Peer-reviewed research spanning neurogenomics, regulatory non-coding RNAs, systems biology, social insect genomics, and translational medicine. Each entry includes a brief research synthesis.
Size reflects prominence across our publications.
This comprehensive review synthesises the emerging field of circular RNA (circRNA) biology in neurological disorders, covering state-of-the-art computational approaches for circRNA identification from RNA-seq data, experimental strategies for functional validation, and their potential as biomarkers and therapeutic targets. The authors provide a systematic appraisal of circRNA evidence across Alzheimer's disease, schizophrenia, Parkinson's disease, and other neurological conditions, highlighting how circRNA regulatory mechanisms — including miRNA sponging, protein scaffolding, and translation into peptides — may contribute to disease pathology.
This interdisciplinary study applies social network analysis — a method central to systems biology — to quantify conflict dynamics within families and communities in post-civil war Mozambique, revealing structural patterns in how disputes propagate, cluster, and resolve across social networks. The computational approach provides novel quantitative insights into reconciliation mechanisms and social resilience in post-conflict societies, demonstrating the cross-disciplinary applicability of network science methods developed in biological research.
This study uncovers a previously unknown regulatory pathway in Natural Killer (NK) cells wherein the unfolded protein response sensor IRE1α governs immune checkpoint expression through a cascade involving XBP1 transcription factor activity and miR-34a-mediated post-transcriptional repression of PD-1. The IRE1α/XBP1/miR-34a axis directly modulates NK cell exhaustion, with immediate implications for understanding why NK cell-based immunotherapies may fail in the tumour microenvironment and how targeting this pathway could enhance cancer immunotherapy efficacy.
The authors developed a non-invasive salivary microRNA signature capable of distinguishing oral cancer patients from healthy controls with high diagnostic accuracy, identifying a panel of circulating miRNAs detectable in saliva that correlate with cancer stage and predict disease progression. This liquid biopsy approach offers a practical, minimally invasive clinical tool for early detection and longitudinal monitoring of oral squamous cell carcinoma, addressing a critical gap in current screening strategies.
This review explores the mechanistic connections between olfactory dysfunction and neuropsychiatric conditions including schizophrenia, autism spectrum disorder, and depression, examining shared molecular pathways, neural circuit disruptions, and genetic factors linking olfactory system impairment to brain disorders. The authors discuss how olfactory deficits may serve as early biomarkers for neuropsychiatric disease and how the accessible olfactory epithelium provides unique experimental entry points for studying neurodevelopmental disease mechanisms without requiring brain biopsies.
Patient-derived olfactory epithelial stem cells were used to establish a disease-relevant non-invasive cellular model of Alzheimer's disease, enabling identification of gene expression signatures in living patients that correlate with cognitive performance and disease stage. The study demonstrates the power of this accessible cell type for capturing disease-specific transcriptomic changes and validates olfactory neurosphere-derived cells as a tractable model for Alzheimer's biomarker discovery and drug testing.
This review comprehensively examines the roles of miRNAs, lncRNAs, circRNAs, and other non-coding RNA classes in the pathogenesis, progression, and therapy resistance of oral cancers, synthesising evidence from sequencing studies and mechanistic investigations. The authors critically evaluate the diagnostic and therapeutic potential of ncRNAs in oral cancer and discuss key challenges — including tissue heterogeneity, lack of standardisation, and delivery barriers — that must be addressed for clinical translation.
This book chapter provides a systematic overview of computational approaches for predicting microRNA target interactions, detailing the algorithms, seed-matching rules, thermodynamic parameters, and curated databases that underpin modern target prediction tools, as well as their individual strengths and limitations. The authors describe both computational validation approaches and experimental methods — including luciferase reporter assays, AGO2-CLIP, and western blotting — for functionally confirming predicted miRNA–target pairs.
This chapter surveys the clinical translation landscape for microRNA-based diagnostics and therapeutics, reviewing circulating miRNA biomarkers across cardiovascular, oncological, and neurological disease applications, alongside the emerging pipeline of miRNA mimics, antagomirs, and miRNA-targeted therapies in clinical trials. The authors examine persistent challenges — including biomarker reproducibility, in vivo delivery systems, off-target effects, and regulatory pathways — that shape the timeline and feasibility of miRNA-based clinical products.
RNA sequencing of peripheral blood mononuclear cells from individuals classified as high or low interferon-alpha producers revealed fundamentally different transcriptomic programs activated upon rhinovirus infection, identifying key gene networks that determine the magnitude of the innate antiviral response. These findings illuminate the molecular basis of individual variation in susceptibility to rhinovirus-triggered asthma exacerbations and suggest candidate pathways for therapeutic modulation of antiviral immunity in respiratory disease.
This study demonstrates that two evolutionarily conserved microRNAs — miR-34 and miR-210 — post-transcriptionally regulate caste-specific expression of hexamerin nutritional storage proteins during early honeybee brain development, providing a molecular link between larval nutrition, miRNA activity, and the developmental fate divergence between queens and workers. The findings place miRNA-mediated regulation of metabolic storage proteins as a key layer of the gene regulatory network governing social insect caste determination.
Transcriptomic profiling of honeybee brains at early developmental stages revealed that differential larval nutrition rapidly reprograms gene expression networks in a caste-specific manner, identifying the primary transcriptional response connecting nutritional input to epigenomic and developmental fate specification programs. This work illuminates the molecular cascade from external environmental cue (diet) to internal genomic response that ultimately determines whether a larva becomes a queen or a worker bee.
This study identifies hnRNPK as a critical regulator of selective miRNA loading into exosomes in cancer cells, and demonstrates that this sorting process is controlled by membrane lipid composition and remodelling events occurring during vesicle biogenesis rather than solely by RNA-binding protein affinity. The findings reveal an upstream lipid-based regulatory mechanism for exosomal miRNA packaging, with implications for how cancer cells exploit extracellular vesicle communication to influence the tumour microenvironment and potentially mediate treatment resistance.
Sex determination pathways in stingless bee species were characterised by analysing alternative splicing variants of the doublesex and feminizer genes, key conserved regulators of sex determination in social Hymenoptera, revealing both conserved features and evolutionary divergences compared to the well-studied honeybee system. The study contributes to understanding how sex determination mechanisms are maintained and modified across the highly diverse stingless bee lineage within the broader context of insect sex determination evolution.
A comprehensive pan-cancer analysis of chromosome arm copy number alterations across thousands of tumour genomes demonstrated that specific aneuploidy patterns drive distinct evolutionary trajectories, correlate with patient prognosis across cancer types, and predict differential sensitivity to targeted therapies. The study provides a genome-scale map of how arm-level genomic instability — acting on entire chromosomal regions rather than individual genes — shapes the cancer phenotype and could be used clinically to stratify patients for therapeutic intervention.
This study reveals a novel viral immune evasion mechanism in EBV-associated lymphoma: a virus-encoded miRNA (BHRF1-2-5p) directly suppresses host expression of PD-L1 and PD-L2, the immune checkpoint ligands that normally inhibit anti-tumour T cell responses. This paradoxical finding — viral miRNA downregulating immunosuppressive ligands — suggests that EBV may modulate immune checkpoint activity to its own advantage, and has direct implications for predicting and potentially improving responses to PD-1/PD-L1 checkpoint blockade therapies in EBV+ lymphomas.
Using genetic models and patient-derived AML samples, this study demonstrates that loss of PTEN function confers robust resistance to MEK inhibitor treatment by enabling compensatory reactivation of the PI3K/AKT survival pathway, bypassing the growth arrest imposed by MEK blockade. The findings establish PTEN status as a critical biomarker for predicting MEK inhibitor efficacy in AML and provide mechanistic rationale for combination strategies incorporating PI3K/AKT pathway co-inhibition to overcome this resistance mechanism.
This study identifies a regulatory network in prostate cancer where miR-3162-5p coordinates the expression of multiple kallikrein-related serine proteases, including PSA (KLK3), through coordinated post-transcriptional repression of shared 3'UTR target sites, creating a miRNA-mediated hub controlling a functionally related gene family. The miR-3162-5p/kallikrein axis influences prostate cancer cell proliferation and invasion, establishing this miRNA as both a mechanistic co-regulator of the kallikrein system and a potential therapeutic target.
This methods chapter provides optimised step-by-step protocols for detecting microRNA expression and subcellular localisation within intact tissue sections using locked nucleic acid (LNA)-based in situ hybridisation, covering probe design, tissue preparation, hybridisation conditions, signal amplification, and quantitative image analysis. The miR-ISH technique enables precise spatial resolution of miRNA activity within heterogeneous tissue microenvironments — distinguishing stromal, epithelial, and immune cell populations — that bulk RNA extraction approaches cannot achieve.
The study characterises the hormonal regulation of the nuclear receptor transcription factor ftz-f1 in honeybees, identifying its downstream gene targets and demonstrating a positive feedback loop wherein juvenile hormone induces ftz-f1, which in turn activates vitellogenin (a key reproductive protein), creating a self-reinforcing regulatory circuit that coordinates reproductive physiology. These findings advance understanding of how hormonal cascades orchestrate the molecular events of social insect reproductive regulation and the physiological differences between reproductive queens and non-reproductive workers.
By integrating whole-genome sequencing data from ASD families with regulatory element annotations including ENCODE cCREs, JASPAR transcription factor binding sites, and eQTL databases, this study identified non-coding variants in gene regulatory regions as significant contributors to ASD genetic risk, extending the disease's molecular architecture well beyond protein-coding mutations. The analysis links ASD-associated regulatory variants to disruption of transcription factor binding and enhancer activity in fetal brain, supporting a model where regulatory genomic dysregulation is central to neurodevelopmental disorder aetiology.
This study measured circulating plasma miRNA levels in DLBCL patients at baseline and during treatment, demonstrating that miR-494 and miR-21 levels correlate with treatment response as assessed by interim PET/CT imaging, qualifying them as non-invasive biomarkers for early response assessment during front-line chemotherapy. The liquid biopsy approach could complement or augment interim PET-based risk stratification, potentially guiding treatment escalation or de-escalation decisions earlier in the treatment course for aggressive lymphoma.
Gene expression profiling of peripheral blood from infants with first-degree genetic risk for type 1 diabetes identified a transcriptomic signature present before the appearance of islet autoantibodies, revealing early innate and adaptive immune dysregulation that precedes clinically detectable autoimmunity by months to years. This pre-autoantibody predictive signature could enable earlier identification of at-risk children for preventive interventions and provides mechanistic insights into the very early immunological events that initiate T1D autoimmune pathogenesis.
Human induced pluripotent stem cell-derived neurons generated from anorexia nervosa patients revealed disease-specific transcriptional alterations in pathways related to synaptic function, neuronal energy sensing, appetite regulation, and neurodevelopmental signalling, providing the first direct neuronal-level transcriptomic evidence for biological differences in AN. This patient iPSC-derived neuronal model establishes a new experimental platform for studying the neurobiological mechanisms of eating disorders and could facilitate identification of molecular targets for an indication with a critical lack of effective pharmacological treatments.
Comparative DNA methylation analysis across multiple schizophrenia patient-derived cell types — including olfactory neurosphere-derived cells, lymphoblastoid cell lines, and fibroblasts — revealed cell-type-specific epigenetic dysregulation patterns, with disease-associated methylation differences concentrated in different genomic regions and gene pathways depending on the cell type examined. This study highlights that the choice of surrogate cell model critically impacts which aspects of schizophrenia epigenomics can be detected, reinforcing the importance of brain-proximal cell types such as olfactory stem cells for epigenetic disease research.
This study demonstrates that miR-34, an evolutionarily ancient and conserved microRNA, targets key pair-rule segmentation genes during honeybee embryonic development, revealing a novel miRNA-mediated regulatory layer overlaid on the ancient Drosophila-like body axis determination genetic cascade in Hymenoptera. The findings establish a role for miR-34 in integrating post-transcriptional gene regulation with the fundamental genetic machinery controlling insect body plan formation, and represent a rare example of miRNA function characterised during social insect embryogenesis.
By meta-analysing multiple subcellular quantitative proteomics datasets, this study identified coordinated functional interactions between cytoskeletal protein networks and lipid raft membrane domains that are specifically dysregulated in cancer, revealing compartment-specific protein complex reorganisation as a driver of oncogenic signalling. The integrative approach demonstrates the value of re-mining published proteomics datasets to extract higher-order systems-level insights beyond what individual studies can identify.
A microRNA expression analysis of honeybee ovaries across queens and workers identified a conserved miRNA signature associated with ovarian activity regardless of caste identity, suggesting that shared post-transcriptional regulatory mechanisms govern core reproductive physiology in both reproductive and functionally sterile castes. These findings reveal a miRNA-based regulatory layer operating independently of the transcription factor networks that control caste identity, contributing a new dimension to the molecular dissection of reproductive division of labour in social insects.
Comparative transcriptomics of haploid (unfertilised, drone-destined) and diploid (fertilised, queen/worker-destined) honeybee embryos provided the first systematic characterisation of genome activation dynamics in this social insect, demonstrating that zygotic transcription initiates earlier during embryonic cleavage than previously recognised. Ploidy-dependent expression differences were also identified, offering molecular insights into the dosage compensation mechanisms and early sex-determination events that operate during embryogenesis in a haplodiploid organism.
This in vivo study demonstrates that long-term potentiation (LTP) — the cellular basis of learning and memory — rapidly induces widespread changes in microRNA expression in the rat hippocampus within minutes to hours, establishing miRNAs as rapid effectors of activity-dependent post-transcriptional gene regulation during synaptic plasticity. The rapid timescale of LTP-induced miRNA regulation, comparable to immediate-early gene induction, implicates miRNAs as key regulators of the translational programme needed for late-phase LTP consolidation and memory formation.
This landmark study identified miR-932 as a novel regulator of memory formation in honeybees, demonstrating that the miRNA targets actin cytoskeletal genes downstream of neuroligin synaptic adhesion molecules to control structural synaptic plasticity required for associative memory consolidation. The work establishes a conserved molecular pathway — neuroligin signalling → miRNA activity → actin dynamics → synaptic remodelling — linking autism-associated synaptic adhesion molecules to memory mechanisms through microRNA regulation, with implications extending to human neurodevelopmental conditions.
Exome sequencing of ASD-affected families combined with protein-protein interaction network analysis identified de novo and inherited rare coding variants that converge on interconnected molecular pathways rather than distributed randomly across the genome, providing a systems-level view of how extreme genetic heterogeneity in ASD can nonetheless produce coherent biological signal through shared pathway membership. The approach demonstrates that network-based integration of sequencing data is essential for extracting biological meaning from highly heterogeneous neurodevelopmental disorders with hundreds of implicated genes.
This study reveals that olfactory memory formation in the brain feeds back to regulate olfactory receptor gene expression in peripheral sensory neurons of the antennae, demonstrating a previously unrecognised bidirectional interaction between central memory circuits and the peripheral sensory organ transcriptome. This feedback mechanism — whereby experience-dependent central neural states shape peripheral receptor expression — represents a novel form of sensory system plasticity relevant to understanding perceptual learning and olfactory habituation.
By mapping genes associated with autism, schizophrenia, ADHD, intellectual disability, and other neuropsychiatric conditions onto a protein-protein interaction network, this study demonstrates that these clinically distinct disorders collectively occupy a highly interconnected and non-random molecular subnetwork, arguing for a "common molecular system" model of mental illness rather than distinct disease entities. The finding has major implications for drug development — suggesting that therapeutic targets relevant to one neuropsychiatric condition may have broader efficacy across the spectrum — and for understanding pleiotropic genetic risk factors.
Transcriptomic analysis of thoracic tissue during the pupal-to-adult metamorphic transition in honeybees identified the gene sets governing cuticle biosynthesis, chitinase activity, and exoskeleton structural remodelling, providing a comprehensive molecular atlas of this developmental process in a social insect model organism. The study identifies both deeply conserved components of the insect moulting programme and honeybee-specific gene expression features associated with the distinctive thoracic morphology of the adult worker bee.
This comprehensive book chapter reviews insect microRNA biology from first principles, covering miRNA biogenesis pathways, Argonaute-mediated gene silencing mechanisms, miRNA gene family evolution across insect phylogeny, and characterised biological functions spanning development, metamorphosis, reproduction, immunity, and behaviour. The chapter contextualises insect miRNA research within broader animal miRNA biology while highlighting insect-specific features — including the absence of certain biogenesis factors present in mammals — that make insects both valuable model organisms and interesting evolutionary comparators.
Small RNA deep sequencing across multiple organs and developmental stages of the German cockroach Blattella germanica — one of the most evolutionarily basal hemimetabolous insects — characterised the complete expressed miRNA repertoire and revealed organ- and stage-specific expression dynamics of both conserved and novel miRNA families. By profiling this ancient insect lineage, the study provides evolutionary insights into miRNA gene family conservation, innovation, and loss across the insect phylogeny, establishing Blattella as a valuable reference point for understanding miRNA evolution in the insect-to-mammal transition.
Comprehensive structural, evolutionary, and expression analyses of all four honeybee hexamerin storage protein genes across castes and sexes revealed distinct functional specialisations consistent with roles in nutritional storage, juvenile hormone binding, and reproductive physiology, and identified caste- and sex-specific expression patterns controlled by both hormonal and nutritional inputs. This study provides the first complete functional annotation of the hexamerin gene family as a cohesive system in a social insect, establishing hexamerins as multifunctional proteins at the nexus of nutrition, endocrinology, and social organisation.
Genome-wide identification and characterisation of detoxification enzyme families (P450s, carboxylesterases, glutathione S-transferases) and chemosensory gene families in the parasitoid wasp Nasonia vitripennis revealed a repertoire shaped by its parasitic lifestyle and host range, with intriguing contractions and expansions relative to the honeybee and Drosophila genomes. The comparative analysis provides insights into how ecological specialisation — in this case, endoparasitism of blowfly puparia — has driven the evolution of metabolic and chemosensory gene toolkits in a non-social Hymenopteran.
Characterisation of hexamerin storage protein genes in Nasonia vitripennis revealed their genomic organisation, phylogenetic relationships to other insect hexamerins, and expression patterns that differ substantially from the social honeybee system, reflecting the distinct non-social life history and endoparasitic ecology of this wasp. The comparative analysis places Nasonia hexamerins within the broader Hymenopteran hexamerin evolutionary context, demonstrating how gene function and regulation within this protein family has diverged in concert with the evolution of different degrees of social organisation.
This landmark comparative genomics paper reports the sequencing and analysis of three closely related Nasonia parasitoid wasp genomes, providing insights into the molecular basis of hybridisation incompatibility, venom composition evolution, unique DNA methylation patterns, and the genetic underpinnings of behavioural differences — including circadian rhythm variation — between species separated by only ~1 million years of evolution. The Nasonia genomes established this genus as a powerful model for studying speciation genetics, the evolution of parasitism, and the genomic basis of complex social and behavioural traits.
Community detection algorithms were applied to the yeast transcriptional regulatory network to identify functional modules — coherent sets of co-regulated genes with related biological functions — revealing hierarchical organisation in the transcription network that reflects the modular architecture of cellular processes. The analysis demonstrates how network topology and graph-theoretic community structure can be exploited to infer biologically meaningful gene regulatory relationships that would be invisible from pairwise interaction data alone.
Microsatellite genotyping of drones collected from multiple congregation areas in southern Brazil revealed significant genetic structure among drone populations, indicating that drones preferentially aggregate at geographically restricted mating sites that reflect the spatial distribution of source colonies in the landscape rather than mixing freely across long distances. These findings have implications for understanding gene flow dynamics and population genetic structure in Africanized honeybee populations that have spread across South and North America since their introduction.
This conceptual review argues for the centrality of complex network theory to systems biology, surveying key network analysis methods — including degree distribution analysis, clustering coefficients, path length analysis, and community detection — and their applications across scales from molecular interaction networks to ecological and social systems. The authors demonstrate how network-based approaches capture emergent properties of biological systems that reductionist analyses of individual components cannot, establishing a framework for the network analysis approaches the lab would subsequently apply to neuropsychiatric and cancer biology.
A rigorous systematic evaluation of candidate reference genes for RT-qPCR normalisation across multiple honeybee tissues, developmental stages, and experimental treatments identified the most stable reference genes for accurate and reproducible gene expression quantification in honeybee research. This methodological contribution established standardised normalisation practices essential for the field and is widely cited by researchers conducting gene expression studies in Apis mellifera, demonstrating the importance of validation studies for ensuring data quality in molecular biology.
Comparative transcriptomic analysis of queen- and worker-destined larvae across the critical nutritional determination window identified the genes and pathways differentially regulated during caste fate specification, revealing that nutritional input (royal jelly) rapidly activates insulin/TOR signalling, epigenetic machinery, and downstream transcription factor networks that irreversibly commit larvae to the queen developmental programme. This study was among the first genome-scale characterisations of the molecular events driving the spectacular phenotypic plasticity of honeybee caste determination, generating hypotheses that remain central to the field.
The sequencing, assembly, and annotation of the complete honeybee genome — the first social insect genome sequenced — revealed a genome marked by expansions in olfactory receptor and gustatory receptor gene families, a reduced immune gene repertoire relative to Drosophila, unique rates of evolution at specific gene families, and genomic features related to learning, memory, and the molecular basis of social behaviour. This landmark paper laid the entire genomic foundation for modern honeybee and social insect biology and is one of the most influential papers in insect genomics.
A genome-wide analysis exploiting the newly released honeybee genome identified and characterised gene sets associated with the evolutionary hallmarks of eusociality — caste determination, reproductive division of labour, and worker altruism — providing early insights into the genomic architecture that underlies social insect organisation. By comparing honeybee social biology-associated gene sets to solitary insect genomes, the study identified candidate molecular innovations that may have enabled the evolution of eusociality in the bee lineage.
Comparative genomic analysis of sex determination genes between the honeybee and Drosophila revealed that while the upstream regulatory pathway controlling sex determination has diverged substantially — with honeybees using a complementary sex determiner (csd) mechanism absent in Drosophila — key downstream effector genes including doublesex show deep conservation in sequence and function across hundreds of millions of years of insect evolution. These findings illuminate the evolutionary dynamics by which sex determination pathways can simultaneously maintain essential downstream outputs while dramatically reorganising upstream regulatory mechanisms.