4 December 2023

Identification of novel biomarkers in obstructive sleep apnea via integrated bioinformatics analysis and experimental validation

Antonella Loperfido, Handling Editor

28 November 2023

A novel long noncoding RNA (lncRNA), LINC02657(LASTR), is a prognostic biomarker associated with immune infiltrates of lung adenocarcinoma based on unsupervised cluster analysis

Zhijie Xu, Handling Editor

27 November 2023

kakapo: easy extraction and annotation of genes from raw RNA-seq reads

"Annotation of sequences from RNA-Seq is sorely needed for the many datasets being submitted to NCBI; this will be a great addition to bioinformatics tools"

Brenda Oppert, Section Editor

24 November 2023

Development of a 5-mRNAsi-related gene signature to predict the prognosis of colon adenocarcinoma

"This study advances the understanding of colon adenocarcinoma (COAD) by developing a prognosis model based on mRNA stemness index (mRNAsi). The researchers identified specific genes correlated with survival rates, clinical stages, and responses to treatments like immunotherapy. By highlighting the connections between these markers and various aspects of the disease, the findings could pave the way for more targeted and effective therapies for COAD, enhancing treatment outcomes."

Peixin Dong, Handling Editor

21 November 2023

Head and neck squamous cell carcinoma-specific prognostic signature and drug sensitive subtypes based on programmed cell death-related genes

"This article innovatively reports a prognostic model involved in the development and treatment of head and neck squamous cell carcinoma. It is useful for clinical management."

Zhijie Xu, Handling Editor

17 November 2023

Genome-wide analysis of sugar transporter genes in maize (Zea mays L.): identification, characterization and their expression profiles during kernel development

"The authors in this study performed a comprehensive search in the maize genome and identified 68 ZmST genes. The authors applied phylogenetic relationship, chromosome location, collinearity analysis, conservative structures, and expression patterns analyses. The study detected that ZmSTs have a substantial role in sugar transportation and seed development. These findings provide fairly robust information for further research on ZmSTs and enhance maize breeding."

Elsayed Mansour, Handling Editor

15 November 2023

In-silico study of antisense oligonucleotide antibiotics

"This study underscores a significant advancement in the ongoing battle against antibiotic-resistant bacteria, a paramount concern in global health due to the dwindling development of new drugs. By pivoting from the traditional focus on small-molecule antibiotics to RNA-based therapeutics, particularly antisense oligonucleotides (ASOs), researchers have paved the way for a novel paradigm in antibiotic design. This research presents a bioinformatics pipeline tailored to identify potent ASO targets within essential bacterial genes, offering an efficient toolset to expedite ASO antibiotic research. By testing the approach on three pertinent bacterial species, the study not only confirms the efficacy of the pipeline but also provides a public database of ASO targets. This is invaluable for future research and holds the potential to significantly impact the development of next-generation antibiotics."

Peixin Dong, Handling Editor

15 November 2023

Seq2science: an end-to-end workflow for functional genomics analysis

"van der Sande and colleagues propose an easier and more reproducible way of conducting computational genomics analyses (like data download capabilities of the download-fastq sub-workflow), which can be expanded by adding workflow components for other genome-wide assays."

Joseph Gillespie, Handling Editor

18 October 2023

Predicting protein and pathway associations for understudied dark kinases using pattern-constrained knowledge graph embedding

"The algorithm provides information on dark kinases that may be involved in disease processes, providing data that may be used to promote new treatments."

Brenda Oppert, Section Editor

3 October 2023

Identification and validation of hub genes involved in foam cell formation and atherosclerosis development via bioinformatics

"Bioinformatics allowed the authors to identify genes involved in atherosclerosis pathogenesis."

Maria Cristina Albertini, Handling Editor