Genetics

Class Balanced Multifactor Dimensionality Reduction to Detect Gene-Gene Interactions.

Detecting gene-gene interactions in single-nucleotide polymorphism data is vital for understanding disease susceptibility. However, existing approaches may be limited by the sample size in case-control studies. Herein, we propose a balance approach for the multifactor dimensionality reduction (BMDR) method to increase the accuracy of estimates of the prediction error rate in small samples. BMDR ex...

EL_LSTM: Prediction of DNA-Binding Residue from Protein Sequence by Combining Long Short-Term Memory and Ensemble Learning.

Most past works for DNA-binding residue prediction did not consider the relationships between residues. In this paper, we propose a novel approach for DNA-binding residue prediction, referred to as EL_LSTM, which includes two main components. The first component is the Long Short-Term Memory (LSTM), which learns pairwise relationships between residues through a bi-gram model and then learns featur...

RNA-seq assistant: machine learning based methods to identify more transcriptional regulated genes.

BACKGROUND: Although different quality controls have been applied at different stages of the sample preparation and data analysis to ensure both repro...

iMethyl-STTNC: Identification of N-methyladenosine sites by extending the idea of SAAC into Chou's PseAAC to formulate RNA sequences.

N- methyladenosine (mA) is a vital post-transcriptional modification, which adds another layer of epigenetic regulation at RNA level. It chemically mo...

GOATOOLS: A Python library for Gene Ontology analyses.

The biological interpretation of gene lists with interesting shared properties, such as up- or down-regulation in a particular experiment, is typicall...

A Machine Learning Approach for Predicting HIV Reverse Transcriptase Mutation Susceptibility of Biologically Active Compounds.

HIV resistance emerging against antiretroviral drugs represents a great threat to the continued prolongation of the lifespans of HIV-infected patients...

Molecular Genotyping of Species Isolated from Patients in Tehran, Iran, by Repetitive Element PCR Fingerprinting.

BACKGROUND & OBJECTIVE: is an opportunistic pathogen with high pathogenic and antibiotic-resistance potential and is also considered as one of the ma...

Deep learning sequence-based ab initio prediction of variant effects on expression and disease risk.

Key challenges for human genetics, precision medicine and evolutionary biology include deciphering the regulatory code of gene expression and understa...

A machine-learned analysis of human gene polymorphisms modulating persisting pain points to major roles of neuroimmune processes.

BACKGROUND: Human genetic research has implicated functional variants of more than one hundred genes in the modulation of persisting pain. Artificial ...

Identification of 170 New Long Noncoding RNAs in .

Long noncoding RNAs (lncRNAs) are transcripts generally longer than 200 nucleotides with no or poor protein coding potential, and most of their functi...

Enabling Precision Medicine through Integrative Network Models.

A key challenge in precision medicine lies in understanding molecular-level underpinnings of complex human disease. Biological networks in multicellul...

Deep learning models for bacteria taxonomic classification of metagenomic data.

BACKGROUND: An open challenge in translational bioinformatics is the analysis of sequenced metagenomes from various environmental samples. Of course, ...

Predicting Post Neoadjuvant Axillary Response Using a Novel Convolutional Neural Network Algorithm.

OBJECTIVES: In the postneoadjuvant chemotherapy (NAC) setting, conventional radiographic complete response (rCR) is a poor predictor of pathologic com...

Scaling up molecular pattern recognition with DNA-based winner-take-all neural networks.

From bacteria following simple chemical gradients to the brain distinguishing complex odour information, the ability to recognize molecular patterns i...

PLANET-SNP pipeline: PLants based ANnotation and Establishment of True SNP pipeline.

Acute prediction of SNPs (Single Nucleotide Polymorphisms) from high throughput sequencing data is a challenging problem, having potential to explore ...

Dynamic Covalent Chemistry at Interfaces: Development of Tougher, Healable Composites through Stress Relaxation at the Resin-Silica Nanoparticles Interface.

The interfacial region in composites that incorporate filler materials of dramatically different modulus relative to the resin phase acts as a stress ...

Prediction of RNA-protein sequence and structure binding preferences using deep convolutional and recurrent neural networks.

BACKGROUND: RNA regulation is significantly dependent on its binding protein partner, known as the RNA-binding proteins (RBPs). Unfortunately, the bin...

HECIL: A Hybrid Error Correction Algorithm for Long Reads with Iterative Learning.

Second-generation DNA sequencing techniques generate short reads that can result in fragmented genome assemblies. Third-generation sequencing platform...

Machine Learning Helps Identify New Drug Mechanisms in Triple-Negative Breast Cancer.

This paper demonstrates the ability of mach- ine learning approaches to identify a few genes among the 23,398 genes of the human genome to experiment ...

A Novel Morphological Marker for the Analysis of Molecular Activities at the Single-cell Level.

For more than a century, hematoxylin and eosin (H&E) staining has been the de facto standard for histological studies. Consequently, the legacy of his...