Preprints (not yet peer-reviewed)

Background: Technological advances in sequencing, assembly and segregation of resulting contigs into species-specific bins has enabled the reconstruction of individual genomes from environmental metagenomic data sets. Though a powerful technique, it is shadowed...

["Bioinformatics","Genomics","Microbiology"]
doi:10.7287/peerj.preprints.2953v1
14 downloads
116 views

Assay for Transposase Accessible Chromatin (ATAC-seq) is an open chromatin profiling assay that is adapted to interrogate chromatin accessibility from small cell numbers. ATAC-seq surmounted a major technical barrier and enabled epigenome profiling of clinical...

["Bioinformatics","Computational Biology","Genomics"]
doi:10.7287/peerj.preprints.2942v1
122 downloads
105 views

Amplicon based taxonomic analysis, which determines the presence of microbial taxa in different environments on the basis of marker gene annotations, often uses percentage identity as the main metric to determine sequence similarity against databases. These data...

["Biodiversity","Bioinformatics","Computational Biology","Microbiology"]
doi:10.7287/peerj.preprints.2941v1
124 downloads
431 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:10.7287/peerj.preprints.2348v2
55 downloads
179 views

Symbiotic microalgae (Symbiodinium spp.) strongly influence the performance and stress-tolerance of their coral hosts, making the analysis of Symbiodinium communities in corals (and metacommunities on reefs) advantageous for many aspects of coral reef research....

["Bioinformatics","Ecology","Marine Biology"]
doi:10.7287/peerj.preprints.2925v1
34 downloads
123 views

Background. DNA sequences are pivotal for a wide array of research in biology. Large sequence databases, like GenBank, provide an amazing resource to utilize DNA sequences for large scale analyses. However, many sequences on GenBank contain more than one gene or...

["Bioinformatics","Evolutionary Studies","Genetics","Taxonomy"]
doi:10.7287/peerj.preprints.2920v1
19 downloads
260 views

Pedigrees, though straightforward and versatile, lack the ability to tell us information about many individuals. Though numerical systems have been developed, there is currently no system to quantify the probability of a pedigree following certain inheritance systems....

["Bioinformatics","Genetics","Mathematical Biology","Statistics"]
doi:10.7287/peerj.preprints.2871v5
23 downloads
125 views

High sensitivity methods such as next generation sequencing and polymerase chain reaction (PCR) are adversely impacted by organismal and DNA contaminants. Current methods for detecting contaminants in microbial materials (genomic DNA and cultures) are not sensitive...

["Bioinformatics","Genomics","Microbiology"]
doi:10.7287/peerj.preprints.2913v1
85 downloads
312 views

The use of online data repositories and the establishment of new data standards that require data to be computer-parsable so that algorithms can reason over them have become increasingly important with the emergence of high-throughput technologies, Big Data and...

["Biodiversity","Bioinformatics","Computational Biology","Zoology","Computational Science"]
doi:10.7287/peerj.preprints.2429v2
189 downloads
933 views

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 phase of these...

["Bioinformatics","Computational Biology"]
doi:10.7287/peerj.preprints.1895v2
736 downloads
2,256 views

A central challenge in the present era of biodiversity loss is to assess and manage human impacts on freshwater ecosystems. Macroinvertebrates are an important group for bioassessment as many taxa show specific responses to environmental conditions. However, generating...

["Biodiversity","Bioinformatics","Ecology","Genetics","Molecular Biology"]
doi:10.7287/peerj.preprints.2044v5
135 downloads
1,148 views

As the generation and use of genomic datasets is becoming increasingly common in all areas of biology, the need for resources to collate, analyse and present data from one or more genome projects is becoming more pressing. The Ensembl platform is a powerful tool...

["Bioinformatics","Genomics"]
doi:10.7287/peerj.preprints.2401v2
57 downloads
241 views

Taxonomic markers such as the 16S ribosomal RNA gene are widely used in microbial community analysis. A common first step in marker-gene analysis is grouping genes into clusters to reduce data sets to a more manageable size and potentially mitigate the effects...

["Bioinformatics","Ecology","Microbiology","Computational Science"]
doi:10.7287/peerj.preprints.2879v1
52 downloads
95 views

Ribulose-1,5-bisphosphate carboxylase/oxygense (RuBisCO) is present in plants and autotrophic organisms like microalgae. The aim of this study was to perform an in silico evaluation of RuBisCo protein in microalgae and cyanobacteria as potential precursors of bioactive...

["Bioinformatics","Biotechnology"]
doi:10.7287/peerj.preprints.2875v1
36 downloads
183 views

A measure of statistical evidence should permit the sample size determination so that the probability M of obtaining (strong) misleading evidence can be held as low as desired. On this desideratum the p-value fails completely, as it leads either to an arbitrary...

["Bioinformatics","Epidemiology","Statistics"]
doi:10.7287/peerj.preprints.2869v1
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