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Comparing genomes with rearrangements and segmental duplications

Publications associées (80)

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The Gene Family-Free Median of Three

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The gene family-free framework for comparative genomics aims at developing methods for gene order analysis that do not require prior gene family assignment, but work directly on a sequence similarity graph. We present a model for constructing a median of t ...

Springer AG2016

Subspace Acceleration For Large-Scale Parameter-Dependent Hermitian Eigenproblems

Daniel Kressner, Petar Sirkovic

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Siam Publications2016

An Exact Algorithm to Compute the Double-Cut-and-Join Distance for Genomes with Duplicate Genes

Bernard Moret, Yu Lin, Mingfu Shao

Computing the edit distance between two genomes is a basic problem in the study of genome evolution. The double-cut-and-join (DCJ) model has formed the basis for most algorithmic research on rearrangements over the last few years. The edit distance under t ...

Mary Ann Liebert2015

Models and Algorithms for Comparative Genomics

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The deluge of sequenced whole-genome data has motivated the study of comparative genomics, which provides global views on genome evolution, and also offers practical solutions in deciphering the functional roles of components of genomes. A fundamental comp ...

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Optimal Hybrid Perimeter and Switching Plans Control for Urban Traffic Networks

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Since centralized control of urban networks with detailed modeling approaches is computationally complex, developing efficient hierarchical control strategies based on aggregate modeling is of great importance. The dynamics of a heterogeneous large-scale u ...

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A Primal-dual Framework For Mixtures Of Regularisers

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Effectively solving many inverse problems in engineering requires to leverage all possible prior information about the structure of the signal to be estimated. This often leads to tackling constrained optimization problems with mixtures of regularizers. Pr ...

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Maximizing Symmetric Submodular Functions

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Symmetric submodular functions are an important family of submodular functions capturing many interesting cases including cut functions of graphs and hypergraphs. In this work, we identify submodular maximization problems for which one can get a better app ...

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A fast and exact algorithm for the exemplar breakpoint distance

Bernard Moret, Mingfu Shao

A fundamental problem in comparative genomics is to compute the distance between two genomes. For two genomes without duplicate genes, we can easily compute a variety of distance measures in linear time, but the problem is NP-hard under most models when ge ...

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Optimal Layered Representation for Adaptive Interactive Multiview Video Streaming

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We consider an interactive multiview video streaming (IMVS) system where clients select their preferred viewpoint in a given navigation window. To provide high quality IMVS, many high quality views should be transmitted to the clients. However, this is not ...

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Improving Christofides' Algorithm for the s-t Path TSP

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We present a deterministic (1+root 5/2)-approximation algorithm for the s-t path TSP for an arbitrary metric. Given a symmetric metric cost on n vertices including two prespecified endpoints, the problem is to find a shortest Hamiltonian path between the t ...

Assoc Computing Machinery2015