AIMC Topic: Software

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miRBaseConverter: an R/Bioconductor package for converting and retrieving miRNA name, accession, sequence and family information in different versions of miRBase.

BMC bioinformatics
BACKGROUND: miRBase is the primary repository for published miRNA sequence and annotation data, and serves as the "go-to" place for miRNA research. However, the definition and annotation of miRNAs have been changed significantly across different vers...

Convolutional neural network based on SMILES representation of compounds for detecting chemical motif.

BMC bioinformatics
BACKGROUND: Previous studies have suggested deep learning to be a highly effective approach for screening lead compounds for new drugs. Several deep learning models have been developed by addressing the use of various kinds of fingerprints and graph ...

iMEGES: integrated mental-disorder GEnome score by deep neural network for prioritizing the susceptibility genes for mental disorders in personal genomes.

BMC bioinformatics
BACKGROUND: A range of rare and common genetic variants have been discovered to be potentially associated with mental diseases, but many more have not been uncovered. Powerful integrative methods are needed to systematically prioritize both variants ...

Gene ontology improves template selection in comparative protein docking.

Proteins
Structural characterization of protein-protein interactions is essential for our ability to study life processes at the molecular level. Computational modeling of protein complexes (protein docking) is important as the source of their structure and a...

Discerning novel splice junctions derived from RNA-seq alignment: a deep learning approach.

BMC genomics
BACKGROUND: Exon splicing is a regulated cellular process in the transcription of protein-coding genes. Technological advancements and cost reductions in RNA sequencing have made quantitative and qualitative assessments of the transcriptome both poss...

NMR-STAR: comprehensive ontology for representing, archiving and exchanging data from nuclear magnetic resonance spectroscopic experiments.

Journal of biomolecular NMR
The growth of the biological nuclear magnetic resonance (NMR) field and the development of new experimental technology have mandated the revision and enlargement of the NMR-STAR ontology used to represent experiments, spectral and derived data, and s...

MILD-Net: Minimal information loss dilated network for gland instance segmentation in colon histology images.

Medical image analysis
The analysis of glandular morphology within colon histopathology images is an important step in determining the grade of colon cancer. Despite the importance of this task, manual segmentation is laborious, time-consuming and can suffer from subjectiv...

PENYEK: Automated brown planthopper detection from imperfect sticky pad images using deep convolutional neural network.

PloS one
Rice is a staple food in Asia and it contributes significantly to the Gross Domestic Product (GDP) of Malaysia and other developing countries. Brown Planthopper (BPH) causes high levels of economic loss in Malaysia. Identification of BPH presence and...

PASNet: pathway-associated sparse deep neural network for prognosis prediction from high-throughput data.

BMC bioinformatics
BACKGROUND: Predicting prognosis in patients from large-scale genomic data is a fundamentally challenging problem in genomic medicine. However, the prognosis still remains poor in many diseases. The poor prognosis may be caused by high complexity of ...

Multi-Institutional Validation of a Knowledge-Based Planning Model for Patients Enrolled in RTOG 0617: Implications for Plan Quality Controls in Cooperative Group Trials.

Practical radiation oncology
PURPOSE: This study aimed to evaluate the feasibility of using a single-institution, knowledge-based planning (KBP) model as a dosimetric plan quality control (QC) for multi-institutional clinical trials. The efficacy of this QC tool was retrospectiv...