Biblio

Modeling, Simulations, and Bioinformatics at the Service of RNA Structure, Dans, Pablo D., Gallego Diego, Balaceanu Alexandra, Darré Leonardo, Gómez Hansel, and Orozco Modesto , Chem, 10/2019, Volume 5, Issue 1, p.51 - 73, (2019)

MiOS, an integrated imaging and computational strategy to model gene folding with nucleosome resolution, Neguembor, Maria Victoria, Arcon Juan Pablo, Buitrago Diana, Lema Rafael, Walther Jurgen, Garate Ximena, Martin Laura, Romero Pablo, Abed Jumana AlHaj, Gut Marta, et al. , Nat Struct Mol Biol , 10/2022, Volume in press, (2022)

MiOS, an integrated imaging and computational strategy to model gene folding with nucleosome resolution, Neguembor, Maria Victoria, Arcon Juan Pablo, Buitrago Diana, Lema Rafael, Walther Jurgen, Garate Ximena, Martin Laura, Romero Pablo, Abed Jumana AlHaj, Gut Marta, et al. , Nat Struct Mol Biol , 10/2022, Volume in press, (2022)

Mechanism of reaction of RNA-dependent RNA polymerase from SARS-CoV-2, Aranda, Juan, Wieczór Milosz, Terrazas Montserrat, Brun-Heath Isabelle, and Orozco Modesto , Chem Catalysis, 05/2022, Volume 2, Issue 5, p.1099, (2022)

Making Canonical Workflow Building Blocks Interoperable across Workflow Languages, Soiland-Reyes, Stian, Bayarri Genis, Andrio Pau, Long Robin, Lowe Douglas, Niewielska Ania, Hospital Adam, and Groth Paul , Data Intelligence, 2022, p.1 - 16, (2022)

Long-timescale dynamics of the Drew-Dickerson dodecamer., Dans, Pablo D., Danilāne Linda, Ivani Ivan, Dršata Tomáš, Lankaš Filip, Hospital Adam, Walther Jurgen, Pujagut Ricard Illa, Battistini Federica, Gelpí Josep-Lluis, et al. , Nucleic Acids Res, 2016 May 19, Volume 44, p.4052-66, (2016)

Ligand-induced dynamical regulation of NO conversion in Mycobacterium tuberculosis truncated hemoglobin-N., Bidon-Chanal, Axel, Martí Marcelo A., Crespo Alejandro, Milani Mario, Orozco Modesto, Bolognesi Martino, F Luque Javier, and Estrin Darío A. , Proteins, 2006 Aug 1, Volume 64, p.457-64, (2006)

Ligand-induced dynamical regulation of NO conversion in Mycobacterium tuberculosis truncated hemoglobin-N., Bidon-Chanal, Axel, Martí Marcelo A., Crespo Alejandro, Milani Mario, Orozco Modesto, Bolognesi Martino, F Luque Javier, and Estrin Darío A. , Proteins, 2006 Aug 1, Volume 64, p.457-64, (2006)

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)

An integrated machine-learning model to predict nucleosome architecture, Sala, Alba, Labrador Mireia, Buitrago Diana, de Jorge Pau, Battistini Federica, Heath Isabelle Brun, and Orozco Modesto , Nucleic Acids Research, 09/2024, Volume 52, Issue 17, p.10132 - 10143, (2024)

An integrated machine-learning model to predict nucleosome architecture, Sala, Alba, Labrador Mireia, Buitrago Diana, de Jorge Pau, Battistini Federica, Heath Isabelle Brun, and Orozco Modesto , Nucleic Acids Research, 09/2024, Volume 52, Issue 17, p.10132 - 10143, (2024)

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 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)

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)

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)

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)

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)

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 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)

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)

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)

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)

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)

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)

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 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 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)

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)

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 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)

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)

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)

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)

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)

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)