Peer-reviewed Articles

Autophagy serves as a turnover mechanism for the recycling of redundant and/or damaged macromolecules present in eukaryotic cells to re-use them under starvation conditions via a double-membrane structure known as autophagosome. A set of eukaryotic genes called...

["Bioinformatics","Cell Biology","Computational Biology"]
doi:10.7717/peerj.2878
30 downloads
192 views

Background Estimates of fishing and natural mortality are important for understanding, and ultimately managing, commercial and recreational fisheries. High reward tags with fixed station acoustic telemetry provides a promising approach to monitoring mortality rates...

["Aquaculture, Fisheries and Fish Science","Computational Biology","Ecology","Statistics"]
doi:10.7717/peerj.2874
20 downloads
243 views

Solar salterns are excellent model ecosystems for studying virus-microbial interactions because of their low microbial diversity, environmental stability, and high viral density. By using the power of CRISPR spacers to link viruses to their prokaryotic hosts, we...

["Bioinformatics","Computational Biology","Ecology","Genomics","Microbiology"]
doi:10.7717/peerj.2844
89 downloads
502 views

Metagenomic experiments attempt to characterize microbial communities using high-throughput DNA sequencing. Identification of the microorganisms in a sample provides information about the genetic profile, population structure, and role of microorganisms within...

["Bioinformatics","Computational Biology"]
doi:10.7717/peerj-cs.104
157 downloads
902 views

A number of different models have been proposed as descriptions of the species-abundance distribution (SAD). Most evaluations of these models use only one or two models, focus on only a single ecosystem or taxonomic group, or fail to use appropriate statistical...

["Computational Biology","Ecology","Statistics"]
doi:10.7717/peerj.2823
94 downloads
262 views

Background The involvement of multiple genes and missing heritability, which are dominant in complex diseases such as multiple sclerosis (MS), entail using network biology to better elucidate their molecular basis and genetic factors. We therefore aimed to integrate...

["Bioinformatics","Computational Biology","Immunology","Neurology"]
doi:10.7717/peerj.2775
57 downloads
328 views

We developed a bio-inspired robot controller combining an artificial genome with an agent-based control system. The genome encodes a gene regulatory network (GRN) that is switched on by environmental cues and, following the rules of transcriptional regulation,...

["Bioinformatics","Computational Biology","Evolutionary Studies"]
doi:10.7717/peerj.2812
140 downloads
490 views

We examined RNA-Seq data on 211 biological samples from 24 different Arabidopsis experiments carried out by different labs. We grouped the samples according to tissue types, and in each of the groups, we identified genes that are stably expressed across biological...

["Bioinformatics","Computational Biology","Genetics","Genomics","Molecular Biology"]
doi:10.7717/peerj.2791
61 downloads
234 views

Major research efforts have been devoted to the discovery and development of new chemical entities that could inhibit the protein–protein interaction between HIF-1α and the von Hippel–Lindau protein (pVHL), which serves as the substrate recognition subunit of an...

["Biochemistry","Computational Biology","Pharmacology"]
doi:10.7717/peerj.2757
107 downloads
606 views

Microbes growing in animal host environments face fluctuations that have elements of both randomness and predictability. In the mammalian gut, fluctuations in nutrient levels and other physiological parameters are structured by the host’s behavior, diet, health...

["Computational Biology","Ecology","Mathematical Biology","Microbiology","Synthetic Biology"]
doi:10.7717/peerj.2716
83 downloads
289 views

As we age, our hearts undergo changes that result in a reduction in complexity of physiological interactions between different control mechanisms. This results in a potential risk of cardiovascular diseases which are the number one cause of death globally. Since...

["Computational Biology","Cardiology"]
doi:10.7717/peerj.2755
112 downloads
650 views

We propose here a working unit for teaching basic concepts of structural bioinformatics and evolution through the example of a wooden snake puzzle, strikingly similar to toy models widely used in the literature of protein folding. In our experience, developed at...

["Bioinformatics","Computational Biology","Computer Education","Scientific Computing and Simulation"]
doi:10.7717/peerj-cs.100
48 downloads
291 views

Tissue microarrays are commonly used in modern pathology for cancer tissue evaluation, as it is a very potent technique. Tissue microarray slides are often scanned to perform computer-aided histopathological analysis of the tissue cores. For processing the image,...

["Computational Biology","Pathology","Histology"]
doi:10.7717/peerj.2741
72 downloads
377 views

The design of experiments and the validation of the results achieved with them are vital in any research study. This paper focuses on the use of different Machine Learning approaches for regression tasks in the field of Computational Intelligence and especially...

["Bioinformatics","Computational Biology","Molecular Biology","Statistics","Computational Science"]
doi:10.7717/peerj.2721
70 downloads
328 views

Background Shugoshins (SGOs) are proteins that protect cohesins located at the centromeres of sister chromatids from their early cleavage during mitosis and meiosis in plants, fungi, and animals. Their function is to prevent premature sister-chromatid disjunction...

["Bioinformatics","Cell Biology","Computational Biology","Evolutionary Studies"]
doi:10.7717/peerj.2736

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