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

Abstract The immune system is professional in recognizing and responding to non‐self, including nanomaterials. Immune responses by professional and nonprofessional immune cells are thus nearly inevitable upon exposure of cells and organisms to such materials. The state of research into taking the immune system into account in nanosafety studies is reviewed and three aspects in…

Driving the nanoinformatics wave

The NanoCommons (https://www.nanocommons.eu/) research e-infrastructure and NanoSolveIT (https://nanosolveit.eu/) projects are developing the knowledge management and nanoinformatics tools to support in silico nanosafety assessment  (published in Scitech Europa www.scitecheuropa.eu) DOI: http://doi.org/10.5281/zenodo.3765525 You can access the article here.

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

Abstract Zeta potential is one of the most critical properties of nanomaterials (NMs) which provides an estimation of the surface charge, and therefore electrostatic stability in medium and, in practical terms, influences the NM’s tendency to form agglomerates and to interact with cellular membranes. This paper describes a robust and accurate read‐across model to predict…

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

Abstract Protein-protein-interaction networks (PPINs) organize fundamental biological processes, but how oncogenic mutations impact these interactions and their functions at a network-level scale is poorly understood. Here, we analyze how a common oncogenic KRAS mutation (KRASG13D) affects PPIN structure and function of the Epidermal Growth Factor Receptor (EGFR) network in colorectal cancer (CRC) cells. Mapping >6000…

Semantic Interoperability and Characterization of Data Provenance in Computational Molecular Engineering

Abstract By introducing a common representational system for metadata that describe the employed simulation workflows, diverse sources of data and platforms in computational molecular engineering, such as workflow management systems, can become interoperable at the semantic level. To achieve semantic interoperability, the present work introduces two ontologies that provide a formal specification of the entities…

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

Abstract A rapid increase of new nanomaterial (NM) products poses new challenges for their risk assessment. Current traditional methods for estimating potential adverse health effect of NMs are complex, time consuming, and expensive. In order to develop new prediction tests for nanotoxicity evaluation, a systems biology approach, and data from high-throughput omics experiments can be…

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

NanoCommons supported paper: Read-across predictions of nanoparticle hazard endpoints: a mathematical optimization approach Abstract In the present study, a novel read-across methodology for the prediction of toxicity related end-points of engineered nanomaterials (ENMs) is developed. The proposed method lies in the interface between the two main read-across approaches, namely the analogue and the grouping methods,…

Mapping connections in signaling networks with ambiguous modularity

Abstract Modular Response Analysis (MRA) is a suite of methods that under certain assumptions permits the precise reconstruction of both the directions and strengths of connections between network modules from network responses to perturbations. Standard MRA assumes that modules are insulated, thereby neglecting the existence of inter-modular protein complexes. Such complexes sequester proteins from different…