12 February 2026

Gene mapping and development of molecular markers for thousand-grain weight in rye based on bulked segregant analysis

"This work provides useful knowledge on the genetic control of thousand-grain weight in rye and provides practical KASP markers for breeding."

Yunfeng Xu, Handling Editor

12 February 2026

Pan-cancer multi-omics profiling of OAS3 reveals its immunological and prognostic associations across human cancers

"This study presents a systematic assessment of OAS3, an enzyme traditionally associated with antiviral responses, in the context of cancer biology across multiple tumor types. By integrating multi-omics data and functional validation, the authors provide a detailed examination of OAS3 expression patterns, its correlation with clinical prognosis, and its involvement in key molecular pathways related to immune regulation and tumor progression. The analysis extends to the exploration of OAS3 mutations and their associations with various genomic features, thereby offering insights into its potential as a biomarker and therapeutic target in specific cancer contexts. The findings regarding OAS3's relationship with immune cell infiltration and immune checkpoints may have implications for understanding tumor-immune interactions. However, the study is primarily exploratory and based on bioinformatic analyses supported by limited experimental validation, which may restrict the immediate translational impact. Nonetheless, the work adds a nuanced perspective to the literature on cancer-associated immune regulators and may serve as a basis for further functional studies."

Fanglin Guan, Section Editor

11 February 2026

A novel analysis workflow for simultaneous parsing prokaryotic and eukaryotic microbial genes from metagenomes

"This article addresses a practical but often underappreciated problem in metagenomic analysis: the difficulty of accurately predicting coding sequences in samples with substantial eukaryotic content. By systematically comparing MetaGeneMark and MetaEuk and then proposing a sequential workflow that masks predicted eukaryotic regions before prokaryotic gene calling, the study offers a technically straightforward solution that can be incorporated into existing pipelines with limited overhead. The reported 14–18% increase in predicted prokaryotic and viral genes, without an obvious loss of eukaryotic gene recovery, suggests that the approach can reduce a specific type of mis-annotation in mixed metagenomes. At the same time, the work relies heavily on a particular combination of tools and custom scripting, and its generalizability across highly complex or low-quality environmental datasets remains to be fully demonstrated. The study is likely to be most useful for practitioners seeking incremental improvements in gene prediction rather than a fundamentally new conceptual framework."

Fanglin Guan, Section Editor

15 January 2026

Molecular characterization of early-stage multi-primary lung adenocarcinoma by transcriptome sequencing—a retrospective study

"The study demonstrates that sMP-LUAD and SP-LUAD can be differentiated by analyzing their gene expression profiles. Furthermore, DUOX1 is downregulated in SP-LUAD, distinguishing it from sMP-LUAD."

Hilal Ozdag, Handling Editor

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

19 December 2025

Identification of hypoxia- and mitochondria-related genes associated with recurrent spontaneous abortion: an integrative bioinformatics analysis and preliminary validation

"This study identifies BSG and TRAK1 as novel hypoxia- and mitochondria-related genes potentially linked to recurrent spontaneous abortion (RSA), integrating multi-omics bioinformatics with preliminary experimental validation. By connecting mitochondrial dysfunction and immune modulation to RSA pathophysiology, it provides new molecular entry points for understanding early pregnancy loss and developing predictive biomarkers. However, its contribution is primarily hypothesis-generating, as functional mechanisms remain to be experimentally verified."

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

29 October 2025

Identification and experimental verification of necroptosis-related prognostic gene signature and characterization of tumor immune infiltration in lung squamous cell carcinoma

"This article provides a systematic evaluation of necroptosis-related genes (NRGs) in lung squamous cell carcinoma (LUSC), offering new insights into their biological and clinical relevance. By integrating transcriptomic and clinical data from large public databases and incorporating both bioinformatics and experimental validation, the study identifies a three-gene NRG signature that may have prognostic value in LUSC. The correlation analysis between these genes and immune infiltration, immune checkpoint activity, and genomic instability further extends the potential implications of NRGs in tumor microenvironment modulation. However, while the methodological approach is comprehensive, the predictive accuracy of the model is only moderate, and the clinical utility of these findings remains to be fully established. The study does not address potential confounders in patient stratification, and the experimental validation, though supportive, is limited in scope. Despite these limitations, the article contributes to the expanding field of cell death mechanisms in cancer and offers a foundation for future research into the role of necroptosis in LUSC."

Fanglin Guan, Section Editor

28 October 2025

Identification of keratinocyte-associated genes for immune characterization and drug response prediction in oral squamous cell carcinoma

"This manuscript addresses the role of keratinocyte-related genes in oral squamous cell carcinoma (OSCC) using a combination of single-cell and bulk transcriptomic analyses, followed by in vitro validation. The study applies established bioinformatics tools to identify keratinocyte gene modules and hub genes, and it explores their potential diagnostic value and association with immune infiltration in OSCC. The integration of multiple analytic approaches and the use of both computational and experimental validation provide a systematic examination of keratinocyte involvement in OSCC, which may add to the understanding of the disease’s cellular microenvironment. However, while the methodology is sound and the manuscript presents coherent results, the novelty and translational relevance of the findings are moderate, given the rapidly advancing landscape of OSCC biomarker research. The identification of several candidate genes and their functional validation are of some interest, but the overall impact on clinical practice and mechanistic insight appears limited at this stage. Thus, this work may be of some value to researchers focused on OSCC biology, but its broader implications are relatively modest."

Fanglin Guan, 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