Biology subjects

Tsaneva-Atanasova, K.

Publications and source records attributed to Tsaneva-Atanasova, K..

At least 19 recordsLinked to original sources

bioRxiv2026

Cellular heterogeneity in the response of Burkholderia thailandensis to antibiotics and phages in synthetic spatial refuges

Understanding the complex interactions between phage, antibiotics and bacteria is vital for the development of rationale phage-antibiotic therapies. These interactions have traditionally been investigated via bulk assays, thus masking eventual cellular heterogeneities and the impact of spatial refuges on phage and antibiotic efficacy. Using microfluidics-based time-lapse microscopy, we reveal large phenotypic heterogeneity in the response of Burkholderia thailandensis to both the bacteriophage {Phi}Bp-AMP1 and sub-inhibitory concentrations of two selected antibiotics ciprofloxacin and trimethoprim. We discover that simultaneous exposure to ciprofloxacin and phage decreases the size of individual B. thailandensis cells, whereas phage and trimethoprim together slow down cell doubling. Exposure to ciprofloxacin also causes extended phage lysis of B. thailandensis which is preceded by a distinguishable pause in cell elongation, whereas exposure to trimethoprim constrains lysis. As a consequence, exposure to ciprofloxacin further hinders the growth of B. thailandensis in the presence of phage, whereas exposure to trimethoprim enhances growth in the presence of phage. These findings help understand the effects of the interactions between antibiotics and phage on bacterial subpopulations in spatial refuges that are notoriously difficult to treat with antibiotics.

microbiology↗

bioRxiv2026

Conserved circadian membrane rhythms arise from divergent cellular mechanisms in pacemaker neurons of mice and Drosophila

Circadian clocks align physiology and behaviour with daily environmental cycles, requiring neuronal networks that reliably encode and transmit time-of-day information. A fundamental yet unresolved question is how membrane properties support this function and whether conserved principles arise across evolutionarily distant organisms. We compared the intrinsic electrophysiological properties of identified circadian neurons from a nocturnal mammal (mouse, Mus musculus SCN VIP neurons) and a diurnal insect (fly, Drosophila melanogaster l-LNv PDF neurons) across the 24-h light-dark cycle. Despite [~]700 million years of evolutionary divergence and opposite temporal niches, we found neurons from both species exhibited similar rhythmic patterns in key parameters for encoding time-of-day, including resting membrane potential, spontaneous firing rate and cell capacitance, indicating convergent strategies for generating daily variation in excitability despite dramatically different network scales ([~]2200 VIPs vs. 8 l-LNvs). These shared outputs arose through distinct mechanisms: flies exhibited higher input resistance, greater excitability and relatively larger A-type potassium currents, while mice displayed larger sustained outward currents and post-inhibitory rebound excitation, absent in flies. Rheobase troughs occurred during the inactive phase in both species, while other parameters did not cycle. These differences likely shape how each neuronal type integrates salient inputs, consistent with their respective roles in processing sustained daytime light (flies) versus nocturnal cues (mice). Our findings reveal conserved functional goals but divergent electrophysiological strategies in circadian neurons, reflecting evolutionary adaptation to species-specific environmental demands. Such neurophysiological diversity highlights how evolution shapes cellular mechanisms to meet the requirements of temporal niche while preserving robust circadian timekeeping.

neuroscience↗

bioRxiv2026

How simple physics drives the earliest stages of embryogenesis

The initial stages of mammalian embryo development involve a single fertilised egg that repeatedly divides to create a solid ball of cells called a morula. Despite the apparent simplicity of this process, which involves only one cell type and a few tens of cells, there are still a host of unanswered questions, particularly around the underlying biophysical mechanisms that are at play. To address this, we here develop a novel type of vertex model that includes cortical tension, cell-to-cell adhesion, membrane curvature and cell volume forces, along with a zona pellucida, cell division and the effect of noise. We fit our model to both mouse and human experimental data, which allows us to address a number of key questions including the relative roles of adhesion and tension, how the cortical tension varies around the cell, the purpose of the zona pellucida, and the rules governing the first few cell divisions. We also determine the biophysical effects responsible for compaction and internalisation, including addressing why the morula does not typically decompact during internalisation. Next, we investigate the position-versus-polarisation debate during trophectoderm differentiation, how the division axis is determined during later divisions, and the role of noise. Finally, we compare human and mouse, focussing on the key similarities that may span all mammals. Our use of a force-based computational model allows us to address fundamental questions relating to mammalian development, particularly the underlying biophysical rules governing early embryogenesis, with important applications to stem cell models such as blastoids, conservation efforts of endangered species and embryo grading during IVF. Significance StatementThe very first stages of embryogenesis are a vital but still poorly understood part of development, with important applications to fertility, fertility lifespan and assisted conception such as IVF. Most research in this area has focussed on experimental approaches, ignoring the potential for biophysical modelling. Here, we address this by developing a novel computer simulation of the first thee-to-four cell divisions of the fertilised egg, resulting in a compact bunch of cells called a morula. In particular, we develop a new type of vertex model for the early embryo that for the first time includes contributions from a range of realistic biophysical forces. By analysing real mouse and human embryo data through our model, we reveal how simple physics drives crucial early developmental processes, including compaction, internalisation, cleavage, noise and species-specific differences.

developmental biology↗

bioRxiv2026

Integrating Models to Decode the GnRH Pulse Generator

The gonadotrophin-releasing hormone (GnRH) pulse generator is a critical neural oscillator that governs reproductive function through the pulsatile release of luteinising hormone (LH) and follicle stimulating hormone (FSH). Early electrophysiological studies, notably by Ernst Knobil, identified multiunit activity (MUA) volleys in the mediobasal hypothalamus that aligned with LH pulses, suggesting a neural basis for GnRH pulsatility. Although GnRH neurons exhibit some intrinsic secretory rhythmicity in vitro, their isolated electrophysiological signatures have proven inconsistent. Recent advances, including GCaMP fibre photometry in freely behaving mice, have revealed a precise correlation between episodic GnRH distal processes and LH pulses. However, it is now well established that a neural oscillator comprising hypothalamic kisspeptin neurones co-expressing neurokinin B and dynorphin, collectively termed the KNDy network, represents the core construct of the GnRH pulse generator. Understanding the dynamics of this network and its modulation by external inputs such as stress, metabolic cues, and circadian rhythms is essential. Computational modelling provides a systematic framework for integrating experimental data with mechanistic and predictive analyses to decode the GnRH pulse generator dynamics.

physiology↗

bioRxiv2025

PhyloAug: An Evolutionary and Structure-Aware Data Augmentation Tool

Genomic Language Models (GLMs) suffer from the inherent problem of data scarcity, due to the cost, time and complexity of wet-lab experiments. Data augmentation offers a solution; however traditional methods may unintentionally affect the underlying structure or function. By combining evolutionary signals with the RNA secondary structure, augmentations can retain original function, and remain structurally coherent. To implement this, we developed PhyloAug, a structure-aware, evolution-inspired augmentation method grounded in neutral theory. We employ Genomic Foundation Models (GFMs) to accurately perturb RNA sequences, and utilise phylogenetic analysis via PAML to provide site-wise restrictions based on evolutionary principles. These principles are obtained through the identification of evolutionarily neutral sites (sequence positions where mutations are unlikely to alter function), which are concatenated with the predicted (or known) secondary structure. We thereby ensure adherence to the underlying structure whilst enabling biologically plausible variation. To validate the biological validity of our augmentations, we compare our predicted neutral sites with Rfam-annotated conserved regions and assess sequence similarity to the underlying multiple sequence alignments. We next fine-tune GLMs on augmented data, yielding significant performance improvements up to 12.9% MCC, and 17.2% F1-Score.

bioinformatics↗

bioRxiv2025

A mechanistically-inspired geometric model to predict microbial growth across environments

Estimating bacterial growth trajectories is essential for bridging mechanistic insights and experimental data. Nevertheless, widely used empirical models tend to be overly simplistic or purely phenomenological. Mechanistic models offer greater detail but still fall short of representing the full spectrum of biochemical processes underlying cellular growth. Here we take a mean-field approach whereby we consider the bacterial cell population as a cascading sequence of biochemical processes. This approach enables the derivation of a geometry-based model of cellular population growth that captures the lag, exponential, and stationary phases observed experimentally, without requiring assumptions about specific cellular mechanisms. Furthermore, parameters estimated from multiple datasets can provide insights into the populations history of cellular stress. We demonstrate the robustness and accuracy of the proposed modelling framework by applying it to existing experimental data for S. aureus and P. aeruginosa grown in closed and open environments. We show that our approach achieves higher accuracy compared to contemporary models.

biophysics↗

bioRxiv2025

Competition with Pseudomonas aeruginosa induces Staphylococcus aureus in an antibiotic-tolerant viable but non culturable state

Interactions between different species of pathogenic microbes often affect clinical outcome by altering the virulence or antibiotic resistance of individual microbes. By investigating the interactions between Staphylococcus aureus and Pseudomonas aeruginosa at the population, single-cell and molecular level we discovered that a sub-population of S. aureus enters in a viable non-culturable state that it is not detected via standard microbiology assays. In the presence of P. aeruginosa, S. aureus adopts a survival lifestyle similar to previously described intracellular S. aureus persisters, downregulating nitrogen metabolism and amino acid biosynthesis, while upregulating protein maturation processes. Entrance in a viable but non culturable state is the primary survival strategy of S. aureus in response to vancomycin treatment, whereas only a minority of the S. aureus population survive ciprofloxacin treatment while in a viable but non culturable state. These bacterial interactions may shape the evolution of resistance traits of co-infecting pathogens. Manipulating these interspecies adaptations could provide new opportunities for early therapeutic interventions.

microbiology↗

bioRxiv2025

Amygdala GABA Neurons: Gatekeepers of Stress and Reproduction

Stress can disrupt menstrual cycles, cause infertility, and lead to other reproductive disorders. The posterodorsal medial amygdala (MePD) processes stress signals and regulates the gonadotropin-releasing hormone (GnRH) pulse generator through GABAergic inhibitory projections to the hypothalamus. However, how stress is processed in the MePD - especially involving its dense GABA and Urocortin-3 (UCN3) neurons - remains poorly understood. In this study, we combine in vivo GRadient-INdex (GRIN) lens mini-endoscopic calcium imaging (to track neuronal activity), optogenetics, clustering analysis, and computational modeling to investigate the MePD circuitry. Our findings reveal two anti-correlated GABA subpopulations in the MePD that dictate responses to both UCN3 neuron stimulation and restraint stress. Our computational modeling suggests that mutual inhibition between these GABA groups drives the anti-correlated activity and predicts how these interactions shape downstream responses to stimulation of GABA and UCN3 neurons. We test these predictions using optogenetics and confirm that GABA neurons are critical for the transmission of UCN3 signals to regulate luteinizing hormone (LH) pulse frequency. Our study is the first to show how GABA neurons in the amygdala mediate stress effects on reproductive health, uncovering key neural mechanisms linking emotional and reproductive functions.

physiology↗

bioRxiv2024

Antibiotic resistant bacteria survive treatment by doubling while shrinking

Many antibiotics that are used in healthcare, farming and aquaculture end up in environments with different spatial structures that might promote heterogeneity in the emergence of antibiotic resistance. However, experimental evolution of microbes at sub-inhibitory concentrations of antibiotics has been mainly carried out at the population level which does not allow capturing heterogeneity within bacterial populations. Here we investigate and compare the emergence of resistance to ciprofloxacin in Escherichia coli in well mixed and structured environments using experimental evolution, genomics and microfluidics-based time-lapse microscopy. We discover that resistance to ciprofloxacin and cross-resistance to other antibiotics is stronger in the well-mixed environment due to the emergence of target mutations, whereas efflux regulator mutations emerge in the structured environment. The latter mutants also harbour sub-populations of persisters that survive high concentrations of ciprofloxacin that inhibit bacterial growth at the population level. In contrast, genetically resistant bacteria that display target mutations also survive high concentrations of ciprofloxacin that inhibit their growth via population-level antibiotic tolerance. These resistant and tolerant bacteria keep doubling while shrinking in size in the presence of ciprofloxacin and regain their original size after antibiotic removal, which constitutes a newly discovered phenotypic response. This new knowledge sheds light on the diversity of strategies employed by bacteria to survive antibiotics and poses a stepping stone for understanding the link between mutations at the population level and phenotypic single-cell responses.

microbiology↗

bioRxiv2024

Heterogeneous efflux pump expression underpins phenotypic resistance to antimicrobial peptides

Antimicrobial resistance threatens the viability of modern medical interventions. There is a dire need of developing novel approaches to counter resistance mechanisms employed by starved or slow-growing pathogens that are refractory to conventional antimicrobial therapies. Antimicrobial peptides have been advocated as potential therapeutic solutions due to low levels of genetic resistance observed in bacteria against these compounds. However, here we show that subpopulations of stationary phase Escherichia coli and Pseudomonas aeruginosa survive tachyplesin treatment without genetic mutations. These phenotypic variants display enhanced efflux activity to limit intracellular peptide accumulation. Differential regulation of genes involved in outer membrane vesicle section, membrane modification, and protease activity were also found between phenotypically resistant and susceptible cells. We discovered that formation of these phenotypic variants could be prevented by administering tachyplesin in combination with sertraline, a clinically used antidepressant, suggesting a novel approach for combatting antimicrobial-refractory stationary phase bacteria.

microbiology↗

bioRxiv2024

Estradiol elicits distinct firing patterns in arcuate nucleus kisspeptin neurons of females through altering ion channel conductances

Hypothalamic kisspeptin (Kiss1) neurons are vital for pubertal development and reproduction. Arcuate nucleus Kiss1 (Kiss1ARH) neurons are responsible for the pulsatile release of Gonadotropin-releasing Hormone (GnRH). In females, the behavior of Kiss1ARH neurons, expressing Kiss1, Neurokinin B (NKB), and Dynorphin (Dyn), varies throughout the ovarian cycle. Studies indicate that 17{beta}-estradiol (E2) reduces peptide expression but increases Vglut2 mRNA and glutamate neurotransmission in these neurons, suggesting a shift from peptidergic to glutamatergic signaling. To investigate this shift, we combined transcriptomics, electrophysiology, and mathematical modeling. Our results demonstrate that E2 treatment upregulates the mRNA expression of voltage-activated calcium channels, elevating the whole-cell calcium current and that contribute to high-frequency burst firing. Additionally, E2 treatment decreased the mRNA levels of Canonical Transient Receptor Potential (TPRC) 5 and G protein-coupled K+ (GIRK) channels. When TRPC5 channels in Kiss1ARH neurons were deleted using CRISPR, the slow excitatory postsynaptic potential (sEPSP) was eliminated. Our data enabled us to formulate a biophysically realistic mathematical model of the Kiss1ARH neuron, suggesting that E2 modifies ionic conductances in Kiss1ARH neurons, enabling the transition from high frequency synchronous firing through NKB-driven activation of TRPC5 channels to a short bursting mode facilitating glutamate release. In a low E2 milieu, synchronous firing of Kiss1ARH neurons drives pulsatile release of GnRH, while the transition to burst firing with high, preovulatory levels of E2 would facilitate the GnRH surge through its glutamatergic synaptic connection to preoptic Kiss1 neurons.

neuroscience↗

bioRxiv2024

Neuronal Network Dynamics in the Posterodorsal Amygdala: Shaping Reproductive Hormone Pulsatility

Normal reproductive function and fertility rely on the rhythmic secretion of gonadotropin-releasing hormone (GnRH), which is driven by the hypothalamic GnRH pulse generator. A key regulator of the GnRH pulse generator is the posterodorsal subnucleus of the medial amygdala (MePD), a brain region which is involved in processing external environmental cues, including the effect of stress. However, the neuronal pathways enabling the dynamic, stress-triggered modulation of GnRH secretion remain largely unknown. Here, we employ in-silico modelling in order to explore the impact of dynamic inputs on GnRH pulse generator activity. We introduce and analyse a mathematical model representing MePD neuronal circuits composed of GABAergic and glutamatergic neuronal populations, integrating it with our GnRH pulse generator model. Our analysis dissects the influence of excitatory and inhibitory MePD projections outputs on the GnRH pulse generators activity and reveals a functionally relevant MePD glutamatergic projection to the GnRH pulse generator, which we probe with in vivo optogenetics. Our study sheds light on how MePD neuronal dynamics affect the GnRH pulse generator activity, and offers insights into stress-related dysregulation.

neuroscience↗

bioRxiv2023

Phage-induced efflux down-regulation boosts antibiotic efficacy

The interactions between a virus and its host vary in space and time and are affected by the presence of molecules that alter the physiology of either the host or the virus. Determining the molecular mechanisms underpinning these interactions is paramount for predicting the fate of bacterial and phage populations and for designing rational phage-antibiotic therapies. We study the interactions between stationary phase Burkholderia thailandensis and the phage {Phi}Bp-AMP1. Although heterogeneous genetic resistance to phage rapidly emerges in B. thailandensis, the presence of phage enhances the efficacy of three major antibiotic classes, the quinolones, the beta-lactams and the tetracyclines, but antagonizes tetrahydrofolate synthesis inhibitors. We discovered that enhanced antibiotic efficacy is underpinned by reduced antibiotic efflux in the presence of phage. This new phage-antibiotic therapy allows for eradication of stationary phase bacteria, whilst requiring reduced antibiotic concentrations, which is crucial for treating infections in sites where it is difficult to achieve high antibiotic concentrations.

microbiology↗

bioRxiv2022

Noradrenergic cross-modular reciprocal inhibition within the Locus Coeruleus.

The Locus Coeruleus (LC) is the primary noradrenergic nucleus in the brain with widespread projections driving changes in cognitive state and animal behaviour. The LC is composed of multiple "modules" with specific efferent target domains enabling discretional neuromodulation. LC neuronal activity releases noradrenaline within the nucleus as a local feedback mechanism, but it is not known how this influences modular output. We address this question using whole-cell recordings and calcium imaging in rat pontine slices in combination with LC neuronal ensemble modelling to assess the influence of local noradrenaline release on cross-modular interactions. Electrophysiological recordings of LC neurons from rats transduced with the optogenetic actuator ChR2 showed auto-inhibition and lateral inhibition (of surrounding non-transduced neurons). This inhibition was strongly frequency dependent and was mediated by noradrenaline acting on alpha2-adrenceptors (2R). To allow calcium-imaging of LC neuronal ensembles a Canine-Adenoviral vector strategy was developed using the PRS promoter to drive selective expression GCaMP6s. Calcium imaging allowed resolution of both increases and decreases in LC activity (to TTX / clonidine or high potassium). Selective chemogenetic-activation of subsets of LC neurons (expressing the ionotropic actuator PSAM) revealed both a direct excitation (after application of PSEM308, 3-30{micro}M) and an 2R-mediated inhibition of neighbouring LC cells (non-transduced). Differential retrograde targeting of PSAM or GCaMP6s to specific LC modules showed the presence of strong, reciprocal cross-modular inhibition (shown for the LC-olfactory bulb vs LC bulbospinal modules) and a subsequent rebound activity inversion. This represents a preferential, targeted, cross-modular, lateral inhibition within the LC rather than a non-specific surround inhibition. Computational modelling showed the emergence of lateral inhibition and biphasic responses to modular activation when 2R signalling and noradrenergic reuptake saturation were included. This interaction may facilitate recruitment of neuronal ensembles by coherent inputs and represents a bottom-up differential contrast-enhancement mechanism within the LC to produce a modality specific focus.

neuroscience↗

bioRxiv2021

Fast bacterial growth reduces antibiotic accumulation and efficacy

Phenotypic variations between individual microbial cells play a key role in the resistance of microbial pathogens to pharmacotherapies. Nevertheless, little is known about cell individuality in antibiotic accumulation. Here we hypothesize that phenotypic diversification can be driven by fundamental cell-to-cell differences in drug transport rates. To test this hypothesis, we employed microfluidics-based single-cell microscopy, libraries of fluorescent antibiotic probes and mathematical modelling. This approach allowed us to rapidly identify phenotypic variants that avoid antibiotic accumulation within populations of Escherichia coli, Pseudomonas aeruginosa, Burkholderia cenocepacia and Staphylococcus aureus. Crucially, we found that fast growing phenotypic variants avoid macrolide accumulation and survive treatment without genetic mutations. These findings are in contrast with the current consensus that cellular dormancy and slow metabolism underlie bacterial survival to antibiotics. Our results also show that fast growing variants display significantly higher expression of ribosomal promoters before drug treatment compared to slow growing variants. Drug-free active ribosomes facilitate essential cellular processes in these fast growing variants, including efflux that can reduce macrolide accumulation. Using this new knowledge, we phenotypically engineered bacterial populations by eradicating variants that displayed low antibiotic accumulation through the chemical manipulation of their outer membrane inspiring new avenues to overcome current antibiotic treatment failures.

microbiology↗

bioRxiv2021

Modulation of pulsatile GnRH dynamics across the ovarian cycle: the role of excitability within the arcuate kisspeptin network

Pulsatile GnRH release is essential for normal reproductive function. Kisspeptin secreting neurons found in the arcuate nucleus, known as KNDy neurons for co-expressing neurokinin B, and dynorphin, drive pulsatile GnRH release. Furthermore, gonadal steroids regulate GnRH pulsatile dynamics across the ovarian cycle by altering KNDy neurons signalling properties. However, the precise mechanism of regulation remains mostly unknown. To better understand these mechanisms we start by perturbing the KNDy system at different stages of the estrous cycle using optogenetics. We find that optogenetic stimulation of KNDy neurons stimulates pulsatile GnRH/LH secretion in estrous mice but inhibits it in diestrous mice. These in-vivo results in combination with mathematical modelling suggest that the transition between estrus and diestrus is underpinned by well-orchestrated changes in neuropeptide signalling and in the excitability of the KNDy population controlled via glutamate signalling. Guided by model predictions, we show that blocking glutamate signalling in diestrous animals inhibits LH pulses, and that optic stimulation of the KNDy population mitigates this inhibition. In estrous mice, disruption of glutamate signalling inhibits pulses generated via sustained low-frequency optic stimulation of the KNDy population, supporting the idea that the level of network excitability is critical for pulse generation. Our results reconcile previous puzzling findings regarding the estradiol-dependent effect that several neuromodulators have on the GnRH pulse generator dynamics. Therefore, we anticipate our model to be a cornerstone for a more quantitative understanding of the pathways via which gonadal steroids regulate GnRH pulse generator dynamics. Finally, our results could inform useful repurposing of drugs targeting the glutamate system in reproductive therapy.

neuroscience↗

bioRxiv2020

Dynamic hormone control of stress and fertility

Neuroendocrine axes display a remarkable diversity of dynamic signalling processes relaying information between the brain, endocrine glands, and peripheral target tissues. These dynamic processes include oscillations, elastic responses to perturbations, and plastic long term changes observed from the cellular to the systems level. While small transient dynamic changes can be considered physiological, larger and longer disruptions are common in pathological scenarios involving more than one neuroendocrine axes, suggesting that a robust control of hormone dynamics would require the coordination of multiple neuroendocrine clocks. The idea of apparently different axes being in fact exquisitely intertwined through neuroendocrine signals can be investigated in the regulation of stress and fertility. The stress response and the reproductive cycle are controlled by the Hypothalamic-Pituitary-Adrenal (HPA) axis and the Hypothalamic-Pituitary-Gonadal (HPG) axis, respectively. Despite the evidence surrounding the effects of stress on fertility, as well as of the reproductive cycle on stress hormone dynamics, there is a limited understanding on how perturbations in one neuroendocrine axis propagate to the other. We hypothesize that the links between stress and fertility can be better understood by considering the HPA and HPG axes as coupled systems. In this manuscript, we investigate neuroendocrine rhythms associated to the stress response and reproduction by mathematically modelling the HPA and HPG axes as a network of interlocked oscillators. We postulate a network architecture based on physiological data and use the model to predict responses to stress perturbations under different hormonal contexts: normal physiological, gonadectomy, hormone replacement with estradiol or corticosterone (CORT), and high excess CORT (hiCORT) similar to hypercortisolism in humans. We validate our model predictions against experiments in rodents, and show how the dynamic responses of these endocrine axes are consistent with our postulated network architecture. Importantly, our model also predicts the conditions that ensure robustness of fertility to stress perturbations, and how chronodisruptions in glucocorticoid hormones can affect the reproductive axis ability to withstand stress. This insight is key to understand how chronodisruption leads to disease, and to design interventions to restore normal rhythmicity and health.

systems biology↗

bioRxiv2020

scReQTL: an approach to correlate SNVs to gene expression from individual scRNA-seq datasets

Recently, pioneering eQTLs studies on single cell RNA-seq (scRNA-seq) data have revealed new and cell-specific regulatory SNVs. Because eQTLs correlate genotypes and gene expression across multiple individuals, they are confined to SNVs with sufficient population frequency. Here, we present an alternative sc-eQTL approach - scReQTL - wherein we substitute the genotypes with expressed Variant Allele Fraction (VAFRNA) at heterozygous SNV sites. Our approach employs the advantage that, when estimated from multiple cells, VAFRNA can be used to assess effects of rare SNVs in a single individual. ScReQTLs are enriched in known genetic interactions, therefore can be used to identify novel regulatory SNVs.

genomics↗