Bioinformatics and Genomics

Comparative Bioinformatics

Group Structure

 Cédric Notredame
 Miquel Orobitg, Darek Kedra
 Jose Espinosa, Pablo Prieto, Maria Hatzou
Ionas Erb, Cedrik Magis, Paolo di Tomaso  


The main focus of the group is the development of novel algorithms for the comparison of multiple biological sequences. Multiple comparisons have the advantage of precisely revealing evolutionary traces, thus allowing the identification of functional constraints imposed on the evolution of biological entities. Most comparisons are currently carried out on the basis of sequence similarity. Our goal is to extend this scope by allowing comparisons based on any relevant biological signal such as sequence homology, structural similarity, genomic structure, functional similarity and more generally any signal that may be identified within biological sequences. Using such heterogeneous signals serves two complementary purposes: (i) producing better models that take advantage of the evolutionary resilience, (ii) improving our understanding of the evolutionary processes that leads to the diversification of biological features. For this purpose we are developing methods for the comparison of protein sequences, protein structures, RNA sequences and structures as well as complete genomes. We apply these methods to a wide range of biological questions that include: Leishmania Donovani resistance, animal and plant domestication, human and other model system gene annotation.  We are also applying similar algorithms to longitudinal data analysis in order to mine recordings for predictive patterns, with a special interest in the obesity onset in murine models. All the tools we develop are open source freeware that can either be downloaded for personal use or accessed through dedicated web interfaces at

Research Projects

  • Homology Modelling of Non Coding RNA
  • Large Scale Protein Sequence Alignments
  • Multiple Genome Alignments
  • Longitudinal data modelling
  • Structure based multiple sequence comparison and classification
  • Development of methods for the estimate of homology and evolutionary model reliability
  • Computation deployment in Cloud environments

Selected Publications

  1. Kemena C, et al.
    “Using tertiary structure for the computation of highly accurate multiple RNA alignments with the SARA-Coffee package”
    Bioinformatics, 29:1112-1119 (2013).
  2. Rachidi N, et al.
    “Pharmacological assessment defines the Leishmania donovani casein kinase 1 as a drug target and reveals important functions in parasite viability and intracellular infection.”
    Antimicrob Agents Chemother, doi: 10.1128/AAC.02022-13. Epub 2013 Dec 23.
  3. Magis C, Di Tommaso P and Notredame C.
    “T-RMSD: a web server for automated fine-grained protein structural classification.”
    Nucleic Acids Research, 41:W358-362 (2013).
  4. Breen M, et al.
    “Reply on The Role of Epistatis in Evolution.”
    Nature, 497, E2-E3 (2013).
  5. Bussotti G, Notredame C and Enright AJ.
    “Detecting and comparing non-coding RNAs in the high-throughput era.”
    International Journal of Molecular Sciences, 14:15423-15458 (2013).