GROUP LEADER: Marc A. Marti-Renom

POSTDOCTORAL FELLOWS: François Serra, Marco di Stefano, Irene Farabella, Juan Rodríguez

PhD STUDENTS: Silvia Galan, Paula Soler, Julen Mendieta, Aleksandra Sparavier, Francesca Mugianesi

PROGRAMMERS / TECHNICIANS: Michael Goodstadt, David Castillo

LABORATORY TECHNICIAN: Yasmina Cuartero

SUMMARY

How biomolecules fold and function in three-dimensional space is one of the most challenging questions in biology. For example, we have limited knowledge of how the 2-meter-long DNA molecule folds in the micro-sized nucleus or how RNA, proteins and small chemical compounds fold and interact to perform their most basic functions of the cell. Our research group employ the laws of physics and the rules of evolution to develop and apply experimental and computational methods for predicting the 3D structures of macromolecules and their complexes.

RESEARCH PROJECTS

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

SELECTED PUBLICATIONS

Nir G, Farabella I, Pérez Estrada C,  Ebeling CG,  Beliveau BJ,  Sasaki HM,  Lee SH,  Nguyen SC,  McCole RB,  Chattoraj S,  Erceg J,  Abed JA,  Martins NMC,   Nguyen HQ,  Hannan MA,  Russell S,  Durand NC,  Rao SSP,  Kishi JY,  Soler-Vila P,  Di Pierro M,  Onuchic JN,  Callahan S,  Schreiner J,  Stuckey J,  Yin P,  Lieberman Aiden E,  Marti-Renom MA and Wu CT.
“Walking along chromosomes with super-resolution imaging, contact maps, and integrative modeling”
PLOS Genetics, 14(12):e1007872, 2018.

Marti-Renom MA, Almouzni G, Bickmore WA, Bystricky K, Cavalli G, Fraser P, Gasser SM, Heard E, Nicodemi M, Orozco M, Pombo A and Torres-Padilla M-E.
“4D Nucleome: challenges and guidelines towards data and model standards.”
Nature Genetics, 50:1352–1358, 2018.

Mas G, Blanco E, Ballaré C, Sansó M, Spill YG, Hu D, Aoi Y, Le Dily F, Shilatifard A, Marti-Renom MA and Di Croce L.
“Promoter bivalency favors an open architecture of the stem cell genome.”
Nature Genetics, 50:1452–1462, 2018.

Kojic A, Cuadrado A, Koninck AM, Gomez-Lopez G, Rodriguez-Corsino M, Le Dily F, Marti-Renom MA and Losada A.
“Distinct roles of cohesin-SA1 and cohesin-SA2 in 3D chromosome organization.”
Nature Structural and Molecular Biology, 25:496–504, 2018.

Stadhouders R, Vidal E, Serra F, Di Stefano B, Le Dily F, Quilez J, Gomez A, Collombet S, Berenguer C, Cuartero Y, Hecht J, Filion G, Beato M, Marti-Renom MA and Graf, T.
“Transcription factors orchestrate dynamic interplay between genome topology and gene regulation during cell reprogramming.”
Nature Genetics, 50:238–249, 2018.