Enhacing TRANslational SAFEty Assessment through Integrative Knowledge Management

Leistungen

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.

Veröffentlichungen

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

Autoren: 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
Veröffentlicht in: iScience, 2023, ISSN 2589-0042
Herausgeber: Elsevier BV
DOI: 10.1016/j.isci.2023.106094

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

Autoren: Jennifer Hemmerich, Gerhard F. Ecker
Veröffentlicht in: WIREs Computational Molecular Science, Ausgabe 10/4, 2020, ISSN 1759-0876
Herausgeber: John Wiley & Sons Inc.
DOI: 10.1002/wcms.1475

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

Autoren: 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
Veröffentlicht in: F1000RESEARCH, 2022, ISSN 2046-1402
Herausgeber: F1000 Research Ltd.
DOI: 10.12688/f1000research.74024.1

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

Autoren: Manuel Pastor, José Carlos Gómez-Tamayo, Ferran Sanz
Veröffentlicht in: Journal of Cheminformatics, Ausgabe 13/1, 2021, ISSN 1758-2946
Herausgeber: Chemistry Central
DOI: 10.1186/s13321-021-00509-z

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

Autoren: Nicolas Bosc, Francis Atkinson, Eloy Felix, Anna Gaulton, Anne Hersey, Andrew R. Leach
Veröffentlicht in: Journal of Cheminformatics, Ausgabe 11/1, 2019, ISSN 1758-2946
Herausgeber: 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”

Autoren: Nicolas Bosc, Francis Atkinson, Eloy Félix, Anna Gaulton, Anne Hersey, Andrew R. Leach
Veröffentlicht in: Journal of Cheminformatics, Ausgabe 11/1, 2019, ISSN 1758-2946
Herausgeber: Chemistry Central
DOI: 10.1186/s13321-019-0388-x

The DisGeNET cytoscape app: Exploring and visualizing disease genomics data

Autoren: Janet Piñero, Josep Saüch, Ferran Sanz, Laura I. Furlong
Veröffentlicht in: Computational and Structural Biotechnology Journal, Ausgabe 19, 2021, Seite(n) 2960-2967, ISSN 2001-0370
Herausgeber: Elsevier
DOI: 10.1016/j.csbj.2021.05.015

The DisGeNET knowledge platform for disease genomics: 2019 update

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

eTRANSAFE: data science to empower translational safety assessment

Autoren: 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
Veröffentlicht in: Nature Reviews Drug Discovery, 2023, ISSN 1474-1776
Herausgeber: Nature Publishing Group
DOI: 10.1038/d41573-023-00099-5

The evolving role of investigative toxicology in the pharmaceutical industry.

Autoren: 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
Veröffentlicht in: Nature Reviews Drug Discovery, 2023, ISSN 1474-1776
Herausgeber: Nature Publishing Group
DOI: 10.1038/s41573-022-00633-x

COVER: conformational oversampling as data augmentation for molecules

Autoren: Jennifer Hemmerich, Ece Asilar, Gerhard F. Ecker
Veröffentlicht in: Journal of Cheminformatics, Ausgabe 12/1, 2020, ISSN 1758-2946
Herausgeber: Chemistry Central
DOI: 10.1186/s13321-020-00420-z

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

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

Assessing network-based methods in the context of system toxicology

Autoren: Jordi Valls-Margarit1, Janet Piñero1, Barbara Füzi2, Natacha Cerisier3, Olivier Taboureau3 and Laura I. Furlong1*
Veröffentlicht in: Frontiers in pharmacology, 2023, ISSN 1663-9812
Herausgeber: 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

Autoren: 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
Veröffentlicht in: Archives of Toxicology, 2021, ISSN 0340-5761
Herausgeber: 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

Autoren: Pablo Rodríguez-Belenguer, Karolina Kopańska, Jordi Llopis-Lorente, Beatriz Trenor, Javier Saiz, Manuel Pastor
Veröffentlicht in: Comput Methods Programs Biomed, 2023, ISSN 0169-2607
Herausgeber: 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

Autoren: 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
Veröffentlicht in: Archives of Toxicology, Ausgabe 93/2, 2019, Seite(n) 385-399, ISSN 0340-5761
Herausgeber: Springer Verlag
DOI: 10.1007/s00204-018-2354-1

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

Autoren: Judith, Pérez-Granado; Janet, Piñero; Laura I, Furlong
Veröffentlicht in: Frontiers in Genetics, 2022, ISSN 1664-8021
Herausgeber: 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

Autoren: 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
Veröffentlicht in: Archives of Toxicology, 2019, ISSN 1432-0738
Herausgeber: Springer
DOI: 10.1007/s00204-019-02552-0

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

Autoren: Steger-Hartmann T, Pognan F.
Veröffentlicht in: PHARMAZEUTISCHE MEDIZIN, 2017, ISSN 2191-6039
Herausgeber: OEMUS MEDIA AG

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

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

Image Based Liver Toxicity Prediction

Autoren: Ece Asilar, Jennifer Hemmerich, Gerhard F. Ecker
Veröffentlicht in: Journal of Chemical Information and Modeling, Ausgabe 60/3, 2020, Seite(n) 1111-1121, ISSN 1549-9596
Herausgeber: American Chemical Society
DOI: 10.1021/acs.jcim.9b00713

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

Autoren: 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
Veröffentlicht in: Nature Reviews Drug Discovery, Ausgabe 16/12, 2017, Seite(n) 811-812, ISSN 1474-1776
Herausgeber: Nature Publishing Group
DOI: 10.1038/nrd.2017.177

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

Autoren: Janet Piñero, Abel Gonzalez-Perez, Emre Guney, Joaquim Aguirre-Plans, Ferran Sanz, Baldo Oliva, Laura I. Furlong
Veröffentlicht in: Frontiers in Genetics, Ausgabe 9, 2018, ISSN 1664-8021
Herausgeber: 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

Autoren: Manuel Pastor, Jordi Quintana, Ferran Sanz
Veröffentlicht in: Frontiers in Pharmacology, Ausgabe 9, 2018, ISSN 1663-9812
Herausgeber: Frontiers Media S.A.
DOI: 10.3389/fphar.2018.01147

Generating Modeling Data From Repeat-Dose Toxicity Reports

Autoren: Oriol López-Massaguer, Kevin Pinto-Gil, Ferran Sanz, Alexander Amberg, Lennart T Anger, Manuela Stolte, Carlo Ravagli, Philippe Marc, Manuel Pastor
Veröffentlicht in: Toxicological Sciences, Ausgabe 162/1, 2017, Seite(n) 287-300, ISSN 1096-6080
Herausgeber: 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

Autoren: Mark D. Pinches, Robert Thomas, Rosemary Porter, Lucinda Camidge, Katharine Briggs
Veröffentlicht in: Regulatory Toxicology and Pharmacology, Ausgabe 107, 2019, Seite(n) 104396, ISSN 0273-2300
Herausgeber: Academic Press
DOI: 10.1016/j.yrtph.2019.05.021

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

Autoren: Gopal Pawar, Judith C. Madden, David Ebbrell, James W. Firman, Mark T. D. Cronin
Veröffentlicht in: Frontiers in Pharmacology, Ausgabe 10, 2019, ISSN 1663-9812
Herausgeber: 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

Autoren: Thomas Steger-Hartmann, Francois Pognan
Veröffentlicht in: Basic & Clinical Pharmacology & Toxicology, Ausgabe 123, 2018, Seite(n) 29-36, ISSN 1742-7835
Herausgeber: Nordic Pharmacological Society
DOI: 10.1111/bcpt.12956

In silico models in drug development: where we are

Autoren: Janet Piñero, Laura I Furlong, Ferran Sanz
Veröffentlicht in: Current Opinion in Pharmacology, Ausgabe 42, 2018, Seite(n) 111-121, ISSN 1471-4892
Herausgeber: Elsevier BV
DOI: 10.1016/j.coph.2018.08.007

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

Autoren: Heldring, M.M, Shaw, A.H. and Beltman, J.B.
Veröffentlicht in: npj Systems Biology and Applications, 2022, ISSN 2056-7189
Herausgeber: 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

Autoren: James Rathman, Chihae Yang, J. Vinicius Ribeiro, Aleksandra Mostrag, Shraddha Thakkar, Weida Tong, Bryan Hobocienski, Oliver Sacher, Tomasz Magdziarz, Bruno Bienfait
Veröffentlicht in: Chemical Research in Toxicology, Ausgabe 34/2, 2021, Seite(n) 601-615, ISSN 0893-228X
Herausgeber: American Chemical Society
DOI: 10.1021/acs.chemrestox.0c00423

Genomic and proteomic biomarker landscape in clinical trials

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

Using Jupyter Notebooks for re-training machine learning models

Autoren: Aljoša Smajić, Melanie Grandits, Gerhard F Ecker
Veröffentlicht in: Journal of Cheminformatics, 2022, ISSN 1758-2946
Herausgeber: 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

Autoren: Naga D, Muster W, Musvasva E, Ecker GF
Veröffentlicht in: Journal of Cheminformatics, 2022, ISSN 1758-2946
Herausgeber: Chemistry Central
DOI: 10.1186/s13321-022-00603-w

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

Autoren: 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
Veröffentlicht in: Pharmaceuticals, Ausgabe 14/3, 2021, Seite(n) 237, ISSN 1424-8247
Herausgeber: Multidisciplinary Digital Publishing Institute (MDPI)
DOI: 10.3390/ph14030237

Introducing the concept of virtual control groups into preclinical toxicology testing

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

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

Autoren: Jennifer Hemmerich, Florentina Troger, Barbara Füzi, Gerhard F.Ecker
Veröffentlicht in: Molecular Informatics, Ausgabe 39/5, 2020, Seite(n) 2000005, ISSN 1868-1743
Herausgeber: Wiley - VCH Verlag GmbH & CO. KGaA
DOI: 10.1002/minf.202000005

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

Autoren: Katharine Briggs
Veröffentlicht in: ALTEX, 2021, ISSN 1868-596X
Herausgeber: 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

Autoren: Jordi Amengol-Estapé, Felipe Soares, Montserrat Marimon, Martin Krallinger
Veröffentlicht in: Genomics & Informatics, Ausgabe 17/2, 2019, Seite(n) e15, ISSN 2234-0742
Herausgeber: 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

Autoren: Janet Piñero; Ferran Sanz; Narcis Fernandez-Fuentes; Joaquim Aguirre-Plans
Veröffentlicht in: Journal of molecular biology, Ausgabe 1, 2019, ISSN 0022-2836
Herausgeber: 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

Autoren: 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
Veröffentlicht in: Archives of Toxicology, 2021, ISSN 1432-0738
Herausgeber: Springer
DOI: 10.1007/s00204-021-03160-7

Ensemble prediction of mitochondrial toxicity using machine learning technology

Autoren: Frank Bringezu, José Carlos Gómez-Tamayo, Manuel Pastor
Veröffentlicht in: Computational Toxicology, Ausgabe 20, 2021, Seite(n) 100189, ISSN 2468-1113
Herausgeber: ScienceDirect, Elsevier
DOI: 10.1016/j.comtox.2021.100189

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

Autoren: Olivier J.M. Béquignon, Gopal Pawar, Bob van de Water, Mark T.D. Cronin, Gerard J.P. van Westen
Veröffentlicht in: Systems Medicine, 2021, Seite(n) 308-329, ISBN 9780128160787
Herausgeber: 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"""

Autoren: Manuel Pastor, Ferran Sanz, Frank Bringezu
Veröffentlicht in: Methods in Molecular Biology, Ausgabe Vol 2425, 2022
Herausgeber: Springer Nature
DOI: 10.1007/978-1-0716-1960-5_5issn:1064-3745

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