Papers

[doi] Rafael Mendes, Bruno Kaelin, Alejo Martínez-Sansigre, Valmir C. Barbosa, Cristiana Bentes, and Claudio L. Amorim, “Faster determination of an initial velocity model for full-waveform inversion based on simulated annealing,” Geophysics 89 (2024), R187–R198.

[doi] Fabio David, José F. de Rezende, and Valmir C. Barbosa, “Exact solution of the full RMSA problem in elastic optical networks,” IEEE Networking Letters 6 (2024), 55–59.

[doi] Gabriel F. C. de Queiroz, José F. de Rezende, and Valmir C. Barbosa, “A flexible algorithm to offload DAG applications for edge computing,” Journal of Network and Computer Applications 222 (2024), 103791.

[arxiv] Eduardo J. Aguilar, Valmir C. Barbosa, Raul Donangelo, and Sergio R. Souza, “Configuration space partitioning in tilings of a bounded region of the plane,” August 2023.

[arxiv] Raphael M. Guedes, José F. de Rezende, and Valmir C. Barbosa, “Near-optimal pilot assignment in cell-free massive MIMO,” August 2023.

[doi] [pdf] [tar.gz, erratum] Eduardo J. Aguilar and Valmir C. Barbosa, “Shape complexity in cluster analysis,” PLoS One 18 (2023), e0286312.

[doi] [acs] Milan A. Clasen, Marlon D. M. Santos, Louise Ulrich Kurt, Juliana Fischer, Amanda C. Camillo-Andrade, 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 34 (2023), 794–796.

[doi] Marlon D. M. Santos, Amanda C. Camillo-Andrade, 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 Chamot-Rooke, Rosario Duran, and Paulo C. Carvalho, “DiagnoMass: a proteomics hub for pinpointing discriminative spectral clusters,” Journal of Proteomics 277 (2023), 104853.

[doi] [pdf] 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.

[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.

[doi] [rdcu] Marlon D. M. Santos, Diogo B. Lima, Juliana S. G. Fischer, Milan A. Clasen, Louise U. Kurt, Amanda Caroline Camillo-Andrade, Leandro C. Monteiro, Priscila F. de Aquino, Ana G. C. Neves-Ferreira, 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.

[doi] [pdf] Raphael M. Guedes, José F. de Rezende, and Valmir C. Barbosa, “Integrated optimization of heterogeneous-network 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 Chamot-Rooke, 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 high-quality 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.

[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 Camillo-Andrade, 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, “Mixed-data acquisition: next-generation 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.

[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 Chamot-Rooke, “Top-Down Garbage Collector: a tool for selecting high-quality top-down proteomics mass spectra,” Bioinformatics 35 (2019), 3489–3490.

[doi] [pdf] 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 isotope-labeled 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 Neves-Ferreira, “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.

[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, corrigendum] 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] [pdf] 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 f-reversible processes on graphs,” Discrete Applied Mathematics 245 (2018), 77–93.

[doi] [pdf] Valmir C. Barbosa, “Information-theoretic 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 Chamot-Rooke, 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 cross-linking mass spectrometry and isotopically labeled proteins,” Nature Protocols 13 (2018), 431–458.

[doi] [pdf] Jefferson Elbert Simões, Daniel R. Figueiredo, and Valmir C. Barbosa, “Power-law decay of the degree-sequence 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 Trevisan-Silva, Aline V. Bednaski, Juliana S. G. Fischer, Silvio S. Veiga, Nuno Bandeira, Adrian Guthals, Fabricio K. Marchini, Felipe V. Leprevost, Valmir C. Barbosa, Andrea Senff-Ribeiro, and Paulo C. Carvalho, “A multi-protease, multi-dissociation, bottom-up-to-top-down 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 Chamot-Rooke, 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 threshold-based interactions,” Complexity (2017), 7046359.

[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 high-demand environments,” April 2016.

[doi] 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.

[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. Neves-Ferreira, Valmir C. Barbosa, Fábio C. Gozzo, and Paulo C. Carvalho, “SIM-XL: a powerful and user-friendly tool for peptide cross-linking 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, “Error-prone 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] Ubiratam de Paula Junior, Lúcia M. A. Drummond, Daniel de Oliveira, Yuri Frota, and Valmir C. Barbosa, “Handling flash-crowd 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. Neves-Ferreira, Valmir C. Barbosa, Fabio C. Gozzo, and Paulo C. Carvalho, “Using SIM-XL to identify and annotate cross-linked peptides analyzed by mass spectrometry,” Protocol Exchange (2015).

[doi] [doi, corrigendum] 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 predecessor-existence problem for k-reversible processes,” Theoretical Computer Science 562 (2015), 406–418.

[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 similarity-driven 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 Perez-Riverol, 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.

[doi] Felipe V. Leprevost, Diogo B. Lima, Juliana Crestani, Yasset Perez-Riverol, 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 CA-rule graphs,” Artificial Life 19 (2013), 255–266.

[doi] [pdf] Diogo Borges, Yasset Perez-Riverol, 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 multi-path routing in wireless mesh networks,” Computer Networks 57 (2013), 273–285.

[doi] Paulo C. Carvalho, Juliana S. G. Fischer, Tao Xu, John R. Yates III, and Valmir C. Barbosa, “PatternLab: from mass spectra to label-free 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. Neves-Ferreira, 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 SCC-Map,” Proceedings of the Third Workshop on Applications for Multi-Core 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.

[doi] [pdf] Luís O. Rigo Jr. and Valmir C. Barbosa, “Evolved preambles for MAX-SAT 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 false-discovery 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 self-assembly 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.

[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] 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 graph-coloring and independent-set 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 label-free data-independent analysis,” Bioinformatics 26 (2010), 847–848.

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

[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 high-resolution 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 two-dimensional sensor network,” Analytical and Stochastic Modeling Techniques and Applications (K. Al-Begain, D. Fiems, and G. Horváth, Eds.), 324–338, Lecture Notes in Computer Science 5513, Springer-Verlag, 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 gene-ontology 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 point-to-point networks,” Parallel Computing 35 (2009), 12–28.

[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 scale-free 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, “V-like formations in flocks of artificial birds,” Artificial Life 14 (2008), 179–188.

[doi] Valmir C. Barbosa, Raul Donangelo, and Sergio R. Souza, “Emergence of scale-free behavior in networks from limited-horizon linking and cost trade-offs,” 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.

[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.

[doi] [pdf] Alexandre O. Stauffer and Valmir C. Barbosa, “Dissemination strategy for immunizing scale-free 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 instruction-memory 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, Springer-Verlag, Berlin, Germany, 2006.

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

[doi] Luís O. Rigo Jr. and Valmir C. Barbosa, “Two-dimensional 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 amino-acid substitution matrices from set covers,” Applications of Evolutionary Computing (F. Rothlauf et al., Eds.), 138–148, Lecture Notes in Computer Science 3907, Springer-Verlag, 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, Springer-Verlag, Berlin, Germany, 2006.

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

[arxiv] Alexandre O. Stauffer and Valmir C. Barbosa, “A study of the edge-switching Markov-chain method for the generation of random graphs,” December 2005.

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

[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 k-dominating 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.

[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.

[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 0-9669530-0-2), 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.

[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, Springer-Verlag, 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.

[pdf] Ayru L. Oliveira Filho and Valmir C. Barbosa, “A graph-theoretic model of shared-memory legality,” Technical Report ES-531/00, 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 first-order theory refinement,” Hybrid Neural System (S. Wermter and R. Sun, Eds.), 92–106, Lecture Notes in Artificial Intelligence 1778, Springer-Verlag, Berlin, Germany, 2000.

[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 time-stepping,” Parallel Computing 25 (1999), 461–489.

[pdf] Romulo M. de Menezes, Gerson Zaverucha, and Valmir C. Barbosa, “A penalty-function approach to rule extraction from knowledge-based 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 graph-theoretic characterization of AND-OR deadlocks,” Technical Report ES-472/98, 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.

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

[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.

[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 photo-interpreters and networks,” Proceedings of the International Symposium on Resource and Environmental Monitoring, 49–55, 1994.

[doi] Nalvo F. de Almeida Junior and Valmir C. Barbosa, “A string-matching 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 Bayesian-network approach to lexical disambiguation,” Cognitive Science 17 (1993), 257–283.

[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 elastic-net algorithm for the traveling salesman problem,” Proceedings of the International Joint Conference on Neural Networks, II-215–220, 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 maximum-flow algorithms on a Transputer hypercube,” Technical Report ES-251/92, Federal University of Rio de Janeiro, Brazil, January 1992.

[pdf] Valmir C. Barbosa, “On the time-driven parallel simulation of two classes of complex systems,” Technical Report ES-248/91, 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 large-scale 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, “Micro-instruction 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, III-62–65, 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, II-183–186, 1991.

[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 Occam-based 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, III-941–946, 1990.

[doi] [pdf] Valmir C. Barbosa and Eli Gafni, “Concurrency in heavily loaded neighborhood-constrained 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 ES-196/89, Federal University of Rio de Janeiro, Brazil, June 1989.

[doi] [better 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.

[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 ES-149/88, Federal University of Rio de Janeiro, Brazil, June 1988.

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

[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.