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ANTENNA, a Multi-Rank, Multi-Layered Recommender System for Inferring Reliable Drug-Gene-Disease Associations: Repurposing Diazoxide as a Targeted Anti-Cancer Therapy.
IEEE/ACM transactions on computational biology and bioinformatics
Mar 16, 2018
Existing drug discovery processes follow a reductionist model of "one-drug-one-gene-one-disease," which is inadequate to tackle complex diseases involving multiple malfunctioned genes. The availability of big omics data offers opportunities to transf...
Computational Prediction of Sigma-54 Promoters in Bacterial Genomes by Integrating Motif Finding and Machine Learning Strategies.
IEEE/ACM transactions on computational biology and bioinformatics
Mar 15, 2018
Sigma factor, as a unit of RNA polymerase holoenzyme, is a critical factor in the process of gene transcriptional regulation. It recognizes the specific DNA sites and brings the core enzyme of RNA polymerase to the upstream regions of target genes. T...
Escherichia coli Proteins
Computational Biology
Machine Learning
Base Sequence
Escherichia coli
Software
Genome, Bacterial
DNA-Directed RNA Polymerases
Promoter Regions, Genetic
False Positive Reactions
Models, Statistical
Reproducibility of Results
Amino Acid Motifs
RNA Polymerase Sigma 54
Transcription, Genetic
Assessing microscope image focus quality with deep learning.
BMC bioinformatics
Mar 15, 2018
BACKGROUND: Large image datasets acquired on automated microscopes typically have some fraction of low quality, out-of-focus images, despite the use of hardware autofocus systems. Identification of these images using automated image analysis with hig...
Development of an information retrieval tool for biomedical patents.
Computer methods and programs in biomedicine
Mar 14, 2018
BACKGROUND AND OBJECTIVE: The volume of biomedical literature has been increasing in the last years. Patent documents have also followed this trend, being important sources of biomedical knowledge, technical details and curated data, which are put to...
iRSpot-PDI: Identification of recombination spots by incorporating dinucleotide property diversity information into Chou's pseudo components.
Genomics
Mar 13, 2018
Recombination spot identification plays an important role in revealing genome evolution and developing DNA function study. Although some computational methods have been proposed, extracting discriminatory information embedded in DNA properties has no...
The design and validation of a hybrid digital-signal-processing plug-in for traditional cochlear implant speech processors.
Computer methods and programs in biomedicine
Mar 12, 2018
BACKGROUND AND OBJECTIVE: Cochlear implants (CIs) are electronic devices restoring partial hearing to deaf individuals with profound hearing loss. In this paper, a new plug-in for traditional IIR filter-banks (FBs) is presented for cochlear implants ...
MUFOLD-SS: New deep inception-inside-inception networks for protein secondary structure prediction.
Proteins
Mar 12, 2018
Protein secondary structure prediction can provide important information for protein 3D structure prediction and protein functions. Deep learning offers a new opportunity to significantly improve prediction accuracy. In this article, a new deep neura...
MetaGO: Predicting Gene Ontology of Non-homologous Proteins Through Low-Resolution Protein Structure Prediction and Protein-Protein Network Mapping.
Journal of molecular biology
Mar 10, 2018
Homology-based transferal remains the major approach to computational protein function annotations, but it becomes increasingly unreliable when the sequence identity between query and template decreases below 30%. We propose a novel pipeline, MetaGO,...
Inferring MicroRNA Targets Based on Restricted Boltzmann Machines.
IEEE journal of biomedical and health informatics
Mar 9, 2018
Predicting the miRNA-target interactions (MTIs) is a critical task for elucidating mechanistic roles of miRNAs in pathophysiology. However, most existing techniques have a higher false positive because the precise miRNA target mechanisms are poorly k...
Deep learning with convolutional neural network in radiology.
Japanese journal of radiology
Mar 1, 2018
Deep learning with a convolutional neural network (CNN) is gaining attention recently for its high performance in image recognition. Images themselves can be utilized in a learning process with this technique, and feature extraction in advance of the...
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