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The Least Cost Path From Landscape Genetics to Landscape Genomics: Challenges and Opportunities to Explore NGS Data in a Spatially Explicit Context

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Open computational landscape genetics

Stéphane Joost, Estelle Rochat, Ivo Widmer

Geographical Information Systems (GIS) are considered to be applications-led technology. Consequently, geographic information scientists commonly find themselves as guest in host disciplines in order to best exploit spatial analysis tools and methods, appr ...

2016

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Modelling the evolution of biological networks is a major challenge. Biological networks are usually represented as graphs; evolutionary events include addition and removal of vertices and edges, but also duplication of vertices and their associated edges. ...

Springer Int Publishing Ag2016

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

Contribution of recombination to the evolutionary history of HIV

Séverine Vuilleumier Varisco

Purpose of review: An improved understanding of how recombination affects the evolutionary history of HIV is crucial to understand its current and future evolution. The present review aims to disentangle the manifold effects of recombination on HIV by disc ...

2015

A Systematic Survey of an Intragenic Epistatic Landscape

Jeffrey David Jensen, Claudia Bank

Mutations are the source of evolutionary variation. The interactions of multiple mutations can have important effects on fitness and evolutionary trajectories. We have recently described the distribution of fitness effects of all single mutations for a nin ...

Oxford Univ Press2015

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East Coast Fever (ECF) is a major livestock disease caused by Theileria parva Theiler, 1904, an emo-parasite protozoan transmitted by the tick Rhipicephalus appendiculatus Neumann, 1901. This disease provokes high mortality in cattle populations of East an ...

2015

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

Biogeoinformatics

Stéphane Joost

GIScience methods and geodata may contribute to the elaboration of efficient decision‐making approaches to favor the conservation of plant/animal genetic diversity and to favor the advancement of our understanding of mechanisms controlling the evolution of ...

2014

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Evolutionary algorithms are widespread heuristic methods inspired by natural evolution to solve difficult problems for which analytical approaches are not suitable. In many domains experimenters are not only interested in discovering optimal solutions, but ...

Public Library of Science2014

A multiscale landscape genomics analytical framework to identify local adaptive variation in the Buckler Mustard

Stéphane Joost, Kevin Leempoel

The question of finding an appropriate scale to study adaptation emerged only recently in landscape genomics, while in landscape ecology its components (extent and resolution or grain) have been addressed in many papers. In fact, in landscape genetics only ...

2013