Peer-reviewed Articles

8 downloads
58 views

C9orf72 is associated with frontotemporal dementia (FTD) and Amyotrophic Lateral Sclerosis (ALS), both of which are devastating neurodegenerative diseases. Findings suggest that an expanded hexanucleotide repeat in the non-coding region of the C9orf72 gene is the...

["Bioinformatics","Computational Biology","Genomics"]
doi:10.7717/peerj.4391
82 downloads
601 views

Complex networks have been successfully applied to the characterization and modeling of complex systems in several distinct areas of Biological Sciences. Nevertheless, their utilization in phylogenetic analysis still needs to be widely tested, using different molecular...

["Bioinformatics","Computational Biology","Evolutionary Studies"]
doi:10.7717/peerj.4349
1 citation
53 downloads
448 views

We introduce LEISR (Likehood Estimation of Individual Site Rates, pronounced “laser”), a tool to infer relative evolutionary rates from protein and nucleotide data, implemented in HyPhy. LEISR is based on the popular Rate4Site (Pupko et al., 2002) approach for...

["Bioinformatics","Computational Biology","Evolutionary Studies","Genomics"]
doi:10.7717/peerj.4339
83 downloads
537 views

The ubiquitous daily rhythms in mammalian physiology are guided by progression of the circadian clock. In mice, systemic disruption of the clock can promote tumor growth. In vitro, multiple oncogenes can disrupt the clock. However, due to the difficulties of studying...

["Bioinformatics","Computational Biology","Genomics","Oncology"]
doi:10.7717/peerj.4327
69 downloads
384 views

Plasma lipid levels are risk factors for cardiovascular disease, a leading cause of death worldwide. While many studies have been conducted on lipid genetics, they mainly focus on Europeans and thus their transferability to diverse populations is unclear. We performed...

["Computational Biology","Genetics","Genomics"]
doi:10.7717/peerj.4314
87 downloads
404 views

Understanding how structural and functional alterations of individual tissues impact on whole-joint function is challenging, particularly in humans where direct invasive experimentation is difficult. Finite element (FE) computational models produce quantitative...

["Bioengineering","Biotechnology","Computational Biology"]
doi:10.7717/peerj.4298
108 downloads
659 views

Genomic signal processing (GSP) methods which convert DNA data to numerical values have recently been proposed, which would offer the opportunity of employing existing digital signal processing methods for genomic data. One of the most used methods for exploring...

["Bioinformatics","Computational Biology","Genomics"]
doi:10.7717/peerj.4264
79 downloads
461 views

Sigmoidal and double-sigmoidal dynamics are commonly observed in many areas of biology. Here we present sicegar, an R package for the automated fitting and classification of sigmoidal and double-sigmoidal data. The package categorizes data into one of three categories,...

["Bioinformatics","Computational Biology","Mathematical Biology","Statistics","Data Science"]
doi:10.7717/peerj.4251
58 downloads
288 views

Background With the continuous discovery of microRNA’s (miRNA) association with a wide range of biological and cellular processes, expression profile-based functional characterization of such post-transcriptional regulation is crucial for revealing its significance...

["Biochemistry","Bioinformatics","Computational Biology","Molecular Biology","Data Mining and Machine Learning"]
doi:10.7717/peerj.4262
82 downloads
305 views

The etiology of cancer includes aberrant cellular homeostasis where a compromised RNA regulatory network is a prominent contributing factor. In particular, noncoding RNAs including microRNAs (miRNAs) and long noncoding RNAs (lncRNAs) were recently shown to play...

["Bioinformatics","Computational Biology","Genomics"]
doi:10.7717/peerj.4254
67 downloads
401 views

Coarse-grained (CG) models have been successful in simulating the chemical properties of lipid bilayers, but accurate treatment of membrane proteins and lipid-protein molecular interactions remains a challenge. The CgProt force field, original developed with the...

["Biophysics","Computational Biology","Computational Science"]
doi:10.7717/peerj.4230
81 downloads
400 views

Von Bertalanffy proposed the differential equation m′(t) = p × m(t)a − q × m(t) for the description of the mass growth of animals as a function m(t) of time t. He suggested that the solution using the metabolic scaling exponent a = 2/3 (Von Bertalanffy growth function...

["Agricultural Science","Aquaculture, Fisheries and Fish Science","Computational Biology","Mathematical Biology"]
doi:10.7717/peerj.4205
52 downloads
311 views

Background Recent research suggests that the CA3 subregion of the hippocampus has properties of both autoassociative network, due to its ability to complete partial cues, tolerate noise, and store associations between memories, and heteroassociative one, due to...

["Computational Biology","Neuroscience"]
doi:10.7717/peerj.4203
72 downloads
282 views

Phosphorylation exerts a crucial role in multiple biological cellular processes which is catalyzed by protein kinases and closely related to many diseases. Identification of kinase–substrate relationships is important for understanding phosphorylation and provides...

["Bioinformatics","Computational Biology"]
doi:10.7717/peerj.4182
1 citation
309 downloads
1,926 views

Systems for collecting image data in conjunction with computer vision techniques are a powerful tool for increasing the temporal resolution at which plant phenotypes can be measured non-destructively. Computational tools that are flexible and extendable are needed...

["Agricultural Science","Bioinformatics","Computational Biology","Plant Science","Data Mining and Machine Learning"]
doi:10.7717/peerj.4088

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