Peer-reviewed Articles

36 downloads
143 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
19 downloads
160 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
269 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
48 downloads
550 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
191 downloads
1,278 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
464 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
125 downloads
819 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
159 downloads
904 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
61 downloads
311 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
86 downloads
354 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
123 downloads
750 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
66 downloads
197 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
64 downloads
728 views

Background Several new programming languages and technologies have emerged in the past few decades in order to ease the task of modelling complex systems. Modelling the dynamics of complex systems requires various levels of abstractions and reductive measures in...

["Computational Biology","Scientific Computing and Simulation","Programming Languages"]
doi:10.7717/peerj-cs.159
83 downloads
383 views

Essential tremor (ET) and Parkinson’s disease (PD) are among the most common adult-onset tremor disorders. Clinical and pathological studies suggest that misdiagnosis of PD for ET, and vice versa, occur in anywhere from 15% to 35% of cases. Complex diagnostic procedures,...

["Computational Biology","Genetics"]
doi:10.7717/peerj.5308

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