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Genome visualization in space

Research output: Contribution in Book/Report/Proceedings - With ISBN/ISSN › Conference contribution/Paper › peer-review

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Genome visualization in space. / Soriano Marcolino, Leandro; Couto, Bráulio R. G. M.; dos Santos, Marcos A.
Advances in Bioinformatics: 4th International Workshop on Practical Applications of Computational Biology and Bioinformatics 2010 (IWPACBB 2010). ed. / Miguel P. Rocha; Florentino Fernández Riverola ; Hagit Shatkay; Juan Manuel Corchado. Springer, 2010. p. 225-232 (Advances in Intelligent and Soft Computing; Vol. 74).

Research output: Contribution in Book/Report/Proceedings - With ISBN/ISSN › Conference contribution/Paper › peer-review

Harvard

Soriano Marcolino, L, Couto, BRGM & dos Santos, MA 2010, Genome visualization in space. in MP Rocha, FF Riverola , H Shatkay & JM Corchado (eds), Advances in Bioinformatics: 4th International Workshop on Practical Applications of Computational Biology and Bioinformatics 2010 (IWPACBB 2010). Advances in Intelligent and Soft Computing, vol. 74, Springer, pp. 225-232. https://doi.org/10.1007/978-3-642-13214-8_29

APA

Soriano Marcolino, L., Couto, B. R. G. M., & dos Santos, M. A. (2010). Genome visualization in space. In M. P. Rocha, F. F. Riverola , H. Shatkay, & J. M. Corchado (Eds.), Advances in Bioinformatics: 4th International Workshop on Practical Applications of Computational Biology and Bioinformatics 2010 (IWPACBB 2010) (pp. 225-232). (Advances in Intelligent and Soft Computing; Vol. 74). Springer. https://doi.org/10.1007/978-3-642-13214-8_29

Vancouver

Soriano Marcolino L, Couto BRGM, dos Santos MA. Genome visualization in space. In Rocha MP, Riverola FF, Shatkay H, Corchado JM, editors, Advances in Bioinformatics: 4th International Workshop on Practical Applications of Computational Biology and Bioinformatics 2010 (IWPACBB 2010). Springer. 2010. p. 225-232. (Advances in Intelligent and Soft Computing). doi: 10.1007/978-3-642-13214-8_29

Author

Soriano Marcolino, Leandro ; Couto, Bráulio R. G. M. ; dos Santos, Marcos A. / Genome visualization in space. Advances in Bioinformatics: 4th International Workshop on Practical Applications of Computational Biology and Bioinformatics 2010 (IWPACBB 2010). editor / Miguel P. Rocha ; Florentino Fernández Riverola ; Hagit Shatkay ; Juan Manuel Corchado. Springer, 2010. pp. 225-232 (Advances in Intelligent and Soft Computing).

Bibtex

@inproceedings{955df089c456421999bbc762ed50f004,
title = "Genome visualization in space",
abstract = "Phylogeny is an important field to understand evolution and the organization of life. However, most methods depend highly on manual study and analysis, making the construction of phylogeny error prone. Linear Algebra methods are known to be efficient to deal with the semantic relationships between a large number of elements in spaces of high dimensionality. Therefore, they can be useful to help the construction of phylogenetic trees. The ability to visualize the relationships between genomes is crucial in this process. In this paper, a linear algebra method, followed by optimization, is used to generate a visualization of a set of complete genomes. Using the proposed method we were able to visualize the relationships of 64 complete mitochondrial genomes, organized as six different groups, and of 31 complete mitochondrial genomes of mammals, organized as nine different groups. The prespecified groups could be seen clustered together in the visualization, and similar species were represented close together. Besides, there seems to be an evolutionary influence in the organization of the graph.",
author = "{Soriano Marcolino}, Leandro and Couto, {Br{\'a}ulio R. G. M.} and {dos Santos}, {Marcos A.}",
note = "The final publication is available at Springer via http://dx.doi.org/10.1007/978-3-642-13214-8_29",
year = "2010",
doi = "10.1007/978-3-642-13214-8_29",
language = "English",
isbn = "9783642132131",
series = "Advances in Intelligent and Soft Computing",
publisher = "Springer",
pages = "225--232",
editor = "Rocha, {Miguel P.} and {Riverola }, {Florentino Fern{\'a}ndez} and Hagit Shatkay and Corchado, {Juan Manuel}",
booktitle = "Advances in Bioinformatics",

}

RIS

TY - GEN

T1 - Genome visualization in space

AU - Soriano Marcolino, Leandro

AU - Couto, Bráulio R. G. M.

AU - dos Santos, Marcos A.

N1 - The final publication is available at Springer via http://dx.doi.org/10.1007/978-3-642-13214-8_29

PY - 2010

Y1 - 2010

N2 - Phylogeny is an important field to understand evolution and the organization of life. However, most methods depend highly on manual study and analysis, making the construction of phylogeny error prone. Linear Algebra methods are known to be efficient to deal with the semantic relationships between a large number of elements in spaces of high dimensionality. Therefore, they can be useful to help the construction of phylogenetic trees. The ability to visualize the relationships between genomes is crucial in this process. In this paper, a linear algebra method, followed by optimization, is used to generate a visualization of a set of complete genomes. Using the proposed method we were able to visualize the relationships of 64 complete mitochondrial genomes, organized as six different groups, and of 31 complete mitochondrial genomes of mammals, organized as nine different groups. The prespecified groups could be seen clustered together in the visualization, and similar species were represented close together. Besides, there seems to be an evolutionary influence in the organization of the graph.

AB - Phylogeny is an important field to understand evolution and the organization of life. However, most methods depend highly on manual study and analysis, making the construction of phylogeny error prone. Linear Algebra methods are known to be efficient to deal with the semantic relationships between a large number of elements in spaces of high dimensionality. Therefore, they can be useful to help the construction of phylogenetic trees. The ability to visualize the relationships between genomes is crucial in this process. In this paper, a linear algebra method, followed by optimization, is used to generate a visualization of a set of complete genomes. Using the proposed method we were able to visualize the relationships of 64 complete mitochondrial genomes, organized as six different groups, and of 31 complete mitochondrial genomes of mammals, organized as nine different groups. The prespecified groups could be seen clustered together in the visualization, and similar species were represented close together. Besides, there seems to be an evolutionary influence in the organization of the graph.

U2 - 10.1007/978-3-642-13214-8_29

DO - 10.1007/978-3-642-13214-8_29

M3 - Conference contribution/Paper

SN - 9783642132131

T3 - Advances in Intelligent and Soft Computing

SP - 225

EP - 232

BT - Advances in Bioinformatics

A2 - Rocha, Miguel P.

A2 - Riverola , Florentino Fernández

A2 - Shatkay, Hagit

A2 - Corchado, Juan Manuel

PB - Springer

ER -