Peer-reviewed Articles - Computer sci

1 citation
273 downloads
507 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
182 downloads
967 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
188 downloads
673 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
2 citations
275 downloads
1,415 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
84 downloads
862 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
148 downloads
1,157 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
96 downloads
637 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
110 downloads
595 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
117 downloads
748 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
1 citation
162 downloads
664 views

Background Clustering is one of the most common techniques in data analysis and seeks to group together data points that are similar in some measure. Although there are many computer programs available for performing clustering, a single web resource that provides...

["Bioinformatics","Computational Biology"]
doi:10.7717/peerj-cs.155
129 downloads
637 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
579 downloads
2,025 views

Cervical cancer remains a significant cause of mortality all around the world, even if it can be prevented and cured by removing affected tissues in early stages. Providing universal and efficient access to cervical screening programs is a challenge that requires...

["Bioinformatics","Computational Biology","Artificial Intelligence","Data Mining and Machine Learning"]
doi:10.7717/peerj-cs.154
280 downloads
901 views

Background Alzheimer’ disease (AD) is an ultimately fatal degenerative brain disorder that has an increasingly large burden on health and social care systems. There are only five drugs for AD on the market, and no new effective medicines have been discovered for...

["Bioinformatics","Computational Biology","Cognitive Disorders"]
doi:10.7717/peerj.4756
2 citations
178 downloads
699 views

Background Using DNA microarrays, we previously identified 451 genes expressed in 19 different human tissues. Although ubiquitously expressed, the variable expression patterns of these “housekeeping genes” (HKGs) could separate one normal human tissue type from...

["Bioinformatics","Computational Biology","Genomics","Oncology","Medical Genetics"]
doi:10.7717/peerj.4719
1 citation
290 downloads
1,011 views

During the past decade, with the significant progress of computational power as well as ever-rising data availability, deep learning techniques became increasingly popular due to their excellent performance on computer vision problems. The size of the Protein Data...

["Bioinformatics","Computational Biology","Genomics","Computational Science"]
doi:10.7717/peerj.4750

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