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Systems Biology

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Tensor Factorization for Precision Medicine in Heart Failure with Preserved Ejection Fraction.

Journal of cardiovascular translational research
Heart failure with preserved ejection fraction (HFpEF) is a heterogeneous clinical syndrome that may benefit from improved subtyping in order to better characterize its pathophysiology and to develop novel targeted therapies. The United States Precis...

Biologically Relevant Heterogeneity: Metrics and Practical Insights.

SLAS discovery : advancing life sciences R & D
Heterogeneity is a fundamental property of biological systems at all scales that must be addressed in a wide range of biomedical applications, including basic biomedical research, drug discovery, diagnostics, and the implementation of precision medic...

Advancing Systems Biology in the International Conference on Intelligent Biology and Medicine (ICIBM) 2015.

BMC systems biology
The 2015 International Conference on Intelligent Biology and Medicine (ICIBM 2015) was held on November 13-15, 2015 in Indianapolis, Indiana, USA. ICIBM 2015 included eight scientific sessions, three tutorial sessions, one poster session, and four ke...

Learning a hierarchical representation of the yeast transcriptomic machinery using an autoencoder model.

BMC bioinformatics
BACKGROUND: A living cell has a complex, hierarchically organized signaling system that encodes and assimilates diverse environmental and intracellular signals, and it further transmits signals that control cellular responses, including a tightly con...

IAS: Interaction Specific GO Term Associations for Predicting Protein-Protein Interaction Networks.

IEEE/ACM transactions on computational biology and bioinformatics
Proteins carry out their function in a cell through interactions with other proteins. A large scale protein-protein interaction (PPI) network of an organism provides static yet an essential structure of interactions, which is valuable clue for unders...

Simulation Experiment Description Markup Language (SED-ML) Level 1 Version 2.

Journal of integrative bioinformatics
The number, size and complexity of computational models of biological systems are growing at an ever increasing pace. It is imperative to build on existing studies by reusing and adapting existing models and parts thereof. The description of the stru...

The CellML Metadata Framework 2.0 Specification.

Journal of integrative bioinformatics
The CellML Metadata Framework 2.0 is a modular framework that describes how semantic annotations should be made about mathematical models encoded in the CellML (www.cellml.org) format, and their elements. In addition to the Core specification, there ...

Managing bioengineering complexity with AI techniques.

Bio Systems
Our capabilities for systematic design and engineering of biological systems are rapidly increasing. Effectively engineering such systems, however, requires the synthesis of a rapidly expanding and changing complex body of knowledge, protocols, and m...

A tree-like Bayesian structure learning algorithm for small-sample datasets from complex biological model systems.

BMC systems biology
BACKGROUND: There are increasing efforts to bring high-throughput systems biology techniques to bear on complex animal model systems, often with a goal of learning about underlying regulatory network structures (e.g., gene regulatory networks). Howev...

Proto-object categorisation and local gist vision using low-level spatial features.

Bio Systems
Object categorisation is a research area with significant challenges, especially in conditions with bad lighting, occlusions, different poses and similar objects. This makes systems that rely on precise information unable to perform efficiently, like...