Preprints (not yet peer-reviewed)

380 downloads
491 views

Pattern recognition is commonly used for identifying an unknown entity from a set of known objects curated in a database, and find use in various applications such as fingerprint matching and microbial identification. Mass spectrometry is increasingly used in identifying...

["Biodiversity","Bioinformatics","Ecology","Microbiology","Science and Medical Education"]
doi:10.7287/peerj.preprints.580v3
5 downloads
54 views

Ecological niche modeling (ENM) is increasingly being used in studying the relationship between species distributions and environmental conditions. The development of ENM software/algorithms is heading toward open-source programming, for the advantage of efficiency...

["Biogeography","Bioinformatics","Ecology","Zoology","Data Science"]
doi:10.7287/peerj.preprints.3346v1
20 downloads
255 views

Background. The number of individuals of each species in a given location forms the basis for many sub-fields of ecology and evolution. Data on individuals, including which species, and where they're found can be used for a large number of research questions. Global...

["Bioinformatics","Ecology","Computational Science"]
doi:10.7287/peerj.preprints.3304v1
28 downloads
108 views

Advances in genomic sequencing technologies resulted in massive microbial diversity data (16S ribosomal gene sequences, rDNA) being generated in every possible environment. However, the majority of microorganisms have never been cultured, and therefore, nor cataloged....

["Biodiversity","Biogeography","Bioinformatics","Ecology","Microbiology"]
doi:10.7287/peerj.preprints.3286v1
60 downloads
238 views

DNA analysis of predator feces using high-throughput amplicon sequencing (HTS) enhances our understanding of predator-prey interactions. However, conclusions drawn from this technique are constrained by biases that occur in multiple steps of the HTS workflow. To...

["Bioinformatics","Ecology","Entomology","Molecular Biology","Zoology"]
doi:10.7287/peerj.preprints.3184v1
118 downloads
343 views

Metabarcoding and metagenomic approaches are becoming routine techniques in biodiversity assessment and ecological studies. The assignment of taxonomic information to sequences is challenging, as many reference libraries are lacking information on certain taxonomic...

["Biodiversity","Bioinformatics","Ecology","Molecular Biology","Data Mining and Machine Learning"]
doi:10.7287/peerj.preprints.3133v1
120 downloads
562 views

Background. Viral metagenomics (viromics) is increasingly used to obtain uncultivated viral genomes, evaluate community diversity, and assess ecological hypotheses. While viromic experimental methods are relatively mature and widely accepted by the research community,...

["Bioinformatics","Ecology","Genomics","Microbiology"]
doi:10.7287/peerj.preprints.3053v1
143 downloads
436 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
1,188 downloads
2,913 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
115 downloads
402 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
121 downloads
480 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
176 downloads
604 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
256 downloads
654 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
2,010 downloads
912 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
143 downloads
573 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
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