Publications by Jacques Fellay

Deciphering the Foundations of Mitochondrial Mutational Spectra: Replication-Driven and Damage-Induced Signatures Across Chordate Classes

Mitochondrial DNA (mtDNA) mutagenesis remains poorly understood despite its crucial role in disease, aging, and evolutionary tracing. In this study, we reconstructed a comprehensive 192-component mtDNA mutational spectrum for chordates by analyzing 118,397 ...

OXFORD UNIV PRESS2025

Types of Myocardial Infarction in People with HIV in Switzerland

Jacques Fellay

Background Of myocardial infarctions (MI) recorded in two large HIV observational studies from North America, approximately half were classified as type 2. In the REPRIEVE clinical trial of pitavastatin vs. placebo in people with HIV (<3% of participant ...

Oxford University Press (OUP)2025

Leukocyte Count and New-onset Diabetes Mellitus in People with Hiv: a Longitudinal Study

Jacques Fellay

Objectives: The risk of diabetes mellitus (DM) is increased in people with HIV. Chronic inflammation contributes to DM risk. High leukocytes are associated with DM in the general population, but in people with HIV, evidence of a leukocyte-DM association is ...

WILEY2025

Granulysin Antimicrobial Activity Promotes Dormancy in Mycobacterium tuberculosis

Jacques Fellay

Human tuberculosis (TB) caused by Mycobacterium tuberculosis (Mtb) remains a global public health threat. Granulomas constitute a hallmark of TB pathogenesis that can clear, contain, or exacerbate an infection. Containment is exploited by Mtb as a hideout ...

2025

Decoding the Interactions and Functions of Non-coding Rna with Artificial Intelligence

Pascal Frossard, Jacques Fellay, Vincent Jung

In addition to encoding proteins, mRNAs have context-specific regulatory roles that contribute to many cellular processes. However, uncovering new mRNA functions is constrained by limitations of traditional biochemical and computational methods. In this Ro ...

NATURE PORTFOLIO2025

Proteome-wide prediction of the mode of inheritance and molecular mechanisms underlying genetic diseases using structural interactomics

Jacques Fellay

Genetic diseases can be classified according to their modes of inheritance and their underlying molecular mechanisms. Autosomal dominant disorders often result from DNA variants that cause loss-of-function, gain-of-function, or dominant-negative effects, w ...

Elsevier BV2025

Fine-tuning protein language models to understand the functional impact of missense variants

Jacques Fellay

Elucidating the functional effects of missense variants is crucial yet challenging. To investigate their impact, we fine-tuned protein language models, including ESM2 and ProtT5, to classify 20 protein features at amino acid resolution. In addition, we tra ...

2025

Low Trauma Fractures in People with Hiv: Longitudinal Time Trends in the Swiss Hiv Cohort Study, 2009-2022

Jacques Fellay, Christian Axel Wandall Thorball

Background People with human immunodeficiency virus (HIV) are at increased risk of low trauma fractures (LTFs). Published data on LTF incidence trends over time have not been uniform. This study sought to analyze LTF time trends in the Swiss HIV Cohort Stu ...

OXFORD UNIV PRESS INC2025

Enhanced TLR7-dependent production of type I interferon by pDCs underlies pandemic chilblains

Jacques Fellay

Outbreaks of chilblains were reported during the COVID-19 pandemic. Given the essential role of type I interferon (I-IFN) in protective immunity against SARS-CoV-2 and the association of chilblains with inherited type I interferonopathies, we hypothesized ...

ROCKEFELLER UNIV PRESS2025

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

Structure-based metabolite function prediction using graph neural networks

Jacques Fellay

Being able to broadly predict the function of novel metabolites based on their structures has applications in systems biology, environmental monitoring and drug discovery. To date, machine learning models aiming to predict functional characteristics of met ...

Oxford University Press (OUP)2025

HIV-phyloTSI: subtype-independent estimation of time since HIV-1 infection for cross-sectional measures of population incidence using deep sequence data

Jacques Fellay

Background Estimating the time since HIV infection (TSI) at population level is essential for tracking changes in the global HIV epidemic. Most methods for determining TSI give a binary classification of infections as recent or non-recent within a window o ...

Springer Science and Business Media LLC2025

Polygenic Risk Scores for Type 2 Diabetes in the Swiss HIV Cohort Study

Jacques Fellay, Christian Axel Wandall Thorball

Background.Type 2 diabetes (T2D) is among the most frequent comorbidities in people with HIV (PWH) and occurs more often in PWH than in people without HIV. Polygenic risk scores (PRS) can be used to summarize the genetic risk for T2D, but it is unknown to ...

Ovid Technologies (Wolters Kluwer Health)2025

Smoking changes adaptive immunity with persistent effects

Jacques Fellay

Individuals differ widely in their immune responses, with age, sex and genetic factors having major roles in this inherent variability1–6. However, the variables that drive such differences in cytokine secretion—a crucial component of the host response to ...

2024

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

Jacques Fellay, Zhi Ming Xu

Springernature2024

SARS-CoV-2 brainstem encephalitis in human inherited DBR1 deficiency

Jacques Fellay

Inherited deficiency of the RNA lariat–debranching enzyme 1 (DBR1) is a rare etiology of brainstem viral encephalitis. The cellular basis of disease and the range of viral predisposition are unclear.We report inherited DBR1 deficiency in a 14-year-old boyw ...

2024

Prevalence of clonal hematopoiesis in people living with HIV

Jacques Fellay, Konstantin Popadin, Valeriia Timonina

Springernature2024

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

Jacques Fellay

Springernature2024

Self-reported neurocognitive complaints in the Swiss HIV Cohort Study: a viral genome-wide association study

Jacques Fellay

People with HIV may report neurocognitive complaints, with or without associated neurocognitive impairment, varying between individuals and populations. While the HIV genome could play a major role, large systematic viral genome-wide screens to date are la ...

OXFORD UNIV PRESS2024

A common NFKB1 variant detected through antibody analysis in UK Biobank predicts risk of infection and allergy

Jacques Fellay, Flavia Aurelia Shoko Hodel

Infectious agents contribute significantly to the global burden of diseases through both acute infection and their chronic sequelae. We leveraged the UK Biobank to identify genetic loci that influence humoral immune response to multiple infections. From 45 ...

2024