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genomics
310 downloads
2,858 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
14 downloads
159 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
50 downloads
291 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
102 downloads
1,183 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
95 downloads
537 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
14 downloads
67 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
191 downloads
805 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
49 downloads
292 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
184 downloads
1,082 views

Viruses of microbes impact all ecosystems where microbes drive key energy and substrate transformations including the oceans, humans and industrial fermenters. However, despite this recognized importance, our understanding of viral diversity and impacts remains...

["Bioinformatics","Genomics","Microbiology","Virology"]
doi:10.7717/peerj.985
50 downloads
265 views

Maintaining high levels of physical function is an important aspect of successful ageing. While muscle mass and strength contribute to functional performance in older adults, little is known about the possible genetic basis for the heterogeneity of physical function...

["Genetics","Genomics","Geriatrics","Kinesiology"]
doi:10.7717/peerj.980
51 downloads
143 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 can be conveniently classified into six groups (V1-V6), based on...

["Aquaculture, Fisheries and Fish Science","Biochemistry","Evolutionary Studies","Genetics","Genomics"]
doi:10.7287/peerj.preprints.1126v1
139 downloads
765 views

An uncultured non-photosynthetic basal lineage of the Cyanobacteria, the Melainabacteria, was recently characterised by metagenomic analyses of aphotic environmental samples. However, a predatory bacterium, Vampirovibrio chlorellavorus, originally described in...

["Genomics","Microbiology"]
doi:10.7717/peerj.968
979 downloads
2,052 views

Large-scale recovery of genomes from isolates, single cells, and metagenomic data has been made possible by advances in computational methods and substantial reductions in sequencing costs. While this increasing breadth of draft genomes is providing key information...

["Bioinformatics","Genomics","Microbiology","Molecular Biology"]
doi:10.7287/peerj.preprints.554v2
46 downloads
367 views

Objective. Bringing together genomics, transcriptomics, proteomics, and other -omics technologies is an important step towards developing highly personalized medicine. However, instrumentation has advances far beyond expectations and now we are able to generate...

["Computational Biology","Genetics","Genomics","Computational Science"]
doi:10.7717/peerj.970
1 citation
249 downloads
2,144 views

The sequencing, assembly, and basic analysis of microbial genomes, once a painstaking and expensive undertaking, has become much easier for research labs with access to standard molecular biology and computational tools. However, there are a confusing variety of...

["Bioinformatics","Genomics","Microbiology"]
doi:10.7717/peerj.960

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