AIMC Topic: Models, Biological

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Development of Decision Forest Models for Prediction of Drug-Induced Liver Injury in Humans Using A Large Set of FDA-approved Drugs.

Scientific reports
Drug-induced liver injury (DILI) presents a significant challenge to drug development and regulatory science. The FDA's Liver Toxicity Knowledge Base (LTKB) evaluated >1000 drugs for their likelihood of causing DILI in humans, of which >700 drugs wer...

Exploring the Impact of Food on the Gut Ecosystem Based on the Combination of Machine Learning and Network Visualization.

Nutrients
Prebiotics and probiotics strongly impact the gut ecosystem by changing the composition and/or metabolism of the microbiota to improve the health of the host. However, the composition of the microbiota constantly changes due to the intake of daily di...

Large-scale automated function prediction of protein sequences and an experimental case study validation on PTEN transcript variants.

Proteins
Recent advances in computing power and machine learning empower functional annotation of protein sequences and their transcript variations. Here, we present an automated prediction system UniGOPred, for GO annotations and a database of GO term predic...

Coupling Matched Molecular Pairs with Machine Learning for Virtual Compound Optimization.

Journal of chemical information and modeling
Matched molecular pair (MMP) analyses are widely used in compound optimization projects to gain insights into structure-activity relationships (SAR). The analysis is traditionally done via statistical methods but can also be employed together with ma...

Morphological and control criteria for self-stable underwater hopping.

Bioinspiration & biomimetics
This paper presents the self-stabilisation features of a hopping gait during underwater legged locomotion. We used a bio-inspired fundamental model of this gait, the underwater spring-loaded inverted pendulum model, to numerically derive quantitative...

Computational Intelligence for Medical Imaging Simulations.

Journal of medical systems
This paper describes how to simulate medical imaging by computational intelligence to explore areas that cannot be easily achieved by traditional ways, including genes and proteins simulations related to cancer development and immunity. This paper ha...

The Wisdom of Networks: A General Adaptation and Learning Mechanism of Complex Systems: The Network Core Triggers Fast Responses to Known Stimuli; Innovations Require the Slow Network Periphery and Are Encoded by Core-Remodeling.

BioEssays : news and reviews in molecular, cellular and developmental biology
I hypothesize that re-occurring prior experience of complex systems mobilizes a fast response, whose attractor is encoded by their strongly connected network core. In contrast, responses to novel stimuli are often slow and require the weakly connecte...

The bacterial interlocked process ONtology (BiPON): a systemic multi-scale unified representation of biological processes in prokaryotes.

Journal of biomedical semantics
BACKGROUND: High-throughput technologies produce huge amounts of heterogeneous biological data at all cellular levels. Structuring these data together with biological knowledge is a critical issue in biology and requires integrative tools and methods...

Physiological based pharmacokinetic modeling to estimate in vivo Ki of ketoconazole on renal P-gp using human drug-drug interaction study result of fesoterodine and ketoconazole.

Drug metabolism and pharmacokinetics
This study was conducted to estimate in vivo inhibition constant (Ki) of ketoconazole on renal P-glycoprotein (P-gp) using human drug-drug interaction (DDI) study result of fesoterodine and ketoconazole. Fesoterodine is a prodrug which is extensively...

The role of neuron-glia interactions in the emergence of ultra-slow oscillations.

Biological cybernetics
Ultra-slow cortical oscillatory activity of 1-100 mHz has been recorded in human by electroencephalography and in dissociated cultures of cortical rat neurons, but the underlying mechanisms remain to be elucidated. This study presents a computational...