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genomics
17 downloads
190 views

The origin and subsequent accumulation of spliceosomal introns are prominent events in the evolution of eukaryotic gene structure. However, the mechanisms underlying intron gain remain unclear because there are few proven cases of recently gained introns. In an...

["Bioinformatics","Computational Biology","Evolutionary Studies","Genomics"]
doi:10.7717/peerj.2272
31 downloads
60 views

The production of hydrogen and methane by geochemical reactions associated with the serpentinization of ultramafic rocks can potentially support subsurface microbial ecosystems independent of the photosynthetic biosphere. Methanogenic and methanotrophic microorganisms...

["Ecology","Environmental Sciences","Genomics","Marine Biology","Microbiology"]
doi:10.7287/peerj.preprints.2315v1
61 downloads
648 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
39 downloads
447 views

Campylobacter jejuni is a major cause of bacterial gastroenteritis worldwide, primarily associated with the consumption of contaminated poultry. C. jejuni lineages vary in host range and prevalence in human infection, suggesting differences in survival throughout...

["Genetics","Genomics","Microbiology"]
doi:10.7287/peerj.preprints.2300v1
56 downloads
230 views

Functional genomics research can give us valuable insights into bacterial gene function. RNA Sequencing (RNA-seq) can generate information on transcript abundance in bacteria following abiotic stress treatments. In this study, we used the RNA-seq technique to study...

["Bioinformatics","Genomics","Microbiology"]
doi:10.7717/peerj.2223
29 downloads
206 views

Understanding the population structure and genetic diversity of plant pathogens, as well as the effect of agricultural practices on pathogen evolution, is important for disease management. Developments in molecular methods have contributed to increase the resolution...

["Agricultural Science","Bioinformatics","Genomics","Microbiology","Taxonomy"]
doi:10.7717/peerj.2222
25 downloads
131 views

Summary. In this article we describe fluff, a software package that allows for simple exploration, clustering and visualization of high-throughput sequencing data mapped to a reference genome. The package contains three command-line tools to generate publication-quality...

["Bioinformatics","Computational Biology","Genomics"]
doi:10.7717/peerj.2209
5 downloads
52 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
26 downloads
169 views

Knockout Sudoku is a method for the construction of whole-genome knockout collections for a wide range of microorganisms with as little as 3 weeks of dedicated labor and at a cost of approximately $10,000. The method uses manual 4-dimensional combinatorial pooling,...

["Computational Biology","Genetics","Genomics","Computational Science"]
doi:10.7287/peerj.preprints.2294v1
8 downloads
88 views

Background. Phylogenetic and barcoding studies usually employ fresh parts of plants as the source of DNA. Successful DNA amplification has been achieved in such investigations for different regions. However, there is need for the utilization of dried samples, due...

["Genomics","Plant Science"]
doi:10.7287/peerj.preprints.2293v1
39 downloads
365 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
79 downloads
417 views

Summary: Clustered regularly interspaced palindromic repeat (CRISPR) systems are prokaryotic adaptive immune systems against viral infection. CRISPR spacer sequences can provide valuable ecological insights by linking environmental viruses to microbial hosts. Despite...

["Bioinformatics","Genomics","Microbiology","Computational Science"]
doi:10.7287/peerj.preprints.2278v2
135 downloads
698 views

Local (within-sample/alpha) diversity is often implicated as a cause of success or failure of a microbial community. However, the relationships between diversity and emergent properties of a community, such as its stability, productivity, or invasibility, are much...

["Ecology","Environmental Sciences","Genomics","Microbiology"]
doi:10.7287/peerj.preprints.2287v1
36 downloads
192 views

Background De novo transcriptome assembly of short reads is now a common step in expression analysis of organisms lacking a reference genome sequence. Several software packages are available to perform this task. Even if their results are of good quality it is...

["Bioinformatics","Genomics","Computational Science"]
doi:10.7287/peerj.preprints.2284v1
44 downloads
351 views

River buffalo (Bubalus bubalis) milk plays an important role in economy and nutritious diet in several developing countries. However, reliable milk-yield genomic markers and their functional insights remain unexposed. Here, we have used a target capture sequencing...

["Agricultural Science","Bioinformatics","Biotechnology","Genetics","Genomics"]
doi:10.7717/peerj.2147

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