Preprints (not yet peer-reviewed)

37 downloads
215 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
159 downloads
520 views

The global deep subsurface biosphere is thought to be one of the largest reservoirs for microbial life on our planet. This study takes advantage of new sampling technologies and couples them with improvements to DNA sequencing and associated informatics tools to...

["Bioinformatics","Environmental Sciences","Genomics","Microbiology"]
doi:10.7287/peerj.preprints.2613v1
66 downloads
351 views

Annually, half of all plant-derived carbon is added to soil where it is microbially respired to CO2. However, understanding of the microbiology of this process is limited because most culture-independent methods cannot link metabolic processes to the organisms...

["Bioinformatics","Environmental Sciences","Genomics","Microbiology","Soil Science"]
doi:10.7287/peerj.preprints.2473v1
133 downloads
511 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
149 downloads
885 views

Biodiversity is currently assessed for environmental characterizations and monitoring through a laborious and time-consuming process of morphological taxonomy. We used rRNA 18S, rRNA 28S and COI, together with NGS and Bioinformatics to identify benthic invertebrate...

["Bioinformatics","Environmental Sciences","Genomics"]
doi:10.7287/peerj.preprints.2103v3
30 downloads
120 views

Barbiturases have scarce structural information available and do not fit in the conventional group of proteins. It is contemplated that they play a role in catabolism of s-triazine herbicide compounds. Structure as well as interaction data information of barbiturase...

["Biochemistry","Bioinformatics","Computational Biology","Environmental Sciences","Microbiology"]
doi:10.7287/peerj.preprints.2070v1
478 downloads
784 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
250 downloads
392 views

Discovery of novel diversity in high-throughput sequencing (HTS) studies is a central task in environmental microbial ecology. To evaluate the effects that amplicon clustering methods have on novel diversity discovery, we clustered an environmental marine protist...

["Biodiversity","Bioinformatics","Environmental Sciences","Microbiology","Molecular Biology"]
doi:10.7287/peerj.preprints.1414v1
756 downloads
736 views

Previously we presented Swarm v1, a novel and open source amplicon clustering program that produced fine-scale molecular operational taxonomic units (OTUs), free of arbitrary global clustering thresholds and input-order dependency. Swarm v1 worked with an initial...

["Biodiversity","Bioinformatics","Environmental Sciences","Microbiology","Molecular Biology"]
doi:10.7287/peerj.preprints.1222v2
350 downloads
344 views

Metagenomics by next generation sequencing has become an important tool for interrogating complex microbial communities. In this study we analyzed several pairs of metagenomic samples obtained by different methods and observed biases, resulting in different nucleotide...

["Bioinformatics","Computational Biology","Environmental Sciences","Genomics","Microbiology"]
doi:10.7287/peerj.preprints.734v1
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