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DanQ: a hybrid convolutional and recurrent deep neural network for quantifying the function of DNA sequences.
Nucleic acids research
Apr 15, 2016
Modeling the properties and functions of DNA sequences is an important, but challenging task in the broad field of genomics. This task is particularly difficult for non-coding DNA, the vast majority of which is still poorly understood in terms of fun...
Extending gene ontology in the context of extracellular RNA and vesicle communication.
Journal of biomedical semantics
Apr 12, 2016
BACKGROUND: To address the lack of standard terminology to describe extracellular RNA (exRNA) data/metadata, we have launched an inter-community effort to extend the Gene Ontology (GO) with subcellular structure concepts relevant to the exRNA domain....
An Effective Antifreeze Protein Predictor with Ensemble Classifiers and Comprehensive Sequence Descriptors.
International journal of molecular sciences
Sep 7, 2015
Antifreeze proteins (AFPs) play a pivotal role in the antifreeze effect of overwintering organisms. They have a wide range of applications in numerous fields, such as improving the production of crops and the quality of frozen foods. Accurate identif...
Enhancing protein function prediction with taxonomic constraints--The Argot2.5 web server.
Methods (San Diego, Calif.)
Aug 28, 2015
Argot2.5 (Annotation Retrieval of Gene Ontology Terms) is a web server designed to predict protein function. It is an updated version of the previous Argot2 enriched with new features in order to enhance its usability and its overall performance. The...
GRYFUN: a web application for GO term annotation visualization and analysis in protein sets.
PloS one
Mar 20, 2015
Functional context for biological sequence is provided in the form of annotations. However, within a group of similar sequences there can be annotation heterogeneity in terms of coverage and specificity. This in turn can introduce issues regarding th...
An ensemble method with hybrid features to identify extracellular matrix proteins.
PloS one
Feb 13, 2015
The extracellular matrix (ECM) is a dynamic composite of secreted proteins that play important roles in numerous biological processes such as tissue morphogenesis, differentiation and homeostasis. Furthermore, various diseases are caused by the dysfu...
Privacy-Protecting Image Classification Within the Web Browser Using Deep Learning Models from Zenodo.
Studies in health technology and informatics
May 15, 2025
Integrating deep learning into clinical workflows for medical image analysis holds promise for improving diagnostic accuracy. However, strict data privacy regulations and the sensitivity of clinical IT infrastructure limit the deployment of cloud-bas...
ARAX: a graph-based modular reasoning tool for translational biomedicine.
Bioinformatics (Oxford, England)
Mar 1, 2023
MOTIVATION: With the rapidly growing volume of knowledge and data in biomedical databases, improved methods for knowledge-graph-based computational reasoning are needed in order to answer translational questions. Previous efforts to solve such challe...
PreTP-EL: prediction of therapeutic peptides based on ensemble learning.
Briefings in bioinformatics
Nov 5, 2021
Therapeutic peptides are important for understanding the correlation between peptides and their therapeutic diagnostic potential. The therapeutic peptides can be further divided into different types based on therapeutic function sharing different cha...
RefRGim: an intelligent reference panel reconstruction method for genotype imputation with convolutional neural networks.
Briefings in bioinformatics
Nov 5, 2021
Genotype imputation is a statistical method for estimating missing genotypes from a denser haplotype reference panel. Existing methods usually performed well on common variants, but they may not be ideal for low-frequency and rare variants. Previous ...
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