Computational Genomics

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Showing 31 - 60 results of 87

2017

PGBD5 promotes site-specific oncogenic mutations in human tumors

Nature Genetics

A. G. Henssen, R. Koche, J. Zhuang, E. Jiang, C. Reed, A. Eisenberg, E. Still, I. C. MacArthur, E. Rodríguez-Fos, S. González, M. Puiggròs, A. N. Blackford, C. E. Mason, E. de Stanchina, M. Gönen, A-K. Emde, M. Shah, K. Arora, C. Reeves, N. D. Socci, E. Perlman, C. R. Antonescu, C. W. M. Roberts, H. Steen, E. Mullen, S. P. Jackson, D. Torrents, Z. Weng, S. A. Armstrong, and A. Kentsis
Metformin alters the gut microbiome of individuals with treatment-naive type 2 diabetes, contributing to the therapeutic effects of the drug

Nature Medicine

H. Wu, E. Esteve, V. Tremaroli, M. Tanweer Khan, R. Caesar, L. Mannerås-Holm, M. Ståhlman, L. M. Olsson, M. Serino, M. Planas-Fèlix, G. Xifra, J. M. Mercader, D. Torrents, R. Burcelin, W. Ricart, R. Perkins, J M. Fernández-Real, and F. Bäckhed

2016

2015

Non-coding recurrent mutations in chronic lymphocytic leukaemia

Nature

X. S. Puente, S. Beà, R. Valdés-Mas, N. Villamor, J. Gutiérrez-Abril, J. I. Martín-Subero, M. Munar, C. Rubio-Pérez, P. Jares, M. Aymerich, T. Baumann, R. Beekman, L. Belver, A. Carrió, G. Castellano, G. Clot, E. Colado, D. Colomer, D. Costa, J. Delgado, A. Enjuanes, X. Estivill, A. A. Ferrando, J L. Gelpí, B. González, S. González, M. González, M. Gut, J. M. Hernández-Rivas, M. López-Guerra, D. Martín-García, A. Navarro, P. Nicolás, M. Orozco, Á. R. Payer, M. Pinyol, D. G. Pisano, D. A. Puente, A. C. Queirós, V. Quesada, C. M. Romeo-Casabona, C. Royo, R. Royo, M. Rozman, N. Russiñol, I. Salaverria, K. Stamatopoulos, H. G. Stunnenberg, D. Tamborero, M. J. Terol, A. Valencia, N. López-Bigas, D. Torrents, I. Gut, A. López-Guillermo, C. López-Otín, and E. Campo

2014

2013

Thyroid hormone receptor alpha gene variants increase the risk of developing obesity and show gene-diet interactions.

Int J Obes (Lond)

J. M. Fernández-Real, D. Corella, L. Goumidi, J. M. Mercader, S. Valdés, R. G Martínez, F. Ortega, M-T. Martinez-Larrad, J. M. Gómez-Zumaquero, J. Salas-Salvadó, M. A. Martinez González, M. I. Covas, P. Botas, E. Delgado, D. Cottel, J. Ferrieres, P. Amouyel, W. Ricart, E. Ros, A. Meirhaeghe, M. Serrano-Rios, F. Soriguer, and R. Estruch
Unravelling the hidden DNA structural/physical code provides novel insights on promoter location.

Nucleic Acids Res

E. Durán, S. Djebali, S. González, O. Flores, J M. Mercader, R. Guigó, D. Torrents, M. Soler-López, and M. Orozco
Targeting the association of calgranulin B (S100A9) with insulin resistance and type 2 diabetes.

J Mol Med (Berl)

F. J. Ortega, J. M. Mercader, J. M. Moreno-Navarrete, M. Sabater, N. Pueyo, S. Valdés, B. Ruiz, E. Luche, M. Serino, D. Naon, W. Ricart, P. Botas, E. Delgado, R. Burcelin, G. Frühbeck, F. Bosch, G. Mingrone, A. Zorzano, and J. M. Fernández-Real
Common genetic variants of surfactant protein-D (SP-D) are associated with type 2 diabetes.

PLoS One

N. Pueyo, F. J. Ortega, J. M. Mercader, J. M. Moreno-Navarrete, M. Sabater, S. Bonàs-Guarch, P. Botas, E. Delgado, W. Ricart, M. T. Martinez-Larrad, M. Serrano-Ríos, D. Torrents, and J. M. Fernández-Real

2012

EMBO Workshop in Computational biology (http://events.embo.org/12-comp-bio/)

2012
The tomato genome sequence provides insights into fleshy fruit evolution.

Nature
Identification of novel type 2 diabetes candidate genes involved in the crosstalk between the mitochondrial and the insulin signaling systems.

PLoS genetics

J. M. Mercader, M. Puiggros, A. V. Segrè, E. Planet, E. Sorianello, D. Sebastian, S. Rodriguez-Cuenca, V. Ribas, S. Bonàs-Guarch, S. Draghici, C. Yang, S. Mora, A. Vidal-Puig, J. Dupuis, J. C. Florez, A. Zorzano, and D. Torrents
Impact of methylation on the physical properties of DNA.

Biophysical journal

A. Pérez, C L. Castellazzi, F. Battistini, K. Collinet, O. Flores, O. Deniz, M L. Ruiz, D. Torrents, R. Eritja, M. Soler-López, and M. Orozco
BLUEPRINT to decode the epigenetic signature written in blood.

Nature biotechnology

D. Adams, L. Altucci, S. E. Antonarakis, J. Ballesteros, S. Beck, A. Bird, C. Bock, B. Boehm, E. Campo, A. Caricasole, F. Dahl, E. T. Dermitzakis, T. Enver, M. Esteller, X. Estivill, A. Ferguson-Smith, J. Fitzgibbon, P. Flicek, C. Giehl, T. Graf, F. Grosveld, R. Guigó, I. Gut, K. Helin, J. Jarvius, R. Küppers, H. Lehrach, T. Lengauer, A. Lernmark, D. Leslie, M. Loeffler, E. Macintyre, A. Mai, J H. Martens, S. Minucci, W. H. Ouwehand, P G. Pelicci, H. Pendeville, B. Porse, V. Rakyan, W. Reik, M. Schrappe, D. Schübeler, M. Seifert, R. Siebert, D. Simmons, N. Soranzo, S. Spicuglia, M. Stratton, H. G. Stunnenberg, A. Tanay, D. Torrents, A. Valencia, E. Vellenga, M. Vingron, J. Walter, and S. Willcocks
ReLA, a local alignment search tool for the identification of distal and proximal gene regulatory regions and their conserved transcription factor binding sites

Bioinformatics

S. González, B. Montserrat, F. Sánchez, M. Puiggros, E. Blanco, A. Ramirez, and D. Torrents

2011

Identification of a potent and selective σ₁ receptor agonist potentiating NGF-induced neurite outgrowth in PC12 cells.

Bioorganic & medicinal chemistry

D. Rossi, A. Pedrali, M. Urbano, R. Gaggeri, M. Serra, L. Fernández, M. Fernández, J. Caballero, S. Ronsisvalle, O. Prezzavento, D. Schepmann, B. Wuensch, M. Peviani, D. Curti, O. Azzolina, and S. Collina
Genetic algorithm optimization in drug design QSAR: Bayesian-regularized genetic neural networks (BRGNN) and genetic algorithm-optimized support vectors machines (GA-SVM).

Molecular diversity

M. Fernández, J. Caballero, L. Fernández, and A. Sarai
Enterotypes of the human gut microbiome.

Nature

M. Arumugam, J. Raes, E. Pelletier, D. Le Paslier, T. Yamada, D. R. Mende, G. R. Fernandes, J. Tap, T. Bruls, J-M. Batto, M. Bertalan, N. Borruel, F. Casellas, L. Fernández, L. Gautier, T. Hansen, M. Hattori, T. Hayashi, M. Kleerebezem, K. Kurokawa, M. Leclerc, F. Levenez, C. Manichanh, B. H. Nielsen, T. Nielsen, N. Pons, J. Poulain, J. Qin, T. Sicheritz-Ponten, S. Tims, D. Torrents, E. Ugarte, E. G. Zoetendal, J. Wang, F. Guarner, O. Pedersen, W. M. de Vos, S. Brunak, J. Doré, M. Antolín, F. Artiguenave, H. M. Blottiere, M. Almeida, C. Brechot, C. Cara, C. Chervaux, A. Cultrone, C. Delorme, G. Denariaz, R. Dervyn, K. U. Foerstner, C. Friss, M. van de Guchte, E. Guedon, F. Haimet, W. Huber, J. van Hylckama-Vlieg, A. Jamet, C. Juste, G. Kaci, J. Knol, O. Lakhdari, S. Layec, K. Le Roux, E. Maguin, A. Mérieux, R. Melo Minardi, C. M'rini, J. Muller, R. Oozeer, J. Parkhill, P. Renault, M. Rescigno, N. Sanchez, S. Sunagawa, A. Torrejon, K. Turner, G. Vandemeulebrouck, E. Varela, Y. Winogradsky, G. Zeller, J. Weissenbach, D. S. Ehrlich, and P. Bork

2010

ZNRD1 (zinc ribbon domain-containing 1) is a host cellular factor that influences HIV-1 replication and disease progression.

Clinical infectious diseases : an official publication of the Infectious Diseases Society of America

E. Ballana, J. Senserrich, E. Pauls, R. Faner, J M. Mercader, F. Uyttebroeck, E. Palou, M P. Mena, E. Grau, B. Clotet, L. Ruiz, A. Telenti, A. Ciuffi, and J. A. Esté
Transferrin receptor-1 gene polymorphisms are associated with type 2 diabetes.

European journal of clinical investigation

J M. Fernández-Real, J M. Mercader, F J. Ortega, J M. Moreno-Navarrete, P. López-Romero, and W. Ricart
Graphical Representations of Protein Sequences for Alignment-Free Comparative and Predictive Studies. Recognition of Protease Inhibition Pattern from H-Depleted Molecular Graph Representat

Bioinformatics

M. Fernández, J. Caballero, L. Fernández, and et. al.

2008

DNAlive: a tool for the physical analysis of DNA at the genomic scale.

Bioinformatics (Oxford, England)

JR. Goñi, C. Fenollosa, A. Pérez, D. Torrents, and M. Orozco
Is there selection for the pace of successive inactivation of the arpAT gene in primates?

Journal of molecular evolution

F. Casals, A. Ferrer-Admetlla, J. Chillarón, D. Torrents, M. Palacín, and J. Bertranpetit
Projection structure of a member of the amino acid/polyamine/organocation transporter superfamily.

The Journal of biological chemistry

F. Casagrande, M. Ratera, A. D. Schenk, M. Chami, E. Valencia, J M. Lopez, D. Torrents, A. Engel, M. Palacín, and D. Fotiadis
Selective maintenance of Drosophila tandemly arranged duplicated genes during evolution.

Genome biology

C. Quijano, P. Tomancak, J. Lopez-Marti, M. Suyama, P. Bork, M. Milan, D. Torrents, and M. Manzanares

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