Publications related to Frequency-dependent selection

Reproductive isolation arises during laboratory adaptation to a novel hot environment

Background: Reproductive isolation can result from adaptive processes (e.g., ecological speciation and mutation-order speciation) or stochastic processes such as "system drift" model. Ecological speciation predicts barriers to gene flow between populations ...

BMC2024

PSGL-1 is an evolutionarily conserved antiviral restriction factor

Ying Liu, Chao Jiang

The arms race between viruses and their hosts shaped the evolutionary history and the genome composition of both parties. Restriction factors are the first-line antiviral effectors encoded by the host genomes and are often conserved through evolution to pr ...

AMER SOC MICROBIOLOGY2023

Individual and combined benefits of different nonequilibrium proofreading mechanisms

Paolo De Los Rios, Daniel Maria Busiello, Stefano Zamuner, Adélaïde Alice Mohr

Genome duplication, transcription, and translation are among many crucial cellular processes that need to be performed with high fidelity. However, those extremely low error rates cannot be explained with simple equilibrium thermodynamic considerations. Th ...

Amer Physical Soc2023

Dynamics of the most common pathogenic mtDNA variant m.3243A > G demonstrate frequency-dependency in blood and positive selection in the germline

Konstantin Popadin

The A-to-G point mutation at position 3243 in the human mitochondrial genome (m.3243A > G) is the most common pathogenic mtDNA variant responsible for disease in humans. It is widely accepted that m.3243A > G levels decrease in blood with age, and an age c ...

Oxford University Press2022

Patron-Driven Acquisition et Evidence-Based Acquisition: Comment implémenter ces modèles afin d’étendre l’offre documentaire dans une bibliothèque ?

Marion Favre, Manon Velasco

Nowadays, usage-based acquisition models for e-books, as PDA and EBA, are quite spread and allow libraries to offer wider collections, without acquiring them. A PDA with Ebook Central was implemented in 2019 and a first EBA with Wiley in 2021. The EPFL Lib ...

Liège Université Library2023

Towards mouse genetic-specific RNA-sequencing read mapping

Maxime Jan, Ioannis Xenarios

Genetic variations affect behavior and cause disease but understanding how these variants drive complex traits is still an open question. A common approach is to link the genetic variants to intermediate molecular phenotypes such as the transcriptome using ...

2022

Frequency selection in a gravitationally stretched capillary jet in the jetting regime

François Gallaire, Isha Shukla

A capillary jet falling under the effect of gravity continuously stretches while thinning downstream. We report here the effect of external periodic forcing on such a spatially varying jet in the jetting regime. Surprisingly, the optimal forcing frequency ...

Cambridge University Press2020

A Global-Local Approach For Detecting Hotspots In Multiple-Response Regression

Anthony Christopher Davison, Hélène Ruffieux, Jörg Hager

We tackle modelling and inference for variable selection in regression problems with many predictors and many responses. We focus on detecting hotspots, that is, predictors associated with several responses. Such a task is critical in statistical genetics, ...

INST MATHEMATICAL STATISTICS2020

HLA Heterozygote Advantage against HIV-1 Is Driven by Quantitative and Qualitative Differences in HLA Allele-Specific Peptide Presentation

Jacques Fellay

Pathogen-mediated balancing selection is regarded as a key driver of host immunogenetic diversity. A hallmark for balancing selection in humans is the heterozygote advantage at genes of the human leukocyte antigen (HLA), resulting in improved HIV-1 control ...

OXFORD UNIV PRESS2020

Canonical Notch signaling controls the early thymic epithelial progenitor cell state and emergence of the medullary epithelia lineage in fetal thymus development

Freddy Radtke, Ute Koch, Dong Liu

Thymus function depends on the epithelial compartment of the thymic stroma. Cortical thymic epithelial cells (cTECs) regulate T cell lineage commitment and positive selection, while medullary (m) TECs impose central tolerance on the T cell repertoire. Duri ...

2020

Gene expression across mammalian organ development

Maria del Carmen Sandi Perez, Ioannis Xenarios

The evolution of gene expression in mammalian organ development remains largely uncharacterized. Here we report the transcriptomes of seven organs (cerebrum, cerebellum, heart, kidney, liver, ovary and testis) across developmental time points from early or ...

2019

Linking a mutation to survival in wild mice

Jeffrey David Jensen, Matthieu Foll, Susanne Petra Pfeifer, Stefan Jean Laurent

Adaptive evolution in new or changing environments can be difficult to predict because the functional connections between genotype, phenotype, and fitness are complex. Here, we make these explicit connections by combining field and laboratory experiments i ...

American Association for the Advancement of Science2019

Tuning the Incorporation of Magnesium into Calcite during Its Crystallization from Additive-Free Aqueous Solution

Esther Amstad, Camelia Borca, Huachuan Du

Under ambient conditions, marine organisms are able to synthesize a variety of functional materials, ranging from eye lenses to protective shells through the meticulous control over magnesium incorporation into calcite during its crystallization. The mecha ...

AMER CHEMICAL SOC2019

A cell fitness selection model for neuronal survival during development

Gioele La Manno

Developmental cell death plays an important role in the construction of functional neural circuits. In vertebrates, the canonical view proposes a selection of the surviving neurons through stochastic competition for target-derived neurotrophic signals, imp ...

Nature Research2019

The Demographic History of African Drosophila melanogaster

Jeffrey David Jensen, Adamantia Kapopoulou, Susanne Petra Pfeifer, Stefan Jean Laurent

As one of the most commonly utilized organisms in the study of local adaptation, an accurate characterization of the demographic history of Drosophila melanogaster remains as an important research question. This owes both to the inherent interest in charac ...

OXFORD UNIV PRESS2018

Signatures of selection and environmental adaptation across the goat genome post-domestication

Stéphane Joost, Estelle Rochat

Background: Since goat was domesticated 10,000 years ago, many factors have contributed to the differentiation of goat breeds and these are classified mainly into two types: (i) adaptation to different breeding systems and/or purposes and (ii) adaptation t ...

2018

Computational and Statistical analyses of Molecular Evolution and Demography using Large-scale Sequencing Data

Adamantia Kapopoulou

Evolution can be described as the change of allele frequencies over time. Four forces - mutation, migration, genetic drift, and selection, drive this change. The aim of my thesis was to accurately estimate and differentiate the parameters governing each of ...

EPFL2018

Pattern formation in thin liquid films: from coating-flow instabilities to microfluidic droplets

Gioele Mariano Nicolò Balestra

Nature and technical applications abound with thin viscous flows, ranging from the lava flow on volcanoes to the lubricating layer around confined bubbles in the microchannels of Lab-on-a-Chip devices. Countless are the examples where coating flows arise i ...

EPFL2018

The corepressor NCOR1 regulates the survival of single-positive thymocytes

Johan Auwerx

Nuclear receptor corepressor 1 (NCOR1) is a transcriptional regulator bridging repressive chromatin modifying enzymes with transcription factors. NCOR1 regulates many biological processes, however its role in T cells is not known. Here we show that Cd4-Cre ...

Nature Research2017

Inferring the age and strength of mutations evolving under positive selection

Nicky Louise Ormond

A fundamental goal of population genetics is to determine and quantify the interplay of mutation, natural selection, genetic drift and migration in shaping allelic frequency changes that underpin evolution-ary change. In this dissertation, I present comput ...

EPFL2017