Peer-reviewed Articles - Computer sci

158 downloads
996 views

Evolutionary biology has entered an era of unprecedented amounts of DNA sequence data, as new sequencing technologies such as Massive Parallel Sequencing (MPS) can generate billions of nucleotides within less than a day. The current bottleneck is how to efficiently...

["Bioinformatics","Computational Biology","Evolutionary Studies","Genetics"]
doi:10.7717/peerj.5175
158 downloads
886 views

Many proteins display complex dynamical properties that are often intimately linked to their biological functions. As the native state of a protein is best described as an ensemble of conformations, it is important to be able to generate models of native state...

["Biochemistry","Computational Biology"]
doi:10.7717/peerj.5125
72 downloads
335 views

Background Optimization of transgene expression can be achieved by designing coding sequences with the synonymous codon usage of genes which are highly expressed in the host organism. The identification of the so-called “favoured codons” generally requires the...

["Bioinformatics","Biotechnology","Computational Biology","Genomics"]
doi:10.7717/peerj.5099
83 downloads
446 views

HLA class II proteins are important elements of human adaptive immune recognition and are associated with numerous infectious and immune-mediated diseases. These highly variable molecules can be classified into DP, DQ and DR groups. It has been proposed that in...

["Computational Biology","Immunology"]
doi:10.7717/peerj.5118
1 citation
80 downloads
449 views

The fates of genetic polymorphisms maintained by balancing selection depend on evolutionary dynamics at linked sites. While coevolution across linked, epigenetically-interacting loci has been extensively explored, such supergenes may be relatively rare. However,...

["Computational Biology","Evolutionary Studies","Genetics"]
doi:10.7717/peerj.5110
287 downloads
664 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
117 downloads
972 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
113 downloads
610 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
195 downloads
1,142 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
51 downloads
400 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
257 downloads
465 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
151 downloads
858 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
165 downloads
613 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
1 citation
232 downloads
1,213 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
75 downloads
815 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

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