Preprints (not yet peer-reviewed)

18 downloads
173 views

Computational biology is rapidly advancing thanks to the many new tools developed and published each month. A systematic benchmarking practice would help biomedical researchers leverage this technological expansion to optimize their projects. Several aspects of...

["Computational Biology","Genetics","Genomics","Computational Science"]
doi:10.7287/peerj.preprints.3236v1
234 downloads
278 views

Generating heatmaps of genes datasets have been known to be a graphical representation of data where the individual values contained in a matrix are represented as colors. Herein, we describe AFCMHeatMap a shiny web App that integrates quantitative interaction...

["Bioinformatics","Genetics","Genomics","Computational Science"]
doi:10.7287/peerj.preprints.2961v1
171 downloads
827 views

Knockout Sudoku is a method for the construction of whole-genome knockout collections for a wide range of microorganisms with as little as 3 weeks of dedicated labor and at a cost of approximately $10,000. The method uses manual 4-dimensional combinatorial pooling,...

["Computational Biology","Genetics","Genomics","Computational Science"]
doi:10.7287/peerj.preprints.2294v1
157 downloads
271 views

Motivations. Building the Burrows-Wheeler transform (BWT) and computing the Lempel-Ziv parsing (LZ77) of huge collections of genomes is becoming an important task in bioinformatic analyses as these datasets often need to be compressed and indexed prior to analysis....

["Bioinformatics","Computational Biology","Genetics","Computational Science"]
doi:10.7287/peerj.preprints.2176v1
44 downloads
259 views

Objective: Bringing together genomics, transcriptomics, proteomics, and other –omics technologies is an important step towards developing highly personalized medicine. However, instrumentation has advances far beyond expectations and now we are able to generate...

["Computational Biology","Genetics","Genomics","Computational Science"]
doi:10.7287/peerj.preprints.1021v1
238 downloads
773 views

Scaffolding errors and incorrect traversals of the de Bruijn graph during de novo assembly can result in large scale misassemblies in draft genomes. Nextera mate pair sequencing data provide additional information to resolve assembly ambiguities during scaffolding....

["Bioinformatics","Genetics","Genomics","Statistics","Computational Science"]
doi:10.7287/peerj.preprints.747v1
1,236 downloads
652 views

Many microbial, fungal, or oomcyete populations violate assumptions for population genetic analysis because these populations are clonal or partially clonal. Furthermore, few tools exist that are specifically designed for analyzing data from clonal populations,...

["Bioinformatics","Genetics","Microbiology","Mycology","Computational Science"]
doi:10.7287/peerj.preprints.161v1
730 downloads
748 views

The Roche 454 GS Junior sequencing platform allows locus-specific DNA methylation analysis using deep bisulfite amplicon sequencing. However, bisulfite-converted DNA reads may contain long T homopolymers, and the main sources of errors on pyrosequencing platforms...

["Bioinformatics","Computational Biology","Genetics","Computational Science"]
doi:10.7287/peerj.preprints.122v2
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