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

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

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

Publications

Iron oxide nanoparticles in bioimaging – an immune perspective

Author(s): Geppert M. and Himly M.
Published in: Front Immunol, 2021, ISSN 1664-3224
Publisher: Front Immunol
DOI: 10.3389/fimmu.2021.688927

Improved characterisation of clinical text through ontology-based vocabulary expansion

Author(s): Luke T. Slater, William Bradlow, Simon Ball, Robert Hoehndorf and Georgios V Gkoutos
Published in: Journal of Biomedical Semantics, Issue 20411480, 2021, ISSN 2041-1480
Publisher: Springer-Nature
DOI: 10.1186/s13326-021-00241-5

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

Author(s): Anna I. Joubert, Mark Geppert, Litty Johnson, Robert Mills-Goodlet, Sara Michelini, Evgeniia Korotchenko, Albert Duschl, Richard Weiss, Jutta Horejs-Höck, Martin Himly
Published in: Frontiers in Immunology, Issue 11, 2020, ISSN 1664-3224
Publisher: Frontiers
DOI: 10.3389/fimmu.2020.01334

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

Author(s): 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
Published in: Plos Computational Biology, Issue 15537358, 2021, ISSN 1553-7358
Publisher: PLOS
DOI: 10.1371/journal.pcbi.1009226

Toxicokinetics of pristine and aged silver nanoparticles in Physa acuta

Author(s): Patrícia V. Silva, Cornelis A. M. van Gestel, Rudo A. Verweij, Anastasios G. Papadiamantis, Sandra F. Gonçalves, Iseult Lynch and Susana Loureiro
Published in: Environmental Science: Nano, 2020, ISSN 2051-8161
Publisher: Royal Society of Chemistry
DOI: 10.1039/d0en00946f

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

Author(s): Zhiling Guo, Swaroop Chakraborty, Fazel Abdolahpur Monikh, Dimitra-Danai Varsou, Andrew J Chetwynd, Antreas Afantitis, Iseult Lynch, Peng Zhang
Published in: Advanced Biology, Issue 27010198, 2021, ISSN 2701-0198
Publisher: 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

Author(s): Papadiamantis, A.G., Afantitis, A., Tsoumanis, A., Valsami-Jones, E., Lynch, I., Melagraki,
Published in: NanoImpact, 2021, ISSN 2452-0748
Publisher: Elsevier
DOI: 10.1016/j.impact.2021.100308

The earthworm microbiome is resilient to exposure to biocidal metal nanoparticles

Author(s): Elmer Swart; Tim Goodall; Peter Kille; David J. Spurgeon; Claus Svendsen;
Published in: Journal: Environmental Pollution, Issue 02697491, 2020, ISSN 0269-7491
Publisher: Pergamon Press Ltd.
DOI: 10.1016/j.envpol.2020.115633

Can Systems Biology Advance Clinical Precision Oncology?

Author(s): Andrea Rocca Boris N. Kholodenko
Published in: Cancers, Issue 20726694, 2021, ISSN 2072-6694
Publisher: Multidisciplinary Digital Publishing Institute (MDPI)
DOI: 10.3390/cancers13246312

Daphnia magna and mixture toxicity with nanomaterials – Current status

Author(s): 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
Published in: NanoToday, 2022, ISSN 1748-0132
Publisher: Elsevier BV
DOI: 10.1016/j.nantod.2022.101430

WikiPathways: connecting communities

Author(s): 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
Published in: Nucleic Acids Research, Issue 49/D1, 2020, Page(s) D613-D621, ISSN 0305-1048
Publisher: 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

Author(s): 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.
Published in: Environ. Sci. Nano., 2020, ISSN 2051-8161
Publisher: Royal Society of Chemistry
DOI: 10.1039/C9EN01353A

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

Author(s): Caterina Thomaseth, Dirk Fey, Tapesh Santra, Oleksii S. Rukhlenko, Nicole E. Radde & Boris N. Kholodenko
Published in: Scientific Reports, Issue 20452322, 2018, ISSN 2045-2322
Publisher: 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

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

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

Author(s): Iseult Lynch, Antreas Afantitis, Dario Greco, Maria Dusinska, Miguel A. Banares, Georgia Melagraki
Published in: Nanomaterials, Issue 11/1, 2021, Page(s) 121, ISSN 2079-4991
Publisher: MDPI
DOI: 10.3390/nano11010121

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

Author(s): Duschl, A., Windgasse, G.
Published in: J Nanopart Res, Issue 13880764, 2018, ISSN 1388-0764
Publisher: 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?

Author(s): 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
Published in: Nanomaterials, Issue 10/12, 2020, Page(s) 2493, ISSN 2079-4991
Publisher: MDPI
DOI: 10.3390/nano10122493

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

Author(s): 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
Published in: BMC Medicine, 2021, ISSN 1741-7015
Publisher: BioMed Central
DOI: 10.1186/s12916-020-01893-3

Apellis: An online tool for read-across model development

Author(s): Dimitra-Danai Varsou, Haralambos Sarimveis
Published in: Computational Toxicology, Issue 17, 2021, Page(s) 100146, ISSN 2468-1113
Publisher: Science Direct
DOI: 10.1016/j.comtox.2020.100146

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

Author(s): 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.
Published in: Nanoscale, 2021, ISSN 2040-3372
Publisher: Nanoscale
DOI: 10.1039/d1nr05958k

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

Author(s): 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
Published in: Nanomaterials, Issue 10/10, 2020, Page(s) 2033, ISSN 2079-4991
Publisher: 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

Author(s): Laura-Jayne A. Ellis and Iseult Lynch
Published in: Environmental Science Nano, Issue 20518161, 2020, ISSN 2051-8161
Publisher: 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

Author(s): Hofstätter N., Hofer S., Duschl A., and Himly M.
Published in: MDPI, 2021, ISSN 2227-9059
Publisher: MDPI
DOI: 10.3390/biomedicines9101414

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

Author(s): Zahra Khodaparast, Cornelis A.M.van Gestel, Anastasios G.Papadiamantis, Sandra F.Gonçalves, Iseult Lynch, Susana Loureiro
Published in: Science Direct, 2021, ISSN 0048-9697
Publisher: Elsevier BV
DOI: 10.1016/j.scitotenv.2021.146071

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

Author(s): Ammar Ammar, Serena Bonaretti, Laurent Winckers, Joris Quik, Martine Bakker, Dieter Maier, Iseult Lynch, Jeaphianne van Rijn, Egon Willighagen
Published in: Nanomaterials, Issue 10/10, 2020, Page(s) 2068, ISSN 2079-4991
Publisher: nanomaterials
DOI: 10.3390/nano10102068

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

Author(s): Oleksii Rukhlenko, Boris N Kholodenko, Walter Kolch
Published in: Current Opinion in Structural Biology, Issue 0959440X, 2021, ISSN 0959-440X
Publisher: Elsevier BV
DOI: 10.1016/j.sbi.2020.09.007

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

Author(s): Luke T. Slater, Georgios V. Gkoutos & Robert Hoehndorf
Published in: BMC Med Inform Decis Mak, Issue 14726947, 2020, ISSN 1472-6947
Publisher: BioMed Central
DOI: 10.1186/s12911-020-01336-2

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

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

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

Author(s): Zhiling Guo, Peng Zhang, Swaroop Chakraborty, Andrew J Chetwynd, Fazel Abdolahpur Monikh, Christopher Stark, Hanene Ali-Boucetta, Sandra Wilson, Iseult Lynch, Eugenia Valsami-Jones
Published in: Proceedings of the National Academy of Sciences, Issue 118/28, 2021, Page(s) e2105245118, ISSN 0027-8424
Publisher: National Academy of Sciences
DOI: 10.1073/pnas.2105245118

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

Author(s): 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,
Published in: nature.com, Issue 11, 2020, ISSN 1476-4687
Publisher: Nature
DOI: 10.1038/s41467-019-14224-9

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

Author(s): Ioannis Xiarchos, Athanasios K. Morozinis, Panagiotis Kavouras, Costas A. Charitidis
Published in: Small, Issue 16/36, 2020, Page(s) 2001590, ISSN 1613-6810
Publisher: 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

Author(s): 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
Published in: eLife Science, Issue 2050084X, 2020, ISSN 2050-084X
Publisher: 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

Author(s): 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.
Published in: Int. J. Mol. Sci., 2021, ISSN 1422-0067
Publisher: Multidisciplinary Digital Publishing Institute (MDPI)
DOI: 10.3390/ijms221910895

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

Author(s): 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.
Published in: Nanomaterials, 2022, ISSN 2079-4991
Publisher: MDPI
DOI: 10.3390/nano12071231

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

Author(s): James D. Ede, Vladimir Lobaskin, Ulla Vogel, Iseult Lynch, Sabina Halappanavar, Shareen H. Doak, Megan G. Roberts, Jo Anne Shatkin
Published in: Nanomaterials, Issue 10/6, 2020, Page(s) 1229, ISSN 2079-4991
Publisher: MDPI
DOI: 10.3390/nano10061229

Environmental dimensions of the protein corona

Author(s): Korin E. Wheeler, Andrew J. Chetwynd, Kira M. Fahy, Brian S. Hong, Jose A. Tochihuitl, Lilah A. Foster & Iseult Lynch
Published in: Nature Nanotecnology, Issue 16, 2021, ISSN 1748-3395
Publisher: Nature
DOI: 10.1038/s41565-021-00924-1

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

Author(s): Dimitra-Danai Varsou, Antreas Afantitis, Andreas Tsoumanis, Georgia Melagraki, Haralambos Sarimveis, Eugenia Valsami-Jones, Iseult Lynch
Published in: Nanoscale Advances, Issue Nanoscale Advances, 2019, ISSN 2516-0230
Publisher: RSC
DOI: 10.1039/C8NA00142A

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

Author(s): Dimitra-Danai Varsou, Antreas Afantitis, Georgia Melagraki, Haralambos Sarimveis
Published in: Nanoscale Advances, 2019, ISSN 2516-0230
Publisher: 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

Author(s): Dimitra‐Danai Varsou, Antreas Afantitis, Andreas Tsoumanis, Anastasios Papadiamantis, Eugenia Valsami‐Jones, Iseult Lynch, Georgia Melagraki
Published in: Small, 2020, Page(s) 1906588, ISSN 1613-6810
Publisher: 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

Author(s): Martin Himly, Mark Geppert, Sabine Hofer, Norbert Hofstätter, Jutta Horejs-Höck, Albert Duschl
Published in: Small, 2020, Page(s) 1907483, ISSN 1613-6810
Publisher: 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

Author(s): 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
Published in: PLOS Computational Biology, Issue 15/1, 2019, Page(s) e1006706, ISSN 1553-7358
Publisher: journal plos org
DOI: 10.1371/journal.pcbi.1006706

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

Author(s): Andrew J. Chetwynd, Iseult Lynch
Published in: Environmental Science: Nano, Issue 7/4, 2020, Page(s) 1041-1060, ISSN 2051-8153
Publisher: Royal Society of Chemistry
DOI: 10.1039/c9en00938h

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

Author(s): Vadim Zhernovkov, Tapesh Santra, Hilary Cassidy, Oleksii Rukhlenko, David Matallanas, Aleksandar Krstic, Walter Kolch, Vladimir Lobaskin, Boris N Kholodenko
Published in: Toxicological Sciences, Issue 171/2, 2019, Page(s) 303-314, ISSN 1096-6080
Publisher: Oxford University Press
DOI: 10.1093/toxsci/kfz151

Mapping connections in signaling networks with ambiguous modularity

Author(s): Daniel Lill, Oleksii S. Rukhlenko, Anthony James Mc Elwee, Eugene Kashdan, Jens Timmer, Boris N. Kholodenko
Published in: npj Systems Biology and Applications, Issue 5/1, 2019, ISSN 2056-7189
Publisher: 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

Author(s): 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,
Published in: Nature Communications, Issue 11/1, 2020, ISSN 2041-1723
Publisher: 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

Author(s): 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
Published in: Cell Systems, Issue 7/2, 2018, Page(s) 161-179.e14, ISSN 2405-4712
Publisher: Science Direct
DOI: 10.1016/j.cels.2018.06.002

Semantic Interoperability and Characterization of Data Provenance in Computational Molecular Engineering

Author(s): 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
Published in: Journal of Chemical & Engineering Data, Issue 65/3, 2020, Page(s) 1313-1329, ISSN 0021-9568
Publisher: 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

Author(s): Dimitra-Danai Varsou, Nikoletta-Maria Koutroumpa, and Haralambos Sarimveis
Published in: J. Chem. Inf. Model., Issue 15499596, 2021, Page(s) 2766–2779, ISSN 1549-9596
Publisher: American Chemical Society
DOI: 10.1021/acs.jcim.1c00199

Nanotechnology and artificial intelligence to enable sustainable and precision agriculture

Author(s): Peng Zhang, Zhiling Guo, Sami Ullah, Georgia Melagraki, Antreas
Published in: Nature Plants, Issue 7, 2021, ISSN 2055-0278
Publisher: Nature
DOI: 10.1038/s41477-021-00946-6

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

Author(s): Shixin Cai, Peng Zhang, Zhiling Guo, Feng Jin, Jingyuan Wang, Zijie Song, Tcyganova Nadezhda, Iseult Lynch and Xiuli Dang
Published in: Environ. Sci.: Nano, Issue 9, 2022, Page(s) 1315-1329, ISSN 2051-8161
Publisher: Royal Society of Chemistry
DOI: 10.1039/d1en01211h

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

Author(s): 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
Published in: Journal of Cheminformatics, Issue 17582946, 2021, ISSN 1758-2946
Publisher: Chemistry Central
DOI: 10.1186/s13321-022-00614-7

Nanotechnology-Based Vaccines for Allergen-Specific Immunotherapy: Potentials and Challenges of Conventional and Novel Adjuvants under Research

Author(s): Johnson L., Duschl A., and Himly M.
Published in: MDPI, Issue 2076393X, 2020, ISSN 2076-393X
Publisher: Multidisciplinary Digital Publishing Institute (MDPI)
DOI: 10.3390/vaccines8020237

The impact of nanoparticles on innate immune activation by live bacteria.

Author(s): 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.
Published in: Int. J. Mol. Sci., 2020, ISSN 1422-0067
Publisher: Multidisciplinary Digital Publishing Institute (MDPI)
DOI: 10.3390/ijms21249695

First principles characterisation of bio–nano interface

Author(s): Ian Rouse, David Power, Erik G. Brandt, Matthew Schneemilch, Konstantinos Kotsis, Nick Quirke, Alexander P. Lyubartsev and Vladimir Lobaskin
Published in: Physical Chemistry Chemical Physics, 2021, ISSN 1463-9084
Publisher: Royal Society of Chemistry
DOI: 10.1039/d1cp01116b

Ecotoxicological read-across models for predicting acute toxicity of freshly dispersed versus medium-aged NMs to Daphnia magna

Author(s): Dimitra-Danai Varsou, Laura-Jayne A. Ellis, Antreas Afantitis, Georgia Melagraki, Iseult Lynch
Published in: Chemosphere, Issue 285, 2021, Page(s) 131452, ISSN 0045-6535
Publisher: 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

Author(s): Olesja Bondarenko, Monika Mortimer, Anne Kahru, Neus Feliu, Ibrahim Javed, Aleksandr Kakinen, Sijie Lin, Tian Xia, Yang Song, Thomas P. Davis, Iseult Lynch, Wolfgang J. Parak, David Tai Leong, Pu Chun Ke,Chunying Chen, Yuliang Zhao
Published in: NanoToday, Issue 17480132, 2021, Page(s) 101, ISSN 1748-0132
Publisher: 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

Author(s): Hasenkopf I., Mills-Goodlet R., Johnson L., Rouse I., Geppert M,. Duschl A., Maier D., Lobaskin V., Lynch I., and Himly M.
Published in: NanoToday, Issue 17480132, 2022, ISSN 1748-0132
Publisher: Elsevier BV
DOI: 10.1016/j.nantod.2022.101561

Ensemble learning for poor prognosis predictions: A case study on SARS-CoV-2

Author(s): Honghan Wu, Huayu Zhang, Andreas Karwath, Zina Ibrahim, Ting Shi, Xin Zhang, Kun Wang, Jiaxing Sun, Kevin Dhaliwal, Daniel Bean, Victor Roth Cardoso, Kezhi Li, James T Teo, Amitava Banerjee, Fang Gao-Smith, Tony Whitehouse, Tonny Veenith, Georgios V Gkoutos, Xiaodong Wu, Richard Dobson, Bruce Guthrie
Published in: J Am Med Inform Assoc, Issue 1527974X, 2021, ISSN 1527-974X
Publisher: Oxfrod Univeristy Press
DOI: 10.1093/jamia/ocaa295

SARS-CoV-2-laden respiratory aerosol deposition in the lung alveolar-interstitial region is a potential risk factor for severe disease: a modeling study

Author(s): Hofer S., Hofstätter N., Duschl A., and Himly M.
Published in: J. Personalized Med., 2021, ISSN 1422-0067
Publisher: Multidisciplinary Digital Publishing Institute (MDPI)
DOI: 10.3390/jpm11050431

Development of a novel cellulose foam augmented with candle-soot derived carbon nanoparticles for solar-powered desalination of brackish water

Author(s): Amrit Kumar Thakur; Ravishankar Sathyamurthy; R. Velraj; Iseult Lynch;
Published in: Environmental Science: Nano, Issue 20518161, 2022, ISSN 2051-8161
Publisher: Royal Society of Chemistry
DOI: 10.1039/d1en01112j

Control of cell state transitions

Author(s): 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
Published in: Nature, Issue 14764687, 2022, ISSN 1476-4687
Publisher: Nature
DOI: 10.1038/s41586-022-05194-y

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

Author(s): Albert Duschl, Gabriele Windgasse
Published in: Journal of Nanoparticle Research, Issue 13880764, 2018, ISSN 1388-0764
Publisher: 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

Author(s): 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
Published in: Environmental Science & Technology, Issue 51/9, 2017, Page(s) 5259-5269, ISSN 0013-936X
Publisher: American Chemical Society
DOI: 10.1021/acs.est.7b00493

Driving the nanoinformatics wave

Author(s): Afantitis, Antreas; Lynch, Iseult;
Published in: Scitech Europa Quarterly, Issue 2516435X, 2019, ISSN 2516-435X
Publisher: Pan European Networks
DOI: 10.5281/zenodo.3765525

INISS-Nano: revised concept and action plan (International Network Initiative on Safe and Sustainable Nanotechnologies) (Version_02)

Author(s): 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.
Published in: Zenodo, 2022
Publisher: Zenodo
DOI: 10.5281/zenodo.6818049

D10.1 Initial draft of data management plan (Open data pilot)

Author(s): Papadiamantis, Anastasios; Farcal, Lucian; Willighagen, Egon; Lynch, Iseult; Exner, Thomas
Published in: Deliverable Report, Issue 1, 2018
Publisher: European Commission
DOI: 10.5281/zenodo.1479556

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

Author(s): Antreas Afantitis, Andreas Tsoumanis, Georgia Melagraki
Published in: National Library of Medicine, Issue 1875533X, 2020, ISSN 1875-533X
Publisher: Bentham Science
DOI: 10.2174/0929867327666200727114410

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