Peer-reviewed Articles

16 downloads
92 views

The cynomolgus macaque (Macaca fascicularis) is an extensively utilised nonhuman primate model for biomedical research due to its biological, behavioural, and genetic similarities to humans. Genomic information of cynomolgus macaque is vital for research in various...

["Bioinformatics","Genomics","Zoology","Immunology"]
doi:10.7717/peerj.3566
28 downloads
326 views

Gene Co-expression Network Analysis (GCNA) is a popular approach to analyze a collection of gene expression profiles. GCNA yields an assignment of genes to gene co-expression modules, a list of gene sets statistically over-represented in these modules, and a gene-to-gene...

["Bioinformatics","Computational Biology","Genomics","Computational Science"]
doi:10.7717/peerj.3678
23 downloads
144 views

Considering complicated microRNA (miRNA) biogenesis and action mechanisms, it was thought so high energy-consuming for a cell to afford simultaneous over-expression of many miRNAs. Thus it prompts that an alternative miRNA regulation pattern on protein-encoding...

["Bioinformatics","Cell Biology","Computational Biology"]
doi:10.7717/peerj.3682
59 downloads
568 views

Species interactions are a key component of ecosystems but we generally have an incomplete picture of who-eats-who in a given community. Different techniques have been devised to predict species interactions using theoretical models or abundances. Here, we explore...

["Bioinformatics","Ecology"]
doi:10.7717/peerj.3644
78 downloads
927 views

It has recently become possible to experimentally measure the effects of all amino-acid point mutations to proteins using deep mutational scanning. These experimental measurements can inform site-specific phylogenetic substitution models of gene evolution in nature....

["Bioinformatics","Computational Biology","Evolutionary Studies"]
doi:10.7717/peerj.3657
63 downloads
536 views

Species in the genus Ganoderma include several ecologically important and pathogenic fungal species whose medicinal and economic value is substantial. Due to the highly similar morphological features within the Ganoderma, identification of species has relied heavily...

["Bioinformatics","Mycology","Taxonomy"]
doi:10.7717/peerj.3596
102 downloads
469 views

Targeted high-throughput sequencing using hybrid-enrichment offers a promising source of data for inferring multiple, meaningfully resolved, independent gene trees suitable to address challenging phylogenetic problems in species complexes and rapid radiations....

["Bioinformatics","Evolutionary Studies","Plant Science"]
doi:10.7717/peerj.3569
63 downloads
486 views

Background This paper is a comment on the idea of matrix-free Cladistics. Demonstration of this idea’s efficiency is a major goal of the study. Within the proposed framework, the ordinary (phenetic) matrix is necessary only as “source” of Hennigian trees, not as...

["Bioinformatics","Taxonomy","Computational Science"]
doi:10.7717/peerj.3578
62 downloads
710 views

Newly emerging influenza viruses continue to threaten public health. A rapid determination of the host range of newly discovered influenza viruses would assist in early assessment of their risk. Here, we attempted to predict the host of influenza viruses using...

["Bioinformatics","Computational Biology","Virology"]
doi:10.7717/peerj.3579
49 downloads
307 views

Background As the fifth most common cancer worldwide, Hepatocellular carcinoma (HCC) is also the third most common cause of cancer-related death in China. Several lncRNAs have been demonstrated to be associated with occurrence and prognosis of HCC. However, identification...

["Bioinformatics","Molecular Biology","Gastroenterology and Hepatology","Oncology"]
doi:10.7717/peerj.3575
41 downloads
447 views

The major virulence factor of the pneumococcus, and target for conjugate vaccines, is the polysaccharide capsule, which is usually encoded by the highly variable cps locus. Serotype 37 is an unusual pneumococcal type in which the single β-glucosyltransferase gene...

["Bioinformatics","Genomics","Microbiology","Infectious Diseases"]
doi:10.7717/peerj.3571
77 downloads
385 views

Background The availability of large databases containing high resolution three-dimensional (3D) models of proteins in conjunction with functional annotation allows the exploitation of advanced supervised machine learning techniques for automatic protein function...

["Bioinformatics","Computational Biology","Data Mining and Machine Learning"]
doi:10.7717/peerj-cs.124
33 downloads
405 views

Background The ferric uptake regulator (Fur) is a transcription factor and the main regulator of iron acquisition in prokaryotes. When bound to ferric iron, Fur recognizes its DNA binding site and generally executes its function by repressing transcription of its...

["Bioinformatics","Genetics","Marine Biology","Microbiology","Molecular Biology"]
doi:10.7717/peerj.3461
248 downloads
1,882 views

The Tara Oceans Expedition has provided large, publicly-accessible microbial metagenomic datasets from a circumnavigation of the globe. Utilizing several size fractions from the samples originating in the Mediterranean Sea, we have used current assembly and binning...

["Bioinformatics","Marine Biology","Microbiology"]
doi:10.7717/peerj.3558
34 downloads
436 views

CodonGenie, freely available from http://codon.synbiochem.co.uk, is a simple web application for designing ambiguous codons to support protein mutagenesis applications. Ambiguous codons are derived from specific heterogeneous nucleotide mixtures, which create sequence...

["Bioengineering","Bioinformatics","Biotechnology","Computational Biology","Synthetic Biology"]
doi:10.7717/peerj-cs.120

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