Publications by Zhi Ming Xu | EPFL Graph Search

Genome-to-genome analysis reveals associations between human and mycobacterial genetic variation in tuberculosis patients from Tanzania

Jacques Fellay, Dylan Lawless, Olivier Noël Marie Naret, Sina Rüeger, Zhi Ming Xu

The risk and prognosis of tuberculosis (TB) are influenced by a complex interplay between human and bacterial genetic factors. While previous genomic studies have largely examined human and bacterial genomes separately, we adopted an integrated approach to ...

Springer Science and Business Media LLC2025

The impact of human genetics on Mycobacterium tuberculosis intra-host evolution

Jacques Fellay, Zhi Ming Xu

Springernature2024

Bacterial diversity dominates variable macrophage responses of tuberculosis patients in Tanzania

Jacques Fellay, Zhi Ming Xu

The Mycobacterium tuberculosis complex (MTBC) comprises nine human-adapted lineages that differ in their geographical distribution. Local adaptation of specific MTBC genotypes to the respective human host population has been invoked in this context. We aim ...

Nature Portfolio2024

EBNA-1 and VCA-p18 immunoglobulin markers link Epstein-Barr virus immune response and brain's myelin content to fatigue in a community-dwelling cohort

Jacques Fellay, Zhi Ming Xu

Given the association of Epstein-Barr virus (EBV) with subjective perception of fatigue and demyelination in clinical conditions, the question about potential subclinical effects in the adult general population remains open. We investigate the association ...

2024

Joint host-pathogen genomic analysis identifies hepatitis B virus mutations associated with human NTCP and HLA class I variation

Jacques Fellay, Dylan Lawless, Olivier Noël Marie Naret, Andreas Scheck, Zhi Ming Xu, Arne Schneuing

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 Press2024

Back-to-Africa introductions of Mycobacterium tuberculosis as the main cause of tuberculosis in Dar es Salaam, Tanzania

Jacques Fellay, Zhi Ming Xu

In settings with high tuberculosis (TB) endemicity, distinct genotypes of the Mycobacterium tuberculosis complex (MTBC) often differ in prevalence. However, the factors leading to these differences remain poorly understood. Here we studied the MTBC populat ...

PUBLIC LIBRARY SCIENCE2023

Viral Genetic Determinants of Prolonged Respiratory Syncytial Virus Infection Among Infants in a Healthy Term Birth Cohort

Thomas Junier, Jacques Fellay, Dylan Lawless, Zhi Ming Xu

Background. Respiratory syncytial virus (RSV) is associated with acute respiratory infection. We sought to identify RSV variants associated with prolonged infection. ...

OXFORD UNIV PRESS INC2023

Associations of genetic and infectious risk factors with coronary heart disease

Roxane De La Harpe, Jacques Fellay, Flavia Aurelia Shoko Hodel, Christian Axel Wandall Thorball, Zhi Ming Xu

Coronary heart disease (CHD) is one of the most pressing health problems of our time and a major cause of preventable death. CHD results from complex interactions between genetic and environmental factors. Using multiplex serological testing for persistent ...

eLIFE SCIENCES PUBL LTD2023

Host-Pathogen Interactions Through the Genomic Lens

Zhi Ming Xu

Hosts and pathogens are involved in a long-standing evolutionary arms race characterized by successive rounds of evolution. Specifically, while hosts evolve resistance against infections, pathogens adapt to re-establish virulence. Since the signatures of t ...

EPFL2023

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

Jacques Fellay, Sina Rüeger, Zhi Ming Xu

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

Improving polygenic prediction with genetically inferred ancestry

Jacques Fellay, Flavia Aurelia Shoko Hodel, Olivier Noël Marie Naret, Zhi Ming Xu

Genome-wide association studies (GWASs) have demonstrated that most common diseases have a strong genetic component from many genetic variants each with a small effect size. GWAS summary statistics have allowed the construction of polygenic scores (PGSs) e ...

ELSEVIER2022

Human genomics of the humoral immune response against polyomaviruses

Jacques Fellay, Flavia Aurelia Shoko Hodel, Christian Hammer, Petar Scepanovic, Christian Axel Wandall Thorball, Olivier Noël Marie Naret, Zhi Ming Xu

Human polyomaviruses are widespread in humans and can cause severe disease in immunocompromised individuals. To identify human genetic determinants of the humoral immune response against polyomaviruses, we performed genome-wide association studies and meta ...

OXFORD UNIV PRESS2021

Human genomics of the humoral response against polyomaviruses

Jacques Fellay, Flavia Aurelia Shoko Hodel, Christian Hammer, Petar Scepanovic, Christian Axel Wandall Thorball, Zhi Ming Xu

SPRINGERNATURE2020

Polygenic modelling of treatment effect heterogeneity

Zhi Ming Xu

Mendelian randomization is the use of genetic variants to assess the effect of intervening on a risk factor using observational data. We consider the scenario in which there is a pharmacomimetic (i.e., treatment-mimicking) genetic variant that can be used ...

2020

Genome-to-genome analysis identifies an Asian-specific variant in the gene encoding NTCP that leads to specific HBV escape mutations during chronic infection

Jacques Fellay, Sina Rüeger, Zhi Ming Xu

SPRINGERNATURE2020

A privacy-preserving solution for compressed storage and selective retrieval of genomic data

Jean-Pierre Hubaux, Adam Molyneaux, Jacques Fellay, Erman Ayday, Zhicong Huang, Huang Lin, Zhi Ming Xu

In clinical genomics, the continuous evolution of bioinformatic algorithms and sequencing platforms makes it beneficial to store patients' complete aligned genomic data in addition to variant calls relative to a reference sequence. Due to the large size of ...

Cold Spring Harbor Laboratory2016