Spanish National Bioinformatics Institute (INB)/ELIXIR-ES, Computational team

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Mostrant 61 - 90 resultats de 106

2014

Comprehensive characterization of complex structural variations in cancer by directly comparing genome sequence reads.

Nat Biotechnol

V. Moncunill, S. González, S. Beà, L. O. Andrieux, I. Salaverria, C. Royo, L. Martinez, M. Puiggros, M. Segura-Wang, A. M. Stütz, A. Navarro, R. Royo, J L. Gelpí, I. G. Gut, C. López-Otín, M. Orozco, J. O. Korbel, E. Campo, X. S. Puente, and D. Torrents
BioSWR--semantic web services registry for bioinformatics.

PLoS One

D. Repchevsky, and J L. Gelpí
Molecular Dynamics Simulations. Going high-throughput

First BCAM Workshop on Non Linear dynamics on biological systems.

J L. Gelpí

2013

NAFlex: a web server for the study of nucleic acid flexibility.

Nucleic Acids Res

A. Hospital, I. Faustino, R. Collepardo-Guevara, C. González, J L. Gelpí, and M. Orozco
Exploring early stages of the chemical unfolding of proteins at the proteome scale.

PLoS Comput Biol

M. Candotti, A. Pérez, C. Ferrer-Costa, M. Rueda, T. Meyer, J L. Gelpí, and M. Orozco
A genome-wide association study on a southern European population identifies a new Crohn's disease susceptibility locus at RBX1-EP300.

Gut

A. Julià, E. Domènech, E. Ricart, R. Tortosa, V. García-Sánchez, J P. Gisbert, P. Nos Mateu, A. Gutiérrez, F. Gomollón, J L. Mendoza, E. García-Planella, M. Barreiro-de Acosta, F. Muñoz, M. Vera, C. Saro, M. Esteve, M. Andreu, A. Alonso, M. López-Lasanta, L. Codó, J L. Gelpí, A. C. García-Montero, J. Bertranpetit, D. Absher, J. Panés, and S. Marsal
Efficient relaxation of protein-protein interfaces by discrete molecular dynamics simulations

Journal of Chemical Theory and Computation

A. Emperador, A. Solernou, P. Sfriso, C. Pons, J L. Gelpí, J. Fernández-Recio, and M. Orozco
High‐throughput molecular dynamics simulations: toward a dynamic view of macromolecular structure

Wiley Interdisciplinary Reviews: Computational Molecular Science

A. Hospital, and J L. Gelpí

2012

DISCRETE – a novel package for the simulation of protein dynamics using the Discrete Molecular Dynamics method

High Performance Computing in Computational Chemistry and Molecular Biology: Challenges and Solutions provided by ScalaLife project

J L. Gelpí
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
Risk variants for psoriasis vulgaris in a large case-control collection and association with clinical subphenotypes.

Human molecular genetics

A. Julià, R. Tortosa, J M. Hernanz, J. D. Cañete, E. Fonseca, C. Ferrándiz, P. Unamuno, L. Puig, J L. Fernández-Sueiro, R. Sanmartí, J. Rodríguez, J. Gratacós, E. Dauden, J L. Sánchez-Carazo, J L. López-Estebaranz, D. Moreno-Ramírez, R. Queiró, C. Montilla, J C. Torre-Alonso, J J. Pérez-Venegas, F. Vanaclocha, E. Herrera, S. Muñoz-Fernández, C. González, D. Roig, A. Erra, I. Acosta, A. Fernández-Nebro, P. Zarco, A. Alonso, M. López-Lasanta, A. García-Montero, J L. Gelpí, D. Absher, and S. Marsal
Unveiling case-control relationships in designing a simple and powerful method for detecting gene-gene interactions.

Genetic epidemiology

O. Canela-Xandri, A. Julià, J L. Gelpí, and S. Marsal
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
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

2011

Infraestructura de Web Services y Supercomputación

Tutoriales Formativos en Biomedicina Computacional. : Lestrove (Coruña) (ESPANYA)

J L. Gelpí
Uso de Herramientas Bioinformáticas y Bases de datos biológicas con soporte de la supercomputación

OMICS aplicada a la Medicina Clínica, Barcelona

J L. Gelpí
HPC approaches to bioinformatics

The 10th Annual Meeting on High Performance Computing and Infrastructure in Norway

J L. Gelpí
Data Management in Massive Genomic Projects

IV International Symposium on BIOMEDICAL INFORMATICS IN EUROPE

J L. Gelpí
Whole-genome sequencing identifies recurrent mutations in chronic lymphocytic leukaemia.

Nature

X. S. Puente, M. Pinyol, V. Quesada, L. Conde, G. R. Ordóñez, N. Villamor, G. Escaramis, P. Jares, S. Beà, M. González-Díaz, L. Bassaganyas, T. Baumann, M. Juan, M. López-Guerra, D. Colomer, J. M. C. Tubío, C. López, A. Navarro, C. Tornador, M. Aymerich, M. Rozman, J. M. Hernández, D. A. Puente, J. M. P. Freije, G. Velasco, A. Gutiérrez-Fernández, D. Costa, A. Carrió, S. Guijarro, A. Enjuanes, L. Hernández, J. Yagüe, P. Nicolás, C. M. Romeo-Casabona, H. Himmelbauer, E. Castillo, J. C. Dohm, S. de Sanjosé, M. A. Piris, E. de Alava, J. San Miguel, R. Royo, J L. Gelpí, D. Torrents, M. Orozco, D. G. Pisano, A. Valencia, R. Guigó, M. Bayés, S. Heath, M. Gut, P. Klatt, J. Marshall, K. Raine, L. A. Stebbings, A. P. Futreal, M. R. Stratton, P. J. Campbell, I. Gut, A. López-Guillermo, X. Estivill, E. Montserrat, C. López-Otín, and E. Campo
Coarse-grained representation of protein flexibility. Foundations, successes, and shortcomings.

Advances in protein chemistry and structural biology

M. Orozco, L. Orellana, A. Hospital, A. N. Naganathan, A. Emperador, O. Carrillo, and J L. Gelpí
Exome sequencing identifies recurrent mutations of the splicing factor SF3B1 gene in chronic lymphocytic leukemia.

Nature genetics

V. Quesada, L. Conde, N. Villamor, G. R. Ordóñez, P. Jares, L. Bassaganyas, A. J. Ramsay, S. Beà, M. Pinyol, A. Martínez-Trillos, M. López-Guerra, D. Colomer, A. Navarro, T. Baumann, M. Aymerich, M. Rozman, J. Delgado, E. Giné, J. M. Hernández, M. González-Díaz, D. A. Puente, G. Velasco, J. M. P. Freije, J. M. C. Tubío, R. Royo, J L. Gelpí, M. Orozco, D. G. Pisano, J. Zamora, M. Vázquez, A. Valencia, H. Himmelbauer, M. Bayés, S. Heath, M. Gut, I. Gut, X. Estivill, A. López-Guillermo, X. S. Puente, E. Campo, and C. López-Otín
MoDEL. Molecular Dynamics Extended Library

nDDB Meeting - Grenoble - France

J L. Gelpí

2010

Enabling HMMER for the Grid with COMP Superscalar

Procedia Computer Science

E. Tejedor, R. M. Badia, R. Royo, and J L. Gelpí
MoDEL (Molecular Dynamics Extended Library): a database of atomistic molecular dynamics trajectories.

Structure (London, England : 1993)

T. Meyer, M. D'Abramo, A. Hospital, M. Rueda, C. Ferrer-Costa, A. Pérez, O. Carrillo, J. Camps, C. Fenollosa, D. Repchevsky, J L. Gelpí, and M. Orozco
MoDEL (Molecular Dynamics Extended Library). A database of atomistic molecular dynamics simulations

T. Meyer, M. D'Abramo, A. Hospital, M. Rueda, C. Ferrer-Costa, A. Pérez, O. Carrillo, C. Fenollosa, D. Perchevsky, J L. Gelpí, and M. Orozco
The EMBRACE web service collection

S. Pettifer, and M. Orozco

2009

FlexServ: an integrated tool for the analysis of protein flexibility.

Bioinformatics (Oxford, England)

J. Camps, O. Carrillo, A. Emperador, L. Orellana, A. Hospital, M. Rueda, D. Cicin-Sain, M. D'Abramo, J L. Gelpí, and M. Orozco
Thienylhalomethylketones: Irreversible glycogen synthase kinase 3 inhibitors as useful pharmacological tools.

Bioorganic & medicinal chemistry

D. I. Perez, S. Conde, C. Pérez, C. Gil, D. Simon, F. Wandosell, F. J. Moreno, J L. Gelpí, F J. Luque, and A. Martínez
Role of Pre-A motif in nitric oxide scavenging by truncated hemoglobin, HbN, of Mycobacterium tuberculosis.

The Journal of biological chemistry

A. Lama, S. Pawaria, A. Bidon-Chanal, A. Anand, J L. Gelpí, S. Arya, M. Martí, D. A. Estrin, F J. Luque, and K. L. Dikshit

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