Peer-reviewed Articles - Biology

21 downloads
121 views

Targeted high-throughput sequencing using hybrid-enrichment offers a promising source of data for inferring multiple, meaningfully resolved, independent gene trees suitable to address challenging phylogenetic problems in species complexes and rapid radiations....

["Bioinformatics","Evolutionary Studies","Plant Science"]
doi:10.7717/peerj.3569
32 downloads
254 views

Background This paper is a comment on the idea of matrix-free Cladistics. Demonstration of this idea’s efficiency is a major goal of the study. Within the proposed framework, the ordinary (phenetic) matrix is necessary only as “source” of Hennigian trees, not as...

["Bioinformatics","Taxonomy","Computational Science"]
doi:10.7717/peerj.3578
48 downloads
567 views

Newly emerging influenza viruses continue to threaten public health. A rapid determination of the host range of newly discovered influenza viruses would assist in early assessment of their risk. Here, we attempted to predict the host of influenza viruses using...

["Bioinformatics","Computational Biology","Virology"]
doi:10.7717/peerj.3579
27 downloads
204 views

Background As the fifth most common cancer worldwide, Hepatocellular carcinoma (HCC) is also the third most common cause of cancer-related death in China. Several lncRNAs have been demonstrated to be associated with occurrence and prognosis of HCC. However, identification...

["Bioinformatics","Molecular Biology","Gastroenterology and Hepatology","Oncology"]
doi:10.7717/peerj.3575
31 downloads
359 views

The major virulence factor of the pneumococcus, and target for conjugate vaccines, is the polysaccharide capsule, which is usually encoded by the highly variable cps locus. Serotype 37 is an unusual pneumococcal type in which the single β-glucosyltransferase gene...

["Bioinformatics","Genomics","Microbiology","Infectious Diseases"]
doi:10.7717/peerj.3571
23 downloads
351 views

Background The ferric uptake regulator (Fur) is a transcription factor and the main regulator of iron acquisition in prokaryotes. When bound to ferric iron, Fur recognizes its DNA binding site and generally executes its function by repressing transcription of its...

["Bioinformatics","Genetics","Marine Biology","Microbiology","Molecular Biology"]
doi:10.7717/peerj.3461
211 downloads
1,638 views

The Tara Oceans Expedition has provided large, publicly-accessible microbial metagenomic datasets from a circumnavigation of the globe. Utilizing several size fractions from the samples originating in the Mediterranean Sea, we have used current assembly and binning...

["Bioinformatics","Marine Biology","Microbiology"]
doi:10.7717/peerj.3558
56 downloads
450 views

Mammalian tears are produced by lacrimal glands to protect eyes and may function in chemical communication and immunity. Recent studies on the house mouse chemical signalling revealed that major urinary proteins (MUPs) are not individually unique in Mus musculus...

["Bioinformatics","Evolutionary Studies","Genetics","Zoology"]
doi:10.7717/peerj.3541
55 downloads
333 views

Coral diseases are a leading factor contributing to the global decline of coral reefs, and yet mechanisms of disease transmission remain poorly understood. This study tested whether zooplankton can act as a vector for white band disease (WBD) in Acropora cervicornis....

["Bioinformatics","Ecology","Environmental Sciences","Marine Biology","Microbiology"]
doi:10.7717/peerj.3502
93 downloads
643 views

There are many steps in analyzing transcriptome data, from the acquisition of raw data to the selection of a subset of representative genes that explain a scientific hypothesis. The data produced can be represented as networks of interactions among genes and these...

["Bioinformatics","Computational Biology"]
doi:10.7717/peerj.3509
53 downloads
228 views

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
45 downloads
297 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
53 downloads
329 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
91 downloads
512 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
79 downloads
437 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

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