Preprints (not yet peer-reviewed)

665 downloads
2,114 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
35 downloads
178 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
40 downloads
227 views

Metatranscriptomics and metaproteomics make it possible to measure gene expression in microbial communities. So far these approaches were mostly used to get a general overview of the dominant metabolism and physiologies of community members. Recently, environmental...

["Bioinformatics","Ecology","Environmental Sciences","Genomics","Microbiology"]
doi:10.7287/peerj.preprints.2846v1
70 downloads
346 views

Cyanobacteria are major contributors to global biogeochemical cycles. The genetic diversity among Cyanobacteria enables them to thrive across many habitats. However, the taxonomy of Cyanobacteria remains unstable because of an inadequate taxonomic classification...

["Bioinformatics","Ecology","Genomics","Microbiology","Taxonomy"]
doi:10.7287/peerj.preprints.2676v1
136 downloads
415 views

To answer many of the major questions in comparative botany, ecology, and global change biology it is necessary to extrapolate across enormous geographic, temporal and taxonomic scales. Yet much ecological knowledge is still based on observations conducted within...

["Biodiversity","Biogeography","Bioinformatics","Ecology","Computational Science"]
doi:10.7287/peerj.preprints.2615v2
1,424 downloads
698 views

The diversity of complex microbial communities can be rapidly assessed by high-throughput DNA sequencing of marker gene (e.g., 16S) PCR amplicon pools, often yielding many thousands of DNA sequences per sample. However, analysis of such community amplicon sequencing...

["Biodiversity","Bioinformatics","Ecology","Microbiology"]
doi:10.7287/peerj.preprints.2196v3
68 downloads
375 views

Microorganisms that reside on and in mammals, such as bats, have the potential to influence their host’s health and to provide potential defenses against invading pathogens. However, we have little to no understanding of the external bacterial microbiome on bats,...

["Biogeography","Bioinformatics","Ecology","Microbiology"]
doi:10.7287/peerj.preprints.2493v1
260 downloads
508 views

To microbiologists, the term macroecology may conjure iconic images of wildebeests grazing in African savannahs or hummingbirds pollinating flowers in a tropical rain forest. Contrary to what the name implies, macroecology is not the ecological study of macroscopic...

["Biodiversity","Biogeography","Bioinformatics","Ecology","Microbiology"]
doi:10.7287/peerj.preprints.2478v1
213 downloads
391 views

1) DNA metabarcoding is a powerful tool to assess biodiversity by amplifying and sequencing a standardized gene marker region. Its success is often limited due to variable binding sites that introduce amplification biases. Thus the development of optimized primers...

["Bioinformatics","Ecology","Genetics","Molecular Biology","Zoology"]
doi:10.7287/peerj.preprints.2352v1
133 downloads
512 views

Understanding the distribution of taxa and associated traits across different environments is one of the central questions in microbial ecology. High-throughput sequencing (HTS) studies are presently generating huge volumes of data to address this biogeographical...

["Bioinformatics","Ecology","Environmental Sciences","Microbiology"]
doi:10.7287/peerj.preprints.2317v1
114 downloads
776 views

Solar salterns are excellent model ecosystems for studying virus-microbial interactions because of their low microbial diversity, environmental stability, and high viral density. By using the power of CRISPR spacers to link viruses to their prokaryotic hosts, we...

["Bioinformatics","Computational Biology","Ecology","Genomics","Microbiology"]
doi:10.7287/peerj.preprints.2106v2
134 downloads
400 views

A variety of methods are available to collapse 16S rRNA gene sequencing reads to the operational taxonomic units (OTUs) used in microbiome analyses. A number of studies have aimed to compare the quality of the resulting OTUs. However, in the absence of a standard...

["Bioinformatics","Ecology","Microbiology"]
doi:10.7287/peerj.preprints.2115v1
283 downloads
2,237 views

Mock communities are an important tool for validating, optimizing, and comparing bioinformatics methods for microbial community analysis. We present mockrobiota, a public resource for sharing, validating, and documenting mock community data resources, available...

["Bioinformatics","Computational Biology","Ecology","Microbiology"]
doi:10.7287/peerj.preprints.2065v1
478 downloads
787 views

North Americans spend the majority of their time indoors where they are exposed to the microbiome of the built environment (BE) they inhabit. Despite the ubiquity of microbes in BEs, and their potential impacts on health and building materials, basic questions...

["Bioinformatics","Ecology","Environmental Sciences","Microbiology"]
doi:10.7287/peerj.preprints.1797v1
716 downloads
369 views

The natural sciences, such as ecology and earth science, study complex interactions between biotic and abiotic systems in order to infer understanding and make predictions. Machine-learning-based methods have an advantage over traditional statistical methods in...

["Bioinformatics","Ecology","Statistics","Computational Science"]
doi:10.7287/peerj.preprints.1720v1
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