Publications

Nature Portfolio:  “A gene regulation model reveals an ancestral adaptation response to particulate exposure triggered by nanomaterials”

2023

AUTHORS: 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.

MDPI:  “How Does the Study MD of pH-Dependent Exposure of Nanoparticles Affect Cellular Uptake of Anticancer Drugs?”

09/02/2023

AUTHORS: Selvaraj Sengottiyan, Alicja Mikolajczyk, Tomasz Puzyn 

Nano Today 48 (2023) 101735:  “Systems toxicology to advance human and environmental hazard assessment: A roadmap for advanced materials”

31/01/2023

AUTHORS: M.J.B. Amorim, W. Peijnenburg, D. Greco, L.A. Saarimäki, V.I. Dumit, A. Bahl, A. Haase, L. Tran, J. Hackermüller, S. Canzler and J.J. Scott-Fordsmand.

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

18/01/2023

AUTHORS: Selvaraj Sengottiyan, Alicja Mikolajczyk, Karolina Jagiełło, Marta Swirog, and Tomasz Puzyn

Int. J. Mol. Sci. 2022, 23(21), 13196:  “One Step before Synthesis: Structure–Property–Condition Relationship Models to Sustainable Design of Efficient TiO₂-Based Multicomponent Nanomaterials”

30/10/2022

AUTHORS: Alicja Mikolajczyk and Dawid Falkowski

Science Direct | “Predicting electrophoretic mobility of TiO₂, ZnO, and CeO₂ nanoparticles in natural waters: The importance of environment descriptors in nanoinformatics models“

20/09/2022

AUTHORS: Marta Swirog, Alicja Mikołajczyk, Karolina Jagiello, Jaak Jänes, Kaido Tämm, Tomasz Puzyn

Science Direct  “Predicting electrophoretic mobility of TiO₂, ZnO, and CeO₂ nanoparticles in natural waters: The importance of environment descriptors in nanoinformatics models“

18/06/2022

AUTHORS: Marta Swirog, Alicja Mikołajczyk, Karolina Jagiello, Jaak Jänes, Kaido Tämm, Tomasz Puzyn

Nanotoxicology 2022, VOL. 16, NO. 3, 276–289:  “NanoMixHamster: a web-based tool for predicting cytotoxicity of TiO2-based multicomponent nanomaterials toward Chinese hamster ovary (CHO-K1) cells”

17/06/2022

AUTHORS: Filip Stoliński, Anna Rybińska-Fryca, Maciej Gromelski, Alicja Mikolajczyk and Tomasz Puzyn.

SSRN: “Predicting Electrophoretic Mobility of Tio2, Zno and Ceo2 Nanoparticles in Natural Waters: The Importance of Environment Descriptors in Nanoinformatics Models”

07/04/2022

AUTHORS: Marta Swirog, Alicja Mikołajczyk, Karolina Jagiello, Jaak Jänes, Kaido Tämm, Tomasz Puzyn

Environmental Toxicology and Chemistry: “Meta-analysis of Bioaccumulation Data for Nondissolvable Engineered Nanomaterials in Freshwater Aquatic Organisms”

21/02/2022

AUTHORS: Zheng, Y.; Nowack, B.

Science Direct: “Effects of natural organic matter on the joint toxicity and accumulation of Cu nanoparticles and ZnO nanoparticles in Daphnia magna”

01/2022

AUTHORS: Qi Yu, Zhuang Wang, Guiyin Wang, Willie J. G. M. Peijnenburg, Martina G. Vijver

Nanomaterials 2021:  “A Multi-Scale Modelling of Aggregation of TiO2 Nanoparticle Suspensions in Water”

15/12/ 2021

AUTHORS: Giulia Mancardi, Matteo Alberghini, Neus Aguilera-Porta, Monica Calatayud, Pietro Asinari, Eliodoro Chiavazzo

Science Direct:  “Effects of natural organic matter on the joint toxicity and accumulation of Cu nanoparticles and ZnO nanoparticles in Daphnia magna“

28/10/2021

AUTHORS: Qi Yu, Zhuang Wang, Guiyin Wang, Willie J. G. M. Peijnenburg, Martina G. Vijver

Science Direct:  “Multiomics assessment in Enchytraeus crypticus exposed to Ag (nano)materials (Ag NM300K and AgNO3) – metabolomics, proteomics (& transcriptomics)”

01/10/2021

AUTHORS: Vera L. Maria, David Licha, Janeck J. Scott-Fordsmand, Christian G. Huber, and Mónica J. B. Amorim

Science Direct: “Alternative test methods for (nano)materials hazards assessment: Challenges and recommendations for regulatory preparedness“

10/2021

AUTHORS: Susana I.L. Gomes, Janeck J. Scott-Fordsmand and Monica J.B. Amorim

Nano Today:  “Alternative test methods for (nano)materials hazards assessment: Challenges and recommendations for regulatory preparedness“

10/2021

AUTHORS: Susana I.L. Gomes, Janeck J. Scott-Fordsmand and Monica J.B. Amorim

Science Direct: “Identification of Monotonic Trends in the Dose-response Relationship of Nanomaterial Toxicity Data using the R package NMTox“

24/09/2021

AUTHORS: Rahmasari Nur Azizah, Geert Verheyen, Sabine Van Miert and Ziv Shkedy

labAnimal: “Annelid genomes: Enchytraeus crypticus, a soil model for the innate (and primed) immune system”

06/09/2021

AUTHORS: Mónica J.B. Amorim, Yannick Gansemans, Susana I.L. Gomes, Filip Van Nieuwerburgh and Janeck J. Scott-Fordsmand

Science Direct: “Probing nano-QSAR to assess the interactions between carbon nanoparticles and a SARS-CoV-2 RNA fragment“

08/2021

AUTHORS: Fan Zhang, Zhuang Wang, Martina G. Vijver, Willie J.G.M. Peijnenburg

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

12/07/2021

AUTHORS: Ioannis Xiarchos, Athanasios K. Morozinis, Panagiotis Kavouras, Costas A. Charitidis

National Library of Medicine:  “Computer Simulations of the Dissociation Mechanism of Gleevec from Abl Kinase with Milestoning”

10/06/2021

AUTHORS: Narayan B, Buchete NV, Elber R.

Science Direct: “Multiomics assessment in Enchytraeus crypticus exposed to Ag nanomaterials (Ag NM300K) and ions (AgNO₃) – Metabolomics, proteomics (& transcriptomics)“

16/06/2021

AUTHORS: Vera L. Maria, David Licha, Janeck J. Scott-Fordsmand, Christian G. Huber, and Mónica J. B. Amorim

Science Direct: “Probing nano-QSAR to assess the interactions between carbon nanoparticles and a SARS-CoV-2 RNA fragment”

19/05/2021

AUTHORS: Fan Zhang, Zhuang Wang, Martina G. Vijver, Willie J.G.M. Peijnenburg

Science Direct: “Zeta potentials of metal oxide nanoparticles: a meta-analysis of experimental data and predictive neural networks modeling”

4/04/2021

AUTHORS: Alicja Mikołajczyk, NataliaSizochenko, Michael Syzochenko, Tomasz Puzyn, Jerzy Leszczynski

Environmental Science & Technology: “Size-Specific, Dynamic, Probabilistic Material Flow Analysis of Titanium Dioxide Releases into the Environment”

4/02/2021

AUTHORS: Yuanfang Zheng, Bernd Nowack

Nanoimpact Journal: “Zeta potentials (ζ) of metal oxide nanoparticles: A meta-analysis of experimental data and a predictive neural networks modeling.”

2021

AUTHORS: Alicja Mikołajczyk, NataliaSizochenko, Michael Syzochenko, Tomasz Puzyn, Jerzy Leszczynski

Editorial: Nanomaterials | Special Issue “From Nanoinformatics to Nanomaterials Risk Assessment and Governance”

07/01/2021

AUTHORS: Iseult Lynch, Antreas Afantitis, Dario Greco, Maria Dusinska, Miguel A.Banares, Georgia Melagraki

Science Direct | “Embryotoxicity of silver nanomaterials (Ag NM300k) in the soil invertebrate Enchytraeus crypticus – Functional assay detects Ca channels shutdown“.

01/2021

AUTHORS: Rita C. Bicho, Augusto M.R. Faustino, Fátima Carvalho, Amadeu M.V.M. Soares, Janeck J. Scott-Fordsmand, Mónica J.B. Amorim

Nanoscale Adv. 2021: “The role of size and nature in nanoparticle binding to a model lung membrane: an atomistic study”

2021

AUTHORS: Singhal A, Agur Sevink GJ

J Phys Chem B:  “Replica Exchange Molecular Dynamics of Diphenylalanine Amyloid Peptides in Electric Fields”

2021

AUTHORS: Narayan B, Herbert C, Rodriguez BJ, Brooks BR, Buchete NV.

Science Direct: “Embryotoxicity of silver nanomaterials (Ag NM300k) in the soil invertebrate Enchytraeus crypticus – Functional assay detects Ca channels shutdown“

2021

AUTHORS: Rita C. Bicho, Augusto M.R. Faustino, Fátima Carvalho, Amadeu M.V.M. Soares, Janeck J. Scott-Fordsmand, Mónica J.B. Amorim

BMC Bioinformatics: “multiGSEA: A GSEA-based pathway enrichment analysis for multi-omics data”

07/12/ 2020

AUTHORS: Sebastian Canzler, Jörg Hackermüller

Environmental Nano: “The effect of Ag, Au, Pt, and Pd on the surface properties, photocatalytic activity and toxicity of multicomponent TiO₂-based nanomaterials”

7/09/2020

AUTHORS: Anna Malankowska, Alicja Mikolajczyk, Joanna Mędrzycka, Izabela Wysocka, Grzegorz Nowaczyk, Marcin Jarek, Tomasz Puzyn, Ewa Mulkiewicz

ASC Publicatiobs: “Prediction of the Joint Toxicity of Multiple Engineered Nanoparticles: The Integration of Classic Mixture Models and In Silico Methods“

14/09/2020

AUTHORS: Fan Zhang, Zhuang Wang, Martina G. Vijver, Willie J.G.M. Peijnenburg

Environmental Nano: “The effect of Ag, Au, Pt, and Pd on the surface properties, photocatalytic activity and toxicity of multicomponent TiO₂-based nanomaterials”

17/09/2020

AUTHORS: Anna Malankowska, Alicja Mikolajczyk, Joanna Mędrzycka, Izabela Wysocka, Grzegorz Nowaczyk, Marcin Jarek, Tomasz Puzyn, Ewa Mulkiewicz

Science Direct: “Developing an epigenetics model species – from blastula to mature adult, life cycle methylation profile of Enchytraeus crypticus (Oligochaete)”

25/08/2020

AUTHORS: Rita C. Bicho, Janeck J. Scott-Fordsmand, Mónica J.B. Amorim

Nano Micro Small: “Nanocharacterization, Materials Modeling, and Research Integrity as Enablers of Sound Risk Assessment: Designing Responsible Nanotechnology”

12/07/2020

AUTHORS: Ioannis Xiarchos, Athanasios K. Morozinis, Panagiotis Kavouras, Costas A. Charitidis

National Library of Medicine: “The transition between active and inactive conformations of Abl kinase studied by rock climbing and Milestoning. Biochim Biophys Acta”

01/04/2020

AUTHORS: Narayan B, Fathizadeh A, Templeton C, He P, Arasteh S, Elber R., Gen Subj. 

Journal of Colloid and interface Science: “How thermal stability of ionic liquids leads to more efficient TiO2-based nanophotocatalysts: theoretical and experimental studies”

Elsevier, 25 March 2020

AUTHORS: Anna Rybińska-Fryca, Alicja Mikołajczyk, Justyna Łuczak, Marta Paszkiewicz-Gawron, manika Paszkiewicz, Adriana Zaleska-Medynska, Tomasz Puzyn

Bioinformatics: “BMDx: a graphical Shiny application to perform Benchmark Dose analysis for transcriptomics data”

17/01/ 2020

AUTHORS: Angela Serra, Laura Aliisa Saarimäki, Michele Fratello, Veer Singh Marwah, Dario Greco

Prog Mol Biol Transl Sci.2:  “Long-time methods for molecular dynamics simulations: Markov State Models and Milestoning”

1/01/ 2020

AUTHORS: Narayan B, Yuan Y, Fathizadeh A, Elber R, Buchete NV. 

Environment International: “Epigenetic effects of (nano)materials in environmental species – Cu case study in Enchytraeus crypticus”

Volume 136 (2020) 105447, Elsevier, January 2020

AUTHORS: Rita C. Bicho, Dick Roelofs, Janine Mariën, Janeck J. Scott-Fordsmand, Mónica J.B. Amorim

Environment Science Nano: “The effect of Ag, Au, Pt, and Pd on the surface properties, photocatalytic activity and toxicity of multicomponent TiO₂-based nanomaterials”

01/2020

AUTHORS: Malankowska A, Mikołajczyk A, Mȩdrzycka J, Wysocka I, Nowaczyk G, Jarek M, et al.

Environment Science Nano: “The effect of Ag, Au, Pt, and Pd on the surface properties, photocatalytic activity and toxicity of multicomponent TiO₂-based nanomaterials”

01/2020

AUTHORS: Malankowska A, Mikołajczyk A, Mȩdrzycka J, Wysocka I, Nowaczyk G, Jarek M, et al.

ACS Publications | “Prediction of the Joint Toxicity of Multiple Engineered Nanoparticles: The Integration of Classic Mixture Models and In Silico Methods“

2020

AUTHORS: Fan Zhang, Zhuang Wang, Martina G. Vijver, Willie J.G.M. Peijnenburg

Environmental Science: Nano, 1661–1669 | “Multivariate Analysis of the Exposure and Hazard of Ceria Nanomaterials in Indoor Aquatic Mesocosms.”

2020

AUTHORS: Nassar, M., Auffan, M., Santaella, C., Masion, A., and Rose, J. 

Bioinformatics, Volume 36, Issue 9, May 2020, Pages 2932–2933, | “BMDx: a graphical Shiny application to perform Benchmark Dose analysis for transcriptomics data”

2020

AUTHORS: Angela Serra, Laura Aliisa Saarimäki, Michele Fratello, Veer Singh Marwah, Dario Greco

Science Direct: “Developing an epigenetics model species – From blastula to mature adult, life cycle methylation profile of Enchytraeus crypticus (Oligochaete)“

2020

AUTHORS: Rita C. Bicho, Janeck J. Scott-Fordsmand, and Mónica J.B. Amorim

“A Chemoinformatics Approach for Characterization of Hybrid Nanomaterials: Safer and Efficient Design Perspective”

Nanoscale, England, 23 May 2019

AUTHORS: Mikolajczyk A., Sizochenko N., Mulkiewicz, E., Malankowska A., Rasulev B., Puzyn T.

“Fostering EU-US Cooperation in Nanosafety”. NanoInformaTIX Project Coordinator wrote the Emerging Materials section

Harvard University (USA), 5-6 March 2019

AUTHOR: Miguel Bañares

Regulatory Toxicology and Pharmacology: “Pulmonary toxicity of silver vapours, nanoparticles and fine dusts: A review”

AUTHORS: Niels Hadrup, Anoop K. Sharma , Katrin Loeschner , and Nicklas R. Jacobsen

Nanomaterials: “Transcriptomics in Toxicogenomics, Part I: Experimental Design, Technologies, Publicly Available Data, Regulatory Aspects”

AUTHORS: Pia Anneli Sofia Kinaret, Angela Serra, Antonio Federico, Pekka Kohonen, Penny Nymark, Irene Liampa, My Kieu Ha , Jang-Sik Choi, Karolina Jagiello, Natasha Sanabri, Georgia Melagraki, Luca Cattelani, Michele Fratello, Haralambos Sarimveis6, Antreas Afantitis , Tae-Hyun Yoon, Mary Gulumian, Roland Grafström, Tomasz Puzyn, Dario Greco

Materials: “Your spreadsheets can be FAIR: a tool and FAIRification workflow for eNanoMapper database”

AUTHORS: Nikolay Kochev, Nina Jeliazkova, Vesselina Paskaleva, Gergana Tancheva, Luchesar Iliev, Peter Ritchie, Vedrin Jeliazkov.

Nanomaterials: “Multigenerational exposure to WCCo nanomaterials – epigenetics in the soil invertebrate Enchytraeus crypticus”

AUTHORS: Rita C. Bicho, Janeck J. Scott-Fordsmand, Mónica J.B. Amorim.

Environmental Science: Nano | “Nano-QSAR modeling for ecosafe design of heterogeneous TiO₂-based nano-photocatalysts”

07/04/2018

AUTHORS: Alicja Mikolajczyk, Agnieszka Gajewicz, Ewa Mulkiewicz, Bakhtiyor Rasulev, Martyna Marchelek, Magdalena Diak, Seishiro Hirano, Adriana Zaleska-Medynska and Tomasz Puzyn