1 download
23 views

Assay for Transposase Accessible Chromatin (ATAC-seq) is an open chromatin profiling assay that is adapted to interrogate chromatin accessibility from small cell numbers. ATAC-seq surmounted a major technical barrier and enabled epigenome profiling of clinical...

["Bioinformatics","Computational Biology","Genomics"]
doi:10.7287/peerj.preprints.2942v1
1 download
13 views

Amplicon based taxonomic analysis, which determines the presence of microbial taxa in different environments on the basis of marker gene annotations, often uses percentage identity as the main metric to determine sequence similarity against databases. These data...

["Biodiversity","Bioinformatics","Computational Biology","Microbiology"]
doi:10.7287/peerj.preprints.2941v1
110 downloads
276 views

Whole genome alignments and comparative analysis are key methods in the quest of unraveling the dynamics of genome evolution. Interactive visualization and exploration of the generated alignments, annotations, and phylogenetic data are important steps in the interpretation...

["Bioinformatics","Computational Biology"]
doi:10.7287/peerj.preprints.2348v2
32 downloads
275 views

The appropriate timing of flowering is crucial for the reproductive success of plants. Hence, intricate genetic networks integrate various environmental and endogenous cues such as temperature or hormonal statues. These signals integrate into a network of floral...

["Bioinformatics","Computational Biology","Developmental Biology","Plant Science"]
doi:10.7717/peerj.3197
53 downloads
701 views

We report the genome sequence of Exiguobacterium chiriqhucha str. N139, isolated from a high-altitude Andean lake. Comparative genomic analyses of the Exiguobacterium genomes available suggest that our strain belongs to the same species as the previously reported...

["Biochemistry","Biodiversity","Bioinformatics","Genomics","Microbiology"]
doi:10.7717/peerj.3162
49 downloads
230 views

Prebiotics are selectively fermentable dietary compounds that result in changes in the composition and/or activity of the intestinal microbiota, thus conferring benefits upon host health. In veterinary medicine, commercially available products containing prebiotics...

["Bioinformatics","Microbiology","Veterinary Medicine","Gastroenterology and Hepatology","Nutrition"]
doi:10.7717/peerj.3184
21 downloads
219 views

Predicting protein structure from sequence remains a major open problem in protein biochemistry. One component of predicting complete structures is the prediction of inter-residue contact patterns (contact maps). Here, we discuss protein contact map prediction...

["Bioinformatics","Computational Biology"]
doi:10.7717/peerj.3139
43 downloads
162 views

Symbiotic microalgae (Symbiodinium spp.) strongly influence the performance and stress-tolerance of their coral hosts, making the analysis of Symbiodinium communities in corals (and metacommunities on reefs) advantageous for many aspects of coral reef research....

["Bioinformatics","Ecology","Marine Biology"]
doi:10.7287/peerj.preprints.2925v1
43 downloads
380 views

Background Geminiviruses (family Geminiviridae) are prevalent plant viruses that imperil agriculture globally, causing serious damage to the livelihood of farmers, particularly in developing countries. The virus evolves rapidly, attributing to its single-stranded...

["Agricultural Science","Bioinformatics","Genomics","Virology"]
doi:10.7717/peerj.3165
22 downloads
120 views

Background. DNA sequences are pivotal for a wide array of research in biology. Large sequence databases, like GenBank, provide an amazing resource to utilize DNA sequences for large scale analyses. However, many sequences on GenBank contain more than one gene or...

["Bioinformatics","Evolutionary Studies","Genetics","Taxonomy"]
doi:10.7287/peerj.preprints.2920v1
19 downloads
254 views

Pedigrees, though straightforward and versatile, lack the ability to tell us information about many individuals. Though numerical systems have been developed, there is currently no system to quantify the probability of a pedigree following certain inheritance systems....

["Bioinformatics","Genetics","Mathematical Biology","Statistics"]
doi:10.7287/peerj.preprints.2871v5
57 downloads
396 views

Background The capacity of visually oriented species to perceive and respond to visual signal is integral to their evolutionary success. Giraffes are closely related to okapi, but the two species have broad range of phenotypic differences including their visual...

["Bioinformatics","Evolutionary Studies","Genomics"]
doi:10.7717/peerj.3145
52 downloads
524 views

Background Maleic acid is a multi-functional chemical widely used in the field of industrial chemistry for producing food additives and food contact materials. As maleic acid may contaminate food by the release from food packages or intentional addition, it raises...

["Bioinformatics","Computational Biology","Food Science and Technology","Genomics"]
doi:10.7717/peerj.3175
94 downloads
688 views

Most reconstruction methods for genomes of ancient origin that are used today require a closely related reference. In order to identify genomic rearrangements or the deletion of whole genes, de novo assembly has to be used. However, because of inherent problems...

["Bioinformatics","Paleontology","Computational Science"]
doi:10.7717/peerj.3126
18 downloads
119 views

High sensitivity methods such as next generation sequencing and polymerase chain reaction (PCR) are adversely impacted by organismal and DNA contaminants. Current methods for detecting contaminants in microbial materials (genomic DNA and cultures) are not sensitive...

["Bioinformatics","Genomics","Microbiology"]
doi:10.7287/peerj.preprints.2913v1

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