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DOI: 10.4230/LIPIcs.WABI.2020.14

The Bourque Distances for Mutation Trees of Cancers

Authors: Katharina Jahn, Niko Beerenwinkel, and Louxin Zhang

Published in: LIPIcs, Volume 172, 20th International Workshop on Algorithms in Bioinformatics (WABI 2020)

Abstract

Mutation trees are rooted trees of arbitrary node degree in which each node is labeled with a mutation set. These trees, also referred to as clonal trees, are used in computational oncology to represent the mutational history of tumours. Classical tree metrics such as the popular Robinson - Foulds distance are of limited use for the comparison of mutation trees. One reason is that mutation trees inferred with different methods or for different patients often contain different sets of mutation labels. Here, we generalize the Robinson - Foulds distance into a set of distance metrics called Bourque distances for comparing mutation trees. A connection between the Robinson - Foulds distance and the nearest neighbor interchange distance is also presented.

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Katharina Jahn, Niko Beerenwinkel, and Louxin Zhang. The Bourque Distances for Mutation Trees of Cancers. In 20th International Workshop on Algorithms in Bioinformatics (WABI 2020). Leibniz International Proceedings in Informatics (LIPIcs), Volume 172, pp. 14:1-14:22, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2020)

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@InProceedings{jahn_et_al:LIPIcs.WABI.2020.14,
  author =	{Jahn, Katharina and Beerenwinkel, Niko and Zhang, Louxin},
  title =	{{The Bourque Distances for Mutation Trees of Cancers}},
  booktitle =	{20th International Workshop on Algorithms in Bioinformatics (WABI 2020)},
  pages =	{14:1--14:22},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-161-0},
  ISSN =	{1868-8969},
  year =	{2020},
  volume =	{172},
  editor =	{Kingsford, Carl and Pisanti, Nadia},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops-dev.dagstuhl.de/entities/document/10.4230/LIPIcs.WABI.2020.14},
  URN =		{urn:nbn:de:0030-drops-128039},
  doi =		{10.4230/LIPIcs.WABI.2020.14},
  annote =	{Keywords: mutation trees, clonal trees, tree distance, phylogenetic trees, tree metric, Robinson - Foulds distance, Bourque distance}
}

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DOI: 10.4230/DagRep.7.11.130

Addressing the Computational Challenges of Personalized Medicine (Dagstuhl Seminar 17472)

Authors: Niko Beerenwinkel, Holger Fröhlich, and Susan A. Murphy

Published in: Dagstuhl Reports, Volume 7, Issue 11 (2018)

Abstract

This report provides an overview of the talks and the working group reports from the Dagstuhl Seminar 17472 "Addressing the Computational Challenges of Personalized Medicine". The seminar brought together leading computational scientists with different backgrounds and perspectives in order to allow for a cross-fertilizing and stimulating discussion. It thus joined expertise that is usually scattered in different research communities. In addition, selected medical researchers, pharmacogenomics researchers and behavioral scientists provided their input and established the link of the computational to the more medical aspects of personalized medicine (PM). The talks and corresponding discussion spanned mainly three areas: 1) how to enhance prediction performance of computational models for PM; 2) how to improve their interpretability; 3) how to validate and implement them in practice.

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Niko Beerenwinkel, Holger Fröhlich, and Susan A. Murphy. Addressing the Computational Challenges of Personalized Medicine (Dagstuhl Seminar 17472). In Dagstuhl Reports, Volume 7, Issue 11, pp. 130-141, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2018)

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@Article{beerenwinkel_et_al:DagRep.7.11.130,
  author =	{Beerenwinkel, Niko and Fr\"{o}hlich, Holger and Murphy, Susan A.},
  title =	{{Addressing the Computational Challenges of Personalized Medicine (Dagstuhl Seminar 17472)}},
  pages =	{130--141},
  journal =	{Dagstuhl Reports},
  ISSN =	{2192-5283},
  year =	{2018},
  volume =	{7},
  number =	{11},
  editor =	{Beerenwinkel, Niko and Fr\"{o}hlich, Holger and Murphy, Susan A.},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops-dev.dagstuhl.de/entities/document/10.4230/DagRep.7.11.130},
  URN =		{urn:nbn:de:0030-drops-86730},
  doi =		{10.4230/DagRep.7.11.130},
  annote =	{Keywords: data science, machine learning, computational modeling, bioinformatics, systems biology}
}

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Documents authored by Beerenwinkel, Niko

The Bourque Distances for Mutation Trees of Cancers

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Addressing the Computational Challenges of Personalized Medicine (Dagstuhl Seminar 17472)

Abstract

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