Preprints (not yet peer-reviewed)

211 downloads
1,270 views

Clustered regularly interspaced short palindromic repeat (CRISPR) systems are the adaptive immune systems of bacteria and archaea against viral infection. While CRISPRs have been exploited as a tool for genetic engineering, their spacer sequences can also provide...

["Bioinformatics","Genomics","Microbiology","Computational Science"]
doi:10.7287/peerj.preprints.2278v4
7 downloads
55 views

Background. Enteroviruses are small non-enveloped viruses with (+) ssRNA genome with one open reading frame. Enterovirus protein 3C (or 3CD for some species) binds replicative element oriL to initiate replication. The replication of enteroviruses features low fidelity...

["Evolutionary Studies","Genomics","Virology"]
doi:10.7287/peerj.preprints.3153v1
12 downloads
111 views

While the benefits of undergraduate research experiences (UREs) are recognized for undergraduates, the advantages of UREs for graduate students, post-doctoral scholars, and faculty are not clearly outlined. The analysis of genomic data is particularly well-suited...

["Bioinformatics","Genomics","Science and Medical Education"]
doi:10.7287/peerj.preprints.3149v1
11 downloads
143 views

We previously demonstrated how CITED1 knockdown in melanoma cells had the capacity to perturb expression of a significant number of genes that comprised MITF and several of its known transcriptional targets. This manifest as a switch from a more invasive to a more...

["Cell Biology","Genomics","Molecular Biology","Oncology"]
doi:10.7287/peerj.preprints.3146v1
30 downloads
106 views

We report here the successful assembly of the complete mitochondrial genomes of the northern spotted owl (Strix occidentalis caurina) and the barred owl (S. varia). We utilized sequence data from two sequencing methodologies, Illumina paired-end sequence data with...

["Genetics","Genomics","Molecular Biology","Zoology"]
doi:10.7287/peerj.preprints.3120v1
15 downloads
114 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
18 downloads
99 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
25 downloads
147 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
22 downloads
147 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
568 downloads
1,458 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
153 downloads
772 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
40 downloads
154 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
295 downloads
1,012 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
23 downloads
310 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
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