Projects & Interests

under development

Similarities and contrasts in the microbial ecology of different habitats

We are interested in looking at different habitats and comparing their microbial ecology.

What are the common features of different microbiota (for example, the gut of different mammals)? Are strains biome-specific?

Relevant papers

Developing tools for very large-scale metagenomic analysis

We are interested both in developing new algorithms with applications to large-scale metagenomics and in exploring tools that enable reproducible science.

In particular, we are interested in the potential of designing domain specific languages to concisely specify data handling pipelines in a way that is (1) intuitive, (2) enables defensive programming, (3) computational efficient, (4) extensible.

Exploring large-scale metagenomics datasets

We are interested in exploiting very large scale metagenomic datasets for basic ecological questions.

What can we learn about microbes and their interaction patterns? Can we use model metatranscriptomes at a community-wide scale?

Relevant papers

  • Paul I Costea, Luis Pedro Coelho, Shinichi Sunagawa, Robin Munch, Jaime Huerta‐Cepas, Kristoffer Forslund, Falk Hildebrand, Almagul Kushugulova, Georg Zeller, Peer Bork Subspecies in the global human gut microbiome
  • Lionel Guidi*, Samuel Chaffron*, Lucie Bittner*, Damien Eveillard*, Abdelhalim Larhlimi, Simon Roux, Youssef Darzi, Stephane Audic, Léo Berline, Jennifer Brum, Luis Pedro Coelho, Julio Cesar Ignacio Espinoza, Shruti Malviya, Shinichi Sunagawa, Céline Dimier, Stefanie Kandels-Lewis, Marc Picheral, Julie Poulain, Sarah Searson, Tara Oceans Consortium Coordinators, Lars Stemmann, Fabrice Not, Pascal Hingamp, Sabrina Speich, Mick Follows, Lee Karp-Boss, Emmanuel Boss, Hiroyuki Ogata, Stephane Pesant, Jean Weissenbach, Patrick Wincker, Silvia G Acinas, Peer Bork, Colomban de Vargas, Daniele Iudicone, Matthew B Sullivan, Jeroen Raes, Eric Karsenti, Chris Bowler, Gabriel Gorsky Plankton networks driving carbon export in the oligotrophic ocean

Pushing the boundaries on bioimage informatics

We want to push the boundaries on bioimage informatics. This can mean work on larger datasets or build detailed models from images or link images and metagenomics or something else you can think of.

Relevant publications

Possible collaborations

We are interested in working with clinical groups on issues of relevance to human health or with groups with access to environmental samples.

Please get in touch.