Preprints (not yet peer-reviewed)

656 downloads
2,071 views

A central challenge in the present era of biodiversity loss is to assess and manage human impacts on freshwater ecosystems. Macroinvertebrates are an important group for bioassessment as many taxa show specific responses to environmental conditions. However, generating...

["Biodiversity","Bioinformatics","Ecology","Genetics","Molecular Biology"]
doi:10.7287/peerj.preprints.2044v5
128 downloads
1,015 views

As the generation and use of genomic datasets is becoming increasingly common in all areas of biology, the need for resources to collate, analyse and present data from one or more genome projects is becoming more pressing. The Ensembl platform is a powerful tool...

["Bioinformatics","Genomics"]
doi:10.7287/peerj.preprints.2401v2
7 downloads
140 views

Pedigrees, though straightforward and versatile, lack the ability to tell us information about many individuals. Though numerical systems have been developed, there has yet to be a system that tells us the probabilities of a pedigree following certain inheritance...

["Bioinformatics","Genetics","Mathematical Biology","Statistics"]
doi:10.7287/peerj.preprints.2871v3
29 downloads
173 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
36 downloads
74 views

Ribulose-1,5-bisphosphate carboxylase/oxygense (RuBisCO) is present in plants and autotrophic organisms like microalgae. The aim of this study was to perform an in silico evaluation of RuBisCo protein in microalgae and cyanobacteria as potential precursors of bioactive...

["Bioinformatics","Biotechnology"]
doi:10.7287/peerj.preprints.2875v1
20 downloads
126 views

A measure of statistical evidence should permit the sample size determination so that the probability M of obtaining (strong) misleading evidence can be held as low as desired. On this desideratum the p-value fails completely, as it leads either to an arbitrary...

["Bioinformatics","Epidemiology","Statistics"]
doi:10.7287/peerj.preprints.2869v1
21 downloads
102 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
46 downloads
146 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
36 downloads
116 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
62 downloads
224 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.2857v1
3 downloads
28 views

Computational analyses for research usually consist of a complicated orchestration of data flows, software libraries, visualization, selection of adequate parameters, etc. Structuring these complex activities into a collaboration of simple, reproducible and well...

["Bioinformatics","Distributed and Parallel Computing"]
doi:10.7287/peerj.preprints.2849v1
38 downloads
220 views

Metatranscriptomics and metaproteomics make it possible to measure gene expression in microbial communities. So far these approaches were mostly used to get a general overview of the dominant metabolism and physiologies of community members. Recently, environmental...

["Bioinformatics","Ecology","Environmental Sciences","Genomics","Microbiology"]
doi:10.7287/peerj.preprints.2846v1
526 downloads
318 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
2 downloads
26 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
111 downloads
152 views

The “reproducibility crisis” has been a highly visible source of scientific controversy and dispute. Here, I propose and review several avenues for identifying and prioritizing research studies for the purpose of targeted validation. Of the various proposals discussed,...

["Bioinformatics","Evidence Based Medicine","Health Policy","Translational Medicine","Science Policy"]
doi:10.7287/peerj.preprints.2830v1
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