Florian Mauffrey

👋 Hi! I'm a computational biologist with a specialization in microbiology 🦠. I have worked for universities, health institutes and hospitals. I participated in various research and diagnostic projects. 🧬

💡I am currently looking for a new position.💡

Papers Resources

Hi! I’m Florian.

I specialized in bacterial genomics and transcriptomics, supporting both research projects and diagnostic analyses for hospital clinicians. My expertise covers a wide range of microorganisms, from microbiota communities to pathogenic species and environmental bacteria.

With over seven years of experience, I’ve had the opportunity to collaborate with research laboratories, public health institutes, and hospitals across Canada and Switzerland.

Whether you’re navigating a complex research challenge, seeking new insights from high-dimensional biological data, or in need of reliable bioinformatics support, I bring a rigorous, research-driven approach to every collaboration.

I also created and manage https://myswissbioinfo.ch.

Do you need bioinformatics expertise on your team?

Interested in collaborating on a research project?

Looking for guidance with bioinformatics data analysis?

Don’t hesitate, let’s connect!

Contact

Current projects

My current project focuses on exploring gene regulation in Pseudomonas aeruginosa.

I study the czcRS regulon (a two-component system sensing zinc, implicated in the development of carbapenem resistance) using ChIP-seq approach. To support this work, I developed a simple and streamlined pipeline tailored for bacterial datasets, available here.

In parallel, I'm working on RNA-seq data to better understand the regulatory response of this bacterium when trapped in macrophages during the immune response.

Portfolio

Genomics analysis of outbreak MRSA

A comprehensive analysis of the progression of a MRSA clone, which emerged during an outbreak, was conducted utilizing machine learning and next-generation sequencing technologies over the course of a decade.

DNA markers for forensic investigations

Comprehensive studies of DIP-STR markers in human DNA have facilitated the identification of the lesser contributor in highly imbalanced blood mixtures, such as those found at crime scenes or during pregnancy testing.

Tracking patients within the hospital

Creation of a web-based tool designed to streamline the generation of patient tracking charts and networks for infection control personnel, thereby enhancing surveillance speed and overall infection management within the hospital setting.

Impact of offshore platforms using NGS

Offshore drilling platforms can cause harm to nearby marine life through spills, leaks, or drilling operations. We assessed the environmental impact using sediment samples and next-gen sequencing techniques to derive ecological status indices.

Plasmids typing with long reads sequencing

Understanding antibiotic resistance spread requires tracking plasmids, which are key transmitters. We employed long-read whole-genome sequencing on carbapenemase-resistant isolates to decode plasmid transmission dynamics in multiple hospital outbreaks.

Metagenomics analysis of infected tissues

The use of mNGS for infection diagnosis is rising due to its ability to rapidly detect pathogens. We investigated the influence of bacterial DNA enrichment on mNGS-based detection and estimation of bacterial abundance in an infected tissue model.

Foraminifera phylogenetic characterization

Foraminifera, a group of eukaryotic protists, have a complex phylogeny partly due to limited genomic data. In an effort to address this, we conducted an analysis of transcriptomic data from 28 species to construct the most comprehensive phylogeny to date.

Serotyping method using WGS

Correctly identifying the serotypes of infectious Streptococcus pneumoniae strains is vital for effective vaccine development. We assessed the efficacy of molecular-based methods (including WGS) compared to the traditional biochemical approach.

Impact of mutations on azithromycin resistance

The emergence of azithromycin resistance poses significant challenges in treating numerous bacterial infections. Our study delved into the effects of genetic mutations on the azithromycin resistance levels exhibited by different strains of Nesseria gonorrhoeae.

Bioinformatics resources

Bioinformatics has become increasingly essential in modern biology, every biologist now benefits from having at least a basic understanding of computational tools. However, finding the right learning resources can often be time-consuming and overwhelming.

To help beginners get started, I’ve compiled a collection of useful resources that I’ve personally found valuable. These are not tutorials, but rather pointers to help you identify what to learn and where to start. There are many excellent tutorials available online, and I aim to update this list regularly to keep it relevant and helpful.

Resources

"Florian possessed remarkable professional knowledge and skills, as well as extensive experience in his field of activity, easily mastering the tasks and responsibilities entrusted to him."

Dominique S. Blanc
– University Hospital of Lausanne

"Florian has provided us with full satisfaction, both in terms of the quality of his work and his commitment. His professional knowledge and skills, particularly in the field of bioinformatics, have been greatly appreciated."

Jacques Schrenzel
– University hospital of Geneva

"Mr. Mauffrey has been able to assume his responsibilities to our complete satisfaction. My group and I would like to warmly thank him for his commitment and the quality of his work."

Diana Hall
– West Swiss University Center of Forensic Medicine