Publications related to Allele frequency

Rigorous Assessment of Natural Frequencies of Fault-Originated Travelling Waves

Mario Paolone, Hamidreza Karami, Zhaoyang Wang, Pier Luigi Dragotti

This paper presents a rigorous assessment of natural frequencies associated with fault-originated travelling waves in power networks, factoring in the presence of multiple junctions and branches. The proposed assessment exploits the Baum-Liu-Tesche (BLT) e ...

2024

Back-to-Africa introductions of Mycobacterium tuberculosis as the main cause of tuberculosis in Dar es Salaam, Tanzania

Jacques Fellay, Zhi Ming Xu

In settings with high tuberculosis (TB) endemicity, distinct genotypes of the Mycobacterium tuberculosis complex (MTBC) often differ in prevalence. However, the factors leading to these differences remain poorly understood. Here we studied the MTBC populat ...

PUBLIC LIBRARY SCIENCE2023

Impact of population size on early adaptation in rugged fitness landscapes

Anne-Florence Raphaëlle Bitbol, Richard Marie Servajean

Owing to stochastic fluctuations arising from finite population size, known as genetic drift, the ability of a population to explore a rugged fitness landscape depends on its size. In the weak mutation regime, while the mean steady-state fitness increases ...

ROYAL SOC2023

A technique for non-intrusive greedy piecewise-rational model reduction of frequency response problems over wide frequency bands

Fabio Nobile, Davide Pradovera

In the field of model order reduction for frequency response problems, the minimal rational interpolation (MRI) method has been shown to be quite effective. However, in some cases, numerical instabilities may arise when applying MRI to build a surrogate mo ...

2022

Dynamics of entrapped microbubbles with multiple openings

Mahmut Selman Sakar, Murat Kaynak, Amit Yedidia Dolev

Microbubbles excited by acoustic fields inside water oscillate, and generate acoustic radiation forces and drag-induced acoustic streaming. These forces can be harnessed in various biomedical applications such as targeted drug delivery and on-chip biomanip ...

2022

Slow-fast Dynamics of Strongly Coupled Adaptive Frequency Oscillators

Auke Ijspeert, Jonas Buchli, Ludovic Righetti

Oscillators have two main limitations: their synchronization properties are limited (i.e., they have a finite synchronization region) and they have no memory of past interactions (i.e., they return to their intrinsic frequency whenever the entraining signa ...

SIAM PUBLICATIONS2021

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

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

Vibration Mode of MEMS Ultrasonic Sensors on Buckled Diaphragms with Piezoelectric Resonance Frequency Modification

Paul Muralt, Kaoru Yamashita

Vibration mode and resonance frequency of piezoelectric MEMS ultrasonic sensors was investigated on buckled diaphragm structures. The buckling of the diaphragms was introduced intrinsically through residual stress control of the piezoelectric film, and ext ...

IEEE2019

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

HIV Transmission Chains Exhibit Greater HLA-B Homogeneity Than Randomly Expected

Jacques Fellay, Christian Axel Wandall Thorball

Background: HIV's capacity to escape immune recognition by human leukocyte antigen (HLA) is a core component of HIV pathogenesis. A better understanding of the distribution of HLA class I in HIV-infected patients would improve our knowledge of pathogenesis ...

LIPPINCOTT WILLIAMS & WILKINS2019

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

The Combined Effect of Oseltamivir and Favipiravir on Influenza A Virus Evolution

Jeffrey David Jensen, Claudia Bank, Sebastian Matuszewski, Nicky Louise Ormond

Influenza virus inflicts a heavy death toll annually and resistance to existing antiviral drugs has generated interest in the development of agents with novel mechanisms of action. Favipiravir is an antiviral drug that acts by increasing the genome-wide mu ...

Oxford University Press (OUP)2017

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 population genomics of rapid adaptation: disentangling signatures of selection and demography in white sands lizards

Jeffrey David Jensen, Susanne Petra Pfeifer, Stefan Jean Laurent, Nicky Louise Ormond

Understanding the process of adaptation during rapid environmental change remains one of the central focal points of evolutionary biology. The recently formed White Sands system of southern New Mexico offers an outstanding example of rapid adaptation, with ...

Wiley-Blackwell2016

Detecting and Quantifying Changing Selection Intensities from Time-Sampled Polymorphism Data

Jeffrey David Jensen, Matthieu Foll, Sebastian Matuszewski, Hyunjin Shim, Stefan Jean Laurent

During his well-known debate with Fisher regarding the phenotypic dataset of Panaxia dominula, Wright suggested fluctuating selection as a potential explanation for the observed change in allele frequencies. This model has since been invoked in a number of ...

Genetics Society of America2016

An Approximate Markov Model for the Wright-Fisher Diffusion and Its Application to Time Series Data

Jeffrey David Jensen, Anna Ferrer Admetlla

The joint and accurate inference of selection and demography from genetic data is considered a particularly challenging question in population genetics, since both process may lead to very similar patterns of genetic diversity. However, additional informat ...

Genetics Society America2016

Inferring the age of a fixed beneficial allele

Jeffrey David Jensen, Matthieu Foll, Susanne Petra Pfeifer, Nicky Louise Ormond, Gregory Bruce Ewing

Estimating the age and strength of beneficial alleles is central to understanding how adaptation proceeds in response to changing environmental conditions. Several haplotype-based estimators exist for inferring the age of segregating beneficial mutations. ...

Wiley-Blackwell2016

Mitochondrial DNA Analyses Indicate High Diversity, Expansive Population Growth and High Genetic Connectivity of Vent Copepods (Dirivultidae) across Different Oceans

Stefan Jean Laurent

Communities in spatially fragmented deep-sea hydrothermal vents rich in polymetallic sulfides could soon face major disturbance events due to deep-sea mineral mining, such that unraveling patterns of gene flow between hydrothermal vent populations will be ...

Public Library of Science2016

Resonance in swirling wakes and sloshing waves : non-normal and sublinear effects

Francesco Viola

Similarly to mechanical structures, stable flows can exhibit resonance when perturbed by an impulsive or harmonic forcing. Swirling wakes and sloshing waves belong to this kind of flows and manifest large energy response when excited close to their natural ...

EPFL2016