Peer-reviewed Articles

Background Amoebiasis is the third most common parasitic cause of morbidity and mortality, particularly in countries with poor hygienic settings. There exists an ambiguity in the diagnosis of amoebiasis, and hence there arises a necessity for a better diagnostic...

["Biochemistry","Bioinformatics","Parasitology","Infectious Diseases"]
doi:10.7717/peerj.3160
11 downloads
95 views

Understanding how proteins mutate is critical to solving a host of biological problems. Mutations occur when an amino acid is substituted for another in a protein sequence. The set of likelihoods for amino acid substitutions is stored in a matrix and input to alignment...

["Bioinformatics","Computational Biology","Human-Computer Interaction"]
doi:10.7717/peerj.3492
10 downloads
99 views

The five community state types (CSTs) first identified by Ravel et al. (2011) offered a powerful scheme to classify the states of human vaginal microbial communities (HVMC). The classification is a significant advance because it devised an effective handle to deal...

["Bioinformatics","Ecology","Microbiology","Women\u2019s Health","Computational Science"]
doi:10.7717/peerj.3366
31 downloads
222 views

Bioinformatics is currently faced with very large-scale data sets that lead to computational jobs, especially sequence similarity searches, that can take absurdly long times to run. For example, the National Center for Biotechnology Information (NCBI) Basic Local...

["Agricultural Science","Bioinformatics","Computational Biology","Plant Science"]
doi:10.7717/peerj.3486
39 downloads
311 views

Symbiotic microalgae (Symbiodinium spp.) strongly influence the performance and stress-tolerance of their coral hosts, making the analysis of Symbiodinium communities in corals (and metacommunities on reefs) advantageous for many aspects of coral reef research....

["Bioinformatics","Ecology","Marine Biology"]
doi:10.7717/peerj.3472
98 downloads
674 views

Oceanic viruses that infect bacteria, or phages, are known to modulate host diversity, metabolisms, and biogeochemical cycling, while the viruses that infect marine Archaea remain understudied despite the critical ecosystem roles played by their hosts. Here we...

["Bioinformatics","Ecology","Microbiology"]
doi:10.7717/peerj.3428
37 downloads
212 views

Background Glutamate decarboxylase (GAD), as a key enzyme in the γ -aminobutyric acid (GABA) shunt, catalyzes the decarboxylation of L-glutamate to form GABA. This pathway has attracted much interest because of its roles in carbon and nitrogen metabolism, stress...

["Bioinformatics","Molecular Biology","Plant Science"]
doi:10.7717/peerj.3439
47 downloads
327 views

Whole genome alignments and comparative analysis are key methods in the quest of unraveling the dynamics of genome evolution. Interactive visualization and exploration of the generated alignments, annotations, and phylogenetic data are important steps in the interpretation...

["Bioinformatics","Computational Biology"]
doi:10.7717/peerj-cs.116
86 downloads
310 views

Gastric cancer is an aggressive cancer that is often diagnosed late. Early detection and treatment require a better understanding of the molecular pathology of the disease. The present study combined data on gene expression and regulatory levels (microRNA, methylation,...

["Bioinformatics","Genetics","Genomics","Gastroenterology and Hepatology","Oncology"]
doi:10.7717/peerj.3385
52 downloads
409 views

Mitogen-activated protein kinases (MAPKs) are an important family of genes which play roles in vital plant processes, and they also help in coping against various kinds of environmental stresses including abiotic as well as biotic factors. The advancement of genomics...

["Bioinformatics","Computational Biology","Evolutionary Studies","Genomics","Plant Science"]
doi:10.7717/peerj.3255
73 downloads
465 views

Background Large-scale molecular evolutionary analyses of protein coding sequences requires a number of preparatory inter-related steps from finding gene families, to generating alignments and phylogenetic trees and assessing selective pressure variation. Each...

["Bioinformatics","Computational Biology"]
doi:10.7717/peerj-cs.118
70 downloads
345 views

The ethylene-insensitive3/ethylene-insensitive3-like (EIN3/EIL) proteins are a type of nuclear-localized protein with DNA-binding activity in plants. Although the EIN3/EIL gene family has been studied in several plant species, little is known about comprehensive...

["Bioinformatics","Genomics","Plant Science"]
doi:10.7717/peerj.3400
72 downloads
265 views

Gerbera hybrida is a cut-flower crop of global importance, and an understanding of the mechanisms underlying petal development is vital for the continued commercial development of this plant species. Brassinosteroids (BRs), a class of phytohormones, are known to...

["Bioinformatics","Developmental Biology","Genetics","Plant Science"]
doi:10.7717/peerj.3382
218 downloads
1,298 views

Coral microbiomes are known to play important roles in organismal health, response to environmental stress, and resistance to disease. The coral microbiome contains diverse assemblages of resident bacteria, ranging from defensive and metabolic symbionts to opportunistic...

["Bioinformatics","Ecology","Marine Biology","Microbiology"]
doi:10.7717/peerj.3315
60 downloads
311 views

Site-specific evolutionary rates can be estimated from codon sequences or from amino-acid sequences. For codon sequences, the most popular methods use some variation of the dN∕dS ratio. For amino-acid sequences, one widely-used method is called Rate4Site, and it...

["Bioinformatics","Computational Biology","Evolutionary Studies","Statistics"]
doi:10.7717/peerj.3391

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