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38 results on '"Brito, Klairton Lima"'

1. Maximum Alternating Balanced Cycle Decomposition and Applications in Sorting by Intergenic Operations Problems

Author

Brito, Klairton Lima, Alexandrino, Alexsandro Oliveira, Siqueira, Gabriel, Oliveira, Andre Rodrigues, Dias, Ulisses, Dias, Zanoni, Goos, Gerhard, Founding Editor, Hartmanis, Juris, Founding Editor, Bertino, Elisa, Editorial Board Member, Gao, Wen, Editorial Board Member, Steffen, Bernhard, Editorial Board Member, Yung, Moti, Editorial Board Member, Scornavacca, Celine, editor, and Hernández-Rosales, Maribel, editor

Published
2024
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3. Block Interchange and Reversal Distance on Unbalanced Genomes

Author

Alexandrino, Alexsandro Oliveira, Siqueira, Gabriel, Brito, Klairton Lima, Oliveira, Andre Rodrigues, Dias, Ulisses, Dias, Zanoni, Goos, Gerhard, Founding Editor, Hartmanis, Juris, Founding Editor, Bertino, Elisa, Editorial Board Member, Gao, Wen, Editorial Board Member, Steffen, Bernhard, Editorial Board Member, Yung, Moti, Editorial Board Member, Reis, Marcelo S., editor, and de Melo-Minardi, Raquel C., editor

Published
2023
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5. A 1.375-Approximation Algorithm for Sorting by Transpositions with Faster Running Time

Author

Alexandrino, Alexsandro Oliveira, Brito, Klairton Lima, Oliveira, Andre Rodrigues, Dias, Ulisses, Dias, Zanoni, Goos, Gerhard, Founding Editor, Hartmanis, Juris, Founding Editor, Bertino, Elisa, Editorial Board Member, Gao, Wen, Editorial Board Member, Steffen, Bernhard, Editorial Board Member, Yung, Moti, Editorial Board Member, Scherer, Nicole M., editor, and de Melo-Minardi, Raquel C., editor

Published
2022
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6. Reversal Distance on Genomes with Different Gene Content and Intergenic Regions Information

Author

Alexandrino, Alexsandro Oliveira, Brito, Klairton Lima, Oliveira, Andre Rodrigues, Dias, Ulisses, Dias, Zanoni, Goos, Gerhard, Founding Editor, Hartmanis, Juris, Founding Editor, Bertino, Elisa, Editorial Board Member, Gao, Wen, Editorial Board Member, Steffen, Bernhard, Editorial Board Member, Woeginger, Gerhard, Editorial Board Member, Yung, Moti, Editorial Board Member, Martín-Vide, Carlos, editor, Vega-Rodríguez, Miguel A., editor, and Wheeler, Travis, editor

Published
2021
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7. Reversals Distance Considering Flexible Intergenic Regions Sizes

Author

Brito, Klairton Lima, Alexandrino, Alexsandro Oliveira, Oliveira, Andre Rodrigues, Dias, Ulisses, Dias, Zanoni, Goos, Gerhard, Founding Editor, Hartmanis, Juris, Founding Editor, Bertino, Elisa, Editorial Board Member, Gao, Wen, Editorial Board Member, Steffen, Bernhard, Editorial Board Member, Woeginger, Gerhard, Editorial Board Member, Yung, Moti, Editorial Board Member, Martín-Vide, Carlos, editor, Vega-Rodríguez, Miguel A., editor, and Wheeler, Travis, editor

Published
2021
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10. Sorting by Reversals and Transpositions with Proportion Restriction

Author

Brito, Klairton Lima, Alexandrino, Alexsandro Oliveira, Oliveira, Andre Rodrigues, Dias, Ulisses, Dias, Zanoni, Goos, Gerhard, Founding Editor, Hartmanis, Juris, Founding Editor, Bertino, Elisa, Editorial Board Member, Gao, Wen, Editorial Board Member, Steffen, Bernhard, Editorial Board Member, Woeginger, Gerhard, Editorial Board Member, Yung, Moti, Editorial Board Member, Setubal, João C., editor, and Silva, Waldeyr Mendes, editor

Published
2020
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11. Block-Interchange Distance Considering Intergenic Regions

Author

Dias, Ulisses, Oliveira, Andre Rodrigues, Brito, Klairton Lima, Dias, Zanoni, Goos, Gerhard, Founding Editor, Hartmanis, Juris, Founding Editor, Bertino, Elisa, Editorial Board Member, Gao, Wen, Editorial Board Member, Steffen, Bernhard, Editorial Board Member, Woeginger, Gerhard, Editorial Board Member, Yung, Moti, Editorial Board Member, Kowada, Luis, editor, and de Oliveira, Daniel, editor

Published
2020
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12. Heuristics for Reversal Distance Between Genomes with Duplicated Genes

Author

Siqueira, Gabriel, Brito, Klairton Lima, Dias, Ulisses, Dias, Zanoni, Goos, Gerhard, Founding Editor, Hartmanis, Juris, Founding Editor, Bertino, Elisa, Editorial Board Member, Gao, Wen, Editorial Board Member, Steffen, Bernhard, Editorial Board Member, Woeginger, Gerhard, Editorial Board Member, Yung, Moti, Editorial Board Member, Martín-Vide, Carlos, editor, Vega-Rodríguez, Miguel A., editor, and Wheeler, Travis, editor

Published
2020
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13. A 3.5-Approximation Algorithm for Sorting by Intergenic Transpositions

Author

Oliveira, Andre Rodrigues, Jean, Géraldine, Fertin, Guillaume, Brito, Klairton Lima, Dias, Ulisses, Dias, Zanoni, Goos, Gerhard, Founding Editor, Hartmanis, Juris, Founding Editor, Bertino, Elisa, Editorial Board Member, Gao, Wen, Editorial Board Member, Steffen, Bernhard, Editorial Board Member, Woeginger, Gerhard, Editorial Board Member, Yung, Moti, Editorial Board Member, Martín-Vide, Carlos, editor, Vega-Rodríguez, Miguel A., editor, and Wheeler, Travis, editor

Published
2020
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15. Sorting by Reversals, Transpositions, and Indels on Both Gene Order and Intergenic Sizes

Author

Brito, Klairton Lima, Jean, Géraldine, Fertin, Guillaume, Oliveira, Andre Rodrigues, Dias, Ulisses, Dias, Zanoni, Hutchison, David, Editorial Board Member, Kanade, Takeo, Editorial Board Member, Kittler, Josef, Editorial Board Member, Kleinberg, Jon M., Editorial Board Member, Mattern, Friedemann, Editorial Board Member, Mitchell, John C., Editorial Board Member, Naor, Moni, Editorial Board Member, Pandu Rangan, C., Editorial Board Member, Steffen, Bernhard, Editorial Board Member, Terzopoulos, Demetri, Editorial Board Member, Tygar, Doug, Editorial Board Member, Goos, Gerhard, Founding Editor, Hartmanis, Juris, Founding Editor, Cai, Zhipeng, editor, Skums, Pavel, editor, and Li, Min, editor

Published
2019
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18. Heuristics for the Sorting Signed Permutations by Reversals and Transpositions Problem

Author

Brito, Klairton Lima, Oliveira, Andre Rodrigues, Dias, Ulisses, Dias, Zanoni, Hutchison, David, Series Editor, Kanade, Takeo, Series Editor, Kittler, Josef, Series Editor, Kleinberg, Jon M., Series Editor, Mattern, Friedemann, Series Editor, Mitchell, John C., Series Editor, Naor, Moni, Series Editor, Pandu Rangan, C., Series Editor, Steffen, Bernhard, Series Editor, Terzopoulos, Demetri, Series Editor, Tygar, Doug, Series Editor, Weikum, Gerhard, Series Editor, Jansson, Jesper, editor, Martín-Vide, Carlos, editor, and Vega-Rodríguez, Miguel A., editor

Published
2018
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19. Sorting by Weighted Reversals and Transpositions

Author

Oliveira, Andre Rodrigues, Brito, Klairton Lima, Dias, Zanoni, Dias, Ulisses, Hutchison, David, Series Editor, Kanade, Takeo, Series Editor, Kittler, Josef, Series Editor, Kleinberg, Jon M., Series Editor, Mattern, Friedemann, Series Editor, Mitchell, John C., Series Editor, Naor, Moni, Series Editor, Pandu Rangan, C., Series Editor, Steffen, Bernhard, Series Editor, Terzopoulos, Demetri, Series Editor, Tygar, Doug, Series Editor, Weikum, Gerhard, Series Editor, and Alves, Ronnie, editor

Published
2018
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34. Reversal and Indel Distance With Intergenic Region Information

Author

Alexandrino, Alexsandro Oliveira, Brito, Klairton Lima, Oliveira, Andre Rodrigues, Dias, Ulisses, and Dias, Zanoni

Abstract

Recent works on genome rearrangements have shown that incorporating intergenic region information along with gene order in models provides better estimations for the rearrangement distance than using gene order alone. The reversal distance is one of the main problems in genome rearrangements. It has a polynomial time algorithm when only gene order is used to model genomes, assuming that repeated genes do not exist and that gene orientation is known, even when the genomes have distinct gene sets. The reversal distance is NP-hard and has a 2-approximation algorithm when incorporating intergenic regions. However, the problem has only been studied assuming genomes with the same set of genes. In this work, we consider the variation that incorporates intergenic regions and that allows genomes to have distinct sets of genes, a scenario that leads us to include indels operations (insertions and deletions). We present a 2.5-approximation algorithm using the labeled intergenic breakpoint graph, which is based on the well-known breakpoint graph structure. We also present an experimental analysis of the proposed algorithm using simulated data, which showed that the practical approximation factor is considerably less than 2.5. Furthermore, we used the algorithm in real genomes to construct a phylogenetic tree.

Published
2023
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38. Heuristics for the Reversal and Transposition Distance Problem.

Author

Brito, Klairton Lima, Oliveira, Andre Rodrigues, Dias, Ulisses, and Dias, Zanoni

Abstract

We present three heuristics-Sliding Window, Look Ahead, and Iterative Sliding Window-to improve solutions for the Sorting Signed Permutations by Reversals and Transpositions Problem. We investigate the classical version of the problem as well as versions restricted to prefix and prefix or suffix operations. To assess the heuristics based on its improvement, we implemented algorithms described in the literature to provide initial solutions. Although we have a limited number of problems, these heuristics can be applied to many others within the area of genome rearrangement. When time is a crucial factor, Sliding Window is a better choice because it runs in linear time. If the quality of the solution is a priority, Look Ahead should be preferred. Iterative Sliding Window is the most flexible heuristic and allows us to find a trade-off for specific scenarios where running time and solution quality are relevant. [ABSTRACT FROM AUTHOR]

Published
2020
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