Background As the world’s second-largest economy, China has launched health reforms for the second time and invested significant funding in medical informatics (MI) since 2010; however, few studies have been conducted on the outcomes of this ambitious cause. Objective...

["Bioinformatics","Clinical Trials","Science and Medical Education"]
doi:10.7717/peerj.4082

Background Tartary buckwheat (TB), a crop rich in protein, dietary fiber, and flavonoids, has been reported to have an effect on Type II diabetes (T2D), hypertension (HT), and hyperlipidemia (HL). However, limited information is available about the relationship...

["Bioinformatics","Diabetes and Endocrinology"]
doi:10.7717/peerj.4042

Transcriptome resources for social insects have the potential to provide new insight into polyphenism, i.e., how divergent phenotypes arise from the same genome. Here we present a transcriptome based on paired-end RNA sequencing data for the ant Formica exsecta...

["Bioinformatics","Computational Biology","Entomology","Evolutionary Studies","Genomics"]
doi:10.7717/peerj.3998
34 downloads
124 views

Normalization is the first critical step in microbiome sequencing data analysis used to account for variable library sizes. Current RNA-Seq based normalization methods that have been adapted for microbiome data fail to consider the unique characteristics of microbiome...

["Bioinformatics","Genomics","Statistics"]
doi:10.7287/peerj.preprints.3417v2
20 downloads
167 views

This paper describes the development and application of a suite of tools, called PBxplore, to analyze the dynamics and deformability of protein structures using Protein Blocks (PBs). Proteins are highly dynamic macromolecules, and a classical way to analyze their...

["Bioinformatics","Computational Biology","Molecular Biology"]
doi:10.7717/peerj.4013
27 downloads
206 views

Modern genome sequencing strategies are highly sensitive to contamination making the detection of foreign DNA sequences an important part of analysis pipelines. Here we use Taxoblast, a simple pipeline with a graphical user interface, for the post-assembly detection...

["Bioinformatics","Genomics","Plant Science"]
doi:10.7717/peerj.4073
16 downloads
124 views

Background Oral tongue squamous cell carcinoma (OTSCC) is the most common subtype of oral cancer. A predictive gene signature is necessary for prognosis of OTSCC. Methods Five microarray data sets of OTSCC from the Gene Expression Omnibus (GEO) and one data set...

["Bioinformatics","Computational Biology","Genetics","Genomics","Oncology"]
doi:10.7717/peerj.4062
24 downloads
162 views

Prophages have been considered genetic units that have an intimate association with novel phenotypic properties of bacterial hosts, such as pathogenicity and genomic variation. Little is known about the genetic information of prophages in the genome of Streptococcus...

["Bioinformatics","Microbiology"]
doi:10.7717/peerj.4057
49 downloads
404 views

The development and application of metagenomic approaches have provided an opportunity to study and define horizontal gene transfer (HGT) on the level of microbial communities. However, no current metagenomic data simulation tools offers the option to introduce...

["Bioinformatics","Evolutionary Studies","Genomics","Microbiology"]
doi:10.7717/peerj.4015
25 downloads
103 views

The hemagglutinin subtypes from Influenza A can be divided into distinct lineages. This is important for tracing the evolutionary history of the gene. It allows regional lineages to be identified and studied. The process of lineage identification depends on phylogenetic...

["Bioinformatics","Virology","Computational Science"]
doi:10.7287/peerj.preprints.3396v1
31 downloads
245 views

In translational medicine, the technology of RNA sequencing (RNA-seq) continues to prove powerful, and transforming the RNA-seq data into biological insights has become increasingly imperative. We present the Transcriptomics profiler for Easy Discovery (TED) toolkit,...

["Bioinformatics","Genomics","Translational Medicine","Computational Science","Data Science"]
doi:10.7287/peerj.preprints.3385v1
54 downloads
287 views

Plant type III polyketide synthase (PKS) can catalyse the formation of a series of secondary metabolites with different structures and different biological functions; the enzyme plays an important role in plant growth, development and resistance to stress. At present,...

["Agricultural Science","Bioinformatics","Genomics","Plant Science"]
doi:10.7717/peerj.3974
12 downloads
121 views

Most evolutionary analyses or structure modeling are based upon pre-estimated multiple sequence alignment (MSA) models. From a computational point of view, it is too complex to estimate a correct alignment. Hence, increasing or identifying signal inside sequence...

["Bioinformatics"]
doi:10.7287/peerj.preprints.3376v1
47 downloads
233 views

Copper plays key roles in plant physiological activities. To maintain copper cellular homeostasis, copper chaperones have important functions in binding and transporting copper to target proteins. Detailed characterization and function analysis of a copper chaperone,...

["Bioinformatics","Molecular Biology","Plant Science"]
doi:10.7717/peerj.3962
99 downloads
578 views

Microorganisms that reside on and in mammals, such as bats, have the potential to influence their host’s health and to provide defenses against invading pathogens. However, we have little understanding of the skin and fur bacterial microbiota on bats, or factors...

["Biogeography","Bioinformatics","Ecology","Microbiology"]
doi:10.7717/peerj.3944

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