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Concept

Constructive neutral evolution

Related publications (17)

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

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

Genetic signatures of divergent selection in European beech (Fagus sylvatica L.) are associated with the variation in temperature and precipitation across its distribution range

Elia Vajana

High genetic variation and extensive gene flow may help forest trees with adapting to ongoing climate change, yet the genetic bases underlying their adaptive potential remain largely unknown. We investigated range-wide patterns of potentially adaptive gene ...

WILEY2021

On the relative roles of background selection and genetic hitchhiking in shaping human cytomegalovirus genetic diversity

Jeffrey David Jensen

A central focus of population genetics has been examining the contribution of selective and neutral processes in shaping patterns of intraspecies diversity. In terms of selection specifically, surveys of higher organisms have shown considerable variation i ...

Wiley-Blackwell2016

The Characteristics of Heterozygous Protein Truncating Variants in the Human Genome

Jacques Fellay, Paul Jack Mc Laren, Istvan Bartha, Nimisha Chaturvedi

Sequencing projects have identified large numbers of rare stop-gain and frameshift variants in the human genome. As most of these are observed in the heterozygous state, they test a gene's tolerance to haploinsufficiency and dominant loss of function. We a ...

Public Library Science2015

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

Unraveling Patterns of Site-to-Site Synonymous Rates Variation and Associated Gene Properties of Protein Domains and Families

Slavica Dimitrieva Janeva

In protein-coding genes, synonymous mutations are often thought not to affect fitness and therefore are not subject to natural selection. Yet increasingly, cases of non-neutral evolution at certain synonymous sites were reported over the last decade. To ev ...

Public Library of Science2014

Inferring the Evolutionary History of Primate microRNA Binding Sites: Overcoming Motif Counting Biases

Jeffrey David Jensen

The first microRNAs (miRNAs) were identified as essential, conserved regulators of gene expression, targeting the same genes across nearly all bilaterians. However, there are also prominent examples of conserved miRNAs whose functions appear to have shifte ...

Oxford Univ Press2014

Robust Demographic Inference from Genomic and SNP Data

Matthieu Foll

We introduce a flexible and robust simulation-based framework to infer demographic parameters from the site frequency spectrum (SFS) computed on large genomic datasets. We show that our composite-likelihood approach allows one to study evolutionary models ...

Public Library of Science2013

A transcript perspective on evolution

Bernard Moret, Yann Christinat

Alternative splicing is now recognized as a major mechanism for transcriptome and proteome diversity in higher eukaryotes, yet its evolution is poorly understood. Most studies focus on the evolution of exons and introns at the gene level, while only few co ...

Ieee Computer Soc2013

CMA-ES with Restarts for Solving CEC 2013 Benchmark Problems

Ilya Loshchilov

This paper investigates the performance of 6 versions of Covariance Matrix Adaptation Evolution Strategy (CMAES) with restarts on a set of 28 noiseless optimization problems (including 23 multi-modal ones) designed for the special session on real-parameter ...

2013

Evidence Of Adaptation From Ancestral Variation In Young Populations Of Beach Mice

Jeffrey David Jensen

To understand how organisms adapt to novel habitats, which involves both demographic and selective events, we require knowledge of the evolutionary history of populations and also selected alleles. There are still few cases in which the precise mutations ( ...

Wiley-Blackwell2012

Inferring transcript phylogenies

Bernard Moret, Yann Christinat

Alternative splicing, an unknown mechanism 20 years ago, is now recognized as a major mechanism for proteome and transcriptome diversity, particularly in mammals-some researchers conjecture that up to 90% of human genes are alternatively spliced. Despite m ...

IEEE Press2011

Does Positive Selection Drive Transcription Factor Binding Site Turnover? A Test with Drosophila Cis-Regulatory Modules

Sebastian Maerkl

Transcription factor binding site(s) (TFBS) gain and loss (i.e., turnover) is a well-documented feature of cis-regulatory module (CRM) evolution, yet little attention has been paid to the evolutionary force(s) driving this turnover process. The predominant ...

Public Library of Science2011

The Interplay between Cytidine Deaminases, HIV and Domesticated Genetic Parasites

"There is more virus in us than us in us". John Coffin's famous sentence illustrates that particular nucleic acid sequences related to exogenous viruses, called retrotransposons, constitute almost half of the human genome and largely exceeds the amount of ...

EPFL2010

Physical constraints affecting bacterial habitats and activity in unsaturated porous media – a review

Dani Or

The immense diversity of microbial life found in the vadose zone reflects the extremely heterogeneous and highly dynamic aquatic and chemical environments formed within soil pore spaces. The notion of planktonian free swimming microbes is unrealistic under ...

2007

A DMSO-sensitive conditional mutant of the fission yeast orthologue of the Saccharomyces cerevisiae SEC13 gene is defective in septation

Viesturs Simanis

Dissection of complex processes using model organisms such as yeasts relies heavily upon the use of conditional mutants. We have generated a collection of fission yeast mutants sensitive to dimethylsulphoxide (DMSO). Among these we have found a mutant in t ...

2002