Peer-reviewed Articles

19 downloads
111 views

Wheat streak mosaic virus (WSMV) causes streak mosaic disease in wheat (Triticum aestivum L.) and has been an important constraint limiting wheat production in many regions around the world. Wsm2 is the only resistance gene discovered in wheat genome and has been...

["Agricultural Science","Bioinformatics","Genomics","Plant Science"]
doi:10.7717/peerj.4678
79 downloads
530 views

Prediction of taxonomy for marker gene sequences such as 16S ribosomal RNA (rRNA) is a fundamental task in microbiology. Most experimentally observed sequences are diverged from reference sequences of authoritatively named organisms, creating a challenge for prediction...

["Bioinformatics","Computational Biology","Microbiology","Taxonomy"]
doi:10.7717/peerj.4652
53 downloads
521 views

The existence of only natural brown and green cotton fibers (BCF and GCF, respectively), as well as poor fiber quality, limits the use of naturally colored cotton (Gossypium hirsutum L.). A better understanding of fiber pigment regulation is needed to surmount...

["Bioinformatics","Genetics","Genomics","Plant Science"]
doi:10.7717/peerj.4537
39 downloads
278 views

Trans-acting small interfering RNAs (ta-siRNAs) are transcribed from protein non-coding genomic TAS loci and belong to a plant-specific class of endogenous small RNAs. These siRNAs have been found to regulate gene expression in most taxa including seed plants,...

["Bioinformatics","Genomics","Molecular Biology","Plant Science"]
doi:10.7717/peerj.4636
38 downloads
364 views

Background Data artifacts due to variations in experimental handling are ubiquitous in microarray studies, and they can lead to biased and irreproducible findings. A popular approach to correct for such artifacts is through post hoc data adjustment such as data...

["Bioinformatics","Genomics","Statistics"]
doi:10.7717/peerj.4584
151 downloads
802 views

Background DNA metabarcoding is used to generate species composition data for entire communities. However, sequencing errors in high-throughput sequencing instruments are fairly common, usually requiring reads to be clustered into operational taxonomic units (OTUs),...

["Biogeography","Bioinformatics","Molecular Biology","Freshwater Biology"]
doi:10.7717/peerj.4644
125 downloads
528 views

The budgerigar (Melopsittacus undulatus) is one of the most widely studied parrot species, serving as an excellent animal model for behavior and neuroscience research. Until recently, it was unknown how sexual differences in the behavior, physiology, and development...

["Biochemistry","Bioinformatics","Genomics","Molecular Biology","Zoology"]
doi:10.7717/peerj.4615
58 downloads
360 views

Many kinases are still ‘orphans,’ which means knowledge about their substrates, and often also about the processes they regulate, is lacking. Here, DIA1/C3orf58, a member of a novel predicted kinase-like family, is shown to be present in the endoplasmic reticulum...

["Bioinformatics","Cell Biology","Molecular Biology"]
doi:10.7717/peerj.4599
49 downloads
308 views

Complex diseases such as cancer are usually the result of a combination of environmental factors and one or several biological pathways consisting of sets of genes. Each biological pathway exerts its function by delivering signaling through the gene network. Theoretically,...

["Bioinformatics","Computational Biology"]
doi:10.7717/peerj.4571
159 downloads
1,213 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:10.7717/peerj.4600
148 downloads
815 views

Background Plasmids play an important role in the dissemination of antibiotic resistance, making their detection an important task. Using whole genome sequencing (WGS), it is possible to capture both bacterial and plasmid sequence data, but short read lengths make...

["Bioinformatics","Computational Biology","Microbiology"]
doi:10.7717/peerj.4588
64 downloads
407 views

Genome rearrangements have played an important role in the evolution of Yersinia pestis from its progenitor Yersinia pseudotuberculosis. Traditional phylogenetic trees for Y. pestis based on sequence comparison have short internal branches and low bootstrap supports...

["Bioinformatics","Genomics","Mathematical Biology"]
doi:10.7717/peerj.4545
49 downloads
226 views

Background Labels are a way to add some information on a text, such as functional annotations such as genes on a DNA sequences. V(D)J recombinations are DNA recombinations involving two or three short genes in lymphocytes. Sequencing this short region (500 bp or...

["Bioinformatics","Computational Biology","Algorithms and Analysis of Algorithms"]
doi:10.7717/peerj-cs.148
108 downloads
451 views

Even with the great advances in immunotherapy in recent years, the response rate to immune checkpoint inhibitor therapy for non-small cell lung cancer is only about 20%. We aimed to identify new features that would better predict which patients can benefit from...

["Bioinformatics","Genomics"]
doi:10.7717/peerj.4546
89 downloads
615 views

Circular RNAs (circRNAs), a class of recently discovered non-coding RNAs, play a role in biological and developmental processes. A recent study showed that circRNAs exist in plants and play a role in their environmental stress responses. However, cotton circRNAs...

["Agricultural Science","Bioinformatics","Molecular Biology","Plant Science"]
doi:10.7717/peerj.4500

Refine by manuscript type

Top subject areas - Articles

Top subject areas - People

View all subject areas