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bioinformatics
31 downloads
84 views

Background: A common research goal in transcriptome projects is to find genes that are differentially expressed in different phenotype classes. Biologists might wish to validate such gene candidates experimentally or use them for downstream systems biology analysis....

["Bioinformatics","Computational Biology","Statistics"]
doi:10.7287/peerj.preprints.1198v1
29 downloads
450 views

Summary. Pylogeny is a cross-platform library for the Python programming language that provides an object-oriented application programming interface for phylogenetic heuristic searches. Its primary function is to permit both heuristic search and analysis of the...

["Bioinformatics","Computational Biology"]
doi:10.7717/peerj-cs.9
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
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
49 downloads
335 views

Deep sequencing of the viral phoH gene, a host-derived auxiliary metabolic gene, was used to track viral diversity throughout the water column at the Bermuda Atlantic Time-series Study (BATS) site in the summer (September) and winter (March) of three years. Viral...

["Biodiversity","Bioinformatics","Microbiology","Virology"]
doi:10.7717/peerj.997
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
25 downloads
245 views

Recently, survival ensembles have found more and more applications in biological and medical research when censored time-to-event data are often confronted. In this research, we investigate the plausibility of extending a rotation forest, originally proposed for...

["Bioinformatics","Computational Biology","Statistics"]
doi:10.7717/peerj.1009
31 downloads
87 views

The genus Halobates includes the only five insect species that have been successful in a pelagic marine environment. Different scenarios of independent colonization events of that environment have been proposed, considering the appearance of pelagic distribution...

["Biodiversity","Bioinformatics","Entomology","Evolutionary Studies","Marine Biology"]
doi:10.7287/peerj.preprints.1164v1
100 downloads
384 views

Background: Data from 16S amplicon sequencing present challenges to ecological and statistical interpretation. In particular, library sizes often vary over several ranges of magnitude, and the data contains many zeroes. Also, since researchers sample a small fraction...

["Bioinformatics","Computational Biology","Ecology","Statistics"]
doi:10.7287/peerj.preprints.1157v1
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
28 downloads
116 views

In modern molecular systematics, matrices of unordered multistate characters, such as DNA sequence alignments, are used for analysis with no further re-coding procedures nor any a priori determination of character polarity. Here we present 1001, a simple freely...

["Bioinformatics","Computational Biology","Theory and Formal Methods"]
doi:10.7287/peerj.preprints.1153v1
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
33 downloads
409 views

Tandem repeat sequences have been found in great numbers in proteins that are conserved in a wide range of living species. In order to reconstruct the evolutionary history of such sequences, it is necessary to develop algorithms and methods that can work with highly...

["Bioinformatics","Computational Biology"]
doi:10.7717/peerj-cs.6
48 downloads
730 views

The growing number of genotyped populations, the advent of high-throughput phenotyping techniques and the development of GWAS analysis software has rapidly accelerated the number of GWAS experimental results. Candidate gene discovery from these results files is...

["Bioinformatics","Computational Biology","Visual Analytics"]
doi:10.7717/peerj-cs.3

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