Barbosa,
“Partially ordered distributed computations on asynchronous pointtopoint
networks,”
Parallel Computing
35 (2009), 12–28.
[2008]

[doi]
[pdf]
Rosa M. V. Figueiredo, Valmir C. Barbosa, Nelson Maculan, and Cid C. de Souza,
“Acyclic orientations with path constraints,”
RAIRO Operations Research
42 (2008), 455–467.

[doi]
[pdf]
Paulo C. Carvalho, Juliana S. G. Fischer, Emily I. Chen, John R. Yates III, and
Valmir C. Barbosa,
“PatternLab for proteomics: a tool for differential shotgun
proteomics,”
BMC Bioinformatics
9 (2008), 316.

[doi]
[pdf]
Elias Bareinboim and Valmir C. Barbosa,
“Descents and nodal load in scalefree networks,”
Physical Review E
77 (2008), 046111.

[doi]
[pdf]
Paulo C. Carvalho, Johannes Hewel, Valmir C. Barbosa, and John R. Yates III,
“Identifying differences in protein expression levels by spectral counting
and feature selection,”
Genetics and Molecular Research
7 (2008), 342–356.

[doi]
[pdf]
Andre Nathan and Valmir C. Barbosa,
“Vlike formations in flocks of artificial birds,”
Artificial Life
14 (2008), 179–188.

[doi]
Valmir C. Barbosa, Raul Donangelo, and Sergio R. Souza,
“Emergence of scalefree behavior in networks from limitedhorizon linking
and cost tradeoffs,”
Physica A
387 (2008), 1016–1024.

[doi]
Valmir C. Barbosa,
“Reachability and recoverability of sink nodes in growing acyclic directed
networks,”
Physica A
387 (2008), 685–693.

[doi]
[pdf]
Valmir C. Barbosa,
“Distributed algorithms,”
The Handbook of Computer Networks
(H. Bidgoli, Ed.), volume 3, 286–297,
John Wiley & Sons, Hoboken, NJ, 2008.
[2007]

[doi]
Alexandre O. Stauffer and Valmir C. Barbosa,
“Probabilistic heuristics for disseminating information in
networks,”
IEEE/ACM Transactions on Networking
15 (2007), 425–435.

[doi]
[pdf]
Paulo C. Carvalho, Juliana S. G. Fischer, Valmir C. Barbosa, Wim Degrave, Maria
G. C. Carvalho, and Gilberto B. Domont,
“Ellipsoid clustering machine: a front line to aid in disease
diagnosis,”
RECIIS: Electronic Journal of Communication, Information & Innovation in
Health
1 (2007), Sup308–Sup315.
[2006]

[doi]
[pdf]
Alexandre O. Stauffer and Valmir C. Barbosa,
“Dissemination strategy for immunizing scalefree networks,”
Physical Review E
74 (2006), 056105.

[doi]
[pdf]
Carlos A. G. Assis, Edil S. T. Fernandes, and Valmir C. Barbosa,
“Modeling the input history of programs for improved instructionmemory
performance,”
The Computer Journal
49 (2006), 744–761.

[doi]
[rdcu]
Rodrigo S. C. Leão and Valmir C. Barbosa,
“Minimal chordal sense of direction and circulant graphs,”
Mathematical Foundations of Computer Science 2006
(R. Královič and P. Urzyczyn, Eds.), 670–680,
Lecture Notes in Computer Science 4162,
SpringerVerlag, Berlin, Germany, 2006.

[doi]
[pdf]
Valmir C. Barbosa, Raul Donangelo, and Sergio R. Souza,
“Emergence of scalefree networks from local connectivity and
communication tradeoffs,”
Physical Review E
74 (2006), 016113.

[doi]
Luís O. Rigo Jr. and Valmir C. Barbosa,
“Twodimensional cellular automata and the analysis of correlated time
series,”
Pattern Recognition Letters
27 (2006), 1353–1360.

[doi]
Renato C. Dutra and Valmir C. Barbosa,
“Finding routes in anonymous sensor networks,”
Information Processing Letters
98 (2006), 139–144.

[doi]
[pdf]
Alexandre O. Stauffer and Valmir C. Barbosa,
“Local heuristics and the emergence of spanning subgraphs in complex
networks,”
Theoretical Computer Science
355 (2006), 80–95.

[doi]
[rdcu]
Alexandre H. L. Porto and Valmir C. Barbosa,
“A methodology for determining aminoacid substitution matrices from set
covers,”
Applications of Evolutionary Computing
(F. Rothlauf et al., Eds.), 138–148,
Lecture Notes in Computer Science 3907,
SpringerVerlag, Berlin, Germany, 2006.

[doi]
[rdcu]
Alexandre H. L. Porto and Valmir C. Barbosa,
“Multiple sequence alignment based on set covers,”
Applications of Evolutionary Computing
(F. Rothlauf et al., Eds.), 127–137,
Lecture Notes in Computer Science 3907,
SpringerVerlag, Berlin, Germany, 2006.

[doi]
Valmir C. Barbosa, Fernando M. N. Miranda, and Matheus C. M. Agostini,
“Cellcentric heuristics for the classification of cellular
automata,”
Parallel Computing
32 (2006), 44–66.
[2005]

[arxiv]
Alexandre O. Stauffer and Valmir C. Barbosa,
“A study of the edgeswitching Markovchain method for the generation of
random graphs,”
December 2005.

[arxiv]
Rodrigo S. C. Leão and Valmir C. Barbosa,
“6cycle double covers of cubic graphs,”
May 2005.
[2004]

[doi]
[rdcu]
Valmir C. Barbosa and Luciana C. D. Campos,
“A novel evolutionary formulation of the maximum independent set
problem,”
Journal of Combinatorial Optimization
8 (2004), 419–437.

[doi]
Valmir C. Barbosa and Rubens G. Ferreira,
“On the phase transitions of graph coloring and independent sets,”
Physica A
343 (2004), 401–423.

[doi]
Luis E. Flores, Eduardo J. Aguilar, Valmir C. Barbosa, and Luís
Alfredo V. de Carvalho,
“A graph model for the evolution of specificity in humoral
immunity,”
Journal of Theoretical Biology
229 (2004), 311–325.

[doi]
[pdf]
Lucia D. Penso and Valmir C. Barbosa,
“A distributed algorithm to find kdominating sets,”
Discrete Applied Mathematics
141 (2004), 243–253.

[doi]
[rdcu]
Valmir C. Barbosa, Carlos A. G. Assis, and Josina O. do Nascimento,
“Two novel evolutionary formulations of the graph coloring problem,”
Journal of Combinatorial Optimization
8 (2004), 41–63.

[doi]
Valmir C. Barbosa, Raul Donangelo, and Sergio R. Souza,
“Directed cycles and related structures in random graphs: II—Dynamic
properties,”
Physica A
334 (2004), 566–582.
[2003]

[doi]
Lúcia M. A. Drummond and Valmir C. Barbosa,
“On reducing the complexity of matrix clocks,”
Parallel Computing
29 (2003), 895–905.

[doi]
Valmir C. Barbosa, Raul Donangelo, and Sergio R. Souza,
“Directed cycles and related structures in random graphs: I—Static
properties,”
Physica A
321 (2003), 381–397.
[2002]

[doi]
Alexandre H. L. Porto and Valmir C. Barbosa,
“Finding approximate palindromes in strings,”
Pattern Recognition
35 (2002), 2581–2591.

[doi]
[rdcu]
Valmir C. Barbosa,
“The interleaved multichromatic number of a graph,”
Annals of Combinatorics
6 (2002), 249–256.

[doi]
Valmir C. Barbosa,
“The combinatorics of resource sharing,”
Models for Parallel and Distributed Computation: Theory, Algorithmic
Techniques and Applications
(R. Corrêa, I. Dutra, M. Fiallos, and F. Gomes, Eds.), 27–52,
Kluwer Academic Publishers, Dordrecht, The Netherlands, 2002.

[pdf]
Edil S. T. Fernandes and Valmir C. Barbosa,
“Monitoring the structure and behavior of programs,”
Proceedings of the International Conference on Massively Parallel
Computing Systems,
paper 21 on CD (ISBN 0966953002), 2002.

[doi]
Edil S. T. Fernandes, Valmir C. Barbosa, and Fabiano Ramos,
“Instruction usage and the memory gap problem,”
Proceedings of the Fourteenth Symposium on Computer Architecture and High
Performance Computing,
169–175, 2002.
[2001]

[doi]
[rdcu]
Rodrigo Basilio, Gerson Zaverucha, and Valmir C. Barbosa,
“Learning logic programs with neural networks,”
Inductive Logic Programming
(C. Rouveirol and M. Sebag, Eds.), 15–26,
Lecture Notes in Artificial Intelligence 2157,
SpringerVerlag, Berlin, Germany, 2001.

[doi]
Valmir C. Barbosa, Mario R. F. Benevides, and Ayru L. Oliveira Filho,
“A priority dynamics for generalized drinking philosophers,”
Information Processing Letters
79 (2001), 189–195.

[doi]
[rdcu]
Valmir C. Barbosa, Mario R. F. Benevides, and Felipe M. G. França,
“Sharing resources at nonuniform access rates,”
Theory of Computing Systems
34 (2001), 13–26.
[2000]

[pdf]
Ayru L. Oliveira Filho and Valmir C. Barbosa,
“A graphtheoretic model of sharedmemory legality,”
Technical Report ES531/00, Federal University of Rio de Janeiro, Brazil,
April 2000.

[doi]
[rdcu]
Nelson A. Hallack, Gerson Zaverucha, and Valmir C. Barbosa,
“Towards a hybrid model of firstorder theory refinement,”
Hybrid Neural System
(S. Wermter and R. Sun, Eds.), 92–106,
Lecture Notes in Artificial Intelligence 1778,
SpringerVerlag, Berlin, Germany, 2000.
[1999]

[doi]
Valmir C. Barbosa and Jayme L. Szwarcfiter,
“Generating all the acyclic orientations of an undirected graph,”
Information Processing Letters
72 (1999), 71–74.

[doi]
[doi, erratum]
Roseli S. Wedemann, Valmir C. Barbosa, and Raul Donangelo,
“Defeasible timestepping,”
Parallel Computing
25 (1999), 461–489.
[1998]

[pdf]
Romulo M. de Menezes, Gerson Zaverucha, and Valmir C. Barbosa,
“A penaltyfunction approach to rule extraction from knowledgebased
neural networks,”
Proceedings of the International Conference on Neural Information
Processing,
1497–1500, 1998.

[doi]
Ricardo J. Machado, Valmir C. Barbosa, and Paulo A. Neves,
“Learning in the combinatorial neural model,”
IEEE Transactions on Neural Networks
9 (1998), 831–847.

[pdf]
Valmir C. Barbosa and Mario R. F. Benevides,
“A graphtheoretic characterization of ANDOR deadlocks,”
Technical Report ES472/98, Federal University of Rio de Janeiro, Brazil,
July 1998.

[doi]
Valmir C. Barbosa, Raul Donangelo, and Roseli S. Wedemann,
“A BUU code for parallel computers,”
International Journal of Modern Physics C
9 (1998), 573–583.
[1996]

[doi]
Lúcia Maria de A. Drummond and Valmir C. Barbosa,
“Distributed breakpoint detection in messagepassing programs,”
Journal of Parallel and Distributed Computing
39 (1996), 153–167.
[1995]

[doi]
Valmir C. Barbosa and Stella C. S. Porto,
“An algorithm for FIFO message delivery among migrating tasks,”
Information Processing Letters
53 (1995), 261–267.
[1994]

[doi]
[pdf]
Valmir C. Barbosa, Ricardo J. Machado, and Frederico dos S. Liporace,
“A neural system for deforestation monitoring on Landsat images of the
Amazon region,”
International Journal of Approximate Reasoning
11 (1994), 321–359.

[doi]
Valmir C. Barbosa, Lúcia Maria de A. Drummond, and Astrid Luise H.
Hellmuth,
“From distributed algorithms to Occam programs by successive
refinements,”
The Journal of Systems and Software
26 (1994), 257–272.

[pdf]
Ricardo J. Machado, Valmir C. Barbosa, Frederico dos S. Liporace, João R.
dos Santos, and Adriano Venturieri,
“Deforestation monitoring of the Amazon region using neural
networks—a comparison between different photointerpreters and
networks,”
Proceedings of the International Symposium on Resource and Environmental
Monitoring,
49–55, 1994.
[1993]

[doi]
Nalvo F. de Almeida Junior and Valmir C. Barbosa,
“A stringmatching algorithm for the CREW PRAM,”
Information Processing Letters
47 (1993), 257–259.

[doi]
Ricardo J. Machado, Valmir C. Barbosa, Frederico dos S. Liporace, and
Cláudia Ferlin,
“Monitoring the deforestation of the Amazon region with neural
networks,”
Proceedings of the International Joint Conference on Neural
Networks,
1239–1242, 1993.

[doi]
[pdf]
Leila M. R. Eizirik, Valmir C. Barbosa, and Sueli B. T. Mendes,
“A Bayesiannetwork approach to lexical disambiguation,”
Cognitive Science
17 (1993), 257–283.
[1992]

[doi]
Eliseu M. Chaves Filho and Valmir C. Barbosa,
“Time sharing in hypercube multiprocessors,”
Proceedings of the IEEE Symposium on Parallel and Distributed
Processing,
354–359, 1992.

[doi]
Maria Claudia S. Boeres, Luís Alfredo V. de Carvalho, and Valmir C.
Barbosa,
“A faster elasticnet algorithm for the traveling salesman problem,”
Proceedings of the International Joint Conference on Neural
Networks,
II215–220, 1992.

[doi]
Luís Alfredo V. de Carvalho and Valmir C. Barbosa,
“Fast linear system solution by neural networks,”
Operations Research Letters
11 (1992), 141–145.

[pdf]
Claudia F. Portella and Valmir C. Barbosa,
“Parallel maximumflow algorithms on a Transputer hypercube,”
Technical Report ES251/92, Federal University of Rio de Janeiro, Brazil,
January 1992.
[1991]

[pdf]
Valmir C. Barbosa,
“On the timedriven parallel simulation of two classes of complex
systems,”
Technical Report ES248/91, Federal University of Rio de Janeiro, Brazil,
December 1991.

[doi]
Valmir C. Barbosa, Lúcia Maria de A. Drummond, and Astrid Luise H.
Hellmuth,
“An integrated software environment for largescale Occam
programming,”
Proceedings of Euromicro'91,
393–400, 1991.

[doi]
Edil S. T. Fernandes, Valmir C. Barbosa, Alberto F. de Souza, and Nelson Q.
Vasconcelos,
“Microinstruction placement by simulated annealing,”
Proceedings of Euromicro'91,
23–28, 1991.

[pdf]
Lélio de P. Sá Freitas and Valmir C. Barbosa,
“Experiments in parallel heuristic search (extended abstract),”
Proceedings of the International Conference on Parallel Processing,
III62–65, 1991.

[doi]
Valmir C. Barbosa and Luís Alfredo V. de Carvalho,
“Learning in analog Hopfield networks,”
Proceedings of the International Joint Conference on Neural
Networks,
II183–186, 1991.
[1990]

[doi]
Valmir C. Barbosa,
“Blocking versus nonblocking interprocess communication: a note on the
effect on concurrency,”
Information Processing Letters
36 (1990), 171–175.

[doi]
Valmir C. Barbosa,
“Strategies for the prevention of communication deadlocks
in distributed parallel programs,”
IEEE Transactions on Software Engineering
16 (1990), 1311–1316.

[doi]
Valmir C. Barbosa and Priscila M. V. Lima,
“On the distributed parallel simulation of Hopfield's neural
networks,”
Software: Practice and Experience
20 (1990), 967–983.

[doi]
Valmir C. Barbosa and Maria Cristina S. Boeres,
“An Occambased evaluation of a parallel version of simulated
annealing,”
Proceedings of Euromicro'90,
85–92, 1990.

[pdf]
Luís Alfredo V. de Carvalho and Valmir C. Barbosa,
“A TSP objective function that ensures feasibility at stable
points,”
Proceedings of the International Neural Network Conference,
volume 1, 249–253, 1990.

[doi]
Valmir C. Barbosa and Luís Alfredo V. de Carvalho,
“Feasible directions linear programming by neural networks,”
Proceedings of the International Joint Conference on Neural
Networks,
III941–946, 1990.
[1989]

[doi]
[acm]
Valmir C. Barbosa and Eli Gafni,
“Concurrency in heavily loaded neighborhoodconstrained systems,”
ACM Transactions on Programming Languages and Systems
11 (1989), 562–584.

[pdf]
Luís Alfredo V. de Carvalho and Valmir C. Barbosa,
“Towards a stochastic neural model for combinatorial optimization,”
Technical Report ES196/89, Federal University of Rio de Janeiro, Brazil,
June 1989.

[doi]
[pdf]
Valmir C. Barbosa and Eli Gafni,
“A distributed implementation of simulated annealing,”
Journal of Parallel and Distributed Computing
6 (1989), 411–434.

[doi]
Edil S. T. Fernandes, Cláudio L. de Amorim, Valmir C. Barbosa, Felipe M.
G. França, and Alberto F. de Souza,
“MPH—a hybrid parallel machine,”
Proceedings of the Euromicro'88 Short Note Programme,
229–232.
[1988]

[doi]
Valmir C. Barbosa and Felipe M. G. França,
“Specification of a communication virtual processor for parallel
processing systems,”
Proceedings of Euromicro'88,
511–518, 1988.

[pdf]
Valmir C. Barbosa and Hung K. Huang,
“Static task allocation in heterogeneous distributed systems,”
Technical Report ES149/88, Federal University of Rio de Janeiro, Brazil,
June 1988.
[1987]

[pdf]
Valmir C. Barbosa and Eli Gafni,
“Concurrency in heavily loaded neighborhoodconstrained systems,”
Proceedings of the International Conference on Distributed Computing
Systems,
448–455, 1987.
[1986]

[pdf]
Eli Gafni and Valmir C. Barbosa,
“Optimal snapshots and the maximum flow in precedence graphs,”
Proceedings of the Annual Allerton Conference on Communication, Control,
and Computing,
1089–1097, 1986.
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[Last edited: March 27, 2023]