A Unified ILP Framework for Genome Median, Halving, and Aliquoting Problems Under DCJ

Avdeyev, Pavel; Alexeev, Nikita; Rong, Yongwu; Alekseyev, Max A.

doi:10.1007/978-3-319-67979-2_9

Cited by 5 publications

(2 citation statements)

References 32 publications

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“…Our approach also provides insights into the combinatorial structure of genome transformations by DCJs and indels with respect to appearance of circular chromosomes. We remark that a similar linearization problem appears in adjacency-based reconstructions of median genomes and is known to be intractable, 10 forcing the existing approaches [10][11][12][13][14] to solve its relaxation and allowing the constructed median genomes to contain circular chromosomes.…”

Section: Introductionmentioning

confidence: 99%

Linearization of Median Genomes Under the Double-Cut-and-Join-Indel Model

Avdeyev

Jiang

Alekseyev

2019

Evol Bioinform Online

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Reconstruction of the median genome consisting of linear chromosomes from three given genomes is known to be intractable. There exist efficient methods for solving a relaxed version of this problem, where the median genome is allowed to have circular chromosomes. We propose a method for construction of an approximate solution to the original problem from a solution to the relaxed problem and prove a bound on its approximation error. Our method also provides insights into the combinatorial structure of genome transformations with respect to appearance of circular chromosomes.

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Section: Introductionmentioning

confidence: 99%

Linearization of Median Genomes Under the Double-Cut-and-Join-Indel Model

Avdeyev

Jiang

Alekseyev

2019

Evol Bioinform Online

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“…On the other hand, the accuracy of the homology-based methods are still worse than the rearrangement-based methods on genomes for which parsimony assumption holds [111,108]. Recently, the promising direction of developing tools which combine the advantages of the homologyand rearrangement-based methods are emerging [107,108,17].…”

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confidence: 99%

Biological computation and computational biology: survey, challenges, and discussion

2021

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Biological computation involves the design and development of computational techniques inspired by natural biota. On the other hand, computational biology involves the development and application of computational techniques to study biological systems. We present a comprehensive review showcasing how biology and computer science can guide and benet each other, resulting in improved understanding of biological processes and at the same time advances in the design of algorithms. Unfortunately, integration between biology and computer science is often challenging, especially due to the cultural idiosyncrasies of these two communities. In this study, we aim at highlighting how nature has inspired the development of various algorithms and techniques in computer science, and how computational techniques and mathematical modeling have helped to better understand various elds in biology. We identied existing gaps between biolog-The discussion in this paper about the challenges and importance of lling the gaps between the biological computation and computational biology communities represents the outcome of an analysis that has been done in the 5 th Heidelberg Laureate Forum; specically during a workshop https://scilogs.spektrum.de/hlf/ experience-learn-share-heidelberg-laureate-forum/ organized by Dr. Zaineb Chelly Dagdia and mentored by Professor Stephen Smale (Fields Medal awardee). After the workshop, a collaboration was formed between Dr. Zaineb Chelly Dagdia who works on biological computation and two participants and contributors to the workshop, Pavel Avdeyev and Dr. Md. Shamsuzzoha Bayzid, who work on dierent areas in computational biology.

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Estimation of the True Evolutionary Distance Under the INFER Model

Zabelkin

Alexeev

2018

Comparative Genomics

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A Unified ILP Framework for Genome Median, Halving, and Aliquoting Problems Under DCJ

Cited by 5 publications

References 32 publications

Linearization of Median Genomes Under the Double-Cut-and-Join-Indel Model

Linearization of Median Genomes Under the Double-Cut-and-Join-Indel Model

Biological computation and computational biology: survey, challenges, and discussion

Estimation of the True Evolutionary Distance Under the INFER Model

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