Preprints (not yet peer-reviewed)

112 downloads
584 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
145 downloads
196 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
41 downloads
225 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
226 downloads
721 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
1,210 downloads
602 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
690 downloads
628 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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