Peer-reviewed Articles - Biology

24 downloads
189 views

Assay for Transposase Accessible Chromatin (ATAC-seq) is an open chromatin profiling assay that is adapted to interrogate chromatin accessibility from small cell numbers. ATAC-seq surmounted a major technical barrier and enabled epigenome profiling of clinical...

["Bioinformatics","Computational Biology","Genomics","Human-Computer Interaction","Computational Science"]
doi:10.7717/peerj.4040
16 downloads
215 views

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
33 downloads
175 views

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
35 downloads
361 views

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
35 downloads
285 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
44 downloads
272 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
22 downloads
199 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
38 downloads
247 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
56 downloads
425 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
55 downloads
296 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
52 downloads
245 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
103 downloads
590 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
196 downloads
1,054 views

Background Differential expression analysis on the basis of RNA-Seq count data has become a standard tool in transcriptomics. Several studies have shown that prior normalization of the data is crucial for a reliable detection of transcriptional differences. Until...

["Bioinformatics","Statistics"]
doi:10.7717/peerj.3859
70 downloads
284 views

Background The emergence of functions in biological systems is a long-standing issue that can now be addressed at the cell level with the emergence of high throughput technologies for genome sequencing and phenotyping. The reconstruction of complete metabolic networks...

["Bioinformatics","Computational Biology","Artificial Intelligence"]
doi:10.7717/peerj.3860
69 downloads
475 views

Understanding how the environment selects a given taxon and the diversity patterns that emerge as a result of environmental filtering can dramatically improve our ability to analyse any environment in depth as well as advancing our knowledge on how the response...

["Biodiversity","Biogeography","Bioinformatics","Microbiology"]
doi:10.7717/peerj.3827

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