Biblio

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)

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 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 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 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)

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 role of glutamate 317 in galactosyl transfer by α3GalT: a computational study., Gómez, Hansel, Lluch José M., and Masgrau Laura , Carbohydr Res, 2012 Jul 15, Volume 356, p.204-8, (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 aberrant super-enhancer DNA methylation in human cancer, Heyn, Holger, Vidal Enrique, Ferreira Humberto J., Vizoso Miguel, Sayols Sergi, Gomez Antonio, Moran Sebastian, Boque-Sastre Raquel, Guil Sonia, Martinez-Cardus Anna, et al. , Genome Biology, 01/2016, Volume 17, p.11, (2016)

Epigenomic analysis detects aberrant super-enhancer DNA methylation in human cancer, Heyn, Holger, Vidal Enrique, Ferreira Humberto J., Vizoso Miguel, Sayols Sergi, Gomez Antonio, Moran Sebastian, Boque-Sastre Raquel, Guil Sonia, Martinez-Cardus Anna, et al. , Genome Biology, 01/2016, Volume 17, p.11, (2016)

Epigenomic analysis detects aberrant super-enhancer DNA methylation in human cancer, Heyn, Holger, Vidal Enrique, Ferreira Humberto J., Vizoso Miguel, Sayols Sergi, Gomez Antonio, Moran Sebastian, Boque-Sastre Raquel, Guil Sonia, Martinez-Cardus Anna, et al. , Genome Biology, 01/2016, Volume 17, p.11, (2016)

Epigenetic loss of RNA-methyltransferase NSUN5 in glioma targets ribosomes to drive a stress adaptive translational program, Janin, Maxime, Ortiz-Barahona Vanessa, de Moura Manuel Castro, Martinez-Cardus Anna, Llinàs-Arias Pere, Soler Marta, Nachmani Daphna, Pelletier Joffrey, Schumann Ulrike, Calleja-Cervantes Maria E., et al. , Acta neuropathologica, 12/2019, Volume 138, Issue 6, p.1053 - 1074, (2019)

Epigenetic loss of RNA-methyltransferase NSUN5 in glioma targets ribosomes to drive a stress adaptive translational program, Janin, Maxime, Ortiz-Barahona Vanessa, de Moura Manuel Castro, Martinez-Cardus Anna, Llinàs-Arias Pere, Soler Marta, Nachmani Daphna, Pelletier Joffrey, Schumann Ulrike, Calleja-Cervantes Maria E., et al. , Acta neuropathologica, 12/2019, Volume 138, Issue 6, p.1053 - 1074, (2019)

Epigenetic loss of RNA-methyltransferase NSUN5 in glioma targets ribosomes to drive a stress adaptive translational program, Janin, Maxime, Ortiz-Barahona Vanessa, de Moura Manuel Castro, Martinez-Cardus Anna, Llinàs-Arias Pere, Soler Marta, Nachmani Daphna, Pelletier Joffrey, Schumann Ulrike, Calleja-Cervantes Maria E., et al. , Acta neuropathologica, 12/2019, Volume 138, Issue 6, p.1053 - 1074, (2019)

Epigenetic loss of RNA-methyltransferase NSUN5 in glioma targets ribosomes to drive a stress adaptive translational program, Janin, Maxime, Ortiz-Barahona Vanessa, de Moura Manuel Castro, Martinez-Cardus Anna, Llinàs-Arias Pere, Soler Marta, Nachmani Daphna, Pelletier Joffrey, Schumann Ulrike, Calleja-Cervantes Maria E., et al. , Acta neuropathologica, 12/2019, Volume 138, Issue 6, p.1053 - 1074, (2019)

Epigenetic loss of RNA-methyltransferase NSUN5 in glioma targets ribosomes to drive a stress adaptive translational program, Janin, Maxime, Ortiz-Barahona Vanessa, de Moura Manuel Castro, Martinez-Cardus Anna, Llinàs-Arias Pere, Soler Marta, Nachmani Daphna, Pelletier Joffrey, Schumann Ulrike, Calleja-Cervantes Maria E., et al. , Acta neuropathologica, 12/2019, Volume 138, Issue 6, p.1053 - 1074, (2019)

Epigenetic loss of RNA-methyltransferase NSUN5 in glioma targets ribosomes to drive a stress adaptive translational program, Janin, Maxime, Ortiz-Barahona Vanessa, de Moura Manuel Castro, Martinez-Cardus Anna, Llinàs-Arias Pere, Soler Marta, Nachmani Daphna, Pelletier Joffrey, Schumann Ulrike, Calleja-Cervantes Maria E., et al. , Acta neuropathologica, 12/2019, Volume 138, Issue 6, p.1053 - 1074, (2019)

Epigenetic loss of RNA-methyltransferase NSUN5 in glioma targets ribosomes to drive a stress adaptive translational program, Janin, Maxime, Ortiz-Barahona Vanessa, de Moura Manuel Castro, Martinez-Cardus Anna, Llinàs-Arias Pere, Soler Marta, Nachmani Daphna, Pelletier Joffrey, Schumann Ulrike, Calleja-Cervantes Maria E., et al. , Acta neuropathologica, 12/2019, Volume 138, Issue 6, p.1053 - 1074, (2019)

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)

Efficient siRNA-peptide conjugation for specific targeted delivery into tumor cells, Gandioso, Albert, Massaguer Anna, Villegas Núria, Salvans Cándida, Sanchez Dani, Brun-Heath Isabelle, Marchan Vicente, Orozco Modesto, and Terrazas Montserrat , Chemical Communications, 03/2017, Volume 53, Issue 19, p.2870 - 2873, (2017)

Efficient siRNA-peptide conjugation for specific targeted delivery into tumor cells, Gandioso, Albert, Massaguer Anna, Villegas Núria, Salvans Cándida, Sanchez Dani, Brun-Heath Isabelle, Marchan Vicente, Orozco Modesto, and Terrazas Montserrat , Chemical Communications, 03/2017, Volume 53, Issue 19, p.2870 - 2873, (2017)

Efficient aminoacylation of the tRNA(Ala) acceptor stem: dependence on the 2:71 base pair., Beuning, Penny J., Nagan Maria C., Cramer Christopher J., Musier-Forsyth Karin, Gelpí Josep-Lluis, and Bashford Donald , RNA, 2002 May, Volume 8, p.659-70, (2002)

Effect of bulky lesions on DNA: solution structure of a DNA duplex containing a cholesterol adduct., Gómez-Pinto, Irene, Cubero Elena, Kalko Susana G., Monaco Vania, van der Marel Gijs, van Boom Jacques H., Orozco Modesto, and González Carlos , J Biol Chem, 2004 Jun 4, Volume 279, p.24552-60, (2004)

Dramatic effect of furanose C2’ substitution on structure and stability: directing the folding of the human telomeric quadruplex with a single fluorine atom., Martín-Pintado, Nerea, Yahyaee-Anzahaee Maryam, Deleavey Glen F., Portella Guillem, Orozco Modesto, Damha Masad J., and González Carlos , J Am Chem Soc, 2013 Apr 10, Volume 135, p.5344-7, (2013)

DNA structure directs positioning of the mitochondrial genome packaging protein Abf2p, Chakraborty, Arka, Lyonnais Sébastien, Battistini Federica, Hospital Adam, Medici Giorgio, Prohens Rafel, Orozco Modesto, Vilardell Josep, and Solà Maria , Nucleic Acids Research, 11/2016, (2016)

A DNA methylation map of human cancer at single base-pair resolution, Vidal, E, Sayols S, Moran S, Guillaumet-Adkins A, Schroeder M P., Royo R, Orozco Modesto, Gut M, Gut I, Lopez-Bigas N, et al. , Oncogene, 06/2017, p.1-10, (2017)

DNA double-strand break-derived RNA drives TIRR/53BP1 complex dissociation, Ketley, Ruth F., Battistini Federica, Alagia Adele, Mondielli Clémence, Iehl Florence, Balikçi Esra, Huber Kilian V. M., Orozco Modesto, and Gullerova Monika , Cell Reports, 10/2022, Volume 41, Issue 4, (2022)

Dispersion and repulsion contributions to the solvation free energy: comparison of quantum mechanical and classical approaches in the polarizable continuum model., Curutchet, Carles, Orozco Modesto, F Luque Javier, Mennucci Benedetta, and Tomasi Jacopo , J Comput Chem, 2006 Nov 30, Volume 27, p.1769-80, (2006)

Differential stability of 2’F-ANA*RNA and ANA*RNA hybrid duplexes: roles of structure, pseudohydrogen bonding, hydration, ion uptake and flexibility., Watts, Jonathan K., Martín-Pintado Nerea, Gómez-Pinto Irene, Schwartzentruber Jeremy, Portella Guillem, Orozco Modesto, González Carlos, and Damha Masad J. , Nucleic Acids Res, 2010 Apr, Volume 38, p.2498-511, (2010)

DFFR: A New Method for High-Throughput Recalibration of Automatic Force-Fields for Drugs, Moreno, David, Zivanovic Sanja, Colizzi Francesco, Hospital Adam, Aranda Juan, Soliva Robert, and Orozco Modesto , Journal of Chemical Theory and Computation, 08/2020, (2020)

Developments and applications of the OPTIMADE API for materials discovery, design, and data exchange, Evans, Matthew, Bergsma Johan, Merkys Andrius, Andersen Casper, Andersson Oskar B., Beltrán Daniel, Blokhin Evgeny, Boland Tara M., Balderas Rubén Castañeda, Choudhary Kamal, et al. , Digital Discovery, 04/2024, p. - , (2024)

Developments and applications of the OPTIMADE API for materials discovery, design, and data exchange, Evans, Matthew, Bergsma Johan, Merkys Andrius, Andersen Casper, Andersson Oskar B., Beltrán Daniel, Blokhin Evgeny, Boland Tara M., Balderas Rubén Castañeda, Choudhary Kamal, et al. , Digital Discovery, 04/2024, p. - , (2024)

Developments and applications of the OPTIMADE API for materials discovery, design, and data exchange, Evans, Matthew, Bergsma Johan, Merkys Andrius, Andersen Casper, Andersson Oskar B., Beltrán Daniel, Blokhin Evgeny, Boland Tara M., Balderas Rubén Castañeda, Choudhary Kamal, et al. , Digital Discovery, 04/2024, p. - , (2024)

Developments and applications of the OPTIMADE API for materials discovery, design, and data exchange, Evans, Matthew, Bergsma Johan, Merkys Andrius, Andersen Casper, Andersson Oskar B., Beltrán Daniel, Blokhin Evgeny, Boland Tara M., Balderas Rubén Castañeda, Choudhary Kamal, et al. , Digital Discovery, 04/2024, p. - , (2024)

Design, synthesis, and biological evaluation of dual binding site acetylcholinesterase inhibitors: new disease-modifying agents for Alzheimer’s disease., Muñoz-Ruiz, Pilar, Rubio Laura, García-Palomero Esther, Dorronsoro Isabel, del Monte-Millán María, Valenzuela Rita, Usán Paola, de Austria Celia, Bartolini Manuela, Andrisano Vincenza, et al. , J Med Chem, 2005 Nov 17, Volume 48, p.7223-33, (2005)

Design, synthesis, and biological evaluation of dual binding site acetylcholinesterase inhibitors: new disease-modifying agents for Alzheimer’s disease., Muñoz-Ruiz, Pilar, Rubio Laura, García-Palomero Esther, Dorronsoro Isabel, del Monte-Millán María, Valenzuela Rita, Usán Paola, de Austria Celia, Bartolini Manuela, Andrisano Vincenza, et al. , J Med Chem, 2005 Nov 17, Volume 48, p.7223-33, (2005)

Design, synthesis, and biological evaluation of dual binding site acetylcholinesterase inhibitors: new disease-modifying agents for Alzheimer’s disease., Muñoz-Ruiz, Pilar, Rubio Laura, García-Palomero Esther, Dorronsoro Isabel, del Monte-Millán María, Valenzuela Rita, Usán Paola, de Austria Celia, Bartolini Manuela, Andrisano Vincenza, et al. , J Med Chem, 2005 Nov 17, Volume 48, p.7223-33, (2005)

A deletion at ADAMTS9-MAGI1 locus is associated with psoriatic arthritis risk., Julià, Antonio, Pinto José Antonio, Gratacós Jordi, Queiró Rubén, Ferrándiz Carlos, Fonseca Eduardo, Montilla Carlos, Torre-Alonso Juan Carlos, Puig Lluís, Venegas José Javier Pé, et al. , Ann Rheum Dis, 2015 Oct, Volume 74, p.1875-81, (2015)

A deletion at ADAMTS9-MAGI1 locus is associated with psoriatic arthritis risk., Julià, Antonio, Pinto José Antonio, Gratacós Jordi, Queiró Rubén, Ferrándiz Carlos, Fonseca Eduardo, Montilla Carlos, Torre-Alonso Juan Carlos, Puig Lluís, Venegas José Javier Pé, et al. , Ann Rheum Dis, 2015 Oct, Volume 74, p.1875-81, (2015)

A deletion at ADAMTS9-MAGI1 locus is associated with psoriatic arthritis risk., Julià, Antonio, Pinto José Antonio, Gratacós Jordi, Queiró Rubén, Ferrándiz Carlos, Fonseca Eduardo, Montilla Carlos, Torre-Alonso Juan Carlos, Puig Lluís, Venegas José Javier Pé, et al. , Ann Rheum Dis, 2015 Oct, Volume 74, p.1875-81, (2015)

A deletion at ADAMTS9-MAGI1 locus is associated with psoriatic arthritis risk., Julià, Antonio, Pinto José Antonio, Gratacós Jordi, Queiró Rubén, Ferrándiz Carlos, Fonseca Eduardo, Montilla Carlos, Torre-Alonso Juan Carlos, Puig Lluís, Venegas José Javier Pé, et al. , Ann Rheum Dis, 2015 Oct, Volume 74, p.1875-81, (2015)

A deletion at ADAMTS9-MAGI1 locus is associated with psoriatic arthritis risk., Julià, Antonio, Pinto José Antonio, Gratacós Jordi, Queiró Rubén, Ferrándiz Carlos, Fonseca Eduardo, Montilla Carlos, Torre-Alonso Juan Carlos, Puig Lluís, Venegas José Javier Pé, et al. , Ann Rheum Dis, 2015 Oct, Volume 74, p.1875-81, (2015)

De novo design of a non-local β-sheet protein with high stability and accuracy, Marcos, Enrique, Chidyausiku Tamuka M., McShan Andrew C., Evangelidis Thomas, Nerli Santrupti, Carter Lauren, Nivón Lucas G., Davis Audrey, Oberdorfer Gustav, Tripsianes Konstantinos, et al. , Nature structural & molecular biology, 11/2018, Volume 25, Issue 11, p.1028 - 1034, (2018)

De novo design of a non-local β-sheet protein with high stability and accuracy, Marcos, Enrique, Chidyausiku Tamuka M., McShan Andrew C., Evangelidis Thomas, Nerli Santrupti, Carter Lauren, Nivón Lucas G., Davis Audrey, Oberdorfer Gustav, Tripsianes Konstantinos, et al. , Nature structural & molecular biology, 11/2018, Volume 25, Issue 11, p.1028 - 1034, (2018)

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)