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genomics
41 downloads
284 views

Comprehensive analysis of shotgun metagenomic assemblies have revolutionized molecular microbial ecology, but few microbiologists command the full suite of bioinformatics skills necessary to process, interact, organize and visualize overlapping DNA sequence contigs....

["Bioinformatics","Biotechnology","Computational Biology","Genomics","Microbiology"]
doi:10.7287/peerj.preprints.1275v1
19 downloads
173 views

A sample of caecal effluent was obtained from a female patient who had undergone a routine colonoscopic examination. Bacteria were isolated anaerobically from the sample, and screened against the remaining filtered caecal effluent in an attempt to isolate bacteriophages...

["Biodiversity","Ecology","Genomics","Microbiology","Virology"]
doi:10.7717/peerj.1061
112 downloads
649 views

Conservation genomics has become an increasingly popular term, yet it remains unclear whether the non-invasive sampling that is essential for many conservation-related studies is compatible with the minimum requirements for harnessing next-generation sequencing...

["Conservation Biology","Ecology","Evolutionary Studies","Genetics","Genomics"]
doi:10.7717/peerj.1106
11 downloads
64 views

Quorum sensing (QS) is a mechanism that plays important roles in gene expression in response to an expanding bacterial population. In many Gram-negative bacteria, N-acyl homoserine lactone is mainly secreted as the diffusible signalling molecules. This QS system...

["Genomics","Microbiology","Molecular Biology"]
doi:10.7287/peerj.preprints.1232v1
25 downloads
129 views

Research on climate change-driven coral disease outbreaks has greatly advanced our understanding of the coral innate immune system, and coral genomics has provided insight into the evolution of metazoan immune systems. However, only recently has next generation...

["Conservation Biology","Genetics","Genomics","Marine Biology","Molecular Biology"]
doi:10.7287/peerj.preprints.1230v1
1 citation
47 downloads
200 views

The funnel-web spider Macrothele calpeiana is a charismatic Mygalomorph with a great interest in basic, applied and translational research. Nevertheless, current scarcity of genomic and transcriptomic data of this species clearly limits the research in this non-model...

["Evolutionary Studies","Genetics","Genomics","Zoology"]
doi:10.7717/peerj.1064
79 downloads
630 views

For tissues to carry out their functions, they rely on the right proteins to be present. Several high-throughput technologies have been used to map out which proteins are expressed in which tissues; however, the data have not previously been systematically compared...

["Computational Biology","Genomics"]
doi:10.7717/peerj.1054
1 citation
453 downloads
4,247 views

The increased availability of genomic and metagenomic data poses challenges at multiple analysis levels, including visualization of very large-scale microbial and microbial community data paired with rich metadata. We developed GraPhlAn (Graphical Phylogenetic...

["Bioinformatics","Computational Biology","Genomics","Microbiology"]
doi:10.7717/peerj.1029
27 downloads
234 views

Group II introns are closely linked to eukaryote evolution because nuclear spliceosomal introns and the small RNAs associated with the spliceosome are thought to trace their ancient origins to these mobile elements. Therefore, elucidating how group II introns move,...

["Biotechnology","Evolutionary Studies","Genetics","Genomics","Marine Biology"]
doi:10.7717/peerj.1017
65 downloads
396 views

The serpin superfamily is characterized by proteins that fold into a conserved tertiary structure and exploits a sophisticated and irreversible suicide-mechanism of inhibition. Vertebrate serpins are classified into six groups (V1–V6), based on three independent...

["Aquaculture, Fisheries and Fish Science","Biochemistry","Evolutionary Studies","Genetics","Genomics"]
doi:10.7717/peerj.1026
147 downloads
1,490 views

As more and more prokaryotic sequencing takes place, a method to quickly and accurately analyze this data is needed. Previous tools are mainly designed for metagenomic analysis and have limitations; such as long runtimes and significant false positive error rates....

["Bioinformatics","Computational Biology","Genomics","Microbiology"]
doi:10.7717/peerj.1025
142 downloads
683 views

Associations between microorganisms occur extensively throughout Earth’s oceans. Understanding how microbial communities are assembled and how the presence or absence of species is related to that of others are central goals of microbial ecology. Here, we investigate...

["Computational Biology","Ecology","Genomics","Marine Biology","Microbiology"]
doi:10.7717/peerj.1008
21 downloads
92 views

Alu elements are sequences of approximately 300 basepairs that combined comprise more than 10% of the human genome. Due to their recent origin in primate evolution some Alu elements are polymorphic in humans, present in some individuals while absent in others....

["Bioinformatics","Computational Biology","Genomics"]
doi:10.7287/peerj.preprints.1174v1
326 downloads
1,362 views

Genomic pipelines consist of several pieces of third party software and, because their experimental nature, frequent changes and updates are commonly necessary thus raising serious distribution and reproducibility issues. Docker containers technology offers an...

["Bioinformatics","Computational Biology","Genomics","Computational Science"]
doi:10.7287/peerj.preprints.1171v2
69 downloads
349 views

Scaffolding errors and incorrect repeat disambiguation during de novo assembly can result in large scale misassemblies in draft genomes. Nextera mate pair sequencing data provide additional information to resolve assembly ambiguities during scaffolding. Here, we...

["Bioinformatics","Genetics","Genomics","Statistics","Computational Science"]
doi:10.7717/peerj.996

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