The European Nanotechnology Community Informatics Platform: Bridging data and disciplinary gaps for industry and regulators (NanoCommons)

CORDIS fornisce collegamenti ai risultati finali pubblici e alle pubblicazioni dei progetti ORIZZONTE.

I link ai risultati e alle pubblicazioni dei progetti del 7° PQ, così come i link ad alcuni tipi di risultati specifici come dataset e software, sono recuperati dinamicamente da .OpenAIRE .

Risultati finali

NERC TA

Delivery of successful User access over 140 days, via 10 User-defined micro-projects each requiring ~1 month of computational effort), plus several physical access visits for workflows of 2 days per User.

1st Annual conference & nano-exploitation day, stakeholder workshop & User call
UM TA

Delivery of successful User access to up to 25 users (40 days in total), including physical access via Open Science workshops to support Users in developing ontology terms specific to their project / data / research needs

EwC TA

Delivery of successful User access to a minimum of 5 user micro-projects (total of 480 days of access via User-defined mini-projects requiring 3-6 months of computational time and effort each). Several User micro-projects will also be undertaken.

7P9-SI TA

Delivery of successful User access to up to 20 users (access duration 1-3 days, average 2 days) leading to 40 days of access in total

UoB TA

Delivery of successful User access to up to 20 users (220 days of total User access, via User micro-project and site-visits), the majority being remote access coupled with short 2-day physical access per User

NUID UCD TA

Delivery of successful User access to up to 5 User mini-projects (total access of 480 days, via User projects requiring 3-6 months of computational time and effort)

LEITAT TA

Delivery of successful User access to up to 10 users (total access time 100 days) including physical access duration of 2 day per User

NM TA

Delivery of successful User access to up to 10 users (100 days of access in total), including physical access (2-days) and computation time via micro-projects (i.e. projects requiring <1 month of computational time and effort)

Year 4 + Project Meetings
NTUA TA

Delivery of successful User access to up to 5 user micro-projects (total access of 360 days, via User projects requiring 3-6 months of computational time and effort)

BIOMAX TA

Delivery of successful User access to up to 30 users (120 days of access in total), including physical access components via User workshops on core topics (data mining, data curation etc.)

Initial draft of Data management plan (Open data pilot)
A workflow and checklist for experimental design and informatics workflow for risk assessment for use in WP9
Training Needs Specification and Proposed Solutions
Report on needs identification for new member states and Action plan proposed
Report on 2nd series demonstration cases and analysis of remaining weaknesses
Initial version of NanoCommons Sustainability Plan
First Testing and Evaluation Results of NanoCommons Sustainability Plan
Description of tools for automated data mining
Dissemination strategy
First TA Resource Access and Use Report
Action Plan for Year 3
3rd Annual conference & nano-exploitation day, social web activities, stakeholder workshop with TA calls/ demonstrations

3rd Annual conference nanoexploitation day social web activities stakeholder workshop with TA calls demonstrations

First Demonstration cases selected
Second Testing and Evaluation Results of NanoCommons Sustainability Plan
First Report on Training Activities, focussing on virtual tools
Community suggestion box and 1st rolling call (and evaluation) –Action plan Year 2
Report on 1st series demonstration cases and 2nd series selected
Workshops with different stakeholders
Action Plan for Year 4
A workflow and checklist of key information needed from modelling tool owners to facilitate integration into KB
Final version of NanoCommons Sustainability Plan
2nd Annual conference & nano-exploitation day, stakeholder workshop with TA calls and demonstrations
Initial NanoCommons Ontology
Final report on utilisation of Helpdesk, Tutorials and FAQ, stakeholder distribution (experimental, modellers, SME / enterprise, regulatory, other) and on TA provision overall

Final report on utilisation of Helpdesk Tutorials and FAQ stakeholder distribution experimental modellers SME enterprise regulatory other and on TA provision overall

Interactions Needs and Goals of Nano Safety Projects and Programs
1st set of stakeholder workshops and Report on Stakeholder feedback on usability of NanoCommons portal & tools
Final Report on Training Activities and analysis of stakeholder groups reached
Final Guidance on Emerging Data and Metadata Standards

AOP-based grouping of ENMs
First corona simulation tools integrated into NanoCommons KnowledgeBase
Firstraw data processing and knowledge extraction tools integrated into KB and first theoretical descriptor calculation services available

Firstraw data processing and knowledge extraction tools integrated into KB and first theoretical descriptor calculation services available

First tools for MIE prediction integrated into NanoCommons KnowledgeBase
First predictive nanoQSAR models integrated into NanoCommons KnowledgeBase
Initial Knowledge Infrastructure Functionalities and Services Implemented
First version of data warehouse & collaborative knowledge infrastructure
Initial integration of decision support system for safe-by-design strategy
Final version of collaborative knowledge infrastructure, including supporting APIs, ontology and data warehouse, and the Functionalities and Services implemented
Initial version of integrated web-based decision support system for regulators
First big data (omics) analysis and mining tools integrated into KnowledgeBase

Final version of Open Data management plan (Open data pilot)

Final version of Open Data management plan Open data pilot

Pubblicazioni

Iron oxide nanoparticles in bioimaging – an immune perspective

Autori: Geppert M. and Himly M.
Pubblicato in: Front Immunol, Numero 16643224, 2021, ISSN 1664-3224
Editore: Front Immunol
DOI: 10.3389/fimmu.2021.688927

Improved characterisation of clinical text through ontology-based vocabulary expansion

Autori: Luke T. Slater, William Bradlow, Simon Ball, Robert Hoehndorf and Georgios V Gkoutos
Pubblicato in: Journal of Biomedical Semantics, Numero 20411480, 2021, ISSN 2041-1480
Editore: Springer-Nature
DOI: 10.1186/s13326-021-00241-5

Mechanisms of Particles in Sensitization, Effector Function and Therapy of Allergic Disease

Autori: Anna I. Joubert, Mark Geppert, Litty Johnson, Robert Mills-Goodlet, Sara Michelini, Evgeniia Korotchenko, Albert Duschl, Richard Weiss, Jutta Horejs-Höck, Martin Himly
Pubblicato in: Frontiers in Immunology, Numero 11, 2020, ISSN 1664-3224
Editore: Frontiers
DOI: 10.3389/fimmu.2020.01334

Ten simple rules for creating reusable pathway models for computational analysis and visualization

Autori: K. Hanspers, M. Kutmon, S. L. Coort, D. Digles, L. J. Dupuis, F. Ehrhart, F. Hu, E. N. Lopes, M. Martens, N. Pham, W. Shin, D. N. Slenter, A. Waagmeester, E. L. Willighagen, L. A. Winckers, C. T. Evelo, A. R. Pico
Pubblicato in: Plos Computational Biology, Numero 15537358, 2021, ISSN 1553-7358
Editore: PLOS
DOI: 10.1371/journal.pcbi.1009226

Toxicokinetics of pristine and aged silver nanoparticles in Physa acuta

Autori: Patrícia V. Silva, Cornelis A. M. van Gestel, Rudo A. Verweij, Anastasios G. Papadiamantis, Sandra F. Gonçalves, Iseult Lynch and Susana Loureiro
Pubblicato in: Environmental Science: Nano, Numero 20518161, 2020, ISSN 2051-8161
Editore: Royal Society of Chemistry
DOI: 10.1039/d0en00946f

Surface Functionalization of Graphene-Based Materials: Biological Behavior, Toxicology, and Safe-By-Design Aspects

Autori: Zhiling Guo, Swaroop Chakraborty, Fazel Abdolahpur Monikh, Dimitra-Danai Varsou, Andrew J Chetwynd, Antreas Afantitis, Iseult Lynch, Peng Zhang
Pubblicato in: Advanced Biology, Numero 27010198, 2021, ISSN 2701-0198
Editore: Wiley
DOI: 10.1002/adbi.202100637

Computational enrichment of physicochemical data for the development of a ζ-potential read-across predictive model with Isalos Analytics Platform

Autori: Papadiamantis, A.G., Afantitis, A., Tsoumanis, A., Valsami-Jones, E., Lynch, I., Melagraki,
Pubblicato in: NanoImpact, Numero 22, 2021, ISSN 2452-0748
Editore: Elsevier
DOI: 10.1016/j.impact.2021.100308

The earthworm microbiome is resilient to exposure to biocidal metal nanoparticles

Autori: Elmer Swart; Tim Goodall; Peter Kille; David J. Spurgeon; Claus Svendsen;
Pubblicato in: Journal: Environmental Pollution, Numero 02697491, 2020, ISSN 0269-7491
Editore: Pergamon Press Ltd.
DOI: 10.1016/j.envpol.2020.115633

Can Systems Biology Advance Clinical Precision Oncology?

Autori: Andrea Rocca Boris N. Kholodenko
Pubblicato in: Cancers, Numero 20726694, 2021, ISSN 2072-6694
Editore: Multidisciplinary Digital Publishing Institute (MDPI)
DOI: 10.3390/cancers13246312

Daphnia magna and mixture toxicity with nanomaterials – Current status

Autori: Diego Stéfani T. Martinez, Laura-Jayne A. Ellis, Gabriela H. Da Silva, Romana Petry, Aline M.Z. Medeiros, Hossein Hayat Davoudi, Anastasios G. Papadiamantis, Adalberto Fazzio, Antreas Afantitis, Georgia Melagraki, Iseult Lynch
Pubblicato in: NanoToday, Numero 17480132, 2022, ISSN 1748-0132
Editore: Elsevier BV
DOI: 10.1016/j.nantod.2022.101430

WikiPathways: connecting communities

Autori: Marvin Martens, Ammar Ammar, Anders Riutta, Andra Waagmeester, Denise N Slenter, Kristina Hanspers, Ryan A. Miller, Daniela Digles, Elisson N Lopes, Friederike Ehrhart, Lauren J Dupuis, Laurent A Winckers, Susan L Coort, Egon L Willighagen, Chris T Evelo, Alexander R Pico, Martina Kutmon
Pubblicato in: Nucleic Acids Research, Numero 49/D1, 2020, Pagina/e D613-D621, ISSN 0305-1048
Editore: Oxford University Press
DOI: 10.1093/nar/gkaa1024

Biological effects of allergen-nanoparticle conjugates: uptake and immune effects determined on hAELVi cells under submerged vs. air-liquid interface conditions

Autori: Mills-Goodlet R., Schenck M., Chary A., Geppert M., Serchi T., Hofer S., Hofstätter N., Feinle A., Hüsing N., Gutleb A.C., Himly M., and Duschl A.
Pubblicato in: Environ. Sci. Nano., Numero 20518161, 2020, ISSN 2051-8161
Editore: Royal Society of Chemistry
DOI: 10.1039/C9EN01353A

Impact of measurement noise, experimental design, and estimation methods on Modular Response Analysis based network reconstruction.

Autori: Caterina Thomaseth, Dirk Fey, Tapesh Santra, Oleksii S. Rukhlenko, Nicole E. Radde & Boris N. Kholodenko
Pubblicato in: Scientific Reports, Numero 20452322, 2018, ISSN 2045-2322
Editore: Nature Publishing Group
DOI: 10.1038/s41598-018-34353-3

Surface functionalization of silica nanoparticles: strategies to optimize the immune-activating profile of biopharmaceutical carrier platforms

Autori: Punz B., Johnson L., Geppert M., Dang H.-H., Horejs-Hoeck J., Duschl A., and Himly M.
Pubblicato in: Pharmaceutics, Numero 19994923, 2022, ISSN 1999-4923
Editore: Multidisciplinary Digital Publishing Institute (MDPI)
DOI: 10.3390/pharmaceutics14051103

Editorial for the Special Issue From Nanoinformatics to Nanomaterials Risk Assessment and Governance

Autori: Iseult Lynch, Antreas Afantitis, Dario Greco, Maria Dusinska, Miguel A. Banares, Georgia Melagraki
Pubblicato in: Nanomaterials, Numero 11/1, 2021, Pagina/e 121, ISSN 2079-4991
Editore: MDPI
DOI: 10.3390/nano11010121

A survey on the state of nanosafety research in the European Union and the United States.

Autori: Duschl, A., Windgasse, G.
Pubblicato in: J Nanopart Res, Numero 13880764, 2018, ISSN 1388-0764
Editore: Kluwer Academic Publishers
DOI: 10.1007/s11051-018-4434-9

Can an InChI for Nano Address the Need for a Simplified Representation of Complex Nanomaterials across Experimental and Nanoinformatics Studies?

Autori: Iseult Lynch, Antreas Afantitis, Thomas Exner, Martin Himly, Vladimir Lobaskin, Philip Doganis, Dieter Maier, Natasha Sanabria, Anastasios G. Papadiamantis, Anna Rybinska-Fryca, Maciej Gromelski, Tomasz Puzyn, Egon Willighagen, Blair D. Johnston, Mary Gulumian, Marianne Matzke, Amaia Green Etxabe, Nathan Bossa, Angela Serra, Irene Liampa, Stacey Harper, Kaido Tämm, Alexander CØ Jensen, Pekka Koh
Pubblicato in: Nanomaterials, Numero 10/12, 2020, Pagina/e 2493, ISSN 2079-4991
Editore: MDPI
DOI: 10.3390/nano10122493

Evaluation and improvement of the National Early Warning Score (NEWS2) for COVID-19: a multi-hospital study

Autori: Ewan Carr, Rebecca Bendayan, Daniel Bean, Matt Stammers, Wenjuan Wang, Huayu Zhang, Thomas Searle, Zeljko Kraljevic, Anthony Shek, Hang T. T. Phan, Walter Muruet, Rishi K. Gupta, Anthony J. Shinton, Mike Wyatt, Ting Shi, Xin Zhang, Andrew Pickles, Daniel Stahl, Rosita Zakeri, Mahdad Noursadeghi, Kevin O’Gallagher, Matt Rogers, Amos Folarin, Andreas Karwath, Kristin E. Wickstrøm, Alvaro Köhn-Lu
Pubblicato in: BMC Medicine, Numero 17417015, 2021, ISSN 1741-7015
Editore: BioMed Central
DOI: 10.1186/s12916-020-01893-3

Apellis: An online tool for read-across model development

Autori: Dimitra-Danai Varsou, Haralambos Sarimveis
Pubblicato in: Computational Toxicology, Numero 17, 2021, Pagina/e 100146, ISSN 2468-1113
Editore: Science Direct
DOI: 10.1016/j.comtox.2020.100146

The nanotopography of SiO2 particles impacts selectivity and 3D fold of bound allergens

Autori: Mills-Goodlet R., Johnson L., Hoppe I.J., Regl C., Geppert M., Schenck M., Huber S., Hauser M., Ferreira F., Hüsing N., Huber C.G., Brandstetter H., Duschl A., and Himly M.
Pubblicato in: Nanoscale, Numero 20403372, 2021, ISSN 2040-3372
Editore: Nanoscale
DOI: 10.1039/d1nr05958k

Metadata Stewardship in Nanosafety Research: Community-Driven Organisation of Metadata Schemas to Support FAIR Nanoscience Data

Autori: Anastasios G. Papadiamantis, Frederick C. Klaessig, Thomas E. Exner, Sabine Hofer, Norbert Hofstaetter, Martin Himly, Marc A. Williams, Philip Doganis, Mark D. Hoover, Antreas Afantitis, Georgia Melagraki, Tracy S. Nolan, John Rumble, Dieter Maier, Iseult Lynch
Pubblicato in: Nanomaterials, Numero 10/10, 2020, Pagina/e 2033, ISSN 2079-4991
Editore: MDPI
DOI: 10.3390/nano10102033

Mechanistic insights into toxicity pathways induced by nanomaterials in Daphnia magna from analysis of the composition of the acquired protein corona

Autori: Laura-Jayne A. Ellis and Iseult Lynch
Pubblicato in: Environmental Science Nano, Numero 20518161, 2020, ISSN 2051-8161
Editore: Royal Society of Chemistry
DOI: 10.1039/d0en00625d

Children’s privilege in COVID-19: The protective role of the juvenile lung morphometry and ventilatory pattern on airborne SARS-CoV-2 transmission and severe pulmonary disease

Autori: Hofstätter N., Hofer S., Duschl A., and Himly M.
Pubblicato in: MDPI, Numero 22279059, 2021, ISSN 2227-9059
Editore: MDPI
DOI: 10.3390/biomedicines9101414

Toxicokinetics of silver nanoparticles in the mealworm Tenebrio molitor exposed via soil or food

Autori: Zahra Khodaparast, Cornelis A.M.van Gestel, Anastasios G.Papadiamantis, Sandra F.Gonçalves, Iseult Lynch, Susana Loureiro
Pubblicato in: Science Direct, Numero 00489697, 2021, ISSN 0048-9697
Editore: Elsevier BV
DOI: 10.1016/j.scitotenv.2021.146071

A Semi-Automated Workflow for FAIR Maturity Indicators in the Life Sciences

Autori: Ammar Ammar, Serena Bonaretti, Laurent Winckers, Joris Quik, Martine Bakker, Dieter Maier, Iseult Lynch, Jeaphianne van Rijn, Egon Willighagen
Pubblicato in: Nanomaterials, Numero 10/10, 2020, Pagina/e 2068, ISSN 2079-4991
Editore: nanomaterials
DOI: 10.3390/nano10102068

Systems biology approaches to macromolecules: the role of dynamic protein assemblies in information processing

Autori: Oleksii Rukhlenko, Boris N Kholodenko, Walter Kolch
Pubblicato in: Current Opinion in Structural Biology, Numero 0959440X, 2021, ISSN 0959-440X
Editore: Elsevier BV
DOI: 10.1016/j.sbi.2020.09.007

Towards semantic interoperability: finding and repairing hidden contradictions in biomedical ontologies

Autori: Luke T. Slater, Georgios V. Gkoutos & Robert Hoehndorf
Pubblicato in: BMC Med Inform Decis Mak, Numero 14726947, 2020, ISSN 1472-6947
Editore: BioMed Central
DOI: 10.1186/s12911-020-01336-2

Investigating the Molecular Processes behind the Cell-Specific Toxicity Response to Titanium Dioxide Nanobelts

Autori: L. A. Winckers, C. T. Evelo, E. L. Willighagen, M. Kutmon
Pubblicato in: International Journal of Molecular Sciences, Numero 14220067, 2021, ISSN 1422-0067
Editore: Multidisciplinary Digital Publishing Institute (MDPI)
DOI: 10.3390/ijms22179432

Biotransformation modulates the penetration of metallic nanomaterials across an artificial blood–brain barrier model

Autori: Zhiling Guo, Peng Zhang, Swaroop Chakraborty, Andrew J Chetwynd, Fazel Abdolahpur Monikh, Christopher Stark, Hanene Ali-Boucetta, Sandra Wilson, Iseult Lynch, Eugenia Valsami-Jones
Pubblicato in: Proceedings of the National Academy of Sciences, Numero 118/28, 2021, Pagina/e e2105245118, ISSN 0027-8424
Editore: National Academy of Sciences
DOI: 10.1073/pnas.2105245118

Extensive rewiring of the EGFR network in colorectal cancer cells expressing transforming levels of KRASG13D

Autori: Susan A. Kennedy, Mohamed-Ali Jarboui, Sriganesh Srihari, Cinzia Raso, Kenneth Bryan, Layal Dernayka, Theodosia Charitou, Manuel Bernal-Llinares, Carlos Herrera-Montavez, Aleksandar Krstic, David Matallanas, Max Kotlyar, Igor Jurisica, Jasna Curak, Victoria Wong, Igor Stagljar, Thierry LeBihan, Lisa Imrie, Priyanka Pillai, Miriam A. Lynn, Erik Fasterius, Cristina Al-Khalili Szigyarto, James Breen,
Pubblicato in: nature.com, Numero 11, 2020, ISSN 1476-4687
Editore: Nature
DOI: 10.1038/s41467-019-14224-9

Nanocharacterization, Materials Modeling, and Research Integrity as Enablers of Sound Risk Assessment: Designing Responsible Nanotechnology

Autori: Ioannis Xiarchos, Athanasios K. Morozinis, Panagiotis Kavouras, Costas A. Charitidis
Pubblicato in: Small, Numero 16/36, 2020, Pagina/e 2001590, ISSN 1613-6810
Editore: Wiley - V C H Verlag GmbbH & Co.
DOI: 10.1002/smll.202001590

Periodic propagating waves coordinate RhoGTPase network dynamics at the leading and trailing edges during cell migration

Autori: Alfonso Bolado-Carrancio, Oleksii S Rukhlenko, Elena Nikonova, Mikhail A Tsyganov, Anne Wheeler, Amaya Garcia-Munoz, Walter Kolch, Alex von Kriegsheim Is a corresponding author, Boris N Kholodenko
Pubblicato in: eLife Science, Numero 2050084X, 2020, ISSN 2050-084X
Editore: eLife Sciences Publications
DOI: 10.7554/elife.58165

Structural alterations of antigens at the material interface: an early decision toolbox facilitating Safe-by-Design nanovaccine development

Autori: Johnson L., Aglas L., Soh W.T., Geppert M., Hofer S., Hofstätter N., Briza P., Ferreira F., Weiss R., Brandstetter H., Duschl A., and Himly M.
Pubblicato in: Int. J. Mol. Sci., Numero 14220067, 2021, ISSN 1422-0067
Editore: Multidisciplinary Digital Publishing Institute (MDPI)
DOI: 10.3390/ijms221910895

Nanomaterials exposure, extracellular vesicles biogenesis and adverse cellular outcomes: a scoping review

Autori: Lima T.S.M., de Souza W., Geaquinto L.R.O., Sanches P.L., Stepień E.L., Meneses J., Fernández de Gortari E., Meisner-Kober N., Himly M., Granjeiro J.M., and Ribeiro A.R.L.P.
Pubblicato in: Nanomaterials, Numero 20794991, 2022, ISSN 2079-4991
Editore: MDPI
DOI: 10.3390/nano12071231

Translating Scientific Advances in the AOP Framework to Decision Making for Nanomaterials

Autori: James D. Ede, Vladimir Lobaskin, Ulla Vogel, Iseult Lynch, Sabina Halappanavar, Shareen H. Doak, Megan G. Roberts, Jo Anne Shatkin
Pubblicato in: Nanomaterials, Numero 10/6, 2020, Pagina/e 1229, ISSN 2079-4991
Editore: MDPI
DOI: 10.3390/nano10061229

Environmental dimensions of the protein corona

Autori: Korin E. Wheeler, Andrew J. Chetwynd, Kira M. Fahy, Brian S. Hong, Jose A. Tochihuitl, Lilah A. Foster & Iseult Lynch
Pubblicato in: Nature Nanotecnology, Numero 16, 2021, ISSN 1748-3395
Editore: Nature
DOI: 10.1038/s41565-021-00924-1

A safe-by-design tool for functionalised nanomaterials through the Enalos Nanoinformatics Cloud platform

Autori: Dimitra-Danai Varsou, Antreas Afantitis, Andreas Tsoumanis, Georgia Melagraki, Haralambos Sarimveis, Eugenia Valsami-Jones, Iseult Lynch
Pubblicato in: Nanoscale Advances, Numero Nanoscale Advances, 2019, ISSN 2516-0230
Editore: RSC
DOI: 10.1039/C8NA00142A

Read-across predictions of nanoparticle hazard endpoints: a mathematical optimization approach

Autori: Dimitra-Danai Varsou, Antreas Afantitis, Georgia Melagraki, Haralambos Sarimveis
Pubblicato in: Nanoscale Advances, 2019, ISSN 2516-0230
Editore: Royal Society of Chemistry
DOI: 10.1039/c9na00242a

Zeta‐Potential Read‐Across Model Utilizing Nanodescriptors Extracted via the NanoXtract Image Analysis Tool Available on the Enalos Nanoinformatics Cloud Platform

Autori: Dimitra‐Danai Varsou, Antreas Afantitis, Andreas Tsoumanis, Anastasios Papadiamantis, Eugenia Valsami‐Jones, Iseult Lynch, Georgia Melagraki
Pubblicato in: Small, 2020, Pagina/e 1906588, ISSN 1613-6810
Editore: Wiley - V C H Verlag GmbbH & Co.
DOI: 10.1002/smll.201906588

When Would Immunologists Consider a Nanomaterial to be Safe? Recommendations for Planning Studies on Nanosafety

Autori: Martin Himly, Mark Geppert, Sabine Hofer, Norbert Hofstätter, Jutta Horejs-Höck, Albert Duschl
Pubblicato in: Small, 2020, Pagina/e 1907483, ISSN 1613-6810
Editore: Wiley - V C H Verlag GmbbH & Co.
DOI: 10.1002/smll.201907483

Modeling cell line-specific recruitment of signaling proteins to the insulin-like growth factor 1 receptor

Autori: Keesha E. Erickson, Oleksii S. Rukhlenko, Md Shahinuzzaman, Kalina P. Slavkova, Yen Ting Lin, Ryan Suderman, Edward C. Stites, Marian Anghel, Richard G. Posner, Dipak Barua, Boris N. Kholodenko, William S. Hlavacek
Pubblicato in: PLOS Computational Biology, Numero 15/1, 2019, Pagina/e e1006706, ISSN 1553-7358
Editore: journal plos org
DOI: 10.1371/journal.pcbi.1006706

The rise of the nanomaterial metabolite corona, and emergence of the complete corona

Autori: Andrew J. Chetwynd, Iseult Lynch
Pubblicato in: Environmental Science: Nano, Numero 7/4, 2020, Pagina/e 1041-1060, ISSN 2051-8153
Editore: Royal Society of Chemistry
DOI: 10.1039/c9en00938h

An Integrative Computational Approach for a Prioritization of Key Transcription Regulators Associated With Nanomaterial-Induced Toxicity

Autori: Vadim Zhernovkov, Tapesh Santra, Hilary Cassidy, Oleksii Rukhlenko, David Matallanas, Aleksandar Krstic, Walter Kolch, Vladimir Lobaskin, Boris N Kholodenko
Pubblicato in: Toxicological Sciences, Numero 171/2, 2019, Pagina/e 303-314, ISSN 1096-6080
Editore: Oxford University Press
DOI: 10.1093/toxsci/kfz151

Mapping connections in signaling networks with ambiguous modularity

Autori: Daniel Lill, Oleksii S. Rukhlenko, Anthony James Mc Elwee, Eugene Kashdan, Jens Timmer, Boris N. Kholodenko
Pubblicato in: npj Systems Biology and Applications, Numero 5/1, 2019, ISSN 2056-7189
Editore: npj Systems Biology and Applications
DOI: 10.1038/s41540-019-0096-1

Extensive rewiring of the EGFR network in colorectal cancer cells expressing transforming levels of KRASG13D

Autori: Susan A. Kennedy, Mohamed-Ali Jarboui, Sriganesh Srihari, Cinzia Raso, Kenneth Bryan, Layal Dernayka, Theodosia Charitou, Manuel Bernal-Llinares, Carlos Herrera-Montavez, Aleksandar Krstic, David Matallanas, Max Kotlyar, Igor Jurisica, Jasna Curak, Victoria Wong, Igor Stagljar, Thierry LeBihan, Lisa Imrie, Priyanka Pillai, Miriam A. Lynn, Erik Fasterius, Cristina Al-Khalili Szigyarto, James Breen,
Pubblicato in: Nature Communications, Numero 11/1, 2020, ISSN 2041-1723
Editore: Nature Publishing Group
DOI: 10.1038/s41467-019-14224-9

Dissecting RAF Inhibitor Resistance by Structure-based Modeling Reveals Ways to Overcome Oncogenic RAS Signaling

Autori: Oleksii S. Rukhlenko, Fahimeh Khorsand, Aleksandar Krstic, Jan Rozanc, Leonidas G. Alexopoulos, Nora Rauch, Keesha E. Erickson, William S. Hlavacek, Richard G. Posner, Silvia Gómez-Coca, Edina Rosta, Cheree Fitzgibbon, David Matallanas, Jens Rauch, Walter Kolch, Boris N. Kholodenko
Pubblicato in: Cell Systems, Numero 7/2, 2018, Pagina/e 161-179.e14, ISSN 2405-4712
Editore: Science Direct
DOI: 10.1016/j.cels.2018.06.002

Semantic Interoperability and Characterization of Data Provenance in Computational Molecular Engineering

Autori: Martin Thomas Horsch, Christoph Niethammer, Gianluca Boccardo, Paola Carbone, Silvia Chiacchiera, Mara Chiricotto, Joshua D. Elliott, Vladimir Lobaskin, Philipp Neumann, Peter Schiffels, Michael A. Seaton, Ilian T. Todorov, Jadran Vrabec, Welchy Leite Cavalcanti
Pubblicato in: Journal of Chemical & Engineering Data, Numero 65/3, 2020, Pagina/e 1313-1329, ISSN 0021-9568
Editore: American Chemical Society
DOI: 10.1021/acs.jced.9b00739

Automated Grouping of Nanomaterials and Read-Across Prediction of Their Adverse Effects Based on Mathematical Optimization

Autori: Dimitra-Danai Varsou, Nikoletta-Maria Koutroumpa, and Haralambos Sarimveis
Pubblicato in: J. Chem. Inf. Model., Numero 15499596, 2021, Pagina/e 2766–2779, ISSN 1549-9596
Editore: American Chemical Society
DOI: 10.1021/acs.jcim.1c00199

Nanotechnology and artificial intelligence to enable sustainable and precision agriculture

Autori: Peng Zhang, Zhiling Guo, Sami Ullah, Georgia Melagraki, Antreas
Pubblicato in: Nature Plants, Numero 7, 2021, ISSN 2055-0278
Editore: Nature
DOI: 10.1038/s41477-021-00946-6

Multi-walled carbon nanotubes improve nitrogen use efficiency and nutritional quality in Brassica campestris†

Autori: Shixin Cai, Peng Zhang, Zhiling Guo, Feng Jin, Jingyuan Wang, Zijie Song, Tcyganova Nadezhda, Iseult Lynch and Xiuli Dang
Pubblicato in: Environ. Sci.: Nano, Numero 20518161, 2022, Pagina/e 1315-1329, ISSN 2051-8161
Editore: Royal Society of Chemistry
DOI: 10.1039/d1en01211h

European Registry of Materials: global, unique identifiers for (undisclosed) nanomaterials

Autori: J. van Rijn, A. Afantitis, M. Culha, M. Dusinska, T. Exner, N. Jeliazkova, E.M. Longhin, I. Lynch, G. Melagraki, P. Nymark, A.G. Papadiamantis, D.A. Winkler, H. Yilmaz, E.L. Willighagen
Pubblicato in: Journal of Cheminformatics, Numero 17582946, 2021, ISSN 1758-2946
Editore: Chemistry Central
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Nanotechnology-Based Vaccines for Allergen-Specific Immunotherapy: Potentials and Challenges of Conventional and Novel Adjuvants under Research

Autori: Johnson L., Duschl A., and Himly M.
Pubblicato in: MDPI, Numero 2076393X, 2020, ISSN 2076-393X
Editore: Multidisciplinary Digital Publishing Institute (MDPI)
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The impact of nanoparticles on innate immune activation by live bacteria.

Autori: Swartzwelter B.J., Fux A.C., Johnson L., Swart E., Hofer S., Hofstätter N., Geppert M., Italiani P., Boraschi D., Duschl A., and Himly M.
Pubblicato in: Int. J. Mol. Sci., Numero 14220067, 2020, ISSN 1422-0067
Editore: Multidisciplinary Digital Publishing Institute (MDPI)
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First principles characterisation of bio–nano interface

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Pubblicato in: Physical Chemistry Chemical Physics, Numero 14639084, 2021, ISSN 1463-9084
Editore: Royal Society of Chemistry
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Ecotoxicological read-across models for predicting acute toxicity of freshly dispersed versus medium-aged NMs to Daphnia magna

Autori: Dimitra-Danai Varsou, Laura-Jayne A. Ellis, Antreas Afantitis, Georgia Melagraki, Iseult Lynch
Pubblicato in: Chemosphere, Numero 285, 2021, Pagina/e 131452, ISSN 0045-6535
Editore: Pergamon Press Ltd.
DOI: 10.1016/j.chemosphere.2021.131452

Nanotoxicology and nanomedicine: The Yin and Yang of nano-bio interactions for the new decade

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Pubblicato in: NanoToday, Numero 17480132, 2021, Pagina/e 101, ISSN 1748-0132
Editore: Elsevier BV
DOI: 10.1016/j.nantod.2021.101184

Computational prediction and experimental analysis of the nanoparticle-protein corona: showcasing an in vitro-in silico workflow providing FAIR data

Autori: Hasenkopf I., Mills-Goodlet R., Johnson L., Rouse I., Geppert M,. Duschl A., Maier D., Lobaskin V., Lynch I., and Himly M.
Pubblicato in: NanoToday, Numero 17480132, 2022, ISSN 1748-0132
Editore: Elsevier BV
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Ensemble learning for poor prognosis predictions: A case study on SARS-CoV-2

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Pubblicato in: J Am Med Inform Assoc, Numero 1527974X, 2021, ISSN 1527-974X
Editore: Oxfrod Univeristy Press
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SARS-CoV-2-laden respiratory aerosol deposition in the lung alveolar-interstitial region is a potential risk factor for severe disease: a modeling study

Autori: Hofer S., Hofstätter N., Duschl A., and Himly M.
Pubblicato in: J. Personalized Med., Numero 14220067, 2021, ISSN 1422-0067
Editore: Multidisciplinary Digital Publishing Institute (MDPI)
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Development of a novel cellulose foam augmented with candle-soot derived carbon nanoparticles for solar-powered desalination of brackish water

Autori: Amrit Kumar Thakur; Ravishankar Sathyamurthy; R. Velraj; Iseult Lynch;
Pubblicato in: Environmental Science: Nano, Numero 20518161, 2022, ISSN 2051-8161
Editore: Royal Society of Chemistry
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Control of cell state transitions

Autori: Rukhlenko, O.S., Halasz, M., Rauch, N. Vadim Zhernovkov, Thomas Prince, Kieran Wynne, Stephanie Maher, Eugene Kashdan, Kenneth MacLeod, Neil O. Carragher, Walter Kolch, Boris N. Kholodenko
Pubblicato in: Nature, Numero 14764687, 2022, ISSN 1476-4687
Editore: Nature
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A survey on the state of nanosafety research in the European Union and the United States

Autori: Albert Duschl, Gabriele Windgasse
Pubblicato in: Journal of Nanoparticle Research, Numero 13880764, 2018, ISSN 1388-0764
Editore: Kluwer Academic Publishers
DOI: 10.1007/s11051-018-4434-9

A Novel Exposure System Termed NAVETTA for In Vitro Laminar Flow Electrodeposition of Nanoaerosol and Evaluation of Immune Effects in Human Lung Reporter Cells

Autori: Evelien Frijns, Sandra Verstraelen, Linda Corinna Stoehr, Jo Van Laer, An Jacobs, Jan Peters, Kristof Tirez, Matthew Samuel Powys Boyles, Mark Geppert, Pierre Madl, Inge Nelissen, Albert Duschl, Martin Himly
Pubblicato in: Environmental Science & Technology, Numero 51/9, 2017, Pagina/e 5259-5269, ISSN 0013-936X
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Driving the nanoinformatics wave

Autori: Afantitis, Antreas; Lynch, Iseult;
Pubblicato in: Scitech Europa Quarterly, Numero 2516435X, 2019, ISSN 2516-435X
Editore: Pan European Networks
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INISS-Nano: revised concept and action plan (International Network Initiative on Safe and Sustainable Nanotechnologies) (Version_02)

Autori: Falk, Andreas; Pogany, Alexander; Aungkavattana, Pavadee; Bañares, Miguel A.; Beitollahi, Ali; Bim, Vinicius; Briffa, Sophie; Bochon, Anthony; Cassee, Flemming; Doridot, Fernand; Exner, Thomas; Farias, Patricia M.A.; Favre, Georges; Franzese, Giancarlo; Friedrichs, Steffi; Hristozov, Danail; Hunt, Neil; Indaraprasirt, Ramjitti; Karim, Md. E.; … Wilkens, Terence A.
Pubblicato in: Zenodo, 2022
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D10.1 Initial draft of data management plan (Open data pilot)

Autori: Papadiamantis, Anastasios; Farcal, Lucian; Willighagen, Egon; Lynch, Iseult; Exner, Thomas
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Editore: European Commission
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INISS-Nano: revised concept and action plan (International Network Initiative on Safe and Sustainable Nanotechnologies) (Version_01)

Enalos Suite of Tools: Enhancing Cheminformatics and Nanoinfor - matics through KNIME

Autori: Antreas Afantitis, Andreas Tsoumanis, Georgia Melagraki
Pubblicato in: National Library of Medicine, Numero 1875533X, 2020, ISSN 1875-533X
Editore: Bentham Science
DOI: 10.2174/0929867327666200727114410

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