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Mining microbe-disease interactions from literature via a transfer learning model

期刊: BMC BIOINFORMATICS, 2021; 22 (1)

Background: Interactions of microbes and diseases are of great importance for biomedical research. However, large-scale of microbe-disease interaction......

SWnet: a deep learning model for drug response prediction from cancer genomic signatures and compound chemical structures

期刊: BMC BIOINFORMATICS, 2021; 22 (1)

Background One of the major challenges in precision medicine is accurate prediction of individual patient's response to drugs. A great number of compu......

MUREN: a robust and multi-reference approach of RNA-seq transcript normalization

期刊: BMC BIOINFORMATICS, 2021; 22 (1)

Background Normalization of RNA-seq data aims at identifying biological expression differentiation between samples by removing the effects of unwanted......

An iteration model for identifying essential proteins by combining comprehensive PPI network with biological information

期刊: BMC BIOINFORMATICS, 2021; 22 (1)

Background Essential proteins have great impacts on cell survival and development, and played important roles in disease analysis and new drug design.......

Instance-based error correction for short reads of disease-associated genes

期刊: BMC BIOINFORMATICS, 2021; 22 (SUPPL 6)

Background Genomic reads from sequencing platforms contain random errors. Global correction algorithms have been developed, aiming to rectify all poss......

scSensitiveGeneDefine: sensitive gene detection in single-cell RNA sequencing data by Shannon entropy

期刊: BMC BIOINFORMATICS, 2021; 22 (1)

Background Single-cell RNA sequencing (scRNA-seq) is the most widely used technique to obtain gene expression profiles from complex tissues. Cell subs......

A novel miRNA-based classification model of risks and stages for clear cell renal cell carcinoma patients

期刊: BMC BIOINFORMATICS, 2021; 22 (SUPPL 10)

Background Clear cell renal cell carcinoma (ccRCC) is the most common subtype of renal carcinoma and patients at advanced stage showed poor survival r......

MSCFS: inferring circRNA functional similarity based on multiple data sources

期刊: BMC BIOINFORMATICS, 2021; 22 (SUPPL 10)

Background: More and more evidence shows that circRNA plays an important role in various biological processes and human health. Therefore, inferring t......

RPocket: an intuitive database of RNA pocket topology information with RNA-ligand data resources

期刊: BMC BIOINFORMATICS, 2021; 22 (1)

Background: RNA regulates a variety of biological functions by interacting with other molecules. The ligand often binds in the RNA pocket to trigger s......

Application of network link prediction in drug discovery

期刊: BMC BIOINFORMATICS, 2021; 22 (1)

Background Technological and research advances have produced large volumes of biomedical data. When represented as a network (graph), these data becom......

DSCMF: prediction of LncRNA-disease associations based on dual sparse collaborative matrix factorization

期刊: BMC BIOINFORMATICS, 2021; 22 (SUPPL 3)

Background: In the development of science and technology, there are increasing evidences that there are some associations between lncRNAs and human di......

Clustering of cancer data based on Stiefel manifold for multiple views

期刊: BMC BIOINFORMATICS, 2021; 22 (1)

Background In recent years, various sequencing techniques have been used to collect biomedical omics datasets. It is usually possible to obtain multip......

Popularity and performance of bioinformatics software: the case of gene set analysis

期刊: BMC BIOINFORMATICS, 2021; 22 (1)

Background Gene Set Analysis (GSA) is arguably the method of choice for the functional interpretation of omics results. The following paper explores t......

A novel end-to-end method to predict RNA secondary structure profile based on bidirectional LSTM and residual neural network

期刊: BMC BIOINFORMATICS, 2021; 22 (1)

BackgroundStudies have shown that RNA secondary structure, a planar structure formed by paired bases, plays diverse vital roles in fundamental life ac......

Comparative analysis and prediction of nucleosome positioning using integrative feature representation and machine learning algorithms

期刊: BMC BIOINFORMATICS, 2021; 22 (SUPPL 6)

Background Nucleosome plays an important role in the process of genome expression, DNA replication, DNA repair and transcription. Therefore, the resea......

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