The BioExcel methodology for developing dynamic, scalable, reliable and portable computational biomolecular workflows

Autor: Jorge Ejarque, Pau Andrio, Adam Hospital, Javier Conejero, Daniele Lezzi, Josep LL. Gelpi, Rosa M. Badia

Developing complex biomolecular workflows is not always straightforward. It requires tedious developments to enable the interoperability between the different biomolecular simulation and analysis tools. Moreover, the need to execute the pipelines on

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::0a36f17c561d526efb97bc98456a62a7
http://arxiv.org/abs/2208.14130

4D Genome Rewiring during Oncogene-Induced and Replicative Senescence

Autor: Franck Pellestor, Jean-Marc Lemaitre, Quentin Szabo, Giorgio L. Papadopoulos, Juan Carlos Rivera-Mulia, Satish Sati, Pauline Bouret, Giacomo Cavalli, Daniel Jost, Modesto Orozco, Frédéric Bantignies, François Serra, Boyan B. Bonev, Lauriane Fritsch, David Castillo, David M. Gilbert, Paul Bensadoun, Josep Ll. Gelpi, Vincent Loubiere, Cédric Vaillant, Marc A. Marti-Renom

Publikováno v: Molecular Cell
Molecular Cell, 2020, 78 (3), pp.522-538.e9. ⟨10.1016/j.molcel.2020.03.007⟩
Dipòsit Digital de la UB
Universidad de Barcelona
Molecular Cell, Elsevier, 2020, 78 (3), pp.522-538.e9. ⟨10.1016/j.molcel.2020.03.007⟩

To understand the role of the extensive senescence-associated 3D genome reorganization, we generated genome-wide chromatin interaction maps, epigenome, replication-timing, whole-genome bisulfite sequencing, and gene expression profiles from cells ent

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::65472d220bf71dddf91a17e3ea08e122

High-throughput molecular dynamics simulations: toward a dynamic view of macromolecular structure

Autor: Josep Ll. Gelpi

Publikováno v: Wiley Interdisciplinary Reviews: Computational Molecular Science. 3:364-377

Molecular dynamics (MD) simulation is nowadays the eligible theoretical technique to account for macromolecular flexibility. Molecular simulations, from ab initio to coarse-grained representation levels, allow having a direct visualization of macromo

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_________::555bfcde7784174eb3642e6a215a6081
https://doi.org/10.1002/wcms.1142

BIGNASim: a NoSQL database structure and analysis portal for nucleic acids simulation data

Autor: Modesto Orozco, Jordi Torres, Yolanda Becerra, Federica Battistini, Cesare Cugnasco, Ramon Goni, Pau Andrio, Pablo D. Dans, Laia Codó, Josep Ll. Gelpi

Publikováno v: Nucleic Acids Research
Recercat. Dipósit de la Recerca de Catalunya
instname
Dipòsit Digital de la UB
Universidad de Barcelona
UPCommons. Portal del coneixement obert de la UPC
Universitat Politècnica de Catalunya (UPC)

Molecular dynamics simulation (MD) is, just behind genomics, the bioinformatics tool that generates the largest amounts of data, and that is using the largest amount of CPU time in supercomputing centres. MD trajectories are obtained after months of

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::ff0348597aad4f060ba2e10b1215cff6
https://pubmed.ncbi.nlm.nih.gov/26612862

Effect of several anions on the activity of mitochondrial malate dehydrogenase from pig heart

Autor: Montserrat Busquets, Marta Cascante, Josep Ll. Gelpi, Antoni Cortés, Ana Ruggia

Publikováno v: Journal of Molecular Catalysis B: Enzymatic. 11:743-755

Mitochondrial malate dehydrogenase (mMDH) shows a complex dependence upon ionic environment that includes kinetic and structural effects. We measured mMDH activity in several buffers (phosphate, MOPS, and MES) at pH 6.5 and 7.5, and in the presence o

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_________::a4beb53a7acf301180a4f3e47ab4992f
https://doi.org/10.1016/s1381-1177(00)00167-3