Research interests

Current research

I am a researcher in bioinformatics and computational biology in the Molecular Assemblies and Genome Integrity team which belongs to the Structural Biology and Radiobiology laboratory at CEA, France. Our team also belongs to the Institute for Integrative Biology of the Cell.

In addition to continuing collaborations with the labs of Johannes Soeding and Patrick Cramer on the projects mentioned below, I am focusing on the evolution, structural prediction and design of protein-protein interactions.

Our team recently developed the InterEvDock server for protein-protein docking using evolutionary information.

Post-doctoral research

From September 2013 to September 2015, I was a post-doctoral researcher in the lab of Johannes Soeding (Gene Center, LMU Munich, and Max Planck Institute for Biophysical Chemistry, Goettingen, Germany). From February 2014 to September 2015, I was the recipient of a Humboldt Research Fellowship for Post-doctoral researchers.

During my postdoc in the Soeding lab, I started working on a project involving high-throughput sequencing data analysis. In collaboration with the laboratory of Prof. Patrick Cramer, I am analyzing data from 4tU-seq (next-generation sequencing of newly synthesized RNA), ChIP-seq (to map the bindings sites of regulatory protein factors over the genome), and PAR-CLIP (to identify the binding sites of RNA-binding proteins), with the goal to study transcription and genomic regulation.

During my postdoc in the Soeding lab, I also worked on the de-novo prediction of residue-residue contacts in proteins from correlated mutations, using statistical modelling. This topic has important applications in the field of protein structure prediction from sequence only.

Methods of global statistical network analysis can explain the observed correlations between columns in a multiple sequence alignment by a small set of directly coupled pairs of columns. Strong couplings are indicative of residue-residue contacts, and from the predicted contacts a structure can be computed. The structural regularity of paired β-strands leads to characteristic patterns in the noisy matrices of couplings. I developed bbcontacts, a tool which predicts β-β contacts by detecting characteristic patterns in the 2D map of predicted coupling scores using hidden Markov models (HMMs). The method was published in Bioinformatics and bbcontacts is open source software under the GNU Affero General Public License v3 (or later).

Similarly, the detection of coupling patterns corresponding to interactions between α-helices was used, together with cryo-EM data and molecular dynamics simulations, to build a structural model of the membrane protein insertase YidC. This is described in Wickles et al. (2014).

Ph.D. research

In July 2013, I completed my Ph.D. in structural bioinformatics, under the supervision of Raphaël Guerois at CEA Saclay (France). I had been working on protein-protein interactions from a structural and evolutionary point of view.

We developed the InterEvol database, which contains all non-redundant protein-protein interfaces with a known structure (retrieved from the PDB). InterEvol was designed to explore 3D structures of homologous interfaces of protein complexes and provides tools to retrieve multiple sequence alignments of orthologous pairs of proteins and to visualize structural and evolutionary information jointly in a PyMOL plugin. InterEvol is described in Faure et al. (2012).

Using a dataset of over 1,000 couples of structural interologs (homologous heteromeric complexes) extracted from InterEvol, I analyzed the conservation of interface contacts and highlighted astonishing plasticity in this respect. I also identified rather invariant features in the evolution of protein interfaces which provide important tracks for extracting meaningful information from the evolutionary history of binding partners. These findings are described in Andreani et al. (2012).

We also developed InterEvScore, an interface scoring function which coupled evolutionary information with a multi-body potential in order to discriminate near-native interfaces from decoys in protein-protein docking. InterEvScore is described in Andreani et al. (2013). The InterEvScore package can be downloaded from this page.

During my Ph.D., I also worked in collaboration with structural biologists and geneticists on projects involving protein-protein docking, remote homology detection, the study of interaction networks and the design of specific peptidic inhibitors. One such collaboration project led to the results described in Lombardi et al. (2013). Another led to the results described in Lisboa, Andreani et al. (2014).


* equal contribution
# co-corresponding authors




Software and servers




Contact information

Laboratoire de Biologie Structurale et Radiobiologie
IBITECS (Institut de Biologie et de Technologie de Saclay)
Batiment 144 p27
Point courrier 22
91191 Gif sur Yvette cedex
Phone: +33 1 69 08 67 17
Email zpJeESrlSoICwAqrz.ftaA%%NDurRg(oEAolhN)