Total of 2,022 results Filter on subject area
bioinformatics

Comprehensive analysis of shotgun metagenomic assemblies have revolutionized molecular microbial ecology, but few microbiologists command the full suite of bioinformatics skills necessary to process, interact, organize and visualize overlapping DNA sequence contigs....

["Bioinformatics","Biotechnology","Computational Biology","Genomics","Microbiology"]
doi:10.7287/peerj.preprints.1275v1
29 downloads
227 views

Changes in hardware or image processing settings are a common issue for large multi-center studies. In order to pool MRI data acquired under these changed conditions, it is necessary to demonstrate that the changes do not affect MRI-based measurements. In these...

["Bioinformatics","Neurology","Radiology and Medical Imaging","Statistics"]
doi:10.7287/peerj.preprints.808v2
6 downloads
50 views

Two Component Systems and Phosphorelays (TCS/PR) are environmental signal transduction cascades in prokaryotes and, less frequently, in eukaryotes. The internal domain organization of proteins and the topology of TCS/PR cascades play an important role in shaping...

["Bioinformatics","Computational Biology","Mathematical Biology","Synthetic Biology"]
doi:10.7287/peerj.preprints.1267v1
139 downloads
258 views

Electroencephalography (EEG) signals’ interpretation is based on waveform analysis, where meaningful information should emerge from a plethora of data. Nonetheless, the continuous increase in computational power and the development of new data processing algorithms...

["Bioengineering","Bioinformatics","Biophysics","Neuroscience","Neurology"]
doi:10.7287/peerj.preprints.1265v1
28 downloads
47 views

We show here that chicken gizzard caldesmon (CaD) and its C-terminal domain (residues 636-771, CaD136) are intrinsically disordered proteins. The computational and experimental analyses of the wild type CaD136 and series of its single tryptophan mutants (W674A,...

["Biochemistry","Bioinformatics","Biophysics","Computational Biology"]
doi:10.7287/peerj.preprints.1261v1
16 downloads
70 views

A significant outbreak of H5N8 avian influenza began in early 2014 in Korea. H5N8 is a highly pathogenic avian influenza that is often fatal to chickens and other domestic poultry but which can be asymptomatic in ducks. The virus was also found in migratory birds...

["Bioinformatics","Evolutionary Studies","Virology"]
doi:10.7287/peerj.preprints.1250v1
28 downloads
122 views

Methods for in-silico screening of large databases of molecules increasingly complement and replace experimental techniques to discover novel compounds to combat diseases. As these techniques become more complex and computationally costly we are faced with an increasing...

["Bioinformatics","Computational Biology","Human-Computer Interaction","Distributed and Parallel Computing"]
doi:10.7287/peerj.preprints.1245v1
19 downloads
61 views

The concept of phylogenetic homology has been criticized of involving circular argumentation resulting from a methodological gap between its ontological definition and its empirical recognition criteria. Based on the role of similarity for the recognition of phylogenetic...

["Biodiversity","Bioinformatics","Computational Biology","Evolutionary Studies","Zoology"]
doi:10.7287/peerj.preprints.1243v1
261 downloads
161 views

Previously we presented Swarm v1, a novel and open source amplicon clustering program that produced fine-scale molecular operational taxonomic units (OTUs), free of arbitrary global clustering thresholds and input-order dependency. Swarm v1 worked with an initial...

["Biodiversity","Bioinformatics","Environmental Sciences","Microbiology","Molecular Biology"]
doi:10.7287/peerj.preprints.1222v2
291 downloads
809 views

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.934v2
72 downloads
136 views

Despite the central role of species distributions in ecology and conservation, occurrence information remains geographically and taxonomically incomplete and biased. Numerous socio-economic and ecological drivers of uneven record collection and mobilization among...

["Biogeography","Bioinformatics","Conservation Biology","Ecology","Zoology"]
doi:10.7287/peerj.preprints.1218v2
78 downloads
781 views

As more than 90% of species in a microbial community could not be isolated and cultivated, the metagenomic methods have become one of the most important methods to analyze microbial community as a whole. With the fast accumulation of metagenomic samples and the...

["Bioinformatics"]
doi:10.7717/peerj.993
8 downloads
57 views

Multiple sequence alignment (MSA) is widely used to reveal structural and functional changes leading to genetic differences among species, and to reconstruct evolutionary histories of related genes, proteins and genomes. Traditionally, proteins and their coding...

["Bioinformatics","Computational Biology"]
doi:10.7287/peerj.preprints.1214v1
51 downloads
293 views

Accurate identification of protein–protein interactions (PPI) is the key step in understanding proteins’ biological functions, which are typically context-dependent. Many existing PPI predictors rely on aggregated features from protein sequences, however only a...

["Bioinformatics"]
doi:10.7717/peerj.1041
26 downloads
143 views

Clustering algorithms are often used to find groups relevant in a specific context; however, they are not informed about this context. We present a simple algorithm, HOODS, which identifies context-specific neighborhoods of entities from a similarity matrix and...

["Bioinformatics","Computational Biology","Computational Science"]
doi:10.7717/peerj.1057

Top subject areas - Articles & Preprints

Top subject areas - People

View all subject areas