AIMC Topic: Systems Biology

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A Systems Toxicology Approach for the Prediction of Kidney Toxicity and Its Mechanisms In Vitro.

Toxicological sciences : an official journal of the Society of Toxicology
The failure to predict kidney toxicity of new chemical entities early in the development process before they reach humans remains a critical issue. Here, we used primary human kidney cells and applied a systems biology approach that combines multidim...

Unsupervised GRN Ensemble.

Methods in molecular biology (Clifton, N.J.)
Inferring gene regulatory networks from expression data is a very challenging problem that has raised the interest of the scientific community. Different algorithms have been proposed to try to solve this issue, but it has been shown that different m...

Tree-Based Learning of Regulatory Network Topologies and Dynamics with Jump3.

Methods in molecular biology (Clifton, N.J.)
Inference of gene regulatory networks (GRNs) from time series data is a well-established field in computational systems biology. Most approaches can be broadly divided in two families: model-based and model-free methods. These two families are highly...

A review on machine learning principles for multi-view biological data integration.

Briefings in bioinformatics
Driven by high-throughput sequencing techniques, modern genomic and clinical studies are in a strong need of integrative machine learning models for better use of vast volumes of heterogeneous information in the deep understanding of biological syste...

A heuristic method for simulating open-data of arbitrary complexity that can be used to compare and evaluate machine learning methods.

Pacific Symposium on Biocomputing. Pacific Symposium on Biocomputing
A central challenge of developing and evaluating artificial intelligence and machine learning methods for regression and classification is access to data that illuminates the strengths and weaknesses of different methods. Open data plays an important...

Conceptual Challenges in the Theoretical Foundations of Systems Biology.

Methods in molecular biology (Clifton, N.J.)
In the last decade, Systems Biology has emerged as a conceptual and explanatory alternative to reductionist-based approaches in molecular biology. However, the foundations of this new discipline need to be fleshed out more carefully. In this paper, w...

Prediction of Growth Factor-Dependent Cleft Formation During Branching Morphogenesis Using A Dynamic Graph-Based Growth Model.

IEEE/ACM transactions on computational biology and bioinformatics
This study considers the problem of describing and predicting cleft formation during the early stages of branching morphogenesis in mouse submandibular salivary glands (SMG) under the influence of varied concentrations of epidermal growth factors (EG...