Peer-reviewed Articles

16 downloads
133 views

High-throughput phenotype assays are a cornerstone of systems biology as they allow direct measurements of mutations, genes, strains, or even different genera. High-throughput methods also require data analytic methods that reduce complex time-series data to a...

["Computational Biology","Microbiology"]
doi:10.7717/peerj.4681
70 downloads
448 views

Prediction of taxonomy for marker gene sequences such as 16S ribosomal RNA (rRNA) is a fundamental task in microbiology. Most experimentally observed sequences are diverged from reference sequences of authoritatively named organisms, creating a challenge for prediction...

["Bioinformatics","Computational Biology","Microbiology","Taxonomy"]
doi:10.7717/peerj.4652
46 downloads
276 views

Complex diseases such as cancer are usually the result of a combination of environmental factors and one or several biological pathways consisting of sets of genes. Each biological pathway exerts its function by delivering signaling through the gene network. Theoretically,...

["Bioinformatics","Computational Biology"]
doi:10.7717/peerj.4571
154 downloads
920 views

Tip-dating, where fossils are included as dated terminal taxa in Bayesian dating inference, is an increasingly popular method. Data for these studies often come from morphological character matrices originally developed for non-dated, and usually parsimony, analyses....

["Computational Biology","Evolutionary Studies","Paleontology"]
doi:10.7717/peerj.4553
143 downloads
775 views

Background Plasmids play an important role in the dissemination of antibiotic resistance, making their detection an important task. Using whole genome sequencing (WGS), it is possible to capture both bacterial and plasmid sequence data, but short read lengths make...

["Bioinformatics","Computational Biology","Microbiology"]
doi:10.7717/peerj.4588
65 downloads
414 views

Background A Rohingya refugee camp in Cox’s Bazar, Bangladesh experienced a large-scale diphtheria epidemic in 2017. The background information of previously immune fraction among refugees cannot be explicitly estimated, and thus we conducted an uncertainty analysis...

["Computational Biology","Mathematical Biology","Epidemiology","Global Health","Infectious Diseases"]
doi:10.7717/peerj.4583
43 downloads
208 views

Background Labels are a way to add some information on a text, such as functional annotations such as genes on a DNA sequences. V(D)J recombinations are DNA recombinations involving two or three short genes in lymphocytes. Sequencing this short region (500 bp or...

["Bioinformatics","Computational Biology","Algorithms and Analysis of Algorithms"]
doi:10.7717/peerj-cs.148
83 downloads
629 views

Membrane-bound fatty acid desaturases perform oxygenated desaturation reactions to insert double bonds within fatty acyl chains in regioselective and stereoselective manners. The Δ9-fatty acid desaturase strictly creates the first double bond between C9 and 10...

["Biotechnology","Computational Biology","Microbiology"]
doi:10.7717/peerj.4347
83 downloads
930 views

Background Real-time quantitative PCR (qPCR) is a broadly used technique in the biomedical research. Currently, few different analysis models are used to determine the quality of data and to quantify the mRNA level across the experimental conditions. Methods We...

["Bioinformatics","Cell Biology","Computational Biology","Molecular Biology"]
doi:10.7717/peerj.4473
88 downloads
895 views

RNA editing modifies transcripts and may alter their regulation or function. In humans, the most common modification is adenosine to inosine (A-to-I). We examined the global characteristics of RNA editing in 4,301 human tissue samples. More than 1.6 million A-to-I...

["Computational Biology","Genetics","Genomics","Cardiology","Computational Science"]
doi:10.7717/peerj.4466
139 downloads
675 views

African swine fever virus (ASFV) is the etiological agent of ASF, a fatal hemorrhagic fever that affects domestic pigs. There is currently no vaccine against ASFV, making it a significant threat to the pork industry. The ASFV genome sequence has been published;...

["Biochemistry","Bioinformatics","Biotechnology","Computational Biology"]
doi:10.7717/peerj.4396
88 downloads
469 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
145 downloads
926 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
80 downloads
633 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
1 citation
166 downloads
791 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

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