Peer-reviewed Articles - Computer sci

24 downloads
186 views

Transcription factors (TFs) and microRNAs (miRNAs) are well-characterized trans-acting essential players in gene expression regulation. Growing evidence indicates that TFs and miRNAs can work cooperatively, and their dysregulation has been associated with many...

["Bioinformatics","Computational Biology","Genomics","Computational Science"]
doi:10.7717/peerj.5951
28 downloads
167 views

Background A positive association between diabetes and breast cancer has been identified by various epidemiological and clinical studies. However, the possible molecular interactions between the two heterogeneous diseases have not been fully determined yet. There...

["Bioinformatics","Computational Biology"]
doi:10.7717/peerj.5917
20 downloads
132 views

The ability of vertebrates to generate rhythm within their spinal neural networks is essential for walking, running, and other rhythmic behaviors. The central pattern generator (CPG) network responsible for these behaviors is well-characterized with experimental...

["Animal Behavior","Bioinformatics","Computational Biology","Neuroscience","Computational Science"]
doi:10.7717/peerj.5849
29 downloads
165 views

We present PromoterPredict, a dynamic multiple regression approach to predict the strength of Escherichia coli promoters binding the σ70 factor of RNA polymerase. σ70 promoters are ubiquitously used in recombinant DNA technology, but characterizing their strength...

["Bioinformatics","Computational Biology","Genomics","Synthetic Biology","Data Mining and Machine Learning"]
doi:10.7717/peerj.5862
57 downloads
396 views

Many important cellular processes involve protein–protein interactions (PPIs) mediated by a Short Linear Motif (SLiM) in one protein interacting with a globular domain in another. Despite their significance, these domain-motif interactions (DMIs) are typically...

["Bioinformatics","Computational Biology","Molecular Biology"]
doi:10.7717/peerj.5858
38 downloads
229 views

Background The need for read-based phasing arises with advances in sequencing technologies. The minimum error correction (MEC) approach is the primary trend to resolve haplotypes by reducing conflicts in a single nucleotide polymorphism-fragment matrix. However,...

["Bioinformatics","Computational Biology","Genomics"]
doi:10.7717/peerj.5852
36 downloads
194 views

Background In both prokaryotic and eukaryotic proteins, repeated occurrence of a single or a group of few amino acids are found. These regions are termed as low complexity regions (LCRs). It has been observed that amino acid bias in LCR is directly linked to their...

["Bioinformatics","Computational Biology"]
doi:10.7717/peerj.5823
47 downloads
336 views

Colorectal cancer (CRC) has a high incident rate in both men and women and is affecting millions of people every year. Genome-wide association studies (GWAS) on CRC have successfully revealed common single-nucleotide polymorphisms (SNPs) associated with CRC risk....

["Bioinformatics","Computational Biology","Genetics","Epidemiology","Data Mining and Machine Learning"]
doi:10.7717/peerj.5854
56 downloads
415 views

Background Bayesian networks are directed acyclic graphical models widely used to represent the probabilistic relationships between random variables. They have been applied in various biological contexts, including gene regulatory networks and protein–protein interactions...

["Bioinformatics","Computational Biology"]
doi:10.7717/peerj.5692
169 downloads
1,353 views

The recognition of the group Archaea as a major branch of the tree of life (ToL) prompted a new view of the evolution of biodiversity. The genomic representation of archaeal biodiversity has since significantly increased. In addition, advances in phylogenetic modeling...

["Biodiversity","Computational Biology","Evolutionary Studies","Paleontology","Taxonomy"]
doi:10.7717/peerj.5770
57 downloads
216 views

Protein backbones occupy diverse conformations, but compact metrics to describe such conformations and transitions between them have been missing. This report re-introduces the Ramachandran number (ℛ) as a residue-level structural metric that could simply the life...

["Bioinformatics","Computational Biology","Mathematical Biology"]
doi:10.7717/peerj.5745
64 downloads
303 views

Background Osteoclast differentiation in the inflamed synovium of rheumatoid arthritis (RA) affected joints leads to the formation of bone lesions. Reconstruction and analysis of protein interaction networks underlying specific disease phenotypes are essential...

["Bioinformatics","Computational Biology","Genomics","Immunology","Rheumatology"]
doi:10.7717/peerj.5743
74 downloads
172 views

Mortality is one of the most important parameters for the study of population dynamics. One of the main sources of information to calculate the mortality of cetaceans arises from the observed age-structure of stranded animals. A method based on an adaptation of...

["Computational Biology","Algorithms and Analysis of Algorithms","Software Engineering"]
doi:10.7717/peerj.5768
57 downloads
223 views

The number of amino acids that occupy a given protein site during evolution reflects the selective constraints operating on the site. This evolutionary variability is strongly influenced by the structural properties of the site in the native structure, and it is...

["Bioinformatics","Biophysics","Computational Biology","Evolutionary Studies"]
doi:10.7717/peerj.5549
63 downloads
306 views

Model-free methods are widely used for the processing of brain fMRI data collected under natural stimulations, sleep, or rest. Among them is the popular fuzzy c-mean algorithm, commonly combined with cluster validity (CV) indices to identify the ‘true’ number of...

["Bioinformatics","Computational Biology","Neuroscience"]
doi:10.7717/peerj.5416

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