Preprints (not yet peer-reviewed)

96 downloads
381 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
22 downloads
234 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
59 downloads
291 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
269 downloads
2,072 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
184 downloads
370 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
25 downloads
208 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
76 downloads
350 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
75 downloads
92 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
99 downloads
723 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
29 downloads
113 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
277 downloads
2,179 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
187 downloads
544 views

Background. Chromosome conformation capture, coupled with high throughput DNA sequencing in protocols like Hi-C and 3C-seq, has been proposed as viable means to generate data to resolve the genomes of microorganisms living in naturally occuring environments. Metagenomic...

["Bioinformatics","Computational Biology","Genomics","Microbiology","Computational Science"]
doi:10.7287/peerj.preprints.1974v2
103 downloads
324 views

Introduction Age is the primary risk factor for major human chronic diseases, including cardiovascular disorders, cancer, type 2 diabetes, and neurodegenerative diseases. Chronic, low-grade, systemic inflammation is associated with aging and the progression of...

["Computational Biology","Microbiology","Geriatrics","Immunology"]
doi:10.7287/peerj.preprints.1754v1
202 downloads
453 views

Bioinformatics software often requires human-generated tabular text files as input and have specific requirements for how those data are formatted. Users frequently manage these data in spreadsheet programs, which is convenient for researchers who are compiling...

["Bioinformatics","Computational Biology","Ecology","Microbiology","Human-Computer Interaction"]
doi:10.7287/peerj.preprints.1670v1
84 downloads
347 views

Background. 16S rRNA gene sequences are routinely assigned to operational taxonomic units (OTUs) that are then used to analyze complex microbial communities. A number of methods have been employed to carry out the assignment of 16S rRNA gene sequences to OTUs leading...

["Computational Biology","Ecology","Microbiology"]
doi:10.7287/peerj.preprints.1511v1
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