Biblio

BioExcel Building Blocks REST API (BioBB REST API), programmatic access to interoperable biomolecular simulation tools, Bayarri, Genis, Andrio Pau, Hospital Adam, Orozco Modesto, and Gelpí Josep Lluis , Bioinformatics, 05/2022, Volume 38, Issue 12, p.3303, (2022)

BioExcel Building Blocks Workflows (BioBB-Wfs), an integrated web-based platform for biomolecular simulations, Bayarri, Genis, Andrio Pau, Hospital Adam, Orozco Modesto, and Gelpí Josep Lluís , Nucleic Acids Res, 05/2022, Volume 50, Issue W1, p.W107, (2022)

The BioExcel methodology for developing dynamic, scalable, reliable and portable computational biomolecular workflows, Ejarque, J., Andrio P., Hospital Adam, Conejero J., Lezzi D., Gelpi J. L., and Badia R. M. , 2022 IEEE 18th International Conference on e-Science (e-Science), 12/2022, (2022)

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)

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)

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)

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)

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)

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)

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)

The structural role of SARS-CoV-2 genetic background in the emergence and success of spike mutations: The case of the spike A222V mutation, Ginex, Tiziana, Marco-Marín Clara, Wieczór Miłosz, Mata Carlos P., Krieger James, Ruiz-Rodriguez Paula, López-Redondo Maria Luisa, Francés-Gómez Clara, Melero Roberto, Sánchez-Sorzano Carlos Óscar, et al. , PLOS Pathogens, 07/2022, Volume 18, Issue 7, p.e1010631 - , (2022)

The structural role of SARS-CoV-2 genetic background in the emergence and success of spike mutations: The case of the spike A222V mutation, Ginex, Tiziana, Marco-Marín Clara, Wieczór Miłosz, Mata Carlos P., Krieger James, Ruiz-Rodriguez Paula, López-Redondo Maria Luisa, Francés-Gómez Clara, Melero Roberto, Sánchez-Sorzano Carlos Óscar, et al. , PLOS Pathogens, 07/2022, Volume 18, Issue 7, p.e1010631 - , (2022)

The structural role of SARS-CoV-2 genetic background in the emergence and success of spike mutations: The case of the spike A222V mutation, Ginex, Tiziana, Marco-Marín Clara, Wieczór Miłosz, Mata Carlos P., Krieger James, Ruiz-Rodriguez Paula, López-Redondo Maria Luisa, Francés-Gómez Clara, Melero Roberto, Sánchez-Sorzano Carlos Óscar, et al. , PLOS Pathogens, 07/2022, Volume 18, Issue 7, p.e1010631 - , (2022)

The structural role of SARS-CoV-2 genetic background in the emergence and success of spike mutations: The case of the spike A222V mutation, Ginex, Tiziana, Marco-Marín Clara, Wieczór Miłosz, Mata Carlos P., Krieger James, Ruiz-Rodriguez Paula, López-Redondo Maria Luisa, Francés-Gómez Clara, Melero Roberto, Sánchez-Sorzano Carlos Óscar, et al. , PLOS Pathogens, 07/2022, Volume 18, Issue 7, p.e1010631 - , (2022)

The structural role of SARS-CoV-2 genetic background in the emergence and success of spike mutations: The case of the spike A222V mutation, Ginex, Tiziana, Marco-Marín Clara, Wieczór Miłosz, Mata Carlos P., Krieger James, Ruiz-Rodriguez Paula, López-Redondo Maria Luisa, Francés-Gómez Clara, Melero Roberto, Sánchez-Sorzano Carlos Óscar, et al. , PLOS Pathogens, 07/2022, Volume 18, Issue 7, p.e1010631 - , (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)

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)

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)

4D Genome Rewiring during Oncogene-Induced and Replicative Senescence, Sati, Satish, Bonev Boyan, Szabo Quentin, Jost Daniel, Bensadoun Paul, Serra Francois, Loubiere Vincent, Papadopoulos Giorgio Lucio, Rivera-Mulia Juan-Carlos, Fritsch Lauriane, et al. , Molecular Cell, 07/2020, Volume 78, Issue 3, p.522 - 538.e9, (2020)

4D Genome Rewiring during Oncogene-Induced and Replicative Senescence, Sati, Satish, Bonev Boyan, Szabo Quentin, Jost Daniel, Bensadoun Paul, Serra Francois, Loubiere Vincent, Papadopoulos Giorgio Lucio, Rivera-Mulia Juan-Carlos, Fritsch Lauriane, et al. , Molecular Cell, 07/2020, Volume 78, Issue 3, p.522 - 538.e9, (2020)

Bioactive Conformational Ensemble Server And Database. A Public Framework To Speed Up In Silico Drug Discovery, Zivanovic, Sanja, Bayarri Genis, Colizzi Francesco, Moreno David, Gelpí Josep Lluis, Soliva Robert, Hospital Adam, and Orozco Modesto , Journal of Chemical Theory and Computation, 08/2020, (2020)

A community proposal to integrate structural bioinformatics activities in ELIXIR (3D-Bioinfo Community), Orengo, C, Velankar S, Wodak S, Zoete V, Bonvin AMJJ, Elofsson A, Feenstra KA, Gerloff DL, Hamelryck T, Hancock JM, et al. , F1000Research, 04/2020, Volume 9, (2020)

An artificial DNAzyme RNA ligase shows a reaction mechanism resembling that of cellular polymerases, Aranda, Juan, Terrazas Montserrat, Gómez Hansel, Villegas Núria, and Orozco Modesto , Nature Catalysis, 06/2019, Volume 2, Issue 6, p.544 - 552, (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)

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)

Deficient Endoplasmic Reticulum-Mitochondrial Phosphatidylserine Transfer Causes Liver Disease, Hernández-Alvarez, María Isabel, Sebastián David, Vives Sara, Ivanova Saška, Bartoccioni Paola, Kakimoto Pamela, Plana Natalia, Veiga Sónia R., Hernández Vanessa, Vasconcelos Nuno, et al. , Cell, 05/2019, Volume 177, Issue 4, p.881 - 895.e17, (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)

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)

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)

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)

Oncogenic mutations at the EGFR ectodomain structurally converge to remove a steric hindrance on a kinase-coupled cryptic epitope, Orellana, Laura, Thorne Amy H., Lema Rafael, Gustavsson Johan, Parisian Alison D., Hospital Adam, Cordeiro Tiago N., Bernadó Pau, Scott Andrew M., Brun-Heath Isabelle, et al. , Proceedings of the National Academy of Sciences, 04/2019, (2019)

The Origins and the Biological Consequences of the Pur/Pyr DNA·RNA Asymmetry, Terrazas, Montserrat, Genna Vito, Portella Guillem, Villegas Núria, Sanchez Dani, Arnan Carme, Pulido-Quetglas Carlos, Johnson Rory, Guigó Roderic, Brun-Heath Isabelle, et al. , Chem, 04/2019, (2019)

The Origins and the Biological Consequences of the Pur/Pyr DNA·RNA Asymmetry, Terrazas, Montserrat, Genna Vito, Portella Guillem, Villegas Núria, Sanchez Dani, Arnan Carme, Pulido-Quetglas Carlos, Johnson Rory, Guigó Roderic, Brun-Heath Isabelle, et al. , Chem, 04/2019, (2019)

Side chain to main chain hydrogen bonds stabilize a polyglutamine helix in a transcription factor, Escobedo, Albert, Topal Busra, Kunze Micha B. A., Aranda Juan, Chiesa Giulio, Mungianu Daniele, Bernardo-Seisdedos Ganeko, Eftekharzadeh Bahareh, Gairí Margarida, Pierattelli Roberta, et al. , Nature Communication, 05/2019, Volume 10, Issue 1, p.2034, (2019)

Side chain to main chain hydrogen bonds stabilize a polyglutamine helix in a transcription factor, Escobedo, Albert, Topal Busra, Kunze Micha B. A., Aranda Juan, Chiesa Giulio, Mungianu Daniele, Bernardo-Seisdedos Ganeko, Eftekharzadeh Bahareh, Gairí Margarida, Pierattelli Roberta, et al. , Nature Communication, 05/2019, Volume 10, Issue 1, p.2034, (2019)

Surviving the deluge of biosimulation data, Hospital, Adam, Battistini Federica, Soliva Robert, Gelpí Josep Lluis, and Orozco Modesto , Wiley Interdisciplinary Reviews: WIREs Comput Mol Sci, 11/2019, Volume n/a, Issue n/a, p.e1449, (2019)

A synthetic genetic polymer with an uncharged backbone chemistry based on alkyl phosphonate nucleic acids, Arangundy-Franklin, Sebastian, Taylor Alexander I., Porebski Benjamin T., Genna Vito, Peak-Chew Sew, Vaisman Alexandra, Woodgate Roger, Orozco Modesto, and Holliger Philipp , Nature Chemistry, 04/2019, (2019)

VeriNA3d: an R package for nucleic acids data mining, Gallego, Diego, Darré Leonardo, Dans Pablo D., and Orozco Modesto , Bioinformatics, 07/2019, (2019)

Challenges and guidelines toward 4D nucleome data and model standards, Marti-Renom, Marc A., Almouzni Genevieve, Bickmore Wendy A., Bystricky Kerstin, Cavalli Giacomo, Fraser Peter, Gasser Susan M., Giorgetti Luca, Heard Edith, Nicodemi Mario, et al. , Nature Genetics, 10/2018, Volume 50, Issue 10, p.1352 - 1358, (2018)

Challenges and guidelines toward 4D nucleome data and model standards, Marti-Renom, Marc A., Almouzni Genevieve, Bickmore Wendy A., Bystricky Kerstin, Cavalli Giacomo, Fraser Peter, Gasser Susan M., Giorgetti Luca, Heard Edith, Nicodemi Mario, et al. , Nature Genetics, 10/2018, Volume 50, Issue 10, p.1352 - 1358, (2018)

Protein Flexibility and Synergy of HMG Domains Underlie U-Turn Bending of DNA by TFAM in Solution, Rubio-Cosials, Anna, Battistini Federica, Gansen Alexander, Cuppari Anna, Bernadó Pau, Orozco Modesto, Langowski Jörg, Tóth Katalin, and Solà Maria , Biophysical Journal, 05/2018, Volume 114, p.2386 - 2396, (2018)

Targeting RNA structure in SMN2 reverses spinal muscular atrophy molecular phenotypes, Garcia-Lopez, Amparo, Tessaro Francesca, Jonker Hendrik R. A., Wacker Anna, Richter Christian, Comte Arnaud, Berntenis Nikolaos, Schmucki Roland, Hatje Klas, Petermann Olivier, et al. , Nature Communication, 2018/05/23, Volume 9, Issue 1, p.2032, (2018)