Valmir C. Barbosa: Selected papers

• 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, to appear.
• 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 PSMs,” Proteomics, to appear.
• Valmir C. Barbosa, Raul Donangelo, and Sergio R. Souza, “Quasispecies dynamics with network constraints,” December 2011.
• 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.
• 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.
• Andre Nathan and Valmir C. Barbosa, “Network algorithmics and the emergence of synchronization in cortical models,” July 2011.
• Andre Nathan and Valmir C. Barbosa, “Network algorithmics and the emergence of information integration in cortical models,” Physical Review E 84 (2011), 011904.
• 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.
• 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.
• Valmir C. Barbosa, Raul Donangelo, and Sergio R. Souza, “Early appraisal of the fixation probability in directed networks,” Physical Review E 82 (2010), 046114.
• Fabiano de S. Oliveira and Valmir C. Barbosa, “Revisiting deadlock prevention: a probabilistic approach,” October 2010.
• 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.
• Valmir C. Barbosa, “Network conduciveness with application to the graph-coloring and independent-set optimization transitions,” PLoS ONE 5 (2010), e11232.
• 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.
• 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.
• 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.
• Andre Nathan and Valmir C. Barbosa, “Network algorithmics and the emergence of the cortical synaptic-weight distribution,” Physical Review E 81 (2010), 021916.
• 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.
• Valmir C. Barbosa, Raul Donangelo, and Sergio R. Souza, “Network growth for enhanced natural selection,” Physical Review E 80 (2009), 026115.
• 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.
• 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.
• 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.
• 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.
• 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.
• Ricardo C. Corrêa and Valmir C. Barbosa, “Partially ordered distributed computations on asynchronous point-to-point networks,” Parallel Computing 35 (2009), 12–28.
• 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.
• 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.
• Elias Bareinboim and Valmir C. Barbosa, “Descents and nodal load in scale-free networks,” Physical Review E 77 (2008), 046111.
• 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.
• Andre Nathan and Valmir C. Barbosa, “V-like formations in flocks of artificial birds,” Artificial Life 14 (2008), 179–188.
• 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.
• Valmir C. Barbosa, “Reachability and recoverability of sink nodes in growing acyclic directed networks,” Physica A 387 (2008), 685–693.
• Valmir C. Barbosa, “Distributed algorithms,” The Handbook of Computer Networks (H. Bidgoli, Ed.), volume 3, 286–297, John Wiley & Sons, Hoboken, NJ, 2008.
• Alexandre O. Stauffer and Valmir C. Barbosa, “Probabilistic heuristics for disseminating information in networks,” IEEE/ACM Transactions on Networking 15 (2007), 425–435.
• 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.
• Alexandre O. Stauffer and Valmir C. Barbosa, “Dissemination strategy for immunizing scale-free networks,” Physical Review E 74 (2006), 056105.
• 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.
• 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.
• 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.
• 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.
• Renato C. Dutra and Valmir C. Barbosa, “Finding routes in anonymous sensor networks,” Information Processing Letters 98 (2006), 139–144.
• 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.
• 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.
• 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.
• 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.
• 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.
• 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.
• Lucia D. Penso and Valmir C. Barbosa, “A distributed algorithm to find k-dominating sets,” Discrete Applied Mathematics 141 (2004), 243–253.
• 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.
• Valmir C. Barbosa and Rubens G. Ferreira, “On the phase transitions of graph coloring and independent sets,” Physica A 343 (2004), 401–423.
• 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.
• 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.
• Lúcia M. A. Drummond and Valmir C. Barbosa, “On reducing the complexity of matrix clocks,” Parallel Computing 29 (2003), 895–905.
• Valmir C. Barbosa, “The interleaved multichromatic number of a graph,” Annals of Combinatorics 6 (2002), 249–256.
• Alexandre H. L. Porto and Valmir C. Barbosa, “Finding approximate palindromes in strings,” Pattern Recognition 35 (2002), 2581–2591.
• 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.
• 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.
• 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.
• 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.
• 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.
• 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.
• 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.
• Roseli S. Wedemann, Valmir C. Barbosa, and Raul Donangelo, “Defeasible time-stepping,” Parallel Computing 25 (1999), 461–489.
• Valmir C. Barbosa and Jayme L. Szwarcfiter, “Generating all the acyclic orientations of an undirected graph,” Information Processing Letters 72 (1999), 71–74.
• 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.
• 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.
• 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.
• 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.
• Valmir C. Barbosa and Stella C. S. Porto, “An algorithm for FIFO message delivery among migrating tasks,” Information Processing Letters 53 (1995), 261–267.
• 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.
• 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.
• 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.
• 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.
• Nalvo F. de Almeida Junior and Valmir C. Barbosa, “A string-matching algorithm for the CREW PRAM,” Information Processing Letters 47 (1993), 257–259.
• 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.
• Luís Alfredo V. de Carvalho and Valmir C. Barbosa, “Fast linear system solution by neural networks,” Operations Research Letters 11 (1992), 141–145.
• 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.
• 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.
• 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.
• 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.
• 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.
• 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.
• 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.
• Valmir C. Barbosa, “Strategies for the prevention of communication deadlocks in distributed parallel programs,” IEEE Transactions on Software Engineering 16 (1990), 1311–1316.
• Valmir C. Barbosa, “Blocking versus nonblocking interprocess communication: a note on the effect on concurrency,” Information Processing Letters 36 (1990), 171–175.
• 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.
• 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, v. 1, 249–253, 1990.
• 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.
• Valmir C. Barbosa and Eli Gafni, “A distributed implementation of simulated annealing,” Journal of Parallel and Distributed Computing 6 (1989), 411–434.
• Valmir C. Barbosa and Eli Gafni, “Concurrency in heavily loaded neighborhord-constrained systems,” ACM Transactions on Programming Languages and Systems 11 (1989), 562–584.
• 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,” Microprocessing and Microprogramming 25 (1989), 229–232.
• 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.
• Valmir C. Barbosa and Eli Gafni, “Concurrency in heavily loaded neighborhood-constrainted systems,” Proceedings of the International Conference on Distributed Computing Systems, 448–455, 1987.
• 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.