Preprints (not yet peer-reviewed)

7 downloads
64 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
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
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
113 downloads
446 views

Background: For more than 25 years the golden mussel Limnoperna fortunei has been an aggressive invader in South America freshwaters, having travelled more than 5,000 km upstream across 5 countries. The mussel has outcompeted native species in the invaded environments...

["Bioinformatics","Computational Biology","Conservation Biology","Genetics","Genomics"]
doi:10.7287/peerj.preprints.2995v1
86 downloads
347 views

Sharing and reusing data in research is a welcome and encouraged practice since it maximises the scientific outcomes given limited financial, material and human resources. Interdisciplinary research is considered to benefit from this practice, uniting researchers...

["Bioinformatics","Computational Biology","Data Science","Spatial and Geographic Information Systems"]
doi:10.7287/peerj.preprints.2248v4
80 downloads
224 views

Digital repositories bring direct impact and influence on the research community and society but measuring their value using formal metrics remains challenging. their value. It is challenging to define a single perfect metric that covers all quality aspects. Here,...

["Bioinformatics","Computational Biology","Digital Libraries","World Wide Web and Web Science"]
doi:10.7287/peerj.preprints.2688v2
15 downloads
113 views

Most biological processes within a cell are carried out by protein-protein interaction (PPI) networks, or so called interactomics. Therefore, identification of PPIs is crucial to elucidating protein functions and further understanding of various cellular biological...

["Bioinformatics","Biotechnology","Computational Biology"]
doi:10.7287/peerj.preprints.2964v1
57 downloads
310 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
401 downloads
228 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
146 downloads
632 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
109 downloads
406 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
232 downloads
1,113 views

Large-scale molecular evolutionary analyses of protein coding sequences requires a number of preparatory inter-related steps from finding gene families, to generating alignments and phylogenetic trees and assessing selective pressure variation. Each phase of these...

["Bioinformatics","Computational Biology"]
doi:10.7287/peerj.preprints.1895v2
49 downloads
162 views

Membrane proteins are the most medicinally important yet to be fully exploited pharmaceutical targets. Here druggability analyses are conducted on three different membrane proteins, namely, the human P2Y12 receptor, glycoprotein-41 that mediates the HIV-1 virus...

["Biochemistry","Bioinformatics","Biophysics","Computational Biology"]
doi:10.7287/peerj.preprints.2868v1
226 downloads
252 views

Incorrect snake identification from the observable visual traits is a major reason of death resulting from snake bites. So far no automatic classification method has been proposed to distinguish snakes by deciphering the taxonomy features of snake for the two major...

["Bioinformatics","Computational Biology","Taxonomy","Zoology"]
doi:10.7287/peerj.preprints.2867v1
What is a PeerJ Preprint?

A PeerJ Preprint is a draft of an article, abstract, or poster that has not yet been peer-reviewed for formal publication. Submit a draft, incomplete, or final version of your work for free.

Submissions today can be approved by Editorial Staff and online in 24 hours.

Establish precedent. Solicit feedback. Publish updates.

Top subject areas - Preprints

Top subject areas - People

View all subject areas