Community-Reviewed Biological Network Models for Toxicology and Drug Discovery Applications

Abstract

Biological network models offer a framework for understanding disease by describing the relationships between the mechanisms involved in the regulation of biological processes. Crowdsourcing can efficiently gather feedback from a wide audience with varying expertise. In the Network Verification Challenge, scientists verified and enhanced a set of 46 biological networks relevant to lung and chronic obstructive pulmonary disease. The networks were built using Biological Expression Language and contain detailed information for each node and edge, including supporting evidence from the literature. Network scoring of public transcriptomics data inferred perturbation of a subset of mechanisms and networks that matched the measured outcomes. These results, based on a computable network approach, can be used to identify novel mechanisms activated in disease, quantitatively compare different treatments and time points, and allow for assessment of data with low signal. These networks are periodically verified by the crowd to maintain an up-to-date suite of networks for toxicology and drug discovery applications.

Whole Blood Expression Levels of Long Noncoding RNAs: HOTAIRM1, GAS5, MZF1-AS1, and OIP5-AS1 as Biomarkers in Adolescents with Obesity-Related Asthma

“…In this context, with the help of powerful bioinformatic tools, several studies have tried to predict different molecular pathways that are directly related lncRNAs, miRNAs, and genes, which have increased the knowledge about interactions between that kind of molecules [ 33 , 34 ]. It is worth mentioning that several databases have been created to systematize and visualize causal relationships between asthma and lung disease [ 35 , 36 ]. Although mathematics and computer science have helped generate much new knowledge in biological sciences, there is still a long way to go, and indeed in the future, much more powerful software and algorithms will be created to help advance disease research.…”

Immunomodulatory and Allergenic Properties of Antimicrobial Peptides

“…A wide spectrum of antimicrobial activities of AMPs inspires researchers to search for new active peptides in biological material [ 252 , 253 ], and also serves as the basis for the design of new synthetic compounds [ 254 , 255 ]. To date, information about AMPs is presented in numerous databases describing the structural, functional, allergenic and toxicological properties of these peptide factors of innate immunity [ 256 , 257 , 258 , 259 , 260 ]. The tools of modern bioinformatic approaches allow one to perform an in-depth analysis of structural homology in order to search for new, not yet discovered AMPs, and also offer additional methods for predicting a putative biological activity in silico [ 261 , 262 , 263 , 264 ].…”

Marine Invertebrate Antimicrobial Peptides and Their Potential as Novel Peptide Antibiotics

“…It has been confirmed that IARR-Anal10 suppressed the virulence of K. pneumoniae to a degree similar to tigecycline, used to treat carbapenemresistant Enterobacteriaceae infections, and did not induce the development of resistance by K. pneumoniae [160]. Notably, AMPs from amphioxus were discovered using bioinformatics and systems biology, which integrate research data and serve as a basis for drug design and novel AMPs [161,162]. It was found that the amphioxus ribosomal polypeptide RPS23, designated as BjRPS23, acted not only as a pattern recognition receptor (PRR) capable of identifying LPS, LTAs, and PGN, but also as an effector killing Gram-negative and Grampositive bacteria.…”