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…
Abstract Receptor tyrosine kinases (RTKs) typically contain multiple autophosphorylation sites in their cytoplasmic domains. Once activated, these autophosphorylation sites can recruit downstream signaling proteins containing Src homology 2 (SH2) and phosphotyrosine-binding (PTB) domains, which recognize phosphotyrosine-containing short linear motifs (SLiMs). These domains and SLiMs have polyspecific or promiscuous binding activities. Thus, multiple signaling proteins may…
NanoCommons supported paper: A safe-by-design tool for functionalised nanomaterials through the Enalos Nanoinformatics Cloud platform Abstract Multi-walled carbon nanotubes are currently used in numerous industrial applications and products, therefore fast and accurate evaluation of their biological and toxicological effects is of utmost importance. Computational methods and techniques, previously applied in the area of cheminformatics for…
The first NanoCommons sponsored eNanoMapper ontology is now online! Version 5 of the eNanoMapper Ontology (ENM) was released on the 13th of September 2018. ENM now covers 12531 classes, compared with 10881 classes in version 4. What’s new in version 5 Now based on BFO 2 New 3rd party ontology versions Includes most JRC nanomaterials…
Abstract Clinically used RAF inhibitors are ineffective in RAS mutant tumors because they enhance homo- and heterodimerization of RAF kinases, leading to paradoxical activation of ERK signaling. Overcoming enhanced RAF dimerization and the resulting resistance is a challenge for drug design. Combining multiple inhibitors could be more effective, but it is unclear how the best combinations can…
At a recent hackathon organised by the European Research Council, GeneWiki, and others, a group of 25 researchers came together in Berlin to work on ontologically modelling research grants in Wikidata. During this meeting the EU NanoSafety Cluster was used as use case study, resulting in new linked data around the cluster. The Scholia platform was extended with a Project…
Tassos Papadiamantis (University of Birmingham) gave a presentation on data curation automation and harmonisation, the CEINT NanoInformatics Knowledge Commons (NIKC) curation templates and the use of online lab-books during every day experimental practice during the EU NanoSafety Cluster Scientific Meeting that took place in Athens, Greece. in conjunction with the NanoFASE consortium meeting, was a member…