Enhacing TRANslational SAFEty Assessment through Integrative Knowledge Management

Livrables

Final version of complete translational system

Report on quantitative weight of evidence methods and software specifications final version

Software implementation of the quantitative weight of evidence methods developed in Task 8.5, as described in deliverable 8.6.

Initial Data and Knowledge Management Plan

Outline for eTRANSAFE data and knowledge management policy especially referring to research data quality sharing and security

D3.9 Progress on preclinical and clinical data donations - action stemming from the Mid-term review

Stemming from the MidTerm Review recommendations to improve project implementation this deliverable provides an update on the progress of data gathering and the actions taken to ensure the quantity and quality of clinical and preclinical data donated The report will serve to monitor the progress of data donation and extraction WP3 Update on data sharing via SEND format WP4 Update on access to access to clinical data WP6

First version of knowledge gathering services

Release of the first version of the knowledge bases including a description of the initial overarching system architecture of these services.

Report on SEND data sharing exercise – first version

The report will include the timelines and the amount of expected data donations, specifying which data will be provided already in SEND format, which data can be obtained in non-SEND format and which report data need to be converted. In addition, the report will set out the principles for curating SEND formatted data including, but not limited to, units conversion, synonym management (controlled terminologies) and data summarisation/ aggregation.

Safety assessment tools - intermediate release

Software implementation of the quantitative weight of evidence methods developed in Task 85 as described in deliverable 86

Project guidelines for sharing of preclinical safety data between industry / academia and guidelines for safety model validation

Report on project requirements analysis, survey of existing guidelines and participant/stakeholder requirements for model validation and iSSC consultation to adopt project guidelines for data sharing and data management, including a data classification system, and model validation.

Knowledge Hub and API specifications - first version

Report describing the software specifications of the knowledge hub and the application program interface.

Consensus position paper on predictive model validations based on stakeholder board opinion

Position paper summarising best practice for validation and use of predictive toxicology models and data classification published for external community consultation (including OECD/ICH)

First version of complete translational system

Release of the first version of the translational system including integration and visualisation

Report on synergies with related initiatives

This document will report on the relationships established to promote alignment and collaboration with other EUinternational projects and initiatives

Report on quantitative weight of evidence methods and software specifications - first version

Report describing the specifications of the software developed for supporting the quantitative weight of evidence computational methods obtained in Task 8.5.

Advanced data mining module - intermediate release

Software implemented in a standard module supporting advanced data mining from the knowledge hub. In addition, this software (so called “Gateway” to Knowledge Hub) will provide centralized access to most of the eTRANSAFE databases and tools.

Guidelines for sharing of safety data and model validations consulted with OECD/ICH and other stakeholders and published

Publication of final guidelines for safety data sharing and model validation subsequent to extensive external consultation

Report on knowledge gathering by analysing preclinical data

Report to provide details on the evolution of the knowledge gained through the analysis of preclinical data as more studies are absorbed into the system.

Final report on results of use cases

Final report on the Use Cases

Report on SEND data sharing exercise – third version

Update on data sharing via SEND format.

Report on quantitative weight of evidence methods and software specifications - final version

Report describing the characteristics of the software developed for supporting the quantitative weight of evidence computational methods obtained in Task 85

Final Data and Knowledge Management Plan including innovation-based access to consortium data

Final document describing the different data processed and the uses identified by the Consortium

Report on SEND data sharing exercise – fourth version

Update on data sharing via SEND format.

Report on release of integrated textual data, identifier and semantic integration services, integrated ontologies, and ontology management and access services to consortium

Report on release of integrated textual data, identifier and semantic integration services, integrated ontologies, and ontology management and access services to consortium, covering input from Task 5.1, 5.2 and 5.3.

Report on knowledge gathering by analysing preclinical data – final version

Report to provide details on the evolution of the knowledge gained through the analysis of preclinical data as more studies are absorbed into the system.

Report on consortium needs, available assets and documented knowledge hub (WP9) interfaces

Requirements analysis: report on consortium needs, available assets, shared pipelines and documented knowledge hub (WP9) interfaces of (1) identifier, ontology and semantic integration services, (2) ontologies and ontology management, available assets, and interfaces to the ontologies, (3) available sources of unstructured information including historical report data, and available assets and key data providers in the consortium, including input from Task 5.1, 5.2 and 5.3.

List on high priority translational safety biomarkers

Report on the list of high priority translational safety biomarkers that bridge between in vitro systems animal models and the human situation based on integration of the mode of action information with coregulated gene network analysis and bioinformatics approaches

Quantitative pharmaco-toxico mode-of-action landscape

Comprehensive compilation on the concentration response relationship on mode of action at the pharmacological and toxicological level for chemicals that cover the relevant chemical drug space related to adverse drug reactions

Second version of knowledge gathering services

Release of the second version of the knowledge bases

Computational read-across workflows- first version

Compilation of computational workflows implementing read across techniques (chemical grouping or analogue identification) for relevant toxic endpoints developed in Task 8.1. The deliverable comprises, for every workflow, both the computational implementation and the documentation, following the guidelines developed in WP2.

Project communication plan and initial tool set

A plan for dissemination that includes the communication objectives, target audiences, activities to be carried out and tools that will support their implementation, with connections among these components. It will also include an initial set of communication materials.

Final report on knowledge extraction and data integration in drug safety assessment

Final report on knowledge extraction and data integration across all services in support of drug safety assessment

Advanced data mining module - first version

Report on data gathering, processing and database – second version

This report will serve to monitor the progress of data donation and extraction; the evolution and development of the database and the incorporation of 3rd party databases into the system.

Tools for the translational assessment of predictive models

Collection of computational tools and methods aimed to assess the translational capability of predictive models developed from preclinical data

Data export and reporting module - first version

Software implemented in a standard module allowing to export data extracted from knowledge hub and to generate reports in standard formats relevant for toxicology.

Deployment of a data infrastructure for consortium partner access

An informatics infrastructure suitable for hosting databases in containerized form will be released and made available to the consortium partners for Internet access.

Report on data gathering, processing and database - final version

This report will serve to monitor the progress of data donation and extraction the evolution and development of the database and the incorporation of 3rd party databases into the system

Report on compound similarity service

Report documenting the compound similarity service used in Use Case 3 (in collaboration with WP8).

Project Assessment

Halfway through the project an assessment of the degree of fulfillment of the project objectives will be carried out and reported in this deliverable

Visualisation module - final version

Software implemented in a standard module for the interactive visualization of data accessible through the knowledge hub

Report on read-across approaches and software specifications

Report describing advances in read-across techniques and similarity metrics for chemical compounds.

Predictive models repository - first version

Compilation of in silico predictive models and read-across workflows generated in Task 8.3 and 8.1, implemented in one or more standard modules.

Report on SEND data sharing exercise - final version

Final update on data sharing via SEND format

Report on the evaluation of priority safety biomarkers

Report on the practical evaluation of priority safety biomarkers in both animal models and the human situation

Visualisation module - first version

Software implemented in a standard module for the interactive visualization of data accessible through the knowledge hub.

Report on SEND data sharing exercise – second version

Update to the report on data shared through SEND.

Report on user requirements and system specifications of database(s)

"This report will result from a series of user questionnaires and interviews based on expected use cases. User Requirements and specifications will be classified according to ""essential"", ""important"", ""nice-to-have"". The report will also summarise the security requirements and technical specification for the solution."

Report on data gathering, processing and database – third version

This report will serve to monitor the progress of data donation and extraction; the evolution and development of the database and the incorporation of 3rd party databases into the system.

Knowledge Hub and API specifications – intermediate release

Report describing the software specifications of the knowledge hub and the application program interface.

Translational adverse outcome pathways for human adversity

A report describing AOPs for the most prevalent human adversities and the comparison of the mechanistic understanding of these AOPs between human and animal models

Machine-learning models - first version

Compilation of predictive models based on machine-learning methods developed in Task 8.2. The deliverable comprises, for every model, both the model implementation and the documentation, following the guidelines developed in WP2.

Methodology, analysis of existing related initiatives, and tools for implementation

A roadmap of synergies with other projects/networks will be established, followed by implementation of the most relevant collaborations.

Predictive models repository - final version

Compilation of in silico predictive models and readacross workflows generated in Task 83 and 81 implemented in one or more standard modules

Report on the procedures for the data donation, extraction, curation and normalisation, ontology mapping, and access to pertinent datasets

This report will describe the pharmaco-toxicological endpoints identified for extraction or collection, how they have been prioritized, the details of extraction (granularity) and the commitment of the different partners in terms of number of reports (confidential & non-confidential). In addition, the report will describe the procedures to be established for quality assurance (e.g. establishment of Clearing House) as well as data curation, normalisation and controlled terminology mapping and assign the responsibilities to achieve these tasks.

Publications

Identifying multiscale translational safety biomarkers using a network-based systems approach

Auteurs: Giulia Callegaro, Johannes P. Schimming, Janet Piñero González, Steven J. Kunnen, Lukas Wijaya, Panuwat Trairatphisan, Linda van den Berk, Kim Beetsma, Laura I. Furlong, Jeffrey J. Sutherland, Jennifer Mollon, James L. Stevens, and Bob van de Water
Publié dans: iScience, 2023, ISSN 2589-0042
Éditeur: Elsevier BV
DOI: 10.1016/j.isci.2023.106094

In silico toxicology: From structure–activity relationships towards deep learning and adverse outcome pathways

Auteurs: Jennifer Hemmerich, Gerhard F. Ecker
Publié dans: WIREs Computational Molecular Science, Numéro 10/4, 2020, ISSN 1759-0876
Éditeur: John Wiley & Sons Inc.
DOI: 10.1002/wcms.1475

eTRANSAFE: Building a sustainable framework to share reproducible drug safety knowledge with the public domain

Auteurs: Sirarat Sarntivijai, Niklas Blomberg, Katharina B. Lauer, Katharine Briggs, Thomas Steger-Hartmann, Johan van der Lei, John-Michael Sauer, Richard Liwski, Miranda Mourby, Montse Camprubi
Publié dans: F1000RESEARCH, 2022, ISSN 2046-1402
Éditeur: F1000 Research Ltd.
DOI: 10.12688/f1000research.74024.1

Flame: an open source framework for model development, hosting, and usage in production environments

Auteurs: Manuel Pastor, José Carlos Gómez-Tamayo, Ferran Sanz
Publié dans: Journal of Cheminformatics, Numéro 13/1, 2021, ISSN 1758-2946
Éditeur: Chemistry Central
DOI: 10.1186/s13321-021-00509-z

Large scale comparison of QSAR and conformal prediction methods and their applications in drug discovery

Auteurs: Nicolas Bosc, Francis Atkinson, Eloy Felix, Anna Gaulton, Anne Hersey, Andrew R. Leach
Publié dans: Journal of Cheminformatics, Numéro 11/1, 2019, ISSN 1758-2946
Éditeur: Chemistry Central
DOI: 10.1186/s13321-018-0325-4

Reply to “Missed opportunities in large scale comparison of QSAR and conformal prediction methods and their applications in drug discovery”

Auteurs: Nicolas Bosc, Francis Atkinson, Eloy Félix, Anna Gaulton, Anne Hersey, Andrew R. Leach
Publié dans: Journal of Cheminformatics, Numéro 11/1, 2019, ISSN 1758-2946
Éditeur: Chemistry Central
DOI: 10.1186/s13321-019-0388-x

The DisGeNET cytoscape app: Exploring and visualizing disease genomics data

Auteurs: Janet Piñero, Josep Saüch, Ferran Sanz, Laura I. Furlong
Publié dans: Computational and Structural Biotechnology Journal, Numéro 19, 2021, Page(s) 2960-2967, ISSN 2001-0370
Éditeur: Elsevier
DOI: 10.1016/j.csbj.2021.05.015

The DisGeNET knowledge platform for disease genomics: 2019 update

Auteurs: Janet Piñero, Juan Manuel Ramírez-Anguita, Josep Saüch-Pitarch, Francesco Ronzano, Emilio Centeno, Ferran Sanz, Laura I Furlong
Publié dans: Nucleic Acids Research, 2019, ISSN 0305-1048
Éditeur: Oxford University Press
DOI: 10.1093/nar/gkz1021

eTRANSAFE: data science to empower translational safety assessment

Auteurs: Ferran Sanz, François Pognan, Thomas Steger-Hartmann, Carlos Díaz, Shoji Asakura, Alexander Amberg, Nathalie Bécourt-Lhote, Niklas Blomberg, Nicolas Bosc, Katharine Briggs, Frank Bringezu, Claire Brulle-Wohlhueter, Søren Brunak, Ruud Bueters, Giulia Callegaro, Salvador Capella-Gutierrez, Emilio Centeno, Javier Corvi, Mark T. D. Cronin, Philip Drew, Guillemette Duchateau-Nguyen, Gerhard F. Ecke
Publié dans: Nature Reviews Drug Discovery, 2023, ISSN 1474-1776
Éditeur: Nature Publishing Group
DOI: 10.1038/d41573-023-00099-5

The evolving role of investigative toxicology in the pharmaceutical industry.

Auteurs: Francois Pognan, Mario Beilmann, Harrie C M Boonen, Andreas Czich, Gordon Dear, Philip Hewitt, Tomas Mow, Teija Oinonen, Adrian Roth, Thomas Steger-Hartmann, Jean-Pierre Valentin, Freddy Van Goethem, Richard J Weaver, Peter Newham
Publié dans: Nature Reviews Drug Discovery, 2023, ISSN 1474-1776
Éditeur: Nature Publishing Group
DOI: 10.1038/s41573-022-00633-x

COVER: conformational oversampling as data augmentation for molecules

Auteurs: Jennifer Hemmerich, Ece Asilar, Gerhard F. Ecker
Publié dans: Journal of Cheminformatics, Numéro 12/1, 2020, ISSN 1758-2946
Éditeur: Chemistry Central
DOI: 10.1186/s13321-020-00420-z

An ensemble learning approach for modeling the systems biology of drug-induced injury

Auteurs: Joaquim Aguirre-Plans, Janet Piñero, Terezinha Souza, Giulia Callegaro, Steven J. Kunnen, Ferran Sanz, Narcis Fernandez-Fuentes, Laura I. Furlong, Emre Guney, Baldo Oliva
Publié dans: Biology Direct, Numéro 16/1, 2021, ISSN 1745-6150
Éditeur: BioMed Central
DOI: 10.1186/s13062-020-00288-x

Assessing network-based methods in the context of system toxicology

Auteurs: Jordi Valls-Margarit1, Janet Piñero1, Barbara Füzi2, Natacha Cerisier3, Olivier Taboureau3 and Laura I. Furlong1*
Publié dans: Frontiers in pharmacology, 2023, ISSN 1663-9812
Éditeur: Frontiers Media S.A.
DOI: 10.3389/fphar.2023.1225697

The human hepatocyte TXG-MAPr: gene co-expression network modules to support mechanism-based risk assessment

Auteurs: Giulia Callegaro, Steven J. Kunnen, Panuwat Trairatphisan, Solène Grosdidier, Marije Niemeijer, Wouter den Hollander, Emre Guney, Janet Piñero Gonzalez, Laura Furlong, Yue W. Webster, Julio Saez-Rodriguez, Jeffrey J. Sutherland, Jennifer Mollon, James L. Stevens, Bob van de Water
Publié dans: Archives of Toxicology, 2021, ISSN 0340-5761
Éditeur: Springer Verlag
DOI: 10.1007/s00204-021-03141-w

Application of machine learning to improve the efficiency of electrophysiological simulations used for the prediction of drug-induced ventricular arrhythmia

Auteurs: Pablo Rodríguez-Belenguer, Karolina Kopańska, Jordi Llopis-Lorente, Beatriz Trenor, Javier Saiz, Manuel Pastor
Publié dans: Comput Methods Programs Biomed, 2023, ISSN 0169-2607
Éditeur: Elsevier BV
DOI: 10.1016/j.cmpb.2023.107345

Characterisation of the NRF2 transcriptional network and its response to chemical insult in primary human hepatocytes: implications for prediction of drug-induced liver injury

Auteurs: Ian M. Copple, Wouter den Hollander, Giulia Callegaro, Fiona E. Mutter, James L. Maggs, Amy L. Schofield, Lucille Rainbow, Yongxiang Fang, Jeffrey J. Sutherland, Ewa C. Ellis, Magnus Ingelman-Sundberg, Stephen W. Fenwick, Christopher E. Goldring, Bob van de Water, James L. Stevens, B. Kevin Park
Publié dans: Archives of Toxicology, Numéro 93/2, 2019, Page(s) 385-399, ISSN 0340-5761
Éditeur: Springer Verlag
DOI: 10.1007/s00204-018-2354-1

Benchmarking post-GWAS analysis tools in major depression: Challenges and implications

Auteurs: Judith, Pérez-Granado; Janet, Piñero; Laura I, Furlong
Publié dans: Frontiers in Genetics, 2022, ISSN 1664-8021
Éditeur: Frontiers Media
DOI: 10.3389/fgene.2022.1006903

High-throughput confocal imaging of differentiated 3D liver-like spheroid cellular stress response reporters for identification of drug-induced liver injury liability

Auteurs: Steven Hiemstra, Sreenivasa C Ramaiahgari, Steven Wink, Giulia Callegaro, Maarten Coonen, John Meerman, Danyel Jennen, Karen van den Nieuwendijk, Anita Dankers, Jan Snoeys, Hans de Bont, Leo Price, Bob van de Water
Publié dans: Archives of Toxicology, 2019, ISSN 1432-0738
Éditeur: Springer
DOI: 10.1007/s00204-019-02552-0

The eTOX Consortium: To Improve the Safety Assessment of New Drug Candidates

Auteurs: Steger-Hartmann T, Pognan F.
Publié dans: PHARMAZEUTISCHE MEDIZIN, 2017, ISSN 2191-6039
Éditeur: OEMUS MEDIA AG

Beyond SEND: Leveraging non-clinical data to drive translational research forward

Auteurs: Briggs K., Friedman B., Ferrara K., Pinches M., Drewe W., Riel C., Thompson M., Hayes A., Gratt J., Wyllie S., Walsh M.
Publié dans: DDW. Drug discovery world, 2019, ISSN 1469-4344
Éditeur: R J Communications & Media World Ltd.

Image Based Liver Toxicity Prediction

Auteurs: Ece Asilar, Jennifer Hemmerich, Gerhard F. Ecker
Publié dans: Journal of Chemical Information and Modeling, Numéro 60/3, 2020, Page(s) 1111-1121, ISSN 1549-9596
Éditeur: American Chemical Society
DOI: 10.1021/acs.jcim.9b00713

Legacy data sharing to improve drug safety assessment: the eTOX project

Auteurs: Ferran Sanz, François Pognan, Thomas Steger-Hartmann, Carlos Díaz, Montserrat Cases, Manuel Pastor, Philippe Marc, Joerg Wichard, Katharine Briggs, David K. Watson, Thomas Kleinöder, Chihae Yang, Alexander Amberg, Maria Beaumont, Anthony J. Brookes, Søren Brunak, Mark T. D. Cronin, Gerhard F. Ecker, Sylvia Escher, Nigel Greene, Antonio Guzmán, Anne Hersey, Pascale Jacques, Lieve Lammens, Jord
Publié dans: Nature Reviews Drug Discovery, Numéro 16/12, 2017, Page(s) 811-812, ISSN 1474-1776
Éditeur: Nature Publishing Group
DOI: 10.1038/nrd.2017.177

Network, Transcriptomic and Genomic Features Differentiate Genes Relevant for Drug Response

Auteurs: Janet Piñero, Abel Gonzalez-Perez, Emre Guney, Joaquim Aguirre-Plans, Ferran Sanz, Baldo Oliva, Laura I. Furlong
Publié dans: Frontiers in Genetics, Numéro 9, 2018, ISSN 1664-8021
Éditeur: Frontiers Media
DOI: 10.3389/fgene.2018.00412

Development of an Infrastructure for the Prediction of Biological Endpoints in Industrial Environments. Lessons Learned at the eTOX Project

Auteurs: Manuel Pastor, Jordi Quintana, Ferran Sanz
Publié dans: Frontiers in Pharmacology, Numéro 9, 2018, ISSN 1663-9812
Éditeur: Frontiers Media S.A.
DOI: 10.3389/fphar.2018.01147

Generating Modeling Data From Repeat-Dose Toxicity Reports

Auteurs: Oriol López-Massaguer, Kevin Pinto-Gil, Ferran Sanz, Alexander Amberg, Lennart T Anger, Manuela Stolte, Carlo Ravagli, Philippe Marc, Manuel Pastor
Publié dans: Toxicological Sciences, Numéro 162/1, 2017, Page(s) 287-300, ISSN 1096-6080
Éditeur: Oxford University Press
DOI: 10.1093/toxsci/kfx254

Curation and analysis of clinical pathology parameters and histopathologic findings from eTOXsys, a large database project (eTOX) for toxicologic studies

Auteurs: Mark D. Pinches, Robert Thomas, Rosemary Porter, Lucinda Camidge, Katharine Briggs
Publié dans: Regulatory Toxicology and Pharmacology, Numéro 107, 2019, Page(s) 104396, ISSN 0273-2300
Éditeur: Academic Press
DOI: 10.1016/j.yrtph.2019.05.021

In Silico Toxicology Data Resources to Support Read-Across and (Q)SAR

Auteurs: Gopal Pawar, Judith C. Madden, David Ebbrell, James W. Firman, Mark T. D. Cronin
Publié dans: Frontiers in Pharmacology, Numéro 10, 2019, ISSN 1663-9812
Éditeur: Frontiers Media S.A.
DOI: 10.3389/fphar.2019.00561

Improving the Safety Assessment of Chemicals and Drug Candidates by the Integration of Bioinformatics and Chemoinformatics Data

Auteurs: Thomas Steger-Hartmann, Francois Pognan
Publié dans: Basic & Clinical Pharmacology & Toxicology, Numéro 123, 2018, Page(s) 29-36, ISSN 1742-7835
Éditeur: Nordic Pharmacological Society
DOI: 10.1111/bcpt.12956

In silico models in drug development: where we are

Auteurs: Janet Piñero, Laura I Furlong, Ferran Sanz
Publié dans: Current Opinion in Pharmacology, Numéro 42, 2018, Page(s) 111-121, ISSN 1471-4892
Éditeur: Elsevier BV
DOI: 10.1016/j.coph.2018.08.007

Unraveling the effect of intra- and intercellular processes on acetaminophen-induced liver injury

Auteurs: Heldring, M.M, Shaw, A.H. and Beltman, J.B.
Publié dans: npj Systems Biology and Applications, 2022, ISSN 2056-7189
Éditeur: Nature Publishing Group
DOI: 10.1038/s41540-022-00238-5

Development of a Battery of In Silico Prediction Tools for Drug-Induced Liver Injury from the Vantage Point of Translational Safety Assessment

Auteurs: James Rathman, Chihae Yang, J. Vinicius Ribeiro, Aleksandra Mostrag, Shraddha Thakkar, Weida Tong, Bryan Hobocienski, Oliver Sacher, Tomasz Magdziarz, Bruno Bienfait
Publié dans: Chemical Research in Toxicology, Numéro 34/2, 2021, Page(s) 601-615, ISSN 0893-228X
Éditeur: American Chemical Society
DOI: 10.1021/acs.chemrestox.0c00423

Genomic and proteomic biomarker landscape in clinical trials

Auteurs: Janet Piñero, Pablo S Rodriguez Fraga, Jordi Valls-Margarit, Francesco Ronzano, Pablo Accuosto, Ricard Lambea Jane, Ferran Sanz, Laura I Furlong
Publié dans: Comput Struct Biotechnol J ., 2023, ISSN 2001-0370
Éditeur: Elsevier
DOI: 10.1016/j.csbj.2023.03.014

Using Jupyter Notebooks for re-training machine learning models

Auteurs: Aljoša Smajić, Melanie Grandits, Gerhard F Ecker
Publié dans: Journal of Cheminformatics, 2022, ISSN 1758-2946
Éditeur: Chemistry Central
DOI: 10.1186/s13321-022-00635-2

Off-targetP ML: an open source machine learning framework for off-target panel safety assessment of small molecules

Auteurs: Naga D, Muster W, Musvasva E, Ecker GF
Publié dans: Journal of Cheminformatics, 2022, ISSN 1758-2946
Éditeur: Chemistry Central
DOI: 10.1186/s13321-022-00603-w

The eTRANSAFE Project on Translational Safety Assessment through Integrative Knowledge Management: Achievements and Perspectives

Auteurs: François Pognan, Thomas Steger-Hartmann, Carlos Díaz, Niklas Blomberg, Frank Bringezu, Katharine Briggs, Giulia Callegaro, Salvador Capella-Gutierrez, Emilio Centeno, Javier Corvi, Philip Drew, William C. Drewe, José M. Fernández, Laura I. Furlong, Emre Guney, Jan A. Kors, Miguel Angel Mayer, Manuel Pastor, Janet Piñero, Juan Manuel Ramírez-Anguita, Francesco Ronzano, Philip Rowell, Josep Sa
Publié dans: Pharmaceuticals, Numéro 14/3, 2021, Page(s) 237, ISSN 1424-8247
Éditeur: Multidisciplinary Digital Publishing Institute (MDPI)
DOI: 10.3390/ph14030237

Introducing the concept of virtual control groups into preclinical toxicology testing

Auteurs: Thomas Steger-Hartmann, Annika Kreuchwig, Lea Vaas, Jörg Wichard, Frank Bringezu, Alexander Amberg, Wolfgang Muster, Francois Pognan, Chris Barber
Publié dans: ALTEX, 2020, ISSN 1868-8551
Éditeur: Spektrum Akademischer Verlag GmbH
DOI: 10.14573/altex.2001311

Using Machine Learning Methods and Structural Alerts for Prediction of Mitochondrial Toxicity

Auteurs: Jennifer Hemmerich, Florentina Troger, Barbara Füzi, Gerhard F.Ecker
Publié dans: Molecular Informatics, Numéro 39/5, 2020, Page(s) 2000005, ISSN 1868-1743
Éditeur: Wiley - VCH Verlag GmbH & CO. KGaA
DOI: 10.1002/minf.202000005

Guidelines for FAIR sharing of preclinical safety and off-target pharmacology data

Auteurs: Katharine Briggs
Publié dans: ALTEX, 2021, ISSN 1868-596X
Éditeur: Springer Spektrum | Springer-Verlag GmbH
DOI: 10.14573/altex.2011181

PharmacoNER Tagger: a deep learning-based tool for automatically finding chemicals and drugs in Spanish medical texts

Auteurs: Jordi Amengol-Estapé, Felipe Soares, Montserrat Marimon, Martin Krallinger
Publié dans: Genomics & Informatics, Numéro 17/2, 2019, Page(s) e15, ISSN 2234-0742
Éditeur: Korea Genome Organization
DOI: 10.5808/gi.2019.17.2.e15

GUILDify v2.0: A Tool to Identify Molecular Networks Underlying Human Diseases, Their Comorbidities and Their Druggable Targets

Auteurs: Janet Piñero; Ferran Sanz; Narcis Fernandez-Fuentes; Joaquim Aguirre-Plans
Publié dans: Journal of molecular biology, Numéro 1, 2019, ISSN 0022-2836
Éditeur: Academic Press
DOI: 10.1016/j.jmb.2019.02.027

Mapping the cellular response to electron transport chain inhibitors reveals selective signaling networks triggered by mitochondrial perturbation

Auteurs: Wanda van der Stel, Huan Yang, Nanette G Vrijenhoek, Johannes P Schimming, Giulia Callegaro, Giada Carta, Salihanur Darici, Johannes Delp, Anna Forsby, Andrew White, Sylvia le Dévédec, Marcel Leist, Paul Jennings, Joost B Beltman, Bob van de Water, Erik H J Danen
Publié dans: Archives of Toxicology, 2021, ISSN 1432-0738
Éditeur: Springer
DOI: 10.1007/s00204-021-03160-7

Ensemble prediction of mitochondrial toxicity using machine learning technology

Auteurs: Frank Bringezu, José Carlos Gómez-Tamayo, Manuel Pastor
Publié dans: Computational Toxicology, Numéro 20, 2021, Page(s) 100189, ISSN 2468-1113
Éditeur: ScienceDirect, Elsevier
DOI: 10.1016/j.comtox.2021.100189

Computational Approaches for Drug-Induced Liver Injury (DILI) Prediction: State of the Art and Challenges

Auteurs: Olivier J.M. Béquignon, Gopal Pawar, Bob van de Water, Mark T.D. Cronin, Gerard J.P. van Westen
Publié dans: Systems Medicine, 2021, Page(s) 308-329, ISBN 9780128160787
Éditeur: Elsevier
DOI: 10.1016/b978-0-12-801238-3.11535-1

"""Development of In Silico Methods for Toxicity Prediction in Collaboration Between Academia and the Pharmaceutical Industry"""

Auteurs: Manuel Pastor, Ferran Sanz, Frank Bringezu
Publié dans: Methods in Molecular Biology, Numéro Vol 2425, 2022
Éditeur: Springer Nature
DOI: 10.1007/978-1-0716-1960-5_5issn:1064-3745

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