Scientist - Bioinformatics

A Bayesian approach to differential prevalence analysis with applications in microbiome studies

How I recovered from a collaboration gone wrong

Host-specific microbiome and genomic signatures in Bifidobacterium reveal co-evolutionary and functional adaptations across diverse animal hosts

Ten species comprise half of the bacteriology literature, leaving most species unstudied

Impact of early life antibiotic and probiotic treatment on gut microbiome and resistome of very-low-birth-weight preterm infants

Functional and evolutionary significance of unknown genes from uncultivated taxa

Ecological factors that drive microbial communities in culturally diverse fermented foods https://www.biorxiv.org/content/10.1101/2024.08.20.608727v1

Paternal and induced gut microbiota seeding complement mother-to-infant transmission

Introduction

Quantifying the daily harvest of fermentation products from the human gut microbiota https://www.biorxiv.org/content/10.1101/2024.01.05.573977v1

'Stickiness' of rarity and the universal dance of dominance

PNAS

Vaginal Lactobacillus fatty acid response mechanisms reveal a novel strategy for bacterial vaginosis treatment https://www.biorxiv.org/content/10.1101/2023.12.30.573720v1

Exposure and resistance to lantibiotics impact microbiota composition and function https://www.biorxiv.org/content/10.1101/2023.12.30.573728v1

Automate microbiome analysis - Automate Microbiome Analysis Using Quarto

Pre‐vaccination immunotypes reveal weak and robust antibody responders to influenza vaccination

Metabolic profiling of petroleum-degrading microbial communities incubated under high-pressure condi...

A catalogue of small proteins from the global microbiome https://www.biorxiv.org/content/10.1101/2023.12.27.573469v1

Benchmarking A Novel Quantitative PCR-based Microbiome Profiling Platform Against Sequencing-based Methods https://www.biorxiv.org/content/10.1101/2023.12.27.573468v1

Bacteroidia and Clostridia perform a progressive cascade of polysaccharide degradation along the hindgut of the herbivorous fish Kyphosus sydneyanus https://www.biorxiv.org/content/10.1101/2023.12.23.570891v1

Evolutionary “Crowdsourcing”: Alignment of Fitness Landscapes Allows for Cross-species Adaptatio...

Gender inequality in cum laude distinctions for PhD students - Scientific Reports

A diet-dependent host metabolite shapes the gut microbiota to protect from autoimmunity

Phylogenetic diversity of the carbon monoxide-utilizing prokaryotes and their divergent carbon monoxide metabolisms in the human gut microbiome https://www.biorxiv.org/content/10.1101/2023.10.23.563559v1

nf-core/taxprofiler: highly parallelised and flexible pipeline for metagenomic taxonomic classificat...

Four functional profiles for fibre and mucin metabolism in the human gut microbiome - Microbiome

Diurnal rhythmicity of fecal microbiota and metabolite profiles in the first year of life: a randomized controlled interventional trial with infant formula https://www.biorxiv.org/content/10.1101/2023.10.19.563092v1

Mechanism of 2-Fucosyllactose degradation by Human-Associated Akkermansia https://www.biorxiv.org/content/10.1101/2023.10.17.562767v1