Vanessa Dumeaux

An agentic AI environment to support biomedical research in collaborative academic environments

The paper introduces Murmurent, an agentic AI environment that supports biomedical research collaboration by providing infrastructure, specialized agents, memory, traceability, SOP enforcement, and multi-user capacity.

Differential requirement for the Ire1 luminal domain in Candida albicans drug susceptibility and pathogenicity

This study shows that the luminal domain of Ire1 in C. albicans is critical for cell wall integrity, thermal stress, and virulence, while the transmembrane domain is sufficient for azole antifungal tolerance.

Distinct Ire1-driven transcriptional responses control morphogenesis in Candida albicans

This study identifies Ire1-driven transcriptional responses distinct from the canonical UPR in C. albicans, revealing HAC1-independent pathways and RIDD activity in morphogenesis.

Deep learning reveals functional archetypes in the adult human gut microbiome that underlie interindividual variability and confound disease signals

The paper uses deep learning to identify three functional archetypes in the adult human gut microbiome, revealing their roles in interindividual variability and disease associations.

Astrocytic Chromatin Remodeler ATRX Gates Hippocampal Memory Consolidation through Metabolic and Synaptic Regulation

This study shows that astrocytic ATRX loss leads to neuronal dysfunction and long-term memory deficits through metabolic and synaptic pathway dysregulation.

Generative and integrative modeling for transcriptomics with formalin fixed paraffin embedded material

The paper introduces PREFFECT, a probabilistic framework to improve analysis of FFPE-derived RNA-seq data by addressing transcript dropout and variance through generative models and graph attention mechanisms.

Mutational landscape of pure ductal carcinoma in situ and associations with disease prognosis and response to radiotherapy

This study identifies genetic alterations associated with recurrence and radiotherapy response in ductal carcinoma in situ using whole-exome sequencing and copy number analysis.

Paternal obesity alters the sperm epigenome and is associated with changes in the placental transcriptome and cellular composition

Paternal obesity alters sperm epigenetic marks at placenta-related genes and is linked to changes in placental gene expression and trophoblast cell composition.

Systemic and intrinsic functions of ATRX in glial cell fate and CNS myelination

This study shows that ATRX loss in oligodendrocyte progenitor cells causes myelination deficits and promotes astrocyte-like features, highlighting ATRX's role in myelination and glial cell fate.

Exposure of Greenlandic Inuit and South African VhaVenda men to the persistent DDT metabolite is associated with an altered sperm epigenome at regions implicated in paternal epigenetic transmission and developmental disease - a cross-sectional study

This study examines the association between p,p-DDE exposure and sperm epigenome alterations in Greenlandic Inuit and South African VhaVenda men, identifying potential impacts on future generations.

Sperm Histone H3 Lysine 4 tri-methylation serves as a metabolic sensor of paternal obesity and is associated with the inheritance of metabolic dysfunction

This study investigates how paternal obesity alters sperm histone methylation and its impact on offspring metabolic health across generations.

Atrx deletion in neurons leads to sexually-dimorphic dysregulation of miR-137 and spatial learning and memory deficits

This study shows that deleting Atrx in mouse forebrain neurons causes male-specific spatial memory deficits linked to miR-137 dysregulation and synaptic abnormalities.

Candida albicans exhibits distinct cytoprotective responses to anti-fungal drugs that facilitate the evolution of drug resistance

This study profiles single-cell transcriptomes of Candida albicans exposed to antifungal drugs to identify epigenetic responses linked to drug resistance evolution.

Reproducible Data Analysis Pipelines for Precision Medicine

The paper introduces a reproducible data analysis system for precision medicine, demonstrating its use in analyzing cancer genomic data.

Candidate SNP analyses integrated with mRNA expression and hormone levels reveal influence on mammographic density and breast cancer risk

The paper identifies SNPs associated with mammographic density and breast cancer risk by integrating SNP analyses with mRNA expression and hormone levels.

Building Applications For Interactive Data Exploration In Systems Biology

The paper presents a microservice-based framework for building interactive data exploration tools in systems biology, demonstrating it with a breast cancer transcriptional analysis web application.