Publications related to Assessment of successful experiments and limitations of phytotechnologies: contaminant uptake, detoxification and sequestration, and consequences for food safety

The cost of adaptability: resource availability constrains functional stability under pulsed disturbances

Global change exposes ecosystems to changes in the frequency, magnitude, and concomitancy of disturbances, which impact the composition and functioning of these systems. Here, we experimentally evaluate the effects of salinity disturbances and eutrophicati ...

Amer Soc Microbiology2024

New and improved methods for integrated models of metabolism and gene expression

Pierre Guy Rémy Salvy

The beginning of the 21st century was marked by the advent of disruptive technologies, which ushered an era of groundbreaking advances in fundamental sciences, carried by the great pace at which computational capabilities spread and evolved. But the new ce ...

EPFL2021

The genetic architecture of complex human traits at the dawn of genomic medicine

Olivier Noël Marie Naret

The focus of the work presented in this thesis is the exploration of the genetic architecture of complex human traits - at the dawn of genomic medicine. The underlying mechanisms explaining the enormously polygenic nature of most human complex traits are ...

EPFL2021

Legacy effect of green manure crops fertilized with calcium phosphite on maize production and soil properties

Alexandre Buttler, Mario Fontana, Luca Bragazza, Thomas Guillaume, Mathieu Raymond Santonja

Recycling phosphorus (P) is crucial to meet future P demand for crop production. We investigated the possibility to use calcium phosphite (Ca-Phi) waste, an industrial by-product, as P fertilizer following the oxidation of phosphite (Phi) to phosphate (Pi) ...

ACADEMIC PRESS LTD- ELSEVIER SCIENCE LTD2021

A fully joint Bayesian quantitative trait locus mapping of human protein abundance in plasma

Anthony Christopher Davison, Hélène Ruffieux, Radu Popescu, Jörg Hager

Molecular quantitative trait locus (QTL) analyses are increasingly popular to explore the genetic architecture of complex traits, but existing studies do not leverage shared regulatory patterns and suffer from a large multiplicity burden, which hampers the ...

PUBLIC LIBRARY SCIENCE2020

Species identity, rather than species mixtures, drives cover crop effects on nutrient partitioning in unfertilized agricultural soil

Alexandre Buttler, Pierre Rémi Mariotte, Lucas Georges Jean-Paul Freund, Mathieu Raymond Santonja

Aims Previous cover crop studies mainly focused on the links between plant uptake and soil fertility, and there is a clear knowledge gap regarding the role of microbes in these processes. Our aim was then to better understand the effects of plant mixtures ...

2021

An Interactive Gameplay to Crowdsource Multiple Sequence Alignment of Genome Sequences: Genenigma

Kalpani Anuradha Welivita

Comparative genomics is a field of research that compares genomes of different organisms to identify common patterns. It is a powerful method used to identify the genetic diseases that cause mutations. Multiple Sequence Alignment (MSA) is an intermediate s ...

ASSOC COMPUTING MACHINERY2019

Privacy-Enhancing Technologies for Medical and Genomic Data: From Theory to Practice

Jean Louis Raisaro

The impressive technological advances in genomic analysis and the significant drop in the cost of genome sequencing are paving the way to a variety of revolutionary applications in modern healthcare. In particular, the increasing understanding of the human ...

EPFL2018

On Secure Cloud Computing for Genomic Data: From Storage to Analysis

Zhicong Huang

Although privacy is generally considered to be the right of an individual or group to control information about themselves, such a right has become challenging to protect in the digital era, this is exemplified by the case of cloud-based genomic computing. ...

EPFL2018

Stoichiometric N:P flexibility and mycorrhizal symbiosis favour plant resistance against drought

Pierre Rémi Mariotte

Drought induces changes in the nitrogen (N) and phosphorus (P) cycle but most plant species have limited flexibility to take up nutrients under such variable or unbalanced N and P availability. Both the degree of flexibility in plant N:P ratio and of ro ...

Wiley2017

Combining genotype, phenotype and environment to infer potential candidate genes: An example using the Loblolly pine (Pinus taeda)

Stéphane Joost

Population genomic analyses can be an important tool in understanding local adaptation. Identification of potential adaptive loci in such analyses is usually based on the survey of a large genomic dataset in combination with environmental variables. Phenot ...

Oxford University Press2017

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

Identification and Characterization of Tyrosine Kinase Nonreceptor 2 Mutations in Leukemia through Integration of Kinase Inhibitor Screening and Genomic Analysis

Oliver Hantschel, Sina Maren Reckel

The amount of genomic information about leukemia cells currently far exceeds our overall understanding of the precise genetic events that ultimately drive disease development and progression. Effective implementation of personalized medicine will require t ...

American Association for Cancer Research2016

Multi-scale landscape genomic models : the role of very high resolution digital elevation models in evolutionary biology

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

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

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

Privacy in the Genomic Era

Jean-Pierre Hubaux, Jacques Fellay, Erman Ayday

Genome sequencing technology has advanced at a rapid pace and it is now possible to generate highlydetailed genotypes inexpensively. The collection and analysis of such data has the potential to support various applications, including personalized medical ...

Assoc Computing Machinery2015

Improving Comparative Genomic Studies : Definitions and Algorithms for Syntenic Blocks

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

Privacy-Preserving Computation of Disease Risk by Using Genomic, Clinical, and Environmental Data

Jean-Pierre Hubaux, Jacques Fellay, Erman Ayday, Paul Jack Mc Laren, Jean Louis Raisaro

According to many scientists and clinicians, genomics is the "next big thing" in the field of medicine. On one hand, decreasing costs in genome sequencing has been paving the way to better preventive and personalized medicine. On the other hand, genomic da ...

2013

Parameterization Models for Pesticide Exposure via Crop Consumption

An approach for estimating human exposure to pesticides via consumption of six important food crops is presented that can be used to extend multimedia models applied in health risk and life cycle impact assessment. We first assessed the variation of model ...

Amer Chemical Soc2012