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.
Feasibility of assessing ultra-short-term pulse rate variability from video recordings
Tjeerd Boonstra –– This work is interesting and relevant to the HRV area. The development of a new method for HRV recording using the technique proposed by the authors may contribute to the development of technologies applied to physical and mental health.
Bioinformatics and Genomics

Section discussions

12 hours ago
Shannon diversity index estimators

Genome of esophageal cancer in Japan via @thePeerJ

I missed this when it came out, but it was something I was wondering if it would be possible only the other day: Tip dating by assigning age uncertainty to fossil formations rather than the species themselves. New(ish) paper by King & Rücklin

Using Bumble Bee Watch to investigate the accuracy and perception of bumble bee (Bombus spp.) identification by community scientists @thePeerJ

Hemogram data as a tool for decision-making in COVID-19 management: applications to resource scarcity scenarios @thePeerJ

New #OA paper by Janis et al. on Thylacosmilus, the sabre-toothed marsupial. The example used in all the textbooks for convergent evolution with the sabre-tooth cat. But their very different ways of being sabre-toothed indicate very different lifestyles