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The mechanistic, diagnostic and therapeutic novel nucleic acids for hepatocellular carcinoma emerging in past score years

期刊: BRIEFINGS IN BIOINFORMATICS, 2021; 22 (2)

Despite The Central Dogma states the destiny of gene as `DNA makes RNA and RNA makes protein', the nucleic acids not only store and transmit genetic i......

Adaptive multi-source multi-view latent feature learning for inferring potential disease-associated miRNAs

期刊: BRIEFINGS IN BIOINFORMATICS, 2021; 22 (2)

Accumulating evidence has shown that microRNAs (miRNAs) play crucial roles in different biological processes, and their mutations and dysregulations h......

GPS-Palm: a deep learning-based graphic presentation system for the prediction of S-palmitoylation sites in proteins

期刊: BRIEFINGS IN BIOINFORMATICS, 2021; 22 (2)

As an important reversible lipid modification, S-palmitoylation mainly occurs at specific cysteine residues in proteins, participates in regulating va......

Inferring microenvironmental regulation of gene expression from single-cell RNA sequencing data using scMLnet with an application to COVID-19

期刊: BRIEFINGS IN BIOINFORMATICS, 2021; 22 (2)

Inferring how gene expression in a cell is influenced by cellular microenvironment is of great importance yet challenging. In this study, we present a......

DeepCPP: a deep neural network based on nucleotide bias information and minimum distribution similarity feature selection for RNA coding potential prediction

期刊: BRIEFINGS IN BIOINFORMATICS, 2021; 22 (2)

The development of deep sequencing technologies has led to the discovery of novel transcripts. Many in silico methods have been developed to assess th......

Cooperative driver pathway discovery via fusion of multi-relational data of genes, miRNAs and pathways

期刊: BRIEFINGS IN BIOINFORMATICS, 2021; 22 (2)

Discovering driver pathways is an essential step to uncover the molecular mechanism underlying cancer and to explore precise treatments for cancer pat......

Application of Bayesian phylogenetic inference modelling for evolutionary genetic analysis and dynamic changes in 2019-nCoV

期刊: BRIEFINGS IN BIOINFORMATICS, 2021; 22 (2)

The novel coronavirus (2019-nCoV) has recently caused a large-scale outbreak of viral pneumonia both in China and worldwide. In this study, we obtaine......

A computational toolset for rapid identification of SARS-CoV-2, other viruses and microorganisms from sequencing data

期刊: BRIEFINGS IN BIOINFORMATICS, 2021; 22 (2)

In this paper, we present a toolset and related resources for rapid identification of viruses and microorganisms from short-read or long-read sequenci......

Biomedical data and computational models for drug repositioning: a comprehensive review

期刊: BRIEFINGS IN BIOINFORMATICS, 2021; 22 (2)

Drug repositioning can drastically decrease the cost and duration taken by traditional drug research and development while avoiding the occurrence of ......

Transcriptome analysis of cepharanthine against a SARS-CoV-2-related coronavirus

期刊: BRIEFINGS IN BIOINFORMATICS, 2021; 22 (2)

Antiviral therapies targeting the pandemic coronavirus disease 2019 (COVID-19) are urgently required. We studied an already-approved botanical drug ce......

NCMCMDA: miRNA-disease association prediction through neighborhood constraint matrix completion

期刊: BRIEFINGS IN BIOINFORMATICS, 2021; 22 (1)

Emerging evidence shows that microRNAs (miRNAs) play a critical role in diverse fundamental and important biological processes associated with human d......

Identifying drug-target interactions based on graph convolutional network and deep neural network

期刊: BRIEFINGS IN BIOINFORMATICS, 2021; 22 (2)

Identification of new drug-target interactions (DTIs) is an important but a time-consuming and costly step in drug discovery. In recent years, to miti......

Integrating multi-network topology for gene function prediction using deep neural networks

期刊: BRIEFINGS IN BIOINFORMATICS, 2021; 22 (2)

Motivation: The emergence of abundant biological networks, which benefit from the development of advanced high-throughput techniques, contributes to d......

EP3: an ensemble predictor that accurately identifies type III secreted effectors

期刊: BRIEFINGS IN BIOINFORMATICS, 2021; 22 (2)

Type III secretion systems (T3SS) can be found in many pathogenic bacteria, such as Dysentery bacillus, Salmonella typhimurium, Vibrio cholera and pat......

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