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A random forest based computational model for predicting novel lncRNA-disease associations

Fri, 27/03/2020 - 5:30am
Accumulated evidence shows that the abnormal regulation of long non-coding RNA (lncRNA) is associated with various human diseases. Accurately identifying disease-associated lncRNAs is helpful to study the mech...
Categories: Bioinformatics Trends

Exploiting sequence labeling framework to extract document-level relations from biomedical texts

Fri, 27/03/2020 - 5:30am
Both intra- and inter-sentential semantic relations in biomedical texts provide valuable information for biomedical research. However, most existing methods either focus on extracting intra-sentential relation...
Categories: Bioinformatics Trends

HeMoQuest: a webserver for qualitative prediction of transient heme binding to protein motifs

Fri, 27/03/2020 - 5:30am
The notion of heme as a regulator of many physiological processes via transient binding to proteins is one that is recently being acknowledged. The broad spectrum of the effects of heme makes it important to i...
Categories: Bioinformatics Trends

QuaDMutNetEx: a method for detecting cancer driver genes with low mutation frequency

Mon, 23/03/2020 - 5:30am
Cancer is caused by genetic mutations, but not all somatic mutations in human DNA drive the emergence or growth of cancers. While many frequently-mutated cancer driver genes have already been identified and ar...
Categories: Bioinformatics Trends

Hellinger distance-based stable sparse feature selection for high-dimensional class-imbalanced data

Mon, 23/03/2020 - 5:30am
Feature selection in class-imbalance learning has gained increasing attention in recent years due to the massive growth of high-dimensional class-imbalanced data across many scientific fields. In addition to r...
Categories: Bioinformatics Trends

Fast tree aggregation for consensus hierarchical clustering

Fri, 20/03/2020 - 5:30am
In unsupervised learning and clustering, data integration from different sources and types is a difficult question discussed in several research areas. For instance in omics analysis, dozen of clustering metho...
Categories: Bioinformatics Trends

Standard machine learning approaches outperform deep representation learning on phenotype prediction from transcriptomics data

Fri, 20/03/2020 - 5:30am
The ability to confidently predict health outcomes from gene expression would catalyze a revolution in molecular diagnostics. Yet, the goal of developing actionable, robust, and reproducible predictive signatu...
Categories: Bioinformatics Trends

Efficient identification of multiple pathways: RNA-Seq analysis of livers from 56Fe ion irradiated mice

Fri, 20/03/2020 - 5:30am
mRNA interaction with other mRNAs and other signaling molecules determine different biological pathways and functions. Gene co-expression network analysis methods have been widely used to identify correlation ...
Categories: Bioinformatics Trends

2D electrophoresis image brightness correction based on gradient interval histogram

Thu, 19/03/2020 - 5:30am
Two-dimensional electrophoresis (2DE) is one of the most widely applied techniques in comparative proteomics. The basic task of 2DE is to identify differential protein expression by quantitative analysis of 2D...
Categories: Bioinformatics Trends

Correction to: Computational assembly of a human Cytomegalovirus vaccine upon experimental epitope legacy

Thu, 19/03/2020 - 5:30am
After publication of the original article [1], we were notified that legends of Fig. 1 and Fig. 2 have been swapped.
Categories: Bioinformatics Trends

Revealing hidden information in osteoblast’s mechanotransduction through analysis of time patterns of critical events

Wed, 18/03/2020 - 5:30am
Mechanotransduction in bone cells plays a pivotal role in osteoblast differentiation and bone remodelling. Mechanotransduction provides the link between modulation of the extracellular matrix by mechanical loa...
Categories: Bioinformatics Trends

SEQing: web-based visualization of iCLIP and RNA-seq data in an interactive python framework

Wed, 18/03/2020 - 5:30am
RNA-binding proteins interact with their target RNAs at specific sites. These binding sites can be determined genome-wide through individual nucleotide resolution crosslinking immunoprecipitation (iCLIP). Subs...
Categories: Bioinformatics Trends

A deep learning-based framework for lung cancer survival analysis with biomarker interpretation

Wed, 18/03/2020 - 5:30am
Lung cancer is the leading cause of cancer-related deaths in both men and women in the United States, and it has a much lower five-year survival rate than many other cancers. Accurate survival analysis is urge...
Categories: Bioinformatics Trends

RASflow: an RNA-Seq analysis workflow with Snakemake

Wed, 18/03/2020 - 5:30am
With the cost of DNA sequencing decreasing, increasing amounts of RNA-Seq data are being generated giving novel insight into gene expression and regulation. Prior to analysis of gene expression, the RNA-Seq da...
Categories: Bioinformatics Trends

LCQS: an efficient lossless compression tool of quality scores with random access functionality

Wed, 18/03/2020 - 5:30am
Advanced sequencing machines dramatically speed up the generation of genomic data, which makes the demand of efficient compression of sequencing data extremely urgent and significant. As the most difficult par...
Categories: Bioinformatics Trends

Joining Illumina paired-end reads for classifying phylogenetic marker sequences

Sat, 14/03/2020 - 5:30am
Illumina sequencing of a marker gene is popular in metagenomic studies. However, Illumina paired-end (PE) reads sometimes cannot be merged into single reads for subsequent analysis. When mergeable PE reads are...
Categories: Bioinformatics Trends

Machine learning prediction of oncology drug targets based on protein and network properties

Sat, 14/03/2020 - 5:30am
The selection and prioritization of drug targets is a central problem in drug discovery. Computational approaches can leverage the growing number of large-scale human genomics and proteomics data to make in-si...
Categories: Bioinformatics Trends

MoAIMS: efficient software for detection of enriched regions of MeRIP-Seq

Sat, 14/03/2020 - 5:30am
Methylated RNA immunoprecipitation sequencing (MeRIP-Seq) is a popular sequencing method for studying RNA modifications and, in particular, for N6-methyladenosine (m6A), the most abundant RNA methylation modif...
Categories: Bioinformatics Trends

A big data approach to metagenomics for all-food-sequencing

Thu, 12/03/2020 - 5:30am
All-Food-Sequencing (AFS) is an untargeted metagenomic sequencing method that allows for the detection and quantification of food ingredients including animals, plants, and microbiota. While this approach avoi...
Categories: Bioinformatics Trends

Network hub-node prioritization of gene regulation with intra-network association

Thu, 12/03/2020 - 5:30am
To identify and prioritize the influential hub genes in a gene-set or biological pathway, most analyses rely on calculation of marginal effects or tests of statistical significance. These procedures may be ina...
Categories: Bioinformatics Trends

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