Preprints (not yet peer-reviewed)

5 downloads
61 views

Microbes are identified based on their distinguishing characteristics such as gene sequence or metabolic profile. Nucleic acid approaches such as 16S rRNA gene sequencing provide the gold standard method for microbial identification in the contemporary era. However,...

["Biochemistry","Bioinformatics","Biotechnology","Computational Biology","Microbiology"]
doi:10.7287/peerj.preprints.3524v1
56 downloads
137 views

The increasing move towards open access full-text scientific literature enhances our ability to utilize advanced text-mining methods to construct information-rich networks that no human will be able to grasp simply from 'reading the literature'. The utility of...

["Computational Biology","Microbiology","Plant Science"]
doi:10.7287/peerj.preprints.3472v1
84 downloads
193 views

Recently, Docker technology has received increasing attention throughout the bioinformatics community. However, its implementation has not yet been mastered by most biologists, and thus its application in biological research has been limited. In order to popularize...

["Bioinformatics","Computational Biology","Genomics","Microbiology"]
doi:10.7287/peerj.preprints.3040v1
459 downloads
358 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
184 downloads
782 views

Numerous investigations of bacterial communities using sequence analysis of environmental DNA have revealed extensive diversity of microbial taxa in an array of different environmental habitats. Community analysis based solely on DNA, however, does not reveal whether...

["Computational Biology","Ecology","Microbiology"]
doi:10.7287/peerj.preprints.2051v2
53 downloads
525 views

Marker gene sequencing of microbial communities has generated big datasets of microbial relative abundances varying across environmental conditions, sample sites and treatments. These data often come with putative phylogenies, providing unique opportunities to...

["Computational Biology","Ecology","Mathematical Biology","Microbiology","Statistics"]
doi:10.7287/peerj.preprints.2685v1
143 downloads
470 views

Genomic heterogeneity of bacterial species is observed and studied in experimental evolution experiments, clinical diagnostics and occurs as micro-diversity of natural habitats. The challenge for genome research is to accurately capture this heterogeneity with...

["Bioinformatics","Computational Biology","Evolutionary Studies","Genomics","Microbiology"]
doi:10.7287/peerj.preprints.2449v1
509 downloads
3,857 views

Background. VSEARCH is an open source and free of charge multithreaded 64-bit tool for processing metagenomics nucleotide sequence data. It is designed as an alternative to the widely used USEARCH tool (Edgar 2010) for which the source code is not publicly available,...

["Biodiversity","Bioinformatics","Computational Biology","Genomics","Microbiology"]
doi:10.7287/peerj.preprints.2409v1
294 downloads
604 views

Identification and quantification of microorganisms is an important step in studying the alpha and beta diversities within and between microbial communities respectively. Both, identification and quantification of a given microbial community can be carried out...

["Bioinformatics","Computational Biology","Genomics","Microbiology","Taxonomy"]
doi:10.7287/peerj.preprints.2378v1
59 downloads
283 views

Phage-therapy is a promising alternative against pathogenic, multiple drug resistant bacteria. In this work we propose an algorithm to determine the optimal bacteriophage dose able to minimize a population of Pseudomonas aeruginosa. Reverse engineering was used...

["Computational Biology","Microbiology"]
doi:10.7287/peerj.preprints.2359v1
104 downloads
470 views

Dormancy is a general microbial life-history trait that leads to the emergence of seed banks across diverse ecosystems. While the primary forces driving seed banks include macroscale factors like resource supply, the importance of microscale factors such as individual...

["Computational Biology","Ecology","Ecosystem Science","Mathematical Biology","Microbiology"]
doi:10.7287/peerj.preprints.2321v1
96 downloads
144 views

With increasing sophistication of instruments and techniques, in addition to the increment in intricacies, girth and complexities of the problems being addressed, simple methods (especially computational biology techniques) are being overlooked, replaced or phased...

["Bioinformatics","Biophysics","Computational Biology","Genomics","Microbiology"]
doi:10.7287/peerj.preprints.2296v1
210 downloads
1,183 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
58 downloads
191 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
342 downloads
2,605 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
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