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bioinformatics

Background: Taxonomic classification of marker-gene (i.e., amplicon) sequences represents an important step for molecular identification of microorganisms.Results: We present three advances in our ability to assign and interpret taxonomic classifications of short...

["Bioinformatics","Computational Biology","Ecology","Microbiology","Taxonomy"]
doi:10.7287/peerj.preprints.934v1
12 downloads
15 views

Recently, a number of protocols extending RNA-sequencing to the single-cell regime have been published. However, we were concerned that the additional steps to deal with such minute quantities of input sample would introduce serious biases that would make analysis...

["Bioinformatics","Biotechnology","Computational Biology","Genomics"]
doi:10.7717/peerj.869
43 downloads
39 views

Dilated cardiomyopathy is a prevalent and often fatal disease in humans and dogs. Indeed dilated cardiomyopathy is the third most common form of cardiac disease in humans, reported to affect approximately 36 individuals per 100,000 individuals. In dogs, dilated...

["Bioinformatics","Genetics","Veterinary Medicine","Cardiology","Medical Genetics"]
doi:10.7717/peerj.842
11 downloads
13 views

Background. The clade Chelidae (Testudines, Pleurodira) is a group of fresh water turtles with representatives in Australasia and South America. Its diversity of extant and fossil species is characterized by two recognized morphotypes: the long-necked and the short-necked...

["Bioinformatics","Evolutionary Studies","Genetics","Taxonomy"]
doi:10.7287/peerj.preprints.930v1
7 downloads
8 views

Mobile accelerometry is more and more being used in clinical trials as a tool to measure outcomes related to physical activity. However, it is still difficult to integrate exercise therapy in controlled clinical trials. We want to explore the option to use a unified...

["Bioengineering","Bioinformatics","Computational Science"]
doi:10.7287/peerj.preprints.929v1
4 downloads
5 views

The ”Gait-&Balance-Box” suggests a standardization for clinical walk and balance tests with the aim to improve quality, applicability and comparability. Heart of the patient monitoring is the actibeltblue, an autonomous wireless accelerometer that is worn like...

["Bioengineering","Bioinformatics","Evidence Based Medicine","Computational Science"]
doi:10.7287/peerj.preprints.928v1
12 downloads
18 views

Currently, monomeric fluorescent proteins (FP) are ideal markers for protein tagging. The prediction of oligomeric states is helpful for enhancing live biomedical imaging. Computational prediction of FP oligomeric states can accelerate the effort of protein engineering...

["Bioinformatics","Computational Biology"]
doi:10.7287/peerj.preprints.922v1
23 downloads
98 views

Protein chemical shifts are routinely used to augment molecular mechanics force fields in protein structure simulations, with weights of the chemical shift restraints determined empirically. These weights, however, might not be an optimal descriptor of a given...

["Biochemistry","Bioinformatics","Computational Biology","Computational Science"]
doi:10.7717/peerj.861
30 downloads
49 views

Protein phosphorylation is one of the most important protein post-translational modifications and plays a role in numerous cellular processes including recognition, signaling and degradation. It can be studied experimentally by various methodologies, like employing...

["Bioinformatics","Biophysics","Computational Biology"]
doi:10.7287/peerj.preprints.916v1
32 downloads
82 views

The perilipins are lipid droplet surface proteins that contribute to fat metabolism by controlling the access of lipids to lipolytic enzymes. Perilipins have been identified in organisms as diverse as metazoa, fungi, and amoebas but strikingly not in nematodes....

["Bioinformatics","Cell Biology","Genomics"]
doi:10.7287/peerj.preprints.904v2
70 downloads
157 views

Amplifications or deletions of genome segments, known as copy number variants (CNVs), have been associated with many diseases. Read depth analysis of next-generation sequencing (NGS) is an essential method of detecting CNVs. However, genome read coverage is frequently...

["Bioinformatics","Computational Biology","Genomics"]
doi:10.7717/peerj.836
39 downloads
175 views

Background. Every new scientific field can be traced back to a single, seminal publication. Therefore, a bibliometric analysis can yield significant insights into the history and potential future of a research field. This year marks 21 years since that first ground-breaking...

["Bioinformatics","Cell Biology","Molecular Biology","Science and Medical Education"]
doi:10.7717/peerj.829
54 downloads
77 views

The growing number of genotyped populations, the advent of high-throughput phenotyping techniques and the development of GWAS analysis software has rapidly accelerated the number of GWAS experimental results. Candidate gene discovery from these results files is...

["Bioinformatics","Computational Biology","Visual Analytics"]
doi:10.7287/peerj.preprints.902v1
64 downloads
195 views

Summary: HapFlow is a python application for visualising haplotypes present in high-throughput sequencing data. HapFlow identifies nucleotide variant profiles in raw read sequences and creates an abstract visual representation of these profiles to make haplotypes...

["Bioinformatics","Genomics","Microbiology"]
doi:10.7287/peerj.preprints.895v1
158 downloads
311 views

We present a semi-streaming algorithm for k-mer spectral analysis of DNA sequencing reads, together with a derivative approach that is fully streaming. The approach can also be applied to genomic, transcriptomic, and metagenomic data sets. We develop two tools...

["Bioinformatics","Computational Biology"]
doi:10.7287/peerj.preprints.890v1

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