Peer-reviewed Articles - Biology

Background Viral metagenomics (viromics) is increasingly used to obtain uncultivated viral genomes, evaluate community diversity, and assess ecological hypotheses. While viromic experimental methods are relatively mature and widely accepted by the research community,...

["Bioinformatics","Ecology","Genomics","Microbiology"]
doi:10.7717/peerj.3817
8 downloads
189 views

Background The rapid increase in antibiotic resistance by various bacterial pathogens underlies the significance of developing new therapies and exploring different drug targets. A fraction of bacterial pathogens abbreviated as ESKAPE by the European Center for...

["Bioinformatics","Computational Biology","Microbiology","Pharmacology"]
doi:10.7717/peerj.3765
19 downloads
182 views

Aquaporins (AQPs) are essential channel proteins that execute multi-functions throughout plant growth and development, including water transport, uncharged solutes uptake, stress response, and so on. Here, we report the first genome-wide identification and characterization...

["Agricultural Science","Bioinformatics","Genomics","Plant Science"]
doi:10.7717/peerj.3747
35 downloads
161 views

Cinnamomum camphora, a member of the Lauraceae family, is a valuable aromatic and timber tree that is indigenous to the south of China and Japan. All parts of Cinnamomum camphora have secretory cells containing different volatile chemical compounds that are utilized...

["Bioinformatics","Conservation Biology","Genetics","Molecular Biology","Plant Science"]
doi:10.7717/peerj.3820
26 downloads
320 views

The Drosophila melanogaster P transposable element provides one of the best cases of horizontal transfer of a mobile DNA sequence in eukaryotes. Invasion of natural populations by the P element has led to a syndrome of phenotypes known as P-M hybrid dysgenesis...

["Bioinformatics","Evolutionary Studies","Genetics","Genomics"]
doi:10.7717/peerj.3824
17 downloads
191 views

Background C-X-C chemokine ligand 12 (CXCL12) has important implications in breast cancer (BC) pathogenesis. It is selectively expressed on B and T lymphocytes and is involved in hematopoiesis, thymocyte trafficking, stem cell motility, neovascularization, and...

["Bioinformatics","Computational Biology","Genetics","Epidemiology"]
doi:10.7717/peerj.3822
29 downloads
268 views

Life science ontologies play an important role in Semantic Web. Given the diversity in fish species and the associated wealth of information, it is imperative to develop an ontology capable of linking and integrating this information in an automated fashion. As...

["Aquaculture, Fisheries and Fish Science","Bioinformatics","Computational Science"]
doi:10.7717/peerj.3811
109 downloads
671 views

Plants play a crucial role in foodstuff, medicine, industry, and environmental protection. The skill of recognising plants is very important in some applications, including conservation of endangered species and rehabilitation of lands after mining activities....

["Bioinformatics","Computational Biology","Plant Science"]
doi:10.7717/peerj.3792
43 downloads
244 views

High sensitivity methods such as next generation sequencing and polymerase chain reaction (PCR) are adversely impacted by organismal and DNA contaminants. Current methods for detecting contaminants in microbial materials (genomic DNA and cultures) are not sensitive...

["Bioinformatics","Genomics","Microbiology"]
doi:10.7717/peerj.3729
47 downloads
258 views

MADS-box transcription factors play significant roles in plant developmental processes such as floral organ conformation, flowering time, and fruit development. Pear (Pyrus), as the third-most crucial temperate fruit crop, has been fully sequenced. However, there...

["Bioinformatics","Genomics","Plant Science"]
doi:10.7717/peerj.3776
55 downloads
279 views

RNA sequencing (RNA-Seq) enables the measurement and comparison of gene expression with isoform-level quantification. Differences in the effect of each isoform may make traditional methods, which aggregate isoforms, ineffective. Here, we introduce a variance component-based...

["Bioinformatics","Statistics"]
doi:10.7717/peerj.3797
60 downloads
699 views

Clustered regularly interspaced short palindromic repeat (CRISPR) systems are the adaptive immune systems of bacteria and archaea against viral infection. While CRISPRs have been exploited as a tool for genetic engineering, their spacer sequences can also provide...

["Bioinformatics","Computational Biology","Ecology","Genomics","Microbiology"]
doi:10.7717/peerj.3788
48 downloads
215 views

Background The endoplasmic reticulum plays an important role in many cellular processes, which includes protein synthesis, folding and post-translational processing of newly synthesized proteins. It is also the site for quality control of misfolded proteins and...

["Bioinformatics","Computational Biology"]
doi:10.7717/peerj.3561
134 downloads
677 views

Whole genome sequencing (WGS) is a very valuable resource to understand the evolutionary history of poorly known species. However, in organisms with large genomes, as most amphibians, WGS is still excessively challenging and transcriptome sequencing (RNA-seq) represents...

["Bioinformatics","Evolutionary Studies","Genomics","Molecular Biology","Zoology"]
doi:10.7717/peerj.3702
36 downloads
245 views

A key step in the transformation of raw sequencing reads into biological insights is the trimming of adapter sequences and low-quality bases. Read trimming has been shown to increase the quality and reliability while decreasing the computational requirements of...

["Bioinformatics","Genomics","Computational Science"]
doi:10.7717/peerj.3720

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