AIMC Topic: Cell Physiological Phenomena

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Moonlighting protein prediction using physico-chemical and evolutional properties via machine learning methods.

BMC bioinformatics
BACKGROUND: Moonlighting proteins (MPs) are a subclass of multifunctional proteins in which more than one independent or usually distinct function occurs in a single polypeptide chain. Identification of unknown cellular processes, understanding novel...

Regression plane concept for analysing continuous cellular processes with machine learning.

Nature communications
Biological processes are inherently continuous, and the chance of phenotypic discovery is significantly restricted by discretising them. Using multi-parametric active regression we introduce the Regression Plane (RP), a user-friendly discovery tool e...

Accurate and fast mitotic detection using an anchor-free method based on full-scale connection with recurrent deep layer aggregation in 4D microscopy images.

BMC bioinformatics
BACKGROUND: To effectively detect and investigate various cell-related diseases, it is essential to understand cell behaviour. The ability to detection mitotic cells is a fundamental step in diagnosing cell-related diseases. Convolutional neural netw...

A portable structural analysis library for reaction networks.

Bio Systems
The topology of a reaction network can have a significant influence on the network's dynamical properties. Such influences can include constraints on network flows and concentration changes or more insidiously result in the emergence of feedback loop...

Computational Analysis of Cell Dynamics in Videos with Hierarchical-Pooled Deep-Convolutional Features.

Journal of computational biology : a journal of computational molecular cell biology
Computational analysis of cellular appearance and its dynamics is used to investigate physiological properties of cells in biomedical research. In consideration of the great success of deep learning in video analysis, we first introduce two-stream co...

Using deep learning to model the hierarchical structure and function of a cell.

Nature methods
Although artificial neural networks are powerful classifiers, their internal structures are hard to interpret. In the life sciences, extensive knowledge of cell biology provides an opportunity to design visible neural networks (VNNs) that couple the ...

Comparison, alignment, and synchronization of cell line information between CLO and EFO.

BMC bioinformatics
BACKGROUND: The Experimental Factor Ontology (EFO) is an application ontology driven by experimental variables including cell lines to organize and describe the diverse experimental variables and data resided in the EMBL-EBI resources. The Cell Line ...

A flexible ontology for inference of emergent whole cell function from relationships between subcellular processes.

Scientific reports
Whole cell responses arise from coordinated interactions between diverse human gene products functioning within various pathways underlying sub-cellular processes (SCP). Lower level SCPs interact to form higher level SCPs, often in a context specific...

Active machine learning-driven experimentation to determine compound effects on protein patterns.

eLife
High throughput screening determines the effects of many conditions on a given biological target. Currently, to estimate the effects of those conditions on other targets requires either strong modeling assumptions (e.g. similarities among targets) or...

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 ...