Publications related to Neutral theory of molecular evolution

Variant-specific pathophysiological mechanisms of AFF3 differently influence transcriptome profiles

Giovanna Ambrosini, Nicolas Jean Philippe Guex, Christian Iseli

Background: We previously described the KINSSHIP syndrome, an autosomal dominant disorder associated with intellectual disability (ID), mesomelic dysplasia and horseshoe kidney,caused by de novo variants in the degron of AFF3. Mouse knock-ins and overexpre ...

BMC2024

Frequent asymmetric migrations suppress natural selection in spatially structured populations

Anne-Florence Raphaëlle Bitbol, Alia Abbara

Natural microbial populations often have complex spatial structures. This can impact their evolution, in particular the ability of mutants to take over. While mutant fixation probabilities are known to be unaffected by sufficiently symmetric structures, ev ...

Oxford Univ Press2023

Molecular reconstruction and simulation of the Neuron-Glia-Vasculature system

Polina Shichkova

The outstanding information processing capacity of the brain relies on numerous molecular mechanisms. It is an extremely energy-expensive function, which involves specialization and collaboration of different cell types. A common framework to study the com ...

EPFL2023

Hydrodynamic flow and concentration gradients in the gut enhance neutral bacterial diversity

Anne-Florence Raphaëlle Bitbol

The gut microbiota features important genetic diversity, and the specific spatial features of the gut may shape evolution within this environment. We investigate the fixation probability of neutral bacterial mutants within a minimal model of the gut that i ...

National Academy of Sciences2022

A self-consistent multi-component model of plasma turbulence and kinetic neutral dynamics for the simulation of the tokamak boundary

Paolo Ricci

A self-consistent model is presented for the simulation of a multi-component plasma in the tokamak boundary. A deuterium plasma is considered, with the plasma species that include electrons, deuterium atomic ions and deuterium molecular ions, while the deu ...

IOP Publishing Ltd2022

Population structure and signals of local adaptation in Eugenia uniflora (Myrtaceae), a widely distributed species in the Atlantic Forest

Elia Vajana

Evolutionary diversity in species can arise in many ways, including local adaptation. Despite the global importance of tropical forest ecosystems, few studies have explored patterns of local adaptation in tropical tree species. We investigated population g ...

OXFORD UNIV PRESS2022

Genomic consequences of colonisation, migration and genetic drift in barn owl insular populations of the eastern Mediterranean

Nicolas Jean Philippe Guex, Eléonore Lavanchy

The study of insular populations was key in the development of evolutionary theory. The successful colonisation of an island depends on the geographic context, and specific characteristics of the organism and the island, but also on stochastic processes. A ...

2022

Unexpected post‐glacial colonisation route explains the white colour of barn owls ( Tyto alba ) from the British Isles

Nicolas Jean Philippe Guex, Christian Iseli

The climate fluctuations of the Quaternary shaped the movement of species in and out of glacial refugia. In Europe, the majority of species followed one of the described traditional postglacial recolonization routes from the southern peninsulas towards the ...

2022

Protein language models trained on multiple sequence alignments learn phylogenetic relationships

Anne-Florence Raphaëlle Bitbol, Umberto Lupo, Damiano Sgarbossa

Self-supervised neural language models with attention have recently been applied to biological sequence data, advancing structure, function and mutational effect prediction. Some protein language models, including MSA Transformer and AlphaFold's EvoFormer, ...

Nature Portfolio2022

Studies of cold chemistry in crossed and merged neutral beams

Silvia Tanteri

In this thesis we present the design of two setups to study low-energy collisions between neutral species: an electron velocity map imaging for chemi-ionisation reactions and a merged electrostatic guide for polar molecules scattering. In the past few yea ...

EPFL2021

Rapid molecular evolution of Spiroplasma symbionts of Drosophila

Bruno Lemaitre, Florent François Masson

Spiroplasma is a genus of Mollicutes whose members include plant pathogens, insect pathogens and endosymbionts of animals. Spiroplasma phenotypes have been repeatedly observed to be spontaneously lost in Drosophila cultures, and several studies have docume ...

2021

Atomic data for the

Carmela Lardo

Context. We describe the atomic and molecular data that were used for the abundance analyses of FGK-type stars carried out within the Gaia-ESO Public Spectroscopic Survey in the years 2012 to 2019. The Gaia-ESO Survey is one among several current and futur ...

EDP SCIENCES S A2021

Self-consistent simulation of multi-component plasma turbulence and neutral dynamics in the tokamak boundary

André Calado Coroado

The interaction between neutral particles and the plasma plays a key role in determining the dynamics of the tokamak boundary that, in turn, significantly impact the overall performance of the device. Leveraging the work in Wersal and Ricci [Nucl. Fusion 5 ...

EPFL2021

Resist or perish: Fate of a microbial population subjected to a periodic presence of antimicrobial

Anne-Florence Raphaëlle Bitbol, Loïc Marrec

The evolution of antimicrobial resistance can be strongly affected by variations of antimicrobial concentration. Here, we study the impact of periodic alternations of absence and presence of antimicrobial on resistance evolution in a microbial population, ...

2020

Feature Learning of Virus Genome Evolution With the Nucleotide Skip-Gram Neural Network

Hyunjin Shim

Recent studies reveal that even the smallest genomes such as viruses evolve through complex and stochastic processes, and the assumption of independent alleles is not valid in most applications. Advances in sequencing technologies produce multiple time-poi ...

2019

Ultrafast nuclear dynamics of the acetylene cation C2H2+ and its impact on the infrared probe pulse induced C-H bond breaking efficiency

Ursula Röthlisberger, Swarnendu Bhattacharyya

The ultrafast nuclear dynamics of the acetylene cation C2H2+ following photoionization of the neutral molecule is investigated using an extreme-ultraviolet pump/infrared probe setup. The observed modulation of the C2H+ fragment ion yield with pump-probe de ...

2019

Allele-specific gene editing prevents deafness in a model of dominant progressive hearing loss

Bernard Schneider, Paola Andrea Solanes Vega, Sofia Carmen Suzanne Spataro

Since most dominant human mutations are single nucleotide substitutions(1,2), we explored gene editing strategies to disrupt dominant mutations efficiently and selectively without affecting wild-type alleles. However, single nucleotide discrimination can b ...

NATURE PUBLISHING GROUP2019

Population structure determines the tradeoff between fixation probability and fixation time

Andreas Pavlogiannis

The rate of biological evolution depends on the fixation probability and on the fixation time of new mutants. Intensive research has focused on identifying population structures that augment the fixation probability of advantageous mutants. But these ampli ...

Springer2019

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

Likelihood-free Inference of Population Genetic Parameters from Time-Sampled Genetic Data

Hyunjin Shim

This thesis consists of five papers published in peer-reviewed journals, two of which focus on method development of time-serial inference, represented by publications in methodology journals, and three others that describe collaborative data applications ...

EPFL2018