Publication

Comparing genomes with rearrangements and segmental duplications

Related publications (80)

Graph Chatbot

Chat with Graph Search

Ask any question about EPFL courses, lectures, exercises, research, news, etc. or try the example questions below.

DISCLAIMER: The Graph Chatbot is not programmed to provide explicit or categorical answers to your questions. Rather, it transforms your questions into API requests that are distributed across the various IT services officially administered by EPFL. Its purpose is solely to collect and recommend relevant references to content that you can explore to help you answer your questions.

The Gene Family-Free Median of Three

Metin Balaban

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

This work is concerned with approximating the smallest eigenvalue of a parameter-dependent Hermitian matrix A(mu) for many parameter values mu in a domain D subset of R-P. The design of reliable and efficient algorithms for addressing this task is of impor ...

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

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

Optimal Hybrid Perimeter and Switching Plans Control for Urban Traffic Networks

Nikolaos Geroliminis, Jack Haddad, Mohammadreza Hajiahmadi

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 ...

Institute of Electrical and Electronics Engineers2015

A Primal-dual Framework For Mixtures Of Regularisers

Volkan Cevher, Cosimo Aprile, Quoc Tran Dinh, Luca Baldassarre, Baran Gözcü

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 ...

2015

Maximizing Symmetric Submodular Functions

Moran Feldman

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 ...

Springer Int Publishing Ag2015

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

Optimal Layered Representation for Adaptive Interactive Multiview Video Streaming

Pascal Frossard, Thomas Maugey, Nikolaos Thomos, Laura Toni, Ana Karina De Abreu Goes

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 ...

Elsevier2015

Improving Christofides' Algorithm for the s-t Path TSP

Hyung Chan An

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