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Documents authored by Swenson, Krister M.

Document
DOI: 10.4230/LIPIcs.WABI.2019.13
Weighted Minimum-Length Rearrangement Scenarios

Authors: Pijus Simonaitis, Annie Chateau, and Krister M. Swenson

Published in: LIPIcs, Volume 143, 19th International Workshop on Algorithms in Bioinformatics (WABI 2019)

Abstract
We present the first known model of genome rearrangement with an arbitrary real-valued weight function on the rearrangements. It is based on the dominant model for the mathematical and algorithmic study of genome rearrangement, Double Cut and Join (DCJ). Our objective function is the sum or product of the weights of the DCJs in an evolutionary scenario, and the function can be minimized or maximized. If the likelihood of observing an independent DCJ was estimated based on biological conditions, for example, then this objective function could be the likelihood of observing the independent DCJs together in a scenario. We present an O(n⁴)-time dynamic programming algorithm solving the Minimum Cost Parsimonious Scenario (MCPS) problem for co-tailed genomes with n genes (or syntenic blocks). Combining this with our previous work on MCPS yields a polynomial-time algorithm for general genomes. The key theoretical contribution is a novel link between the parsimonious DCJ (or 2-break) scenarios and quadrangulations of a regular polygon. To demonstrate that our algorithm is fast enough to treat biological data, we run it on syntenic blocks constructed for Human paired with Chimpanzee, Gibbon, Mouse, and Chicken. We argue that the Human and Gibbon pair is a particularly interesting model for the study of weighted genome rearrangements.
Cite as

Pijus Simonaitis, Annie Chateau, and Krister M. Swenson. Weighted Minimum-Length Rearrangement Scenarios. In 19th International Workshop on Algorithms in Bioinformatics (WABI 2019). Leibniz International Proceedings in Informatics (LIPIcs), Volume 143, pp. 13:1-13:17, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2019)

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@InProceedings{simonaitis_et_al:LIPIcs.WABI.2019.13,
  author =	{Simonaitis, Pijus and Chateau, Annie and Swenson, Krister M.},
  title =	{{Weighted Minimum-Length Rearrangement Scenarios}},
  booktitle =	{19th International Workshop on Algorithms in Bioinformatics (WABI 2019)},
  pages =	{13:1--13:17},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-123-8},
  ISSN =	{1868-8969},
  year =	{2019},
  volume =	{143},
  editor =	{Huber, Katharina T. and Gusfield, Dan},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.WABI.2019.13},
  URN =		{urn:nbn:de:0030-drops-110436},
  doi =		{10.4230/LIPIcs.WABI.2019.13},
  annote =	{Keywords: Weighted genome rearrangement, Double cut and join (DCJ), Edge switch, Minimum-weight quadrangulation}
}
Document
DOI: 10.4230/LIPIcs.WABI.2019.20
Rapidly Computing the Phylogenetic Transfer Index

Authors: Jakub Truszkowski, Olivier Gascuel, and Krister M. Swenson

Published in: LIPIcs, Volume 143, 19th International Workshop on Algorithms in Bioinformatics (WABI 2019)

Abstract
Given trees T and T_o on the same taxon set, the transfer index phi(b,T_o) is the number of taxa that need to be ignored so that the bipartition induced by branch b in T is equal to some bipartition in T_o. Recently, Lemoine et al. [Lemoine et al., 2018] used the transfer index to design a novel bootstrap analysis technique that improves on Felsenstein’s bootstrap on large, noisy data sets. In this work, we propose an algorithm that computes the transfer index for all branches b in T in O(n log^3 n) time, which improves upon the current O(n^2)-time algorithm by Lin, Rajan and Moret [Lin et al., 2012]. Our implementation is able to process pairs of trees with hundreds of thousands of taxa in minutes and considerably speeds up the method of Lemoine et al. on large data sets. We believe our algorithm can be useful for comparing large phylogenies, especially when some taxa are misplaced (e.g. due to horizontal gene transfer, recombination, or reconstruction errors).
Cite as

Jakub Truszkowski, Olivier Gascuel, and Krister M. Swenson. Rapidly Computing the Phylogenetic Transfer Index. In 19th International Workshop on Algorithms in Bioinformatics (WABI 2019). Leibniz International Proceedings in Informatics (LIPIcs), Volume 143, pp. 20:1-20:12, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2019)

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@InProceedings{truszkowski_et_al:LIPIcs.WABI.2019.20,
  author =	{Truszkowski, Jakub and Gascuel, Olivier and Swenson, Krister M.},
  title =	{{Rapidly Computing the Phylogenetic Transfer Index}},
  booktitle =	{19th International Workshop on Algorithms in Bioinformatics (WABI 2019)},
  pages =	{20:1--20:12},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-123-8},
  ISSN =	{1868-8969},
  year =	{2019},
  volume =	{143},
  editor =	{Huber, Katharina T. and Gusfield, Dan},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.WABI.2019.20},
  URN =		{urn:nbn:de:0030-drops-110505},
  doi =		{10.4230/LIPIcs.WABI.2019.20},
  annote =	{Keywords: large phylogenies, bootstrap analysis, tree comparison, data structures on trees}
}
Document
DOI: 10.4230/LIPIcs.WABI.2017.24
Finding Local Genome Rearrangements

Authors: Pijus Simonaitis and Krister M. Swenson

Published in: LIPIcs, Volume 88, 17th International Workshop on Algorithms in Bioinformatics (WABI 2017)

Abstract
The Double Cut and Join (DCJ) model of genome rearrangement is well studied due to its mathematical simplicity and power to account for the many events that transform genome architecture. These studies have mostly been devoted to the understanding of minimum length scenarios transforming one genome into another. In this paper we search instead for DCJ rearrangement scenarios that minimize the number of rearrangements whose breakpoints are unlikely due to some biological criteria. We establish a link between this Minimum Local Scenario (MLS) problem and the problem of finding a Maximum Edge-disjoint Cycle Packing (MECP) on an undirected graph. This link leads us to a 3/2-approximation for MLS, as well as an exact integer linear program. From a practical perspective, we briefly report on the applicability of our methods and the potential for computation of distances using a more general DCJ cost function.
Cite as

Pijus Simonaitis and Krister M. Swenson. Finding Local Genome Rearrangements. In 17th International Workshop on Algorithms in Bioinformatics (WABI 2017). Leibniz International Proceedings in Informatics (LIPIcs), Volume 88, pp. 24:1-24:13, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2017)

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@InProceedings{simonaitis_et_al:LIPIcs.WABI.2017.24,
  author =	{Simonaitis, Pijus and Swenson, Krister M.},
  title =	{{Finding Local Genome Rearrangements}},
  booktitle =	{17th International Workshop on Algorithms in Bioinformatics (WABI 2017)},
  pages =	{24:1--24:13},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-050-7},
  ISSN =	{1868-8969},
  year =	{2017},
  volume =	{88},
  editor =	{Schwartz, Russell and Reinert, Knut},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.WABI.2017.24},
  URN =		{urn:nbn:de:0030-drops-76604},
  doi =		{10.4230/LIPIcs.WABI.2017.24},
  annote =	{Keywords: genome rearrangement, double cut and join, maximum edge-disjoint cycle packing, Hi-C, NP-complete, approximation algorithm}
}
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