Big Data Biology Lab Projects & Interests
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?
- Luis Pedro Coelho, Jens Kultima, Paul Costea, Coralie Fournier, Yuanlong Pan, Gail Czarnecki-Maulden, Matthew Hayward, Sofia K. Forslund, Patrick Descombes, Janet Jackson, Qinghong Li, and Peer Bork Similarity of the dog and human gut microbiomes in gene content and response to diet
- Shinichi Sunagawa*, Luis Pedro Coelho*, Samuel Chaffron*, […] Matthew B. Sullivan, Jean Weissenbach, Patrick Wincker, Eric Karsenti, Jeroen Raes, Silvia G. Acinas, Peer Bork, Structure and function of the global ocean microbiome
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.
Relevant papers & Links
- Luis Pedro Coelho Jug: Software for parallel reproducible computation in Python
- NG-meta-profiler: fast processing of metagenomes using NGLess, a domain-specific language by Luis Pedro Coelho, Renato Alves, Paulo Monteiro, Jaime Huerta-Cepas, Ana Teresa Freitas, Peer Bork bioRxiv 367755; doi: https://doi.org/10.1101/367755. See also the NGLess webpage
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?
- 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
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.