Peer-reviewed Articles - Computer sci

123 downloads
421 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
201 downloads
868 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
76 downloads
228 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
82 downloads
845 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
106 downloads
446 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
207 downloads
1,186 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
186 downloads
996 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
89 downloads
378 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
111 downloads
539 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
1 citation
98 downloads
525 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
2 citations
332 downloads
800 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
143 downloads
1,131 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
145 downloads
696 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
246 downloads
1,261 views

Salt bridges form between pairs of ionisable residues in close proximity and are important interactions in proteins. While salt bridges are known to be important both for protein stability, recognition and regulation, we still do not have fully accurate predictive...

["Biochemistry","Computational Biology"]
doi:10.7717/peerj.4967
62 downloads
440 views

Supertree methods enable the reconstruction of large phylogenies. The supertree problem can be formalized in different ways in order to cope with contradictory information in the input. Some supertree methods are based on encoding the input trees in a matrix; other...

["Bioinformatics","Computational Biology","Evolutionary Studies","Taxonomy","Computational Science"]
doi:10.7717/peerj.4987

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