Bioinformatics and Genomics

SCelVis: exploratory single cell data analysis on the desktop and in the cloud
Elena Papaleo –– Tools like this are very much needed by the community for the first exploration of single-cell RNA data
The expression of small RNAs in exosomes of follicular fluid altered in human polycystic ovarian syndrome
Walter de Azevedo Jr. –– In this work by Hu et al., the authors carried out a study focused on small RNAs of exosomes’ role on human polycystic ovary syndrome. Their results indicated that six MiRNAs may give an important addition regarding the mechanism of polycystic ovary syndrome pathogenesis. These RNAs could be chosen as molecular biomarkers for polycystic ovary syndrome diagnosis in the future.
SpeciesPrimer: a bioinformatics pipeline dedicated to the design of qPCR primers for the quantification of bacterial species
Cindy Smith –– SpeciesPrimer is a welcome user-friendly software solution for the design of species specific quantitative PCR primers, demonstrated for use in food microbiology, but of use more widely.
Co-expression network analysis reveals the pivotal role of mitochondrial dysfunction and interferon signature in juvenile dermatomyositis
Marcin Grynberg –– It shows a good piece of work, results can be used by diverse players.
A transcriptional co-expression network-based approach to identify prognostic biomarkers in gastric carcinoma
Walter de Azevedo Jr. –– In this paper, the authors applied a system biology-based WGCNA methodology to identify the hub biomarkers indicative of gastric cancer patient prognosis. Application of this methodology could favor future personalized therapies.
LINC00958 and HOXC13-AS as key candidate biomarkers in head and neck squamous cell carcinoma by integrated bioinformatics analysis
Walter de Azevedo Jr. –– In this study by Xiong et al., the authors applied bioinformatics tools to analyze data focused on head and neck squamous cell carcinoma. They found two long non-coding RNAs, LINC00958 and HOXC13-AS, as novel candidate biomarkers for cancer patients by bioinformatics analysis. Their results indicated that the transcript levels of LINC00958 and HOXC13-AS may be suitable biomarkers of head and neck squamous cell carcinoma.
Integrated analysis of the roles and prognostic value of RNA binding proteins in lung adenocarcinoma
Walter de Azevedo Jr. –– Here, Li et al. report a study where they investigated the expression and prognostic significance of differently expressed RNA binding proteins using bioinformatics approaches in lung adenocarcinoma data. Their results have the potential to contribute to show the pathogenesis of lung adenocarcinoma and to develop treatment targets and diagnostic molecular markers.
ViSiElse: an innovative R-package to visualize raw behavioral data over time
Claus Wilke –– This paper introduces a new type of visualization that could be quite useful to a wide range of researchers working on many different problems.
Genome-wide identification and expression analysis of NADPH oxidase genes in response to ABA and abiotic stresses, and in fibre formation in Gossypium
Jesús Campos-García –– The findings contribute with elucidating the functions and regulation mechanisms of NADPH oxidases and their roles in adaptation to stresses, growth and development in Gossypium plants.
Gene co-expression network for analysis of plasma exosomal miRNAs in the elderly as markers of aging and cognitive decline
Walter de Azevedo Jr. –– In this paper, Ye et al. described interesting research about the participation of microRNA (miRNAs) in pathways related to aging and cognitive decline. The authors used miRNA-seq based expression dataset GSE97644 available in the NCBI Gene Expression Omnibus (GEO) to explore the relationship between variations in miRNA expression with age. In their results, the authors show strong evidence that several plasma miRNAs have essential regulatory roles in the development of aging and may operate as biomarkers and putative new therapeutic targets for aging and cognitive decline.
Bioinformatics and Genomics

Section discussions

24 days ago
A great article I helped peer review published today in @thePeerJ #Bioinformatics #ComputationalBiology #Virology #Immunology #InfectiousDiseases

Depicting the mating system and patterns of contemporary pollen flow in trees of the genus Anadenanthera (Fabaceae) @thePeerJ

Diversity structure of the microbial communities in the guts of four neotropical termite species @thePeerJ

Analysis of differences in the transcriptomic profiles of eutopic and ectopic endometriums in women with ovarian endometriosis @thePeerJ

My paper on tarantula biogeography was released today! Though I hesitate to speak in absolutes, we suggest some answers towards when and where the group emerged: #tarantula #evolution

Extensive microbial diversity within the chicken gut microbiome revealed by metagenomics and culture [PeerJ]