Preprints (not yet peer-reviewed)

5 downloads
78 views

Scientific terms should be as accurate and meaningful as possible for both researchers and the general science readership. Currently, some scientific terms do not properly describe the activity or function to which they are associated to, being frequently characterized...

["Biochemistry","Genetics","Genomics","Molecular Biology"]
doi:10.7287/peerj.preprints.3102v1
6 downloads
69 views

Recently, a novel phenomenon of horizontal gene transfer of helicase-encoding sequence from positive-stranded RNA viruses to LINE transposons in insect genomes was described. TRAS family transposons encoding an ORF2 protein, which comprised all typical functional...

["Entomology","Genomics","Molecular Biology","Virology"]
doi:10.7287/peerj.preprints.3101v1
16 downloads
98 views

The Class Bivalvia is a highly successful and ancient group including 20,000+ known species. They represent a good model for studying adaptation (anoxia/hypoxia, salinity, temperature, ...), and they are useful bioindicators for monitoring the concentration of...

["Aquaculture, Fisheries and Fish Science","Evolutionary Studies","Genomics","Marine Biology","Zoology"]
doi:10.7287/peerj.preprints.3096v1
8 downloads
93 views

We have developed a machine learning approach to predict context specific enhancer-promoter interactions using evidence from changes in genomic protein occupancy over time. The occupancy of estrogen receptor alpha (ERα), RNA polymerase (Pol II) and histone marks...

["Bioinformatics","Computational Biology","Genomics"]
doi:10.7287/peerj.preprints.3093v1
296 downloads
574 views

Oxford Nanopore Technologies' MinION sequencer was launched in pre-release form in 2014 and represents an exciting new sequencing paradigm. The device offers multi-kilobase reads and a streamed mode of operation that allows processing of reads as they are generated....

["Bioinformatics","Genomics"]
doi:10.7287/peerj.preprints.3090v1
135 downloads
671 views

A key step in the transformation of raw sequencing reads into biological insights is the trimming of adapter sequences and low-quality bases. Read trimming has been shown to increase the quality and reliability while decreasing the computational requirements of...

["Bioinformatics","Genomics","Computational Science"]
doi:10.7287/peerj.preprints.2452v4
23 downloads
113 views

The consumption of raw fish has been increasing considerably in the West, since it has an appeal to be potentially healthier (omega 3 and 6, essential amino acids and vitamins). However this potential benefit, as well as the taste, value and even the risk of extinction...

["Food Science and Technology","Genomics"]
doi:10.7287/peerj.preprints.3085v1
268 downloads
869 views

The outstanding biodiversity found in the American tropics (the Neotropics) has attracted the attention of naturalists for centuries. Despite major advances in the generation of biodiversity data, many questions remain to be answered. In this review, we first summarize...

["Biodiversity","Biogeography","Ecology","Evolutionary Studies","Genomics"]
doi:10.7287/peerj.preprints.3074v1
18 downloads
279 views

Recent years have witnessed the discovery of protein–coding genes which appear to have evolved de novo from previously non-coding sequences. This has changed the long-standing view that coding sequences can only evolve from other coding sequences. However, there...

["Bioinformatics","Computational Biology","Evolutionary Studies","Genetics","Genomics"]
doi:10.7287/peerj.preprints.3031v2
35 downloads
220 views

Background. Viral metagenomics (viromics) is increasingly used to obtain uncultivated viral genomes, evaluate community diversity, and assess ecological hypotheses. While viromic experimental methods are relatively mature and widely accepted by the research community,...

["Bioinformatics","Ecology","Genomics","Microbiology"]
doi:10.7287/peerj.preprints.3053v1
17 downloads
135 views

Potamopyrgus antipodarum, a New Zealand freshwater snail, is a powerful system to study the maintenance of sexual reproduction. Obligate asexual P. antipodarum (herein, Pa) lineages include both triploids and tetraploids that are products of multiple separate transitions...

["Evolutionary Studies","Genomics"]
doi:10.7287/peerj.preprints.3046v1
10 downloads
80 views

Aminoacyl-tRNA synthetases (aaRS) are enzymes that catalyze the ligation of tRNAs to their cognate amino acids. There are aaRSs specific to each of the 20 standard amino acids. These enzymes are divided into two classes, class I and class II, which are unrelated...

["Bioinformatics","Computational Biology","Evolutionary Studies","Genomics"]
doi:10.7287/peerj.preprints.3045v1
34 downloads
214 views

The advent of next-generation sequencing tools has made it possible to conduct fine-scale surveys of population differentiation and genome-wide scans for signatures of selection in non-model organisms. Such surveys are of particular importance in sharply declining...

["Conservation Biology","Genomics","Marine Biology"]
doi:10.7287/peerj.preprints.3043v1
41 downloads
108 views

Recently, Docker technology has received increasing attention throughout the bioinformatics community. However, its implementation has not yet been mastered by most biologists, and thus its application in biological research has been limited. In order to popularize...

["Bioinformatics","Computational Biology","Genomics","Microbiology"]
doi:10.7287/peerj.preprints.3040v1
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