Bioinformatics and Genomics

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.
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.
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.
Studying the impact of young age on prognosis and treatment in laryngeal squamous cell carcinomas using the SEER database
Cheng Zhan –– Young patients usually have a different pattern of prognosis compared with old ones.
SLCV–a supervised learning—computer vision combined strategy for automated muscle fibre detection in cross-sectional images
Henkjan Huisman –– The method described in this paper will help advance the scientific analysis of cross-sectional muscular histopathology.
Construction and integrated analysis of crosstalking ceRNAs networks in laryngeal squamous cell carcinoma
Cheng Zhan –– The authors constructed a crosstalking ceRNAs networks in laryngeal squamous cell carcinoma
Evolutionary couplings detect side-chain interactions
Elena Papaleo –– A nice study on the predictive power of sequence-based contact prediction, highlight that evolutionary coupling-based analyses are more prone to identify structural contacts mediated by side-chain atoms than by backbone atom.
Global transcriptomic analysis identifies SERPINE1 as a prognostic biomarker associated with epithelial-to-mesenchymal transition in gastric cancer
Obul Bandapalli –– The authors have shown that SERPINE1 is a potent biomarker associated with EMT and a poor prognosis in GC and FN1, TIMP1, MMP2, and SPARC are correlated with SERPINE1 and may serve as therapeutic targets in reversing EMT in GC.
Bioinformatics and Genomics

Section discussions

Comparative transcriptome and histological analyses provide insights into the skin pigmentation in Minxian black fur sheep (Ovis aries) @thePeerJ

Artículo original de la LCF: Dysregulation of miR-381-3p and miR-23b-3p in skeletal muscle could be a possible estimator of early post-mortem interval in rats. Disponible en:

HiCEnterprise: identifying long range chromosomal contacts in Hi-C data @thePeerJ