Gene Regulation, Stems Cells and Cancer

marc-marti-renom
Structural Genomics (Group with dual affiliation CRG-CNAG)

Group Structure

GROUP LEADER:
Marc A. Marti-Renom (ICREA Research Professor)
STAFF SCIENTIST:
Davide Baù
POSTDOCTORAL FELLOWS:
François Serra, François le Dily
PhD STUDENTS:
David Dufour, Gireesh K. Bogu, Francisco Martínez-Jiménez
PROGRAMMER/TECHNICIAN:
Michael Goodstadt

Summary

Our group is interested in the molecular mechanisms that regulate cell fate. To study such mechanisms, we employ the laws of physics and the rules of evolution to develop and apply computational methods for predicting the 3D structures of macromolecules and their complexes.


Research Projects

  • Protein-Ligand interactions. We develop methods for comparative docking of small chemical compounds and their target proteins.
  • Comparative RNA structure prediction. We develop a series of tools for the alignment of RNA structures and the prediction of their structures and functions.
  • Structure determination of genomes. We develop methods for determining the 3D organization of the chromatin

Selected Publications

  1. Köser CU, Bryant JM, Becq J, Török ME, Ellington MJ, Marti-Renom MA, Carmichael AJ, Parkhill J, Smith GP, Peacock SJ.
    “Whole-genome sequencing for rapid susceptibility testing of M. tuberculosis.”
    N Engl J Med, 369(3):290-2 (2013).
  2. López-Pelegrín M, Cerdà-Costa N, Martínez-Jiménez F, Cintas-Pedrola A, Canals A, Peinado JR, Marti-Renom MA, López-Otín C, Arolas JL, Gomis-Rüth FX.
    “A novel family of soluble minimal scaffolds provides structural insight into the catalytic domains of integral membrane metallopeptidases.”
    J Biol Chem, 288(29):21279-94 (2013).
  3. Dekker J, Marti-Renom MA, Mirny LA.
    “Exploring the three-dimensional organization of genomes: interpreting chromatin interaction data.”
    Nat Rev Genet, 14(6):390-403 (2013).
  4. Martínez-Jiménez F, Papadatos G, Yang L, Wallace IM, Kumar V, Pieper U, Sali A, Brown JR, Overington JP, Marti-Renom MA.
    “Target prediction for an open access set of compounds active against Mycobacterium tuberculosis.”
    PLoS Comput Biol, 9(10):e1003253 (2013).
  5. Kemena C, Bussotti G, Capriotti E, Marti-Renom MA, Notredame C.
    “Using tertiary structure for the computation of highly accurate multiple RNA alignments with the SARA-Coffee package.”
    Bioinformatics, 29(9):1112-9 (2013).