Peer-reviewed Articles - Biology

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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
1 download
1 view

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
39 downloads
190 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
22 downloads
168 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
44 downloads
188 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
39 downloads
270 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
53 downloads
553 views

The increase in atmospheric CO2 due to anthropogenic activities is generating climate change, which has resulted in a subsequent rise in global temperatures with severe environmental impacts. Biological mitigation has been considered as an alternative for environmental...

["Computational Biology","Climate Change Biology"]
doi:10.7717/peerj.5528
195 downloads
1,296 views

Potential natural vegetation (PNV) is the vegetation cover in equilibrium with climate, that would exist at a given location if not impacted by human activities. PNV is useful for raising public awareness about land degradation and for estimating land potential....

["Biogeography","Computational Biology","Plant Science","Data Mining and Machine Learning","Spatial and Geographic Information Science"]
doi:10.7717/peerj.5457
75 downloads
466 views

The development of methods to estimate rates of speciation and extinction from time-calibrated phylogenies has revolutionized evolutionary biology by allowing researchers to correlate diversification rate shifts with causal factors. A growing number of researchers...

["Bioinformatics","Computational Biology","Evolutionary Studies"]
doi:10.7717/peerj.5495
126 downloads
820 views

The CHARMM36 force field for lipids is widely used in simulations of lipid bilayers. The CHARMM family of force fields were developed for use with the mTIP3P water model. This water model has an anomalously high dielectric constant and low viscosity, which limits...

["Biochemistry","Biophysics","Computational Biology"]
doi:10.7717/peerj.5472
162 downloads
908 views

Piwi-interacting RNAs (piRNAs) are the largest class of small non-coding RNAs discovered in germ cells. Identifying piRNAs from small RNA data is a challenging task due to the lack of conserved sequences and structural features of piRNAs. Many programs have been...

["Bioinformatics","Computational Biology","Data Mining and Machine Learning"]
doi:10.7717/peerj.5429
64 downloads
313 views

Analysing the relationships between biomolecules and the genetic diseases is a highly active area of research, where the aim is to identify the genes and their products that cause a particular disease due to functional changes originated from mutations. Biological...

["Bioinformatics","Computational Biology"]
doi:10.7717/peerj.5298
88 downloads
358 views

Genome-scale diversity data are increasingly available in a variety of biological systems, and can be used to reconstruct the past evolutionary history of species divergence. However, extracting the full demographic information from these data is not trivial, and...

["Biogeography","Computational Biology","Evolutionary Studies","Genetics"]
doi:10.7717/peerj.5198
128 downloads
757 views

Although most of the cervical cancer cases are reported to be closely related to the Human Papillomavirus (HPV) infection, there is a need to study genes that stand up differentially in the final actualization of cervical cancers following HPV infection. In this...

["Bioinformatics","Computational Biology","Pathology","Computational Science","Data Mining and Machine Learning"]
doi:10.7717/peerj.5285
68 downloads
199 views

Missing data are frequently encountered in molecular phylogenetics, but there has been no accurate distance imputation method available for distance-based phylogenetic reconstruction. The general framework for distance imputation is to explore tree space and distance...

["Bioinformatics","Computational Biology","Evolutionary Studies"]
doi:10.7717/peerj.5321

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