Preprints (not yet peer-reviewed)

211 downloads
1,327 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
2,286 downloads
19,835 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
21 downloads
112 views

In studies of human movement control, an important question is how the central nervous system (CNS) controls movements in the presence of a large number of degrees of freedom (DoFs) at all levels of the control architecture. It is known that CNS groups the multiple...

["Bioengineering","Neuroscience","Kinesiology","Computational Science"]
doi:10.7287/peerj.preprints.3080v1
153 downloads
778 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
489 downloads
2,245 views

This essay proposes mathematical answers to meta-scientific questions including "how much knowledge is produced by research?", "how rapidly is a field making progress?", "what is the expected reproducibility of a result?", "what do we mean by soft science?", "what...

["Computational Biology","Evolutionary Studies","Science Policy","Statistics","Computational Science"]
doi:10.7287/peerj.preprints.1968v3
63 downloads
137 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
99 downloads
131 views

Emerging infectious diseases caused by fungal taxa are increasing and are placing a substantial burden on economies and ecosystems worldwide. Of the emerging fungal diseases, chytridomycosis caused by the fungus Batrachochytrium dendrobatidis (hereafter Bd) is...

["Ecology","Microbiology","Mycology","Computational Science"]
doi:10.7287/peerj.preprints.3017v1
233 downloads
500 views

In this review, we present a summary of how computer modeling has been used in the development of covalent modifier drugs. Covalent modifier drugs bind by forming a chemical bond with their target. This covalent binding can improve the selectivity of the drug for...

["Biochemistry","Bioinformatics","Biophysics","Pharmacology","Computational Science"]
doi:10.7287/peerj.preprints.2857v2
192 downloads
221 views

Generating heatmaps of genes datasets have been known to be a graphical representation of data where the individual values contained in a matrix are represented as colors. Herein, we describe AFCMHeatMap a shiny web App that integrates quantitative interaction...

["Bioinformatics","Genetics","Genomics","Computational Science"]
doi:10.7287/peerj.preprints.2961v1
116 downloads
422 views

The use of online data repositories and the establishment of new data standards that require data to be computer-parsable so that algorithms can reason over them have become increasingly important with the emergence of high-throughput technologies, Big Data and...

["Biodiversity","Bioinformatics","Computational Biology","Zoology","Computational Science"]
doi:10.7287/peerj.preprints.2429v2
125 downloads
1,111 views

Background. The goals of this study were (1) to present the set of data evaluating running biomechanics (kinematics and kinetics), including data on running habits, demographics, and levels of muscle strength and flexibility made available at Figshare (DOI: 10.6084/m9.figshare.4543435);...

["Bioengineering","Neuroscience","Kinesiology","Computational Science"]
doi:10.7287/peerj.preprints.2888v1
71 downloads
370 views

Background. High talker variability (i.e. multiple voices in the input) has been found effective in training non-native phonetic contrasts in adults. A small number of studies suggest that children also benefit from high-variability phonetic training with some...

["Psychiatry and Psychology","Computational Science"]
doi:10.7287/peerj.preprints.2870v2
106 downloads
354 views

Taxonomic markers such as the 16S ribosomal RNA gene are widely used in microbial community analysis. A common first step in marker-gene analysis is grouping genes into clusters to reduce data sets to a more manageable size and potentially mitigate the effects...

["Bioinformatics","Ecology","Microbiology","Computational Science"]
doi:10.7287/peerj.preprints.2879v1
278 downloads
434 views

This document summarizes a series of authoritative views on research data management, sharing and citation, developed in Expert Groups, Working Groups, and other activities organized through FORCE11 (http://force11.org), an international community of over 2,000...

["Translational Medicine","Science Policy","Human-Computer Interaction","Computational Science"]
doi:10.7287/peerj.preprints.2836v1
32 downloads
201 views

Hydrolysis of ATP by Na+/K+-ATPase, a P-Type ATPase, catalyzing active Na+ and K+ transport through cellular membranes leads transiently to a phosphorylation of its catalytical α-subunit. Surprisingly, 3-dimensional molecular structure analysis of P-type ATPases...

["Biochemistry","Bioinformatics","Biophysics","Computational Biology","Computational Science"]
doi:10.7287/peerj.preprints.2812v1
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