Peer-reviewed Articles - Biology

1 citation
224 downloads
787 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
2 citations
919 downloads
2,485 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
151 downloads
770 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
200 downloads
1,116 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
3 citations
1,216 downloads
2,807 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
163 downloads
1,549 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
4 citations
350 downloads
2,428 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
435 downloads
1,803 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
319 downloads
1,316 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
334 downloads
1,831 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
6 citations
620 downloads
3,250 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
13 citations
1,606 downloads
7,469 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
682 downloads
2,552 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
12 citations
643 downloads
3,424 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
8 citations
558 downloads
3,187 views

Ascribing function to sequence in the absence of biological data is an ongoing challenge in bioinformatics. Differentiating the toxins of venomous animals from homologues having other physiological functions is particularly problematic as there are no universally...

["Bioinformatics","Computational Biology","Data Mining and Machine Learning"]
doi:10.7717/peerj-cs.90

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