Innovative Nanoinformatics models and tools: towards a Solid, verified and Integrated Approach to Predictive (eco)Toxicology (NanoSolveIT)

Deliverables

Collection of system requirements and specifications
AOP-level grouping, AOP fingerprints, minimal feature sets and inputs into IATAs
Report on developed dissemination activities
Final version of IATA with full documentation & training modules
Report detailing descriptors for NMs that are based on electronic images
Definition of omics-derived predictive models and biomarkers

Definition of omicsderived predictive models and biomarkers

Report summarizing the integrated modelling strategy: connecting materials modelling, chemoinformatics & bioinformatics.
Report detailing meta-models development and outputs from the intrinsic and extrinsic properties modelling
Full business development plan for NanoSolveIT tools and IATA
Set of intrinsic descriptors of selected NM
Documentation and training material for the NanoSolveIT e-platform
Datasets from bespoke NMs synthesis and characterization studies in appropriate formats for the models in WPs 3-5 and the IATA (WP6)
Initial version of NanoSolveIT cloud platform
Completion of existing omics data preprocessing and transfer of data to WP1
Methodology of calculation of intrinsic descriptors of NM
Maintenance and Evaluation Report
Two case studies submitted to OECD for consideration as OECD IATA Case study projects
Report on the first half-yearly ontology releases and guidance

Report on the first halfyearly ontology releases and guidance

Set of extrinsic descriptors of NMs, descriptors of bionano interface

Set of extrinsic descriptors of NMs descriptors of bionano interface

Report summarizing the types of NM descriptors (existing and newly developed), which are not based on the experimental measurements.

Report summarizing the types of NM descriptors existing and newly developed which are not based on the experimental measurements

Report on two IATA demonstration workshops (one for SMEs, one for regulators)

Report on two IATA demonstration workshops one for SMEs one for regulators

Structural alerts report describing methods that can identify the MoA structural alerts
Report on developed dissemination activities (update)
Report on the final ontology releases and guidance
Initial report on automated data completeness testing and delivered data sets
Datasets from bespoke ecotoxicity studies in appropriate formats for the models in WPs 3-5 and the IATA (WP6)
Exposure/ PBTK models and relevant NM forms linked into IATA

Exposure PBTK models and relevant NM forms linked into IATA

Report on the implementation of tools as microservices
CG force fields for selected representative NMs/biomolecules

CG force fields for selected representative NMsbiomolecules

Demonstration version of IATA with models linked
Report on outcome of international RR for model benchmarking
Atomistic force fields for selected NMs
Datasets from bespoke toxicity studies in appropriate formats for the models in WPs 3-5 and the IATA (WP6)
Report on the 3 rounds of DoE covering synthesis (1st only), characterization, tox and ecotox gap filling (2nd and 3rd rounds)

Report on the 3 rounds of DoE covering synthesis 1st only characterization tox and ecotox gap filling 2nd and 3rd rounds

Definition of hybrid predictive models comprising MOA & molecular descriptors/intrinsic properties

Definition of hybrid predictive models comprising MOA molecular descriptorsintrinsic properties

An ontology-backed data completeness standard for curation use
Report on exploitation activities
Final report on delivered data sets
Architecture of NanoSolveIT e-platform and API specifications
Initial inventory of MoAs, MIEs and predictive NMs descriptors
Materials models coupling for calculation of advanced descriptors from 1st principles
Documentation on use of Design of Experiments for end-users of the IATA to support optimized generation of input data for the IATA

Final Data Management Plan
Initial data management plan (DMP) as part of the open data pilot

Final version of NanoSolveIT cloud platform
NanoSolveIT Knowledge infrastructure API
Project web site
NanoSolveIT standalone software application

Publications

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

Author(s): Jeaphianne van Rijn; Antreas Afantitis; Mustafa Culha; Maria Dusinska; Thomas Exner; Nina Jeliazkova; Eleonora Longhin; Iseult Lynch; Georgia Melagraki; Penny Nymark; Anastasios G. Papadiamantis; David A. Winkler; Hulya Yilmaz; Egon Willighagen
Published in: Nanoscience, 2021
Publisher: ChemRxiv
DOI: 10.33774/chemrxiv-2021-65894

International Network Initiative on Safe and Sustainable Nanotechnologies (INISS-nano)

Author(s): Andreas Falk
Published in: INISS-nano, Issue 1, 2021
Publisher: INISS-nano
DOI: 10.5281/zenodo.5004928

Driving the nanoinformatics wave

Author(s): Afantitis, Antreas; Lynch, Iseult
Published in: SciTech Europa Quarterly, Issue 10, 2019
Publisher: Scitech Europa
DOI: 10.5281/zenodo.3765524

RDF version of the data from Saarimaki et al. Manually curated transcriptomics data collection for toxicogenomic assessment of engineered nanomaterials (Version 1.0.0) [Zenodo Dataset] (2020)

Author(s): Ammar Ammar
Published in: 2021
Publisher: Zenodo
DOI: 10.5281/zenodo.5744003

RDF version of the data from Anastasios G. et al. Computational enrichment of physicochemical data for the development of a zeta-potential read-across predictive model with Isalos Analytics Platform. NanoImpact (2021)

Author(s): Ammar Ammar
Published in: 2021
Publisher: Zenodo
DOI: 10.5281/zenodo.5744082

RDF version of the data from Choi, JS. et al. Towards a generalized toxicity prediction model for oxide nanomaterials using integrated data from different sources (2018)

Author(s): Ammar Ammar
Published in: 2021
Publisher: Zenodo
DOI: 10.5281/zenodo.5743204

"Data & code repository for the article ""An ancestral molecular response to nanomaterial particulates"""

Author(s): Giusy del Giudice; Dario Greco
Published in: 2023
Publisher: Zenodo
DOI: 10.5281/zenodo.7674573

RDF version of the data from Anastasios G. Papadiamantis et al. Predicting Cytotoxicity of Metal Oxide Nanoparticles Using Isalos Analytics Platform (2020)

Author(s): Ammar Ammar
Published in: 2021
Publisher: Zenodo
DOI: 10.5281/zenodo.5743788

Two real use cases of FAIR maturity indicators in the life sciences

Author(s): Bonaretti, Serena; Willighagen, Egon
Published in: bioRxiv, Issue 1, 2019
Publisher: bioRxiv
DOI: 10.1101/739334

RDF version of the data from Hagar I. Labouta et al. Meta-Analysis of Nanoparticle Cytotoxicity via Data-Mining the Literature. NanoImpact (2019)

Author(s): Ammar Ammar
Published in: 2021
Publisher: Zenodo
DOI: 10.5281/zenodo.5744302

Nanoinformatics: Artificial intelligence and nanotechnology in the new decade

Author(s): Afantitis A.
Published in: Combinatorial Chemistry and High Throughput Screening, Issue 23, 1, 2020, Page(s) 4-5, ISSN 1386-2073
Publisher: Bentham Science
DOI: 10.2174/138620732301200316112000

A gene regulation model reveals an ancestral adaptation response to particulate exposure triggered by nanomaterials

Author(s): Giusy del Giudice Angela Serra Laura Saarimäki Konstantinos Kotsis Ian Rouse Anais Colibaba Karolina Jagiello Alicja Mikolajczyk Anastasios Papadiamantis Natasha Sanabria Pia Kinaret Evangelos Voyiatzis Georgia Melagraki Antreas Afantitis Kaido Tamm Tomasz Puzyn Mary Gulumian Vladimir Lobaskin Iseult Lynch Antonio Federico Dario Greco
Published in: Research Square, 2022, ISSN 2693-5015
Publisher: Research Square
DOI: 10.21203/rs.3.rs-1547187/v1

Machine-learning based prediction of small molecule -- surface interaction potentials

Author(s): Rouse, Ian; Lobaskin, Vladimir
Published in: Arxiv, Issue 4, 2022
Publisher: Arxiv
DOI: 10.48550/arxiv.2211.07999

Advanced in silico characterization of nanomaterials for nanoparticle toxicology

Author(s): Rouse, Ian; Power, David; Brandt, Erik G.; Schneemilch, Matthew; Kotsis, Konstantinos; Quirke, Nick; Lyubartsev, Alexander P.; Lobaskin, Vladimir
Published in: arXiv, Issue 2, 2020
Publisher: arXiv

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

Author(s): Papadiamantis, A.G.; Klaessig, F.C.; Exner, T.E.; Hofer, S.; Hofstaetter, N.; Himly, M.; Williams, M.A.; Doganis, P.; Hoover, M.D.; Afantitis, A.; Melagraki, G.; Nolan, T.S.; Rumble, J.; Maier, D.; Lynch, I.
Published in: Nanomaterials, Issue 10, 2020, Page(s) 2033, ISSN 2079-4991
Publisher: MDPI
DOI: 10.3390/nano10102033

Quantitative Estimation of Cell-Associated Silver Nanoparticles using the Normalized Side Scattering Intensities of Flow Cytometry.

Author(s): Yoo Jin Shim; My Kieu Ha; Tae Hyun Yoon
Published in: 2079-4991, Issue 11, 2021, ISSN 2079-4991
Publisher: MDPI
DOI: 10.3390/nano11113079

A data reusability assessment in the nanosafety domain based on the NSDRA framework followed by an exploratory quantitative structure activity relationships (QSAR) modeling targeting cellular viability

Author(s): Furxhi I.; Willighagen E.; Evelo C.; Costa A.; Gardini D.; Ammar A.
Published in: NanoImpact, Issue 31, 2023, Page(s) 100475, ISSN 2452-0748
Publisher: Elsevier
DOI: 10.1016/j.impact.2023.100475

Hazard identification of nanomaterials: In silico unraveling of descriptors for cytotoxicity and genotoxicity

Author(s): El Yamani N.; Mariussen E.; Gromelski M.; Wyrzykowska E.; Grabarek D.; Puzyn T.; Tanasescu S.; Dusinska M.; Rundén-Pran E.
Published in: Nano Today, Issue 46, 2022, Page(s) 101581, ISSN 1748-0132
Publisher: Elsevier BV
DOI: 10.1016/j.nantod.2022.101581

The miniaturized enzyme-modified comet assay for genotoxicity testing of nanomaterials

Author(s): El Yamani N.; Rundén-Pran E.; Collins A.R.; Longhin E.M.; Elje E.; Hoet P.; Vinković Vrček I.; Doak S.H.; Fessard V.; Dusinska M.
Published in: Frontiers in Toxicology, Issue 4, 2022, Page(s) 986318, ISSN 2673-3080
Publisher: Frontiers
DOI: 10.3389/ftox.2022.986318

Milk Protein Adsorption on Metallic Iron Surfaces

Author(s): Mosaddeghi Amini P.; Subbotina J.; Lobaskin V.
Published in: Nanomaterials, Issue 13, 12, 2023, Page(s) 1857, ISSN 2079-4991
Publisher: MDPI
DOI: 10.3390/nano13121857

Maternal Responses and Adaptive Changes to Environmental Stress via Chronic Nanomaterial Exposure: Differences in Inter and Transgenerational Interclonal Broods of Daphnia magna

Author(s): Laura-Jayne. A. Ellis, Stephen Kissane, Iseult Lynch
Published in: International Journal of Molecular Sciences, Issue 22/1, 2021, Page(s) 15, ISSN 1422-0067
Publisher: Multidisciplinary Digital Publishing Institute (MDPI)
DOI: 10.3390/ijms22010015

Core, Coating, or Corona? The Importance of Considering Protein Coronas in nano-QSPR Modeling of Zeta Potential

Author(s): Sengottiyan S.; Mikolajczyk A.; Jagiełło K.; Swirog M.; Puzyn T.
Published in: ACS Nano, Issue 17, 3, 2023, Page(s) 1989–1997, ISSN 1936-0851
Publisher: American Chemical Society
DOI: 10.1021/acsnano.2c06977

Engineered Zn-based nano-pesticides as an opportunity for treatment of phytopathogens in agriculture

Author(s): Zhao W.; Liu Y.; Zhang P.; Zhou P.; Wu Z.; Lou B.; Jiang Y.; Shakoor N.; Li M.; Li Y.; Lynch I.; Rui Y.; Tan Z.
Published in: NanoImpact, Issue 28, 2022, Page(s) 100420, ISSN 2452-0748
Publisher: Elsevier
DOI: 10.1016/j.impact.2022.100420

Rapid identification of in vitro cell toxicity using an electrochemical membrane screening platform

Author(s): Kohl Y.; William N.; Elje E.; Backes N.; Rothbauer M.; Srancikova A.; Rundén-Pran E.; El Yamani N.; Korenstein R.; Madi L.; Barbul A.; Kozics K.; Sramkova M.; Steenson K.; Gabelova A.; Ertl P.; Dusinska M.; Nelson A.
Published in: Bioelectrochemistry, Issue 153, 2023, Page(s) 108467, ISSN 1567-5394
Publisher: Elsevier BV
DOI: 10.1016/j.bioelechem.2023.108467

Manually curated transcriptomics data collection for toxicogenomic assessment of engineered nanomaterials

Author(s): Laura Aliisa Saarimäki, Antonio Federico, Iseult Lynch, Anastasios G. Papadiamantis, Andreas Tsoumanis, Georgia Melagraki, Antreas Afantitis, Angela Serra & Dario Greco
Published in: Scientific data, Issue 8, 2021, Page(s) 49, ISSN 2052-4463
Publisher: Springer Nature Limited
DOI: 10.1038/s41597-021-00808-y

Remediation of Water Using a Nanofabricated Cellulose Membrane Embedded with Silver Nanoparticles

Author(s): Shad S.; Lynch I.; Shah S.W.H.; Bashir N.
Published in: Membranes, Issue 12, 11, 2022, Page(s) 1035, ISSN 2077-0375
Publisher: Molecular Diversity Preservation International
DOI: 10.3390/membranes12111035

Design of cryogel based CNTs-anchored polyacrylonitrile honeycomb film with ultra-high S-NZVI incorporation for enhanced synergistic reduction of Cr(VI)

Author(s): Yang K.; Wang X.; Lynch I.; Guo Z.; Zhang P.; Wu L.; Ma J.
Published in: Journal of Hazardous Materials, Issue 442, 2023, Page(s) 129923, ISSN 0304-3894
Publisher: Elsevier BV
DOI: 10.1016/j.jhazmat.2022.129923

Risk Governance of Emerging Technologies Demonstrated in Terms of its Applicability to Nanomaterials

Author(s): Panagiotis Isigonis, Antreas Afantitis, Dalila Antunes, Alena Bartonova, Ali Beitollahi, Nils Bohmer, Evert Bouman, Qasim Chaudhry, Mihaela Roxana Cimpan, Emil Cimpan, Shareen Doak, Damien Dupin, Doreen Fedrigo, Valérie Fessard, Maciej Gromelski, Arno C. Gutleb, Sabina Halappanavar, Peter Hoet, Nina Jeliazkova, Stéphane Jomini, Sabine Lindner, Igor Linkov, Eleonora Marta Longhin, Iseult Lynch, I
Published in: Small, Issue 16/36, 2020, Page(s) 2003303, ISSN 1613-6810
Publisher: Wiley - V C H Verlag GmbbH & Co.
DOI: 10.1002/smll.202003303

Nextcast: A software suite to analyse and model toxicogenomics data

Author(s): AngelaSerra, Laura Aliisa Saarimäki, Alisa Pavel, Giusy del Giudice, Michele Fratello, Luca Cattelani, Antonio Federico, Omar Laurino, Veer Singh Marwah, Vittorio Fortino, Giovanni Scala, Pia Anneli Sofia Kinaret, Dario Greco
Published in: Computational and Structural Biotechnology Journal, Issue 20, 2022, Page(s) 1413-1426, ISSN 2001-0370
Publisher: Elsevier
DOI: 10.1016/j.csbj.2022.03.014

Construction of urchin-like core-shell Fe/Fe2O3@UiO-66 hybrid for effective tetracycline reduction and photocatalytic oxidation

Author(s): Wang X.; Jiang M.; Lynch I.; Guo Z.; Zhang P.; Wu L.; Ma J.
Published in: Environmental Pollution, Issue 336, 2023, Page(s) 122280, ISSN 0269-7491
Publisher: Pergamon Press Ltd.
DOI: 10.1016/j.envpol.2023.122280

ELIXIR and Toxicology: a community in development

Author(s): Marvin Martens; Rob Stierum; Emma L. Schymanski; Chris T. Evelo; Reza Aalizadeh; Hristo Aladjov; Kasia Arturi; Karine Audouze; Pavel Babica; Karel Berka; Jos Bessems; Ludek Blaha; Evan E Bolton; Montserrat Cases; Dimitrios Damalas; Kirtan Dave; Marco Dilger; Thomas Exner; Daan P. Geerke; Roland C. Grafström; Alasdair J. G. Gray; John M. Hancock; Henner Hollert; Nina Jeliazkova; Danyel Jennen; Fab
Published in: F1000 Research, Issue 10, 2021, Page(s) 1129, ISSN 2046-1402
Publisher: F1000 Research Ltd.
DOI: 10.12688/f1000research.74502.1

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

Representing and describing nanomaterials in predictive nanoinformatics

Author(s): Wyrzykowska E.; Mikolajczyk A.; Lynch I.; Jeliazkova N.; Kochev N.; Sarimveis H.; Doganis P.; Karatzas P.; Afantitis A.; Melagraki G.; Serra A.; Greco D.; Subbotina J.; Lobaskin V.; Bañares M.A.; Valsami-Jones E.; Jagiello K.; Puzyn T.
Published in: Nature Nanotechnology, Issue 17, 9, 2022, Page(s) 924-932, ISSN 1748-3387
Publisher: Nature Publishing Group
DOI: 10.1038/s41565-022-01173-6

Genotoxicity of Nanomaterials: Advanced In VitroModels and High Throughput Methods for HumanHazard Assessment—A Review

Author(s): Yvonne Kohl, Elise Rundén-Pran, Espen Mariussen, Michelle Hesler, Naouale El Yamani, Eleonora Marta Longhin and Maria Dusinska
Published in: NANOMATERIALS, 2020, ISSN 2079-4991
Publisher: MDPI

NanoMixHamster: a web-based tool for predicting cytotoxicity of TiO2-based multicomponent nanomaterials toward Chinese hamster ovary (CHO-K1) cells

Author(s): Stoliński F.; Rybińska-Fryca A.; Gromelski M.; Mikolajczyk A.; Puzyn T.
Published in: Nanotoxicology, Issue 16, 3, 2022, Page(s) 276 289, ISSN 1743-5390
Publisher: Informa Healthcare
DOI: 10.1080/17435390.2022.2080609

Apellis: An online tool for read-across model development

Author(s): Dimitra-Danai Varsou, Haralambos Sarimveis
Published in: Computational Toxicology, Issue 17, 2020, Page(s) 100146, ISSN 2468-1113
Publisher: Elsevier
DOI: 10.1016/j.comtox.2020.100146

An ancestral molecular response to nanomaterial particulates

Author(s): G. del Giudice, A. Serra, L. A. Saarimäki, K. Kotsis, I. Rouse, S. A. Colibaba, K. Jagiello, A. Mikolajczyk, M. Fratello, A. G. Papadiamantis, N. Sanabria, M. E. Annala, J. Morikka, P. A. S. Kinaret, E. Voyiatzis, G. Melagraki, A. Afantitis, K. Tämm, T. Puzyn, M. Gulumian, V. Lobaskin, I. Lynch, A. Federico & D. Greco
Published in: Nature Nanotechnology, Issue 18, 2023, Page(s) 957-966, ISSN 1748-3387
Publisher: Nature Publishing Group
DOI: 10.1038/s41565-023-01393-4

1,3-Dimethyl-imidazolium dimethyl phosphate ([MMIM]+[DMP]−) analyzed by XPS and HAXPES

Author(s): Xenia Knigge; Jörg Radnik
Published in: Crossref, Issue 37, 2023, ISSN 1055-5269
Publisher: AVS Science and Technology Society
DOI: 10.1116/6.0002297

Toxicogenomics analysis of dynamic dose-response in macrophages highlights molecular alterations relevant for multi-walled carbon nanotube-induced lung fibrosis

Author(s): Laura A. Saarimäki. Pia A.S. Kinaret, Giovanni Scala, Giusy del Giudice, Antonio Federico, Angela Serra, Dario Greco
Published in: NanoImpact, Issue 20, 2020, Page(s) 100274, ISSN 2452-0748
Publisher: Elsevier
DOI: 10.1016/j.impact.2020.100274

Stress Response and Nutrient Homeostasis in Lettuce (Lactuca sativa) Exposed to Graphene Quantum Dots Are Modulated by Particle Surface Functionalization.

Author(s): Peng Zhang; Xinyue Wu; Zhiling Guo; Xiaonan Yang; Xiangang Hu; Iseult Lynch
Published in: Advanced Biology, Issue 1, 2021, ISSN 2701-0198
Publisher: Wiley-VCH GmbH
DOI: 10.1002/adbi.202000778

Multigenerational Exposure to Nano‐TiO2 Induces Ageing as a Stress Response Mitigated by Environmental Interactions

Author(s): Laura-Jayne A. Ellis; Stephen Kissane; Elijah Hoffman; Eugenia Valsami-Jones; James B. Brown; James B. Brown; John K. Colbourne; Iseult Lynch
Published in: Advanced NanoBiomed Research, Vol 1, Iss 6, Pp n/a-n/a (2021), Issue 1, 2021, ISSN 2699-9307
Publisher: Wiley-VCH GmbH
DOI: 10.1002/anbr.202000083

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; Iseult Lynch
Published in: Environmental Science: Nano, Issue 7, 2020, Page(s) 3343-3359, ISSN 2051-8161
Publisher: Royal Society of Chemistry
DOI: 10.1039/d0en00625d

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

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

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.; Himly M.
Published in: Nanotoday, Issue 46, 2022, Page(s) 101561, ISSN 1748-0132
Publisher: Elsevier BV
DOI: 10.1016/j.nantod.2022.101561

The alamar blue assay in the context of safety testing of nanomaterials

Author(s): Longhin E.M.; El Yamani N.; Rundén-Pran E.; Dusinska M.
Published in: Frontiers in Toxicology, Issue 4, 2022, Page(s) 981701, ISSN 2673-3080
Publisher: Frontiers
DOI: 10.3389/ftox.2022.981701

Current Approaches and Techniques in Physiologically Based Pharmacokinetic (PBPK) Modelling of Nanomaterials

Author(s): Wells Utembe, Harvey Clewell, Natasha Sanabria, Philip Doganis, Mary Gulumian
Published in: Nanomaterials, Issue 10/7, 2020, Page(s) 1267, ISSN 2079-4991
Publisher: MDPI
DOI: 10.3390/nano10071267

Using the Isalos platform to develop a (Q)SAR model that predicts metal oxide toxicity utilizing facet-based electronic, image analysis-based, and periodic table derived properties as descriptors

Author(s): M. M. Thwala; A. Afantitis; A. G. Papadiamantis; A. Tsoumanis; G. Melagraki; L. N. Dlamini; C. N. M. Ouma; P. Ramasami; R. Harris; T. Puzyn; N. Sanabria; I. Lynch; M. Gulumian
Published in: Structural Chemistry, Issue 33, 2021, Page(s) 527–538, ISSN 1572-9001
Publisher: Springer
DOI: 10.1007/s11224-021-01869-w

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: Journal of Chemical Information and Modeling, 2021, ISSN 1549-9596
Publisher: American Chemical Society
DOI: 10.1021/acs.jcim.1c00199

The potential of a data centred approach & knowledge graph data representation in chemical safety and drug design

Author(s): Pavel A.; Saarimäki L.A.; Möbus L.; Federico A.; Serra A.; Greco D.
Published in: Computational and Structural Biotechnology Journal, Issue 20, 2022, Page(s) 4837 4849, ISSN 2001-0370
Publisher: Elsevier
DOI: 10.1016/j.csbj.2022.08.061

Uncertainties in the antibacterial mechanisms of graphene family materials

Author(s): Zhang P.; Guo Z.; Chen C.; Lynch I.
Published in: Nano Today, Issue 43, 2022, Page(s) 101436, ISSN 1748-0132
Publisher: Elsevier BV
DOI: 10.1016/j.nantod.2022.101436

Green synthesis of metal-based nanoparticles for sustainable agriculture

Author(s): Jiang Y.; Zhou P.; Zhang P.; Adeel M.; Shakoor N.; Li Y.; Li M.; Guo M.; Zhao W.; Lou B.; Wang L.; Lynch I.; Rui Y.
Published in: Environmental Pollution, Issue 309, 2022, Page(s) 119755, ISSN 0269-7491
Publisher: Pergamon Press Ltd.
DOI: 10.1016/j.envpol.2022.119755

Structure-activity prediction networks (SAPNets): a step beyond Nano-QSAR for effective implementation of the safe-by-design concept.

Author(s): Anna Rybińska-Fryca; Alicja Mikolajczyk; Tomasz Puzyn
Published in: Nanoscale, Issue 1, 2020, ISSN 2040-3372
Publisher: Royal Society of Chemistry
DOI: 10.1039/d0nr05220e

Atomistic Molecular Dynamics Simulations of Lipids Near TiO2 Nanosurfaces

Author(s): Mikhail Ivanov, Alexander P. Lyubartsev
Published in: Journal of Physical Chemistry B, Issue 125-29, 2021, Page(s) 8048–8059, ISSN 1520-5207
Publisher: ACS publications
DOI: 10.1021/acs.jpcb.1c04547

Passage of exogeneous fine particles from the lung into the brain in humans and animals

Author(s): Qi Y.; Wei S.; Xin T.; Huang C.; Pu Y.; Ma J.; Zhang C.; Liu Y.; Lynch I.; Liu S.
Published in: Proceedings of the National Academy of Sciences of the United States of America, Issue 119, 2022, Page(s) 26 e2117083119, ISSN 1091-6490
Publisher: PNAS
DOI: 10.1073/pnas.2117083119

Recent trends in carbon nanotube (CNT)-based biosensors for the fast and sensitive detection of human viruses: a critical review

Author(s): Hicham Meskher; Hussain Chaudhery Mustansar; Amrit Kumar Thakur; Ravishankar Sathyamurthy; Iseult Lynch; Punit Singh; Tan Kim Han; Rahman Saidur
Published in: Crossref, Issue 16, 2022, ISSN 2516-0230
Publisher: RSC
DOI: 10.1039/d2na00236a

Mass Cytometry and Single‐Cell RNA‐seq Profiling of the Heterogeneity in Human Peripheral Blood Mononuclear Cells Interacting with Silver Nanoparticles

Author(s): My Kieu Ha, Sook Jin Kwon, Jang‐Sik Choi, Nguyen Thanh Nguyen, Jaewoo Song, Yangsoon Lee, Young‐Eun Kim, Incheol Shin, Jin‐Wu Nam, Tae Hyun Yoon
Published in: Small, Issue 16/21, 2020, Page(s) 1907674, ISSN 1613-6810
Publisher: Wiley - V C H Verlag GmbbH & Co.
DOI: 10.1002/smll.201907674

Advances in De Novo Drug Design: From Conventional to Machine Learning Methods

Author(s): Mouchlis, V.D.; Afantitis, A.; Serra, A.; Fratello, M.; Papadiamantis, A.G.; Aidinis, V.; Lynch, I.; Greco, D.; Melagraki, G.
Published in: International Journal of Molecular Sciences, Issue 22, 2021, Page(s) 1676, ISSN 1422-0067
Publisher: Multidisciplinary Digital Publishing Institute (MDPI)
DOI: 10.3390/ijms22041676

Linking Nanomaterial-Induced Mitochondrial Dysfunction to Existing Adverse Outcome Pathways for Chemicals

Author(s): Murugadoss S.; Vrček I.V.; Schaffert A.; Paparella M.; Pem B.; Sosnowska A.; Stępnik M.; Martens M.; Willighagen E.L.; Puzyn T.; Cimpan M.R.; Lemaire F.; Mertens B.; Dusinska M.; Fessard V.; Hoet P.H.
Published in: Altex, Issue 40, 2023, Page(s) 4, ISSN 1868-596X
Publisher: Springer Spektrum
DOI: 10.14573/altex.2305011

Nano-enabled strategies to enhance biological nitrogen fixation

Author(s): Li M.; Gao L.; White J.C.; Haynes C.L.; O’Keefe T.L.; Rui Y.; Ullah S.; Guo Z.; Lynch I.; Zhang P.
Published in: Nature Nanotechnology, Issue 18, 7, 2023, Page(s) 688 691, ISSN 1748-3387
Publisher: Nature Publishing Group
DOI: 10.1038/s41565-023-01392-5

High-efficiency removal of tetracycline from water by electrolysis-assisted NZVI: mechanism of electron transfer and redox of iron

Author(s): Wang X.; Wang X.; Lynch I.; Ma J.
Published in: RSC Advances, Issue 13, 2023, ISSN 2046-2069
Publisher: Royal Society of Chemistry
DOI: 10.1039/d3ra00954h

Computationally prioritized drugs inhibit SARS-CoV-2 infection and syncytia formation

Author(s): Angela Serra, Michele Fratello, Antonio Federico, Ravi Ojha, Riccardo Provenzani, Ervin Tasnadi, Luca Cattelani, Giusy del Giudice, Pia A S Kinaret, Laura A Saarimäki, Alisa Pavel, Suvi Kuivanen, Vincenzo Cerullo, Olli Vapalahti, Peter Horvath, Antonio Di Lieto, Jari Yli-Kauhaluoma, Giuseppe Balistreri, Dario Greco
Published in: Briefings in Bioinformatics, Issue 23, 2021, Page(s) bbab507, ISSN 1477-4054
Publisher: Oxford University Press
DOI: 10.1093/bib/bbab507

FAIR assessment tools: evaluating use and performance

Author(s): Krans N.A.; Ammar A.; Nymark P.; Willighagen E.L.; Bakker M.I.; Quik J.T.K.
Published in: NanoImpact, Issue 27, 2022, Page(s) 100402, ISSN 2452-0748
Publisher: Elsevier
DOI: 10.1016/j.impact.2022.100402

Exceptional photo-elimination of antibiotic by a novel Z-scheme heterojunction catalyst composed of nanoscale zero valent iron embedded with carbon quantum dots (CQDs)-black TiO2

Author(s): Wu X.; Wang X.; Lynch I.; Guo Z.; Zhang P.; Wu L.; Ning P.; Ren N.
Published in: Journal of Hazardous Materials, Issue 460, 2023, Page(s) 132323, ISSN 0304-3894
Publisher: Elsevier BV
DOI: 10.1016/j.jhazmat.2023.132323

Toxicogenomics Data for Chemical Safety Assessment and Development of New Approach Methodologies: An Adverse Outcome Pathway-Based Approach

Author(s): Saarimäki L.A.; Morikka J.; Pavel A.; Korpilähde S.; del Giudice G.; Federico A.; Fratello M.; Serra A.; Greco D.
Published in: Advanced Science, Issue 10, 2, 2023, Page(s) 2203984, ISSN 2198-3844
Publisher: Wiley
DOI: 10.1002/advs.202203984

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 Rybińska-Fryca; Maciej Gromelski; Tomasz Puzyn; Egon Willighagen; Blair Johnston; Mary Gulumian; Marianne Matzke; Amaia Green Etxabe; Nathan Bossa; Angela Serra; Irene Liampa; Stacey L. Harper; Kaido Tämm; Alexander Cø Jensen; Pekka Ko
Published in: Nanomaterials, Issue 12, 2020, Page(s) 2493, ISSN 2079-4991
Publisher: MDPI
DOI: 10.26181/5fd82a0837ea2

Transcriptomics in Toxicogenomics, Part II: Preprocessing and Differential Expression Analysis for High Quality Data

Author(s): Federico, A.; Serra, A.; Ha, M.K.; Kohonen, P.; Choi, J.-S.; Liampa, I.; Nymark, P.; Sanabria, N.; Cattelani, L.; Fratello, M.; Kinaret, P.A.S.; Jagiello, K.; Puzyn, T.; Melagraki, G.; Gulumian, M.; Afantitis, A.; Sarimveis, H.; Yoon, T.-H.; Grafström, R.; Greco, D.
Published in: Nanomaterials, Issue 10, 2020, Page(s) 903, ISSN 2079-4991
Publisher: MDPI
DOI: 10.3390/nano10050903

Nickel Oxide Nanoparticles Improve Soybean Yield and Enhance Nitrogen Assimilation

Author(s): Zhou P.; Jiang Y.; Adeel M.; Shakoor N.; Zhao W.; Liu Y.; Li Y.; Li M.; Azeem I.; Rui Y.; Tan Z.; White J.C.; Guo Z.; Lynch I.; Zhang P.
Published in: Environmental Science and Technology, Issue 57, 19, 2023, Page(s) 7547 7558, ISSN 0013-936X
Publisher: American Chemical Society
DOI: 10.1021/acs.est.3c00959

Predicting Cytotoxicity of Metal Oxide Nanoparticles Using Isalos Analytics Platform

Author(s): Papadiamantis, A.G.; Jänes, J.; Voyiatzis, E.; Sikk, L.; Burk, J.; Burk, P.; Tsoumanis, A.; Ha, M.K.; Yoon, T.H.; Valsami-Jones, E.; Lynch, I.; Melagraki, G.; Tämm, K.; Afantitis, A.
Published in: Nanomaterials, Issue 2020, 2020, Page(s) 2017, ISSN 2079-4991
Publisher: MDPI
DOI: 10.3390/nano10102017

Strategies to improve photocatalytic activity of nanoscale zero valent iron decorated MoS2: Construction of novel S-scheme nanoflower heterojunction with advanced visible-light degradation of tetracycline

Author(s): Wu X.; Wang X.; Lynch I.; Guo Z.; Zhang P.; Wu L.; Deng Y.; Xie Y.; Ning P.; Ren N.
Published in: Journal of Cleaner Production, Issue 388, 2023, Page(s) 135865, ISSN 0959-6526
Publisher: Elsevier BV
DOI: 10.1016/j.jclepro.2023.135865

Development of Deep Learning Models for Predicting the Effects of Exposure to Engineered Nanomaterials on Daphnia magna

Author(s): Pantelis Karatzas, Georgia Melagraki, Laura‐Jayne A. Ellis, Iseult Lynch, Dimitra‐Danai Varsou, Antreas Afantitis, Andreas Tsoumanis, Philip Doganis, Haralambos Sarimveis
Published in: Small, Issue 16/36, 2020, Page(s) 2001080, ISSN 1613-6810
Publisher: Wiley - V C H Verlag GmbbH & Co.
DOI: 10.1002/smll.202001080

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, Vladimir Lobaskin
Published in: Physical Chemistry Chemical Physics, Issue 23, 2021, Page(s) 13473-13482, ISSN 1463-9084
Publisher: Royal Society of Chemistry
DOI: 10.1039/d1cp01116b

Expanding adverse outcome pathways towards one health models for nanosafety

Author(s): Saarimäki L.A.; del Giudice G.; Greco D.
Published in: Frontiers in Toxicology, Issue 5, 2023, Page(s) 1176745, ISSN 2673-3080
Publisher: Frontiers
DOI: 10.3389/ftox.2023.1176745

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

In Silico Prediction of Protein Adsorption Energy on Titanium Dioxide and Gold Nanoparticles

Author(s): Shada Ali Alsharif; David A. Power; Ian Rouse; Vladimir Lobaskin
Published in: Nanomaterials, Issue 10, 2020, Page(s) 1967, ISSN 2079-4991
Publisher: MDPI
DOI: 10.3390/nano10101967

TinderMIX: Time-dose integrated modelling of toxicogenomics data

Author(s): Angela Serra, Michele Fratello, Giusy del Giudice, Laura Aliisa Saarimäki, Michelangelo Paci, Antonio Federico, Dario Greco
Published in: GigaScience, Issue 9/5, 2020, ISSN 2047-217X
Publisher: Oxford Academic
DOI: 10.1093/gigascience/giaa055

NanoSolveIT Project: Driving nanoinformatics research to develop innovative and integrated tools for in silico nanosafety assessment

Author(s): Antreas Afantitis, Georgia Melagraki, Panagiotis Isigonis, Andreas Tsoumanis, Dimitra Danai Varsou, Eugenia Valsami-Jones, Anastasios Papadiamantis, Laura-Jayne A. Ellis, Haralambos Sarimveis, Philip Doganis, Pantelis Karatzas, Periklis Tsiros, Irene Liampa, Vladimir Lobaskin, Dario Greco, Angela Serra, Pia Anneli Sofia Kinaret, Laura Aliisa Saarimäki, Roland Grafström, Pekka Kohonen, Penny Nyma
Published in: Computational and Structural Biotechnology Journal, Issue 18, 2020, Page(s) 583-602, ISSN 2001-0370
Publisher: Elsevier
DOI: 10.1016/j.csbj.2020.02.023

Principles and requirements for nanomaterial representations to facilitate machine processing and cooperation with nanoinformatics tools

Author(s): Blekos K.; Chairetakis K.; Lynch I.; Marcoulaki E.
Published in: Journal of Cheminformatics, Issue 15, 1, 2023, Page(s) 44, ISSN 1758-2946
Publisher: Chemistry Central
DOI: 10.1186/s13321-022-00669-6

From principles to reality. FAIR implementation in the nanosafety community

Author(s): Dumit V.I.; Ammar A.; Bakker M.I.; Bañares M.A.; Bossa C.; Costa A.; Cowie H.; Drobne D.; Exner T.E.; Farcal L.; Friedrichs S.; Furxhi I.; Grafström R.; Haase A.; Himly M.; Jeliazkova N.; Lynch I.; Maier D.; Noorlander C.W.; Shin H.K.; Soler-Illia G.J.A.A.; Suarez-Merino B.; Willighagen E.; Nymark P.
Published in: Nano Today, Issue 51, 2023, Page(s) 101923, ISSN 1748-0132
Publisher: Elsevier BV
DOI: 10.1016/j.nantod.2023.101923

Extra-Pulmonary Translocation of Exogenous Ambient Nanoparticles in the Human Body

Author(s): Qi Y.; Chen Y.; Xia T.; Lynch I.; Liu S.
Published in: ACS Nano, Issue 17, 2023, Page(s) 1, 12-19, ISSN 1936-0851
Publisher: American Chemical Society
DOI: 10.1021/acsnano.2c09299

Prospects and challenges for FAIR toxicogenomics data

Author(s): Laura A. Saarimäki, Georgia Melagraki, Antreas Afantitis, Iseult Lynch & Dario Greco
Published in: Nature nanotechnology, Issue 17, 2022, Page(s) 17-18, ISSN 1748-3395
Publisher: Springer Nature Limited
DOI: 10.1038/s41565-021-01049-1

Lack of mutagenicity of TiO2 nanoparticles in vitro despite cellular and nuclear uptake

Author(s): El Yamani N.; Rubio L.; García-Rodríguez A.; Kažimírová A.; Rundén-Pran E.; Magdalena B.; Marcos R.; Dusinska M.
Published in: Mutation Research - Genetic Toxicology and Environmental Mutagenesis, Issue 882, 2022, Page(s) 503545, ISSN 1383-5718
Publisher: Elsevier BV
DOI: 10.1016/j.mrgentox.2022.503545

Metadata stewardship in nanosafety research: learning from the past, preparing for an “on-the-fly” FAIR future

Author(s): Exner T.E.; Papadiamantis A.G.; Melagraki G.; Amos J.D.; Bossa N.; Gakis G.P.; Charitidis C.A.; Cornelis G.; Costa A.L.; Doganis P.; Farcal L.; Friedrichs S.; Furxhi I.; Klaessig F.C.; Lobaskin V.; Maier D.; Rumble J.; Sarimveis H.; Suarez-Merino B.; Vázquez S.; Wiesner M.R.; Afantitis A.; Lynch I.
Published in: Frontiers in Physics, Issue 11, 2023, Page(s) 1233879, ISSN 2296-424X
Publisher: Frontiers
DOI: 10.3389/fphy.2023.1233879

In silico identification and evaluation of natural products as potential tumor necrosis factor function inhibitors using advanced enalos asclepios KNIME nodes

Author(s): Papadopoulou D.; Drakopoulos A.; Lagarias P.; Melagraki G.; Kollias G.; Afantitis A.
Published in: International Journal of Molecular Sciences, Issue 22, 2021, Page(s) 10220, ISSN 1422-0067
Publisher: Multidisciplinary Digital Publishing Institute (MDPI)
DOI: 10.3390/ijms221910220

Transcriptomics in Toxicogenomics, Part III: Data Modelling for Risk Assessment

Author(s): Angela Serra, Michele Fratello, Luca Cattelani, Irene Liampa, Georgia Melagraki, Pekka Kohonen, Penny Nymark, Antonio Federico, Pia Anneli Sofia Kinaret, Karolina Jagiello, My Kieu Ha, Jang-Sik Choi, Natasha Sanabria, Mary Gulumian, Tomasz Puzyn, Tae-Hyun Yoon, Haralambos Sarimveis, Roland Grafström, Antreas Afantitis, Dario Greco
Published in: Nanomaterials, Issue 10/4, 2020, Page(s) 708, ISSN 2079-4991
Publisher: MDPI
DOI: 10.3390/nano10040708

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, Issue 16/21, 2020, Page(s) 1906588, ISSN 1613-6810
Publisher: Wiley - V C H Verlag GmbbH & Co.
DOI: 10.1002/smll.201906588

Daphnia as a model organism to probe biological responses to nanomaterials—from individual to population effects via adverse outcome pathways

Author(s): Katie Reilly; Laura-Jayne A. Ellis; Hossein Hayat Davoudi; Suffeiya Supian; Marcella T. Maia; Gabriela H. Silva; Zhiling Guo; Diego Stéfani T. Martinez; Iseult Lynch
Published in: Crossref, Issue 16, 2023, ISSN 2673-3080
Publisher: Frontier
DOI: 10.3389/ftox.2023.1178482

A curated gene and biological system annotation of adverse outcome pathways related to human health

Author(s): Laura Aliisa Saarimäki, Michele Fratello, Alisa Pavel, Seela Korpilähde, Jenni Leppänen, Angela Serra, Dario Greco
Published in: Scientific Data, Issue 10, 2023, Page(s) 409, ISSN 2052-4463
Publisher: Springer Nature Limited
DOI: 10.1038/s41597-023-02321-w

Dynamic intracellular exchange of nanomaterials’ protein corona perturbs proteostasis and remodels cell metabolism

Author(s): Cai R.; Ren J.; Guo M.; Wei T.; Liu Y.; Xie C.; Zhang P.; Guo Z.; Chetwynd A.J.; Ke P.C.; Lynch I.; Chen C.
Published in: Proceedings of the National Academy of Sciences of the United States of America, Issue 119, 2022, Page(s) 23, e2200363119, ISSN 1091-6490
Publisher: National Academy of Science
DOI: 10.1073/pnas.2200363119

A hard-sphere model of protein corona formation on spherical and cylindrical nanoparticles

Author(s): Ian Rouse, Vladimir Lobaskin
Published in: Biophysical journal, Issue 20, 2021, Page(s) 4457-4471, ISSN 1542-0086
Publisher: CellPress
DOI: 10.1016/j.bpj.2021.09.002

Transcriptomics in Toxicogenomics, Part I: Experimental Design, Technologies, Publicly Available Data, and Regulatory Aspects

Author(s): Pia Anneli Sofia Kinaret, Angela Serra, Antonio Federico, Pekka Kohonen, Penny Nymark, Irene Liampa, My Kieu Ha, Jang-Sik Choi, Karolina Jagiello, Natasha Sanabria, Georgia Melagraki, Luca Cattelani, Michele Fratello, Haralambos Sarimveis, Antreas Afantitis, Tae-Hyun Yoon, Mary Gulumian, Roland Grafström, Tomasz Puzyn, Dario Greco
Published in: Nanomaterials, Issue 10/4, 2020, Page(s) 750, ISSN 2079-4991
Publisher: MDPI
DOI: 10.3390/nano10040750

In silico prediction of protein binding affinities onto core-shell PEGylated noble metal nanoparticles for rational design of drug nanocarriers

Author(s): Subbotina J.; Rouse I.; Lobaskin V.
Published in: Nanoscale, Issue 15, 2023, ISSN 2040-3372
Publisher: RSC
DOI: 10.1039/d3nr03264g

WikiPathways: connecting communities.

Author(s): Martens, Marvin; Ammar, Ammar; Riutta, Anders; Waagmeester, Andra; Slenter, Denise N; Hanspers, Kristina; A. Miller, Ryan; Digles, Daniela; Lopes, Elisson N; Ehrhart, Friederike; Dupuis, Lauren J; Winckers, Laurent A; Coort, Susan L; Willighagen, Egon L; Evelo, Chris T; Pico, Alexander R; Kutmon, Martina
Published in: Nucleic Acids Research, Issue 49, 2020, Page(s) D613–D621, ISSN 1362-4962
Publisher: Oxford University Press
DOI: 10.1093/nar/gkaa1024

Defining the Surface Oxygen Threshold That Switches the Interaction Mode of Graphene Oxide with Bacteria

Author(s): Guo Z.; Zhang P.; Xie C.; Voyiatzis E.; Faserl K.; Chetwynd A.J.; Monikh F.A.; Melagraki G.; Zhang Z.; Peijnenburg W.J.G.M.; Afantitis A.; Chen C.; Lynch I.
Published in: ACS nano, Issue 17, 7,, 2023, Page(s) 6350–6361, ISSN 1936-0851
Publisher: American Chemical Society
DOI: 10.1021/acsnano.2c10961

Homogeneous dispersion of amorphous nanoscale zero-valent iron supported on chlorella-derived biochar: In-situ synthesis and application mechanism for Cr(VI) removal over a wide pH range

Author(s): Deng Y.; Wang X.; Lynch I.; Guo Z.; Zhang P.; Wu L.; Wu X.; Li T.
Published in: Separation and Purification Technology, Issue 330, 2024, Page(s) 125207, ISSN 1383-5866
Publisher: Pergamon Press Ltd.
DOI: 10.1016/j.seppur.2023.125207

Improved freshwater generation via hemispherical solar desalination unit using paraffin wax as phase change material encapsulated in waste aluminium cans

Author(s): Thamarai Kannan B.; Madhu B.; Kabeel A.E.; Thakur A.K.; Velraj R.; Lynch I.; Saidur R.; Sathyamurthy R.
Published in: Desalination, Issue 538, 2022, Page(s) 115907, ISSN 1873-4464
Publisher: elsevier
DOI: 10.1016/j.desal.2022.115907

Increase in the active ingredients of traditional Chinese medicine <i>Isatis indigotica</i> through iron nanoparticles supplementation <i>versus</i> carbon nanotubes: a comparative study

Author(s): Pingfan Zhou; Binbin Long; Ruisi Wang; Yaqi Jiang; Weichen Zhao; Yuanbo Li; Mingshu Li; Zhiling Guo; Peng Zhang; Yukui Rui; Iseult Lynch
Published in: Crossref, Issue 37, 2022, ISSN 2051-8161
Publisher: Royal Society of Chemistry
DOI: 10.1039/d2en00488g

Nanotechnology and artificial intelligence to enable sustainable and precision agriculture

Author(s): Peng Zhang, Zhiling Guo, Sami Ullah, Georgia Melagraki, Antreas Afantitis & Iseult Lynch
Published in: Nature plants, Issue 7, 2021, Page(s) 864–876, ISSN 2055-0278
Publisher: Springer Nature Limited
DOI: 10.1038/s41477-021-00946-6

Daphnia magna and mixture toxicity with nanomaterials – Current status and perspectives in data-driven risk prediction

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: Nano Today, Issue 43, 2022, Page(s) 101430, ISSN 1748-0132
Publisher: Elsevier BV
DOI: 10.1016/j.nantod.2022.101430

Emerging investigator series: perspectives on toxicokinetics of nanoscale plastic debris in organisms

Author(s): Abdolahpur Monikh F.; Vijver M.G.; Kortet R.; Lynch I.; Peijnenburg W.J.G.M.
Published in: Environmental Science: Nano, Issue 9, 2022, Page(s) 1566-1577, ISSN 2051-8161
Publisher: RSC
DOI: 10.1039/d1en00425e

Importance of Surface Topography in Both Biological Activity and Catalysis of Nanomaterials: Can Catalysis by Design Guide Safe by Design?

Author(s): Gulumian, M.; Andraos, C.; Afantitis, A.; Puzyn, T.; Coville, N.J.
Published in: International Journal of Molecular Sciences, Issue 22, 2021, Page(s) 8347, ISSN 1422-0067
Publisher: Multidisciplinary Digital Publishing Institute (MDPI)
DOI: 10.3390/ijms22158347

Reliable Surface Analysis Data of Nanomaterials in Support of Risk Assessment Based on Minimum Information Requirements.

Author(s): Jörg Radnik; Reinhard Kersting; Birgit Hagenhoff; Francesca Bennet; Dmitri Ciornii; Penny Nymark; Roland C. Grafström; Vasile-Dan Hodoroaba
Published in: Nanomaterials, Issue 11, 2021, Page(s) 639, ISSN 2079-4991
Publisher: MDPI
DOI: 10.3390/nano11030639

Toward Rigorous Materials Production: New Approach Methodologies Have Extensive Potential to Improve Current Safety Assessment Practices

Author(s): Penny Nymark, Martine Bakker, Susan Dekkers, Remy Franken, Wouter Fransman, Amaia García‐Bilbao, Dario Greco, Mary Gulumian, Niels Hadrup, Sabina Halappanavar, Vesa Hongisto, Karin Sørig Hougaard, Keld Alstrup Jensen, Pekka Kohonen, Antti Joonas Koivisto, Miikka Dal Maso, Thies Oosterwijk, Mikko Poikkimäki, Isabel Rodriguez‐Llopis, Rob Stierum, Jorid Birkelund Sørli, Roland Grafström
Published in: Small, Issue 16/6, 2020, Page(s) 1904749, ISSN 1613-6810
Publisher: Wiley - V C H Verlag GmbbH & Co.
DOI: 10.1002/smll.201904749

Computational modelling of bionano interface

Author(s): Lobaskin V.; Subbotina J.; Rouse I.
Published in: Europhysics Letters, Issue 143, 2023, Page(s) 5, ISSN 0295-5075
Publisher: EDP Sciences
DOI: 10.1209/0295-5075/acf33f

Towards an in silico integrated approach for testing and assessment of nanomaterials: from predicted indoor air concentrations to lung dose and biodistribution

Author(s): P. Tsiros, N. Cheimarios, A. Tsoumanis, A. C. Ø. Jensen, G. Melagraki, I. Lynch, H. Sarimveis and A. Afantitis
Published in: Environmental Science: Nano, Issue 9, 2019, Page(s) 13757-13764, ISSN 2051-8161
Publisher: RSC publishing
DOI: 10.1039/d1en00956g

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

Author(s): Cai S.; Zhang P.; Guo Z.; Jin F.; Wang J.; Song Z.; Nadezhda T.; Lynch I.; Dang X.
Published in: Environmental Science: Nano, Issue 9, 2022, Page(s) 1315 1329, ISSN 2051-8161
Publisher: RSC
DOI: 10.1039/d1en01211h

Biomarkers of nanomaterials hazard from multi-layer data

Author(s): Vittorio Fortino, Pia Anneli Sofia Kinaret, Michele Fratello, Angela Serra, Laura Aliisa Saarimäki, Audrey Gallud, Govind Gupta, Gerard Vales, Manuel Correia, Omid Rasool, Jimmy Ytterberg, Marco Monopoli, Tiina Skoog, Peter Ritchie, Sergio Moya, Socorro Vázquez-Campos, Richard Handy, Roland Grafström, Lang Tran, Roman Zubarev, Riitta Lahesmaa, Kenneth Dawson, Katrin Loeschner, Erik Husfeldt Lar
Published in: Nature Communications, Issue 13, 2022, Page(s) 3798, ISSN 2041-1723
Publisher: Nature Publishing Group
DOI: 10.1038/s41467-022-31609-5

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

Author(s): Anastasios G. Papadiamantis, Antreas Afantitis, Andreas Tsoumanis, Eugenia Valsami-Jones, Iseult Lynch, Georgia Melagraki
Published in: NanoImpact, Issue 22, 2021, Page(s) 100308, ISSN 2452-0748
Publisher: Elsevier
DOI: 10.1016/j.impact.2021.100308

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, 2021, Page(s) 202100637, ISSN 2701-0198
Publisher: Wiley-VCH GmbH
DOI: 10.1002/adbi.202100637

MaNGA: a novel multi-niche multi-objective genetic algorithm for QSAR modelling

Author(s): Angela Serra, Serli Önlü, Paola Festa, Vittorio Fortino, Dario Greco
Published in: Bioinformatics, Issue 36, 2020, Page(s) 145–153, ISSN 1460-2059
Publisher: Oxford University Press
DOI: 10.1093/bioinformatics/btz521

Exposure medium and particle ageing moderate the toxicological effects of nanomaterials to Daphnia magna over multiple generations: a case for standard test review?

Author(s): Laura-Jayne A. Ellis, Eugenia Valsami-Jones, Iseult Lynch
Published in: Environmental Science: Nano, Issue 7/4, 2020, Page(s) 1136-1149, ISSN 2051-8153
Publisher: Royal Society of Chemistry
DOI: 10.1039/d0en00049c

Covid-19 acute responses and possible long term consequences: What nanotoxicology can teach us

Author(s): Pia A.S.Kinaret, Giusy del Giudice, Dario Greco
Published in: Nanotoday, Issue 35, 2020, Page(s) 100945, ISSN 1748-0132
Publisher: Elsevier BV
DOI: 10.1016/j.nantod.2020.100945

Upconversion Nanomaterials in Bioimaging and Biosensor Applications and Their Biological Response

Author(s): Gerelkhuu Z.; Lee Y.-I.; Yoon T.H.
Published in: Nanomaterials, Issue 12, 2022, Page(s) 3470, ISSN 2079-4991
Publisher: MDPI
DOI: 10.3390/nano12193470

FAIR assessment of nanosafety data reusability with community standards

Author(s): Ammar Ammar; Chris Evelo; Egon Willighagen
Published in: Crossref, Issue 5, 2022, ISSN 2573-2293
Publisher: ChemRxiv
DOI: 10.26434/chemrxiv-2022-l8vk8

Correction: Recent trends in carbon nanotube (CNT)-based biosensors for the fast and sensitive detection of human viruses: a critical review

Author(s): Hicham Meskher; Hussain Chaudhery Mustansar; Amrit Kumar Thakur; Ravishankar Sathyamurthy; Iseult Lynch; Punit Singh; Tan Kim Han; Rahman Saidur
Published in: Crossref, Issue 3, 2023, ISSN 2516-0230
Publisher: RSC
DOI: 10.1039/d3na90097e

In Silico Characterization of Nanomaterials

Author(s): Colibaba A.; Kotsis K.; Lobaskin V.
Published in: World Congress on Recent Advances in Nanotechnology, Issue ICNNFC 170, 2022
Publisher: ICNNFC
DOI: 10.11159/icnnfc22.170

If you want to go far go together - Collaborative research supported by NanoCommons transnational access

Author(s): Iseult Lynch; Thomas Exner; Claus Svendsen; Irini Furxhi; Dieter Maier; Felice Simeone; Haralambos Sarimveis; Philip Doganis; Antreas Afantitis; Martin Himly
Published in: NanoCommons Nanoinformatics data services & tools, Issue 1, 2021
Publisher: NanoCommons
DOI: 10.5281/zenodo.5752072

Multi-Scale Modelling Of the Formation of the Nanoparticle-Protein Corona

Author(s): Rouse I.; Power D.; Poggio S.; Brandt E.; Lopez H.; Lyubartsev A.; Lobaskin V.
Published in: World Congress on Recent Advances in Nanotechnology, Issue ICNNFC 172, 2022
Publisher: ICNNFC
DOI: 10.11159/icnnfc22.172

Hamaker Constants for Bionano Interactions in Water

Author(s): Kotsis K.; Lobaskin V.
Published in: World Congress on Recent Advances in Nanotechnology, 2022
Publisher: ICNNFC
DOI: 10.11159/icnnfc22.171

Advanced Computational Modelling Of Interface Properties

Author(s): Konstantinos Kotsis
Published in: Proceedings of the 8th World Congress on Recent Advances in Nanotechnology (RAN'23), 2023
Publisher: ICNNFC
DOI: 10.11159/icnnfc23.164

Everything You Always Wanted to Know About Data Citations* (*But Were Afraid to Ask)

Author(s): Jeliazkova, Nina; Exner, Thomas; Willighagen, Egon
Published in: Joint workshop RiskGONE, NanoCommons, NanoSolveIT, 2020
Publisher: NanoSolveIT
DOI: 10.5281/zenodo.3648169

FAIR data assessment tools: an evaluation

Author(s): Ammar Ammar
Published in: DANS Data Trail Workshop, Issue 1, 2021
Publisher: UM
DOI: 10.5281/zenodo.5721388

The eNanoMapper Ontology v9.0: Semi-automated and Community-based Ontology Development

Author(s): Javier Millán Acosta; Egon Willighagen
Published in: Issue 61, 2023
Publisher: Maastricht University
DOI: 10.5281/zenodo.8032202

NanoSolveIT integration of tools for assessment of human and environmental exposure to nanomaterials

Author(s): Nikolaos Cheimarios, Sam Harrison, Alexander C.Ø Jensen, Pantelis Karatzas, Andreas Tsoumanis, Philip Doganis, Periklis Tsiros, David A. Winkler, Stephen Lofts, Keld A. Jensen, Haralambos Sarimveis, Antreas Afantitis, Iseult Lynch, Georgia Melagraki
Published in: Handbook of Functionalized Nanomaterials, 2021, Page(s) 81-120, ISBN 978-0-12-822415-1
Publisher: Elsevier
DOI: 10.1016/b978-0-12-822415-1.00001-9

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