Preprints (not yet peer-reviewed)

93 downloads
692 views

The website Sci-Hub provides access to scholarly literature via full text PDF downloads. The site enables users to access articles that would otherwise be paywalled. Since its creation in 2011, Sci-Hub has grown rapidly in popularity. However, until now, the extent...

["Bioinformatics","Legal Issues","Science and Medical Education","Statistics","Computational Science"]
doi:10.7287/peerj.preprints.3100v1
7 downloads
72 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
135 downloads
432 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
134 downloads
666 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
8 downloads
165 views

Human papillomavirus type 16 (HPV16) is the most carcinogenic HPV, causing >50% of cervical cancers. Its unique oncogenicity is unsolved, e.g., the second most carcinogenic type (HPV18, causing ~16% of cancers) is relatively distantly related to HPV16. Mirabello...

["Bioinformatics","Evolutionary Studies","Infectious Diseases","Oncology","Women's Health"]
doi:10.7287/peerj.preprints.3070v1
32 downloads
156 views

Symbiotic interactions between insects and bacteria are ubiquitous and form a continuum from loose facultative symbiosis to greatly intimate and stable obligate symbiosis. In blood-sucking insects living exclusively on vertebrate blood, obligate endosymbionts are...

["Biodiversity","Bioinformatics","Evolutionary Studies"]
doi:10.7287/peerj.preprints.3057v1
18 downloads
274 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
32 downloads
212 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
61 downloads
291 views

Species diversity of metazoan bulk samples can be rapidly assessed using Cytochrome c oxidase I (COI) metabarcoding. However, in cases where only degraded DNA is available, e.g. from poorly conserved museum specimens, eDNA filtered from water or gut content analyses,...

["Biodiversity","Bioinformatics","Molecular Biology"]
doi:10.7287/peerj.preprints.3037v1
10 downloads
77 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
40 downloads
100 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
29 downloads
116 views

The Arabian Peninsula (AP) is the first site of human migration and habitation outside of Africa. As a major crossroad for human populations, the AP provides an opportunity to better understand early to modern changes in human demographic patterns through selections,...

["Bioinformatics","Evolutionary Studies","Genomics"]
doi:10.7287/peerj.preprints.3039v1
27 downloads
126 views

Many difficulties are encountered by people with disabilities, especially when a diagnosis is made up of more than one dysfunction, as is the case of visually impaired wheelchair users. In fact, this scenario generates a degree of incapacity in terms of the performing...

["Bioengineering","Bioinformatics","Neuroscience","Clinical Trials","Human-Computer Interaction"]
doi:10.7287/peerj.preprints.3036v1
10 downloads
151 views

In de novo gene emergence, a segment of non-coding DNA undergoes a series of changes which enables transcription, potentially leading to a new protein that could eventually acquire a novel function. Due to their recent origins, young de novo genes have no homology...

["Bioinformatics","Evolutionary Studies","Genomics"]
doi:10.7287/peerj.preprints.3030v1
44 downloads
119 views

Life science ontologies play an important role in semantic web. In the fish and fisheries research field, it is imperative to have an ontology that can automatically provide information for biological objects annotations and links to relevant data pieces. As such,...

["Aquaculture, Fisheries and Fish Science","Bioinformatics","Computational Science"]
doi:10.7287/peerj.preprints.3020v1
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