Publications associées à Haplotype

Rapid molecular evolution of Spiroplasma symbionts of Drosophila

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

Ultrafast homomorphic encryption models enable secure outsourcing of genotype imputation

Jean-Pierre Hubaux, Juan Ramón Troncoso-Pastoriza, David Jules Froelicher, Jean-Philippe Léonard Bossuat, Yiping Ma

Genotype imputation is a fundamental step in genomic data analysis, where missing variant genotypes are predicted using the existing genotypes of nearby "tag"variants. Although researchers can outsource genotype imputation, privacy concerns may prohibit ge ...

CELL PRESS2021

A high-resolution HLA reference panel capturing global population diversity enables multi-ancestry fine-mapping in HIV host response

Jacques Fellay, John Wilson, Yang Luo, Xinyi Li

A high-resolution reference panel based on whole-genome sequencing data enables accurate imputation of HLA alleles across diverse populations and fine-mapping of HLA association signals for HIV-1 host response. ...

NATURE PORTFOLIO2021

Multi-omics reveals abundant mitochondrial genomic and circadian expression variation in the Drosophila Genetic Reference Panel

Maria Litovchenko

Modern biology rapidly generates a wealth of data,which can only be analysed computationally.Despite the variety of available data types,most of them aim to provide an answer to one question: how does genotypic diversity translates into phenotypes? This qu ...

EPFL2020

Mitochondrial haplotypes affect metabolic phenotypes in the Drosophila Genetic Reference Panel

Johan Auwerx, Bart Deplancke, Virginie Sandra Braman, Adamantia Kapopoulou, Maria Litovchenko, Brian Dennis Hollis, Roel Paulus Josephus Bevers

The nature and extent of mitochondrial DNA variation in a population and how it affects traits is poorly understood. Here we resequence the mitochondrial genomes of 169 Drosophila Genetic Reference Panel lines, identifying 231 variants that stratify along ...

2019

Discoidin domain receptor 1 gene variants are associated with decreased white matter fractional anisotropy and decreased processing speed in schizophrenia

Erick Jorge Canales Rodriguez

DDR1 has been linked to schizophrenia (SZ) and myelination. Here, we tested whether DDR1 variants in people at risk for SZ influence white matter (WM) structural variations and cognitive processing speed (PS). First, following a case-control design (Study ...

2019

The phenotypic impact of naturally occurring genetic and molecular mitochondrial variation in a Drosophila Genetic Reference Population

Roel Paulus Josephus Bevers

Genome-wide association (GWA) studies aim to dissect the relationship between genotype and phenotype. So far, the focus has been on nuclear genetic determinants as variation in the mitochondrial genome is often low in the study cohorts. Despite this observ ...

EPFL2018

High performance computation of landscape genomic models including local indicators of spatial association

Stéphane Joost, Sylvie Stucki, Pierre Taberlet, Solange Catherine Gaillard

With the increasing availability of both molecular and topo-climatic data, the main challenges facing landscape genomics — i.e. the combination of landscape ecology with population genomics — include processing large numbers of models and distinguishing be ...

Wiley-Blackwell2017

On the Analysis of Intrahost and Interhost Viral Populations: Human Cytomegalovirus as a Case Study of Pitfalls and Expectations

Jeffrey David Jensen, Sebastian Matuszewski, Susanne Petra Pfeifer

Intrahost and interhost assessments of viral diversity are often treated as measures of separate and distinct evolutionary processes, with numerous investigations reporting seemingly incompatible results between the two. For example, in human cytomegalovir ...

American Society for Microbiology2017

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

The Impact of Linked Selection in Chimpanzees: A Comparative Study

Jeffrey David Jensen, Susanne Petra Pfeifer

Levels of nucleotide diversity vary greatly across the genomes of most species owing to multiple factors. These include variation in the underlying mutation rates, as well as the effects of both direct and linked selection. Fundamental to interpreting the ...

Oxford University Press (OUP)2016

On Detecting Incomplete Soft or Hard Selective Sweeps Using Haplotype Structure

Anna Ferrer Admetlla

We present a new haplotype-based statistic (nS(L)) for detecting both soft and hard sweeps in population genomic data from a single population. We compare our new method with classic single-population haplotype and site frequency spectrum (SFS)-based metho ...

Oxford Univ Press2014

Personal receptor repertoires: olfaction as a model

Sebastian Martin Waszak

Background: Information on nucleotide diversity along completely sequenced human genomes has increased tremendously over the last few years. This makes it possible to reassess the diversity status of distinct receptor proteins in different human individual ...

BioMed Central2012

COI gene reveals size-dependent high dispersal and low intra-specific diversity in free-living terrestrial protists (Euglyphida; Assulina)

Edward Mitchell, Enrique Lara, Thierry Jean Heger

Aim Propagule size and ecological requirements are believed to be major factors influencing the passive dispersal of free-living terrestrial protists. We compared the colonization potential of three closely related testate amoeba species (Assulina muscoru ...

Wiley-Blackwell2011

Visual backward masking deficits in schizophrenic patients are associated with polymorphisms in the nicotinic receptor α7 subunit gene (CHRNA7)

Michael Herzog, Maya Roinishvili

Visual backward masking (BM) deficits are often proposed to be trait markers for schizophrenia revealing the genetic underpinnings of the disease. Here, we show that, indeed, masking deficits in the shine-through effect are associated with polymorphisms in ...

2010

Comparative genomic and phylogeographic analysis of Mycobacterium leprae

Stewart Cole, Jacques Rougemont, Pushpendra Singh, Philippe Busso, Alexandre Gattiker

Reductive evolution and massive pseudogene formation have shaped the 3.31-Mb genome of Mycobacterium leprae, an unculturable obligate pathogen that causes leprosy in humans. The complete genome sequence of M. leprae strain Br4923 from Brazil was obtained b ...

2009