28 Publikationen
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2024 | Sammelwerksbeitrag | Veröffentlicht | PUB-ID: 2990270Dias Vieira Braga, Marília, Doerr, Daniel, Rubert, Diego P., and Stoye, Jens. “Family-Free Genome Comparison”. Comparative Genomics. Methods and Protocols. Ed. João Carlos Setubal, Peter F. Stadler, and Jens Stoye. 2nd ed. New York, NY: Humana, 2024.Vol. 2802. Methods in Molecular Biology. 57-72.PUB | DOI
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2024 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2985702Dias Vieira Braga, Marília, Brockmann, Leonie Ruth, Klerx, Katharina, and Stoye, Jens. “Investigating the complexity of the double distance problems”. Algorithms for Molecular Biology 19 (2024): 1.PUB | PDF | DOI | WoS | PubMed | Europe PMC
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2023 | Konferenzbeitrag | Veröffentlicht | PUB-ID: 2981606Dias Vieira Braga, Marília, Brockmann, Leonie Ruth, Klerx, Katharina, and Stoye, Jens. “On the Class of Double Distance Problems”. Comparative Genomics. 20th International Conference, RECOMB-CG 2023, Istanbul, Turkey, April 14–15, 2023, Proceedings. Ed. Katharina Jahn and Tomáš Vinař. Cham: Springer Nature , 2023.Vol. 13883. Lecture Notes in Computer Science. 35-50.PUB | DOI | WoS
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2022 | Konferenzbeitrag | Veröffentlicht | PUB-ID: 2968237Rubert, Diego, and Dias Vieira Braga, Marília. “Gene Orthology Inference via Large-Scale Rearrangements for Partially Assembled Genomes”. 22nd International Workshop on Algorithms in Bioinformatics (WABI 2022). Ed. Christina Boucher and Sven Rahmann. Dagstuhl: Schloss Dagstuhl, Leibniz-Zentrum für Informatik, 2022.Vol. 242. Leibniz International Proceedings in Informatics (LIPIcs).PUB | PDF | DOI | Download (ext.)
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2022 | Konferenzbeitrag | Veröffentlicht | PUB-ID: 2965398Dias Vieira Braga, Marília, Brockmann, Leonie Ruth, Klerx, Katharina, and Stoye, Jens. “A Linear Time Algorithm for an Extended Version of the Breakpoint Double Distance”. 22nd International Workshop on Algorithms in Bioinformatics (WABI 2022). Ed. Christina Boucher and Sven Rahmann. Dagstuhl: Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2022.Vol. 242. Leibniz International Proceedings in Informatics. LIPIcs. 13:1-13:16.PUB | DOI
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2021 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2959611Rubert, Diego, Doerr, Daniel, and Dias Vieira Braga, Marília. “The potential of family-free rearrangements towards gene orthology inference”. Journal of Bioinformatics and Computational Biology 19.6 (2021): 2140014.PUB | DOI | WoS | PubMed | Europe PMC
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2021 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2942686Willing, Eyla, Stoye, Jens, and Dias Vieira Braga, Marília. “Computing the Inversion-Indel Distance”. IEEE/ACM Transactions on Computational Biology and Bioinformatics 18.6 (2021): 2314-2326.PUB | DOI | WoS | PubMed | Europe PMC | arXiv
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2021 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2946303Bohnenkämper, Leonard, Dias Vieira Braga, Marília, Dörr, Daniel, and Stoye, Jens. “Computing the rearrangement distance of natural genomes”. Journal of Computational Biology 28.4 (2021): 410-431.PUB | DOI | WoS | PubMed | Europe PMC
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2020 | Konferenzbeitrag | Veröffentlicht | PUB-ID: 2965072Rubert, Diego, Martinez, Fábio V., and Dias Vieira Braga, Marília. “Natural Family-Free Genomic Distance”. 20th International Workshop on Algorithms in Bioinformatics (WABI 2020). Ed. Carl Kingsford and Nadia Pisanti. Dagstuhl, Germany: Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2020.Vol. 172. Leibniz International Proceedings in Informatics (LIPIcs). 3:1-3:23.PUB | PDF | DOI | Download (ext.)
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2020 | Preprint | Veröffentlicht | PUB-ID: 2939861Bohnenkämper, Leonard, Dias Vieira Braga, Marília, Dörr, Daniel, and Stoye, Jens. “Computing the rearrangement distance of natural genomes”. arXiv:2001.02139 (2020).PUB | Download (ext.) | arXiv
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2018 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2919006Rubert, Diego, Hoshino, Edna A., Dias Vieira Braga, Marília, Stoye, Jens, and Martinez, Fábio Henrique Viduani. “Computing the family-free DCJ similarity”. BMC Bioinformatics 19.Suppl. 6 (2018): 152.PUB | PDF | DOI | WoS | PubMed | Europe PMC
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2017 | Konferenzbeitrag | Veröffentlicht | PUB-ID: 2913015Rubert, Diego, Medeiros, Gabriel L., Hoshino, Edna A., Dias Vieira Braga, Marília, Stoye, Jens, and Martinez, Fábio Henrique Viduani. “Algorithms for Computing the Family-Free Genomic Similarity under DCJ”. Comparative Genomics. RECOMB-CG 2017. Ed. Joao Meidanis and Luay Nakhleh. Cham: Springer Verlag, 2017.Vol. 10562. Lecture Notes in Bioinformatics. 76-100.PUB | DOI
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2017 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2909057Rubert, Diego, Feijão, Pedro, Dias Vieira Braga, Marília, Stoye, Jens, and Martinez, Fábio Henrique Viduani. “Approximating the DCJ distance of balanced genomes in linear time”. Algorithms for Molecular Biology 12.1 (2017): 3.PUB | PDF | DOI | WoS | PubMed | Europe PMC
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2017 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2916552da Silva, Poly H., Machado, Raphael, Dantas, Simone, and Dias Vieira Braga, Marília. “Genomic Distance with High Indel Costs”. IEEE/ACM Transactions on Computational Biology and Bioinformatics 14.3 (2017): 728-732.PUB | DOI | WoS | PubMed | Europe PMC
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2016 | Konferenzbeitrag | Veröffentlicht | PUB-ID: 2903708Rubert, Diego, Feijão, Pedro, Dias Vieira Braga, Marília, Stoye, Jens, and Martinez, Fábio Henrique Viduani. “A Linear Time Approximation Algorithm for the DCJ Distance for Genomes with Bounded Number of Duplicates”. Algorithms in Bioinformatics. WABI 2016. Ed. Martin Frith and Christian Nørgaard Storm Pedersen. Cham: Springer, 2016.Vol. 9838. Lecture Notes in Bioinformatics. 293-306.PUB | DOI
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2015 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2726366Viduani Martinez, Fábio Henrique, Feijão, Pedro, Dias Vieira Braga, Marília, and Stoye, Jens. “On the family-free DCJ distance and similarity”. Algorithms for Molecular Biology 10.1 (2015): 13.PUB | PDF | DOI | WoS | PubMed | Europe PMC
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2015 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2677844Dias Vieira Braga, Marília, and Stoye, Jens. “Sorting linear genomes with rearrangements and indels”. IEEE/ACM Transactions on Computational Biology and Bioinformatics 12.3 (2015): 500-506.PUB | DOI | WoS | PubMed | Europe PMC
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2013 | Sammelwerksbeitrag | Veröffentlicht | PUB-ID: 2611648Dias Vieira Braga, Marília, Chauve, Cedric, Dörr, Daniel, Jahn, Katharina, Stoye, Jens, Thévenin, Annelyse, and Wittler, Roland. “The Potential of Family-Free Genome Comparison”. Models and Algorithms for Genome Evolution. Ed. Cedric Chauve, Nadia El-Mabrouk, and Eric Tannier. London: Springer Verlag, 2013.Vol. 19. Computational Biology Series. 287-307.PUB | DOI
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2011 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2091794Dias Vieira Braga, Marília, Willing, Eyla, and Stoye, Jens. “Double Cut and Join with Insertions and Deletions”. Journal of Computational Biology 18.9 (2011): 1167-1184.PUB | DOI | WoS | PubMed | Europe PMC
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2011 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2091790Kovac, Jakub, Warren, Robert, Dias Vieira Braga, Marília, and Stoye, Jens. “Restricted DCJ Model. Rearrangement Problems with Chromosome Reincorporation”. Journal of Computational Biology 18.9 (2011): 1231-1241.PUB | DOI | WoS | PubMed | Europe PMC
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2010 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 1898025Dias Vieira Braga, Marília, and Stoye, Jens. “The Solution Space of Sorting by DCJ”. Journal of Computational Biology 17.9 (2010): 1145-1165.PUB | DOI | WoS | PubMed | Europe PMC
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2009 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 1588760Dias Vieira Braga, Marília, Gautier, Christian, and Sagot, Marie-France. “An asymmetric approach to preserve common intervals while sorting by reversals”. Algorithms for Molecular Biology 4.1 (2009): 16.PUB | PDF | DOI | WoS | PubMed | Europe PMC