Our Research Projects

The Computational Biology group adresses biological problems using computational methods. We pursue several lines of research:

1. we are interested in large-scale data integration, focusing on mitochondrial function in development and disease

2. we are interested in evolutionary computational biology and work among others on the prediction and evolution of motifs, the evolution of epithelia, bacterial evolution, and with remote sequence similarity

1. Integration of -omics data

We work on the integration of -omics data from different sources to extract meaningful biological information. We use mostly NGS-data, integrating differential expression with ChIP-seq or interactome data to provide biologists with testable hypothesis for further experimental studies. To this end, we develop data integration methods that are easy to use for non-experts.

mitoXplorer - exploring the dynamics of mitochondrial gene expression by visual data mining

We have developed the mitoXplorer platform, a visual data mining web-server that allows us to mine the expression dynamics of mitochondria-associated genes in the vast amount of available -omics data. A manually curated, mitochondrial interactome is at the heart of this web-tool ... more

mitoXplorer is available at http://mitoxplorer.ibdm.univ-mrs.fr

This project was supported by DFG grant ‘CancerSysDB’ and is currently supported by ANR grant ‘MITO-DYNAMICS’ and the CNRS.

Biological networks in time and space

Biological networks such as protein-protein interaction networks or gene regulatory networks are an integral part to understand biological systems. We use such networks to interpret and integrate -omics data. We currently work on integrating time (and space) in interaction networks ... more


These projects are supported by ANR grant 'MYOCHRONIC' and by CENTURI.

Annotation and integration of epigenetic data

With NGS, sequencing also became functional. We can now describe also the non-coding part of a genome, for instance by looking at histone marks, transcription factor binding events, or chromatin states. These new techniques also require new tools for annotating and integrating data from such epigenetic studies. With the web-tool AnnoMiner, we introduce an annotation and integration tools for epigenetic data that offers the user flexibility and choice in determining the association of a genomic peak and a genomic feature. more

AnnoMiner is available at http://chimborazo.ibdm.univ-mrs.fr/AnnoMiner

2. Evolutionary Computational Biology

Our Darwinian view on evolution states that evolution is the result of random changes of our genetic code combined with the process of natural selection. Many small changes over a long period of time have a major evolutionary impact. As a result, even true orthologs can share only low sequence similarity, which we refer to as conservation in the twilight or midnight zone.

Our group is interested in detecting sequence relationships in the twilight and midnight zone.

Motif evolution and motif detection in proteins

HH-MOTiF: de novo detection of short linear motifs in proteins using HMM-comparisons

Protein motifs are defined as self-sufficient functional units. They are typically only between 3 and 23 amino acids long and have various functions in proteins. We have developed an easy-to-use, efficient de novo search engine for short linear motifs in a set of proteins. Our method is based on the comparison of Hidden-Markov-Models (HMM) and uses a hierarchical model, so-called motif trees, to identify conserved motifs ... more

HH-motif is available at http://hh-motif.ibdm.univ-mrs.fr

This project was supported by the Max Planck Society and the CNRS.

evolution of short linear motifs in proteins

Protein motifs are essential for the interaction between proteins with each other or other molecules in the cell. As self-sufficient functional units, a newly evolving motif could in principle also provide the protein with a novel interaction partner and in consequence, with a novel function. In this project, we are looking at motif evolution in the context of its structural neighborhood, as well as newly evolved phenotypes.

As more and more large-scale datasets, for instance from Cross-link Mass spectrometry (XL-MS) become available, we are also able to study the evolution of protein motifs more systematically.

Working with remote sequence similarity

Our Darwinian view on evolution states that evolution is the result of random changes of our genetic code combined with the process of natural selection. Many small changes over a long period of time have a major evolutionary impact. As a result, even true orthologs can share only low sequence similarity, which we refer to as conservation in the twilight or midnight zone.

Our group is interested in detecting sequence relationships in the twilight and midnight zone.

morFeus: finding remotely conserved orthologs using iterative, relaxed BLAST-searches and network scoring

We are interested in discovering remote orthologs. We have developed the web-based method morFeus for the detection of orthologs in the twilight and midnight zone of sequence similarity ... more


This project was supported by BMBF grant NGS goes HPC and the Max Planck Society.

RemOtF - finding orthologs on proteome-scale

With RemOtF, we want to scale up the search for remote orthologs to proteome-level. Using comparisons of Hidden Markov Models (HMMs), we search for remote orthologs on genome-scale.

The evolution of epithelia

In this CENTURI funded project, we want to identify the basic components of primitive epithelial cells as found in sponges. We use single-cell RNA sequencing for identifying epithelial components in the marine sponge Oscarella lobularis. The project is a close collaboration between Andre le Bivic (IBDM), Carole Borchiellini (IMBE) and our team.

Predator-prey co-evolution

In this CENTURi funded project, we are exploring the co-evolution of predatory bacteria with their prey. We use Myxococcus xanthus as a model system, exploring its evolutionary arms-race for survival with different more or less resistant preys. This project is a close collaboration between our team and the team of Tam Mignot (LBC).

Genome sequencing and annotation

Our group is also involved in several genome and transcriptome de novo sequencing and annotation projects, from bacteria, as well as vertebrates. Find out more ...