Bioinformatics and Genomics

consensusDE: an R package for assessing consensus of multiple RNA-seq algorithms with RUV correction
Elena Papaleo –– The paper describes a useful new package, consensusDE to perform differential expression analysis with three popular methods and compare the results. COnsensusDE also includes integration of RUV into the DE workflow.
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.
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.
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.
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.
EnContact: predicting enhancer-enhancer contacts using sequence-based deep learning model
Yong Wang –– Deep learning model boosts the enhancer interaction prediction in epigenomic study.
Risk assessment of FLT3 and PAX5 variants in B-acute lymphoblastic leukemia: a case–control study in a Pakistani cohort
Obul Bandapalli –– The authors showed an association of B-cell acute lymphoblastic leukemia with rs35958982 and rs12430881 polymorphisms. However, rs3780135 polymorphism showed the protective effect which needs to be checked in the background of family history, smoking and consanguinity. This may help in risk stratification and therapeutic improvements
HiLDA: a statistical approach to investigate differences in mutational signatures
Jun Chen –– Detecting differences in mutational signatures is a fundamental problem in oncology. A powerful method as the proposed could not only help understand the biology of cancers but also point to potential therapeutic targets.
Bioinformatics and Genomics

Section discussions

39 days ago
My first first-author paper is finally published!

Prediction of DNA binding proteins using local features and long-term dependencies with primary sequences based on deep learning @thePeerJ

Centromere protein N may be a novel malignant prognostic biomarker for hepatocellular carcinoma @thePeerJ

Wang et al. examine how barley grain size impacts storage capacity during grain filling with the use of molecular markers Read the full @PeerJLife article #AgriculturalScience #Genetics #MolecularBiology #PlantScience

45 days ago
Gilda Valiero's article has been published today in @thePeerJ #Bioinformatics #Microbiology #MolecularBiology Congratulations !!!

Yang et al. present identification of a five-gene signature in association with overall survival for #hepatocellular #carcinoma Read the full @PeerJLife article #HCC #Bioinformatics #Gastroenterology #MedicalGenetics

Phenotypic, molecular and pathogenic characterization of Colletotrichum scovillei infecting Capsicum species in Rio de Janeiro, Brazil @thePeerJ