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On Computing Breakpoint Distances for Genomes with Duplicate Genes

Publications associées (84)

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Models and Algorithms for Comparative Genomics

Mingfu Shao

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 ...

EPFL2015

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 ...

Springer2015

Comparing genomes with rearrangements and segmental duplications

Bernard Moret, Mingfu Shao

Motivation: Large-scale evolutionary events such as genomic rearrange. ments and segmental duplications form an important part of the evolution of genomes and are widely studied from both biological and computational perspectives. A basic computational pro ...

Oxford University Press2015

Centrality of trees for capacitated -center

Ola Nils Anders Svensson, Hyung Chan An, Aditya Bhaskara

We consider the capacitated -center problem. In this problem we are given a finite set of locations in a metric space and each location has an associated non-negative integer capacity. The goal is to choose (open) locations (called centers) and assign each ...

Springer Heidelberg2015

Whole genome duplications and recruitment of ecologically relevant genes in alpine Mustards

Stéphane Joost, Kevin Leempoel, Béatrice North

Polyploid taxa represent excellent models to address the underpinnings of genome evolution and the building up of new species in heterogeneous environments. Here, we present an overview of recent works in the alpine Biscutella laevigata autopolyploid compl ...

2015

An Exact Algorithm to Compute the DCJ 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 ...

Springer Verlag2014

Node-weighted network design and maximum sub-determinants

Carsten Moldenhauer

We consider the Node-weighted Steiner Forest problem on planar graphs. Demaine et al. showed that a generic primal-dual algorithm gives a 6-approximation. We present two different proofs of an approximation factor of~

3

. Then, we draw a connection to Goem ...

EPFL2014

Centrality of Trees for Capacitated k-Center

Ola Nils Anders Svensson, Hyung Chan An, Aditya Bhaskara

We consider the capacitated k-center problem. In this problem we are given a finite set of locations in a metric space and each location has an associated non-negative integer capacity. The goal is to choose (open) k locations (called centers) and assign e ...

Springer2014

Improving Comparative Genomic Studies

Cristina Gabriela Ghiurcuta

Comparative genomics aims to understand the structure of genomes and the function of various genomic fragments, by transferring knowledge gained from well studied genomes, to the new object of study. Rapid and inexpensive high-throughput sequencing is maki ...

EPFL2014

Right-Protected Data Publishing with Provable Distance-Based Mining

Michail Vlachos, Nikolaos Freris

Protection of one's intellectual property is a topic with important technological and legal facets. We provide mechanisms for establishing the ownership of a dataset consisting of multiple objects. The algorithms also preserve important properties of the d ...

Ieee Computer Soc2014

Node-weighted network design and maximum sub-determinants

Carsten Moldenhauer

3

. Then, we draw a connection to Goem ...

EPFL2014