Bioinformatics and Genomics

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.
Identification of crucial genes based on expression profiles of hepatocellular carcinomas by bioinformatics analysis
Maria Cristina Albertini –– This bioinformatics study can provide important information on hepatocellular carcinoma pathogenesis.
Validity of the iLOAD® app for resistance training monitoring
Scotty Butcher –– This new app solves a problem with current apps in the resistance monitoring literature by allowing real-time velocity feedback. The authors have shown excellent validity compared with direct velocity measures.
miRDRN—miRNA disease regulatory network: a tool for exploring disease and tissue-specific microRNA regulatory networks
Ramy Aziz –– A major resource of miRNA and it connects it to diseases in a statistically supported way.
Identification of a novel four-lncRNA signature as a prognostic indicator in cirrhotic hepatocellular carcinoma
Obul Bandapalli –– Several studies have showed the association of noncoding RNAs ( lncRNA) with the occurrence and development of various tumors and have the potential to be prognostic markers. Thought there are some studies to predict overall survival (OS) and recurrence-free survival (RFS) in patients with hepatocellular carcinoma (HCC), no one has constructed a prognostic lncRNA model only in patients with cirrhotic HCC. The finds of this study showed that four lncRNAs may be potentially involved in multiple metabolic processes, such as amino acid, lipid, and glucose metabolism in cirrhotic HCC.
A 3-mRNA-based prognostic signature of survival in oral squamous cell carcinoma
Abhiram Maddi –– Establishes novel prognostication of oral squamous cell carcinoma based on mRNA signature.
Mobile learning in dentistry: usage habits, attitudes and perceptions of undergraduate students
Abhiram Maddi –– It may well be one of the first articles to address mobile based learning attitudes among dental students.
MetaBAT 2: an adaptive binning algorithm for robust and efficient genome reconstruction from metagenome assemblies
Elena Papaleo –– MetaBAT2 has been one of the most used software for metagenomic binning. This paper explains the different steps behind this tool and its algorithm. An important article for anyone working with metagenomics.
Bioinformatics and Genomics

Section discussions

7 days ago
New publication from Haigh lab and his collaborators identify SARS-CoV-2 founder mutations in samples from China, USA, Australia and GenBank sequences with the greatest number of mutations in the US samples. #covid19 via @thePeerJ

Another interesting article I handled as editor has been published today @thePeerJ #Biotechnology #MolecularBiology #Toxicology #Pharmacology #Histology

High expression of stromal signatures correlated with macrophage infiltration, angiogenesis and poor prognosis in glioma microenvironment @thePeerJ

Distribution of the acoustic occurrence of dolphins during the summers 2011 to 2015 in the Upper Gulf of California, Mexico @thePeerJ

Impact of cost distance and habitat fragmentation on the daily path length of Rhinopithecus bieti @thePeerJ