AIMC Topic: Evolution, Molecular
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Large-scale inference of gene function through phylogenetic annotation of Gene Ontology terms: case study of the apoptosis and autophagy cellular processes.
Database : the journal of biological databases and curation
Dec 26, 2016
We previously reported a paradigm for large-scale phylogenomic analysis of gene families that takes advantage of the large corpus of experimentally supported Gene Ontology (GO) annotations. This 'GO Phylogenetic Annotation' approach integrates GO ann...
WORMHOLE: Novel Least Diverged Ortholog Prediction through Machine Learning.
PLoS computational biology
Nov 3, 2016
The rapid advancement of technology in genomics and targeted genetic manipulation has made comparative biology an increasingly prominent strategy to model human disease processes. Predicting orthology relationships between species is a vital componen...
Can computational efficiency alone drive the evolution of modularity in neural networks?
Scientific reports
Aug 30, 2016
Some biologists have abandoned the idea that computational efficiency in processing multipart tasks or input sets alone drives the evolution of modularity in biological networks. A recent study confirmed that small modular (neural) networks are relat...
Machine Learning of Protein Interactions in Fungal Secretory Pathways.
PloS one
Jul 21, 2016
In this paper we apply machine learning methods for predicting protein interactions in fungal secretion pathways. We assume an inter-species transfer setting, where training data is obtained from a single species and the objective is to predict prote...
A new approach to the automatic identification of organism evolution using neural networks.
Bio Systems
Mar 11, 2016
Automatic identification of organism evolution still remains a challenging task, which is especially exiting, when the evolution of human is considered. The main aim of this work is to present a new idea to allow organism evolution analysis using neu...
Protein folds recognized by an intelligent predictor based-on evolutionary and structural information.
Journal of computational chemistry
Oct 27, 2015
Protein fold recognition is an important and essential step in determining tertiary structure of a protein in biological science. In this study, a model termed NiRecor is developed for recognizing protein folds based on artificial neural networks inc...
Systematic Analysis and Prediction of In Situ Cross Talk of O-GlcNAcylation and Phosphorylation.
BioMed research international
Oct 27, 2015
Reversible posttranslational modification (PTM) plays a very important role in biological process by changing properties of proteins. As many proteins are multiply modified by PTMs, cross talk of PTMs is becoming an intriguing topic and draws much at...
Protein contact prediction by integrating joint evolutionary coupling analysis and supervised learning.
Bioinformatics (Oxford, England)
Aug 14, 2015
MOTIVATION: Protein contact prediction is important for protein structure and functional study. Both evolutionary coupling (EC) analysis and supervised machine learning methods have been developed, making use of different information sources. However...
Better prediction of functional effects for sequence variants.
BMC genomics
Jun 18, 2015
Elucidating the effects of naturally occurring genetic variation is one of the major challenges for personalized health and personalized medicine. Here, we introduce SNAP2, a novel neural network based classifier that improves over the state-of-the-a...
Toll-like receptor signaling in vertebrates: testing the integration of protein, complex, and pathway data in the protein ontology framework.
PloS one
Apr 20, 2015
The Protein Ontology (PRO) provides terms for and supports annotation of species-specific protein complexes in an ontology framework that relates them both to their components and to species-independent families of complexes. Comprehensive curation o...
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