Peer-reviewed Articles - Biology

3 downloads
3 views

Gene expression profiling data provide useful information for the investigation of biological function and process. However, identifying a specific expression pattern from extensive time series gene expression data is not an easy task. Clustering, a popular method,...

["Bioinformatics","Computational Biology"]
doi:10.7717/peerj.4927
7 downloads
52 views

Background Mitogen-activated protein kinase (MAPK) cascades, an important type of pathway in eukaryotic signaling networks, play a key role in plant defense responses, growth and development. Methods Phylogenetic analysis and conserved motif analysis of the MKK...

["Bioinformatics","Plant Science"]
doi:10.7717/peerj.5037
21 downloads
188 views

Multilocus sequence typing (MLST) is a standard tool in population genetics and bacterial epidemiology that assesses the genetic variation present in a reduced number of housekeeping genes (typically seven) along the genome. This methodology assigns arbitrary integer...

["Bioinformatics","Ecology","Genomics","Microbiology","Population Biology"]
doi:10.7717/peerj.5098
21 downloads
156 views

Background Cervical cancer is one of the most common cancers in women worldwide. Malignant tumors develop resistance mechanisms and are less sensitive to or do not respond to irradiation. With the development of high-throughput sequencing technologies, circular...

["Bioinformatics","Oncology"]
doi:10.7717/peerj.5011
24 downloads
268 views

A robust and accurate gene expression signature is essential to assist oncologists to determine which subset of patients at similar Tumor-Lymph Node-Metastasis (TNM) stage has high recurrence risk and could benefit from adjuvant therapies. Here we applied a two-step...

["Bioinformatics","Gastroenterology and Hepatology","Oncology","Data Mining and Machine Learning"]
doi:10.7717/peerj.4942
42 downloads
328 views

Soil microbial communities’ assembly is strongly tied to changes in temperature and moisture. Although microbial functional redundancy seems to overcome taxonomical composition changes, the sensitivity and resilience of soil microbial communities from subtropical...

["Agricultural Science","Biodiversity","Bioinformatics","Ecology","Microbiology"]
doi:10.7717/peerj.4991
32 downloads
166 views

Nowadays DNA meta-barcoding is a powerful instrument capable of quickly discovering the biodiversity of an environmental sample by integrating the DNA barcoding approach with High Throughput Sequencing technologies. It mainly consists of the parallel reading of...

["Biodiversity","Bioinformatics","Environmental Sciences"]
doi:10.7717/peerj.4845
68 downloads
428 views

Sequencing of the 16S ribosomal RNA (rRNA) gene is widely used to survey microbial communities. Specialized 16S rRNA databases have been developed to support this approach including Greengenes, RDP and SILVA. Most taxonomy annotations in these databases are predictions...

["Bioinformatics","Microbiology","Taxonomy"]
doi:10.7717/peerj.5030
25 downloads
207 views

Supertree methods enable the reconstruction of large phylogenies. The supertree problem can be formalized in different ways in order to cope with contradictory information in the input. Some supertree methods are based on encoding the input trees in a matrix; other...

["Bioinformatics","Computational Biology","Evolutionary Studies","Taxonomy","Computational Science"]
doi:10.7717/peerj.4987
71 downloads
299 views

Circadian rhythms maintain a 24 h oscillation pattern in metabolic, physiological and behavioral processes in all living organisms. Circadian rhythms are organized as biochemical networks located in hypothalamus and peripheral tissues. Rhythmicity in the expression...

["Bioinformatics","Computational Biology"]
doi:10.7717/peerj.4877
62 downloads
638 views

Dot plots are widely used to quickly compare sequence sets. They provide a synthetic similarity overview, highlighting repetitions, breaks and inversions. Different tools have been developed to easily generated genomic alignment dot plots, but they are often limited...

["Bioinformatics","Genomics","Computational Science"]
doi:10.7717/peerj.4958
28 downloads
444 views

Tumor samples obtained from a single cancer patient spatially or temporally often consist of varying cell populations, each harboring distinct mutations that uniquely characterize its genome. Thus, in any given samples of a tumor having more than two haplotypes,...

["Bioinformatics","Computational Biology"]
doi:10.7717/peerj.4838
66 downloads
512 views

After transitioning to a new environment, species often exhibit rapid phenotypic innovation. One of the fastest mechanisms for this is duplication followed by specialization of existing genes. When this happens to a member of a gene family, it tends to leave a...

["Bioinformatics","Computational Biology","Evolutionary Studies"]
doi:10.7717/peerj.4873
29 downloads
300 views

As a DNA binding transcriptional activator, Gal4 promotes the expression of genes responsible for galactose metabolism. The Gal4 protein from Saccharomyces cerevisiae (baker’s yeast) has become a model for studying eukaryotic transcriptional activation in general...

["Bioinformatics","Computational Biology","Data Mining and Machine Learning"]
doi:10.7717/peerj.4844
37 downloads
244 views

The reconstruction of genomes using mapping-based approaches with short reads experiences difficulties when resolving repetitive regions. These repetitive regions in genomes result in low mapping qualities of the respective reads, which in turn lead to many unresolved...

["Bioinformatics","Computational Biology"]
doi:10.7717/peerj.4742

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