Publications related to Linkage disequilibrium

The HLA-B*57:01 allele corresponds to a very large MHC haploblock likely explaining its massive effect for HIV-1 elite control

Introduction: We have reanalyzed the genomic data of the International Collaboration for the Genomics of HIV (ICGH), centering on HIV-1 Elite Controllers.Methods: We performed a genome-wide Association Study comparing 543 HIV Elite Controllers with 3,272 u ...

Frontiers Media Sa2023

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

C-shells: Deployable Gridshells with Curved Beams

Mark Pauly, Seiichi Eduardo Suzuki Erazo, Quentin Christian Becker, Yingying Ren, Francis Julian Panetta, Davide Pellis

We introduce a computational pipeline for simulating and designing C-shells, a new class of planar-to-spatial deployable linkage structures. A C-shell is composed of curved flexible beams connected at rotational joints that can be assembled in a stress-fre ...

2023

Systematic screening of viral and human genetic variation identifies antiretroviral resistance and immune escape link

Jacques Fellay, Christian Axel Wandall Thorball

Background: Considering the remaining threat of drug-resistantmutations (DRMs) to antiretroviral treatment (ART) efficacy, we investigated how the selective pressure of human leukocyte antigen (HLA)-restricted cytotoxic T lymphocytes drives certain DRMs' e ...

2021

Method of encoding a 3d shape into a 2d surface

Mark Pauly, Mina Konakovic Lukovic, Francis Julian Panetta

The present invention concerns a method for encoding a given 3D shape into a target 2D linkage. The method comprises: (a) providing an initial 2D surface; and (b) defining on the initial 2D surface an auxetic pattern of geometric elements planarly linked b ...

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

Genome-wide gene-based analyses of weight loss interventions identify a potential role for NKX6.3 in metabolism

Patrick Descombes, Hélène Ruffieux, Sylviane Métairon, Jörg Hager, Nele Gheldof

Hundreds of genetic variants have been associated with Body Mass Index (BMI) through genome-wide association studies (GWAS) using observational cohorts. However, the genetic contribution to efficient weight loss in response to dietary intervention remains ...

Springer2019

Limits and patterns of cytomegalovirus genomic diversity in humans

Jeffrey David Jensen, Cornelia Pokalyuk

Human cytomegalovirus (HCMV) exhibits surprisingly high genomic diversity during natural infection although little is known about the limits or patterns of HCMV diversity among humans. To address this deficiency, we analyzed genomic diversity among congeni ...

National Academy of Sciences2015

Adaptations to Climate-Mediated Selective Pressures in Sheep

Stéphane Joost, Sylvie Stucki

Following domestication, sheep (Ovis aries) have become essential farmed animals across the world through adaptation to a diverse range of environments and varied production systems. Climate-mediated selective pressure has shaped phenotypic variation and h ...

Oxford Univ Press2014

Single locus of control in a tangible paper-based tabletop application: An Exploratory Study

Pierre Dillenbourg, Luis Pablo Prieto Santos, Daniela Caballero Díaz, Yun Wen

Multiple loci of control is one of the main affordances of tangible tabletop UIs due to their capability for simultaneous manipulation. However, there is a tension between the efficiency given by simultaneous manipulation and the need to coordinate and ref ...

ACM2014

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

Genetic interplay between HLA-C and MIR148A in HIV control and Crohn disease

Jacques Fellay, Paul Jack Mc Laren

Variation in the 3' untranslated region (3'UTR) of the HLA-C locus determines binding of the microRNA Hsa-miR-148a, resulting in lower cell surface expression of alleles that bind miR-148a relative to those alleles that escape its binding. The HLA-C 3'UTR ...

National Academy of Sciences2013

Influence of HLA-C Expression Level on HIV Control

Jacques Fellay, Paul Jack Mc Laren

A variant upstream of human leukocyte antigen C (HLA-C) shows the most significant genome-wide effect on HIV control in European Americans and is also associated with the level of HLA-C expression. We characterized the differential cell surface expression ...

American Association for the Advancement of Science2013

Rapid Intrahost Evolution of Human Cytomegalovirus Is Shaped by Demography and Positive Selection

Jeffrey David Jensen

Populations of human cytomegalovirus (HCMV), a large DNA virus, are highly polymorphic in patient samples, which may allow for rapid evolution within human hosts. To understand HCMV evolution, longitudinally sampled genomic populations from the urine and p ...

Public Library of Science2013

Theoretical and Experimental Studies of Dendritic Metacommunities

Francesco Carrara

The present thesis deals with the understanding of the origins and the mechanisms of maintenance of biodiversity in natural landscapes, in particular by identifying key processes that define large-scale patterns of abundance and diversity. Biological commu ...

EPFL2013

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

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

Inference about the number of contributors to a DNA mixture: Comparative analyses of a Bayesian network approach and the maximum allele count method

Kjell Konis

In the forensic examination of DNA mixtures, the question of how to set the total number of contributors (N) presents a topic of ongoing interest. Part of the discussion gravitates around issues of bias, in particular when assessments of the number of cont ...

Elsevier2012

Return mobility and scientific productivity of researchers working abroad: The role of home country linkages

Stefano Horst Baruffaldi

Through an analysis of 497 foreign researchers in Italy and Portugal we verify the impact of home linkages on return mobility choices and scientific productivity. We consider the presence of several different types of linkages of the researchers working ab ...

Elsevier Science Bv2012

Clinical and genetic investigation of a large Tunisian family with complete achromatopsia: identification of a new nonsense mutation in GNAT2 gene

Farah Ouechtati

Complete achromatopsia is a rare autosomal recessive disease associated with CNGA3, CNGB3, GNAT2 and PDE6C mutations. This retinal disorder is characterized by complete loss of color discrimination due to the absence or alteration of the cones function. Th ...

2011