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Optical Genome Mapping: A New Tool for Cytogenomic Analysis -
Genomic Regions Associated with Respiratory Disease in Holstein Calves in the Southern United States -
ABCC6 Involvement in Cerebral Small Vessel Disease: Potential Mechanisms and Associations -
Increased Prevalence of Psychiatric Disorders in Children with RASopathies: Comparing NF1, Noonan Syndrome Spectrum Disorder, and the General Population -
Identification of Key Genes Associated with Overall Survival in Glioblastoma Multiforme Using TCGA RNA-Seq Expression Data
Journal Description
Genes
Genes
is a peer-reviewed, open access journal of genetics and genomics published monthly online by MDPI. The Spanish Society for Nitrogen Fixation (SEFIN) is affiliated with Genes and its members receive discounts on the article processing charges.
- Open Access— free for readers, with article processing charges (APC) paid by authors or their institutions.
- High Visibility: indexed within Scopus, SCIE (Web of Science), PubMed, MEDLINE, PMC, Embase, PubAg, and other databases.
- Journal Rank: JCR - Q2 (Genetics and Heredity) / CiteScore - Q2 (Genetics (clinical))
- Rapid Publication: manuscripts are peer-reviewed and a first decision is provided to authors approximately 14.6 days after submission; acceptance to publication is undertaken in 2.5 days (median values for papers published in this journal in the first half of 2025).
- Recognition of Reviewers: Reviewers who provide timely, thorough peer-review reports receive vouchers entitling them to a discount on the APC of their next publication in any MDPI journal, in appreciation of the work done.
Impact Factor:
2.8 (2024);
5-Year Impact Factor:
3.2 (2024)
Latest Articles
Genetic, Clinical and Neuroradiological Spectrum of MED-Related Disorders: An Updated Review
Genes 2025, 16(12), 1444; https://doi.org/10.3390/genes16121444 - 2 Dec 2025
Abstract
Background/Objectives: The Mediator (MED) complex is an essential regulator of RNA polymerase II transcription. There is increasing evidence that pathogenic variants in several MED subunits are the cause of neurodegenerative and neurodevelopmental phenotypes, collectively referred to as “MEDopathies”. This review aims to summarize
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Background/Objectives: The Mediator (MED) complex is an essential regulator of RNA polymerase II transcription. There is increasing evidence that pathogenic variants in several MED subunits are the cause of neurodegenerative and neurodevelopmental phenotypes, collectively referred to as “MEDopathies”. This review aims to summarize current knowledge on the genetic basis, clinical manifestations, and neuroradiological features of MED-related disorders. Methods: We undertook a narrative synthesis of the literature focusing on the MED subunits most commonly associated with neurological disorders, including MED1, MED8, MED11, MED12/MED12L, MED13/MED13L, MED14, MED17, MED20, MED23, MED25, MED27, and CDK8. Sources included peer-reviewed genetic, clinical, and imaging studies, supplemented by relevant case reports and cohort analyses. In addition, representative facial phenotypes associated with selected MED variants (MED11, MED12, MED13, MED13L, MED25) were visualized for educational purposes using artificial intelligence-based image generation derived from standardized clinical descriptors. Results: All MEDopathies show converging clinical patterns: global developmental delay/intellectual disability, hypotonia, epilepsy, speech disorders, and behavioral comorbidity. Non-neurological involvement, such as craniofacial or cardiac anomalies, is subunit-specific. Neuroradiological features include callosal abnormalities (agenesis, thinning, dysmorphia), delayed or hypomyelination, progressive cerebral and cerebellar atrophy, basal ganglia signaling changes, pontine hypoplasia, and, in MED27 deficiency, a “hot cross bun” sign. Gene-specific constellations emphasize catastrophic infantile progression (MED11), X-linked syndromes with callosal defects (MED12/MED12L), language-dominant phenotypes (MED13), and syndromic intellectual disability with systemic features (MED13L). Conclusions: The growing spectrum of MEDopathies argues for their recognition as a unified nosological group with overlapping clinical and radiological signatures. Characteristic MRI constellations may serve as diagnostic clues and guide targeted molecular testing. Future directions include longitudinal imaging to describe disease progression and the integration of genomic data with curated clinical radiological datasets to refine genotype-phenotype correlations.
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(This article belongs to the Collection Study on Genotypes and Phenotypes of Pediatric Clinical Rare Diseases)
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Open AccessReview
Role of Genetic and Epigenetic Biomarkers in Treatment-Resistant Depression: A Literature Review
by
Petra Sulić, Andrea Ražić Pavičić, Biljana Đapić Ivančić, Tamara Božina, Nada Božina and Maja Živković
Genes 2025, 16(12), 1443; https://doi.org/10.3390/genes16121443 - 2 Dec 2025
Abstract
Background: Treatment-resistant depression (TRD) affects up to 30–40% of patients with major depressive disorder and remains a major therapeutic challenge. Genetic and epigenetic factors are increasingly recognized as key contributors to both vulnerability and treatment response. Methods: We conducted a narrative review of
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Background: Treatment-resistant depression (TRD) affects up to 30–40% of patients with major depressive disorder and remains a major therapeutic challenge. Genetic and epigenetic factors are increasingly recognized as key contributors to both vulnerability and treatment response. Methods: We conducted a narrative review of studies published between 2021 and 2025, focusing exclusively on DNA- and RNA-based biomarkers of TRD. Twelve studies met the inclusion criteria, covering candidate gene analyses, genome-wide association studies (GWAS), neuroimaging–genetic approaches, and microRNA profiling. Results: Genetic investigations consistently implicate neuroplasticity-related genes (BDNF, NTRK2, PTEN, SYN1, MAPK1, and GSK3B) in the risk of TRD and its relapse. Variants in glutamatergic receptor genes (GRIN2A, GRIN2B, GRIA2, GRIA3) were predicted to result in a rapid and sustained response to ketamine. Genomic approaches further demonstrated that composite genetic panels outperform single-variant predictors. In parallel, microRNAs such as miR-1202, miR-16, miR-135, miR-124, miR-223, and miR-146a emerged as dynamic biomarkers of treatment response, particularly in cohorts treated with ketamine or electroconvulsive therapy. Conclusions: DNA- and RNA-based biomarkers provide promising avenues for improving the understanding and management of TRD. Their integration into clinical frameworks could support patient stratification, individualized treatment selection, and real-time monitoring of therapeutic efficacy. Future research should prioritize replication, methodological harmonization, and longitudinal validation to facilitate the translation of findings into precision psychiatry.
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(This article belongs to the Special Issue Psychiatric Pharmacogenomics)
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Open AccessReview
From Metabolic to Epigenetic Memory: The Impact of Hyperglycemia-Induced Epigenetic Signature on Kidney Disease Progression and Complications
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Sara Cannito, Ida Giardino, Maria D’Apolito, Alessandra Ranaldi, Francesca Scaltrito, Massimo Pettoello-Mantovani and Annamaria Piscazzi
Genes 2025, 16(12), 1442; https://doi.org/10.3390/genes16121442 - 2 Dec 2025
Abstract
Chronic kidney disease is a significant global health burden and a leading cause of cardiovascular morbidity and mortality. Diabetes mellitus is the primary cause of kidney disease, driving the progression of both micro- and macrovascular complications. Sustained hyperglycemia initiates a cascade of deleterious
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Chronic kidney disease is a significant global health burden and a leading cause of cardiovascular morbidity and mortality. Diabetes mellitus is the primary cause of kidney disease, driving the progression of both micro- and macrovascular complications. Sustained hyperglycemia initiates a cascade of deleterious molecular and cellular events, including mitochondrial dysfunction, inflammation, oxidative stress, and dysregulated apoptosis and autophagy, which collectively contribute to the progression of renal injury. Beyond these well-established mechanisms, a compelling body of evidence highlights the pivotal role of epigenetic alterations (such as DNA methylation, histone post-translational modifications, and non-coding RNAs) in mediated long-term kidney damage. The interplay between transcriptional and epigenetic regulation underlies the phenomenon of the “metabolic memory”, wherein cellular dysfunction persists even after glycemic control is achieved. This review synthesizes the current knowledge on mechanisms sustaining metabolic and epigenetic memory, with a particular focus on the epigenetic machinery that establishes and maintains these signals, a concept increasingly termed “epigenetic memory.” Given their reversible nature, epigenetic determinants are emerging as promising biomarkers and a compelling therapeutic avenue. Targeting these “epifactors” offers a novel strategy to halt progression to end-stage renal disease, thereby paving the way for precision medicine approaches in diabetes-related renal disease.
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(This article belongs to the Section Epigenomics)
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Open AccessReview
Plant-Derived miRNAs as Potential Cross-Kingdom Cancer Regulators
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Aizhan Rakhmetullina, Zuzanna Lubas and Piotr Zielenkiewicz
Genes 2025, 16(12), 1441; https://doi.org/10.3390/genes16121441 - 2 Dec 2025
Abstract
MicroRNAs (miRNAs) are key posttranscriptional regulators of gene expression that influence cancer initiation, progression, and therapeutic response. While most studies have focused on endogenous miRNAs, emerging evidence has highlighted the role of plant-derived miRNAs as exogenous dietary regulators capable of cross-kingdom gene modulation.
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MicroRNAs (miRNAs) are key posttranscriptional regulators of gene expression that influence cancer initiation, progression, and therapeutic response. While most studies have focused on endogenous miRNAs, emerging evidence has highlighted the role of plant-derived miRNAs as exogenous dietary regulators capable of cross-kingdom gene modulation. This review summarises current knowledge regarding plant-derived miRNAs and their ability to regulate human cancer-related genes. Experimental findings indicate that plant miRNAs can withstand gastrointestinal digestion, enter the circulation, and regulate the expression of oncogenes, tumour suppressors, long noncoding RNAs, and immune checkpoint molecules via canonical RNA-induced silencing mechanisms. Specific examples include miR-156a, miR-159a-3p, miR-166a, miR-167e-5p, miR-171, miR-395e, miR-2911, miR-4995 and miR-5754, which exhibit anticancer activities across various cancer types and modulate key signalling pathways in mammalian cells, highlighting their potential as cross-kingdom regulators with therapeutic relevance. In addition to these characterised miRNAs, certain plant groups, which are rich in bioactive compounds, remain unexplored as sources of functional miRNAs, representing a promising avenue for future research. Collectively, these studies underscore the ability of plant-derived miRNAs to modulate mammalian gene expression and suggest their potential as diet-based or synthetic therapeutic agents. Further investigations into their bioavailability, target specificity, and functional relevance could inform innovative strategies for cancer prevention, integrating nutritional, molecular biological, and therapeutic approaches.
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(This article belongs to the Special Issue Function and Regulatory Mechanism of MicroRNAs in Cancers)
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Open AccessArticle
Host Immunogenetics and Chronic HCV Infection Shape Atopic Risk in Pediatric Beta-Thalassemia: A Genotype–Phenotype Study
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Caterina Cuppari, Alessio Mancuso, Laura Colavita, Clelia Cusmano, Valeria Tallarico, Valerio Caruso, Roberto Chimenz, Mimma Caloiero, Mariarosa Calafiore, Antonina La Mazza and Luciana Rigoli
Genes 2025, 16(12), 1440; https://doi.org/10.3390/genes16121440 - 2 Dec 2025
Abstract
Background: Pediatric patients with beta-thalassemia (BT) face unique immunologic challenges due to chronic transfusions and viral exposure. Hepatitis C virus (HCV), a common infection in polytransfused individuals, may influence immune polarization. However, the combined effect of chronic HCV and host immunogenetics on allergic
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Background: Pediatric patients with beta-thalassemia (BT) face unique immunologic challenges due to chronic transfusions and viral exposure. Hepatitis C virus (HCV), a common infection in polytransfused individuals, may influence immune polarization. However, the combined effect of chronic HCV and host immunogenetics on allergic sensitization remains incompletely understood. Objective: To assess total serum IgE levels and allergic manifestations in HCV-positive vs. HCV-negative BT patients, and explore associations with common polymorphisms in IL10, TLR7, IL4, and IFNG genes Methods: This cross-sectional observational study enrolled 46 BT patients (37 HCV-positive, 9 HCV-negative) and 50 healthy controls. Clinical allergy history, total IgE levels (ELISA), and skin prick tests (SPT) for aeroallergens were collected. Genotyping for IL10 −1082, TLR7 rs179008, IL4 −589, and IFNG +874 polymorphisms was performed. Associations between genotypes, HCV status, and IgE levels were analyzed descriptively due to small sample size Results: HCV-positive BT patients had lower mean IgE levels (18.73 ± 4.2 IU/mL) and fewer reported allergic symptoms (21.6%) compared to HCV-negative counterparts (118.76 ± 7.9 IU/mL; 55.5%). The IL10 −1082 AA and TLR7 rs179008 TT genotypes were more common in the HCV-positive group and were associated with lower IgE levels. No associations were noted for IL4 or IFNG variants. Splenectomy appeared to further modify IgE levels in HCV-negative patients. Due to limited power and absence of multivariate analysis, findings are exploratory. These preliminary observations may inform future studies of immune deviation in chronically infected pediatric cohorts. Conclusions: Chronic HCV infection may contribute to immune tolerance and reduced allergic expression in BT patients, potentially modulated by IL10 and TLR7 genotypes. Further studies with functional immune profiling and larger cohorts are required.
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(This article belongs to the Section Human Genomics and Genetic Diseases)
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What Do Single-Cell Models Already Know About Perturbations?
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Andreas Bjerregaard, Iñigo Prada-Luengo, Vivek Das and Anders Krogh
Genes 2025, 16(12), 1439; https://doi.org/10.3390/genes16121439 - 2 Dec 2025
Abstract
Background: Virtual cells are embedded in widely used single-cell generative models. Nonetheless, the models’ implicit knowledge of perturbations remains unclear. Methods: We train variational autoencoders on three gene expression datasets spanning genetic, chemical, and temporal perturbations, and infer perturbations by differentiating
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Background: Virtual cells are embedded in widely used single-cell generative models. Nonetheless, the models’ implicit knowledge of perturbations remains unclear. Methods: We train variational autoencoders on three gene expression datasets spanning genetic, chemical, and temporal perturbations, and infer perturbations by differentiating decoder outputs with respect to latent variables. This yields vector fields of infinitesimal change in gene expression. Furthermore, we probe a publicly released scVI decoder trained on the Discover Census ( M mouse cells) and score genes by the alignment between local gradients and an empirical healthy-to-disease axis, followed by a novel large language model-based evaluation of pathways. Results: Gradient flows recover known transitions in Irf8 knockout microglia, cardiotoxin-treated muscle, and worm embryogenesis. In the pretrained Census model, gradients help identify pathways with stronger statistical support and higher type 2 diabetes relevance than an average expression baseline. Conclusions: Trained single-cell decoders already contain rich perturbation-relevant information that can be accessed by automatic differentiation, enabling in-silico perturbation simulations and principled ranking of genes along observed disease or treatment axes without bespoke architectures or perturbation labels.
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(This article belongs to the Special Issue Machine Learning in Cancer and Disease Genomics)
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Global Transcriptome Analysis Reveals the Molecular Mechanism Underlying Seed Physical Dormancy Formation in Medicago sativa
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He Li, Xiaoying Kang, Xu Li, Feng Yuan, Zeng-Yu Wang and Maofeng Chai
Genes 2025, 16(12), 1438; https://doi.org/10.3390/genes16121438 - 1 Dec 2025
Abstract
Seed physical dormancy, also known as hard-seededness, is a characteristic commonly found in higher plants, which functions to prevent water and oxygen from passing through the impermeable seed coat. Background: Notably, seed dormancy has emerged as a critical factor in the domestication
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Seed physical dormancy, also known as hard-seededness, is a characteristic commonly found in higher plants, which functions to prevent water and oxygen from passing through the impermeable seed coat. Background: Notably, seed dormancy has emerged as a critical factor in the domestication of leguminous plants. Alfalfa (Medicago sativa L.) is a globally cultivated high-quality legume forage crop, while the seeds from different varieties maintain varying degrees of hard-seededness. However, the molecular mechanisms underlying physical dormancy in alfalfa seeds remain poorly understood. In particular, the regulatory mechanisms at the transcriptomic level remain unclear, which has hindered the breeding process of varieties with low hard-seededness. Methods: In this study, we performed global transcriptome analysis to discover the genes specifically expressed in the alfalfa seed coat and provide insights into alfalfa seeds’ physical dormancy domestication traits. RNA sequencing was performed on various alfalfa tissues, including roots, stems, leaves, flowers, and seed coats. Results: This analysis led to the identification of 4740 seed coat-specific expressed genes, including key genes such as KNOX4 (a class II KNOTTED-like homeobox gene), qHs1 (encoding endo-1,4-β-glucanase), GmHs1-1 (encoding a calcineurin-like metallophosphoesterase), and KCS12 (β-ketoacyl-CoA synthase). In addition, several seed coat-specific transcription factor families were identified, including ERF, B3, and NAC, among others. Furthermore, a comparison of gene expression profiles between seeds with and without physical dormancy revealed 60 upregulated and 197 downregulated genes associated with physical dormancy. Crucially, functional enrichment analysis demonstrated that these genes are predominantly associated with lipid metabolism pathways, particularly those involved in the formation of “monolayer-surrounding lipid storage bodies.” Conclusions: This key finding suggests that the establishment of physical dormancy is closely linked to the biosynthesis and deposition of specialized lipid-based layers in the seed coat, which likely constitute the primary barrier to water penetration. Our study thus provides fundamental insights and a valuable genetic resource for future functional studies aimed at deciphering and manipulating physical dormancy in alfalfa.
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(This article belongs to the Special Issue Genetics and Breeding of Forage)
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Molecular Cargo of Exosomes in Prostate Cancer: A Multi-Omics Perspective on Liquid Biopsies
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Roxana Andra Coman, Andreea Nutu, Stefan Strilciuc, Liviuta Budisan and Ioana Berindan-Neagoe
Genes 2025, 16(12), 1437; https://doi.org/10.3390/genes16121437 - 1 Dec 2025
Abstract
Prostate cancer is one of the most common cancers affecting men, and finding better ways to detect and monitor it remains a top priority in oncology. In recent years, scientists have focused their attention on different classes of extracellular bodies, among them the
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Prostate cancer is one of the most common cancers affecting men, and finding better ways to detect and monitor it remains a top priority in oncology. In recent years, scientists have focused their attention on different classes of extracellular bodies, among them the small ones called exosomes. Exosomes are nanoscale extracellular vesicles (30–200 nm) released into body fluids, where they transport molecular cargo reflective of their cell of origin. Instead of serving as liquid biopsies themselves, exosomes present in accessible fluids such as plasma and urine can be analyzed as part of minimally invasive liquid biopsy strategies without the need for surgery or tissue sampling. In prostate cancer, exosomes are not just passive carriers: they actively influence how cancer grows, spreads, and responds to treatment. Exosomes can be extracted from simple fluid samples, opening the door to faster, safer, and more personalised approaches to diagnosis and care. Exosome content is analysed for the molecular profiling of tumours, including genomics, transcriptomics, proteomics, and metabolomics. This has led to the discovery of new biomarkers that may help detect prostate cancer earlier, predict its aggressiveness, and monitor the effectiveness of treatment. This review synthesizes current multi-omics data on exosomal cargo in prostate cancer, highlighting diagnostic, prognostic, and therapeutic implications as well as existing challenges to clinical translation.
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(This article belongs to the Section Human Genomics and Genetic Diseases)
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Barriers, Limitations, and Experiences with Clinical Trials—Treatment in Rare Diseases with Prader–Willi Syndrome as an Example
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Merlin G. Butler, Spencer Silvey and Harold J. P. van Bosse
Genes 2025, 16(12), 1436; https://doi.org/10.3390/genes16121436 - 1 Dec 2025
Abstract
Background/Objectives: Developing and implementing clinical trials for rare diseases is complicated by the incomplete understanding of the varied genotype and subsequent phenotypic differences of a condition, particularly when low numbers of subjects are enrolled in a study. Moreover, a small-scale clinical study
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Background/Objectives: Developing and implementing clinical trials for rare diseases is complicated by the incomplete understanding of the varied genotype and subsequent phenotypic differences of a condition, particularly when low numbers of subjects are enrolled in a study. Moreover, a small-scale clinical study may indicate a positive outcome but have too small of a sampling population to adequately evaluate unwanted outcomes. Prader–Willi syndrome (PWS) is one such genetic disorder with varied subtypes and heterogeneity, where little progress has been made in treatment discoveries. Recently, the FDA approved diazoxide choline for treating key features of hyperphagia and obesity associated with PWS based on clinical trial experience. Diazoxide choline activates the ATP-sensitive potassium channel (KATP) of pancreatic beta cells, inhibiting the release of insulin. One of the subunits of KATP is the protein Kir6.2, the gene product of KCNJ11. Methods: Web-based programs and datasets were used to study the gene and protein functional enrichments of Kir6.2 and KCNJ11, including shared gene and/or protein–protein interactions, and biological processes and functions. Results: Four essential domains of related functions were identified: (1) apoptosis, protein degradation, and inflammation; (2) the coupling of G proteins needed for KATP channel activation; (3) glucose metabolism and control; and (4) the maintenance of intracellular ionic homeostasis. Conclusions: Cellular metabolism in the pancreas is linked to membrane excitability by KATP, which regulates insulin production, energy production and storage, appetite regulation, and fatty acid synthesis. As such, diazoxide choline may influence several biological systems beyond pancreatic and metabolic functions.
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(This article belongs to the Special Issue Molecular Basis in Rare Genetic Disorders)
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Gene Regulation in Comorbid Migraine and Myogenic Temporomandibular Disorder Pain
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Ran Tao, Sufang Liu, Hui Maltezos and Feng Tao
Genes 2025, 16(12), 1435; https://doi.org/10.3390/genes16121435 - 1 Dec 2025
Abstract
Background/Objectives: Previous studies have demonstrated an association between migraine headache and temporomandibular joint disorders (TMDs), with a higher prevalence of TMD symptoms in patients with migraine. Methods: In this study, we conducted RNA sequencing to identify differentially expressed genes (DEGs) in the spinal
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Background/Objectives: Previous studies have demonstrated an association between migraine headache and temporomandibular joint disorders (TMDs), with a higher prevalence of TMD symptoms in patients with migraine. Methods: In this study, we conducted RNA sequencing to identify differentially expressed genes (DEGs) in the spinal trigeminal nucleus caudalis of mice with migraine-like pain and/or myogenic TMD. Results: We observed 204 upregulated and 274 downregulated genes in the comorbid migraine and TMD group compared to the control group. We identified 15 ferroptosis-related DEGs enriched in the pathways of neurodegeneration, cellular homeostasis, interleukin signaling, and pain response. Gene Ontology analysis highlighted the involvement of neuroinflammatory response and monoamine transmembrane transporter activity, while Gene Set Enrichment analysis showed enrichment in chemokine signaling, cell cycle, and calcium signaling pathways. Immune infiltration analysis identified M0 macrophages, immature dendritic cells, neutrophils, and eosinophils as key responders. Hub genes in the protein–protein interaction network included Gm7536, Rpl17, Rpl22l1, Rpl14, Rps8, Rps29, Rpl35, Gm4889, Gm11808, Rps27rt, Rps12-ps3, Rpl10-ps3, Gm9843, Oas1c, Il1b, and Serpine1, indicating their synergistic roles in such orofacial pain comorbidity. Conclusions: Our results suggest that the comorbid migraine and TMD can regulate gene expressions involving ferroptosis and immune cell responses and the identified DEGs could be targeted to develop novel therapies for this painful comorbidity.
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(This article belongs to the Section Neurogenomics)
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Identification and Characterization of the Efbzip Gene Family in Erianthus fulvus and Exploration of Functional Genes Involved in Sucrose Metabolism
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Changzu Zhao, Weiyou Nong, Zhenfeng Qian, Qian Ding, Yujie Wang, Lilian He and Fusheng Li
Genes 2025, 16(12), 1434; https://doi.org/10.3390/genes16121434 - 1 Dec 2025
Abstract
Background/Objectives: Sugarcane (Saccharum spp.) is a major global sugar crop, and improving sucrose accumulation is critical for industry and bioenergy. Due to its high Brix content, Erianthus fulvus (E. fulvus) is valuable for genetic improvement of sugarcane. The bZIP
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Background/Objectives: Sugarcane (Saccharum spp.) is a major global sugar crop, and improving sucrose accumulation is critical for industry and bioenergy. Due to its high Brix content, Erianthus fulvus (E. fulvus) is valuable for genetic improvement of sugarcane. The bZIP transcription factor family critically regulates plant sucrose metabolism, but its roles in sugarcane remain largely unexplored. Methods: Through bioinformatics methods, Efbzip gene family members were systematically identified within the genome of E. fulvus. Gene expression patterns in distinct plant tissues were examined by RNA-seq and quantitative real-time PCR (qRT-PCR). Furthermore, genes potentially involved in sucrose metabolism were screened using transient expression assays and subcellular localization studies conducted in tobacco. Results: Seventy-nine Efbzip genes were identified and classified into nine subgroups, showing uneven distribution across ten chromosomes. Among ten conserved motifs, Motif1 was most conserved. Subcellular localization and physicochemical analyses showed most Efbzip proteins were hydrophilic and nuclear-localized. Cis-regulatory element analysis suggested Efbzip proteins regulate sucrose metabolism through hormone and light-responsive pathways. Segmental duplication primarily drove Efbzip gene family expansion. qRT-PCR showed predominant expression in stems and leaves, with subgroup-specific patterns. Nuclear localization of Efbzip52 was confirmed. Transient overexpression of Efbzip52, Efbzip61, and Efbzip64 significantly increased sucrose content in tobacco leaves, with highly statistically significant (p < 0.0001). Conclusions: In this study, the Efbzip gene family of E. fulvus was systematically characterized for the first time. Key candidate genes potentially involved in sucrose metabolism were identified, providing potential targets for the genetic improvement of sugarcane.
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(This article belongs to the Section Plant Genetics and Genomics)
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Secondary Ophthalmic Features Represent Diagnostic Clues and Potential Points of Intervention for Inherited Retinal Diseases (Target 5000 Report 3)
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Kirk A. J. Stephenson, Julia Zhu, Marcus Conway, Bridget Moran, Adrian Dockery, Laura Whelan, Jacqueline Turner, James J. O’Byrne, D. Ian Flitcroft, G. Jane Farrar and David J. Keegan
Genes 2025, 16(12), 1433; https://doi.org/10.3390/genes16121433 - 1 Dec 2025
Abstract
Background/Objective: Inherited retinal degenerations (IRDs) are the leading cause of blind registration in children and adults, yet 30–40% of cases remain genetically unresolved. Deep ophthalmic phenotyping may help to address this shortfall by identifying characteristic phenotypes. We describe the ophthalmic features of patients
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Background/Objective: Inherited retinal degenerations (IRDs) are the leading cause of blind registration in children and adults, yet 30–40% of cases remain genetically unresolved. Deep ophthalmic phenotyping may help to address this shortfall by identifying characteristic phenotypes. We describe the ophthalmic features of patients with stationary or progressive inherited retinal diseases other than outer retinal degeneration (i.e., secondary ophthalmic features, SOFs). Methods: This is a retrospective review of all patients attending an ophthalmic genetics clinic with a genetically confirmed IRD focusing on SOFs including refractive error, cataract, retinal detachment (RRD), cystoid macular lesions (CML) and epiretinal membrane (ERM). These features were assessed in the context of phenotype and genotype. Results: In a cohort of 429 genotyped patients, ≥1 SOFs were seen in 70.2% of patients, with 36.6% being affected by multiple SOFs. Refractive error (63.3%) and cataract (43.4%) were the most common secondary features, with a subset affected by CML (14.7%), ERM (10%) and RRD (4.7%). Conclusions: SOFs are common in patients with IRDs and most are amenable to therapeutic intervention even when no primary treatment (e.g., gene therapy) is available. We highlight patterns associated with genotypes and disease groups which may aid harmonisation of clinical and genetic diagnoses.
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(This article belongs to the Special Issue Genetic Diagnosis and Therapeutics of Eye Diseases)
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Endometrial Microbial Profile in Infertile Women with Chronic Endometritis: Intensified Culturomics and 16S rDNA Gene Sequencing
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Bárbara Lara-del-Río, Rocío Sánchez-Ruiz, Mónica Bernal-Sánchez, Francisco Ruiz-Cabello-Osuna, José María Navarro-Marí and José Gutiérrez-Fernández
Genes 2025, 16(12), 1432; https://doi.org/10.3390/genes16121432 - 1 Dec 2025
Abstract
Background/Objectives: Chronic endometritis (CE) has been linked to implantation failure, recurrent pregnancy loss, and endometrial dysbiosis with low Lactobacillus abundance. We assessed the endometrial microbiota in infertile women with CE and the added value of combining intensified culturomics with 16S rDNA NGS. Methods:
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Background/Objectives: Chronic endometritis (CE) has been linked to implantation failure, recurrent pregnancy loss, and endometrial dysbiosis with low Lactobacillus abundance. We assessed the endometrial microbiota in infertile women with CE and the added value of combining intensified culturomics with 16S rDNA NGS. Methods: Cross-sectional study with descriptive results of 15 endometrial biopsies analyzed in parallel by intensified culture and 16S rDNA (V3–V6) sequencing (RA threshold ≥ 5%). Results: Culture yielded growth in 13/15 samples (86.7%), whereas NGS reported findings in 15/15 (100%). NGS provided additional taxa beyond culture in 14/15 (93.3%), while culture identified taxa missed by NGS in 10/15 (66.7%). In both culture-negative cases, NGS detected ≥1 taxon. Lactobacillus spp. appeared exclusively by NGS in 26.7% of samples; Fannyhessea vaginae showed the highest mean RA by NGS and did not grow in culture, underscoring complementarity. Conclusions: 16S NGS complements intensified culturomics for characterizing the endometrial microbiota in CE, enhancing detection—especially when culture is negative—and supports a combined, clinically contextualized interpretation. Larger, controlled cohorts are warranted to validate diagnostic and prognostic utility.
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(This article belongs to the Section Molecular Genetics and Genomics)
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Unveiling Novel Traits Associated with Ulcerative Colitis via Phenome-Wide Associations Enhanced by Polygenic Risk Statistics
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Yiming Wu, Ling Liu, Meltem Ece Kars, Rui Li, Menglong Li and Yuval Itan
Genes 2025, 16(12), 1431; https://doi.org/10.3390/genes16121431 - 30 Nov 2025
Abstract
Background: Ulcerative colitis (UC) is a major form of inflammatory bowel disease affecting the gastrointestinal tract. Increasing evidence suggests UC is predisposed to co-occurring with other autoimmune diseases, yet its pathogenesis remains insufficiently understood. Large-scale biobank-based cross-trait genetic analyses may provide insights
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Background: Ulcerative colitis (UC) is a major form of inflammatory bowel disease affecting the gastrointestinal tract. Increasing evidence suggests UC is predisposed to co-occurring with other autoimmune diseases, yet its pathogenesis remains insufficiently understood. Large-scale biobank-based cross-trait genetic analyses may provide insights into the origins of UC and its comorbidities. Methods: Using the UK Biobank and Mount Sinai BioMe Biobank, we conducted genome-wide association studies (GWASs) in individuals of European ancestry. High-impact rare variants were aggregated for collapsing analysis. Genome-wide significant variants were tested in a phenome-wide association study (PheWAS) to explore UC comorbidities. Polygenic risk scores (PRSs) were derived from large-scale GWASs under different thresholds and functionalities, and the best-performing PRS was further applied in a PRS-based PheWAS. Genetic correlation between UC and highly associated traits was evaluated. Results: GWASs identified four genome-wide significant loci, including two novel variants (rs2314757, p = 4.82 × 10−11, OR = 0.81; rs6869382, p = 2.48 × 10−8, OR = 0.83) and two previously reported UC-associated sites (rs4654925, p = 1.85 × 10−8, OR = 0.84; rs2836882, p = 1.23 × 10−11, OR = 0.78) outside the HLA region. The optimal PRS, constructed with SNPs at p < 0.05, conferred an odds ratio of 5.86 (95% CI: 5.05–6.86) for UC in individuals with the highest versus lowest quintile. Both variant- and PRS-based PheWASs consistently highlighted type 1 diabetes (T1D) as the most significant comorbidity, confirmed by genetic correlation analysis. Conclusions: This study reveals novel loci contributing to UC and highlights comorbidities with shared genetic bases. UC PRSs demonstrated strong utility beyond risk prediction, effectively identifying UC-associated traits. A robust genetic correlation was established between UC and T1D.
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(This article belongs to the Section Technologies and Resources for Genetics)
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Open AccessArticle
Generation of a Compendium of Transcription Factor Cascades and Identification of Potential Therapeutic Targets Using Graph Machine Learning
by
Sonish Sivarajkumar, Romy Roy, Pratyush Tandale, Ankit Bhardwaj, Kipp W. Johnson, Anoop Titus, Benjamin S. Glicksberg, Shameer Khader, Kamlesh K. Yadav and Lakshminarayanan Subramanian
Genes 2025, 16(12), 1430; https://doi.org/10.3390/genes16121430 - 30 Nov 2025
Abstract
Background: Transcription factors (TFs) are critical regulators of gene expression, and their dysregulation is implicated in diseases like cancer. This study aims to create a comprehensive resource of TF cascades to identify potential therapeutic targets. Methods: We extracted TF interactions from the STRING
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Background: Transcription factors (TFs) are critical regulators of gene expression, and their dysregulation is implicated in diseases like cancer. This study aims to create a comprehensive resource of TF cascades to identify potential therapeutic targets. Methods: We extracted TF interactions from the STRING database, constructed a knowledge graph using graph machine learning, and performed pathway enrichment analysis with Enrichr. Network analysis and PageRank identified influential TFs. Results: We generated 81,488 unique TF cascades, with the longest containing 62 TFs. Key TFs (e.g., MYC, TP53, STAT3) were identified, and enriched pathways included cancer-related processes. A knowledge graph and dataset were made publicly available. Conclusions: This compendium of TF cascades provides a valuable resource for understanding TF interactions and identifying novel drug targets for precision therapeutics.
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(This article belongs to the Section Bioinformatics)
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Open AccessArticle
Surviving the Heat: Genetic Diversity and Adaptation in Sudanese Butana Cattle
by
Guilherme B. Neumann, Paula Korkuć, Siham A. Rahmatalla, Monika Reißmann, Elhady A. M. Omer, Salma Elzaki and Gudrun A. Brockmann
Genes 2025, 16(12), 1429; https://doi.org/10.3390/genes16121429 - 30 Nov 2025
Abstract
Background: Butana are native Sudanese Bos indicus cattle that are well adapted to arid environments and valued for their relatively high milk performance and resilience under harsh conditions. Despite their adaptive advantages, Butana cattle face the risk of genetic erosion due to low
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Background: Butana are native Sudanese Bos indicus cattle that are well adapted to arid environments and valued for their relatively high milk performance and resilience under harsh conditions. Despite their adaptive advantages, Butana cattle face the risk of genetic erosion due to low production performance and the absence of structured breeding programs underscoring the urgent need to conserve their unique genetic potential for climate-resilient livestock development. Methods: In this study, we analyzed whole-genome sequencing data from 40 Butana cattle to assess their genetic diversity, population structure, signatures of selection, and potential pathogen load. Results: Butana cattle exhibited high nucleotide diversity and low levels of inbreeding, indicating a stable gene pool shaped by natural selection rather than by intensive breeding. Signatures of selection and functional variant analysis revealed candidate genes involved in heat stress adaptation (COL6A5, HSPA1L, TUBA8, XPOT), metabolic processes (G6PD, FAM3A, SLC10A3), and immune regulation (IKBKG, IRAK3, IL18RAP). Enrichment analyses and RoH island mapping consistently highlighted immune and thermoregulatory pathways as key selection targets, distinguishing Butana from both the geographically neighbored Kenana cattle and the specialized dairy cattle breed Holstein. Furthermore, metagenomic screening of unmapped reads detected the tick-borne parasite Theileria annulata and the opportunistic pathogen Burkholderia cenocepacia in all animals, underscoring the importance of integrating pathogen surveillance into genomic studies. Conclusions: Taken together, our findings highlight the distinct adaptive genomic profile of Butana cattle and reinforce their value in breeding programs aimed at improving climate resilience and disease resistance in livestock through the utilization of local breeds.
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(This article belongs to the Section Animal Genetics and Genomics)
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Open AccessArticle
Genetic Insight into Expression-Defined Melanoma Subtypes and Network Mechanisms: An in Silico Study
by
Desirèe Speranza, Mariapia Marafioti, Martina Musarra, Vincenzo Cianci, Cristina Mondello, Maria Francesca Astorino, Mariacarmela Santarpia, Natasha Irrera, Mario Vaccaro, Nicola Silvestris, Concetta Crisafulli, Marco Calabrò and Silvana Briuglia
Genes 2025, 16(12), 1428; https://doi.org/10.3390/genes16121428 - 30 Nov 2025
Abstract
Background: Melanoma is a highly heterogeneous neoplasia in which transcriptional profile encodes much of the biological diversity that determines tumor progression and therapeutic response. To refine its molecular stratification and profiles characterization, we conducted an in silico transcriptomic analysis. Methods: Public microarray datasets
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Background: Melanoma is a highly heterogeneous neoplasia in which transcriptional profile encodes much of the biological diversity that determines tumor progression and therapeutic response. To refine its molecular stratification and profiles characterization, we conducted an in silico transcriptomic analysis. Methods: Public microarray datasets from the GEO and ArrayExpress were examined, and the E-MTAB-6697 expression dataset was selected. We used a K-Means clustering algorithm to stratify 194 tumor samples into expression-driven subgroups and analyzed each one to define their transcriptional and biological profiles. Differential expression analysis between identified clusters and controls was performed. Additionally, we applied Weighted-Gene correlation analysis to identify coordinated expression hubs in the tumor dataset and tested the resulting modules for correlation with the identified clusters. Results: Unsupervised clustering of melanoma transcriptomic profiles identified three distinct molecular subtypes characterized by divergent biological programs. While all clusters shared the dysregulation of pathways involved in epidermal differentiation, immune response, and lipid metabolism, they diverged in proliferation, phenotypic plasticity, metabolic adaptation, and apoptotic regulation. Cluster A was characterized by enrichment in DNA replication, repair, and mitochondrial metabolism modules, suggesting a proliferative yet genomically stable state. Cluster B showed enrichment in immune and cytokine signaling pathways alongside reduced proliferative activity, consistent with a quiescent or transitional phenotype. Cluster C displayed coordinated enrichment in cell-cycle, DNA-maintenance, and neuroectodermal reprogramming pathways, indicating a highly plastic and proliferative subtype. Despite these molecular distinctions, all clusters retained an “immunologically hot” profile (IPS 7–8), indicating potential responsiveness to immunotherapy. Conclusions: These findings provide an overview of the functional characteristics of melanoma heterogeneity and identify biological processes that could be targeted by drugs for the development of tailored therapies for each subtype. Nevertheless, future studies in independent clinically annotated cohorts would be required.
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(This article belongs to the Section Bioinformatics)
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Open AccessArticle
Characterization of the Mitochondrial Genome of Cavariella salicicola: Insight into the Codon Usage Bias and Phylogenetic Implications in Aphidinae
by
Tian-Xing Jing, Yan-Jin Zhang, Pei-Xuan Li, Qian Wang, Jin Yang, Hong-Hua Su and Shuai Zhang
Genes 2025, 16(12), 1427; https://doi.org/10.3390/genes16121427 - 29 Nov 2025
Abstract
Background: Cavariella salicicola (Hemiptera: Aphidinae) is a pest on Salix spp. and various Umbelliferae (Apiaceae) vegetables. However, the taxonomic status and phylogenetic relationship of the genus Cavariella within Aphidinae remain controversial due to the small body size and easily confused external morphology.
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Background: Cavariella salicicola (Hemiptera: Aphidinae) is a pest on Salix spp. and various Umbelliferae (Apiaceae) vegetables. However, the taxonomic status and phylogenetic relationship of the genus Cavariella within Aphidinae remain controversial due to the small body size and easily confused external morphology. Methods: The complete mitochondrial genome of C. salicicola collected from Oenanthe javanica was sequenced using the Illumina platform and compared with C. theobaldi. The codon usage bias of two Cavariella aphids was assessed through Enc plot, PR2 plot, and neutrality plot analyses. Furthermore, phylogenetic trees were constructed based on both Maximum Likelihood and Bayesian Inference analysis. Results: The C. salicicola mitochondrial genome comprises 15,720 bp and represents a typical circular DNA molecule with a high AT content of 83.8%. It contains the standard 37 genes, including 2 ribosomal RNAs (rRNAs), 13 protein-coding genes (PCGs), 22 transfer RNAs (tRNAs), and 2 long non-coding regions (control and repeat regions). Varying degrees of codon usage bias were found across different PCGs, and the bias was predominantly influenced by natural selection rather than mutational pressure. The ratio of nonsynonymous to synonymous substitutions (Ka/Ks) indicated that all PCGs in C. salicicola, as well as most other Aphidinae species, are under strong purifying selection. The phylogenetic analysis based on Maximum Likelihood and Bayesian Inference both strongly supported the monophyly of Aphidinae, Macrosiphini, and Aphidini. Crucially, the monophyletic genus Cavariella was resolved as a sister group to all other sampled species within the tribe Macrosiphini. Conclusions: This study provides new molecular data to support the sister relationship of the genus Cavariella to other Macrosiphini aphids. This study will enhance our understanding of phylogenetic relationships within the subfamily Aphidinae.
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(This article belongs to the Special Issue Molecular Evolution, Mitochondrial Genomics and Mitochondrial Genome Expression in Animals: 2024–2025)
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The Methylation of the CYP11A1 Gene Affects the Expression Pattern in Different-Diameter Granulosa Cells of Qira Black Sheep
by
Chunjie Liu, Peilin Guo, Linlin Pei, Wenhao Wang, Andi Qiao and Xin Xu
Genes 2025, 16(12), 1426; https://doi.org/10.3390/genes16121426 - 29 Nov 2025
Abstract
Background: CYP11A1 (a key enzyme in the process of progesterone synthesis) expression is a crucial factor that promotes the proliferation and progressive differentiation of granulosa cells (GCs) to support oocyte maturation and ovulation in livestock. Changes in its expression may be related to
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Background: CYP11A1 (a key enzyme in the process of progesterone synthesis) expression is a crucial factor that promotes the proliferation and progressive differentiation of granulosa cells (GCs) to support oocyte maturation and ovulation in livestock. Changes in its expression may be related to DNA methylation, but the specific regulatory mechanism of this remains unclear. Methods: The qRT-PCR, western-blot, CCK-8 assay, RNAi, dual-luciferase activity assay and sulfite sequening were used to explore the effect of the activity and methylation level of the CYP11A promoter on the proliferation of GCs. Results: Our studies first identified that the activity of CYP11A1 promoted the core genes that affected the superior growth of follicles in Qira Black sheep, and activity changes were related to the degree of DNA methylation. We further revealed that the DNA methylation of GCs at different developmental stages was mainly regulated by the promoter region, and also clearly defined the optimal window period for CYP11A1 to affect the proliferation of GCs. Conclusions: In summary, our data reveals the epigenetic regulatory mechanism of GCs in follicle development provides a new perspective for understanding the molecular basis of reproductive cell differentiation, and offers important theoretical support for future research and basic application in the field of livestock reproduction. Discussion: This not only helps to improve the efficient breeding and production system of sheep and the process of genetic improvement, but also provides a theoretical basis for fundamentally accelerating the expansion, breeding, and genetic quality innovation of superior sheep breeds in China, and also offers accurate targets for sheep genetic breeding.
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(This article belongs to the Special Issue Genetics and Breeding Improvements in Sheep and Goat)
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Open AccessArticle
Identification of the FLA Gene Family in Soybean and Preliminary Functional Analysis of Its Drought-Responsive Candidate Genes
by
Jiyue Zhang, Lina Yang, Jingxuan Dou, Cong Wang and Zhengpei Yao
Genes 2025, 16(12), 1425; https://doi.org/10.3390/genes16121425 - 29 Nov 2025
Abstract
Background/Objectives: Fasciclin-like arabinogalactan proteins (FLAs) are critical components of the plant cell wall, playing vital roles in development and abiotic stress responses. However, a systematic genome-wide analysis of the FLA family in soybean (Glycine max L.), a major legume crop susceptible to
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Background/Objectives: Fasciclin-like arabinogalactan proteins (FLAs) are critical components of the plant cell wall, playing vital roles in development and abiotic stress responses. However, a systematic genome-wide analysis of the FLA family in soybean (Glycine max L.), a major legume crop susceptible to drought, is lacking. This study aimed to comprehensively identify GmFLA members and investigate their potential functions in drought tolerance. Methods: We identified GmFLA genes via BLASTP (v2.16.0) and Hidden Markov Model (HMM) searches against the soybean genome. Subsequent analyses encompassed their physicochemical properties, chromosomal distribution, gene structure, phylogenetic relationships, conserved domains, cis-acting elements, and subcellular localization. Drought-responsive candidates were screened using a Gene Expression Omnibus (GEO) dataset, and their expression profiles were validated under drought stress using quantitative real-time PCR (qRT-PCR). Results: A total of 55 GmFLA genes were identified and unevenly distributed across 14 chromosomes. Most genes featured a single-exon structure and contained a conserved Fasciclin domain, with predicted localization primarily to the chloroplast. Phylogenetic analysis grouped them into three distinct subclasses with Arabidopsis homologs, suggesting lineage-specific expansion. Promoter analysis revealed an abundance of stress- and hormone-related cis-elements. Expression analysis identified five candidate genes (GmFLA5, GmFLA15, GmFLA40, GmFLA47, and GmFLA54) that showed tissue-specific expression changes under drought treatment. Conclusions: This study provides the first comprehensive genomic characterization of the GmFLA gene family and identifies candidate GmFLAs with drought-responsive expression patterns. Our findings establish a foundation for future functional research to investigate their potential roles in soybean drought response. Furthermore, these candidates serve as potential targets for further investigation in strategies aimed at improving soybean drought tolerance.
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(This article belongs to the Section Plant Genetics and Genomics)
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