Bioinformatics and Genomics

Identification of key genes in non-small cell lung cancer by bioinformatics analysis
Vasco Azevedo –– manuscript that has identified genes implicated in cancer and give excellent clues to the area.
Unprofessional peer reviews disproportionately harm underrepresented groups in STEM
Robert Toonen –– This study provides empirical evidence that unprofessional reviews can negatively impact career advancement and discourage researchers. As pointed out by the referees, it confirms what many have long suspected. This work highlights the importance of training researchers on how to conduct professional reviews and for editors to take responsibility for unprofessional peer reviewer comments that are passed along to authors.
TEffectR: an R package for studying the potential effects of transposable elements on gene expression with linear regression model
Elena Papaleo –– The authors developed a R-based package to study the effects of transposable elements on gene expression using a linear regression model. This is an important aspect to address in genomics and the availability of packages to facilitate and standardize these analyses is of great value for the community.
A systematic review on literature-based discovery workflow
Tzung-Pei Hong –– It is a good review paper in this field and may provide some reference value to readers.
A Sparse-Modeling Based Approach for Class Specific Feature Selection
Tzung-Pei Hong –– It is a good paper and may provide some reference values to the scholars in this field.
Identification of key genes and pathways associated with cholangiocarcinoma development based on weighted gene correlation network analysis
Yezaz Ghouri –– The article expands upon some genetic pathogenesis and pathways involved with development of cholangiocarcinoma which is has a high mortality rate and limited curative options.
ncRNA2MetS: a manually curated database for non-coding RNAs associated with metabolic syndrome
Elena Papaleo –– A huge effort of manual curation for a database on noncoding RNAs associated with metabolic syndrome. This work is relevance since metabolic syndrome has become a global threat to human health.
A prognostic nomogram for overall survival in male breast cancer with histology of infiltrating duct carcinoma after surgery
Antonio Palazón-Bru –– A novel nomogram to predict mortality in male breast cancer with histology of infiltrating duct carcinoma after surgery.
Levels of toothache-related interests of Google and YouTube users from developed and developing countries over time
Abhiram Maddi –– This may be one of the first articles related to tooth ache and search habits of users of Google and YouTube. The methods used in the study are unique and may be universally applied for gathering data related to user habits for educational study. This would be very helpful in understanding behaviors of patients with specific oral disorders by dentists, policy makers and marketing firms.
Identification of crucial genes in abdominal aortic aneurysm by WGCNA
Yong Wang –– The authors performed cop-expression network analysis on three gene expression datasets on AAA disease to identify crucial genes.
Bioinformatics and Genomics

Section discussions

250 visitors to my 'Human milk microbiota associated with early colonization of the neonatal gut in Mexican newborns' article published in #OpenAccess journal @thePeerJ #

250 visitors to my 'VIRdb: a comprehensive database for interactive analysis of genes/proteins involved in the pathogenesis of vitiligo' article published in #OpenAccess journal @thePeerJ

It is hard to name new species! Even for bacteria! Debbie Brock valiantly guided this one to publication today in @thePeerJ #Ecology #EvolutionaryStudies #Microbiology #Taxonomy

Congrats to Danial! His article has been published today in @thePeerJ #Genomics #Taxonomy #Virology #InfectiousDiseases

Bioinformatics analyses of retinoblastoma reveal the retinoblastoma progression subtypes @thePeerJ

New Scientist: "Harsh peer reviewer comments disproportionately affect minorities"

‘Rude’ peer reviews inflict most damage on women and minorities

Science Magazine: "Rude paper reviews are pervasive and sometimes harmful, study finds"