Peer-reviewed Articles

36 downloads
531 views

Background Carbonic anhydrases (CAs) are ubiquitous, essential enzymes which catalyze the conversion of carbon dioxide and water to bicarbonate and H+ ions. Vertebrate genomes generally contain gene loci for 15–21 different CA isoforms, three of which are enzymatically...

["Biochemistry","Bioinformatics","Evolutionary Studies"]
doi:10.7717/peerj.4128
41 downloads
215 views

Abscisic acid (ABA) receptor pyrabactin resistance1/PYR1-like/regulatory components of ABA receptor (PYR1/PYL/RCAR) (named PYLs for simplicity) are core regulators of ABA signaling, and have been well studied in Arabidopsis and rice. However, knowledge is limited...

["Bioinformatics","Evolutionary Studies","Genomics","Plant Science"]
doi:10.7717/peerj.4126
258 downloads
5,208 views

Background Modern advances in sequencing technology have enabled the census of microbial members of many natural ecosystems. Recently, attention is increasingly being paid to the microbial residents of human-made, built ecosystems, both private (homes) and public...

["Bioinformatics","Ecology","Microbiology"]
doi:10.7717/peerj.4029
48 downloads
143 views

Availability of snake genome sequences has opened up exciting areas of research on comparative genomics and gene diversity. One of the challenges in studying snake genomes is the acquisition of biological material from live animals, especially from the venomous...

["Biodiversity","Bioinformatics","Evolutionary Studies","Genomics"]
doi:10.7717/peerj.4104
42 downloads
286 views

SDMtoolbox 2.0 is a software package for spatial studies of ecology, evolution, and genetics. The release of SDMtoolbox 2.0 allows researchers to use the most current ArcGIS software and MaxEnt software, and reduces the amount of time that would be spent developing...

["Biodiversity","Biogeography","Bioinformatics","Conservation Biology"]
doi:10.7717/peerj.4095
106 downloads
822 views

Systems for collecting image data in conjunction with computer vision techniques are a powerful tool for increasing the temporal resolution at which plant phenotypes can be measured non-destructively. Computational tools that are flexible and extendable are needed...

["Agricultural Science","Bioinformatics","Computational Biology","Plant Science","Data Mining and Machine Learning"]
doi:10.7717/peerj.4088
33 downloads
322 views

Background Lung cancer is considered as one of the most frequent and deadly cancers with high mortality all around the world. It is critical to find new biomarkers for early diagnosis of lung cancer, especially lung squamous cell carcinoma (LUSC). The Cancer Genome...

["Bioinformatics","Genomics","Molecular Biology","Public Health"]
doi:10.7717/peerj.4101
65 downloads
610 views

The amino acid content of the proteins encoded by a genome may predict the coding potential of that genome and may reflect lifestyle restrictions of the organism. Here, we calculated the Kullback–Leibler divergence from the mean amino acid content as a metric to...

["Bioinformatics","Computational Biology","Genomics","Microbiology","Statistics"]
doi:10.7717/peerj.4026
45 downloads
223 views

Recently, Docker technology has received increasing attention throughout the bioinformatics community. However, its implementation has not yet been mastered by most biologists; accordingly, its application in biological research has been limited. In order to popularize...

["Bioinformatics","Computational Biology","Genomics","Microbiology"]
doi:10.7717/peerj.3948
64 downloads
286 views

Background Streptomyces are well known for their capability to produce many bioactive secondary metabolites with medical and industrial importance. Here we report a novel bioactive phenazine compound, 6-((2-hydroxy-4-methoxyphenoxy) carbonyl) phenazine-1-carboxylic...

["Bioinformatics","Biotechnology","Genomics","Drugs and Devices"]
doi:10.7717/peerj.3738
95 downloads
398 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
51 downloads
503 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
52 downloads
254 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
76 downloads
524 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
63 downloads
363 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

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