Biblio

Flexibility in PAM recognition expands DNA targeting in xCas9, Hossain, Kazi A., Nierzwicki Lukasz, Orozco Modesto, Czub Jacek, and Palermo Giulia , eLife, 02/2025, Volume 13, p.RP102538, (2025)

Naphthalene diimide-naphthalimide dyads promote telomere damage by selectively targeting multimeric G-quadruplexes, Pirota, Valentina, Iachettini Sara, Platella Chiara, Zizza Pasquale, Fracchioni Giorgia, Di Vito Serena, Carachino Alice, Battistini Federica, Orozco Modesto, Freccero Mauro, et al. , Nucleic Acids Research, 04/2025, Volume 53, Issue 7, p.gkaf301, (2025)

Naphthalene diimide-naphthalimide dyads promote telomere damage by selectively targeting multimeric G-quadruplexes, Pirota, Valentina, Iachettini Sara, Platella Chiara, Zizza Pasquale, Fracchioni Giorgia, Di Vito Serena, Carachino Alice, Battistini Federica, Orozco Modesto, Freccero Mauro, et al. , Nucleic Acids Research, 04/2025, Volume 53, Issue 7, p.gkaf301, (2025)

The need to implement FAIR principles in biomolecular simulations, Amaro, Rommie E., Åqvist Johan, Bahar Ivet, Battistini Federica, Bellaiche Adam, Beltrán Daniel, Biggin Philip C., Bonomi Massimiliano, Bowman Gregory R., Bryce Richard A., et al. , Nature Methods, 04/2025, Volume 22, Issue 4, p.641 - 645, (2025)

The need to implement FAIR principles in biomolecular simulations, Amaro, Rommie E., Åqvist Johan, Bahar Ivet, Battistini Federica, Bellaiche Adam, Beltrán Daniel, Biggin Philip C., Bonomi Massimiliano, Bowman Gregory R., Bryce Richard A., et al. , Nature Methods, 04/2025, Volume 22, Issue 4, p.641 - 645, (2025)

The need to implement FAIR principles in biomolecular simulations, Amaro, Rommie E., Åqvist Johan, Bahar Ivet, Battistini Federica, Bellaiche Adam, Beltrán Daniel, Biggin Philip C., Bonomi Massimiliano, Bowman Gregory R., Bryce Richard A., et al. , Nature Methods, 04/2025, Volume 22, Issue 4, p.641 - 645, (2025)

The need to implement FAIR principles in biomolecular simulations, Amaro, Rommie E., Åqvist Johan, Bahar Ivet, Battistini Federica, Bellaiche Adam, Beltrán Daniel, Biggin Philip C., Bonomi Massimiliano, Bowman Gregory R., Bryce Richard A., et al. , Nature Methods, 04/2025, Volume 22, Issue 4, p.641 - 645, (2025)

Developments and applications of the OPTIMADE API for materials discovery, design, and data exchange, Evans, Matthew L., Bergsma Johan, Merkys Andrius, Andersen Casper W., Andersson Oskar B., Beltrán Daniel, Blokhin Evgeny, Boland Tara M., Balderas Rubén Castañeda, Choudhary Kamal, et al. , Digital Discovery, 04/2024, Volume 3, Issue 8, p.1509 - 1533, (2024)

Developments and applications of the OPTIMADE API for materials discovery, design, and data exchange, Evans, Matthew L., Bergsma Johan, Merkys Andrius, Andersen Casper W., Andersson Oskar B., Beltrán Daniel, Blokhin Evgeny, Boland Tara M., Balderas Rubén Castañeda, Choudhary Kamal, et al. , Digital Discovery, 04/2024, Volume 3, Issue 8, p.1509 - 1533, (2024)

Developments and applications of the OPTIMADE API for materials discovery, design, and data exchange, Evans, Matthew L., Bergsma Johan, Merkys Andrius, Andersen Casper W., Andersson Oskar B., Beltrán Daniel, Blokhin Evgeny, Boland Tara M., Balderas Rubén Castañeda, Choudhary Kamal, et al. , Digital Discovery, 04/2024, Volume 3, Issue 8, p.1509 - 1533, (2024)

Developments and applications of the OPTIMADE API for materials discovery, design, and data exchange, Evans, Matthew L., Bergsma Johan, Merkys Andrius, Andersen Casper W., Andersson Oskar B., Beltrán Daniel, Blokhin Evgeny, Boland Tara M., Balderas Rubén Castañeda, Choudhary Kamal, et al. , Digital Discovery, 04/2024, Volume 3, Issue 8, p.1509 - 1533, (2024)

Developments and applications of the OPTIMADE API for materials discovery, design, and data exchange, Evans, Matthew L., Bergsma Johan, Merkys Andrius, Andersen Casper W., Andersson Oskar B., Beltrán Daniel, Blokhin Evgeny, Boland Tara M., Balderas Rubén Castañeda, Choudhary Kamal, et al. , Digital Discovery, 04/2024, Volume 3, Issue 8, p.1509 - 1533, (2024)

Formation of left-handed helices by C2′-fluorinated nucleic acids under physiological salt conditions, El-Khoury, Roberto, Cabrero Cristina, Movilla Santiago, Kaur Harneesh, Friedland David, Domínguez Arnau, Thorpe James D., Roman Morgane, Orozco Modesto, González Carlos, et al. , Nucleic Acids Research, 06/2024, Volume 52, Issue 13, p.7414 - 7428, (2024)

Formation of left-handed helices by C2′-fluorinated nucleic acids under physiological salt conditions, El-Khoury, Roberto, Cabrero Cristina, Movilla Santiago, Kaur Harneesh, Friedland David, Domínguez Arnau, Thorpe James D., Roman Morgane, Orozco Modesto, González Carlos, et al. , Nucleic Acids Research, 06/2024, Volume 52, Issue 13, p.7414 - 7428, (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 Rhodium Analogue of Coenzyme B12 as an Anti-Photoregulatory Ligand Inhibiting Bacterial CarH Photoreceptors, Pérez-Castaño, Ricardo, Aranda Juan, Widner Florian J., Kieninger Christoph, Deery Evelyne, Warren Martin J., Orozco Modesto, Elías-Arnanz Montserrat, Padmanabhan S., and Kräutler Bernhard , Angewandte Chemie International Edition, 04/2024, Volume 63, Issue 18, p.e202401626, (2024)

RNA dynamics from experimental and computational approaches, Bussi, Giovanni, Bonomi Massimiliano, Gkeka Paraskevi, Sattler Michael, Al-Hashimi Hashim M., Auffinger Pascal, Duca Maria, Foricher Yann, Incarnato Danny, Jones Alisha N., et al. , Structure, 09/2024, Volume 32, Issue 9, p.1281 - 1287, (2024)

SETD8 inhibition targets cancer cells with increased rates of ribosome biogenesis, Murga, Matilde, Lopez-Pernas Gema, Soliva Robert, Fueyo-Marcos Elena, Amor Corina, Faustino Ignacio, Serna Marina, Serrano Alicia G., Díaz Lucía, Martínez Sonia, et al. , Cell Death & Disease, 09/2024, Volume 15, Issue 9, p.694, (2024)

Special issue: Multiscale simulations of DNA from electrons to nucleosomes, Maddocks, John H., Dans Pablo D., Cheatham Thomas H., Harris Sarah, Laughton Charles, Orozco Modesto, Pollack Lois, and Olson Wilma K. , Biophysical Reviews, 06/2024, Volume 16, Issue 3, p.259 - 262, (2024)

Characterization of p38α autophosphorylation inhibitors that target the non-canonical activation pathway, González, Lorena, Díaz Lucía, Pous Joan, Baginski Blazej, Duran-Corbera Anna, Scarpa Margherita, Brun-Heath Isabelle, Igea Ana, Martin-Malpartida Pau, Ruiz Lidia, et al. , Nature Communications, 06/2023, Volume 14, Issue 1, p.3318, (2023)

Characterization of p38α autophosphorylation inhibitors that target the non-canonical activation pathway, González, Lorena, Díaz Lucía, Pous Joan, Baginski Blazej, Duran-Corbera Anna, Scarpa Margherita, Brun-Heath Isabelle, Igea Ana, Martin-Malpartida Pau, Ruiz Lidia, et al. , Nature Communications, 06/2023, Volume 14, Issue 1, p.3318, (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)

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)

The pseudotorsional space of RNA, Grille, Leandro, Gallego Diego, Darré Leonardo, da Rosa Gabriela, Battistini Federica, Orozco Modesto, and Dans Pablo D. , RNA, 12/2023, Volume 29, Issue 12, p.1896 - 1909, (2023)

The pseudotorsional space of RNA, Grille, Leandro, Gallego Diego, Darré Leonardo, da Rosa Gabriela, Battistini Federica, Orozco Modesto, and Dans Pablo D. , RNA, 12/2023, Volume 29, Issue 12, p.1896 - 1909, (2023)

The pseudotorsional space of RNA, Grille, Leandro, Gallego Diego, Darré Leonardo, da Rosa Gabriela, Battistini Federica, Orozco Modesto, and Dans Pablo D. , RNA, 12/2023, Volume 29, Issue 12, p.1896 - 1909, (2023)

Splice variants of mitofusin 2 shape the endoplasmic reticulum and tether it to mitochondria, Naón, Déborah, Hernández-Alvarez María Isabel, Shinjo Satoko, Wieczor Milosz, Ivanova Saška, de Brito Olga Martins, Quintana Albert, Hidalgo Juan, Palacín Manuel, Aparicio Pilar, et al. , Science, 07/2023, Volume 380, Issue 6651, p.eadh9351, (2023)

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)

Molecular basis of Arginine and Lysine DNA sequence-dependent thermo-stability modulation, Martin, Benjamin, Dans Pablo D., Wieczór Milosz, Villegas Núria, Brun-Heath Isabelle, Battistini Federica, Terrazas Montserrat, and Orozco Modesto , PLoS computational biology, 01/2022, Volume 18, Issue 1, p.e1009749 - e1009749, (2022)

Pre-exascale HPC approaches for molecular dynamics simulations. Covid-19 research: A use case, Wieczór, Miłosz, Genna Vito, Aranda Juan, Badia Rosa M., Gelpí Josep Lluis, Gapsys Vytautas, de Groot Bert L., Lindahl Erik, Municoy Martí, Hospital Adam, et al. , WIREs Computational Molecular Science, 05/2022, Volume In Press, p.e1622, (2022)

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)

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)

Mutation in KARS: A novel mechanism for severe anaphylaxis, Ribó, Pau, Guo Yanru, Aranda Juan, Ainsua-Enrich Erola, Navinés-Ferrer Arnau, Guerrero Mario, Pascal Mariona, de la Cruz Cinthia, Orozco Modesto, Muñoz-Cano Rosa, et al. , Journal of Allergy and Clinical Immunology, 05/2021, Volume 147, Issue 5, p.1855 - 1864.e9, (2021)

Sequence-dependent structural properties of B-DNA: what have we learned in 40 years?, da Rosa, Gabriela, Grille Leandro, Calzada Victoria, Ahmad Katya, Arcon Juan Pablo, Battistini Federica, Bayarri Genis, Bishop Thomas, Carloni Paolo, III Thomas Cheatham, et al. , Biophysical Reviews, 11/2021, (2021)

Sequence-dependent structural properties of B-DNA: what have we learned in 40 years?, da Rosa, Gabriela, Grille Leandro, Calzada Victoria, Ahmad Katya, Arcon Juan Pablo, Battistini Federica, Bayarri Genis, Bishop Thomas, Carloni Paolo, III Thomas Cheatham, et al. , Biophysical Reviews, 11/2021, (2021)

Colibactin DNA-damage signature indicates mutational impact in colorectal cancer, Dziubańska-Kusibab, Paulina J., Berger Hilmar, Battistini Federica, Bouwman Britta A. M., Iftekhar Amina, Katainen Riku, Cajuso Tatiana, Crosetto Nicola, Orozco Modesto, Aaltonen Lauri A., et al. , Nature Medicine, 07/2020, Volume 26, Issue 7, p.1063 - 1069, (2020)

A multi-modal coarse grained model of DNA flexibility mappable to the atomistic level, Walther, Jurgen, Dans Pablo D., Balaceanu Alexandra, Hospital Adam, Bayarri Genis, and Orozco Modesto , Nucleic Acids Research, 01/2020, (2020)

AutoDock Bias: improving binding mode prediction and virtual screening using known protein–ligand interactions, Arcon, Juan Pablo, Modenutti Carlos P., Avendaño Demian, Lopez Elias D., Defelipe Lucas A., Ambrosio Francesca Alessandra, Turjanski Adrian G., Forli Stefano, and Martí Marcelo A. , Bioinformatics, 2019, Volume 35, Issue 19, p.3836 - 3838, (2019)

BioExcel Building Blocks, a software library for interoperable biomolecular simulation workflows, Andrio, Pau, Hospital Adam, Conejero Javier, Jordá Luis, Del Pino Marc, Codó Laia, Soiland-Reyes Stian, Goble Carole, Lezzi Daniele, Badia Rosa M., et al. , Nature Scientific Data, 09/2019, Volume 6, Issue 1, p.169, (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)

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)

An In-Depth Look at DNA Crystals through the Prism of Molecular Dynamics Simulations, Kuzmanic, Antonija, Dans Pablo D., and Orozco Modesto , Chem, 03/2019, Volume 5, Issue 3, p.649 - 663, (2019)

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)

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)

Modulation of the helical properties of DNA: next-to-nearest neighbour effects and beyond, Balaceanu, Alexandra, Buitrago Diana, Walther Jurgen, Hospital Adam, Dans Pablo D., and Orozco Modesto , 01/2019, (2019)

Nucleosome Dynamics: a new tool for the dynamic analysis of nucleosome positioning, Buitrago, Diana, Codó Laia, Illa Ricard, de Jorge Pau, Battistini Federica, Flores Oscar, Bayarri Genis, Royo Romina, Del Pino Marc, Heath Simon, et al. , Nucleic Acids Research, 08/2019, (2019)

Nucleosome Dynamics: a new tool for the dynamic analysis of nucleosome positioning, Buitrago, Diana, Codó Laia, Illa Ricard, de Jorge Pau, Battistini Federica, Flores Oscar, Bayarri Genis, Royo Romina, Del Pino Marc, Heath Simon, et al. , Nucleic Acids Research, 08/2019, (2019)