Peer-reviewed Articles - Biology

52 downloads
377 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
85 downloads
720 views

Background Mass Spectrometry (MS) based chemoproteomics has recently become a main tool to identify and quantify cellular target protein interactions with ligands/drugs in drug discovery. The complexity associated with these new types of data requires scientists...

["Bioinformatics"]
doi:10.7717/peerj-cs.129
249 downloads
1,006 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
57 downloads
743 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
1 citation
113 downloads
804 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
165 downloads
895 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
138 downloads
615 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
151 downloads
1,011 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
1 citation
260 downloads
1,428 views

Data in the life sciences are extremely diverse and are stored in a broad spectrum of repositories ranging from those designed for particular data types (such as KEGG for pathway data or UniProt for protein data) to those that are general-purpose (such as FigShare,...

["Bioinformatics","Data Science","Databases","Emerging Technologies","World Wide Web and Web Science"]
doi:10.7717/peerj-cs.110
370 downloads
1,297 views

Electroencephalography (EEG) is a rich source of information regarding brain function. However, the preprocessing of EEG data can be quite complicated, due to several factors. For example, the distinction between true neural sources and noise is indeterminate;...

["Bioinformatics","Brain\u2013Computer Interface"]
doi:10.7717/peerj-cs.108
1 citation
299 downloads
1,624 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
4 citations
722 downloads
3,493 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
327 downloads
1,357 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
3 citations
329 downloads
1,962 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
3 citations
345 downloads
1,620 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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