AIMC Topic: Computational Biology

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Mem-mEN: Predicting Multi-Functional Types of Membrane Proteins by Interpretable Elastic Nets.

IEEE/ACM transactions on computational biology and bioinformatics
Membrane proteins play important roles in various biological processes within organisms. Predicting the functional types of membrane proteins is indispensable to the characterization of membrane proteins. Recent studies have extended to predicting si...

SAMSVM: A tool for misalignment filtration of SAM-format sequences with support vector machine.

Journal of bioinformatics and computational biology
Sequence alignment/map (SAM) formatted sequences [Li H, Handsaker B, Wysoker A et al., Bioinformatics 25(16):2078-2079, 2009.] have taken on a main role in bioinformatics since the development of massive parallel sequencing. However, because misalign...

Practical Guidelines for Incorporating Knowledge-Based and Data-Driven Strategies into the Inference of Gene Regulatory Networks.

IEEE/ACM transactions on computational biology and bioinformatics
Modeling gene regulatory networks (GRNs) is essential for conceptualizing how genes are expressed and how they influence each other. Typically, a reverse engineering approach is employed; this strategy is effective in reproducing possible fitting mod...

Accurate contact predictions using covariation techniques and machine learning.

Proteins
Here we present the results of residue-residue contact predictions achieved in CASP11 by the CONSIP2 server, which is based around our MetaPSICOV contact prediction method. On a set of 40 target domains with a median family size of around 40 effectiv...

OVA: integrating molecular and physical phenotype data from multiple biomedical domain ontologies with variant filtering for enhanced variant prioritization.

Bioinformatics (Oxford, England)
MOTIVATION: Exome sequencing has become a de facto standard method for Mendelian disease gene discovery in recent years, yet identifying disease-causing mutations among thousands of candidate variants remains a non-trivial task.

A tool for developing an automatic insect identification system based on wing outlines.

Scientific reports
For some insect groups, wing outline is an important character for species identification. We have constructed a program as the integral part of an automated system to identify insects based on wing outlines (DAIIS). This program includes two main fu...

Evolution of Self-Organized Task Specialization in Robot Swarms.

PLoS computational biology
Division of labor is ubiquitous in biological systems, as evidenced by various forms of complex task specialization observed in both animal societies and multicellular organisms. Although clearly adaptive, the way in which division of labor first evo...

A methodological evaluation and predictive in silico investigation into the multi-functionality of arginine in directly compressed tablets.

European journal of pharmaceutics and biopharmaceutics : official journal of Arbeitsgemeinschaft fur Pharmazeutische Verfahrenstechnik e.V
The acceleration of solid dosage form product development can be facilitated by the inclusion of excipients that exhibit poly-/multi-functionality with reduction of the time invested in multiple excipient optimisations. Because active pharmaceutical ...

First Trimester Noninvasive Prenatal Diagnosis: A Computational Intelligence Approach.

IEEE journal of biomedical and health informatics
The objective of this study is to examine the potential value of using machine learning techniques such as artificial neural network (ANN) schemes for the noninvasive estimation, at 11-13 weeks of gestation, the risk for euploidy, trisomy 21 (T21), a...

idDock+: Integrating Machine Learning in Probabilistic Search for Protein-Protein Docking.

Journal of computational biology : a journal of computational molecular cell biology
Predicting the three-dimensional native structures of protein dimers, a problem known as protein-protein docking, is key to understanding molecular interactions. Docking is a computationally challenging problem due to the diversity of interactions an...