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bioinformatics
35 downloads
49 views

Comparing inferences among datasets generated using short read sequencing may provide insight into the concerted effects of evolutionary processes across organisms, but comparisons are complicated by biases introduced during dataset assembly. Sequence similarity...

["Bioinformatics","Evolutionary Studies","Genetics","Genomics","Molecular Biology"]
doi:10.7287/peerj.preprints.864v1
10 downloads
7 views

Severe gaps and biases in digital accessible information (DAI) of species distributions hamper prospects of safeguarding biodiversity and ecosystem services and reliably addressing central questions in ecology and evolution. Accordingly, governments have agreed...

["Biodiversity","Biogeography","Bioinformatics","Conservation Biology","Ecology"]
doi:10.7287/peerj.preprints.856v1
25 downloads
117 views

Background. Studies of ancestry are difficult in the tomato because it crosses with many wild relatives and species in the tomato clade that have diverged very recently. As a result, the phylogeny in relation to its closest relatives remains uncertain. By using...

["Agricultural Science","Bioinformatics","Evolutionary Studies","Genomics","Plant Science"]
doi:10.7717/peerj.793
15 downloads
124 views

CITED1 is a non-DNA binding transcriptional co-regulator whose expression can distinguish the ‘proliferative’ from ‘invasive’ signature in the phenotype-switching model of melanoma. We have found that, in addition to other ‘proliferative’ signature genes, CITED1...

["Bioinformatics","Cell Biology","Genomics","Molecular Biology"]
doi:10.7717/peerj.788
179 downloads
226 views

Background: Establishing health-related causal relationships is a central pursuit in biomedical research. Yet, the interdependent non-linearity of biological systems renders causal dynamics laborious and at times impractical to disentangle. This pursuit is further...

["Bioinformatics","Mathematical Biology","Computational Science","Coupled Natural and Human Systems"]
doi:10.7287/peerj.preprints.583v2
14 downloads
85 views

Biological data analysis is frequently performed with command line software. While this practice provides considerable flexibility for computationally savy individuals, such as investigators trained in bioinformatics, this also creates a barrier to the widespread...

["Bioinformatics","Human\u2013Computer Interaction","Computational Science"]
doi:10.7717/peerj.800
16 downloads
49 views

A traditional random variable X is a function that maps from a stochastic process to the real line. Here, "real line" refers to the structure (R,<=,|x-y|), where R is the set of real numbers, <= is the standard linear order relation on R, and d(x,y)=|x-y| is the...

["Bioinformatics","Computational Biology"]
doi:10.7287/peerj.preprints.844v1
48 downloads
151 views

LRRK2 was identified in 2004 as the causative protein product of the Parkinson’s disease locus designated PARK8. In the decade since then, genetic studies have revealed at least 6 dominant mutations in LRRK2 linked to Parkinson’s disease, alongside one associated...

["Biochemistry","Bioinformatics","Computational Biology","Neuroscience","Neurology"]
doi:10.7717/peerj.778
31 downloads
131 views

Biogenic amine receptors play critical roles in regulating behavior and physiology in both vertebrates and invertebrates, particularly within the central nervous system. Members of the G-protein coupled receptor (GPCR) family, these receptors interact with endogenous...

["Bioinformatics","Computational Biology","Evolutionary Studies","Pharmacology"]
doi:10.7717/peerj.773
21 downloads
87 views

The ability of Shiga toxin-producing Escherichia coli (STEC) to cause severe illness in humans is determined by multiple host factors and bacterial characteristics, including Shiga toxin (Stx) subtype. Given the link between Stx2a subtype and disease severity,...

["Bioinformatics","Genetics","Genomics","Microbiology"]
doi:10.7717/peerj.739
54 downloads
29 views

One necessary step of metagenome analysis is to assign sequences to classes according to their taxonomic origins. Unsupervised binning method is one of the two binning categories. However existing unsupervised binning methods yield to estimate the species number...

["Bioinformatics","Computational Biology","Computational Science"]
doi:10.7287/peerj.preprints.839v1
361 downloads
553 views

The whale shark (Rhincodon typus) has by far the largest body size of any elasmobranch (shark or ray) species and is therefore also the largest extant species of the paraphyletic assemblage commonly referred to as “fishes”. As both a phenotypic extreme and a member...

["Aquaculture, Fisheries and Fish Science","Bioinformatics","Genomics","Marine Biology","Immunology"]
doi:10.7287/peerj.preprints.837v1
15 downloads
27 views

Background: A major goal of RNA-Seq data analysis is to reconstruct the full set of gene transcripts expressed in a biological sample in order to quantify their expression levels. The process typically involves multiple steps including mapping short sequence reads...

["Bioinformatics","Genomics","Pediatrics"]
doi:10.7287/peerj.preprints.833v1
52 downloads
41 views

The origin of recent parallel outbreaks of the high pathogenicity H5N8 avian flu virus in Europe and in Japan can be traced to a single source population, which has most likely been spread by migratory birds. By using Bayesian coalescence methods to analyze the...

["Agricultural Science","Bioinformatics","Computational Biology","Genetics","Virology"]
doi:10.7287/peerj.preprints.822v1
86 downloads
211 views

Biomedical research networks need to integrate research data among their members and with external partners. To support such data sharing activities, an adequate information technology infrastructure is necessary. To facilitate the establishment of such an infrastructure,...

["Bioinformatics","Computational Science"]
doi:10.7717/peerj.755

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