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Sorting genomes with rearrangements and segmental duplications through trajectory graphs

Related publications (32)

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Multi-scale landscape genomic models

Kevin Leempoel

Environmental heterogeneity is one of the main actors of biodiversity and species adaptation as it exerts a selective pressure on observable characteristics of living organisms. Consequently, local adaptation favours certain genetic variants and, by doing ...

EPFL2015

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

Worldwide Population Structure, Long-Term Demography, and Local Adaptation of Helicobacter pylori

Jeffrey David Jensen, Matthieu Foll, Valeria Montano

Helicobacter pylori is an important human pathogen associated with serious gastric diseases. Owing to its medical importance and close relationship with its human host, understanding genomic patterns of global and local adaptation in H. pylori may be of pa ...

Genetics Society America2015

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

Adaptation on a genomic scale

Jacques Fellay, Istvan Bartha

Sequencing the genome of Candida albicans as it evolves in a patient reveals the genetic changes that allow the yeast to adapt to its environment. ...

2015

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

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

Adaptive, convergent origins of the pygmy phenotype in African rainforest hunter-gatherers

Matthieu Foll, Xin Zhou

The evolutionary history of the human pygmy phenotype (small body size), a characteristic of African and Southeast Asian rainforest hunter-gatherers, is largely unknown. Here we use a genome-wide admixture mapping analysis to identify 16 genomic regions th ...

Natl Acad Sciences2014

Patient Privacy in the Genomic Era

Jean-Pierre Hubaux, Erman Ayday, Jean Louis Raisaro

According to many scientists and clinicians, genomics is taking on a key role in the field of medicine. Impressive advances in genome sequencing have opened the way to a variety of revolutionary applications in modern healthcare. In particular, the increas ...

2014

The characterization of goat genetic diversity: Towards a genomic approach

Stéphane Joost, Pierre Taberlet

The investigation of genetic diversity at molecular level has been proposed as a valuable complement and sometimes proxy to phenotypic diversity of local breeds and is presently considered as one of the FAO priorities for breed characterization. By recomme ...

Elsevier2014