Institut Pasteur

Workflow management systems and reproducible pipelines for Plasmodium falciparum genomic surveillance: tools, design principles and infrastructure challenges

Genomic data are increasingly leveraged to enable malaria genomic surveillance, with many teams now generating Plasmodium falciparum sequence data for routine analysis. However, downstream analysis remains dependent on ad-hoc scripts and local infrastructure. This reliance limits...

Proteoforms in Disease: Biomedical Applications of Top‐Down Proteomics

ABSTRACT The proteome is a dynamic landscape of proteoforms arising from genetic mutations, alternative splicing, and post‐translational modifications (PTMs), which collectively drive biological function and disease phenotypes. Mass spectrometry (MS)‐based proteomics has emerged...

Evolutionary Dynamics-Aware De Novo Design of a Thermostable NS1-Derived Diagnostic Protein for Yellow Fever Virus

Abstract Serological diagnosis of neglected arboviruses remains hindered by extensive intra-genus cross-reactivity, compromising both assay specificity and epidemiological accuracy. In this study, we focused on yellow fever virus (YFV) as a model system to design and validate a g...

Coupling of stable isotope probing and metagenomics reveals the diversity of viruses infecting formatotrophs during anaerobic digestion process

Abstract Background Viruses play a major role in regulating microbial community composition and activity, yet their diversity and host associations in anaerobic digestion (AD)—a complex biotechnological process converting organic waste into biogas—remain poorly characterized. Lin...

Delivery of multiple PspA fragments by CyaA toxoid induces broad protection against Streptococcus pneumoniae

Abstract Streptococcus pneumoniae is a leading cause of lower respiratory tract (LRT) infections and invasive pneumococcal diseases (IPD). Conjugate vaccines are effective against IPD and nasal colonization but offer coverage limited to serotypes included in the formulations. Pne...

ViroSeek: a viral detection pipeline for second-generation sequencing

Abstract Arbovirus emergences represent a rising public health issue and are exacerbated by climate change and globalization. Virome analysis has become a key approach for monitoring and managing infectious diseases, yet existing tools often remain technically complex and inacces...

A nationally representative One Health multi-pathogen serosurvey in Cambodia: study protocol for the RACSMEI mixed-methods study

Abstract Background Cambodia faces a high and complex burden of zoonotic, vector-borne, vaccine-preventable and environmentally transmitted infections, driven by intensive human–animal–environment interactions. However, nationally representative data integrating human, animal and...

Estimating differing causal roles of glutamate and GABA genes on brain and behavior in autism

Abstract The excitatory/inhibitory (E/I) imbalance theory suggests that excitatory and inhibitory alterations underlies autism characteristics. However, genetic underpinnings of this imbalance and its impact on brain function and behavior remains unclear. We explored causal links...

Constitutive natural killer cell features associated with post-treatment control of SIV infection in the pVISCONTI study

Abstract Post-treatment HIV controllers (PTC) offer a unique opportunity to uncover the determinants of durable remission after antiretroviral therapy (ART) interruption. Here, using six PTC and six post-treatment non-controllers from the pVISCONTI study in cynomolgus macaques, w...

Covalently Linked Peptides and Membrane Potential Enable CyaA Segment Translocation

The adenylate cyclase toxin (CyaA) from Bordetella pertussis intoxicates host cells by directly translocating its N-terminal catalytic domain across the plasma membrane; however, the forces driving this unique process remain poorly defined. Here, we dissect the membrane transloca...

A modern toolbox to elucidate the role of the human microbiome in modulating mycobacterial gut infections

Abstract Inflammatory bowel diseases (IBDs) are a major public and veterinary health concern, but the causes are poorly understood. In this review, we discuss the potential of mycobacteria as causative factors for such diseases. We focus on similarities between the most common hu...

European S2k guidelines for hidradenitis suppurativa/acne inversa Part 1. Epidemiology, diagnosis and clinical assessment

BACKGROUND: This first part of the S2k guidelines is an update of the 2015 S1 European guidelines based on the structured assessment of clinically relevant topics by the panel of experts. It is complemented by Part 2, which deals with treatments. OBJECTIVES: These guidelines aim...

The limitations of non-mechanistic methods for characterizing pathogen-pathogen interactions: A simulation study

Abstract Pathogen-pathogen interactions occur when infection with one pathogen influences one’s chance of infection or disease due to another. Increasingly, evidence suggests that interactions are a common feature of infectious disease epidemiology. However, due to both the nonli...

A network-driven antiviral discovery pipeline for emerging RNA viruses: a critical perspective from the Red Mexicana de Desarrollo de Antivirales (RMDA)

INTRODUCTION: RNA viruses impose a disproportionate burden of emerging and reemerging infectious diseases in Latin America, yet antiviral discovery in the region remains fragmented, target-limited, and frequently disconnected from translational pathways. This perspective discusse...

Nuclear activities and interactome of the NS5 protein of tick-borne encephalitis virus

Orthoflaviviruses are RNA viruses responsible for significant diseases in humans, domesticated animals, and wildlife. Their NS5 protein is central in viral replication, functioning both as an RNA-dependent RNA polymerase and a methyltransferase, while also modulating cellular pro...

Transient Cytoskeletal Anisotropy Encodes Short‐Term Mechanical Memory in Glioblastoma Cells

ABSTRACT Cells experience time‐varying mechanical cues when navigating complex microenvironments, yet whether and how they retain a short‐term memory of recent deformations remains unclear. Here, we show that glioblastoma cells encode such memory through transient cytoskeletal an...

Guidelines for Studying Mutagenesis in Quiescent Schizosaccharomyces pombe

All living organisms can enter a non-dividing state known as quiescence, which often functions as a survival strategy. In many cases, quiescent cells retain the ability to re-enter the cell cycle when conditions become favorable. Therefore, preserving the integrity of non-dividin...

Community engagement in epidemics – experiences from the SoNAR-Global COVID-19 vulnerability assessment

Since the largest outbreak of Ebola Virus Disease 2014–2016, the concept of community engagement (CE) gained popularity in global frameworks and strategies to tackle infectious disease. Recent studies suggest that CE might be a useful approach to understand and resolve vulnerabil...