AIMC Topic: Software

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DEEPre: sequence-based enzyme EC number prediction by deep learning.

Bioinformatics (Oxford, England)
MOTIVATION: Annotation of enzyme function has a broad range of applications, such as metagenomics, industrial biotechnology, and diagnosis of enzyme deficiency-caused diseases. However, the time and resource required make it prohibitively expensive t...

Chromatin accessibility prediction via a hybrid deep convolutional neural network.

Bioinformatics (Oxford, England)
MOTIVATION: A majority of known genetic variants associated with human-inherited diseases lie in non-coding regions that lack adequate interpretation, making it indispensable to systematically discover functional sites at the whole genome level and p...

DeepGO: predicting protein functions from sequence and interactions using a deep ontology-aware classifier.

Bioinformatics (Oxford, England)
MOTIVATION: A large number of protein sequences are becoming available through the application of novel high-throughput sequencing technologies. Experimental functional characterization of these proteins is time-consuming and expensive, and is often ...

Machine learning and data science in soft materials engineering.

Journal of physics. Condensed matter : an Institute of Physics journal
In many branches of materials science it is now routine to generate data sets of such large size and dimensionality that conventional methods of analysis fail. Paradigms and tools from data science and machine learning can provide scalable approaches...

Gramene 2018: unifying comparative genomics and pathway resources for plant research.

Nucleic acids research
Gramene (http://www.gramene.org) is a knowledgebase for comparative functional analysis in major crops and model plant species. The current release, #54, includes over 1.7 million genes from 44 reference genomes, most of which were organized into 62,...

Computational Identification of Chemical Compounds with Potential Activity against Leishmania amazonensis using Nonlinear Machine Learning Techniques.

Current topics in medicinal chemistry
Leishmaniasis is a poverty-related disease endemic in 98 countries worldwide, with morbidity and mortality increasing daily. All currently used first-line and second-line drugs for the treatment of leishmaniasis exhibit several drawbacks including to...

Ontology-Guided Markerless Navigation and Situational Awareness for Endoscopic Surgery.

Studies in health technology and informatics
Optical navigation systems help surgeons find their way through the complex anatomy of a patient. However, such systems are accident-sensitive, time-consuming and difficult to use because of their complicated technical requirements such as the settin...

Metadata Import from RDF to i2b2.

Studies in health technology and informatics
Metadata management is an important task in medical informatics and highly affects the gain out of existing health information data. Data Warehouse solutions like Informatics for Integrating Biology and the Bedside (i2b2) are common tools for identif...

Computing and Visualizing Gene Function Similarity and Coherence with NaviGO.

Methods in molecular biology (Clifton, N.J.)
Gene ontology (GO) is a controlled vocabulary of gene functions across all species, which is widely used for functional analyses of individual genes and large-scale proteomic studies. NaviGO is a webserver for visualizing and quantifying the relation...