Preprints (not yet peer-reviewed)

12 downloads
78 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
771 downloads
648 views

The past influences the present and future; for example, in computational chemistry, simplifying assumptions and approximations important in the pre-computing era remains relevant today in allowing simulation of larger systems with reasonable amount of computer...

["Biochemistry","Bioengineering","Biophysics","Computational Biology","Computational Science"]
doi:10.7287/peerj.preprints.365v4
24 downloads
90 views

Colony counting to estimate colony forming units (CFUs) is a standard microbiology procedure used for determining the number of viable microbes in a system. Typically this process is done manually, which is time consuming, tedious, and sometimes error prone. Alternate...

["Microbiology","Medical Genetics","Computational Science"]
doi:10.7287/peerj.preprints.2792v1
8 downloads
75 views

Basic idea of science is reproducibility of phenomena and experiments. Reproducibility of data analyses and reports is becoming more and more important. It requires structured organization of data, augmented with enought metadata for future re-use of data. Our...

["Bioinformatics","Genomics","Plant Science","Statistics","Computational Science"]
doi:10.7287/peerj.preprints.2791v1
122 downloads
207 views

As part of a recent workshop entitled "Imagining Tomorrow's University”, we were asked to visualize the future of universities as research becomes increasingly data- and computation-driven and identify a set of principles characterizing pertinent opportunities...

["Ethical Issues","Science and Medical Education","Science Policy","Computational Science"]
doi:10.7287/peerj.preprints.2781v1
8 downloads
122 views

Background. The phytohormone jasmonates (JAs) regulate fundamental plant processes; such as the anthocyanin accumulation during ripening of strawberry, a non-climacteric fruit model. Jasmonoyl-isoleucine (JA-Ile), one of the bioactive JA molecules, mediates binding...

["Biochemistry","Bioinformatics","Computational Biology","Computational Science"]
doi:10.7287/peerj.preprints.2772v1
51 downloads
204 views

Background RNA sequencing (RNA-Seq) is a powerful technique for transcriptome profiling of the organisms that uses the capabilities of next-generation sequencing (NGS) technologies. Recent advances in NGS let to measure the expression levels of tens to thousands...

["Bioinformatics","Genomics","Statistics","Computational Science"]
doi:10.7287/peerj.preprints.2761v1
9 downloads
50 views

In the health self-management services it is beneficial to identify and address the already existing healthy activity patterns of the user. Some of these healthy activity patterns might be of a utilitarian nature, e.g. commuting to work by bike or on foot, or might...

["Kinesiology","Public Health","Computational Science"]
doi:10.7287/peerj.preprints.2751v1
51 downloads
170 views

Introduction Next Generation Sequencing (NGS) platforms have radically changed the field of genomics and are routinely applied to a variety of functional genomics problems. Although NGS has markedly accelerated multiple areas of genomics research it is a massively...

["Bioinformatics","Genomics","Molecular Biology","Computational Science"]
doi:10.7287/peerj.preprints.2752v1
25 downloads
152 views

The scientific literature contains an historic record of the changing ways in which we describe the world. Shifts in understanding of scientific concepts are reflected in the introduction of new terms and the changing usage and context of existing ones. We conducted...

["Biodiversity","Bioinformatics","Computational Biology","Computational Science"]
doi:10.7287/peerj.preprints.2747v1
15 downloads
73 views

Natural product libraries are important tools for drug discovery. However, until now, there has not been a system to allow projections of the potential number of hits from creating these libraries. The objective of this study was to develop a stochastic model system...

["Biodiversity","Biotechnology","Microbiology","Drugs and Devices","Computational Science"]
doi:10.7287/peerj.preprints.2734v1
19 downloads
178 views

Background In the era of semantic web, life science ontologies play an important role in tasks such as annotating biological objects, linking relevant data pieces, and verifying data consistency. Understanding ontology structures and overlapping ontologies is essential...

["Bioinformatics","Computational Science"]
doi:10.7287/peerj.preprints.2715v1
101 downloads
569 views

Access to consistent, high-quality metadata is critical to finding, understanding, and reusing scientific data. However, while there are many relevant vocabularies for the annotation of a dataset, none sufficiently captures all the necessary metadata. This prevents...

["Bioinformatics","Taxonomy","Computational Science"]
doi:10.7287/peerj.preprints.1982v2
38 downloads
200 views

This document is my attempt at distilling some of the information in two papers published by Anthony Nicholls (J. Comput. Aided Mol. Des. 2014, 28, 887; ibid 2016, 30, 103). Anthony also very kindly provided some new equations, not found in the papers, in response...

["Biophysics","Computational Biology","Mathematical Biology","Computational Science"]
doi:10.7287/peerj.preprints.2693v1
68 downloads
353 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","Computational Biology","Genomics","Computational Science"]
doi:10.7287/peerj.preprints.2452v3
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