Preprints (not yet peer-reviewed)

5 downloads
53 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
3 downloads
40 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
111 downloads
278 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
49 downloads
174 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
218 downloads
1,163 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
84 downloads
309 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
8 downloads
140 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
187 downloads
916 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
307 downloads
956 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
107 downloads
531 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
29 downloads
122 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
64 downloads
195 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
45 downloads
137 views

Emerging viruses cause a lot of fatalities as they jump to humans from other species. Here we develop a novel technique to computationally estimate an important parameter of within-host viral infection: the lifespan of infected cells. Our approach is general and...

["Bioinformatics","Computational Biology"]
doi:10.7287/peerj.preprints.2621v2
648 downloads
528 views

ATLAS (Automatic Tool for Local Assembly Structures) is a comprehensive multi-omics data analysis pipeline that is massively parallel and scalable. ATLAS contains a modular analysis pipeline for assembly, annotation, quantification and genome binning of metagenomics...

["Bioinformatics","Computational Biology","Data Science","Scientific Computing and Simulation","Software Engineering"]
doi:10.7287/peerj.preprints.2843v1
4 downloads
40 views

Modern biomedical research aims at drawing biological conclusions from large, highly complex biological datasets. Nowadays, it is common practice to make extensive use of high-throughput technologies that produce big amounts of heterogeneous data. In addition to...

["Bioinformatics","Computational Biology","Data Science","Databases","Distributed and Parallel Computing"]
doi:10.7287/peerj.preprints.2839v1
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