Peer-reviewed Articles - Computer sci

153 downloads
1,056 views

Background Indigenous populations of the circumpolar Arctic are considered to be endemically infected (>2% prevalence) with hepatitis B virus (HBV), with subgenotype B5 (formerly B6) unique to these populations. The distinctive properties of HBV/B5, including high...

["Computational Biology","Evolutionary Studies","Virology","Infectious Diseases"]
doi:10.7717/peerj.3757
1 citation
211 downloads
1,889 views

Gene Co-expression Network Analysis (GCNA) is a popular approach to analyze a collection of gene expression profiles. GCNA yields an assignment of genes to gene co-expression modules, a list of gene sets statistically over-represented in these modules, and a gene-to-gene...

["Bioinformatics","Computational Biology","Genomics","Computational Science"]
doi:10.7717/peerj.3678
185 downloads
912 views

Considering complicated microRNA (miRNA) biogenesis and action mechanisms, it was thought so high energy-consuming for a cell to afford simultaneous over-expression of many miRNAs. Thus it prompts that an alternative miRNA regulation pattern on protein-encoding...

["Bioinformatics","Cell Biology","Computational Biology"]
doi:10.7717/peerj.3682
5 citations
251 downloads
2,271 views

It has recently become possible to experimentally measure the effects of all amino-acid point mutations to proteins using deep mutational scanning. These experimental measurements can inform site-specific phylogenetic substitution models of gene evolution in nature....

["Bioinformatics","Computational Biology","Evolutionary Studies"]
doi:10.7717/peerj.3657
1 citation
273 downloads
1,172 views

Introduction Different types of headaches and TMJ click influence the masseter muscle activity. The aim of this study was to assess the trend of energy level of the electromyography (EMG) activity of the masseter muscle during open-close clench cycles in migraine...

["Bioengineering","Computational Biology","Evidence Based Medicine","Radiology and Medical Imaging","Translational Medicine"]
doi:10.7717/peerj.3556
194 downloads
1,377 views

Newly emerging influenza viruses continue to threaten public health. A rapid determination of the host range of newly discovered influenza viruses would assist in early assessment of their risk. Here, we attempted to predict the host of influenza viruses using...

["Bioinformatics","Computational Biology","Virology"]
doi:10.7717/peerj.3579
1 citation
347 downloads
1,221 views

The skyline plot is a graphical representation of historical effective population sizes as a function of time. Past population sizes for these plots are estimated from genetic data, without a priori assumptions on the mathematical function defining the shape of...

["Computational Biology","Evolutionary Studies","Genetics","Statistics"]
doi:10.7717/peerj.3530
1 citation
263 downloads
1,147 views

Gastric cancer (GC) is a complex disease with heterogeneous genetic mechanisms. Genomic mutational profiling of gastric cancer not only expands our knowledge about cancer progression at a fundamental genetic level, but also could provide guidance on new treatment...

["Computational Biology","Genomics","Oncology"]
doi:10.7717/peerj.3585
2 citations
962 downloads
2,448 views

Background The availability of large databases containing high resolution three-dimensional (3D) models of proteins in conjunction with functional annotation allows the exploitation of advanced supervised machine learning techniques for automatic protein function...

["Bioinformatics","Computational Biology","Data Mining and Machine Learning"]
doi:10.7717/peerj-cs.124
2 citations
127 downloads
1,345 views

CodonGenie, freely available from http://codon.synbiochem.co.uk, is a simple web application for designing ambiguous codons to support protein mutagenesis applications. Ambiguous codons are derived from specific heterogeneous nucleotide mixtures, which create sequence...

["Bioengineering","Bioinformatics","Biotechnology","Computational Biology","Synthetic Biology"]
doi:10.7717/peerj-cs.120
2 citations
425 downloads
2,255 views

There are many steps in analyzing transcriptome data, from the acquisition of raw data to the selection of a subset of representative genes that explain a scientific hypothesis. The data produced can be represented as networks of interactions among genes and these...

["Bioinformatics","Computational Biology"]
doi:10.7717/peerj.3509
2 citations
276 downloads
1,333 views

Artifacts removal and rhythms extraction from electroencephalography (EEG) signals are important for portable and wearable EEG recording devices. Incorporating a novel grouping rule, we proposed an adaptive singular spectrum analysis (SSA) method for artifacts...

["Bioengineering","Computational Biology","Neuroscience"]
doi:10.7717/peerj.3474
211 downloads
1,050 views

Colorectal cancer (CRC) is the third commonest malignant tumor. Previous studies have revealed that the composition change of the human gut microbiome, measured by community diversity, is associated with the progression of CRC. However, a further question, whether...

["Computational Biology","Ecology","Microbiology","Computational Science"]
doi:10.7717/peerj.3383
245 downloads
970 views

Understanding how proteins mutate is critical to solving a host of biological problems. Mutations occur when an amino acid is substituted for another in a protein sequence. The set of likelihoods for amino acid substitutions is stored in a matrix and input to alignment...

["Bioinformatics","Computational Biology","Human-Computer Interaction"]
doi:10.7717/peerj.3492
362 downloads
1,372 views

Bioinformatics is currently faced with very large-scale data sets that lead to computational jobs, especially sequence similarity searches, that can take absurdly long times to run. For example, the National Center for Biotechnology Information (NCBI) Basic Local...

["Agricultural Science","Bioinformatics","Computational Biology","Plant Science"]
doi:10.7717/peerj.3486

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