5 January 2026

Cholesterol and steroid synthesis pathways may be involved in the inhibition of osteosarcoma cell viability by calcium-sensing receptor antagonism

"For an exploratory molecular oncology study, it is meaningful, solid, and useful to the field. Some limitations that do not undermine scientific integrity and rigour. This study provides the first transcriptomic-level evidence that blocking the calcium-sensing receptor (CaSR) alters cholesterol and steroid biosynthesis pathways in osteosarcoma cells, revealing a previously unrecognized metabolic link between CaSR signaling and tumor cell viability. By identifying coordinated, stage-specific upregulation of multiple cholesterol-synthesis genes after CaSR antagonism, the work highlights cholesterol metabolism as a plausible mechanistic target and establishes CaSR antagonists as exploratory metabolic modulators with potential relevance for osteosarcoma therapy."

Sonia Oliveira, Handling Editor

5 December 2025

The Nextflow nf-core/metatdenovo pipeline for reproducible annotation of metatranscriptomes, and more

"While metagenomic analysis pipelines gained lots of attention in recent years, metatranscriptome pipelines are still sparse. Hence, providing an analysis pipeline, that even follows the nf-core standards will be a valuable contribution to the field and will certainly be used by many researchers."

Daniel Fischer, Handling Editor

20 October 2025

Genome-wide identification of calcium-dependent protein kinase (CDPK) family members in Phaseolus vulgaris L. and expression analysis during abiotic stresses

"This research is important as it may offer insights into climate change mediated responses in plants important for consumption, and genomic ways to potentially select for more stress resistant crops."

Barbara Langille, Handling Editor

22 September 2025

Predicting the prognosis of hepatocellular carcinoma based on genes related to polyamine metabolism

"This manuscript presents a comprehensive analysis of polyamine metabolism-related genes (PMRGs) in hepatocellular carcinoma (HCC), utilizing both bulk and single-cell RNA sequencing datasets. The study identifies distinct molecular subtypes and constructs a prognostic risk model, integrating bioinformatics analyses with experimental validation. The identification of key genes such as G6PD, ADH4, S100A9, and AKR1B15, as well as the development of a nomogram for survival prediction, demonstrate a methodical approach that combines computational and laboratory techniques. The findings offer additional understanding of the heterogeneity of HCC and provide potential biomarkers that may inform future research on molecular subtyping and personalized treatment strategies. While the study addresses an area of ongoing interest and incorporates several well-established analytical methods, the novelty and translational potential remain to be further substantiated by larger-scale clinical validation. The work contributes to the growing body of knowledge regarding the molecular landscape of HCC and supports further investigation into polyamine metabolism as a potentially relevant pathway in the prognosis and treatment of this malignancy."

Fanglin Guan, Handling Editor

18 September 2025

Expression characterization of the guanylate-binding protein gene family in breast cancer and its association with the immune microenvironment

"This article addresses an important aspect of breast cancer prognostic assessment by focusing on the involvement of guanylate-binding protein (GBP) genes and their association with the tumor immune microenvironment. The study employs a combination of bioinformatics approaches, including ssGSEA, WGCNA, and regression analyses, to construct a risk model based on GBP-related genes. The integration of immune infiltration analysis and experimental validation of DACT2 function in breast cancer cell lines provides additional biological context to the findings. While the methodology is comprehensive and the risk model appears to offer prognostic value, the novelty and clinical applicability of the results would benefit from further validation in independent cohorts and real-world clinical settings. The study presents a methodologically sound framework for exploring immune-related prognostic markers in breast cancer, which could contribute to improved risk stratification and potentially inform individualized treatment strategies, though its immediate translational impact may be limited at this stage."

Fanglin Guan, Handling Editor

3 September 2025

BMP2 alterations in mucinous cystadenocarcinoma of the breast: insights from whole-exome sequencing

"The article presents a rare and understudied breast cancer subtype, and the integrative approach using whole exome sequencing (WES) and immunohistochemistry (IHC) provides valuable initial insights into its possible molecular pathogenesis. However, limited sample size (n=3) and lack of downstream functional analyses are limiting factors."

Mehmet Burak Ateş, Handling Editor

28 August 2025

Uncovering tissue-specific endophytic microbiota composition and activity in Rhizophora mangle L.: a metagenomic and metatranscriptomic approach

"Understanding the structure and functional activity of mangrove tree-associated microbiomes paves the way for mangrove ecosystem conservation and future biotechnological applications"

Paripok Phitsuwan, Handling Editor

27 August 2025

Exploration of prognostic genes associated with lymphangiogenesis in breast cancer based on transcriptomics and experimental verification

"This research contributes to precision medicine in BC by identifying actionable biomarkers, elucidating their biological roles, and suggesting potential treatments, all of which could enhance diagnosis, prognosis, and therapy for patients with breast cancer."

Rodolfo García-Contreras, Handling Editor

18 August 2025

Genomewide analysis of the Class III peroxidase gene family in apple (Malus domestica)

"The manuscript presents a robust genome-wide analysis of Class III peroxidases in Malus domestica, uncovering their structural diversity, evolution, and expression patterns. It highlights antagonistic roles of PRX subgroups in rootstock vigor and bud differentiation, offering valuable insights into ROS-mediated regulation and apple breeding strategies."

Ganesh Nikalje, Handling Editor

11 July 2025

An R package for survival-based gene set enrichment analysis

"This article presents SGSEA, a novel adaptation of traditional GSEA that incorporates survival data into pathway enrichment analysis. The development of both an R package and Shiny App makes this method accessible to researchers across disciplines. While standard GSEA has been effective for comparing differential expression between experimental conditions, SGSEA addresses the need to link transcriptomic variations with clinical outcomes like patient survival. The authors demonstrate the method's utility through a case study of kidney renal clear cell carcinoma, where pathways identified by SGSEA align with previously documented survival associations. This alignment with existing knowledge helps validate the approach. The method enables researchers to identify pathways relevant to disease progression and mortality risk in a systematic way, complementing insights from traditional GSEA. The provision of standardized tools addresses a gap in the current analytical landscape. While the approach shows promise, further validation across different cancer types and diseases would help establish its broader applicability. The development of SGSEA represents a practical contribution to the field of functional genomics and survival analysis, potentially aiding in the identification of clinically relevant pathways."

Fanglin Guan, Section Editor