AIMC Topic: Deep Learning

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Deep learning identifies and quantifies recombination hotspot determinants.

Bioinformatics (Oxford, England)
MOTIVATION: Recombination is one of the essential genetic processes for sexually reproducing organisms, which can happen more frequently in some regions, called recombination hotspots. Although several factors, such as PRDM9 binding motifs, are known...

deepHPI: a comprehensive deep learning platform for accurate prediction and visualization of host-pathogen protein-protein interactions.

Briefings in bioinformatics
Host-pathogen protein interactions (HPPIs) play vital roles in many biological processes and are directly involved in infectious diseases. With the outbreak of more frequent pandemics in the last couple of decades, such as the recent outburst of Covi...

D3AI-CoV: a deep learning platform for predicting drug targets and for virtual screening against COVID-19.

Briefings in bioinformatics
Target prediction and virtual screening are two powerful tools of computer-aided drug design. Target identification is of great significance for hit discovery, lead optimization, drug repurposing and elucidation of the mechanism. Virtual screening ca...

Do deep learning models make a difference in the identification of antimicrobial peptides?

Briefings in bioinformatics
In the last few decades, antimicrobial peptides (AMPs) have been explored as an alternative to classical antibiotics, which in turn motivated the development of machine learning models to predict antimicrobial activities in peptides. The first genera...

S2Snet: deep learning for low molecular weight RNA identification with nanopore.

Briefings in bioinformatics
Ribonucleic acid (RNA) is a pivotal nucleic acid that plays a crucial role in regulating many biological activities. Recently, one study utilized a machine learning algorithm to automatically classify RNA structural events generated by a Mycobacteriu...

Protein design via deep learning.

Briefings in bioinformatics
Proteins with desired functions and properties are important in fields like nanotechnology and biomedicine. De novo protein design enables the production of previously unseen proteins from the ground up and is believed as a key point for handling rea...

deepNEC: a novel alignment-free tool for the identification and classification of nitrogen biochemical network-related enzymes using deep learning.

Briefings in bioinformatics
Nitrogen is essential for life and its transformations are an important part of the global biogeochemical cycle. Being an essential nutrient, nitrogen exists in a range of oxidation states from +5 (nitrate) to -3 (ammonium and amino-nitrogen), and it...

Deep learning based on biologically interpretable genome representation predicts two types of human adaptation of SARS-CoV-2 variants.

Briefings in bioinformatics
Explosively emerging SARS-CoV-2 variants challenge current nomenclature schemes based on genetic diversity and biological significance. Genomic composition-based machine learning methods have recently performed well in identifying phenotype-genotype ...

AggMapNet: enhanced and explainable low-sample omics deep learning with feature-aggregated multi-channel networks.

Nucleic acids research
Omics-based biomedical learning frequently relies on data of high-dimensions (up to thousands) and low-sample sizes (dozens to hundreds), which challenges efficient deep learning (DL) algorithms, particularly for low-sample omics investigations. Here...

SynPathy: Predicting Drug Synergy through Drug-Associated Pathways Using Deep Learning.

Molecular cancer research : MCR
UNLABELLED: Drug combination therapy has become a promising therapeutic strategy for cancer treatment. While high-throughput drug combination screening is effective for identifying synergistic drug combinations, measuring all possible combinations is...