Peer-reviewed Articles - Biology

142 downloads
466 views

Cervical cancer is the fourth most common cancer in women worldwide with human papillomavirus (HPV) being the main cause the disease. Chromosomal amplifications have been identified as a source of upregulation for cervical cancer driver genes but cannot fully explain...

["Computational Biology","Microbiology","Oncology"]
doi:10.7717/peerj.5590
120 downloads
749 views

The increasing move towards open access full-text scientific literature enhances our ability to utilize advanced text-mining methods to construct information-rich networks that no human will be able to grasp simply from ‘reading the literature’. The utility of...

["Computational Biology","Microbiology","Plant Science"]
doi:10.7717/peerj.4806
93 downloads
638 views

High-throughput phenotype assays are a cornerstone of systems biology as they allow direct measurements of mutations, genes, strains, or even different genera. High-throughput methods also require data analytic methods that reduce complex time-series data to a...

["Computational Biology","Microbiology"]
doi:10.7717/peerj.4681
6 citations
651 downloads
3,230 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
532 downloads
1,898 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
1 citation
223 downloads
1,292 views

Membrane-bound fatty acid desaturases perform oxygenated desaturation reactions to insert double bonds within fatty acyl chains in regioselective and stereoselective manners. The Δ9-fatty acid desaturase strictly creates the first double bond between C9 and 10...

["Biotechnology","Computational Biology","Microbiology"]
doi:10.7717/peerj.4347
259 downloads
1,488 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
212 downloads
3,129 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
13 citations
1,666 downloads
12,101 views

Next-generation sequencing of 16S ribosomal RNA is widely used to survey microbial communities. Sequences are typically assigned to Operational Taxonomic Units (OTUs). Closed- and open-reference OTU assignment matches reads to a reference database at 97% identity...

["Bioinformatics","Computational Biology","Microbiology"]
doi:10.7717/peerj.3889
1 citation
223 downloads
1,076 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
212 downloads
2,151 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
1 citation
226 downloads
1,089 views

Colorectal cancer (CRC) is the third commonest malignant tumor. Previous studies have revealed that the composition change of the human gut microbiome, measured by community diversity, is associated with the progression of CRC. However, a further question, whether...

["Computational Biology","Ecology","Microbiology","Computational Science"]
doi:10.7717/peerj.3383
5 citations
660 downloads
2,187 views

Background Fast, accurate and high-throughput identification of bacterial isolates is in great demand. The present work was conducted to investigate the possibility of identifying isolates from unassembled next-generation sequencing reads using custom-made guide...

["Bioinformatics","Computational Biology","Microbiology"]
doi:10.7717/peerj.3353
5 citations
210 downloads
1,574 views

Metagenomics-based studies have provided insight into many of the complex microbial communities responsible for maintaining life on this planet. Sequencing efforts often uncover novel genetic content; this is most evident for phage communities, in which upwards...

["Bioinformatics","Computational Biology","Microbiology","Virology"]
doi:10.7717/peerj.3281
5 citations
548 downloads
3,431 views

Identification and quantification of microorganisms is a significant step in studying the alpha and beta diversities within and between microbial communities respectively. Both identification and quantification of a given microbial community can be carried out...

["Bioinformatics","Computational Biology","Genomics","Microbiology","Taxonomy"]
doi:10.7717/peerj.3138

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