Peer-reviewed Articles - Computer sci

76 downloads
615 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
116 downloads
783 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
41 downloads
233 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
66 downloads
288 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
85 downloads
639 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
53 downloads
168 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
60 downloads
316 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
123 downloads
849 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
119 downloads
763 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
58 downloads
281 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
58 downloads
333 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
69 downloads
397 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
247 downloads
549 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
95 downloads
828 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
87 downloads
507 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

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