Peer-reviewed Articles - Biology

40 downloads
229 views

Background Biological interactions between varicella (chickenpox) and herpes zoster (shingles), two diseases caused by the varicella zoster virus (VZV), continue to be debated including the potential effect on shingles cases following the introduction of universal...

["Computational Biology","Epidemiology","Infectious Diseases","Public Health"]
doi:10.7717/peerj.5012
28 downloads
219 views

Gene expression profiling data provide useful information for the investigation of biological function and process. However, identifying a specific expression pattern from extensive time series gene expression data is not an easy task. Clustering, a popular method,...

["Bioinformatics","Computational Biology"]
doi:10.7717/peerj.4927
30 downloads
259 views

Npas4 is an activity dependent transcription factor which is responsible for gearing the expression of target genes involved in neuro-transmission. Despite the importance of Npas4 in many neuronal diseases, the tertiary structure of Npas4 protein along with its...

["Computational Biology","Neuroscience"]
doi:10.7717/peerj.4978
57 downloads
486 views

Salt bridges form between pairs of ionisable residues in close proximity and are important interactions in proteins. While salt bridges are known to be important both for protein stability, recognition and regulation, we still do not have fully accurate predictive...

["Biochemistry","Computational Biology"]
doi:10.7717/peerj.4967
27 downloads
230 views

Supertree methods enable the reconstruction of large phylogenies. The supertree problem can be formalized in different ways in order to cope with contradictory information in the input. Some supertree methods are based on encoding the input trees in a matrix; other...

["Bioinformatics","Computational Biology","Evolutionary Studies","Taxonomy","Computational Science"]
doi:10.7717/peerj.4987
223 downloads
273 views

We evaluated allometric relationships in length, diameter, and mass of branches for two variably managed orchard tree species (tart cherry, Prunus cerasus; apple, Malus spp.). The empirically estimated allometric exponents (a) of the orchard trees were described...

["Agricultural Science","Computational Biology","Ecology","Plant Science"]
doi:10.7717/peerj.4949
70 downloads
363 views

Quantitative analysis of shape and form is critical in many biological disciplines, as context-dependent morphotypes reflect changes in gene expression and physiology, e.g., in comparisons of environment-dependent phenotypes, forward/reverse genetic assays or shape...

["Computational Biology","Ecology","Computational Science"]
doi:10.7717/peerj.4861
75 downloads
329 views

Circadian rhythms maintain a 24 h oscillation pattern in metabolic, physiological and behavioral processes in all living organisms. Circadian rhythms are organized as biochemical networks located in hypothalamus and peripheral tissues. Rhythmicity in the expression...

["Bioinformatics","Computational Biology"]
doi:10.7717/peerj.4877
151 downloads
781 views

The pond turtle Emys trinacris is an endangered endemic species of Sicily showing a fragmented distribution throughout the main island. In this study, we applied “Ensemble Niche Modelling”, combining more classical statistical techniques as Generalized Linear Models...

["Computational Biology","Ecology","Zoology","Climate Change Biology","Spatial and Geographic Information Science"]
doi:10.7717/peerj.4969
29 downloads
467 views

Tumor samples obtained from a single cancer patient spatially or temporally often consist of varying cell populations, each harboring distinct mutations that uniquely characterize its genome. Thus, in any given samples of a tumor having more than two haplotypes,...

["Bioinformatics","Computational Biology"]
doi:10.7717/peerj.4838
68 downloads
542 views

After transitioning to a new environment, species often exhibit rapid phenotypic innovation. One of the fastest mechanisms for this is duplication followed by specialization of existing genes. When this happens to a member of a gene family, it tends to leave a...

["Bioinformatics","Computational Biology","Evolutionary Studies"]
doi:10.7717/peerj.4873
30 downloads
320 views

As a DNA binding transcriptional activator, Gal4 promotes the expression of genes responsible for galactose metabolism. The Gal4 protein from Saccharomyces cerevisiae (baker’s yeast) has become a model for studying eukaryotic transcriptional activation in general...

["Bioinformatics","Computational Biology","Data Mining and Machine Learning"]
doi:10.7717/peerj.4844
39 downloads
265 views

The reconstruction of genomes using mapping-based approaches with short reads experiences difficulties when resolving repetitive regions. These repetitive regions in genomes result in low mapping qualities of the respective reads, which in turn lead to many unresolved...

["Bioinformatics","Computational Biology"]
doi:10.7717/peerj.4742
45 downloads
433 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
75 downloads
381 views

Elucidating the molecular mechanism of helix–coil transitions of short peptides is a long-standing conundrum in physical chemistry. Although the helix–coil transitions of poly-glutamic acid (PGA) have been extensively studied, the molecular details of its unfolding...

["Biophysics","Computational Biology"]
doi:10.7717/peerj.4769

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