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

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Cis-regulatory effect of HPV integration is constrained by host chromatin architecture in cervical cancers

Human papillomavirus (HPV) infections are the primary drivers of cervical cancers, and often HPV DNA gets integrated into the host genome. Although the oncogenic impact of HPV encoded genes is relatively well known, the cis-regulatory effect of integrated ...

Wiley2023

Leukocyte Count and Coronary Artery Disease Events in People With Human Immunodeficiency Virus: A Longitudinal Study

Jacques Fellay, Christian Axel Wandall Thorball

Leukocyte count is associated with coronary artery disease (CAD) events in the general population. Here we show that leukocytes are independently associated with CAD events in people with HIV in Switzerland, after adjusting for traditional and HIVrelated r ...

OXFORD UNIV PRESS INC2023

Inborn errors of type I interferon immunity in patients with symptomatic acute hepatitis E

Jacques Fellay

Background and Aims:The clinical spectrum of human infection by HEV ranges from asymptomatic to severe acute hepatitis. Furthermore, HEV can cause diverse neurological manifestations, especially Parsonage-Turner syndrome. Here, we used a large-scale human ...

Lippincott Williams & Wilkins2023

Energy-harnessing problem solving of primordial life: Modeling the emergence of catalytic host-nested parasite life cycles

Christian Iseli

All life forms on earth ultimately descended from a primordial population dubbed the last universal common ancestor or LUCA via Darwinian evolution. Extant living systems share two salient functional features, a metabolism extracting and transforming energ ...

2023

Genomics of Preaxostyla Flagellates Illuminates the Path Towards the Loss of Mitochondria

Marek Elias, Shweta Vinodrai Pipaliya

The notion that mitochondria cannot be lost was shattered with the report of an oxymonad Monocercomonoides exilis, the first eukaryote arguably without any mitochondrion. Yet, questions remain about whether this extends beyond the single species and how th ...

Public Library Science2023

Towards mouse genetic-specific RNA-sequencing read mapping

Maxime Jan, Ioannis Xenarios

Genetic variations affect behavior and cause disease but understanding how these variants drive complex traits is still an open question. A common approach is to link the genetic variants to intermediate molecular phenotypes such as the transcriptome using ...

2022

Phylogenetic estimation of the viral fitness landscape of HIV-1 set-point viral load

Jacques Fellay, Luca Ferretti

Set-point viral load (SPVL), a common measure of human immunodeficiency virus (HIV)-1 virulence, is partially determined by viral genotype. Epidemiological evidence suggests that this viral property has been under stabilising selection, with a typical opti ...

OXFORD UNIV PRESS2022

Using population-specific add-on polymorphisms to improve genotype imputation in underrepresented populations

Jacques Fellay, Zhi Ming Xu, Sina Rüeger

Genome-wide association studies rely on the statistical inference of untyped variants, called imputation, to increase the coverage of genotyping arrays. However, the results are often suboptimal in populations underrepresented in existing reference panels ...

Public Library Science2022

A Phylogeny-aware GWAS Framework to Correct for Heritable Pathogen Effects on Infectious Disease Traits

Jacques Fellay, Christian Axel Wandall Thorball

Infectious diseases are particularly challenging for genome-wide association studies (GWAS) because genetic effects from two organisms (pathogen and host) can influence a trait. Traditional GWAS assume individual samples are independent observations. Howev ...

OXFORD UNIV PRESS2022

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Leukocyte Count and Coronary Artery Disease Events in People With Human Immunodeficiency Virus: A Longitudinal Study

Jacques Fellay, Christian Axel Wandall Thorball

OXFORD UNIV PRESS INC2023

Cis-regulatory effect of HPV integration is constrained by host chromatin architecture in cervical cancers

Daniele Tavernari, Giovanni Ciriello

Wiley2023

Energy-harnessing problem solving of primordial life: Modeling the emergence of catalytic host-nested parasite life cycles

Christian Iseli

2023