Publication
GuavaH: a compendium of host genomic data in HIV biology and disease
Publications associées (187)
Comparison of Three Viral Nucleic Acid Preamplification Pipelines for Sewage Viral Metagenomics
Tamar Kohn, Xavier Fernandez Cassi
Viral metagenomics is a useful tool for detecting multiple human viruses in urban sewage. However, more refined protocols are required for its effective use in disease surveillance. In this study, we investigated the performance of three different preampli ...
2024Joint host-pathogen genomic analysis identifies hepatitis B virus mutations associated with human NTCP and HLA class I variation
Jacques Fellay, Bruno Emanuel Ferreira De Sousa Correia, Zhi Ming Xu, Andreas Scheck, Dylan Lawless, Olivier Noël Marie Naret, Arne Schneuing, David Gfeller, Thomas Junier, Sina Rüeger
Evolutionary changes in the hepatitis B virus (HBV) genome could reflect its adaptation to host -induced selective pressure. Leveraging paired human exome and ultra -deep HBV genome-sequencing data from 567 affected individuals with chronic hepatitis B, we ...
Cell Press2024The 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 ...
Lausanne2023Modeling, analysis, and design of complex biological networks
Automating experimental procedures has resulted in an unprecedented increase in the volume of generated data, which, in turn, has caused an accumulation of unprocessed data. As a result, the need to develop tools to analyze data systematically has been ris ...
EPFL2023PSGL-1 is an evolutionarily conserved antiviral restriction factor
The arms race between viruses and their hosts shaped the evolutionary history and the genome composition of both parties. Restriction factors are the first-line antiviral effectors encoded by the host genomes and are often conserved through evolution to pr ...
AMER SOC MICROBIOLOGY2023Viral Genetic Determinants of Prolonged Respiratory Syncytial Virus Infection Among Infants in a Healthy Term Birth Cohort
Jacques Fellay, Zhi Ming Xu, Dylan Lawless, Thomas Junier
Background. Respiratory syncytial virus (RSV) is associated with acute respiratory infection. We sought to identify RSV variants associated with prolonged infection. Methods. Among healthy term infants we identified those with prolonged RSV infection and c ...
OXFORD UNIV PRESS INC2023Association of a Polygenic Risk Score With Osteoporosis in People Living With HIV: The Swiss HIV Cohort Study
Jacques Fellay, Christian Axel Wandall Thorball
An individual polygenic risk score was associated with osteoporosis in people living with HIV. The genetic effect was robust, as it persisted after multivariable adjustment for established traditional and HIV-related osteoporosis risk factors, including te ...
OXFORD UNIV PRESS INC2023Epigenetic ageing accelerates before antiretroviral therapy and decelerates after viral suppression in people with HIV in Switzerland: a longitudinal study over 17 years
Jacques Fellay, Christian Axel Wandall Thorball
Background Accelerated epigenetic ageing can occur in untreated HIV infection and is partially reversible with effective antiretroviral therapy (ART). We aimed to make a long-term comparison of epigenetic ageing dynamics in people with HIV during untreated ...
ELSEVIER2023KRAB zinc-finger proteins and their transposable element targets: between antagonism and cooperation
Jonas Caspar De Tribolet-Hardy
There are 377 Krüppel-associated box (KRAB) domain-containing zinc finger proteins (KZFPs) in the human genome, making them the largest family of transcription factors. KZFPs are defined by a N-terminal KRAB domain and several zinc-finger domains arranged ...
EPFL2022Using 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 ...
San Francisco2022