Peer-reviewed Articles

141 downloads
671 views

Background De novo transcriptome assembly of short reads is now a common step in expression analysis of organisms lacking a reference genome sequence. Several software packages are available to perform this task. Even if their results are of good quality it is...

["Bioinformatics","Computational Biology","Genomics","Computational Science"]
doi:10.7717/peerj.2988
60 downloads
577 views

Genomic heterogeneity of bacterial species is observed and studied in experimental evolution experiments and clinical diagnostics, and occurs as micro-diversity of natural habitats. The challenge for genome research is to accurately capture this heterogeneity with...

["Bioinformatics","Computational Biology","Evolutionary Studies","Genomics","Microbiology"]
doi:10.7717/peerj.2997
63 downloads
503 views

Metastatic cutaneous melanoma is an aggressive skin cancer with some progression-slowing treatments but no known cure. The omics data explosion has created many possible drug candidates; however, filtering criteria remain challenging, and systems biology approaches...

["Bioinformatics","Computational Biology","Data Science","World Wide Web and Web Science"]
doi:10.7717/peerj-cs.106
210 downloads
1,058 views

Marker gene sequencing of microbial communities has generated big datasets of microbial relative abundances varying across environmental conditions, sample sites and treatments. These data often come with putative phylogenies, providing unique opportunities to...

["Computational Biology","Ecology","Mathematical Biology","Microbiology","Statistics"]
doi:10.7717/peerj.2969
120 downloads
432 views

Rhodomyrtone, a natural antimicrobial compound, displays potent activity against many Gram-positive pathogenic bacteria, comparable to last-defence antibiotics including vancomycin and daptomycin. Our previous studies pointed towards effects of rhodomyrtone on...

["Biochemistry","Computational Biology","Microbiology","Drugs and Devices","Infectious Diseases"]
doi:10.7717/peerj.2962
70 downloads
459 views

Bioinformaticians have implemented different strategies to distinguish cancer driver genes from passenger genes. One of the more recent advances uses a pathway-oriented approach. Methods that employ this strategy are highly dependent on the quality and size of...

["Bioinformatics","Computational Biology","Statistics","Computational Science"]
doi:10.7717/peerj.2568
145 downloads
573 views

Background Few studies have investigated the gut microbiome of infants, fewer still preterm infants. In this study we sought to quantify and interrogate the resistome within a cohort of premature infants using shotgun metagenomic sequencing. We describe the gut...

["Computational Biology","Genomics","Microbiology","Pediatrics","Public Health"]
doi:10.7717/peerj.2928
61 downloads
438 views

Type I restriction-modification enzymes are multisubunit, multifunctional molecular machines that recognize specific DNA target sequences, and their multisubunit organization underlies their multifunctionality. EcoR124I is the archetype of Type I restriction-modification...

["Biochemistry","Biophysics","Computational Biology","Molecular Biology"]
doi:10.7717/peerj.2887
95 downloads
672 views

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
46 downloads
298 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
65 downloads
648 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
161 downloads
864 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
218 downloads
1,141 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
126 downloads
350 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
84 downloads
395 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

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