Biblio

A genome-wide association study on a southern European population identifies a new Crohn’s disease susceptibility locus at RBX1-EP300., Julià, Antonio, Domènech Eugeni, Ricart Elena, Tortosa Raül, García-Sánchez Valle, Gisbert Javier P., Mateu Pilar Nos, Gutiérrez Ana, Gomollón Fernando, Mendoza Juan Luís, et al. , Gut, 2013 Oct, Volume 62, p.1440-5, (2013)

Light on the structural communication in Ras GTPases., Raimondi, Francesco, Felline Angelo, Portella Guillem, Orozco Modesto, and Fanelli Francesca , J Biomol Struct Dyn, 2013, Volume 31, p.142-57, (2013)

Epigenomic analysis detects widespread gene-body DNA hypomethylation in chronic lymphocytic leukemia., Kulis, Marta, Heath Simon, Bibikova Marina, Queirós Ana C., Navarro Alba, Clot Guillem, Martínez-Trillos Alejandra, Castellano Giancarlo, Brun-Heath Isabelle, Pinyol Magda, et al. , Nat Genet, 2012 Nov, Volume 44, p.1236-42, (2012)

Epigenomic analysis detects widespread gene-body DNA hypomethylation in chronic lymphocytic leukemia., Kulis, Marta, Heath Simon, Bibikova Marina, Queirós Ana C., Navarro Alba, Clot Guillem, Martínez-Trillos Alejandra, Castellano Giancarlo, Brun-Heath Isabelle, Pinyol Magda, et al. , Nat Genet, 2012 Nov, Volume 44, p.1236-42, (2012)

Epigenomic analysis detects widespread gene-body DNA hypomethylation in chronic lymphocytic leukemia., Kulis, Marta, Heath Simon, Bibikova Marina, Queirós Ana C., Navarro Alba, Clot Guillem, Martínez-Trillos Alejandra, Castellano Giancarlo, Brun-Heath Isabelle, Pinyol Magda, et al. , Nat Genet, 2012 Nov, Volume 44, p.1236-42, (2012)

Epigenomic analysis detects widespread gene-body DNA hypomethylation in chronic lymphocytic leukemia., Kulis, Marta, Heath Simon, Bibikova Marina, Queirós Ana C., Navarro Alba, Clot Guillem, Martínez-Trillos Alejandra, Castellano Giancarlo, Brun-Heath Isabelle, Pinyol Magda, et al. , Nat Genet, 2012 Nov, Volume 44, p.1236-42, (2012)

Evidence for transcript networks composed of chimeric RNAs in human cells., Djebali, Sarah, Lagarde Julien, Kapranov Philipp, Lacroix Vincent, Borel Christelle, Mudge Jonathan M., Howald Cédric, Foissac Sylvain, Ucla Catherine, Chrast Jacqueline, et al. , PLoS One, 2012, Volume 7, p.e28213, (2012)

Evidence for transcript networks composed of chimeric RNAs in human cells., Djebali, Sarah, Lagarde Julien, Kapranov Philipp, Lacroix Vincent, Borel Christelle, Mudge Jonathan M., Howald Cédric, Foissac Sylvain, Ucla Catherine, Chrast Jacqueline, et al. , PLoS One, 2012, Volume 7, p.e28213, (2012)

Exome sequencing identifies recurrent mutations of the splicing factor SF3B1 gene in chronic lymphocytic leukemia., Quesada, Víctor, Conde Laura, Villamor Neus, Ordóñez Gonzalo R., Jares Pedro, Bassaganyas Laia, Ramsay Andrew J., Beà Sílvia, Pinyol Magda, Martínez-Trillos Alejandra, et al. , Nat Genet, 2012 Jan, Volume 44, p.47-52, (2012)

Exome sequencing identifies recurrent mutations of the splicing factor SF3B1 gene in chronic lymphocytic leukemia., Quesada, Víctor, Conde Laura, Villamor Neus, Ordóñez Gonzalo R., Jares Pedro, Bassaganyas Laia, Ramsay Andrew J., Beà Sílvia, Pinyol Magda, Martínez-Trillos Alejandra, et al. , Nat Genet, 2012 Jan, Volume 44, p.47-52, (2012)

Exome sequencing identifies recurrent mutations of the splicing factor SF3B1 gene in chronic lymphocytic leukemia., Quesada, Víctor, Conde Laura, Villamor Neus, Ordóñez Gonzalo R., Jares Pedro, Bassaganyas Laia, Ramsay Andrew J., Beà Sílvia, Pinyol Magda, Martínez-Trillos Alejandra, et al. , Nat Genet, 2012 Jan, Volume 44, p.47-52, (2012)

htSeqTools: high-throughput sequencing quality control, processing and visualization in R., Planet, Evarist, Attolini Camille Stephan- Ot, Reina Oscar, Flores Oscar, and Rossell David , Bioinformatics, 2012 Feb 15, Volume 28, p.589-90, (2012)

htSeqTools: high-throughput sequencing quality control, processing and visualization in R., Planet, Evarist, Attolini Camille Stephan- Ot, Reina Oscar, Flores Oscar, and Rossell David , Bioinformatics, 2012 Feb 15, Volume 28, p.589-90, (2012)

Impact of methylation on the physical properties of DNA., Pérez, Alberto, Castellazzi Chiara Lara, Battistini Federica, Collinet Kathryn, Flores Oscar, Deniz Ozgen, Ruiz Maria Luz, Torrents David, Eritja Ramon, Soler-López Montserrat, et al. , Biophys J, 2012 May 2, Volume 102, p.2140-8, (2012)

Risk variants for psoriasis vulgaris in a large case-control collection and association with clinical subphenotypes., Julià, Antonio, Tortosa Raül, Hernanz José Manuel, Cañete Juan D., Fonseca Eduardo, Ferrándiz Carlos, Unamuno Pablo, Puig Lluís, Fernández-Sueiro José Luís, Sanmartí Raimon, et al. , Hum Mol Genet, 2012 Oct 15, Volume 21, p.4549-57, (2012)

Risk variants for psoriasis vulgaris in a large case-control collection and association with clinical subphenotypes., Julià, Antonio, Tortosa Raül, Hernanz José Manuel, Cañete Juan D., Fonseca Eduardo, Ferrándiz Carlos, Unamuno Pablo, Puig Lluís, Fernández-Sueiro José Luís, Sanmartí Raimon, et al. , Hum Mol Genet, 2012 Oct 15, Volume 21, p.4549-57, (2012)

Structure of triplex DNA in the gas phase., Arcella, Annalisa, Portella Guillem, Ruiz Maria Luz, Eritja Ramon, Vilaseca Marta, Gabelica Valérie, and Orozco Modesto , J Am Chem Soc, 2012 Apr 18, Volume 134, p.6596-606, (2012)

Molecular basis of substrate-induced permeation by an amino acid antiporter., Kowalczyk, Lukasz, Ratera Mercè, Paladino Antonella, Bartoccioni Paola, Errasti-Murugarren Ekaitz, Valencia Eva, Portella Guillem, Bial Susanna, Zorzano Antonio, Fita Ignacio, et al. , Proc Natl Acad Sci U S A, 2011 Mar 8, Volume 108, p.3935-40, (2011)

Nucleotide binding switches the information flow in ras GTPases., Raimondi, Francesco, Portella Guillem, Orozco Modesto, and Fanelli Francesca , PLoS Comput Biol, 2011 Mar, Volume 7, p.e1001098, (2011)

A systematic study of the energetics involved in structural changes upon association and connectivity in protein interaction networks., Stein, Amelie, Rueda Manuel, Panjkovich Alejandro, Orozco Modesto, and Aloy Patrick , Structure, 2011 Jun 8, Volume 19, p.881-9, (2011)

Whole-genome sequencing identifies recurrent mutations in chronic lymphocytic leukaemia., Puente, Xose S., Pinyol Magda, Quesada Víctor, Conde Laura, Ordóñez Gonzalo R., Villamor Neus, Escaramis Georgia, Jares Pedro, Beà Sílvia, González-Díaz Marcos, et al. , Nature, 2011 Jul 7, Volume 475, p.101-5, (2011)

Whole-genome sequencing identifies recurrent mutations in chronic lymphocytic leukaemia., Puente, Xose S., Pinyol Magda, Quesada Víctor, Conde Laura, Ordóñez Gonzalo R., Villamor Neus, Escaramis Georgia, Jares Pedro, Beà Sílvia, González-Díaz Marcos, et al. , Nature, 2011 Jul 7, Volume 475, p.101-5, (2011)

Whole-genome sequencing identifies recurrent mutations in chronic lymphocytic leukaemia., Puente, Xose S., Pinyol Magda, Quesada Víctor, Conde Laura, Ordóñez Gonzalo R., Villamor Neus, Escaramis Georgia, Jares Pedro, Beà Sílvia, González-Díaz Marcos, et al. , Nature, 2011 Jul 7, Volume 475, p.101-5, (2011)

Whole-genome sequencing identifies recurrent mutations in chronic lymphocytic leukaemia., Puente, Xose S., Pinyol Magda, Quesada Víctor, Conde Laura, Ordóñez Gonzalo R., Villamor Neus, Escaramis Georgia, Jares Pedro, Beà Sílvia, González-Díaz Marcos, et al. , Nature, 2011 Jul 7, Volume 475, p.101-5, (2011)

Approaching Elastic Network Models to Molecular Dynamics Flexibility, Orellana, Laura, Rueda Manuel, Ferrer-Costa Carles, Lopez-Blanco José Ramón, Chacón Pablo, and Orozco Modesto , Journal of Chemical Theory and Computation, Volume 6, p.2910-2923, (2010)

Deciphering the deformation modes associated with function retention and specialization in members of the Ras superfamily., Raimondi, Francesco, Orozco Modesto, and Fanelli Francesca , Structure, 2010 Mar 10, Volume 18, p.402-14, (2010)

The EMBRACE web service collection, Pettifer, Steve, Ison Jon, Kalaš Matúš, Thorne Dave, McDermott Philip, Jonassen Inge, Liaquat Ali, Fernández José M., Rodriguez Jose M., Partners INB-, et al. , Nucleic Acids Research, Volume 38, p.W683-W688, (2010)

The EMBRACE web service collection, Pettifer, Steve, Ison Jon, Kalaš Matúš, Thorne Dave, McDermott Philip, Jonassen Inge, Liaquat Ali, Fernández José M., Rodriguez Jose M., Partners INB-, et al. , Nucleic Acids Research, Volume 38, p.W683-W688, (2010)

The EMBRACE web service collection, Pettifer, Steve, Ison Jon, Kalaš Matúš, Thorne Dave, McDermott Philip, Jonassen Inge, Liaquat Ali, Fernández José M., Rodriguez Jose M., Partners INB-, et al. , Nucleic Acids Research, Volume 38, p.W683-W688, (2010)

Enabling HMMER for the Grid with COMP Superscalar, Tejedor, Enric, Badia Rosa M., Royo Romina, and Gelpí Josep-Lluis , Procedia Computer Science, Volume 1, p.2629–2638, (2010)

MoDEL (Molecular Dynamics Extended Library): a database of atomistic molecular dynamics trajectories., Meyer, Tim, D’Abramo Marco, Hospital Adam, Rueda Manuel, Ferrer-Costa Carles, Pérez Alberto, Carrillo Oliver, Camps Jordi, Fenollosa Carles, Repchevsky Dmitry, et al. , Structure, 2010 Nov 10, Volume 18, p.1399-409, (2010)

MoDEL (Molecular Dynamics Extended Library): a database of atomistic molecular dynamics trajectories., Meyer, Tim, D’Abramo Marco, Hospital Adam, Rueda Manuel, Ferrer-Costa Carles, Pérez Alberto, Carrillo Oliver, Camps Jordi, Fenollosa Carles, Repchevsky Dmitry, et al. , Structure, 2010 Nov 10, Volume 18, p.1399-409, (2010)

Comparison of molecular dynamics and superfamily spaces of protein domain deformation., Velázquez-Muriel, Javier A., Rueda Manuel, Cuesta Isabel, Pascual-Montano Alberto, Orozco Modesto, and Carazo José-María , BMC Struct Biol, 2009, Volume 9, p.6, (2009)

FlexServ: an integrated tool for the analysis of protein flexibility., Camps, Jordi, Carrillo Oliver, Emperador Agustí, Orellana Laura, Hospital Adam, Rueda Manuel, Cicin-Sain Damjan, D’Abramo Marco, Gelpí Josep-Lluis, and Orozco Modesto , Bioinformatics, 2009 Jul 1, Volume 25, p.1709-10, (2009)

On the Use of low-resolution Data to Improve Structure Prediction of Proteins and Protein Complexes, D’Abramo, Marco, Meyer Tim, Bernadó Pau, Pons Carles, Recio Juan Fernánde, and Orozco Modesto , Journal of Chemical Theory and Computation, 2009/11/10, Volume 5, Issue 11, p.3129 - 3137, (2009)

Exploring the suitability of coarse-grained techniques for the representation of protein dynamics., Emperador, Agustí, Carrillo Oliver, Rueda Manuel, and Orozco Modesto , Biophys J, 2008 Sep, Volume 95, p.2127-38, (2008)

Interoperability with Moby 1.0–it’s better than sharing your toothbrush!, Wilkinson, Mark D., Senger Martin, Kawas Edward, Bruskiewich Richard, Gouzy Jerome, Noirot Celine, Bardou Philippe, Ng Ambrose, Haase Dirk, Saiz Enrique de Andres, et al. , Brief Bioinform, 2008 May, Volume 9, p.220-31, (2008)

Interoperability with Moby 1.0–it’s better than sharing your toothbrush!, Wilkinson, Mark D., Senger Martin, Kawas Edward, Bruskiewich Richard, Gouzy Jerome, Noirot Celine, Bardou Philippe, Ng Ambrose, Haase Dirk, Saiz Enrique de Andres, et al. , Brief Bioinform, 2008 May, Volume 9, p.220-31, (2008)

Interoperability with Moby 1.0–it’s better than sharing your toothbrush!, Wilkinson, Mark D., Senger Martin, Kawas Edward, Bruskiewich Richard, Gouzy Jerome, Noirot Celine, Bardou Philippe, Ng Ambrose, Haase Dirk, Saiz Enrique de Andres, et al. , Brief Bioinform, 2008 May, Volume 9, p.220-31, (2008)

Interoperability with Moby 1.0–it’s better than sharing your toothbrush!, Wilkinson, Mark D., Senger Martin, Kawas Edward, Bruskiewich Richard, Gouzy Jerome, Noirot Celine, Bardou Philippe, Ng Ambrose, Haase Dirk, Saiz Enrique de Andres, et al. , Brief Bioinform, 2008 May, Volume 9, p.220-31, (2008)

Target flexibility: an emerging consideration in drug discovery and design., Cozzini, Pietro, Kellogg Glen E., Spyrakis Francesca, Abraham Donald J., Costantino Gabriele, Emerson Andrew, Fanelli Francesca, Gohlke Holger, Kuhn Leslie A., Morris Garrett M., et al. , J Med Chem, 2008 Oct 23, Volume 51, p.6237-55, (2008)

Binding affinities of oligonucleotides and PNAs containing phenoxazine and G-clamp cytosine analogues are unusually sequence-dependent., Ortega, José-Antonio, Blas José Ramón, Orozco Modesto, Grandas Anna, Pedroso Enrique, and Robles Jordi , Org Lett, 2007 Oct 25, Volume 9, p.4503-6, (2007)

A consensus view of protein dynamics., Rueda, Manuel, Ferrer-Costa Carles, Meyer Tim, Pérez Alberto, Camps Jordi, Hospital Adam, Gelpí Josep-Lluis, and Orozco Modesto , Proc Natl Acad Sci U S A, 2007 Jan 16, Volume 104, p.796-801, (2007)

Functional and structural characterization of the first prokaryotic member of the L-amino acid transporter (LAT) family: a model for APC transporters., Reig, Núria, del Rio César, Casagrande Fabio, Ratera Mercè, Gelpí Josep-Lluis, Torrents David, Henderson Peter J. F., Xie Hao, Baldwin Stephen A., Zorzano Antonio, et al. , J Biol Chem, 2007 May 4, Volume 282, p.13270-81, (2007)

Functional and structural characterization of the first prokaryotic member of the L-amino acid transporter (LAT) family: a model for APC transporters., Reig, Núria, del Rio César, Casagrande Fabio, Ratera Mercè, Gelpí Josep-Lluis, Torrents David, Henderson Peter J. F., Xie Hao, Baldwin Stephen A., Zorzano Antonio, et al. , J Biol Chem, 2007 May 4, Volume 282, p.13270-81, (2007)

Thorough validation of protein normal mode analysis: a comparative study with essential dynamics., Rueda, Manuel, Chacón Pablo, and Orozco Modesto , Structure, 2007 May, Volume 15, p.565-75, (2007)

Data mining of molecular dynamics trajectories of nucleic acids., Noy, Agnes, Meyer Tim, Rueda Manuel, Ferrer Carles, Valencia Antonion, Pérez Alberto, de la Cruz Xavier, López-Bes J M., Pouplana R, Fernandez-Recio J, et al. , J Biomol Struct Dyn, 2006 Feb, Volume 23, p.447-56, (2006)

Destabilization of quadruplex DNA by 8-aminoguanine., de la Osa, Jaime Lopez, González Carlos, Gargallo Raimundo, Rueda Manuel, Cubero Elena, Orozco Modesto, Aviñó Anna, and Eritja Ramon , Chembiochem, 2006 Jan, Volume 7, p.46-8, (2006)

Essential Dynamics: A Tool for Efficient Trajectory Compression and Management, Meyer, Tim, Ferrer-Costa Carles, Pérez Alberto, Rueda Manuel, Bidon-Chanal Axel, F. Luque Javier, Laughton Charles. A., and Orozco Modesto , Journal of Chemical Theory and Computation, 2006/03/01, Volume 2, Issue 2, p.251 - 258, (2006)

G-quadruplexes can maintain their structure in the gas phase., Rueda, Manuel, F Luque Javier, and Orozco Modesto , J Am Chem Soc, 2006 Mar 22, Volume 128, p.3608-19, (2006)