Peer-reviewed Articles - Computer sci

25 downloads
231 views

Background Bayesian networks are directed acyclic graphical models widely used to represent the probabilistic relationships between random variables. They have been applied in various biological contexts, including gene regulatory networks and protein–protein interactions...

["Bioinformatics","Computational Biology"]
doi:10.7717/peerj.5692
79 downloads
762 views

The recognition of the group Archaea as a major branch of the tree of life (ToL) prompted a new view of the evolution of biodiversity. The genomic representation of archaeal biodiversity has since significantly increased. In addition, advances in phylogenetic modeling...

["Biodiversity","Computational Biology","Evolutionary Studies","Paleontology","Taxonomy"]
doi:10.7717/peerj.5770
39 downloads
160 views

Protein backbones occupy diverse conformations, but compact metrics to describe such conformations and transitions between them have been missing. This report re-introduces the Ramachandran number (ℛ) as a residue-level structural metric that could simply the life...

["Bioinformatics","Computational Biology","Mathematical Biology"]
doi:10.7717/peerj.5745
46 downloads
260 views

Background Osteoclast differentiation in the inflamed synovium of rheumatoid arthritis (RA) affected joints leads to the formation of bone lesions. Reconstruction and analysis of protein interaction networks underlying specific disease phenotypes are essential...

["Bioinformatics","Computational Biology","Genomics","Immunology","Rheumatology"]
doi:10.7717/peerj.5743
60 downloads
154 views

Mortality is one of the most important parameters for the study of population dynamics. One of the main sources of information to calculate the mortality of cetaceans arises from the observed age-structure of stranded animals. A method based on an adaptation of...

["Computational Biology","Algorithms and Analysis of Algorithms","Software Engineering"]
doi:10.7717/peerj.5768
53 downloads
198 views

The number of amino acids that occupy a given protein site during evolution reflects the selective constraints operating on the site. This evolutionary variability is strongly influenced by the structural properties of the site in the native structure, and it is...

["Bioinformatics","Biophysics","Computational Biology","Evolutionary Studies"]
doi:10.7717/peerj.5549
50 downloads
245 views

Model-free methods are widely used for the processing of brain fMRI data collected under natural stimulations, sleep, or rest. Among them is the popular fuzzy c-mean algorithm, commonly combined with cluster validity (CV) indices to identify the ‘true’ number of...

["Bioinformatics","Computational Biology","Neuroscience"]
doi:10.7717/peerj.5416
117 downloads
588 views

Secondary contact is the reestablishment of gene flow between sister populations that have diverged. For instance, at the end of the Quaternary glaciations in Europe, secondary contact occurred during the northward expansion of the populations which had found refugia...

["Computational Biology","Ecology","Evolutionary Studies","Population Biology"]
doi:10.7717/peerj.5325
42 downloads
171 views

Xeno-miRNAs are microRNAs originating from exogenous species detected in host biofluids. A growing number of studies have suggested that many of these xeno-miRNAs may be involved in cross-species interactions and manipulations. To date, hundreds of xeno-miRNAs...

["Bioinformatics","Computational Biology","Genetics","Genomics","Parasitology"]
doi:10.7717/peerj.5650
28 downloads
199 views

The variation between the actual and perceived lightness of a stimulus has strong dependency on its background, a phenomena commonly known as lightness induction in the literature of visual neuroscience and psychology. For instance, a gray patch may perceptually...

["Computational Biology","Neuroscience"]
doi:10.7717/peerj.5626
115 downloads
500 views

Background Dengue fever has rapidly manifested into a serious global health concern. The emergence of various viral serotypes has prompted the urgent need for innovative drug design techniques. Of the viral non-structural enzymes, the NS5 RNA-dependent RNA polymerase...

["Bioinformatics","Computational Biology","Genomics","Infectious Diseases"]
doi:10.7717/peerj.5068
112 downloads
398 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
59 downloads
307 views

Background High myopia is a common ocular disease worldwide. To expand our current understanding of the genetic basis of high myopia, we carried out a whole exome sequencing (WES) study to identify potential causal gene mutations. Methods A total of 20 individuals...

["Bioinformatics","Computational Biology","Genetics","Genomics","Translational Medicine"]
doi:10.7717/peerj.5552
66 downloads
246 views

The ε subunit from ATP synthases acts as an ATP sensor in the bacterial cell to prevent ATP hydrolysis and thus the waste of ATP under conditions of low ATP concentration. However, the ATP binding affinities from various bacterial organisms differ markedly, over...

["Biophysics","Computational Biology","Molecular Biology"]
doi:10.7717/peerj.5505
56 downloads
318 views

In single-cell RNA-sequencing, it is important to know the frequency at which the sequenced transcriptomes actually derive from multiple cells. A common method to estimate this multiplet frequency is to mix two different types of cells (e.g., human and mouse),...

["Bioinformatics","Computational Biology","Genomics","Mathematical Biology"]
doi:10.7717/peerj.5578

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