Peer-reviewed Articles - Computer sci

73 downloads
771 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
139 downloads
608 views

Background Clustering is one of the most common techniques in data analysis and seeks to group together data points that are similar in some measure. Although there are many computer programs available for performing clustering, a single web resource that provides...

["Bioinformatics","Computational Biology"]
doi:10.7717/peerj-cs.155
468 downloads
1,873 views

Cervical cancer remains a significant cause of mortality all around the world, even if it can be prevented and cured by removing affected tissues in early stages. Providing universal and efficient access to cervical screening programs is a challenge that requires...

["Bioinformatics","Computational Biology","Artificial Intelligence","Data Mining and Machine Learning"]
doi:10.7717/peerj-cs.154
115 downloads
702 views

Background Labels are a way to add some information on a text, such as functional annotations such as genes on a DNA sequences. V(D)J recombinations are DNA recombinations involving two or three short genes in lymphocytes. Sequencing this short region (500 bp or...

["Bioinformatics","Computational Biology","Algorithms and Analysis of Algorithms"]
doi:10.7717/peerj-cs.148
1 citation
172 downloads
1,026 views

Cataloging mutated driver genes that confer a selective growth advantage for tumor cells from sporadic passenger mutations is a critical problem in cancer genomic research. Previous studies have reported that some driver genes are not highly frequently mutated...

["Bioinformatics","Computational Biology"]
doi:10.7717/peerj-cs.133
2 citations
1,015 downloads
2,499 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
130 downloads
1,378 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
289 downloads
2,009 views

Whole genome alignments and comparative analysis are key methods in the quest of unraveling the dynamics of genome evolution. Interactive visualization and exploration of the generated alignments, annotations, and phylogenetic data are important steps in the interpretation...

["Bioinformatics","Computational Biology"]
doi:10.7717/peerj-cs.116
1 citation
384 downloads
1,652 views

Background Large-scale molecular evolutionary analyses of protein coding sequences requires a number of preparatory inter-related steps from finding gene families, to generating alignments and phylogenetic trees and assessing selective pressure variation. Each...

["Bioinformatics","Computational Biology"]
doi:10.7717/peerj-cs.118
275 downloads
1,233 views

Shotgun metagenomics of microbial communities reveal information about strains of relevance for applications in medicine, biotechnology and ecology. Recovering their genomes is a crucial but very challenging step due to the complexity of the underlying biological...

["Bioinformatics","Computational Biology","Data Science"]
doi:10.7717/peerj-cs.117
3 citations
279 downloads
1,694 views

We developed a web-based cloud-hosted system that allow users to archive, listen, visualize, and annotate recordings. The system also provides tools to convert these annotations into datasets that can be used to train a computer to detect the presence or absence...

["Bioinformatics","Computational Biology","Data Mining and Machine Learning"]
doi:10.7717/peerj-cs.113
3 citations
546 downloads
2,982 views

Metastatic cutaneous melanoma is an aggressive skin cancer with some progression-slowing treatments but no known cure. The omics data explosion has created many possible drug candidates; however, filtering criteria remain challenging, and systems biology approaches...

["Bioinformatics","Computational Biology","Data Science","World Wide Web and Web Science"]
doi:10.7717/peerj-cs.106
8 citations
1,393 downloads
6,440 views

Metagenomic experiments attempt to characterize microbial communities using high-throughput DNA sequencing. Identification of the microorganisms in a sample provides information about the genetic profile, population structure, and role of microorganisms within...

["Bioinformatics","Computational Biology"]
doi:10.7717/peerj-cs.104
1 citation
599 downloads
2,260 views

We propose here a working unit for teaching basic concepts of structural bioinformatics and evolution through the example of a wooden snake puzzle, strikingly similar to toy models widely used in the literature of protein folding. In our experience, developed at...

["Bioinformatics","Computational Biology","Computer Education","Scientific Computing and Simulation"]
doi:10.7717/peerj-cs.100
9 citations
557 downloads
3,057 views

Background Large scale metagenomic projects aim to extract biodiversity knowledge between different environmental conditions. Current methods for comparing microbial communities face important limitations. Those based on taxonomical or functional assignation rely...

["Bioinformatics","Computational Biology"]
doi:10.7717/peerj-cs.94

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