Publications

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2012

A Multilevel Strategy for the Exploration of the Conformational Flexibility of Small Molecules

J. Chem. Theory Comput

F. Forti, C. N. Cavasotto, M. Orozco, X. Barril, and J. F. Luque
Application of Drug-Perturbed Essential Dynamics/Molecular Dynamics (ED/MD) to Virtual Screening and Rational Drug Design

J. Chem. Theory Comput.

R. Chaudhuri, C. Anthony Laughton, O. Carrillo, and M. Orozco
Small Molecule Docking from Theoretical Structural Models

Computational Modeling of Biological Systems Biological and Medical Physics, Biomedical Engineering

E. MariaNovoa, L R. de Pouplana, and M. Orozco
Fast Atomistic Molecular Dynamics Simulations from Essential Dynamics Samplings

J. Chem. Theory Comput.

O. Carrillo, C. A. Laughton, and M. Orozco
Geometry, Dynamics, and Electronic Structure of DNA–Carbon Nanotube Hybrids

J. Phys. Chem. C

N. Utz, T. Meyer, G. Rink, M. Orozco, and T. Koslowski
Finding Conformational Transition Pathways from Discrete Molecular Dynamics Simulations

Journal of Chemical Theory and Computation

P. Sfriso, A. Emperador, L. Orellana, A. Hospital, J L. Gelpí, and M. Orozco
MDWeb and MDMoby: an integrated web-based platform for molecular dynamics simulations.

Bioinformatics (Oxford, England)

A. Hospital, P. Andrio, C. Fenollosa, D. Cicin-Sain, M. Orozco, and J L. Gelpí
Epigenomic analysis detects widespread gene-body DNA hypomethylation in chronic lymphocytic leukemia.

Nature genetics

M. Kulis, S. Heath, M. Bibikova, A. C. Queirós, A. Navarro, G. Clot, A. Martínez-Trillos, G. Castellano, I. Brun-Heath, M. Pinyol, S. Barberán-Soler, P. Papasaikas, P. Jares, S. Beà, D. Rico, S. Ecker, M. Rubio, R. Royo, V. Ho, B. Klotzle, L. Hernández, L. Conde, M. López-Guerra, D. Colomer, N. Villamor, M. Aymerich, M. Rozman, M. Bayés, M. Gut, J L. Gelpí, M. Orozco, J-B. Fan, V. Quesada, X. S. Puente, D. G. Pisano, A. Valencia, A. López-Guillermo, I. Gut, C. López-Otín, E. Campo, and J. I. Martín-Subero
Hog1 bypasses stress-mediated down-regulation of transcription by RNA polymerase II redistribution and chromatin remodeling.

Genome biology

M. Nadal-Ribelles, N. Conde, O. Flores, J. González-Vallinas, E. Eyras, M. Orozco, E. de Nadal, and F. Posas
Evidence for transcript networks composed of chimeric RNAs in human cells.

PloS one

S. Djebali, J. Lagarde, P. Kapranov, V. Lacroix, C. Borel, J. M. Mudge, C. Howald, S. Foissac, C. Ucla, J. Chrast, P. Ribeca, D. Martin, R. R. Murray, X. Yang, L. Ghamsari, C. Lin, I. Bell, E. Dumais, J. Drenkow, M. L. Tress, J L. Gelpí, M. Orozco, A. Valencia, N. L. van Berkum, B. R. Lajoie, M. Vidal, J. Stamatoyannopoulos, P. Batut, A. Dobin, J. Harrow, T. Hubbard, J. Dekker, A. Frankish, K. Salehi-Ashtiani, A. Reymond, S. E. Antonarakis, R. Guigó, and T. R. Gingeras

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