Biblio

The Impact of the HydroxyMethylCytosine epigenetic signature on DNA structure and function, Battistini, Federica, Dans Pablo D., Terrazas Montserrat, Castellazzi Chiara L., Portella Guillem, Labrador Mireia, Villegas Núria, Brun-Heath Isabelle, González Carlos, and Orozco Modesto , PLOS Computational Biology, 11/2021, Volume 17, Issue 11, p.e1009547 - , (2021)

The impact of monovalent ion force field model in nucleic acids simulations., Noy, Agnes, Soteras Ignacio, F Luque Javier, and Orozco Modesto , Phys Chem Chem Phys, 2009 Dec 7, Volume 11, p.10596-607, (2009)

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)

Impact of DNA methylation on 3D genome structure, Buitrago, Diana, Labrador Mireia, Arcon Juan Pablo, Lema Rafael, Flores Oscar, Esteve-Codina Anna, Blanc Julie, Villegas Núria, Bellido David, Gut Marta, et al. , Nature Communications, 05/2021, Volume 12, Issue 1, p.3243, (2021)

i-Motif folding intermediates with zero-nucleotide loops are trapped by 2′-fluoroarabinocytidine via F···H and O···H hydrogen bonds, El-Khoury, Roberto, Macaluso Veronica, Hennecker Christopher, Mittermaier Anthony K., Orozco Modesto, González Carlos, Garavís Miguel, and Damha Masad J. , Communications Chemistry, 02/2023, Volume 6, Issue 1, p.31, (2023)

Identification of risk loci for Crohn’s disease phenotypes using a genome-wide association study, Alonso, Arnald, Domènech Eugeni, Julià Antonio, Panés Julián, García-Sánchez Valle, Mateu Pilar Nos, Gutiérrez Ana, Gomollón Fernando, Mendoza Juan L., Garcia-Planella Esther, et al. , Gastroenterology, 2015 Apr, Volume 148, p.794-805, (2015)

Hydrophobic similarity between molecules: a MST-based hydrophobic similarity index., Muñoz, J, Barril X, Hernández B, Orozco Modesto, and F Luque Javier , J Comput Chem, 2002 Apr 15, Volume 23, p.554-63, (2002)

A hydrophobic similarity analysis of solvation effects on nucleic acid bases., Muñoz-Muriedas, Jordi, Barril Xavier, López José María, Orozco Modesto, and Luque Francisco Javier , J Mol Model, 2007 Feb, Volume 13, p.357-65, (2007)

Hydrophobic molecular similarity from MST fractional contributions to the octanol/water partition coefficient., Muñoz-Muriedas, Jordi, Perspicace Samantha, Bech Nuria, Guccione Salvatore, Orozco Modesto, and F Luque Javier , J Comput Aided Mol Des, 2005 Jun, Volume 19, p.401-19, (2005)

A hybrid all-atom/coarse grain model for multiscale simulations of DNA, Machado, Matías Rodrigo, Dans Pablo Daniel, and Pantano Sergio , Physical Chemistry Chemical Physics, Volume 13, Number 40, p.18134–18144, (2011)

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)

How B-DNA Dynamics Decipher Sequence-Selective Protein Recognition, Battistini, Federica, Hospital Adam, Buitrago Diana, Gallego Diego, Dans Pablo D., Gelpí Josep Lluis, and Orozco Modesto , Journal of Molecular Biology, 07/2019, (2019)

How accurate are accurate force-fields for B-DNA?, Dans, Pablo D., Ivani Ivan, Hospital Adam, Portella Guillem, González Carlos, and Orozco Modesto , Nucleic Acids Research, 01/2017, Volume 45, Issue 7, p.4217-4230, (2017)

Hoogsteen-based parallel-stranded duplexes of DNA. Effect of 8-amino-purine derivatives., Cubero, Elena, Aviñó Anna, de la Torre Beatriz G., Frieden Miriam, Eritja Ramon, F Luque Javier, González Carlos, and Orozco Modesto , J Am Chem Soc, 2002 Mar 27, Volume 124, p.3133-42, (2002)

Hog1 bypasses stress-mediated down-regulation of transcription by RNA polymerase II redistribution and chromatin remodeling., Nadal-Ribelles, Mariona, Conde Núria, Flores Oscar, González-Vallinas Juan, Eyras Eduardo, Orozco Modesto, de Nadal Eulàlia, and Posas Francesc , Genome Biol, 2012, Volume 13, p.R106, (2012)

Histone H3 serine-57 is a CHK1 substrate whose phosphorylation affects DNA repair, Parisis, Nikolaos, Dans Pablo D., Jbara Muhammad, Singh Balveer, Schausi-Tiffoche Diane, Molina-Serrano Diego, Brun-Heath Isabelle, Hendrychová Denisa, Maity Suman Kumar, Buitrago Diana, et al. , Nature Communications, 08/2023, Volume 14, Issue 1, p.5104, (2023)

High-Throughput Prediction of the Impact of Genetic Variability on Drug Sensitivity and Resistance Patterns for Clinically Relevant Epidermal Growth Factor Receptor Mutations from Atomistic Simulations, Suriñach, Aristarc, Hospital Adam, Westermaier Yvonne, Jordá Luis, Orozco-Ruiz Sergi, Beltrán Daniel, Colizzi Francesco, Andrio Pau, Soliva Robert, Municoy Martí, et al. , Journal of Chemical Information and Modeling, 12/2022, Volume In press, (2022)

High-throughput molecular dynamics simulations: toward a dynamic view of macromolecular structure, Hospital, Adam, and Gelpí Josep-Lluis , Wiley Interdisciplinary Reviews: Computational Molecular Science, Volume 3, p.364–377, (2013)

GRID-MD-A tool for massive simulation of protein channels., Carrillo, Oliver, and Orozco Modesto , Proteins, 2008 Feb 15, Volume 70, p.892-9, (2008)

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)

Glutaryl-CoA dehydrogenase deficiency in Spain: evidence of two groups of patients, genetically, and biochemically distinct., Busquets, C, Merinero B, Christensen E, Gelpí Josep-Lluis, Campistol J, Pineda M, Fernández-Alvarez E, Prats J M., Sans A, Arteaga R, et al. , Pediatr Res, 2000 Sep, Volume 48, p.315-22, (2000)

Geometrical and electronic structure variability of the sugar-phosphate backbone in nucleic acids., Svozil, Daniel, Sponer Judit E., Marchán Ivan, Pérez Alberto, Cheatham Thomas E., Forti F, F Luque Javier, Orozco Modesto, and Sponer Jiri , J Phys Chem B, 2008 Jul 10, Volume 112, p.8188-97, (2008)

A genomics method to identify pathogenicity-related proteins. Application to aminoacyl-tRNA synthetase-like proteins., Novoa, Eva Maria, de Moura Manuel Castro, Orozco Modesto, and de Pouplana Lluís Ribas , FEBS Lett, 2010 Jan 21, Volume 584, p.460-6, (2010)

Genome-Wide Pathway Analysis Identifies Genetic Pathways Associated with Psoriasis., Aterido, Adrià, Julià Antonio, Ferrándiz Carlos, Puig Lluís, Fonseca Eduardo, Fernández-López Emilia, Dauden Esteban, Sánchez-Carazo José Luís, López-Estebaranz José Luís, Moreno-Ramírez David, et al. , J Invest Dermatol, 2016 Mar, Volume 136, Issue 3, p.593-602, (2016)

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)

A genome-wide association study identifies SLC8A3 as a susceptibility locus for ACPA-positive rheumatoid arthritis., Julià, Antonio, González Isidoro, Fernández-Nebro Antonio, Blanco Francisco, Rodriguez Luis, González Antonio, Cañete Juan D., Maymó Joan, Alperi-López Mercedes, Olivé Alejandro, et al. , Rheumatology (Oxford), 2016 Jun, Volume 55, p.1106-11, (2016)

A genome-wide association study identifies a novel locus at 6q22.1 associated with ulcerative colitis., Julià, Antonio, Domènech Eugeni, Chaparro María, García-Sánchez Valle, Gomollón Fernando, Panés Julián, Mañosa Míriam, de Acosta Manuel Barreiro-, Gutiérrez Ana, Garcia-Planella Esther, et al. , Hum Mol Genet, 2014 Dec 20, Volume 23, p.6927-34, (2014)

Fuzziness and noise in nucleosomal architecture., Flores, Oscar, Deniz Ozgen, Soler-López Montserrat, and Orozco Modesto , Nucleic Acids Res, 2014 Apr, Volume 42, p.4934-46, (2014)

Functionalization of the 3’-ends of DNA and RNA strands with N-ethyl-N-coupled nucleosides: a promising approach to avoid 3’-exonuclease-catalyzed hydrolysis of therapeutic oligonucleotides., Terrazas, Montserrat, Alagia Adele, Faustino Ignacio, Orozco Modesto, and Eritja Ramon , Chembiochem, 2013 Mar 4, Volume 14, p.510-20, (2013)

Functional and structural conservation of CBS domains from CLC chloride channels., Estévez, Raúl, Pusch Michael, Ferrer-Costa Carles, Orozco Modesto, and Jentsch Thomas J. , J Physiol, 2004 Jun 1, Volume 557, p.363-78, (2004)

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)

Frontiers in molecular dynamics simulations of DNA., Pérez, Alberto, F Luque Javier, and Orozco Modesto , Acc Chem Res, 2012 Feb 21, Volume 45, p.196-205, (2012)

Four-stranded DNA structure stabilized by a novel G:C:A:T tetrad., Escaja, Núria, Gelpí Josep-Lluis, Orozco Modesto, Rico Manuel, Pedroso Enrique, and González Carlos , J Am Chem Soc, 2003 May 14, Volume 125, p.5654-62, (2003)

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)

Finding Conformational Transition Pathways from Discrete Molecular Dynamics Simulations, Sfriso, Pedro, Emperador Agustí, Orellana Laura, Hospital Adam, Gelpí Josep-Lluis, and Orozco Modesto , Journal of Chemical Theory and Computation, 2012/11/13, Volume 8, p.4707 - 4718, (2012)

A fast method for the determination of fractional contributions to solvation in proteins., Talavera, David, Morreale Antonio, Meyer Tim, Hospital Adam, Ferrer-Costa Carles, Gelpí Josep-Lluis, de la Cruz Xavier, Soliva Robert, F Luque Javier, and Orozco Modesto , Protein Sci, 2006 Nov, Volume 15, p.2525-33, (2006)

Fast estimation of hydrogen-bonding donor and acceptor propensities: a GMIPp study., Salichs, Albert, López M, Segarra V, Orozco Modesto, and F Luque Javier , J Comput Aided Mol Des, 2002 Aug-Sep, Volume 16, p.569-83, (2002)

Extension of the MST continuum solvation model to the RM1 semiempirical Hamiltonian., Forti, Flavio, Barril Xavier, F Luque Javier, and Orozco Modesto , J Comput Chem, 2008 Mar, Volume 29, p.578-87, (2008)

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)

Exploring the reasons for the large density of triplex-forming oligonucleotide target sequences in the human regulatory regions., J Goñi, Ramon, Vaquerizas Juan Manuel, Dopazo Joaquin, and Orozco Modesto , BMC Genomics, 2006, Volume 7, p.63, (2006)

Exploring the dynamics of calix[4]pyrrole: effect of solvent and fluorine substitution., J Blas, Ramón, López-Bes Jose Maria, Márquez Manuel, Sessler Jonathan L., F Luque Javier, and Orozco Modesto , Chemistry, 2007, Volume 13, p.1108-16, (2007)

Exploring the counterion atmosphere around DNA: what can be learned from molecular dynamics simulations?, Rueda, Manuel, Cubero Elena, Laughton Charles A., and Orozco Modesto , Biophys J, 2004 Aug, Volume 87, p.800-11, (2004)

Exploring The Conformational Landscape Of Bioactive Small Molecules, Zivanovic, Sanja, Colizzi Francesco, Moreno David, Hospital Adam, Soliva Robert, and Orozco Modesto , Journal of Chemical Theory and Computation, 08/2020, (2020)

Exploring the Complete Mutational Space of the LDL receptor LA5 Domain Using Molecular Dynamics: Linking SNPs with Disease Phenotypes in Familial Hypercholesterolemia, Angarica, Vladimir Espinosa, Orozco Modesto, and Sancho Javier , Human Molecular Genetics, (2016)

Exploring the binding mode of semicarbazide-sensitive amine oxidase/VAP-1: identification of novel substrates with insulin-like activity., Marti, Luc, Abella Anna, de la Cruz Xavier, García-Vicente Silvia, Unzeta Mercedes, Carpéné Christian, Palacín Manuel, Testar Xavier, Orozco Modesto, and Zorzano Antonio , J Med Chem, 2004 Sep 23, Volume 47, p.4865-74, (2004)

Exploring polymorphisms in B-DNA helical conformations., Dans, Pablo D., Pérez Alberto, Faustino Ignacio, Lavery Richard, and Orozco Modesto , Nucleic Acids Res, 2012 Nov, Volume 40, p.10668-78, (2012)

Exploring early stages of the chemical unfolding of proteins at the proteome scale., Candotti, Michela, Pérez Alberto, Ferrer-Costa Carles, Rueda Manuel, Meyer Tim, Gelpí Josep-Lluis, and Orozco Modesto , PLoS Computational Biology, 2013/00/01, Volume 9, p.e1003393, (2013)

Exploration of conformational transition pathways from coarse-grained simulations., Sfriso, Pedro, Hospital Adam, Emperador Agustí, and Orozco Modesto , Bioinformatics, 2013 Aug 15, Volume 29, p.1980-6, (2013)

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)

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)