2 Search Results for "Cornwell, Steffen"

Document
DOI: 10.4230/LIPIcs.IPEC.2025.11
Parameterized Algorithms for Diversity of Networks with Ecological Dependencies

Authors: Mark Jones and Jannik Schestag

Published in: LIPIcs, Volume 358, 20th International Symposium on Parameterized and Exact Computation (IPEC 2025)

Abstract
For a phylogenetic tree, the phylogenetic diversity of a set A of taxa is the total weight of edges on paths to A. Finding small sets of maximal diversity is crucial for conservation planning, as it indicates where limited resources can be invested most efficiently. In recent years, efficient algorithms have been developed to find sets of taxa that maximize phylogenetic diversity either in a phylogenetic network or in a phylogenetic tree subject to ecological constraints, such as a food web. However, these aspects have mostly been studied independently. Since both factors are biologically important, it seems natural to consider them together. In this paper, we introduce decision problems where, given a phylogenetic network, a food web, and integers k, and D, the task is to find a set of k taxa with phylogenetic diversity of at least D under the maximize all paths measure, while also satisfying viability conditions within the food web. Here, we consider different definitions of viability, which all demand that a "sufficient" number of prey species survive to support surviving predators. We investigate the parameterized complexity of these problems and present several fixed-parameter tractable (FPT) algorithms. Specifically, we provide a complete complexity dichotomy characterizing which combinations of parameters - out of the size constraint k, the acceptable diversity loss D̄, the scanwidth of the food web sw_ℱ, the maximum in-degree δ in the network, and the network height h - lead to W[1]-hardness and which admit FPT algorithms. Our primary methodological contribution is a novel algorithmic framework for solving phylogenetic diversity problems in networks where dependencies (such as those from a food web) impose an order, using a color coding approach.
Cite as

Mark Jones and Jannik Schestag. Parameterized Algorithms for Diversity of Networks with Ecological Dependencies. In 20th International Symposium on Parameterized and Exact Computation (IPEC 2025). Leibniz International Proceedings in Informatics (LIPIcs), Volume 358, pp. 11:1-11:21, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2025)

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@InProceedings{jones_et_al:LIPIcs.IPEC.2025.11,
  author =	{Jones, Mark and Schestag, Jannik},
  title =	{{Parameterized Algorithms for Diversity of Networks with Ecological Dependencies}},
  booktitle =	{20th International Symposium on Parameterized and Exact Computation (IPEC 2025)},
  pages =	{11:1--11:21},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-407-9},
  ISSN =	{1868-8969},
  year =	{2025},
  volume =	{358},
  editor =	{Agrawal, Akanksha and van Leeuwen, Erik Jan},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.IPEC.2025.11},
  URN =		{urn:nbn:de:0030-drops-251439},
  doi =		{10.4230/LIPIcs.IPEC.2025.11},
  annote =	{Keywords: Phylogenetic Diversity, Fixed-Parameter Tractability, Phylogenetic Networks, Food Webs, Color Coding}
}
Document
DOI: 10.4230/LIPIcs.WABI.2017.10
Yanagi: Transcript Segment Library Construction for RNA-Seq Quantification

Authors: Mohamed K. Gunady, Steffen Cornwell, Stephen M. Mount, and Héctor Corrada Bravo

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

Abstract
Analysis of differential alternative splicing from RNA-seq data is complicated by the fact that many RNA-seq reads map to multiple transcripts, and that annotated transcripts from a given gene are often a small subset of many possible complete transcripts for that gene. Here we describe Yanagi, a tool which segments a transcriptome into disjoint regions to create a segments library from a complete transcriptome annotation that preserves all of its consecutive regions of a given length L while distinguishing annotated alternative splicing events in the transcriptome. In this paper, we formalize this concept of transcriptome segmentation and propose an efficient algorithm for generating segment libraries based on a length parameter dependent on specific RNA-Seq library construction. The resulting segment sequences can be used with pseudo-alignment tools to quantify expression at the segment level. We characterize the segment libraries for the reference transcriptomes of Drosophila melanogaster and Homo sapiens. Finally, we demonstrate the utility of quantification using a segment library based on an analysis of differential exon skipping in Drosophila melanogaster and Homo sapiens. The notion of transcript segmentation as introduced here and implemented in Yanagi will open the door for the application of lightweight, ultra-fast pseudo-alignment algorithms in a wide variety of analyses of transcription variation.
Cite as

Mohamed K. Gunady, Steffen Cornwell, Stephen M. Mount, and Héctor Corrada Bravo. Yanagi: Transcript Segment Library Construction for RNA-Seq Quantification. In 17th International Workshop on Algorithms in Bioinformatics (WABI 2017). Leibniz International Proceedings in Informatics (LIPIcs), Volume 88, pp. 10:1-10:14, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2017)

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@InProceedings{gunady_et_al:LIPIcs.WABI.2017.10,
  author =	{Gunady, Mohamed K. and Cornwell, Steffen and Mount, Stephen M. and Bravo, H\'{e}ctor Corrada},
  title =	{{Yanagi: Transcript Segment Library Construction for RNA-Seq Quantification}},
  booktitle =	{17th International Workshop on Algorithms in Bioinformatics (WABI 2017)},
  pages =	{10:1--10:14},
  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.2017.10},
  URN =		{urn:nbn:de:0030-drops-76487},
  doi =		{10.4230/LIPIcs.WABI.2017.10},
  annote =	{Keywords: RNA-Seq, Genome Sequencing, Kmer-based alignment, Transcriptome Quantification, Differential Alternative Splicing}
}
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