6 Search Results for "Doerr¹, Daniel"

Document
DOI: 10.4230/LIPIcs.WABI.2024.12
Reconstructing Rearrangement Phylogenies of Natural Genomes

Authors: Leonard Bohnenkämper, Jens Stoye, and Daniel Dörr

Published in: LIPIcs, Volume 312, 24th International Workshop on Algorithms in Bioinformatics (WABI 2024)

Abstract
We study the classical problem of inferring ancestral genomes from a set of extant genomes under a given phylogeny, known as the Small Parsimony Problem (SPP). Genomes are represented as sequences of oriented markers, organized in one or more linear or circular chromosomes. Any marker may appear in several copies, without restriction on orientation or genomic location, known as the natural genomes model. Evolutionary events along the branches of the phylogeny encompass large scale rearrangements, including segmental inversions, translocations, gain and loss (DCJ-indel model). Even under simpler rearrangement models, such as the classical breakpoint model without duplicates, the SPP is computationally intractable. Nevertheless, the SPP for natural genomes under the DCJ-indel model has been studied recently, with limited success. Here, we improve on that earlier work, giving a highly optimized ILP that is able to solve the SPP for sufficiently small phylogenies and gene families. A notable improvement w.r.t. the previous result is an optimized way of handling both circular and linear chromosomes. This is especially relevant to the SPP, since the chromosomal structure of ancestral genomes is unknown and the solution space for this chromosomal structure is typically large. We benchmark our method on simulated and real data. On simulated phylogenies we observe a considerable performance improvement on problems that include linear chromosomes. And even when the ground truth contains only one circular chromosome per genome, our method outperforms its predecessor due to its optimized handling of the solution space. The practical advantage becomes also visible in an analysis of seven Anopheles taxa.
Cite as

Leonard Bohnenkämper, Jens Stoye, and Daniel Dörr. Reconstructing Rearrangement Phylogenies of Natural Genomes. In 24th International Workshop on Algorithms in Bioinformatics (WABI 2024). Leibniz International Proceedings in Informatics (LIPIcs), Volume 312, pp. 12:1-12:16, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2024)

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@InProceedings{bohnenkamper_et_al:LIPIcs.WABI.2024.12,
  author =	{Bohnenk\"{a}mper, Leonard and Stoye, Jens and D\"{o}rr, Daniel},
  title =	{{Reconstructing Rearrangement Phylogenies of Natural Genomes}},
  booktitle =	{24th International Workshop on Algorithms in Bioinformatics (WABI 2024)},
  pages =	{12:1--12:16},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-340-9},
  ISSN =	{1868-8969},
  year =	{2024},
  volume =	{312},
  editor =	{Pissis, Solon P. and Sung, Wing-Kin},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.WABI.2024.12},
  URN =		{urn:nbn:de:0030-drops-206564},
  doi =		{10.4230/LIPIcs.WABI.2024.12},
  annote =	{Keywords: genome rearrangement, ancestral reconstruction, small parsimony, integer linear programming, double-cut-and-join}
}
Document
DOI: 10.4230/LIPIcs.WABI.2024.23
AlfaPang: Alignment Free Algorithm for Pangenome Graph Construction

Authors: Adam Cicherski, Anna Lisiecka, and Norbert Dojer

Published in: LIPIcs, Volume 312, 24th International Workshop on Algorithms in Bioinformatics (WABI 2024)

Abstract
The success of pangenome-based approaches to genomics analysis depends largely on the existence of efficient methods for constructing pangenome graphs that are applicable to large genome collections. In the current paper we present AlfaPang, a new pangenome graph building algorithm. AlfaPang is based on a novel alignment-free approach that allows to construct pangenome graphs using significantly less computational resources than state-of-the-art tools. The code of AlfaPang is freely available at https://github.com/AdamCicherski/AlfaPang.
Cite as

Adam Cicherski, Anna Lisiecka, and Norbert Dojer. AlfaPang: Alignment Free Algorithm for Pangenome Graph Construction. In 24th International Workshop on Algorithms in Bioinformatics (WABI 2024). Leibniz International Proceedings in Informatics (LIPIcs), Volume 312, pp. 23:1-23:18, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2024)

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@InProceedings{cicherski_et_al:LIPIcs.WABI.2024.23,
  author =	{Cicherski, Adam and Lisiecka, Anna and Dojer, Norbert},
  title =	{{AlfaPang: Alignment Free Algorithm for Pangenome Graph Construction}},
  booktitle =	{24th International Workshop on Algorithms in Bioinformatics (WABI 2024)},
  pages =	{23:1--23:18},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-340-9},
  ISSN =	{1868-8969},
  year =	{2024},
  volume =	{312},
  editor =	{Pissis, Solon P. and Sung, Wing-Kin},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.WABI.2024.23},
  URN =		{urn:nbn:de:0030-drops-206673},
  doi =		{10.4230/LIPIcs.WABI.2024.23},
  annote =	{Keywords: pangenome, variation graph, genome alignment, population genomics}
}
Document
DOI: 10.4230/LIPIcs.MFCS.2024.75
Edit and Alphabet-Ordering Sensitivity of Lex-Parse

Authors: Yuto Nakashima, Dominik Köppl, Mitsuru Funakoshi, Shunsuke Inenaga, and Hideo Bannai

Published in: LIPIcs, Volume 306, 49th International Symposium on Mathematical Foundations of Computer Science (MFCS 2024)

Abstract
We investigate the compression sensitivity [Akagi et al., 2023] of lex-parse [Navarro et al., 2021] for two operations: (1) single character edit and (2) modification of the alphabet ordering, and give tight upper and lower bounds for both operations (i.e., we show Θ(log n) bounds for strings of length n). For both lower bounds, we use the family of Fibonacci words. For the bounds on edit operations, our analysis makes heavy use of properties of the Lyndon factorization of Fibonacci words to characterize the structure of lex-parse.
Cite as

Yuto Nakashima, Dominik Köppl, Mitsuru Funakoshi, Shunsuke Inenaga, and Hideo Bannai. Edit and Alphabet-Ordering Sensitivity of Lex-Parse. In 49th International Symposium on Mathematical Foundations of Computer Science (MFCS 2024). Leibniz International Proceedings in Informatics (LIPIcs), Volume 306, pp. 75:1-75:15, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2024)

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@InProceedings{nakashima_et_al:LIPIcs.MFCS.2024.75,
  author =	{Nakashima, Yuto and K\"{o}ppl, Dominik and Funakoshi, Mitsuru and Inenaga, Shunsuke and Bannai, Hideo},
  title =	{{Edit and Alphabet-Ordering Sensitivity of Lex-Parse}},
  booktitle =	{49th International Symposium on Mathematical Foundations of Computer Science (MFCS 2024)},
  pages =	{75:1--75:15},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-335-5},
  ISSN =	{1868-8969},
  year =	{2024},
  volume =	{306},
  editor =	{Kr\'{a}lovi\v{c}, Rastislav and Ku\v{c}era, Anton{\'\i}n},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.MFCS.2024.75},
  URN =		{urn:nbn:de:0030-drops-206314},
  doi =		{10.4230/LIPIcs.MFCS.2024.75},
  annote =	{Keywords: Compression sensitivity, Lex-parse, Fibonacci words}
}
Document
DOI: 10.4230/LIPIcs.WABI.2023.22
Bridging Disparate Views on the DCJ-Indel Model for a Capping-Free Solution to the Natural Distance Problem

Authors: Leonard Bohnenkämper

Published in: LIPIcs, Volume 273, 23rd International Workshop on Algorithms in Bioinformatics (WABI 2023)

Abstract
One of the most fundamental problems in genome rearrangement is the (genomic) distance problem. It is typically formulated as finding the minimum number of rearrangements under a model that are needed to transform one genome into the other. A powerful multi-chromosomal model is the Double Cut and Join (DCJ) model. While the DCJ model is not able to deal with some situations that occur in practice, like duplicated or lost regions, it was extended over time to handle these cases. First, it was extended to the DCJ-indel model, solving the issue of lost markers. Later ILP-solutions for so called natural genomes, in which each genomic region may occur an arbitrary number of times, were developed, enabling in theory to solve the distance problem for any pair of genomes. However, some theoretical and practical issues remained unsolved. On the theoretical side of things, there exist two disparate views of the DCJ-indel model, motivated in the same way, but with different conceptualizations that could not be reconciled so far. On the practical side, while the solutions for natural genomes typically perform well on telomere to telomere resolved genomes, they have been shown in recent years to quickly loose performance on genomes with a large number of contigs or linear chromosomes. This has been linked to a particular technique increasing the solution space superexponentially named capping. Recently, we introduced a new conceptualization of the DCJ-indel model within the context of another rearrangement problem. In this manuscript, we will apply this new conceptualization to the distance problem. In doing this, we uncover the relation between the disparate conceptualizations of the DCJ-indel model. We are also able to derive an ILP solution to the distance problem that does not rely on capping and therefore significantly improves upon the performance of previous solutions for genomes with high numbers of contigs while still solving the problem exactly. To the best of our knowledge, our approach is the first allowing for an exact computation of the DCJ-indel distance for natural genomes with large numbers of linear chromosomes. We demonstrate the performance advantage as well as limitations in comparison to an existing solution on simulated genomes as well as showing its practical usefulness in an analysis of 11 Drosophila genomes.
Cite as

Leonard Bohnenkämper. Bridging Disparate Views on the DCJ-Indel Model for a Capping-Free Solution to the Natural Distance Problem. In 23rd International Workshop on Algorithms in Bioinformatics (WABI 2023). Leibniz International Proceedings in Informatics (LIPIcs), Volume 273, pp. 22:1-22:18, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2023)

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@InProceedings{bohnenkamper:LIPIcs.WABI.2023.22,
  author =	{Bohnenk\"{a}mper, Leonard},
  title =	{{Bridging Disparate Views on the DCJ-Indel Model for a Capping-Free Solution to the Natural Distance Problem}},
  booktitle =	{23rd International Workshop on Algorithms in Bioinformatics (WABI 2023)},
  pages =	{22:1--22:18},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-294-5},
  ISSN =	{1868-8969},
  year =	{2023},
  volume =	{273},
  editor =	{Belazzougui, Djamal and Ouangraoua, A\"{i}da},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.WABI.2023.22},
  URN =		{urn:nbn:de:0030-drops-186484},
  doi =		{10.4230/LIPIcs.WABI.2023.22},
  annote =	{Keywords: Comparative Genomics, Genome Rearrangement, Double-Cut-And-Join, Indels, Integer Linear Programming, Capping}
}
Document
DOI: 10.4230/LIPIcs.WABI.2022.6
Constructing Founder Sets Under Allelic and Non-Allelic Homologous Recombination

Authors: Konstantinn Bonnet, Tobias Marschall, and Daniel Doerr¹

Published in: LIPIcs, Volume 242, 22nd International Workshop on Algorithms in Bioinformatics (WABI 2022)

Abstract
Homologous recombination between the maternal and paternal copies of a chromosome is a key mechanism for human inheritance and shapes population genetic properties of our species. However, a similar mechanism can also act between different copies of the same sequence, then called non-allelic homologous recombination (NAHR). This process can result in genomic rearrangements - including deletion, duplication, and inversion - and is underlying many genomic disorders. Despite its importance for genome evolution and disease, there is a lack of computational models to study genomic loci prone to NAHR. In this work, we propose such a computational model, providing a unified framework for both (allelic) homologous recombination and NAHR. Our model represents a set of genomes as a graph, where human haplotypes correspond to walks through this graph. We formulate two founder set problems under our recombination model, provide flow-based algorithms for their solution, and demonstrate scalability to problem instances arising in practice.
Cite as

Konstantinn Bonnet, Tobias Marschall, and Daniel Doerr¹. Constructing Founder Sets Under Allelic and Non-Allelic Homologous Recombination. In 22nd International Workshop on Algorithms in Bioinformatics (WABI 2022). Leibniz International Proceedings in Informatics (LIPIcs), Volume 242, pp. 6:1-6:23, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2022)

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@InProceedings{bonnet_et_al:LIPIcs.WABI.2022.6,
  author =	{Bonnet, Konstantinn and Marschall, Tobias and Doerr¹, Daniel},
  title =	{{Constructing Founder Sets Under Allelic and Non-Allelic Homologous Recombination}},
  booktitle =	{22nd International Workshop on Algorithms in Bioinformatics (WABI 2022)},
  pages =	{6:1--6:23},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-243-3},
  ISSN =	{1868-8969},
  year =	{2022},
  volume =	{242},
  editor =	{Boucher, Christina and Rahmann, Sven},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.WABI.2022.6},
  URN =		{urn:nbn:de:0030-drops-170403},
  doi =		{10.4230/LIPIcs.WABI.2022.6},
  annote =	{Keywords: founder set reconstruction, variation graph, pangenomics, NAHR, homologous recombination}
}
Document
DOI: 10.4230/LIPIcs.WABI.2022.13
A Linear Time Algorithm for an Extended Version of the Breakpoint Double Distance

Authors: Marília D. V. Braga, Leonie R. Brockmann, Katharina Klerx, and Jens Stoye

Published in: LIPIcs, Volume 242, 22nd International Workshop on Algorithms in Bioinformatics (WABI 2022)

Abstract
Two genomes over the same set of gene families form a canonical pair when each of them has exactly one gene from each family. A genome is circular when it contains only circular chromosomes. Different distances of canonical circular genomes can be derived from a structure called breakpoint graph, which represents the relation between the two given genomes as a collection of cycles of even length. Then, the breakpoint distance is equal to n-c_2, where n is the number of genes and c_2 is the number of cycles of length 2. Similarly, when the considered rearrangements are those modeled by the double-cut-and-join (DCJ) operation, the rearrangement distance is n-c, where c is the total number of cycles. The distance problem is a basic unit for several other combinatorial problems related to genome evolution and ancestral reconstruction, such as median or double distance. Interestingly, both median and double distance problems can be solved in polynomial time for the breakpoint distance, while they are NP-hard for the rearrangement distance. One way of exploring the complexity space between these two extremes is to consider a σ_k distance, defined to be n-(c_2+c_4+…+c_k), and increasingly investigate the complexities of median and double distance for the σ₄ distance, then the σ₆ distance, and so on. While for the median much effort was done in our and in other research groups but no progress was obtained even for the σ₄ distance, for solving the double distance under σ₄ and σ₆ distances we could devise linear time algorithms, which we present here.
Cite as

Marília D. V. Braga, Leonie R. Brockmann, Katharina Klerx, and Jens Stoye. A Linear Time Algorithm for an Extended Version of the Breakpoint Double Distance. In 22nd International Workshop on Algorithms in Bioinformatics (WABI 2022). Leibniz International Proceedings in Informatics (LIPIcs), Volume 242, pp. 13:1-13:16, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2022)

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@InProceedings{braga_et_al:LIPIcs.WABI.2022.13,
  author =	{Braga, Mar{\'\i}lia D. V. and Brockmann, Leonie R. and Klerx, Katharina and Stoye, Jens},
  title =	{{A Linear Time Algorithm for an Extended Version of the Breakpoint Double Distance}},
  booktitle =	{22nd International Workshop on Algorithms in Bioinformatics (WABI 2022)},
  pages =	{13:1--13:16},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-243-3},
  ISSN =	{1868-8969},
  year =	{2022},
  volume =	{242},
  editor =	{Boucher, Christina and Rahmann, Sven},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.WABI.2022.13},
  URN =		{urn:nbn:de:0030-drops-170472},
  doi =		{10.4230/LIPIcs.WABI.2022.13},
  annote =	{Keywords: Comparative genomics, genome rearrangement, breakpoint distance, double-cut-and-join (DCJ) distance, double distance}
}
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