A Centre of Excellence in Computational Biomedicine

CORDIS provides links to public deliverables and publications of HORIZON projects.

Links to deliverables and publications from FP7 projects, as well as links to some specific result types such as dataset and software, are dynamically retrieved from OpenAIRE .

Deliverables

Final Report on Training Activities

A report that summarise the training activities conducted in the project.

Third Report on Fast Track Application

Third report on research outcomes on Fast Track applications, including ‘best practices’ to help external users of the underlying codes to quickly set up their own applications (e.g. in the context of task 2.4).

Software Incubation Report

Definition of the incubation plan, description of its components and implementation strategy. Software documentation and usage summary. Best practice for documentation, regression tests, benchmarking, etc.

First Report on Applications Stack Service

Report on the applications service, mainly focused on supercomputing centres.

Final Dissemination and Innovation Report

A report on dissemination and innovation activities produced by the project at the end of the project

Report on Training Programme Design

A report on the design and delivery of the material used for the HPC training events aimed at advanced and industrial users.

Report on Long-term Sustainability

This report will summarise the strategy and operational arrangements for long-term sustainability of CompBioMed.

Second Report on Fast Track Applications

Second report on research outcomes from fast track applications including a first best practices section to help external users of the underlying codes to quickly set up their own applications eg in the context of task 24

Dissemination Action Plan

A detailed and comprehensive report on the dissemination actions that will be carried out by the project.

Final Public Report

A summary of the final status of the project.

Final Report on Fast Track Applications

Final report on research outcomes on Fast Track applications, including a final ‘best practices’ section to help external users of the underlying codes to quickly set up their own applications.

Intermediate Report on VVUQ, Exemplar Research Integration and Community Applications

This report will describe the results of VVUQ technique application in Task 25 and the exemplar integration research as well as review achievements with community application codes

CompBioMed2 Compute and Data Services Strategic Plan

This deliverable will define of the strategies for the design of services portfolio and the operational service processes needed for the maintenance and delivery of CompBioMed compute and data services.

First Report on VVUQ Strategies and Community Application Codes

This report will describe the VVUQ strategies and techniques developed in Task 25 and review the community application codes with best prospects for parallelisation and deployment by Task 24

Final Report on Engagement

A report that summarises the results of the engagement activities conducted in the project.

Report on Exascale Readiness

This report will describe the work of Task 4.6 and the Exascale readiness of the diverse set of CompBioMed2 applications

Final Release of CompBioMed Compute and Data Services

This report will summarize the developments of the CompBioMed2 services and creation of new service components and tools used to promote the uptake of biomedicine applications on various European e-infrastructures.

Project Handbook

WP1 will produce a project handbook outlining the project’s procedures, legal obligations and reporting processes, to assist each partner.

First Report on Fast Track Application Readiness

Report on the applications and research being undertaken within the CompBioMed2 environment based on the initial, Fast Track deployment.

Data Curation Strategies Report

This report will describe the projects data curation strategy, including a metadata schema for project data.

Final Report on Applications Stack Service

Report on the applications service, primarily focused on cloud providers.

Report on Uptake of CompBioMed Services

This report will describe the integration of the CompBioMed2 services with the computational and data infrastructures available in Europe. We will present the results of Task 4.3 and Task 4.4, focussing in particular on the work done to promote availability of CompBioMed2 service.

Report on Dissemination and Innovation

A report on dissemination and innovation activities produced by the project at the midterm point

Quality Assurance Plan

To manage the project’s quality control process, a Quality Assurance Plan will be created to assist internal reviewers in monitoring all deliverables before they are finalised and submitted to the Commission. The deliverable will also contain a detailed risk analysis and contingency planning.

Report on Establishment of the Community Engagement

A report on the report on the establishment of the users’ engagement portal and of the HPC-M community of practice.

Ethics Report

This report will be initiated in M6 and maintained as a running log of the types of data used in CompBioMed2. The report will keep detailed information on the procedures for data collection, storage, protection, retention, and destruction, and confirmation that they comply with national and EU legislation.

Advanced Report on Biomedical Applications

Technical report on results of code improvement focussing on robustness efficiency usability etc Report on software incubation

Report on Maintenance and Development of CompBioMed Computational Services

This report will describe the status of the CompBioMed service portfolio at the halfway point of the project lifetime For each of the identified services we will provide a technical description of its components access mechanism used and einfrastructure usage

Report on Content for External Use and Commercialisation

Report on preparing content for external use and commercialisation, including both code and training material.

Analytics Requirements Analysis

This report will assess the potential for applying analytics techniques to CompBioMed2 project data

Final Report on VVUQ, Exemplar Research Integration and Community Application Codes

This report will describe the final results of the VVUQ technique application in Task 2.5. It will also outline ‘best practices’ to help external users to quickly set up their own applications incorporating VVUQ and complex workflows.

Report on Analytics Techniques

This report will describe the success of applying analytics techniques to CompBioMed2 research data and in silico clinical trials

Innovation Plan

A detailed innovation plan, to be adhered to by all members of the consortium, to promote the innovation and commercialisation aspects of this project.

Data Management Plan

Task 3.1 will produce an initial Data Management Plan for the project. This will be updated over the course of the project as its needs evolve.

Publications

Investigating the mechanical response of paediatric bone under bending and torsion using finite element analysis

Author(s): Zainab Altai, Marco Viceconti, Amaka C. Offiah, Xinshan Li
Published in: Biomechanics and Modeling in Mechanobiology, Issue 17/4, 2018, Page(s) 1001-1009, ISSN 1617-7959
Publisher: Springer Verlag
DOI: 10.1007/s10237-018-1008-9

Time-efficient three-dimensional transmural scar assessment provides relevant substrate characterization for ventricular tachycardia features and long-term recurrences in ischemic cardiomyopathy

Author(s): Susana Merino-Caviedes, Lilian K. Gutierrez, José Manuel Alfonso-Almazán, Santiago Sanz-Estébanez, Lucilio Cordero-Grande, Jorge G. Quintanilla, Javier Sánchez-González, Manuel Marina-Breysse, Carlos Galán-Arriola, Daniel Enríquez-Vázquez, Carlos Torres, Gonzalo Pizarro, Borja Ibáñez, Rafael Peinado, Jose Luis Merino, Julián Pérez-Villacastín, José Jalife, Mariña López-Yunta, Maria
Published in: Scientific Reports, Issue 11, 2022, ISSN 2045-2322
Publisher: Nature Publishing Group
DOI: 10.1038/s41598-021-97399-w

Three-dimensional analysis of blood platelet spreading using digital holographic microscopy: a statistical study of the differential effect of coatings in healthy volunteers and dialyzed patients

Author(s): Jérôme Dohet-Eraly, Karim Zouaoui Boudjeltia, Alexandre Rousseau, Patrick Queeckers, Christophe Lelubre, Jean-Marc Desmet, Bastien Chopard, Catherine Yourassowsky, Frank Dubois
Published in: Biomedical Optics Express, Issue 13, 2022, Page(s) 502, ISSN 2156-7085
Publisher: The Optical Society
DOI: 10.1364/boe.448817

Coarse graining molecular dynamics with graph neural networks

Author(s): Brooke E. Husic, Nicholas E. Charron, Dominik Lemm, Jiang Wang, Adrià Pérez, Maciej Majewski, Andreas Krämer, Yaoyi Chen, Simon Olsson, Gianni de Fabritiis, Frank Noé, Cecilia Clementi
Published in: The Journal of Chemical Physics, Issue 153/19, 2020, Page(s) 194101, ISSN 0021-9606
Publisher: American Institute of Physics
DOI: 10.1063/5.0026133

HPC compact quasi-Newton algorithm for interface problems

Author(s): Alfonso Santiago, Miguel Zavala-Aké, Ricard Borrell, Guillaume Houzeaux, Mariano Vázquez
Published in: Journal of Fluids and Structures, Issue 96, 2020, Page(s) 103009, ISSN 0889-9746
Publisher: Academic Press
DOI: 10.1016/j.jfluidstructs.2020.103009

Uncertainty quantification in classical molecular dynamics

Author(s): Shunzhou Wan, Robert C. Sinclair, Peter V. Coveney
Published in: Philosophical Transactions of the Royal Society A: Mathematical, Physical and Engineering Sciences, Issue 379/2197, 2021, ISSN 1364-503X
Publisher: Royal Society of London
DOI: 10.1098/rsta.2020.0082

Rapid, accurate, precise and reproducible ligand–protein binding free energy prediction

Author(s): Shunzhou Wan, Agastya P. Bhati, Stefan J. Zasada, Peter V. Coveney
Published in: Interface Focus, Issue 10, 2023, Page(s) 20200007, ISSN 2042-8898
Publisher: Royal Society Publishing
DOI: 10.1098/rsfs.2020.0007

Equivariant Graph Neural Networks for Toxicity Prediction

Author(s): Julian Cremer; Leonardo Medrano Sandonas; Alexandre Tkatchenko; Djork-Arné Clevert; Gianni De Fabritiis
Published in: Crossref, Issue 40, 2023, ISSN 0000-0000
Publisher: ACS
DOI: 10.26434/chemrxiv-2023-9kb55

Experimental validation of a subject-specific finite element model of lumbar spine segment using digital image correlation

Author(s): Chiara Garavelli, Cristina Curreli, Marco Palanca, Alessandra Aldieri, Luca Cristofolini, Marco Viceconti
Published in: PLOS ONE, Issue 17, 2022, Page(s) e0272529, ISSN 1932-6203
Publisher: Public Library of Science
DOI: 10.1371/journal.pone.0272529

Large‐Scale Molecular Dynamics Elucidates the Mechanics of Reinforcement in Graphene‐Based Composites

Author(s): James L. Suter, Maxime Vassaux, Peter V. Coveney
Published in: Advanced Materials, Issue 35, 2023, ISSN 0935-9648
Publisher: United Nations Industrial Developement Organization
DOI: 10.1002/adma.202302237

Human Purkinje in silico model enables mechanistic investigations into automaticity and pro-arrhythmic abnormalities

Author(s): Cristian Trovato, Elisa Passini, Norbert Nagy, András Varró, Najah Abi-Gerges, Stefano Severi, Blanca Rodriguez
Published in: Journal of Molecular and Cellular Cardiology, Issue 142, 2020, Page(s) 24-38, ISSN 0022-2828
Publisher: Academic Press
DOI: 10.1016/j.yjmcc.2020.04.001

Development and performance of a HemeLB GPU code for human-scale blood flow simulation

Author(s): I. Zacharoudiou, J.W.S. McCullough, P.V. Coveney
Published in: Computer Physics Communications, Issue 282, 2024, Page(s) 108548, ISSN 0010-4655
Publisher: Elsevier BV
DOI: 10.1016/j.cpc.2022.108548

A particle-based model for endothelial cell migration under flow conditions

Author(s): P. S. Zun, A. J. Narracott, P. C. Evans, B. J. M. van Rooij, A. G. Hoekstra
Published in: Biomechanics and Modeling in Mechanobiology, Issue 19/2, 2020, Page(s) 681-692, ISSN 1617-7959
Publisher: Springer Verlag
DOI: 10.1007/s10237-019-01239-w

Location-Specific Comparison Between a 3D In-Stent Restenosis Model and Micro-CT and Histology Data from Porcine In Vivo Experiments

Author(s): P. S. Zun, A. J. Narracott, C. Chiastra, J. Gunn, A. G. Hoekstra
Published in: Cardiovascular Engineering and Technology, Issue 10/4, 2019, Page(s) 568-582, ISSN 1869-408X
Publisher: Springer Pub. Co.,
DOI: 10.1007/s13239-019-00431-4

Statistical Properties of a Virtual Cohort for In Silico Trials Generated with a Statistical Anatomy Atlas

Author(s): Antonino A. La Mattina, Fabio Baruffaldi, Mark Taylor, Marco Viceconti
Published in: Annals of Biomedical Engineering, Issue 51, 2023, Page(s) 117-124, ISSN 0090-6964
Publisher: Kluwer Academic Publishers
DOI: 10.1007/s10439-022-03050-8

Machine learning coarse-grained potentials of protein thermodynamics

Author(s): Majewski; Maciej; Pérez; Adrià; Thölke; Philipp; Doerr; Stefan; Charron; Nicholas E.; Giorgino; Toni; Husic; Brooke E.; Clementi; Cecilia; Noe; Frank; De Fabritiis; Gianni
Published in: Nature communications 14 (2023): 1–13. doi:10.1038/s41467-023-41343-1, Issue 37, 2023, ISSN 0000-0000
Publisher: Nature
DOI: 10.1038/s41467-023-41343-1

Stochastic PCA-Based Bone Models from Inverse Transform Sampling: Proof of Concept for Mandibles and Proximal Femurs

Author(s): Giulia Pascoletti, Alessandra Aldieri, Mara Terzini, Pinaki Bhattacharya, Michele Calì, Elisabetta M. Zanetti
Published in: Applied Sciences, Issue 11, 2024, Page(s) 5204, ISSN 2076-3417
Publisher: MDPI
DOI: 10.3390/app11115204

Reducing the Complexity of Musculoskeletal Models Using Gaussian Process Emulators

Author(s): Ivan Benemerito, Erica Montefiori, Alberto Marzo and Claudia Mazzà
Published in: Applied Sciences, 2022, ISSN 2076-3417
Publisher: MDPI
DOI: 10.3390/app122412932

Evaluation of patient tissue selection methods for deriving equivalent density calibration for femoral bone quantitative CT analyses

Author(s): C. Winsor, X. Li, M. Qasim, C.R. Henak, P.J. Pickhardt, H. Ploeg, M. Viceconti
Published in: Bone, Issue 143, 2021, Page(s) 115759, ISSN 8756-3282
Publisher: Elsevier BV
DOI: 10.1016/j.bone.2020.115759

Large Scale Study of Ligand–Protein Relative Binding Free Energy Calculations: Actionable Predictions from Statistically Robust Protocols

Author(s): Agastya P. Bhati, Peter V. Coveney
Published in: Journal of Chemical Theory and Computation, Issue 18, 2023, Page(s) 2687-2702, ISSN 1549-9618
Publisher: American Chemical Society
DOI: 10.1021/acs.jctc.1c01288

A multiscale computational framework to evaluate flow alterations during mechanical thrombectomy for treatment of ischaemic stroke

Author(s): Ivan Benemerito; Ivan Benemerito; Ahmed Mustafa; Ahmed Mustafa; Ning Wang; Ning Wang; Ana Paula Narata; Andrew Narracott; Andrew Narracott; Alberto Marzo; Alberto Marzo
Published in: Frontiers in Cardiovascular Medicine, Vol 10 (2023), Issue 50, 2023, ISSN 0000-0000
Publisher: Frontiers
DOI: 10.3389/fcvm.2023.1117449

Application of the ESMACS Binding Free Energy Protocol to a Multi‐Binding Site Lactate Dehydogenase A Ligand Dataset

Author(s): David W. Wright, Fouad Husseini, Shunzhou Wan, Christophe Meyer, Herman van Vlijmen, Gary Tresadern, Peter V. Coveney
Published in: Advanced Theory and Simulations, Issue 3/1, 2019, Page(s) 1900194, ISSN 2513-0390
Publisher: John Wiley & Sons
DOI: 10.1002/adts.201900194

Computational biomedicine. Part II: organs and systems

Author(s): Peter V. Coveney, Alfons Hoekstra, Blanca Rodriguez, Marco Viceconti
Published in: Interface Focus, Issue 11, 2021, Page(s) 20200082, ISSN 2042-8898
Publisher: Royal Society Publishing
DOI: 10.1098/rsfs.2020.0082

Supporting_material_compbiomed_conference_paper3_clean.pdf from Haemodynamic flow conditions at the initiation of high-shear platelet aggregation: a combined in vitro and cellular in silico study

Author(s): Rooij, B.J.M. Van; Závodszky, G.; Hoekstra, A.G.; Ku, D.N.
Published in: Interface Focus, Issue 7, 2020, ISSN 0000-0000
Publisher: The Royal Society
DOI: 10.6084/m9.figshare.13272993

Ensembles Are Required to Handle Aleatoric and Parametric Uncertainty in Molecular Dynamics Simulation

Author(s): Maxime Vassaux, Shunzhou Wan, Wouter Edeling, Peter V. Coveney
Published in: Journal of Chemical Theory and Computation, Issue 17, 2023, Page(s) 5187-5197, ISSN 1549-9618
Publisher: American Chemical Society
DOI: 10.1021/acs.jctc.1c00526

Thermodynamic and structural insights into the repurposing of drugs that bind to SARS-CoV-2 main protease

Author(s): Shunzhou Wan, Agastya P. Bhati, Alexander D. Wade, Dario Alfè, Peter V. Coveney
Published in: Molecular Systems Design & Engineering, Issue 7, 2024, Page(s) 123-131, ISSN 2058-9689
Publisher: The Royal Society of Chemistry
DOI: 10.1039/d1me00124h

Large scale relative protein ligand binding affinities using non-equilibrium alchemy

Author(s): Vytautas Gapsys, Laura Pérez-Benito, Matteo Aldeghi, Daniel Seeliger, Herman van Vlijmen, Gary Tresadern, Bert L. de Groot
Published in: Chemical Science, Issue 11/4, 2020, Page(s) 1140-1152, ISSN 2041-6520
Publisher: Royal Society of Chemistry
DOI: 10.1039/c9sc03754c

High arrhythmic risk in antero-septal acute myocardial ischemia is explained by increased transmural reentry occurrence

Author(s): Hector Martinez-Navarro, Ana Mincholé, Alfonso Bueno-Orovio, Blanca Rodriguez
Published in: Scientific Reports, Issue 9/1, 2019, ISSN 2045-2322
Publisher: Nature Publishing Group
DOI: 10.1038/s41598-019-53221-2

Uncertainty quantification of the lattice Boltzmann method focussing on studies of human-scale vascular blood flow

Author(s): Jon W. S. McCullough, Peter V. Coveney
Published in: Scientific Reports, Issue 14, 2024, ISSN 2045-2322
Publisher: Nature Publishing Group
DOI: 10.1038/s41598-024-61708-w

TIES 2.0: A Dual-Topology Open Source Relative Binding Free Energy Builder with Web Portal

Author(s): Mateusz K. Bieniek, Alexander D. Wade, Agastya P. Bhati, Shunzhou Wan, Peter V. Coveney
Published in: Journal of Chemical Information and Modeling, Issue 63, 2023, Page(s) 718-724, ISSN 1549-9596
Publisher: American Chemical Society
DOI: 10.1021/acs.jcim.2c01596

A porous circulation model of the human brain for in silico clinical trials in ischaemic stroke

Author(s): T. I. Józsa, R. M. Padmos, N. Samuels, W. K. El-Bouri, A. G. Hoekstra, S. J. Payne
Published in: Interface Focus, Issue 11, 2021, Page(s) 20190127, ISSN 2042-8898
Publisher: Royal Society Publishing
DOI: 10.1098/rsfs.2019.0127

Predicting antibiotic resistance in complex protein targets using alchemical free energy methods

Author(s): Alice E. Brankin, Philip W. Fowler
Published in: Journal of Computational Chemistry, Issue 43, 2023, Page(s) 1771-1782, ISSN 0192-8651
Publisher: John Wiley & Sons Inc.
DOI: 10.1002/jcc.26979

Comparison of Equilibrium and Nonequilibrium Approaches for Relative Binding Free Energy Predictions

Author(s): Shunzhou Wan, Agastya P. Bhati, Peter V. Coveney
Published in: Journal of Chemical Theory and Computation, Issue 19, 2023, Page(s) 7846-7860, ISSN 1549-9618
Publisher: American Chemical Society
DOI: 10.1021/acs.jctc.3c00842

SkeleDock: A Web Application for Scaffold Docking in PlayMolecule

Author(s): Alejandro Varela-Rial, Maciej Majewski, Alberto Cuzzolin, Gerard Martínez-Rosell, Gianni De Fabritiis
Published in: Journal of Chemical Information and Modeling, Issue 60/6, 2020, Page(s) 2673-2677, ISSN 1549-9596
Publisher: American Chemical Society
DOI: 10.1021/acs.jcim.0c00143

Comparison of the Simulated Response of Three in Silico Human Stem Cell-Derived Cardiomyocytes Models and in Vitro Data Under 15 Drug Actions

Author(s): Michelangelo Paci, Jussi T. Koivumäki, Hua Rong Lu, David J. Gallacher, Elisa Passini, Blanca Rodriguez
Published in: Frontiers in Pharmacology, Issue 12, 2021, ISSN 1663-9812
Publisher: Frontiers Media S.A.
DOI: 10.3389/fphar.2021.604713

Applicability assessment of a stent-retriever thrombectomy finite-element model

Author(s): Giulia Luraghi, Jose Felix Rodriguez Matas, Gabriele Dubini, Francesca Berti, Sara Bridio, Sharon Duffy, Anushree Dwivedi, Ray McCarthy, Behrooz Fereidoonnezhad, Patrick McGarry, Charles B. L. M. Majoie, Francesco Migliavacca, null null
Published in: Interface Focus, Issue 11, 2021, Page(s) 20190123, ISSN 2042-8898
Publisher: Royal Society Publishing
DOI: 10.1098/rsfs.2019.0123

The effect of protein mutations on drug binding suggests ensuing personalised drug selection

Author(s): Shunzhou Wan, Deepak Kumar, Valentin Ilyin, Ussama Al Homsi, Gulab Sher, Alexander Knuth, Peter V. Coveney
Published in: Scientific Reports, Issue 11, 2022, ISSN 2045-2322
Publisher: Nature Publishing Group
DOI: 10.1038/s41598-021-92785-w

Deep medical image analysis with representation learning and neuromorphic computing

Author(s): N. Getty, T. Brettin, D. Jin, R. Stevens, F. Xia
Published in: Interface Focus, Issue 11, 2021, ISSN 2042-8898
Publisher: Royal Society Publishing
DOI: 10.1098/rsfs.2019.0122

High fidelity blood flow in a patient-specific arteriovenous fistula

Author(s): J. W. S. McCullough, P. V. Coveney
Published in: Scientific Reports, Issue 11, 2023, ISSN 2045-2322
Publisher: Nature Publishing Group
DOI: 10.1038/s41598-021-01435-8

Drug‐induced shortening of the electromechanical window is an effective biomarker for in silico prediction of clinical risk of arrhythmias

Author(s): Elisa Passini, Cristian Trovato, Pierre Morissette, Frederick Sannajust, Alfonso Bueno‐Orovio, Blanca Rodriguez
Published in: British Journal of Pharmacology, Issue 176, 2023, Page(s) 3819-3833, ISSN 0007-1188
Publisher: Wiley-Blackwell
DOI: 10.1111/bph.14786

Bridging the computational gap between mesoscopic and continuum modeling of red blood cells for fully resolved blood flow

Author(s): Christos Kotsalos, Jonas Latt, Bastien Chopard
Published in: Journal of Computational Physics, Issue 398, 2019, Page(s) 108905, ISSN 0021-9991
Publisher: Academic Press
DOI: 10.1016/j.jcp.2019.108905

Pandemic drugs at pandemic speed: infrastructure for accelerating COVID-19 drug discovery with hybrid machine learning- and physics-based simulations on high-performance computers

Author(s): Agastya P. Bhati, Shunzhou Wan, Dario Alfè, Austin R. Clyde, Mathis Bode, Li Tan, Mikhail Titov, Andre Merzky, Matteo Turilli, Shantenu Jha, Roger R. Highfield, Walter Rocchia, Nicola Scafuri, Sauro Succi, Dieter Kranzlmüller, Gerald Mathias, David Wifling, Yann Donon, Alberto Di Meglio, Sofia Vallecorsa, Heng Ma, Anda Trifan, Arvind Ramanathan, Tom Brettin, Alexander Partin, Fangfang Xia, Xiaot
Published in: Interface Focus, Issue 11, 2023, ISSN 2042-8901
Publisher: The Royal Society
DOI: 10.1098/rsfs.2021.0018

Human biventricular electromechanical simulations on the progression of electrocardiographic and mechanical abnormalities in post-myocardial infarction

Author(s): Zhinuo J Wang, Alfonso Santiago, Xin Zhou, Lei Wang, Francesca Margara, Francesc Levrero-Florencio, Arka Das, Chris Kelly, Erica Dall'Armellina, Mariano Vazquez, Blanca Rodriguez
Published in: EP Europace, Issue 23, 2021, Page(s) i143-i152, ISSN 1099-5129
Publisher: Oxford University Press
DOI: 10.1093/europace/euaa405

Biorheology of occlusive thrombi formation under high shear: in vitro growth and shrinkage

Author(s): Britt J. M. van Rooij, Gábor Závodszky, Alfons G. Hoekstra, David N. Ku
Published in: Scientific Reports, Issue 10/1, 2020, ISSN 2045-2322
Publisher: Nature Publishing Group
DOI: 10.1038/s41598-020-74518-7

Implementation Details of the Reconstruction Pipeline and Electrophysiological Inference Results from A completely automated pipeline for 3D reconstruction of human heart from 2D cine magnetic resonance slices

Author(s): Banerjee, Abhirup; Camps, Julià; Zacur, Ernesto; Andrews, Christopher M.; Rudy, Yoram; Choudhury, Robin P.; Rodriguez, Blanca; Grau, Vicente
Published in: Philosophical Transactions A, Issue 32, 2021, ISSN 0000-0000
Publisher: The Royal Society
DOI: 10.6084/m9.figshare.15656924

Characterizing Interhelical Interactions of G-Protein Coupled Receptors with the Fragment Molecular Orbital Method

Author(s): Alexander Heifetz, Inaki Morao, M. Madan Babu, Tim James, Michelle W. Y. Southey, Dmitri G. Fedorov, Matteo Aldeghi, Michael J. Bodkin, Andrea Townsend-Nicholson
Published in: Journal of Chemical Theory and Computation, Issue 16/4, 2020, Page(s) 2814-2824, ISSN 1549-9618
Publisher: American Chemical Society
DOI: 10.1021/acs.jctc.9b01136

TorchMD: A Deep Learning Framework for Molecular Simulations

Author(s): Stefan Doerr, Maciej Majewski, Adrià Pérez, Andreas Krämer, Cecilia Clementi, Frank Noe, Toni Giorgino, Gianni De Fabritiis
Published in: Journal of Chemical Theory and Computation, Issue 17/4, 2021, Page(s) 2355-2363, ISSN 1549-9618
Publisher: American Chemical Society
DOI: 10.1021/acs.jctc.0c01343

Parallel Multiphysics Coupling: Algorithmic and Computational Performances

Author(s): G. Houzeaux, M. Garcia-Gasulla, J. C. Cajas, R. Borrell, A. Santiago, C. Moulinec, M. Vázquez
Published in: International Journal of Computational Fluid Dynamics, Issue 34, 2023, Page(s) 486-507, ISSN 1061-8562
Publisher: Taylor & Francis
DOI: 10.1080/10618562.2020.1783440

Binding-and-Folding Recognition of an Intrinsically Disordered Protein Using Online Learning Molecular Dynamics

Author(s): Pablo Herrera-Nieto; Adrià Pérez; Gianni De Fabritiis
Published in: Crossref, Issue 28, 2023, ISSN 0000-0000
Publisher: ACS
DOI: 10.1021/acs.jctc.3c00008

Enhanced single-node lattice Boltzmann boundary condition for fluid flows

Author(s): Francesco Marson, Yann Thorimbert, Bastien Chopard, Irina Ginzburg, Jonas Latt
Published in: Physical Review E, Issue 103, 2021, ISSN 2470-0045
Publisher: APS
DOI: 10.1103/physreve.103.053308

Multi-Domain Variational Autoencoders for Combined Modeling of MRI-Based Biventricular Anatomy and ECG-Based Cardiac Electrophysiology

Author(s): Marcel Beetz, Abhirup Banerjee, Vicente Grau
Published in: Frontiers in Physiology, Issue 13, 2022, ISSN 1664-042X
Publisher: Frontiers Research Foundation
DOI: 10.3389/fphys.2022.886723

Long Time Scale Ensemble Methods in Molecular Dynamics: Ligand–Protein Interactions and Allostery in SARS-CoV-2 Targets

Author(s): Agastya P. Bhati, Art Hoti, Andrew Potterton, Mateusz K. Bieniek, Peter V. Coveney
Published in: Journal of Chemical Theory and Computation, Issue 19, 2023, Page(s) 3359-3378, ISSN 1549-9618
Publisher: American Chemical Society
DOI: 10.1021/acs.jctc.3c00020

A systematic approach to the scale separation problem in the development of multiscale models

Author(s): Pinaki Bhattacharya, Qiao Li, Damien Lacroix, Visakan Kadirkamanathan, Marco Viceconti
Published in: PLOS ONE, Issue 16, 2021, Page(s) e0251297, ISSN 1932-6203
Publisher: Public Library of Science
DOI: 10.1371/journal.pone.0251297

AdaptiveBandit: A Multi-armed Bandit Framework for Adaptive Sampling in Molecular Simulations

Author(s): Pablo Herrera-Nieto; Adrià Pérez; Gianni De Fabritiis; Gianni De Fabritiis; Stefan Doerr
Published in: Crossref, Issue 59, 2020, ISSN 0000-0000
Publisher: ACS
DOI: 10.1021/acs.jctc.0c00205

A completely automated pipeline for 3D reconstruction of human heart from 2D cine magnetic resonance slices.

Author(s): Banerjee, A; Camps, J; Zacur, E; Andrews, CM; Rudy, Y; Choudhury, RP; Rodriguez, B; Grau, V
Published in: Philosophical Transactions of the Royal Society A: Mathematical, Physical and Engineering Sciences, Issue 41, 2021, ISSN 1471-2962
Publisher: The Royal Society
DOI: 10.1098/rsta.2020.0257

Supplemental Figures and Table from How quickly can we predict trimethoprim resistance using alchemical free energy methods?

Author(s): Fowler, Philip W
Published in: Interface Focus, Issue 2, 2020, ISSN 0000-0000
Publisher: The Royal Society
DOI: 10.6084/m9.figshare.12979029

Interpretable cardiac anatomy modeling using variational mesh autoencoders

Author(s): Marcel Beetz, Jorge Corral Acero, Abhirup Banerjee, Ingo Eitel, Ernesto Zacur, Torben Lange, Thomas Stiermaier, Ruben Evertz, Sören J. Backhaus, Holger Thiele, Alfonso Bueno-Orovio, Pablo Lamata, Andreas Schuster, Vicente Grau
Published in: Frontiers in Cardiovascular Medicine, Issue 9, 2022, ISSN 2297-055X
Publisher: Frontiers
DOI: 10.3389/fcvm.2022.983868

Sensitivity analysis of a strongly-coupled human-based electromechanical cardiac model: Effect of mechanical parameters on physiologically relevant biomarkers

Author(s): F. Levrero-Florencio, F. Margara, E. Zacur, A. Bueno-Orovio, Z.J. Wang, A. Santiago, J. Aguado-Sierra, G. Houzeaux, V. Grau, D. Kay, M. Vázquez, R. Ruiz-Baier, B. Rodriguez
Published in: Computer Methods in Applied Mechanics and Engineering, Issue 361, 2020, Page(s) 112762, ISSN 0045-7825
Publisher: Elsevier BV
DOI: 10.1016/j.cma.2019.112762

Fluid–structure interaction simulations outperform computational fluid dynamics in the description of thoracic aorta haemodynamics and in the differentiation of progressive dilation in Marfan syndrome patients

Author(s): R. Pons, A. Guala, J. F. Rodríguez-Palomares, J. C. Cajas, L. Dux-Santoy, G. Teixidó-Tura, J. J. Molins, M. Vázquez, A. Evangelista, J. Martorell
Published in: Royal Society Open Science, Issue 7/2, 2020, Page(s) 191752, ISSN 2054-5703
Publisher: Royal Society Publishing
DOI: 10.1098/rsos.191752

Parametric Analysis of an Efficient Boundary Condition to Control Outlet Flow Rates in Large Arterial Networks

Author(s): Sharp Chim Yui Lo, J. W. S. McCullough, P. V. Coveney
Published in: Scientific Reports, 2022, ISSN 2045-2322
Publisher: Nature Publishing Group
DOI: 10.1038/s41598-022-21923-9

Electrophysiological and anatomical factors determine arrhythmic risk in acute myocardial ischaemia and its modulation by sodium current availability

Author(s): Hector Martinez-Navarro, Xin Zhou, Alfonso Bueno-Orovio, Blanca Rodriguez
Published in: Interface Focus, Issue 11, 2021, Page(s) 20190124, ISSN 2042-8898
Publisher: Royal Society Publishing
DOI: 10.1098/rsfs.2019.0124

The effect of stiffened diabetic red blood cells on wall shear stress in a reconstructed 3D microaneurysm

Author(s): Benjamin Czaja, Jonathan de Bouter, Morgan Heisler, Gábor Závodszky, Sonja Karst, Marinko Sarunic, David Maberley, Alfons Hoekstra
Published in: Computer Methods in Biomechanics and Biomedical Engineering, Issue 25, 2022, Page(s) 1691-1709, ISSN 1025-5842
Publisher: Taylor & Francis
DOI: 10.1080/10255842.2022.2034794

DeltaDelta neural networks for lead optimization of small molecule potency

Author(s): José Jiménez-Luna, Laura Pérez-Benito, Gerard Martínez-Rosell, Simone Sciabola, Rubben Torella, Gary Tresadern, Gianni De Fabritiis
Published in: Chemical Science, Issue 10/47, 2019, Page(s) 10911-10918, ISSN 2041-6520
Publisher: Royal Society of Chemistry
DOI: 10.1039/c9sc04606b

AdaptiveBandit: A Multi-armed Bandit Framework for Adaptive Sampling in Molecular Simulations

Author(s): Adrià Pérez, Pablo Herrera-Nieto, Stefan Doerr, Gianni De Fabritiis
Published in: Journal of Chemical Theory and Computation, Issue 16/7, 2020, Page(s) 4685-4693, ISSN 1549-9618
Publisher: American Chemical Society
DOI: 10.1021/acs.jctc.0c00205#

Analysis of mechanotransduction dynamics during combined mechanical stimulation and modulation of the extracellular-regulated kinase cascade uncovers hidden information within the signalling noise

Author(s): Gianluca Ascolani, Timothy M. Skerry, Damien Lacroix, Enrico Dall'Ara, Aban Shuaib
Published in: Interface Focus, Issue 11, 2021, Page(s) 20190136, ISSN 2042-8898
Publisher: Royal Society Publishing
DOI: 10.1098/rsfs.2019.0136

Delivering computationally-intensive digital patient applications to the clinic: An exemplar solution to predict femoral bone strength from CT data

Author(s): I. Benemerito, W. Griffiths, J. Allsopp, W. Furnass, P. Bhattacharya, X. Li, A. Marzo, S. Wood, M. Viceconti, A. Narracott
Published in: Computer Methods and Programs in Biomedicine, Issue 208, 2021, Page(s) 106200, ISSN 0169-2607
Publisher: Elsevier BV
DOI: 10.1016/j.cmpb.2021.106200

Finite element analysis informed variable selection for femoral fracture risk prediction

Author(s): Mark Taylor, Marco Viceconti, Pinaki Bhattacharya, Xinshan Li
Published in: Journal of the Mechanical Behavior of Biomedical Materials, Issue 118, 2021, Page(s) 104434, ISSN 1751-6161
Publisher: Elsevier BV
DOI: 10.1016/j.jmbbm.2021.104434

Determining Clinically-Viable Biomarkers for Ischaemic Stroke Through a Mechanistic and Machine Learning Approach

Author(s): Benemerito, I.; Narata, A.P.; Narracott, A.; Marzo, A.
Published in: 0090-6964, Issue 47, 2022, ISSN 0000-0000
Publisher: Springer
DOI: 10.1007/s10439-022-02956-7

Computational prediction of GPCR oligomerization

Author(s): Andrea Townsend-Nicholson, Nojood Altwaijry, Andrew Potterton, Inaki Morao, Alexander Heifetz
Published in: Current Opinion in Structural Biology, Issue 55, 2019, Page(s) 178-184, ISSN 0959-440X
Publisher: Elsevier BV
DOI: 10.1016/j.sbi.2019.04.005

Digital Blood in Massively Parallel CPU/GPU Systems for the Study of Platelet Transport: Supplementary Material

Author(s): Kotsalos, Christos; Latt, Jonas; Beny, Joel; Chopard, Bastien
Published in: Interface Focus, Issue 9, 2020, ISSN 0000-0000
Publisher: The Royal Society
DOI: 10.6084/m9.figshare.13213333.v1

Improving the clinical understanding of hypertrophic cardiomyopathy by combining patient data, machine learning and computer simulations: A case study

Author(s): A. Lyon, A. Mincholé, A. Bueno-Orovio, B. Rodriguez
Published in: Morphologie, Issue 103, 2019, Page(s) 169-179, ISSN 1286-0115
Publisher: Elsevier Masson
DOI: 10.1016/j.morpho.2019.09.001

Unified directional parabolic-accurate lattice Boltzmann boundary schemes for grid-rotated narrow gaps and curved walls in creeping and inertial fluid flows

Author(s): Irina Ginzburg, Goncalo Silva, Francesco Marson, Bastien Chopard, Jonas Latt
Published in: Physical Review E, Issue 107, 2023, ISSN 2470-0045
Publisher: APS
DOI: 10.1103/physreve.107.025303

Multi-modality cardiac image computing: A survey

Author(s): Lei Li, Wangbin Ding, Liqin Huang, Xiahai Zhuang, Vicente Grau
Published in: Medical Image Analysis, Issue 88, 2024, Page(s) 102869, ISSN 1361-8415
Publisher: Elsevier BV
DOI: 10.1016/j.media.2023.102869

Shear induced diffusion of platelets revisited

Author(s): Christos Kotsalos, Franck Raynaud, Jonas Lätt, Ritabrata Dutta, Frank Dubois, Karim Zouaoui Boudjeltia, Bastien Chopard
Published in: Frontiers in Physiology, Issue 13, 2023, ISSN 1664-042X
Publisher: Frontiers Research Foundation
DOI: 10.3389/fphys.2022.985905

Ensemble-Based Steered Molecular Dynamics Predicts Relative Residence Time of A 2A Receptor Binders

Author(s): Andrew Potterton, Fouad S. Husseini, Michelle W. Y. Southey, Mike J. Bodkin, Alexander Heifetz, Peter V. Coveney, Andrea Townsend-Nicholson
Published in: Journal of Chemical Theory and Computation, Issue 15/5, 2019, Page(s) 3316-3330, ISSN 1549-9618
Publisher: American Chemical Society
DOI: 10.1021/acs.jctc.8b01270

Large-scale binding affinity calculations on commodity compute clouds

Author(s): S. J. Zasada, D. W. Wright, P. V. Coveney
Published in: Interface Focus, Issue 10, 2021, Page(s) 20190133, ISSN 2042-8898
Publisher: Royal Society Publishing
DOI: 10.1098/rsfs.2019.0133

TIES 20: Relative Binding Free Energy with a Flexible Superimposition Algorithm and Partial Ring Morphing

Author(s): Mateusz K. Bieniek, Agastya P. Bhati, Shunzhou Wan, Peter V. Coveney
Published in: Journal of Chemical Theory and Computation, Issue 17/2, 2021, Page(s) 1250-1265, ISSN 1549-9618
Publisher: American Chemical Society
DOI: 10.1021/acs.jctc.0c01179

Spherization of red blood cells and platelet margination in COPD patients

Author(s): Karim Zouaoui Boudjeltia, Christos Kotsalos, Daniel Ribeiro Sousa, Alexandre Rousseau, Christophe Lelubre, Olivier Sartenaer, Michael Piagnerelli, Jérôme Dohet‐Eraly, Frank Dubois, Nicole Tasiaux, Bastien Chopard, Alain Van Meerhaeghe
Published in: Annals of the New York Academy of Sciences, Issue 1485/1, 2021, Page(s) 71-82, ISSN 0077-8923
Publisher: New York Academy of Sciences
DOI: 10.1111/nyas.14489

Characterising GPCR–ligand interactions using a fragment molecular orbital-based approach

Author(s): Alexander Heifetz, Tim James, Michelle Southey, Inaki Morao, Matteo Aldeghi, Laurie Sarrat, Dmitri G Fedorov, Mike J Bodkin, Andrea Townsend-Nicholson
Published in: Current Opinion in Structural Biology, Issue 55, 2019, Page(s) 85-92, ISSN 0959-440X
Publisher: Elsevier BV
DOI: 10.1016/j.sbi.2019.03.021

NNP/MM: Accelerating Molecular Dynamics Simulations with Machine Learning Potentials and Molecular Mechanics

Author(s): Raimondas Galvelis, Alejandro Varela-Rial, Stefan Doerr, Roberto Fino, Peter Eastman, Thomas E. Markland, John D. Chodera, Gianni De Fabritiis
Published in: Journal of Chemical Information and Modeling, Issue 63, 2023, Page(s) 5701-5708, ISSN 1549-9596
Publisher: American Chemical Society
DOI: 10.1021/acs.jcim.3c00773

Hotspot Identification and Drug Design of Protein–Protein Interaction Modulators Using the Fragment Molecular Orbital Method

Author(s): Stefania Monteleone, Dmitri G. Fedorov, Andrea Townsend-Nicholson, Michelle Southey, Michael Bodkin, Alexander Heifetz
Published in: Journal of Chemical Information and Modeling, Issue 62, 2023, Page(s) 3784-3799, ISSN 1549-9596
Publisher: American Chemical Society
DOI: 10.1021/acs.jcim.2c00457

Personalised 3D Assessment of Trochanteric Soft Tissues Improves HIP Fracture Classification Accuracy

Author(s): Alessandra Aldieri, Mara Terzini, Alberto L. Audenino, Cristina Bignardi, Margaret Paggiosi, Richard Eastell, Marco Viceconti, Pinaki Bhattacharya
Published in: Annals of Biomedical Engineering, Issue 50, 2022, Page(s) 303-313, ISSN 0090-6964
Publisher: Kluwer Academic Publishers
DOI: 10.1007/s10439-022-02924-1

All-Optical Electrophysiology Refines Populations of In Silico Human iPSC-CMs for Drug Evaluation

Author(s): Michelangelo Paci, Elisa Passini, Aleksandra Klimas, Stefano Severi, Jari Hyttinen, Blanca Rodriguez, Emilia Entcheva
Published in: Biophysical Journal, Issue 118, 2022, Page(s) 2596-2611, ISSN 0006-3495
Publisher: Biophysical Society
DOI: 10.1016/j.bpj.2020.03.018

The influence of external electric fields on proton transfer tautomerism in the guanine–cytosine base pair

Author(s): Alexander Gheorghiu, Peter V. Coveney, Alya A. Arabi
Published in: Physical Chemistry Chemical Physics, Issue 23/10, 2021, Page(s) 6252-6265, ISSN 1463-9076
Publisher: Royal Society of Chemistry
DOI: 10.1039/d0cp06218a

Ensemble-Based Approaches Ensure Reliability and Reproducibility

Author(s): Shunzhou Wan, Agastya P. Bhati, Alexander D. Wade, Peter V. Coveney
Published in: Journal of Chemical Information and Modeling, Issue 63, 2023, Page(s) 6959-6963, ISSN 1549-9596
Publisher: American Chemical Society
DOI: 10.1021/acs.jcim.3c01654

Small Molecule Modulation of Intrinsically Disordered Proteins Using Molecular Dynamics Simulations

Author(s): Pablo Herrera-Nieto, Adrià Pérez, Gianni De Fabritiis
Published in: Journal of Chemical Information and Modeling, Issue 60/10, 2020, Page(s) 5003-5010, ISSN 1549-9596
Publisher: American Chemical Society
DOI: 10.1021/acs.jcim.0c00381

Applying the CiPA approach to evaluate cardiac proarrhythmia risk of some antimalarials used off‐label in the first wave of COVID‐19

Author(s): Annie Delaunois, Matthew Abernathy, Warren D. Anderson, Kylie A. Beattie, Khuram W. Chaudhary, Julie Coulot, Vitalina Gryshkova, Simon Hebeisen, Mark Holbrook, James Kramer, Yuri Kuryshev, Derek Leishman, Isabel Lushbough, Elisa Passini, Will S. Redfern, Blanca Rodriguez, Eric I. Rossman, Cristian Trovato, Caiyun Wu, Jean‐Pierre Valentin
Published in: Clinical and Translational Science, Issue 14, 2023, Page(s) 1133-1146, ISSN 1752-8054
Publisher: Wiley-Blackwell
DOI: 10.1111/cts.13011

Design and execution of a verification, validation, and uncertainty quantification plan for a numerical model of left ventricular flow after LVAD implantation

Author(s): Alfonso Santiago; Constantine Butakoff; Beatriz Eguzkitza; Richard A. Gray; Karen May-Newman; Pras Pathmanathan; Vi Vu; Mariano Vázquez
Published in: instname:Universitat Politècnica de Catalunya (UPC), Issue 62, 2022, ISSN 0000-0000
Publisher: PLOS
DOI: 10.1371/journal.pcbi.1010141

Principles of Small-Molecule Transport through Synthetic Nanopores

Author(s): Tim Diederichs, Katya Ahmad, Jonathan R. Burns, Quoc Hung Nguyen, Zuzanna S. Siwy, Marc Tornow, Peter V. Coveney, Robert Tampé, Stefan Howorka
Published in: ACS Nano, Issue 15, 2023, Page(s) 16194-16206, ISSN 1936-0851
Publisher: American Chemical Society
DOI: 10.1021/acsnano.1c05139

In-silico human electro-mechanical ventricular modelling and simulation for drug-induced pro-arrhythmia and inotropic risk assessment

Author(s): Francesca Margara, Zhinuo J. Wang, Francesc Levrero-Florencio, Alfonso Santiago, Mariano Vázquez, Alfonso Bueno-Orovio, Blanca Rodriguez
Published in: Progress in Biophysics and Molecular Biology, Issue 159, 2021, Page(s) 58-74, ISSN 0079-6107
Publisher: Pergamon Press Ltd.
DOI: 10.1016/j.pbiomolbio.2020.06.007

The performance of ensemble-based free energy protocols in computing binding affinities to ROS1 kinase

Author(s): Shunzhou Wan, Agastya P. Bhati, David W. Wright, Alexander D. Wade, Gary Tresadern, Herman van Vlijmen, Peter V. Coveney
Published in: Scientific Reports, Issue 12, 2022, ISSN 2045-2322
Publisher: Nature Publishing Group
DOI: 10.1038/s41598-022-13319-6

Modeling 3D Cardiac Contraction and Relaxation With Point Cloud Deformation Networks

Author(s): Marcel Beetz; Abhirup Banerjee; Vicente Grau
Published in: IEEE Journal of Biomedical and Health Informatics, Issue 22, 2024, ISSN 0000-0000
Publisher: IEEE
DOI: 10.1109/jbhi.2024.3389871

Teaching genomics to life science undergraduates using cloud computing platforms with open datasets

Author(s): Toryn M. Poolman, Andrea Townsend‐Nicholson, Amanda Cain
Published in: Biochemistry and Molecular Biology Education, Issue 50, 2023, Page(s) 446-449, ISSN 1470-8175
Publisher: American Society for Biochemistry and Molecular Biology Inc.
DOI: 10.1002/bmb.21646

Dynamic resource allocation for efficient parallel CFD simulations

Author(s): G. Houzeaux, R.M. Badia, R. Borrell, D. Dosimont, J. Ejarque, M. Garcia-Gasulla, V. López
Published in: Computers & Fluids, Issue 245, 2023, Page(s) 105577, ISSN 0045-7930
Publisher: Pergamon Press Ltd.
DOI: 10.1016/j.compfluid.2022.105577

Lattice-Boltzmann interactive blood flow simulation pipeline

Author(s): Sahar S. Esfahani, Xiaojun Zhai, Minsi Chen, Abbes Amira, Faycal Bensaali, Julien AbiNahed, Sarada Dakua, Georges Younes, Abdulla Baobeid, Robin A. Richardson, Peter V. Coveney
Published in: International Journal of Computer Assisted Radiology and Surgery, Issue 15, 2021, Page(s) 629-639, ISSN 1861-6410
Publisher: Springer Verlag
DOI: 10.1007/s11548-020-02120-3

A Multi-view Crossover Attention U-Net Cascade with Fourier Domain Adaptation for Multi-domain Cardiac MRI Segmentation

Author(s): Beetz, Marcel; Corral Acero, Jorge; Grau, Vicente
Published in: Lecture Notes in Computer Science ISBN: 9783030937218, Issue 57, 2022, ISSN 0000-0000
Publisher: Springer
DOI: 10.1007/978-3-030-93722-5_35

Investigating rolling as mechanism for humeral fractures in non-ambulant infants: a preliminary finite element study

Author(s): Z. Altai, M. Viceconti, X. Li, A.C. Offiah
Published in: Clinical Radiology, Issue 75/1, 2020, Page(s) 78.e9-78.e16, ISSN 0009-9260
Publisher: W. B. Saunders Co., Ltd.
DOI: 10.1016/j.crad.2019.08.026

Educating and engaging new communities of practice with high performance computing through the integration of teaching and research

Author(s): Andrea Townsend-Nicholson
Published in: Interface Focus, Issue 10/6, 2020, Page(s) 20200003, ISSN 2042-8898
Publisher: Royal Society Publishing
DOI: 10.1098/rsfs.2020.0003

Hierarchically Structured Bioinspired Nanocomposites

Author(s): D. Nepal, S Kang, K. M. Adstedt, K. Kanhaiya, M. R. Bockstaller, L. C. Brinson, M. J. Buehler, P. V. Coveney, K. Dayal, J. A. El-Awady, L. C. Henderson, D. L. Kaplan, S. Keten, N. A. Kotov, G. C. Schatz, S. Vignolini, F. Vollrath, Y. Wang, B. I. Yakobson, V. V. Tsukruk, H. Heinz
Published in: Nature Materials, 2022, ISSN 1476-4660
Publisher: Nature
DOI: 10.1038/s41563-022-01384-1

Concomitant Respiratory Failure Can Impair Myocardial Oxygenation in Patients with Acute Cardiogenic Shock Supported by VA-ECMO

Author(s): Prisco, Anthony R.; Aguado Sierra, Jazmín; Butakoff, Constantine; Vázquez, Mariano; Houzeaux, Guillaume; Eguzkitza, Beatriz; Bartos, Jason A.; Yannopoulos, Demetris; Raveendran, Ganesh; Holm, Mikayle; Iles, Tinen; Mahr, Claudius; Iaizzo, Paul A.
Published in: Journal of Cardiovascular Translational Research, Issue 31, 2021, ISSN 0000-0000
Publisher: Springer
DOI: 10.1007/s12265-021-10110-2

Accuracy and Precision of Alchemical Relative Free Energy Predictions with and without Replica‐Exchange

Author(s): Shunzhou Wan, Gary Tresadern, Laura Pérez‐Benito, Herman Vlijmen, Peter V. Coveney
Published in: Advanced Theory and Simulations, Issue 3/1, 2019, Page(s) 1900195, ISSN 2513-0390
Publisher: John Wiley & Sons
DOI: 10.1002/adts.201900195

Dual Transcriptomic and Molecular Machine Learning Predicts all Major Clinical Forms of Drug Cardiotoxicity

Author(s): Polina Mamoshina, Alfonso Bueno-Orovio, Blanca Rodriguez
Published in: Frontiers in Pharmacology, Issue 11, 2020, ISSN 1663-9812
Publisher: Frontiers Media S.A.
DOI: 10.3389/fphar.2020.00639

PlayMolecule Glimpse: Understanding Protein–Ligand Property Predictions with Interpretable Neural Networks

Author(s): Alejandro Varela-Rial, Iain Maryanow, Maciej Majewski, Stefan Doerr, Nikolai Schapin, José Jiménez-Luna, Gianni De Fabritiis
Published in: Journal of Chemical Information and Modeling, Issue 62, 2023, Page(s) 225-231, ISSN 1549-9596
Publisher: American Chemical Society
DOI: 10.1021/acs.jcim.1c00691

An efficient, localised approach for the simulation of elastic blood vessels using the lattice Boltzmann method

Author(s): J. W. S. McCullough, P. V. Coveney
Published in: Scientific Reports, Issue 11, 2023, ISSN 2045-2322
Publisher: Nature Publishing Group
DOI: 10.1038/s41598-021-03584-2

The EurValve model execution environment

Author(s): M. Bubak, K. Czechowicz, T. Gubała, D. R. Hose, M. Kasztelnik, M. Malawski, J. Meizner, P. Nowakowski, S. Wood
Published in: Interface Focus, Issue 11, 2021, Page(s) 20200006, ISSN 2042-8898
Publisher: Royal Society Publishing
DOI: 10.1098/rsfs.2020.0006

Structure based virtual screening: Fast and slow

Author(s): Alejandro Varela‐Rial, Maciej Majewski, Gianni De Fabritiis
Published in: WIREs Computational Molecular Science, Issue 12, 2023, ISSN 1759-0876
Publisher: John Wiley & Sons Inc.
DOI: 10.1002/wcms.1544

Ensemble Simulations and Experimental Free Energy Distributions: Evaluation and Characterization of Isoxazole Amides as SMYD3 Inhibitors

Author(s): S. Wan, A. Bhati, D. Wright, I. Wall, A. Graves, D. Green, P. V. Coveney
Published in: J. Chem. Inf. Model., 2022, ISSN 1549-960X
Publisher: ACS
DOI: 10.1021/acs.jcim.2c00255

In silico trials for treatment of acute ischemic stroke: Design and implementation

Author(s): Claire Miller, Raymond M. Padmos, Max van der Kolk, Tamás I. Józsa, Noor Samuels, Yidan Xue, Stephen J. Payne, Alfons G. Hoekstra
Published in: Computers in Biology and Medicine, Issue 137, 2022, Page(s) 104802, ISSN 0010-4825
Publisher: Pergamon Press Ltd.
DOI: 10.1016/j.compbiomed.2021.104802

When we can trust computers (and when we can't)

Author(s): Peter V. Coveney, Roger R. Highfield
Published in: Philosophical Transactions of the Royal Society A: Mathematical, Physical and Engineering Sciences, Issue 379/2197, 2021, ISSN 1364-503X
Publisher: Royal Society of London
DOI: 10.1098/rsta.2020.0067

PlayMolecule Viewer: A Toolkit for the Visualization of Molecules and Other Data

Author(s): Mariona Torrens-Fontanals, Panagiotis Tourlas, Stefan Doerr, Gianni De Fabritiis
Published in: Journal of Chemical Information and Modeling, Issue 64, 2024, Page(s) 584-589, ISSN 1549-9596
Publisher: American Chemical Society
DOI: 10.1021/acs.jcim.3c01776

Understanding and Improving Risk Assessment After Myocardial Infarction Using Automated Left Ventricular Shape Analysis

Author(s): Jorge Corral Acero, Andreas Schuster, Ernesto Zacur, Torben Lange, Thomas Stiermaier, Sören J. Backhaus, Holger Thiele, Alfonso Bueno-Orovio, Pablo Lamata, Ingo Eitel, Vicente Grau
Published in: JACC: Cardiovascular Imaging, Issue 15, 2022, Page(s) 1563-1574, ISSN 1936-878X
Publisher: Elsevier BV
DOI: 10.1016/j.jcmg.2021.11.027

Multi-class point cloud completion networks for 3D cardiac anatomy reconstruction from cine magnetic resonance images

Author(s): Marcel Beetz, Abhirup Banerjee, Julius Ossenberg-Engels, Vicente Grau
Published in: Medical Image Analysis, Issue 90, 2024, Page(s) 102975, ISSN 1361-8415
Publisher: Elsevier BV
DOI: 10.1016/j.media.2023.102975

Are CT-Based Finite Element Model Predictions of Femoral Bone Strengthening Clinically Useful?

Author(s): Marco Viceconti, Muhammad Qasim, Pinaki Bhattacharya, Xinshan Li
Published in: Current Osteoporosis Reports, Issue 16/3, 2018, Page(s) 216-223, ISSN 1544-1873
Publisher: Current Science Inc.
DOI: 10.1007/s11914-018-0438-8

Cardiac computational modelling

Author(s): Bragard, Jean R.; Cámara, Óscar; Echebarria, Blas; Giorda, Luca Gerardo; Pueyo, Esther; Saiz Rodríguez, Francisco Javier; Sebastián, Rafael; Soudah, Eduardo; Vázquez, Mariano
Published in: reponame:RiuNet. Repositorio Institucional de la Universitat Politécnica de Valéncia, Issue 43, 2021, ISSN 0000-0000
Publisher: ScienceDirect
DOI: 10.1016/j.rec.2020.05.024

The ‘Digital Twin’ to enable the vision of precision cardiology

Author(s): Jorge Corral-Acero, Francesca Margara, Maciej Marciniak, Cristobal Rodero, Filip Loncaric, Yingjing Feng, Andrew Gilbert, Joao F Fernandes, Hassaan A Bukhari, Ali Wajdan, Manuel Villegas Martinez, Mariana Sousa Santos, Mehrdad Shamohammdi, Hongxing Luo, Philip Westphal, Paul Leeson, Paolo DiAchille, Viatcheslav Gurev, Manuel Mayr, Liesbet Geris, Pras Pathmanathan, Tina Morrison, Richard Cornelusse
Published in: European Heart Journal, Issue 41, 2022, Page(s) 4556-4564, ISSN 0195-668X
Publisher: Oxford University Press
DOI: 10.1093/eurheartj/ehaa159

FabSim3: An automation toolkit for verified simulations using high performance computing

Author(s): D. Groen, H. Arabnejad, D. Suleimenova, W. Edeling, E. Raffin, Y. Xue, K. Bronik, N. Monnier, P. V. Coveney
Published in: Computer Physics Communications, 2022, ISSN 0010-4655
Publisher: Elsevier BV
DOI: 10.1016/j.cpc.2022.108596

The effect of boundary and loading conditions on patient classification using finite element predicted risk of fracture

Author(s): Zainab Altai, Muhammad Qasim, Xinshan Li, Marco Viceconti
Published in: Clinical Biomechanics, Issue 68, 2019, Page(s) 137-143, ISSN 0268-0033
Publisher: Pergamon Press Ltd.
DOI: 10.1016/j.clinbiomech.2019.06.004

Continuum model for flow diverting stents in 3D patient-specific simulation of intracranial aneurysms

Author(s): Sha Li, Bastien Chopard, Jonas Latt
Published in: Journal of Computational Science, Issue 38, 2019, Page(s) 101045, ISSN 1877-7503
Publisher: Elsevier BV
DOI: 10.1016/j.jocs.2019.101045

Segment anything model for medical images?

Author(s): Yuhao Huang, Xin Yang, Lian Liu, Han Zhou, Ao Chang, Xinrui Zhou, Rusi Chen, Junxuan Yu, Jiongquan Chen, Chaoyu Chen, Sijing Liu, Haozhe Chi, Xindi Hu, Kejuan Yue, Lei Li, Vicente Grau, Deng-Ping Fan, Fajin Dong, Dong Ni
Published in: Medical Image Analysis, Issue 92, 2024, Page(s) 103061, ISSN 1361-8415
Publisher: Elsevier BV
DOI: 10.1016/j.media.2023.103061

Effect of Suboptimal Neuromuscular Control on the Risk of Massive Wear in Total Knee Replacement

Author(s): Viceconti M.; Curreli C.; Bottin F.; Davico G.
Published in: Annals of Biomedical Engineering, Issue 2, 2021, ISSN 0000-0000
Publisher: Springer
DOI: 10.1007/s10439-021-02795-y

Image-based flow simulation of platelet aggregates under different shear rates

Author(s): Yue Hao, Gábor Závodszky, Claudia Tersteeg, Mojtaba Barzegari, Alfons G. Hoekstra
Published in: PLOS Computational Biology, Issue 19, 2023, Page(s) e1010965, ISSN 1553-7358
Publisher: PLOS
DOI: 10.1371/journal.pcbi.1010965

From digital hype to analogue reality: Universal simulation beyond the quantum and exascale eras

Author(s): Peter V. Coveney, Roger R. Highfield
Published in: Journal of Computational Science, Issue 46, 2020, Page(s) 101093, ISSN 1877-7503
Publisher: Elsevier BV
DOI: 10.1016/j.jocs.2020.101093

Blinded In Silico Drug Trial Reveals the Minimum Set of Ion Channels for Torsades de Pointes Risk Assessment

Author(s): Xin Zhou, Yusheng Qu, Elisa Passini, Alfonso Bueno-Orovio, Yang Liu, Hugo M. Vargas, Blanca Rodriguez
Published in: Frontiers in Pharmacology, Issue 10, 2020, ISSN 1663-9812
Publisher: Frontiers Media S.A.
DOI: 10.3389/fphar.2019.01643

Computational biomedicine. Part 1: molecular medicine

Author(s): Peter V. Coveney
Published in: Interface Focus, Issue 10, 2021, Page(s) 20200047, ISSN 2042-8898
Publisher: Royal Society Publishing
DOI: 10.1098/rsfs.2020.0047

The influence of base pair tautomerism on single point mutations in aqueous DNA

Author(s): A. Gheorghiu, P. V. Coveney, A. A. Arabi
Published in: Interface Focus, Issue 10, 2022, Page(s) 20190120, ISSN 2042-8898
Publisher: Royal Society Publishing
DOI: 10.1098/rsfs.2019.0120

Haemodynamic flow conditions at the initiation of high-shear platelet aggregation: a combined in vitro and cellular in silico study

Author(s): B. J. M. van Rooij, G. Závodszky, A. G. Hoekstra, D. N. Ku
Published in: Interface Focus, Issue 11/1, 2021, Page(s) 20190126, ISSN 2042-8898
Publisher: Royal Society Publishing
DOI: 10.1098/rsfs.2019.0126

Femoral neck strain prediction during level walking using a combined musculoskeletal and finite element model approach

Author(s): Zainab Altai, Erica Montefiori, Bart van Veen, Margaret A. Paggiosi, Eugene V. McCloskey, Marco Viceconti, Claudia Mazzà, Xinshan Li
Published in: PLOS ONE, Issue 16/2, 2021, Page(s) e0245121, ISSN 1932-6203
Publisher: Public Library of Science
DOI: 10.1371/journal.pone.0245121

Inference of ventricular activation properties from non-invasive electrocardiography

Author(s): Julia Camps, Brodie Lawson, Christopher Drovandi, Ana Minchole, Zhinuo Jenny Wang, Vicente Grau, Kevin Burrage, Blanca Rodriguez
Published in: Medical Image Analysis, Issue 73, 2024, Page(s) 102143, ISSN 1361-8415
Publisher: Elsevier BV
DOI: 10.1016/j.media.2021.102143

How quickly can we predict trimethoprim resistance using alchemical free energy methods?

Author(s): Philip W. Fowler
Published in: Interface Focus, Issue 10/6, 2020, Page(s) 20190141, ISSN 2042-8898
Publisher: Royal Society Publishing
DOI: 10.1098/rsfs.2019.0141

Towards blood flow in the virtual human: efficient self-coupling of HemeLB

Author(s): J. W. S. McCullough, R. A. Richardson, A. Patronis, R. Halver, R. Marshall, M. Ruefenacht, B. J. N. Wylie, T. Odaker, M. Wiedemann, B. Lloyd, E. Neufeld, G. Sutmann, A. Skjellum, D. Kranzlmüller, P. V. Coveney
Published in: Interface Focus, Issue 11/1, 2021, Page(s) 20190119, ISSN 2042-8898
Publisher: Royal Society Publishing
DOI: 10.1098/rsfs.2019.0119

Hybrid parallelization of molecular dynamics simulations to reduce load imbalance

Author(s): Julian Morillo, Maxime Vassaux, Peter V. Coveney, Marta Garcia-Gasulla
Published in: The Journal of Supercomputing, Issue 78, 2022, Page(s) 9184-9215, ISSN 0920-8542
Publisher: Kluwer Academic Publishers
DOI: 10.1007/s11227-021-04214-4

Structure and dynamics of an archetypal DNA nanoarchitecture revealed via cryo-EM and molecular dynamics simulations

Author(s): Katya Ahmad, Abid Javed, Conor Lanphere, Peter V. Coveney, Elena V. Orlova, Stefan Howorka
Published in: Nature Communications, Issue 14, 2023, ISSN 2041-1723
Publisher: Nature Publishing Group
DOI: 10.1038/s41467-023-38681-5

What determines the optimal pharmacological treatment of atrial fibrillation? Insights from in silico trials in 800 virtual atria

Author(s): Albert Dasí, Michael T.B. Pope, Rohan S. Wijesurendra, Tim R. Betts, Rafael Sachetto, Alfonso Bueno‐Orovio, Blanca Rodriguez
Published in: The Journal of Physiology, Issue 601, 2023, Page(s) 4013-4032, ISSN 0022-3751
Publisher: Blackwell Publishing Inc.
DOI: 10.1113/jp284730

Possible Contexts of Use for In Silico Trials Methodologies: A Consensus-Based Review

Author(s): Marco Viceconti, Luca Emili, Payman Afshari, Eulalie Courcelles, Cristina Curreli, Nele Famaey, Liesbet Geris, Marc Horner, Maria Cristina Jori, Alexander Kulesza, Axel Loewe, Michael Neidlin, Markus Reiterer, Cecile F. Rousseau, Giulia Russo, Simon J. Sonntag, Emmanuelle M. Voisin, Francesco Pappalardo
Published in: IEEE Journal of Biomedical and Health Informatics, Issue 25, 2021, Page(s) 3977-3982, ISSN 2168-2194
Publisher: Institute of Electrical and Electronics Engineers Inc.
DOI: 10.1109/jbhi.2021.3090469

Effect of particularisation size on the accuracy and efficiency of a multiscale tumours' growth model

Author(s): Varella, Vinicius; Quintela, Barbara de M; Kasztelnik, Marek; Viceconti, Marco
Published in: International Journal for Numerical Methods in Biomedical Engineering, Issue 48, 2022, ISSN 0000-0000
Publisher: Wiley
DOI: 10.1002/cnm.3657

Hit-to-lead and lead optimization binding free energy calculations for G protein-coupled receptors

Author(s): Shunzhou Wan, Andrew Potterton, Fouad S. Husseini, David W. Wright, Alexander Heifetz, Maciej Malawski, Andrea Townsend-Nicholson, Peter V. Coveney
Published in: Interface Focus, Issue 10/6, 2020, Page(s) 20190128, ISSN 2042-8898
Publisher: Royal Society Publishing
DOI: 10.1098/rsfs.2019.0128

The impact of uncertainty on predictions of the CovidSim epidemiological code

Author(s): Wouter Edeling, Hamid Arabnejad, Robbie Sinclair, Diana Suleimenova, Krishnakumar Gopalakrishnan, Bartosz Bosak, Derek Groen, Imran Mahmood, Daan Crommelin, Peter V. Coveney
Published in: Nature Computational Science, Issue 1, 2022, Page(s) 128-135, ISSN 2662-8457
Publisher: Nature
DOI: 10.1038/s43588-021-00028-9

Hydrodynamic Resistance of Intracranial Flow-Diverter Stents: Measurement Description and Data Evaluation

Author(s): Benjamin Csippa, Dániel Gyürki, Gábor Závodszky, István Szikora, György Paál
Published in: Cardiovascular Engineering and Technology, Issue 11/1, 2020, Page(s) 1-13, ISSN 1869-408X
Publisher: Springer Pub. Co.,
DOI: 10.1007/s13239-019-00445-y

The Effects of Micro-vessel Curvature Induced Elongational Flows on Platelet Adhesion

Author(s): Christian J. Spieker, Gábor Závodszky, Clarisse Mouriaux, Max van der Kolk, Christian Gachet, Pierre H. Mangin, Alfons G. Hoekstra
Published in: Annals of Biomedical Engineering, Issue 49, 2021, Page(s) 3609-3620, ISSN 0090-6964
Publisher: Kluwer Academic Publishers
DOI: 10.1007/s10439-021-02870-4

Characterization of partially ordered states in the intrinsically disordered N-terminal domain of p53 using millisecond molecular dynamics simulations

Author(s): Pablo Herrera-Nieto, Adrià Pérez, Gianni De Fabritiis
Published in: Scientific Reports, Issue 10/1, 2020, ISSN 2045-2322
Publisher: Nature Publishing Group
DOI: 10.1038/s41598-020-69322-2

Gordon Research Conference on Cardiac Arrhythmia Mechanisms 2023: early career investigators’ views on emerging concepts and technologies

Author(s): Ahmed Ramadan, Enaam Chleilat, Hector Martinez‐Navarro, Jaclyn Brennan‐McLean, Jaël Copier, Jessica Caldwell, Joachim Greiner, Patricia Martínez Díaz, Vladimír Sobota
Published in: The Journal of Physiology, 2023, ISSN 0022-3751
Publisher: Blackwell Publishing Inc.
DOI: 10.1113/jp284666

In-silico drug trials for precision medicine in atrial fibrillation: From ionic mechanisms to electrocardiogram-based predictions in structurally-healthy human atria

Author(s): Albert Dasí, Aditi Roy, Rafael Sachetto, Julia Camps, Alfonso Bueno-Orovio, Blanca Rodriguez
Published in: Frontiers in Physiology, Issue 13, 2022, ISSN 1664-042X
Publisher: Frontiers Research Foundation
DOI: 10.3389/fphys.2022.966046

The influence of red blood cell deformability on hematocrit profiles and platelet margination

Author(s): Benjamin Czaja, Mario Gutierrez, Gábor Závodszky, David de Kanter, Alfons Hoekstra, Omolola Eniola-Adefeso
Published in: PLOS Computational Biology, Issue 16/3, 2020, Page(s) e1007716, ISSN 1553-7358
Publisher: PLOS
DOI: 10.1371/journal.pcbi.1007716

Digital blood in massively parallel CPU/GPU systems for the study of platelet transport

Author(s): Christos Kotsalos, Jonas Latt, Joel Beny, Bastien Chopard
Published in: Interface Focus, Issue 11/1, 2021, Page(s) 20190116, ISSN 2042-8898
Publisher: Royal Society Publishing
DOI: 10.1098/rsfs.2019.0116

High resolution simulation of basilar artery infarct and flow within the circle of Willis

Author(s): Jon W. S. McCullough, Peter V. Coveney
Published in: Scientific Reports, Issue 13, 2023, ISSN 2045-2322
Publisher: Nature Publishing Group
DOI: 10.1038/s41598-023-48776-0

Coupling one-dimensional arterial blood flow to three-dimensional tissue perfusion models for in silico trials of acute ischaemic stroke

Author(s): Raymond M. Padmos, Tamás I. Józsa, Wahbi K. El-Bouri, Praneeta R. Konduri, Stephen J. Payne, Alfons G. Hoekstra
Published in: Interface Focus, Issue 11, 2021, Page(s) 20190125, ISSN 2042-8898
Publisher: Royal Society Publishing
DOI: 10.1098/rsfs.2019.0125

Enhanced optimization-based method for the generation of patient-specific models of Purkinje networks

Author(s): Lucas Arantes Berg, Bernardo Martins Rocha, Rafael Sachetto Oliveira, Rafael Sebastian, Blanca Rodriguez, Rafael Alves Bonfim de Queiroz, Elizabeth M. Cherry, Rodrigo Weber dos Santos
Published in: Scientific Reports, Issue 13, 2023, ISSN 2045-2322
Publisher: Nature Publishing Group
DOI: 10.1038/s41598-023-38653-1

Supplementary Information from Identifying the start of a platelet aggregate by the shear rate and the cell-depleted layer

Author(s): B.J.M. Van Rooij; G. Závodszky; V.W. Azizi Tarksalooyeh; A.G. Hoekstra
Published in: The Royal Society Interface, Issue 24, 2019, ISSN 0000-0000
Publisher: The Royal Society
DOI: 10.6084/m9.figshare.9831245

Modelización computacional cardiaca

Author(s): Jean R. Bragard, Oscar Camara, Blas Echebarria, Luca Gerardo Giorda, Esther Pueyo, Javier Saiz, Rafael Sebastián, Eduardo Soudah, Mariano Vázquez
Published in: Revista Española de Cardiología, Issue 74, 2020, Page(s) 65-71, ISSN 0300-8932
Publisher: Ediciones Doyma S.A.
DOI: 10.1016/j.recesp.2020.05.040

Cost-Effectiveness Analysis of CT-Based Finite Element Modeling for Osteoporosis Screening in Secondary Fracture Prevention: An Early Health Technology Assessment in the Netherlands

Author(s): Jieyi Li, Marco Viceconti, Xinshan Li, Pinaki Bhattacharya, David M. J. Naimark, Anwar Osseyran
Published in: MDM Policy & Practice, Issue 8, 2023, ISSN 2381-4683
Publisher: Sage
DOI: 10.1177/23814683231202993

Alchemical Free Energy Estimators and Molecular Dynamics Engines: Accuracy, Precision and Reproducibility

Author(s): A. Wade, A. P. Bhati, S. Wan, P. V. Coveney
Published in: J. Chem. Theory Comput, 2022, ISSN 1549-9626
Publisher: ACS
DOI: 10.1021/acs.jctc.2c00114

Fluid-structure interaction analysis of eccentricity and leaflet rigidity on thrombosis biomarkers in bioprosthetic aortic valve replacements

Author(s): David Oks; Mariano Vázquez; Guillaume Houzeaux; Constantine Butakoff; Cristóbal Samaniego
Published in: Crossref, Issue 56, 2022, ISSN 0000-0000
Publisher: Wiley
DOI: 10.1101/2022.01.06.475272

Palabos: Parallel Lattice Boltzmann Solver

Author(s): Jonas Latt, Orestis Malaspinas, Dimitrios Kontaxakis, Andrea Parmigiani, Daniel Lagrava, Federico Brogi, Mohamed Ben Belgacem, Yann Thorimbert, Sébastien Leclaire, Sha Li, Francesco Marson, Jonathan Lemus, Christos Kotsalos, Raphaël Conradin, Christophe Coreixas, Rémy Petkantchin, Franck Raynaud, Joël Beny, Bastien Chopard
Published in: Computers & Mathematics with Applications, Issue 81, 2022, Page(s) 334-350, ISSN 0898-1221
Publisher: Pergamon Press Ltd.
DOI: 10.1016/j.camwa.2020.03.022

Initial platelet aggregation in the complex shear environment of a punctured vessel model

Author(s): Christian J. Spieker, Gábor Závodszky, Clarisse Mouriaux, Pierre H. Mangin, Alfons G. Hoekstra
Published in: Physics of Fluids, Issue 35, 2023, ISSN 1070-6631
Publisher: American Institute of Physics
DOI: 10.1063/5.0157814

Palabos-npFEM: Software for the Simulation of Cellular Blood Flow (Digital Blood)

Author(s): Christos Kotsalos, Jonas Latt, Bastien Chopard
Published in: Journal of Open Research Software, Issue 9, 2022, Page(s) 16, ISSN 2049-9647
Publisher: Ubiquity Press
DOI: 10.5334/jors.343

Personalized pathology test for Cardio-vascular disease: Approximate Bayesian computation with discriminative summary statistics learning

Author(s): Ritabrata Dutta, Karim Zouaoui Boudjeltia, Christos Kotsalos, Alexandre Rousseau, Daniel Ribeiro de Sousa, Jean-Marc Desmet, Alain Van Meerhaeghe, Antonietta Mira, Bastien Chopard
Published in: PLOS Computational Biology, Issue 18, 2022, Page(s) e1009910, ISSN 1553-7358
Publisher: PLOS
DOI: 10.1371/journal.pcbi.1009910

Identifying the start of a platelet aggregate by the shear rate and the cell-depleted layer

Author(s): B. J. M. van Rooij, G. Závodszky, V. W. Azizi Tarksalooyeh, A. G. Hoekstra
Published in: Journal of The Royal Society Interface, Issue 16/159, 2019, Page(s) 20190148, ISSN 1742-5689
Publisher: The Royal Society
DOI: 10.1098/rsif.2019.0148

Enhancing Protein–Ligand Binding Affinity Predictions Using Neural Network Potentials

Author(s): Francesc Sabanés Zariquiey, Raimondas Galvelis, Emilio Gallicchio, John D. Chodera, Thomas E. Markland, Gianni De Fabritiis
Published in: Journal of Chemical Information and Modeling, Issue 64, 2024, Page(s) 1481-1485, ISSN 1549-9596
Publisher: American Chemical Society
DOI: 10.1021/acs.jcim.3c02031

Automated 3D Whole-Heart Mesh Reconstruction From 2D Cine MR Slices Using Statistical Shape Model

Author(s): Banerjee, A; Zacur, E; Choudhury, RP; Grau, V
Published in: Crossref, Issue 28, 2022, ISBN 978-1-7281-2782-8
Publisher: IEEE
DOI: 10.1109/embc48229.2022.9871327

Generating Subpopulation-Specific Biventricular Anatomy Models Using Conditional Point Cloud Variational Autoencoders

Author(s): Beetz, M; Banerjee, A; Grau, V
Published in: Lecture Notes in Computer Science ISBN: 9783030937218, Issue 29, 2022, ISBN 9783030937218
Publisher: Springer
DOI: 10.1007/978-3-030-93722-5_9

Generation of 12-Lead Electrocardiogram with Subject-Specific, Image-Derived Characteristics Using a Conditional Variational Autoencoder

Author(s): Yuling Sang, Marcel Beetz, Vicente Grau
Published in: 2022 IEEE 19th International Symposium on Biomedical Imaging (ISBI), 2022
Publisher: IEEE
DOI: 10.1109/isbi52829.2022.9761431

Automated Torso Contour Extraction from Clinical Cardiac MR Slices for 3D Torso Reconstruction

Author(s): Hannah J. Smith, Abhirup Banerjee, Robin P. Choudhury, Vicente Grau
Published in: 2022 44th Annual International Conference of the IEEE Engineering in Medicine & Biology Society (EMBC), 2022
Publisher: IEEE
DOI: 10.1109/embc48229.2022.9871643

Biventricular Surface Reconstruction From Cine Mri Contours Using Point Completion Networks

Author(s): Marcel Beetz, Abhirup Banerjee, Vicente Grau
Published in: 2021 IEEE 18th International Symposium on Biomedical Imaging (ISBI), 2022
Publisher: IEEE
DOI: 10.1109/isbi48211.2021.9434040

Semi-Supervised Coronary Vessels Segmentation from Invasive Coronary Angiography with Connectivity-Preserving Loss Function

Author(s): Haorui He, Abhirup Banerjee, Marcel Beetz, Robin P. Choudhury, Vicente Grau
Published in: 2022 IEEE 19th International Symposium on Biomedical Imaging (ISBI), 2022, ISBN 978-1-6654-2923-8
Publisher: IEEE
DOI: 10.1109/isbi52829.2022.9761695

Combined Generation of Electrocardiogram and Cardiac Anatomy Models Using Multi-Modal Variational Autoencoders

Author(s): Beetz, M; Banerjee, A; Sang, Y; Grau, V
Published in: Crossref, Issue 26, 2022, ISSN 0000-0000
Publisher: IEEE
DOI: 10.1109/isbi52829.2022.9761590

Hemelb Acceleration and Visualization for Cerebral Aneurysms

Author(s): Sahar Soheilian Esfahani, Peter V. Coveney, Xiaojun Zhai, Minsi Chen, Abbes Amira, Faycal Bensaali, Julien AbiNahed, Sarada Dakua, Georges Younes, Robin A. Richardson
Published in: 2019 IEEE International Conference on Image Processing (ICIP), 2022
Publisher: IEEE
DOI: 10.1109/icip.2019.8803712

3D Shape-Based Myocardial Infarction Prediction Using Point Cloud Classification Networks

Author(s): Beetz, M; Yang, Y; Banerjee, A; Li, L; Grau, V
Published in: Crossref, Issue 17, 2022
Publisher: IEEE
DOI: 10.1109/embc40787.2023.10340878

IMPECCABLE: Integrated Modeling PipelinE for COVID Cure by Assessing Better LEads

Author(s): Aymen Al Saadi, Dario Alfe, Yadu Babuji, Agastya Bhati, Ben Blaiszik, Alexander Brace, Thomas Brettin, Kyle Chard, Ryan Chard, Austin Clyde, Peter Coveney, Ian Foster, Tom Gibbs, Shantenu Jha, Kristopher Keipert, Dieter Kranzlmüller, Thorsten Kurth, Hyungro Lee, Zhuozhao Li, Heng Ma, Gerald Mathias, Andre Merzky, Alexander Partin, Arvind Ramanathan, Ashka Shah, Abraham Stern, Rick Stevens, Li Tan
Published in: 50th International Conference on Parallel Processing, 2023
Publisher: ACM
DOI: 10.1145/3472456.3473524

Exascale potholes for HPC: Execution performance and variability analysis of the flagship application code HemeLB

Author(s): Brian J. N. Wylie
Published in: 2020 IEEE/ACM International Workshop on HPC User Support Tools (HUST) and Workshop on Programming and Performance Visualization Tools (ProTools), 2022
Publisher: IEEE
DOI: 10.1109/hustprotools51951.2020.00014

Scalable HPC & AI infrastructure for COVID-19 therapeutics

Author(s): Hyungro Lee, Andre Merzky, Li Tan, Mikhail Titov, Matteo Turilli, Dario Alfe, Agastya Bhati, Alex Brace, Austin Clyde, Peter Coveney, Heng Ma, Arvind Ramanathan, Rick Stevens, Anda Trifan, Hubertus Van Dam, Shunzhou Wan, Sean Wilkinson, Shantenu Jha
Published in: Proceedings of the Platform for Advanced Scientific Computing Conference, 2023
Publisher: ACM
DOI: 10.1145/3468267.3470573

Inference of Number and Location of Purkinje Root Nodes and Ventricular Conduction Properties from Clinical 12-Lead ECGs for Cardiac Digital Twinning

Author(s): """Julia Camps, Zhinuo Jenny Wang, Rafael Sebastian, Xin Zhou, Brodie Lawson, Lucas Arantes Berg, Kevin Burrage, Vicente Grau, Rodrigo Weber, Blanca Rodriguez"""
Published in: Computing in Cardiology Conference (CinC), 2022 Computing in Cardiology Conference (CinC), 2023
Publisher: Computing in Cardiology
DOI: 10.22489/cinc.2022.235

A Heterogeneous Multi-scale Model for Blood Flow

Author(s): Benjamin Czaja, Gábor Závodszky, Alfons Hoekstra
Published in: Computational Science – ICCS 2020 - 20th International Conference, Amsterdam, The Netherlands, June 3–5, 2020, Proceedings, Part VI, Issue 12142, 2020, Page(s) 403-409, ISBN 978-3-030-50432-8
Publisher: Springer International Publishing
DOI: 10.1007/978-3-030-50433-5_31

Point2Mesh-Net: Combining Point Cloud and Mesh-Based Deep Learning for Cardiac Shape Reconstruction

Author(s): Marcel Beetz, Abhirup Banerjee, Vicente Grau
Published in: Statistical Atlases and Computational Models of the Heart. Regular and CMRxMotion Challenge Papers, Lecture Notes in Computer Science, 2023, Page(s) 280-290
Publisher: Springer Nature Switzerland
DOI: 10.1007/978-3-031-23443-9_26

Predicting Residence Time of GPCR Ligands with Machine Learning

Author(s): Andrew Potterton, Alexander Heifetz, Andrea Townsend-Nicholson
Published in: Artificial Intelligence in Drug Design, Methods in Molecular Biology, 2022, Page(s) 191-205
Publisher: Springer US
DOI: 10.1007/978-1-0716-1787-8_8

Post-Infarction Risk Prediction with Mesh Classification Networks

Author(s): Marcel Beetz, Jorge Corral Acero, Abhirup Banerjee, Ingo Eitel, Ernesto Zacur, Torben Lange, Thomas Stiermaier, Ruben Evertz, Sören J. Backhaus, Holger Thiele, Alfonso Bueno-Orovio, Pablo Lamata, Andreas Schuster, Vicente Grau
Published in: Statistical Atlases and Computational Models of the Heart. Regular and CMRxMotion Challenge Papers, Lecture Notes in Computer Science, 2023, Page(s) 291-301
Publisher: Springer Nature Switzerland
DOI: 10.1007/978-3-031-23443-9_27

Characterizing Rhodopsin-Arrestin Interactions with the Fragment Molecular Orbital (FMO) Method

Author(s): Alexander Heifetz, Andrea Townsend-Nicholson
Published in: Quantum Mechanics in Drug Discovery, Issue 2114, 2020, Page(s) 177-186, ISBN 978-1-0716-0281-2
Publisher: Springer US
DOI: 10.1007/978-1-0716-0282-9_12

Analyzing GPCR-Ligand Interactions with the Fragment Molecular Orbital (FMO) Method

Author(s): Alexander Heifetz, Tim James, Michelle Southey, Inaki Morao, Dmitri G. Fedorov, Mike J. Bodkin, Andrea Townsend-Nicholson
Published in: Quantum Mechanics in Drug Discovery, Issue 2114, 2020, Page(s) 163-175, ISBN 978-1-0716-0281-2
Publisher: Springer US
DOI: 10.1007/978-1-0716-0282-9_11

des-ist: A Simulation Framework to Streamline Event-Based In Silico Trials

Author(s): Max van der Kolk, Claire Miller, Raymond Padmos, Victor Azizi, Alfons Hoekstra
Published in: Computational Science – ICCS 2021, Lecture Notes in Computer Science, 2021, Page(s) 648-654
Publisher: Springer International Publishing
DOI: 10.1007/978-3-030-77967-2_53

Deep Learning-Based Emulation of Human Cardiac Activation Sequences

Author(s): Ambre Bertrand, Julia Camps, Vicente Grau, Blanca Rodriguez
Published in: Functional Imaging and Modeling of the Heart, Lecture Notes in Computer Science, 2023, Page(s) 213-222
Publisher: Springer Nature Switzerland
DOI: 10.1007/978-3-031-35302-4_22

Predicting 3D Cardiac Deformations with Point Cloud Autoencoders

Author(s): Marcel Beetz, Julius Ossenberg-Engels, Abhirup Banerjee, Vicente Grau
Published in: Lecture Notes in Computer Science, Statistical Atlases and Computational Models of the Heart. Multi-Disease, Multi-View, and Multi-Center Right Ventricular Segmentation in Cardiac MRI Challenge, 2023, Page(s) 219-228
Publisher: Springer International Publishing
DOI: 10.1007/978-3-030-93722-5_24

Simulating Initial Steps of Platelet Aggregate Formation in a Cellular Blood Flow Environment

Author(s): Christian J. Spieker, Konstantinos Asteriou, Gab́or Zav́odszky
Published in: Computational Science – ICCS 2023, Lecture Notes in Computer Science, 2024, Page(s) 323-336
Publisher: Springer Nature Switzerland
DOI: 10.1007/978-3-031-36024-4_26

Multi-objective Point Cloud Autoencoders for Explainable Myocardial Infarction Prediction

Author(s): Marcel Beetz, Abhirup Banerjee, Vicente Grau
Published in: Lecture Notes in Computer Science, Medical Image Computing and Computer Assisted Intervention – MICCAI 2023, 2024, Page(s) 532-542
Publisher: Springer Nature Switzerland
DOI: 10.1007/978-3-031-43895-0_50

Mesh U-Nets for 3D Cardiac Deformation Modeling

Author(s): Marcel Beetz, Jorge Corral Acero, Abhirup Banerjee, Ingo Eitel, Ernesto Zacur, Torben Lange, Thomas Stiermaier, Ruben Evertz, Sören J. Backhaus, Holger Thiele, Alfonso Bueno-Orovio, Pablo Lamata, Andreas Schuster, Vicente Grau
Published in: Statistical Atlases and Computational Models of the Heart. Regular and CMRxMotion Challenge Papers, Lecture Notes in Computer Science, 2023, Page(s) 245-257
Publisher: Springer Nature Switzerland
DOI: 10.1007/978-3-031-23443-9_23

Optimised Misalignment Correction from Cine MR Slices Using Statistical Shape Model

Author(s): Abhirup Banerjee, Ernesto Zacur, Robin P. Choudhury, Vicente Grau
Published in: Medical Image Understanding and Analysis, Lecture Notes in Computer Science, 2024, Page(s) 201-209
Publisher: Springer International Publishing
DOI: 10.1007/978-3-030-80432-9_16

Characterizing Protein-Protein Interactions with the Fragment Molecular Orbital Method

Author(s): Alexander Heifetz, Vladimir Sladek, Andrea Townsend-Nicholson, Dmitri G. Fedorov
Published in: Quantum Mechanics in Drug Discovery, Issue 2114, 2020, Page(s) 187-205, ISBN 978-1-0716-0281-2
Publisher: Springer US
DOI: 10.1007/978-1-0716-0282-9_13

Conformational Searching with Quantum Mechanics

Author(s): Matthew Habgood, Tim James, Alexander Heifetz
Published in: Quantum Mechanics in Drug Discovery, Issue 2114, 2020, Page(s) 207-229, ISBN 978-1-0716-0281-2
Publisher: Springer US
DOI: 10.1007/978-1-0716-0282-9_14

Deep Computational Model for the Inference of Ventricular Activation Properties

Author(s): Lei Li; Julia Camps; Abhirup Banerjee; Marcel Beetz; Blanca Rodriguez; Vicente Grau
Published in: Statistical Atlases and Computational Models of the Heart. Regular and CMRxMotion Challenge Papers ISBN: 9783031234422, Issue 16, 2023
Publisher: Springer
DOI: 10.1007/978-3-031-23443-9_34

Personalized pathology test for Cardio-vascular disease: Approximate Bayesian computation with discriminative summary statistics learning

Author(s): Ritabrata Dutta, Karim Zouaoui-Boudjeltia, Christos Kotsalos, Alexandre Rousseau, Daniel Ribeiro de Sousa, Jean-Marc Desmet, Alain Van Meerhaeghe, Antonietta Mira, Bastien Chopard
Published in: arXiv, 2020
Publisher: arXiv
DOI: 10.48550/arxiv.2010.06465

In Silico Evaluation of Cell Therapy in Acute versus Chronic Infarction: Role of Automaticity, Heterogeneity and Purkinje in Human

Author(s): Leto Luana Riebel, Zhinuo Jenny Wang, Hector Martinez-Navarro, Cristian Trovato, Julia Camps, Lucas Arantes Berg, Xin Zhou, Ruben Doste, Rafael Sachetto Oliveira, Rodrigo Weber dos Santos, Jacopo Biasetti, Blanca Rodriguez
Published in: bioRxiv, 2023
Publisher: bioRxiv
DOI: 10.1101/2023.12.11.570780

High fidelity blood flow in a patient-specific arteriovenous fistula

Author(s): J. W. S. McCullough, P. V. Coveney
Published in: arXiv, 2020
Publisher: arXiv
DOI: 10.48550/arxiv.2012.04639

Prediction of pyrazinamide resistance in Mycobacterium tuberculosis using structure-based machine learning approaches

Author(s): Joshua J Carter, Timothy M Walker, A Sarah Walker, Michael G. Whitfield, Glenn P. Morlock, Charlotte I. Lynch, Dylan Adlard, Timothy EA Peto, James E. Posey, Derrick W Crook, Philip W Fowler
Published in: bioRxiv, 2023
Publisher: bioRxiv
DOI: 10.1101/518142

Clinical phenotypes in acute and chronic infarction explained through human ventricular electromechanical modelling and simulations

Author(s): Xin Zhou, Zhinuo Jenny Wang, Julia Camps, Jakub Tomek, Alfonso Santiago, Adria Quintanas, Mariano Vazquez, Marmar Vaseghi, Blanca Rodriguez
Published in: bioRxiv, 2023
Publisher: bioRxiv
DOI: 10.1101/2022.02.15.480392

Proximal femur bone mineral density in osteoporotic patients a review of placebo groups in clinical trials

Author(s): Sara Oliviero
Published in: Zenodo, 2022
Publisher: Zenodo
DOI: 10.5281/zenodo.7248964

Digital Twinning of the Human Ventricular Activation Sequence to Clinical 12-lead ECGs and Magnetic Resonance Imaging Using Realistic Purkinje Networks for in Silico Clinical Trials

Author(s): Julia Camps, Lucas Arantes Berg, Zhinuo Jenny Wang, Rafael Sebastian, Leto Luana Riebel, Ruben Doste, Xin Zhou, Rafael Sachetto, James Coleman, Brodie Lawson, Vicente Grau, Kevin Burrage, Alfonso Bueno-Orovio, Rodrigo Weber, Blanca Rodriguez
Published in: arXiv, 2023
Publisher: arXiv
DOI: 10.48550/arxiv.2306.13740

TorchMD-NET: Equivariant Transformers for Neural Network based Molecular Potentials

Author(s): Thölke, Philipp; De Fabritiis, Gianni
Published in: arXiv, Issue 21, 2022, ISSN 0000-0000
Publisher: arXiv
DOI: 10.48550/arxiv.2202.02541

HPC framework for in-silico trials on 3D virtual human cardiac population to assess drug-induced arrhythmic risk

Author(s): Jazmin Aguado-Sierra; Constantine Butakoff; Renee Brigham; Apollo K. Baron; Guillaume Houzeaux; Jose M. Guerra; Francesc Carreras; David Filgueiras-Rama; Paul A. Iaizzo; Tinen L. Iles; Mariano Vazquez
Published in: Crossref, Issue 1, 2022, ISSN 0000-0000
Publisher: medRxiv
DOI: 10.1101/2021.04.21.21255870

Enhanced single-node boundary condition for the Lattice Boltzmann Method

Author(s): Marson, Francesco; Thorimbert, Yann; Latt, Jonas; Chopard, Bastien
Published in: arXiv, Issue 9, 2021, ISSN 0000-0000
Publisher: arXiv
DOI: 10.48550/arxiv.2009.04604

Towards Enabling Cardiac Digital Twins of Myocardial Infarction Using Deep Computational Models for Inverse Inference

Author(s): Li, Lei; Camps, Julia; Zhinuo; Wang; Banerjee, Abhirup; Beetz, Marcel; Rodriguez, Blanca; Grau, Vicente
Published in: arXiv, Issue 6, 2023, ISSN 0000-0000
Publisher: arXiv
DOI: 10.48550/arxiv.2307.04421

TensorNet: Cartesian Tensor Representations for Efficient Learning of Molecular Potentials

Author(s): Simeon, Guillem; de Fabritiis, Gianni
Published in: arXiv, Issue 29, 2023, ISSN 0000-0000
Publisher: arXiv
DOI: 10.48550/arxiv.2306.06482

Binding Affinity Prediction with 3D Machine Learning: Training Data and Challenging External Testing

Author(s): Jose Carlos Gómez-Tamayo; Lili Cao; Mazen Ahmad; Gary Tresadern
Published in: Crossref, Issue 1, 2024, ISSN 0000-0000
Publisher: ChemRxiv
DOI: 10.26434/chemrxiv-2024-s5sbs

Influence of Myocardial Infarction on QRS Properties: A Simulation Study

Author(s): Li, Lei; Camps, Julia; Zhinuo; Wang; Banerjee, Abhirup; Rodriguez, Blanca; Grau, Vicente
Published in: arXiv, Issue 27, 2023, ISSN 0000-0000
Publisher: arXiv
DOI: 10.48550/arxiv.2304.01796

Anomalous Platelet Transport & Fat-Tailed Distributions

Author(s): Kotsalos, Christos; Boudjeltia, Karim Zouaoui; Dutta, Ritabrata; Latt, Jonas; Chopard, Bastien
Published in: arXiv, Issue 14, 2020, ISSN 0000-0000
Publisher: arXiv
DOI: 10.48550/arxiv.2006.11755

Orchestration of multiscale models for computational oncology

Author(s): Varella, Vinicius
Published in: UNIBO, Issue 37, 2023
Publisher: UNIBO
DOI: 10.5281/zenodo.8025197

Directional lattice Boltzmann boundary conditions

Author(s): Marson, Francesco
Published in: Issue 31, 2022
Publisher: UNIGE
DOI: 10.13097/archive-ouverte/unige:160770

Searching for OpenAIRE data...

Deliverables

Publications

Share this page Share this page on social networks

Download Download the content of the page