We are honored to be recipient of the ERC Starting grant 2016 and we are looking for motivated computational scientists, PhD students, and postdoctoral fellows to join the lab. Take a look at the call and contact me if interested!

Meta'omics for hacking the human microbiome

  • "The diversity of the microbiome" (Nature 2012, TiM 2013)
  • The laboratory and our little friends as of 2016
  • MetaMLST strain analysis (Zolfo et al, NAR, 2016)
  • Microbiome signatures (Pasolli et al, PLOS ComBio, 2016)
  • Strain diversity on the skin (Tett et al, 2016)

Our body harbours ~100 trillion microbes which outnumber our own cells. This microbial diversity (the "microbiome") and its functions are still largely uncharachterized but we can now try to mine it using cultivation-free sequencing-based metagenomic tools.

We employ experimental meta'omic tools and novel computational approaches to study the diversity of the microbiome and its role in human dysbiosis and infections. Our projects bring together computer scientists, microbiologists, statisticians, and clinicians.

Main research directions

Next generation computational metagenomic tools. The potential of metagenomics is only partially expressed due to computational challenges. We are working on novel methods to profile microbiomes at increased resolution (e.g. strains) and perform large-scale comparative genomics on uncharacterized microbes.

Integrative and machine learning meta'omic approaches. We develop new machine learning tools to cope with the variability and dimensionality of microbiome profiles and provide clinically relevant signatures by integrating complementary meta'omic approaches (e.g. metatrasncriptomics or metaproteomics).

Microbiome-pathogen interaction in human infections. The role of the microbiome in the acquisition and development of infections is largely unknown. By coupling longitudinal pathogen/microbiome sequencing we aim understand how the microbiome can modulate the virulence profile and antibiotic resistance of human infections.

Vertical microbiome transmission. We study how microbes can be transmitted between different environments with specific focus on how members of the microbiome are vertically transmitted from mothers to infants at birth and during the first years of age. .

Our Keywords (from our papers)

Wordle: CibioCM