Biology subjects

Liu, B.

Publications and source records attributed to Liu, B..

At least 19 recordsLinked to original sources

bioRxiv2026

Ratio-preserving super-resolution FLIM for quantitative live-cell lifetime imaging

Super-resolution (SR) fluorescence lifetime imaging promises nanoscale maps of molecular environment and function, but photon-limited acquisition and computational reconstruction can distort lifetime estimates, particularly for ratio-derived frequency-domain measurements under SR conditions. Here we introduce structured-illumination frequency-domain FLIM (SIM-fdFLIM), an SR lifetime imaging platform that combines commercial dual-tap fdFLIM detection with ratio-preserving reconstruction. SIM-fdFLIM uses direct-current (DC)-stabilized lifetime estimation to improve reconstruction robustness under low signal-to-noise conditions, followed by ratio-domain integrated variational estimation (RIVE) to correct channel misregistration and suppress noise amplification after SR reconstruction. The method achieves ~100 nm spatial resolution in lifetime maps and enables live-cell imaging at 2.8 Hz over a 56 x 56 {micro}m2 field of view. Across representative fluorophore standards, RIVE reduces lifetime standard deviation by approximately threefold relative to non-RIVE SIM-fdFLIM while preserving mean lifetime agreement with calibrated widefield fdFLIM. In living cells, SIM-fdFLIM resolves mitochondrial cristae-scale lifetime heterogeneity, mitochondrion-to-mitochondrion functional dynamics, nanoscale lipid-environment variations and perturbation-sensitive organelle-contact signatures. These results establish SIM-fdFLIM as a ratio-preserving platform for quantitative SR lifetime imaging, extending live-cell FLIM into a regime that combines nanoscale spatial resolution, Hz-rate acquisition, and preserved lifetime fidelity.

bioengineering↗

bioRxiv2026

Heat-dependent engagement of a buried mitophagy motif in prohibitin 2

Mitophagy receptors are generally switched on by upstream enzymes rather than by the receptor itself. Whether a receptor can instead respond directly to a physical stimulus has not been established. Here we show that a second LC3-interacting region (LIR) in prohibitin 2 (PHB2) is regulated by temperature. It lies in a marginally stable helix that holds its two anchor residues about 5 angstrom apart, whereas a bound LIR spans about 9 angstrom. Replica-scaling simulations showed that this helix, but not a matched control from the same protein under identical scaling, samples that geometry; purified PHB2 bound ATG8-family proteins only at 313 K and above. Substitutions designed from this geometry to stabilise (K253A/R255A) or destabilise (I254G) the helix altered binding, mitochondrial recruitment and respiration in PHB2-null cardiomyocytes. Mice carrying the stabilising substitutions in cardiomyocytes sustained greater cardiac injury during heat stroke despite matched thermal load and comparable systemic injury. Motif accessibility may therefore be a regulated variable rather than a fixed property of a fold.

molecular biology↗

bioRxiv2026

Acetylation of NDUFA13 at K7 Senses OXPHOS Dysfunction to Disrupt Prohibitin Scaffolds and Drive Cristae Remodelling in Heart Failure

Mitochondrial cristae disintegration is a hallmark of heart failure, yet how oxidative phosphorylation (OXPHOS) dysfunction triggers this structural collapse remains unclear. Here we identify acetylation of the complex I subunit NDUFA13 at lysine 7 (K7) as a metabolic sensor coupling OXPHOS dysfunction to cristae remodelling. OXPHOS inhibition drove NDUFA13-K7 hyperacetylation, inducing conformational compaction and translocation to the intermembrane space. Acetylated NDUFA13 competitively engaged PHB2 through its coiled-coil domain, displacing PHB1 and disassembling prohibitin scaffolds. The acetylation-mimetic NDUFA13-K7Q induced cristae fragmentation in vitro, and cardiomyocyte-specific K7Q knock-in mice showed accelerated mortality and cristae loss under pressure overload, accompanied by impaired TCA cycle flux, defective fatty acid oxidation and selective depletion of polyunsaturated cardiolipins. These findings establish NDUFA13-K7 acetylation as a reversible switch converting bioenergetic failure into pathological cristae remodelling and metabolic reprogramming, highlighting therapeutic potential for targeted deacetylation.

cell biology↗

bioRxiv2026

Neuronal Hyperactivity Induces Tau Phosphorylation Selectively in Excitatory Pyramidal Neurons Which Contributes to GluA2 Regulation

While tau plays a role in regulating neuronal network excitability, a process thought to be dysregulated in Alzheimers disease (AD), the molecular mechanisms linking tau and hyperexcitability remain unclear. To investigate interactions between endogenous tau and neuronal activity, we increased neuronal activity using bicuculline or suppressed activity using tetrodotoxin for 24 hours in rat hippocampal neurons. Chronic neuronal hyperactivity increased dendritic tau phosphorylation at S202/T205. This response was observed only in excitatory CA1 and CA3 pyramidal neurons, but not in inhibitory or dentate granule neurons. Dendritic phospho-tau positively correlated with neuronal activation after bicuculline treatment, as measured by cfos expression, and was prevented with inhibition of protein kinase A (PKA). To examine the functional consequences of tau S202/T205 phosphorylation, hippocampal neurons were transfected with wild-type tau or tau containing mutations preventing phosphorylation at these sites. Wildtype tau overexpression increased tau phosphorylation and reduced neuronal surface GluA2, which was prevented by phospho-site mutation. Extending these findings to mice, chronic low-dose picrotoxin treatment increased endogenous S202/T205 tau phosphorylation in CA3 neurons. In picrotoxin-treated mice, cfos expression was associated with increased tau phosphorylation specifically in CA3 and CA1 neurons. Together, these findings identify activity-dependent, endogenous tau phosphorylation as a selective response to hyperexcitation in excitatory hippocampal neurons downstream of PKA activation. The data further link tau phosphorylation to altered GluA2 regulation, suggesting a potential molecular connection between neuronal hyperactivity, tau phosphorylation, and synaptic dysfunction relevant to AD.

neuroscience↗

bioRxiv2026

Function-preserving CD8⁺ T Cell Immunogenicity minimization through protein design

Rapid advances in protein design enable new approaches in adoptive cell therapy, but foreign proteins can elicit cytotoxic T cell responses, and hence there is considerable need for approaches which reduce immunogenicity without compromising protein function. Here, we develop a computational framework integrating structure-guided sequence design with MHC class I epitope prediction to efficiently tune protein immunogenicity while preserving function. Using a de novo-designed luciferase as a model, we demonstrate epitope elimination while preserving function across 5 common mouse alleles and extend our computational optimization to 25 common human MHC-I alleles. In mice immunized with mRNA-lipid nanoparticles, variants designed to have few MHC-I epitopes elicited little detectable CD8 T cell response, whereas variants designed to include multiple epitopes induced robust responses. Together, these results demonstrate that the CD8 T cell immunogenicity of designed proteins can be tuned while preserving function, opening the door to incorporation of designed proteins in a next generation of adoptive cell therapies.

bioengineering↗

bioRxiv2026

Charting sex divergence in the human brain across the lifespan

Biological sex fundamentally shapes human brain organization, but sex-specific normative neuroanatomical trajectories across the lifespan remain largely uncharted. Here, we constructed independent, sex-specific lifespan brain charts using structural neuroimaging data from 59,915 healthy individuals (29,760 males and 30,155 females) ranging in age from 266 postconception days to 100 years. By examining 296 structural phenotypes across global, cortical, and subcortical measures, these models revealed widespread sex differences in maturational timing, with males reaching peak milestones later than females. These trajectories demonstrate that sex differences evolve dynamically, with phenotype-specific windows of emergence and maximal separation. Compared with conventional sex-pooled references, sex-specific models achieved superior predictive accuracy and reduced misestimation of individual deviations in healthy populations. Across five neuropsychiatric conditions, sex-specific models improved the detection of extreme deviations and revealed both shared and sex-dependent patterns of disorder-related neuroanatomical abnormalities. These sex-specific charts establish tailored normative references for assessing brain development, ageing, and disease.

neuroscience↗

bioRxiv2026

Reduced emerin expression marks gastric cancer progression and invasive nuclear remodeling

Altered nuclear morphology is a defining diagnostic feature of malignancy, and nuclear structure is increasingly recognized as a functional regulator of cancer cell invasion. The inner nuclear membrane protein emerin maintains nuclear architecture and restrains invasive phenotypes in breast cancer models, but whether emerin expression is similarly altered in gastric cancer has not been established. Here, we analyzed emerin protein expression, nuclear morphology, and impeded migration in nonmalignant and malignant gastric cell lines. In parallel, emerin protein expression and nuclear envelope localization across gastric cancer was determined using patient tissue microarrays. Emerin was abundant at the nuclear envelope in cancer-adjacent and noncancerous gastric epithelium but was reduced across multiple gastric cancer histologies, including adenocarcinoma, signet-ring cell carcinoma, mucinous adenocarcinoma, neuroendocrine carcinoma, squamous cell carcinoma, and metastatic lesions. Reduced emerin at the nuclear envelope was most strongly associated with higher-grade tumors, with grade 2 and grade 3 cancers exhibiting significantly lower nuclear envelope scores than noncancerous tissue and grade 1 tumors. Consistent with the patient tissue data, the gastric cancer cell lines AGS and MKN1 expressed less emerin protein than noncancerous gastric epithelial control cells HFE-145. Consistent with studies in breast cancer cells, gastric cells with reduced emerin expression also had smaller nuclei and increased impeded migration through 8 micron pores. These findings support a model in which reduced nuclear envelope emerin is a conserved feature of invasive epithelial tumor progression and a candidate biomarker of gastric cancer nuclear remodeling.

cancer biology↗

bioRxiv2026

Human single-neuron correlates of somatosensation

Understanding the neural correlates of consciousness poses a central challenge in neuroscience, with longstanding debate over which cortical areas underlie subjective sensory perception. In the tactile domain, posterior parietal cortex (PPC) and primary somatosensory cortex (S1) are candidate cortical substrates for neural correlates of consciousness due to their crucial roles in somatosensory processing. Yet whether and how these regions contribute to conscious tactile perception remains unclear. Here, to address this issue, we leveraged chronic intracortical recordings to simultaneously monitor large ensembles of single neurons in grasp related cortical areas from three participants with tetraplegia while natural vibrotactile stimuli were delivered to a sensate region of the upper limb. We demonstrate that an orchestration of neural activity emerged across the grasp-related parietal-frontal network at near-threshold perception. Within this distributed network, we then focused on PPC and S1. While S1 responses closely tracked the amplitude of the physical stimulus, PPC activity covaried more strongly with awareness and confidence. This single-neuron evidence reveals PPC and S1 have complementary neural codes with PPC transforming physical stimulation into conscious perception whereas S1 is more sensitive to stimulus amplitude.

neuroscience↗

bioRxiv2026

DEPICT enables sample-centric therapeutic prioritization across evolving and spatially heterogeneous tumor states

Accurate treatment selection remains a major challenge in precision oncology because tumors with similar genomic alterations can respond differently to therapy. Most drug-response models evaluate individual drugs or drug-sample pairs, whereas clinical decision-making requires therapies to be prioritized within each tumor context. Here we present DEPICT (Drug Efficacy Prediction via Integrated ConText), a sample-centric deep learning framework that reframes drug-response prediction as the relative prioritization of therapies within an individual tumor context. DEPICT integrates transcriptomic and mutational features with prior alteration-therapy relationship and was trained on 231,880 cell line-drug pairs comprising 941 cancer cell lines and 289 compounds. Without retraining, DEPICT retained predictive performance in independently profiled cell lines, experimentally induced drug-resistant states and matched primary lung tumors and patient-derived organoids. Representations learned exclusively from bulk pharmacogenomic data further captured progressive drug-response states at single-cell resolution and outperformed existing single-cell drug-response inference methods. Applied to spatial transcriptomic data, DEPICT resolved clone-associated therapeutic heterogeneity within individual lung tumors, and predicted regional differences were recapitulated in matched multiregional organoid drug-response assays. These findings establish sample-centric therapeutic prioritization as a transferable strategy for modeling dynamic and spatially heterogeneous drug vulnerabilities across biological scales.

bioinformatics↗

bioRxiv2026

SEEKER: A genome-scale library-on-library screening platform for deciphering T cell recognition of antigen

Decoding which antigens activate a given T cell receptor (TCR) is a central challenge in immunology. We present SEEKER, a functional genome-scale library-on-library screening platform built on three elements: a Jurkat-derived T-APC cell (TAPCell) that combinatorially expresses one TCR and one peptide-MHC drawn from separate libraries together with an NFAT activation reporter; encapsulation of single TAPCells in a thermos-reversible hydrogel for isolated clonal expansion, so recognition is read out as intraclonal activation; and dual-asymmetric PCR that links TCR- and pMHC-encoding sequences into a heritable unit, enabling progressive hit enrichment over screening rounds. SEEKER interrogates ~10^8 TCR-pMHC combinations per run without prior knowledge. Screening joint-infiltrating CD8+ T cells from HLA-B*27+ ankylosing spondylitis patients against proteome-wide libraries validated 53 TCR-peptide pairs, uncovered extensive cross-recognition of self and common viral epitopes, and revealed highly polyreactive T cells recognizing up to 80 autoantigens, implicating virus-triggered poly-autoreactivity in multi-organ autoimmune diseases.

immunology↗

bioRxiv2026

ctDNA Release Heterogeneity in Luminal Breast Cancer Revealed by Single-Cell Multi-Omics Spatial Analysis

Backgroud Breast cancer is a leading cause of cancer-related mortality, and HR+/HER2-; is the predominant subtype. Molecular pathology, including PIK3CA and ESR1 mutation, informs prognosis and treatment selection. Circulating tumor DNA (ctDNA) offers a non-invasive approach for cancer monitoring, but its clinical utility is limited by tissue plasma discordance, reflecting heterogeneous ctDNA release. The cellular and spatial determinants of this release remain poorly understood, particularly in HR+/HER2-; subtype, where heterogeneity across subclones complicates liquid biopsy interpretation. Results To identify the cellular and spatial determinants of ctDNA release, we developed scMASTER, integrating single-cell transcriptomes and mutations, spatial transcriptomics and matched tumor and plasma DNA sequencing. In ten patients with non-metastatic HR+/HER2- breast cancer, eight recurrent malignant epithelial states showed distinct ctDNA release potential. Antigen-presentation, stress, mitosis and mesenchymal-like states showed high release. PIK3CA and ESR1 mutations were linked to distinct functional states and altered ctDNA detectability. Three spatial architectures, EMT-enriched regions, intraductal luminal progenitors and avascular hypoxic zones, showed high release. Tumor-microenvironment interactions were bidirectional: anti-tumoral immunity correlated with reduced release, whereas immunomodulatory components correlated with increased release. A stratification model based on these features identified high-risk, immunosuppressed patients with poor prognosis, validated across external cohorts. Conclusions Our study establishes a single-cell spatial framework for decoding ctDNA release heterogeneity, linking tumor states, somatic mutations, spatial architecture, and immune interactions to ctDNA release. These findings provide mechanistic insights into tissue-plasma discordance, offer a biological rationale for interpreting ctDNA dynamics, refine patient risk stratification and liquid biopsy-based monitoring in HR+/HER2-; breast cancer.

cancer biology↗

bioRxiv2026

Simvastatin and Primaquine Identified as Potential Endometriosis Therapeutics via a Novel Epithelial-Stromal Assembloid Drug Screening Assay

Background: Endometriosis is an estrogen-driven, inflammatory disorder affecting ~10% of menstruators, causing severe pain. Current treatments that reduce estrogen or inflammation have inconsistent efficacy and poor tolerability. Therapies identified via drug-repositioning methods, which target patient-specific pathways, offer a promising alternative. Simvastatin and primaquine were identified as potential treatments, strongly reversing endometriosis-associated gene expression pathways, and behavioral testing in an animal model showed that these drugs diminish endometriosis-associated pain. This paper examines their effects in human assembloids to provide proof-of-concept validation and insights into their mechanisms of action relevant to endometriosis. Methods: We established human endometrial assembloids using immortalized epithelial (12Z) and stromal fibroblast (iEc) cell lines, as well as primary tissue from patients. Assembloids were generated in 96-well agarose molds with both cell types. We tested ibuprofen, fenoprofen, primaquine, and simvastatin. Following a 24-hour exposure, assembloids and monolayer cultures were harvested and stranded mRNA-seq libraries were sequenced on an Illumina NovaSeqX Plus System. Results: Gene set enrichment analysis showed key pathway reversals: Primaquine reversed the chemical carcinogenesis ROS pathway in assembloids. Simvastatin reversed cytokine-cytokine receptor interaction in both epithelial and stromal cell lines, and the cytoskeleton in muscle cells pathway in stromal cell lines. Fenoprofen reversed the calcium signaling pathway in stromal cell lines. Conclusion: Simvastatin induced the most significant gene expression changes, notably reversing cytokine-cytokine receptor interactions in both cell lines, mirroring findings from our rat model. Despite the small sample size limitation, these experiments highlight the promise of assembloid models to test therapeutic candidates for endometriosis.

molecular biology↗

bioRxiv2026

The diversity, evolution, and conservation of African plants

Africa hosts remarkable biodiversity across diverse biomes, yet its evolutionary history at continental-scale remains poorly understood. We integrate a time-calibrated phylogeny covering 93% of African vascular plant genera with continental-scale distribution data to jointly evaluate phylogenetic diversity (PD), endemism, and diversification rates (DR). We reveal a pronounced decoupling between DR and accumulated evolutionary history across Africa. Mountain, arid, and semi-arid areas emerge as centers of neo-endemism and elevated diversification, whereas lowland and humid regions, particularly the Guineo-Congolian zone, are dominated by older lineages with low recent diversification. Several DR hotspots do not overlap with Global Biodiversity Hotspots, indicating a mismatch between rapid diversification and accumulated evolutionary history. High net diversification and speciation rates during the last 15 million years were likely driven by cooling, aridification, and mountain uplift that created new ecological gradients and isolation barriers. These abiotic changes, interacting with lineage-specific traits, shaped African modern flora and highlight conservation gaps, especially in arid regions

evolutionary biology↗

bioRxiv2026

In vivo Quantitative Tomography of 225Ac Daughters in a Prostate Cancer Mouse Model with a Compton Camera

Targeted alpha therapy with 225Ac is a promising modality for cancer treatment, as shown in recent preclinical and clinical studies. Preclinical imaging of 225Ac is essential to fully understand the biokinetics of developmental 225Ac radiopharmaceuticals. Although single photon emission computed tomography (SPECT) is typically used to achieve this in vivo, conventional preclinical scanners struggle to provide high contrast and accurate quantification for 225Ac imaging due to the very low injected activities (below 1 kBq/g), the unfavorable gamma-ray branching ratios (<26%), and its complex decay chain with several gamma-ray emissions. In this work, we employ a compact CZT-based Compton camera to achieve quantitative tomography of 225Ac daughters in live mice at 18.5 kBq (0.5 Ci) injected activities. Three mice bearing 22Rv1 prostate cancer subcutaneous xenografts were scanned in a single bed position for 30 minutes following intravenous administration of 18.5 kBq of the Anti-CD46 225Ac-Macropa-PEG4-YS5 conjugate. We successfully visualized the in vivo biodistributions of the 225Ac daughters 221Fr and 213Bi, distinguishing between the tumor xenograft and the central organs. Quantification of the tumor uptake from the images revealed an activity as low as 1.1 kBq. In vivo activity quantification computed from the images was compared to ex vivo biodistribution measurements using a gamma counter after harvesting the tissue, showing strong agreement.

bioengineering↗

bioRxiv2026

DiffGSP: reversing mRNA diffusion to unlock high-fidelity spatial transcriptomics

Spatial transcriptomics enables gene expression profiling within intact tissues while preserving spatial context, providing unprecedented insights into cellular organization and function. However, mRNA diffusion during tissue processing can cause transcripts originating from adjacent cells to be captured at a given spot. This spatial misalignment challenges a fundamental premise of spatial transcriptomics that measured gene expression faithfully corresponds to its spatial origin, thereby compromising spatial fidelity and potentially biasing biological interpretation. Here, we present DiffGSP, a physics-informed framework that integrates Fick's law with graph signal processing to explicitly model diffusion-induced distortions and recover the underlying spatial gene expression landscape. Comprehensive benchmarking across diverse datasets and evaluation metrics demonstrates the consistent ability of DiffGSP to restore spatial gene expression patterns. By computationally reversing diffusion-induced distortions, DiffGSP enables the discovery of fine anatomical structures in the mouse brain, spatially organized gene modules in the kidney, intratumoral heterogeneity in colorectal cancer, and tertiary lymphoid structures in lung adenocarcinoma. Built on a physically interpretable framework and broadly applicable to sequencing-based spatial transcriptomics technologies, DiffGSP improves the fidelity of spatial gene expression reconstruction and enables more reliable biological interpretation.

bioinformatics↗

bioRxiv2026

Loss of PKN2 drives fibroblast reprogramming and extracellular matrix remodelling in pulmonary fibrosis

Introduction Idiopathic pulmonary fibrosis (IPF) is a progressive fibrotic lung disease characterised by aberrant fibroblast function, extracellular matrix (ECM) remodelling and defective tissue repair. Protein kinase N2 (PKN2) is associated with accelerated forced vital capacity decline in IPF, but its functional role in pulmonary fibrosis remains unknown. We hypothesised that PKN2 regulates fibroblast phenotype and tissue repair. Methods PKN2 expression was assessed in human lung tissue, induced sputum and primary airway and parenchymal fibroblasts from non-fibrotic controls and patients with interstitial lung disease (ILD). DNA methylation was profiled using the Illumina HumanMethylationEPIC array. PKN2 function was investigated by siRNA-mediated depletion in primary human lung fibroblasts using transcriptomic, proteomic and functional analyses. Tissue repair was assessed following pharmacological PKN inhibition in zebrafish. Results PKN2 expression was reduced in ILD lung tissue and primary airway and parenchymal fibroblasts and further suppressed by TGF-{beta}1. Differential methylation was identified across the PKN2 locus in both fibroblast populations. Integrated transcriptomic and proteomic profiling following PKN2 depletion revealed coordinated remodelling of ECM, cell adhesion, non-canonical WNT and VEGF pathways, including dysregulation of COL1A1, WNT, VEGF and MMP1. PKN2 loss increased VEGF and MMP-1 secretion and accelerated fibroblast wound closure. PKN inhibition altered epithelial organisation and collagen fibre alignment during zebrafish wound repair. Conclusion PKN2 loss drives fibroblast reprogramming and aberrant ECM remodelling, establishing PKN2 as an important regulator of pulmonary fibroblast homeostasis and tissue repair.

cell biology↗

bioRxiv2026

Automatic bioinformatic software named entity recognition from literature

Bioinformatics software and databases are essential components of modern life science research, yet their mentions in the scientific literature are often inconsistent and difficult to systematically identify at scale. The lack of a comprehensive and up-to-date catalog of bioinformatics resources hinders efforts toward automated biomedical knowledge extraction and streamlined data analysis. Here we present SNAIL, a hybrid named entity recognition framework designed to automatically identify bioinformatics software and database (SW/DB) names from biomedical texts. SNAIL integrates complementary lexical and semantic modeling strategies. The lexical component captures orthographic patterns and contextual cues characteristic of SW/DB names, while the semantic component leverages contextual embeddings generated by transformer-based language models such as SciBERT, combined with an explicit token-masking strategy to enhance entity-focused representations. A large training corpus was constructed automatically through a hybrid pipeline that integrates citation-hinted extraction with large language model-assisted distillation. Evaluation on two independent benchmark datasets and real-world research articles demonstrates that SNAIL substantially outperforms existing approaches, including domain-specific methods such as bioNerDS2 and general-purpose large language models such as ChatGPT, Gemini, Grok and Claude. Applying SNAIL to large-scale literature analysis further reveals distinct journal-level preferences across bioinformatics subfields. These results demonstrate that SNAIL provides an accurate and scalable solution for identifying bioinformatics resources in scientific texts and enables systematic meta-analysis of tool usage and research trends.

bioinformatics↗

bioRxiv2026

FOCUS-3D: Robust, generalizable volumetric cell segmentation for three-dimensional fluorescence microscopy

Understanding how cells establish spatial organization within tissues is a fundamental question in life sciences. While modern three-dimensional fluorescence microscopy captures large-volume tissue architecture, extracting quantitative cellular insights from complex volumetric datasets remains a major barrier. Here, we introduce FOCUS-3D, a robust, broadly generalizable volumetric cell segmentation framework built on a large, diverse manually annotated cell resource and advanced AI designs. Integrating volumetric representation learning, multi-scale feature extraction, and query-based mask prediction, FOCUS-3D achieves state-of-the-art performance across diverse species, tissues, fluorescent reporters and imaging modalities. During zebrafish (Danio rerio) development, FOCUS-3D uncovers three successive phases of notochord morphogenesis. We disentangle early motility-driven rearrangements from later cell shape remodeling and tissue repacking, and further link these morphological states to spatial and developmental transcriptional programs across independent datasets.

bioinformatics↗