Publication

A Fast and Exact Algorithm for the Exemplar Breakpoint Distance

Related publications (40)

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.

KRAB zinc-finger proteins contribute to the evolution of gene regulatory networks

Didier Trono, Michaël Imbeault, Pierre-Yves Joseph Laurent Helleboid

The human genome encodes some 350 Kruppel-associated box (KRAB) domain-containing zinc-finger proteins (KZFPs), the products of a rapidly evolving gene family that has been traced back to early tetrapods(1,2). The function of most KZFPs is unknown, but a f ...

Nature Publishing Group2017

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

, ,

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

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

Understanding the metabolism of tetrachloroethene-respiring Dehalobacter restrictus

Aamani Rupakula Boyanapalli

Tetra- and trichloroethene (PCE, TCE) are organohalides polluting the environment as a result of inappropriate use, storage, and disposal by various industries. Anthropogenic pollution by organohalides is a major source of concern because of their undesira ...

EPFL2015

An Exact Algorithm to Compute the DCJ Distance for Genomes with Duplicate Genes

Bernard Moret, Yu Lin, Mingfu Shao

Springer Verlag2014

Proteins are a ubiquitous and indispensable element for every living organism, from simple bacteria to mammals. Already in the simplest organisms, there exist some thousands of different protein species that take up a great variety of structures, and thus ...

EPFL2014

Recent advancements in DNA sequencing technologies, accompanied by parallel development of sophisticated computational methods, offer an unprecedented opportunity to explore and study the genetic material of many organisms. However, despite the tremendous ...

EPFL2013

In the field of robust optimization, the goal is to provide solutions to combinatorial problems that hedge against variations of the numerical parameters. This constitutes an effort to design algorithms that are applicable in the presence of uncertainty in ...

2013