Preprints (not yet peer-reviewed)

75 downloads
273 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
148 downloads
264 views

Landscape genetics combines population genetics, landscape ecology, and spatial analysis to identify landscape and genetic factors that influence genetic and genomic variation. Progress in the field depends on a strong conceptual foundation and the means of identifying...

["Computational Biology","Scientific Computing and Simulation","Spatial and Geographic Information Systems"]
doi:10.7287/peerj.preprints.2225v4
74 downloads
174 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
10 downloads
104 views

Movement in proteins requires energy. To this end, natural selection has selected phosphate as the principal energy currency in cells. On the other hand, depicting the state of transcription could come in the form of epigenetic markers, which are modifications...

["Biochemistry","Cell Biology","Computational Biology","Genetics","Molecular Biology"]
doi:10.7287/peerj.preprints.2966v1
10 downloads
99 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
37 downloads
237 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
379 downloads
185 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
137 downloads
565 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
61 downloads
235 views

An immune system inspired Artificial Immune System (AIS) algorithm is presented, and is used for the purposes of automated program verification. Relevant immunological concepts are discussed and the field of AIS is briefly reviewed. It is proposed to use this AIS...

["Computational Biology","Adaptive and Self-Organizing Systems","Theory and Formal Methods"]
doi:10.7287/peerj.preprints.2690v2
226 downloads
1,245 views

1. Stable isotope analysis is a widely used tool for the reconstruction and interpretation of animal diets and trophic relationships. Analytical tools have improved the robustness of inferring the relative contribution of different prey sources to an animal’s diet...

["Computational Biology","Ecology","Ecosystem Science","Zoology","Statistics"]
doi:10.7287/peerj.preprints.1950v3
97 downloads
360 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
10 downloads
169 views

Motion detection and position tracking of animal behavior over a period of time produce massive amount of information, but analysis and interpretation of such huge datasets are challenging. Here we describe statistical methods to extract major movement structures...

["Animal Behavior","Computational Biology"]
doi:10.7287/peerj.preprints.2908v1
201 downloads
1,026 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
310 downloads
1,002 views

The dynamics of ecological communities have been described by neutral and niche theories that are now increasingly integrated into unified models. It is known that a critical transition exists between these two states, but the spatial aspect of this transition...

["Biodiversity","Computational Biology","Ecology","Mathematical Biology"]
doi:10.7287/peerj.preprints.1589v4
143 downloads
583 views

A detailed review of a recent data science book by Hadley Wickham and Garrett Grolemund is developed herein. Technical book reviews should provide a guide to the readers, a sense of the appropriate audience, the specifics of the software/language, and identify...

["Computational Biology","Data Science"]
doi:10.7287/peerj.preprints.2873v1
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