Biology subjects

Yang, C.

Publications and source records attributed to Yang, C..

At least 91 records · Page 5Linked to original sources

bioRxiv2026

Stimulated human cortical waves: spatiotemporal dynamics across development

Traveling waves of neural activity are fundamental to cortical function, yet their spatiotemporal dynamics and structural constraints remain less understood in human brain. Conventional analyses focus on network topology and spatial geometry of neural signals, with limited emphasis on wave dynamics at high spatiotemporal resolutions. Here, we applied a manifold-based optical flow algorithm to an open-access intracranial electroencephalography (iEEG) dataset from the single-pulse stimulation cortico-cortical evoked potentials (CCEPs) paradigm, enabling direct construction of high-temporal-resolution cortical neural activity velocity fields. Spatiotemporal mode decomposition revealed a hierarchical organization: large-scale plane waves (mediating global propagation) dominate, complemented by local patterns for local computation. Dominant plane wave directions correlate with underlying white matter fibre tract orientations, indicating anatomical guidance of cortical dynamics. Velocity field singularities (sources, sinks, spirals and saddles) are non-randomly distributed, associating with default mode network (DMN) hubs. We further identified a nonlinear relationship between cortical wave speed and age, with developmental phases paralleling white matter maturation and aging. Our findings link cortical wave dynamics to anatomy, functional networks, and neurodevelopment, establishing wave speed as a potential yet important biomarker for brain function and health.

neuroscience↗

bioRxiv2026

Diet-Driven Gut Microbiome Differences Between Cohabiting Han and Yi Ethnic Groups in Liangshan, China

BackgroundWhile ethnic variations in gut microbiota are well-documented, their persistence in genetically distinct populations sharing the same geographic environment remains poorly understood. This study investigates the Han and Yi ethnic groups cohabiting rural Southwest China, where contrasting dietary traditions persist under identical environmental conditions. MethodsWe analyzed fecal samples from 100 healthy adults (50 Yi/50 Han) using 16S rRNA gene sequencing (V3-V4 region). Dietary intake was quantified via three 24-hour recalls validated with plasma biomarkers. Multivariate analyses (DESeq2, PERMANOVA) controlled for age, sex, and BMI covariates. ResultsYi individuals exhibited significantly higher Prevotellaceae (log2FC=1.82, padj=0.028) and Succinivibrionaceae (log2FC=2.15, padj=0.013) abundances, corresponding to their buckwheat-rich diet (58.5 {+/-} 12.3% vs Han 3.3{+/-}1.8%, p<0.001) Han microbiota showed enriched Bacteroidaceae (log2FC=1.24, padj=0.041), associated with higher animal fat intake (23.6% vs Yi 1.8%, p<0.001) Dietary factors (buckwheat/animal fat intake) explained greater microbiota variation than ethnic genetic ancestry (PERMANOVA R{superscript 2}=0.10 vs 0.07, p < 0.05) ConclusionCohabiting Han and Yi populations maintain distinct gut microbiota compositions primarily driven by dietary differences. These findings highlight diet as a stronger determinant than genetic ancestry in shaping microbial communities under shared environments. Future studies should validate these observations with metagenomic sequencing.

microbiology↗

bioRxiv2026

Acute deletion of PLIN5 in brown adipocytes causes mitochondrial dysfunction and cold intolerance

Cold exposure of mice is associated with adaptive molecular and organellar changes in brown adipose tissue (BAT) that promote thermogenesis to defend body temperature. We previously reported that the lipid droplet protein Perilipin 5 (PLIN5) robustly increases in BAT during acute exposure of mice to cold. We demonstrated that chronic induction of BAT PLIN5 within the physiological range in mice housed at room temperature mimics the effects of cold exposure in terms of increased thermogenic gene expression in BAT, increased BAT mitochondria cristae packing, and increased uncoupled mitochondrial respiration. Additionally, BAT PLIN5 overexpression led to healthy remodeling of inguinal white adipose tissue with improved systemic glucose tolerance and reduced diet-induced hepatic steatosis. Conversely, PLIN5 constitutive deletion in brown adipose tissue resulted in decreased BAT thermogenic gene expression and in BAT mitochondrial dysfunction but did not lead to cold intolerance or changes in glucose tolerance. We hypothesized that preserved cold tolerance despite chronic deficiency of PLIN5 in BAT was the result of compensatory white adipose tissue (WAT) beiging, as suggested by the observed increase in thermogenic gene expression in inguinal WAT (iWAT). To test this hypothesis, we developed a mouse model of doxycycline-inducible, acute deficiency of PLIN5 in BAT of adult mice (BiKOPLIN5 mice). After 7 days of doxycycline treatment and housing at 6 {degrees}C, PLIN5 was significantly reduced in the BAT of BiKOPLIN5 mice compared with littermate control mice but was unchanged in the iWAT of these experimental groups. Under these conditions, thermogenic gene expression was reduced significantly in the BAT of BiKOPLIN5 mice compared to Control mice, as were mitochondrial cristae density and uncoupled BAT mitochondrial respiration. These effects of acute PLIN5 deficiency in BAT were associated with cold intolerance, which was consistent with the observed failure in iWAT of thermogenic gene expression to increase beyond that of Controls. These findings clarify the essential role of BAT PLIN5 in the physiological adaptive responses of mice to cold ambient temperature.

cell biology↗

bioRxiv2025

A Comprehensive Treatment-Induced Resistance Atlas of Glioblastoma Reveals a Fibrotic Niche Shielding the Tumor from Immunotherapy

Therapeutic resistance in IDH-wildtype glioblastoma (GBM) is driven by an intricate interplay between cellular plasticity and protective microenvironmental niches. By constructing the GRIT-Atlas--a massive transcriptomic compendium encompassing nearly one million high-quality single cells across 17 cohorts--and cross-analyzing it with 48 independent Visium spatial transcriptomics sections, we discover a recurrent "Spatial Resistance Triad" comprising mesenchymal-like (MES-like) malignant cells, myeloid-derived suppressor cells (MDSCs), and collagen-secreting cancer-associated fibroblasts (CAFs). This large-scale spatial integration reveals that the triad physically fortifies microvascular proliferation (MVP) and pseudopalisading necrosis (PAN) niches. To substantiate these findings at true single-cell resolution, we deploy high-plex spatial molecular imaging (CosMx SMI) to map over 400,000 single cells across a clinical validation cohort. This high-resolution architecture firmly validates the triads geography and, critically, provides structural gradient evidence unmasking a spatiotemporal continuum wherein PAN emerges as a direct functional consequence of MVP advancement and subsequent vascular collapse. Mechanistically, stromal CAF-derived COL6A1 engages CD44 receptors on MES-like cells to accelerate a potent neural stemness cascade within these protective domains. Utilizing a blood-brain barrier (BBB)-penetrant multi-library compound screen, we identify Lacidipine as a multi-modal stromal disruptor that successfully silences CAF activation and halts matrix secretion. Incorporating Lacidipine into the standard chemo-immunotherapy backbone (TMZ + anti-CSF1R) completely dismantles the protective desmoplastic matrix niche, forcing a profound collapse of intracranial tumor burden and dramatically extending overall survival in orthotopic models. Collectively, our study leverages unprecedented single-cell and spatial scale to provide a definitive blueprint of GBM therapeutic evasion, establishing matrix-targeted intervention as a mandatory prerequisite for successful glioblastoma eradication.

cancer biology↗

bioRxiv2025

FlashDeconv enables atlas-scale, multi-resolution spatial deconvolution via structure-preserving sketching

Coarsening Visium HD resolution from 8 to 64 m can flip cell-type co-localization from negative to positive (r = -0.12 [->] +0.80), yet many widely used compositional deconvolution workflows require coarsening or subsampling at million-bin scale. Here we introduce FlashDeconv, which combines leverage-score importance sampling with sparse spatial regularization to achieve competitive benchmark accuracy while processing 1.6 million bins in 153 seconds on commodity hardware. Systematic multi-resolution analysis of Visium HD mouse intestine reveals a tissue-specific resolution horizon (8-16 m), the scale at which this sign inversion occurs, validated by Xenium ground truth. Below this horizon, FlashDeconv provides, to our knowledge, the first sequencing-based quantification of Tuft cell chemosensory niches (15.3-fold stem cell enrichment). In a 1.6-million-bin human colorectal cancer cohort, FlashDeconv uncovers neutrophil inflammatory microdomains co-localized with immunoregulatory dendritic cells (mRegDC) at the tumor-stroma interface, spatial niches largely missed by discrete-label summaries, with RCTD doublet mode labeling only 2.3% of hotspot bins as neutrophil singlets.

bioinformatics↗

bioRxiv2025

Two Small Proteins Enable N2O Reduction in Acidic Environments

Denitrifying bacteria are major contributors to nitrous oxide (N2O) emissions, which rise with global soil acidification, likely because low pH impairs maturation of the periplasmic enzyme N2O reductase (NosZ) in most bacteria. While some bacteria can reduce N2O under acidic conditions, the underlying mechanism remain unclear. Here, we isolated bacteria from acidic soils and identified strains that efficiently reduce N2O at low pH. They carry two novel proteins, NosP and NosQ, along with NosZ clade I. Functional analyses of deletion mutants demonstrated that NosP and NosQ are essential for the maturation of NosZ at low pH, but are not required at circumneutral pH. Cryo-EM analysis indicates that NosPQ forms a protective complex with NosZ, safeguarding its maturation under acidic conditions. Metagenomic analysis shows that nosPQ genes are widely distributed across diverse bacterial taxa and soil types. Our findings reveal a key molecular adaptation mechanism for N2O reduction in acidic environments and provide valuable insights for developing efficient N2O mitigation strategies.

biochemistry↗

bioRxiv2025

Exudate-Guided Janus Trilayer Bioelectronic Dressing for Multimodal Sensing and Therapy of Chronic Wounds

Chronic wound treatment remains challenging because conventional dressings and systemic therapies typically lack real-time adaptability to the dynamic changes in the wound microenvironment. Here, we report a breathable self-adhesive multifunctional wound dressing based on a gradient-wettable Janus trilayer fibrous membrane, which integrates real-time biochemical sensing, on-demand drug release, and low-voltage electrical stimulation therapy simultaneously. The dressing features a vertically integrated trilayer architecture with hierarchical partitioning, where the three vertically stacked layers integrate a multiplex electrochemical sensor array (glucose, lactate, pH), a silver-sulfadiazine drug reservoir, and stimulation electrodes. Specifically, a hydrophilic sensing layer, intermediate drug-storage layer, and hydrophobic adhesivelayer are assembled to achieve spatially resolved functionalities. The membranes gradient wettability and asymmetric porous structure enable directional exudate transport, thereby triggering stepwise activation of sensing, drug release, and electrical stimulation in a spatiotemporally controlled manner. The dressing is thin, breathable, stretchable, self-adhesive and biocompatible, enabling conformal contact and stable signal acquisition on deformable skin without tapes. This design ensures continuous bio-signal monitoring while maintaining a favorable wound healing microenvironment. Preclinical tests demonstrate its effectiveness in promoting wound closure, reducing infection, and providing continuous wound status monitoring. This integrated system offers a promising approach for next-generation wound care and regenerative medicine.

bioengineering↗

bioRxiv2025

Super-CUT&Tag: A Sensitive, Spatially Resolved Approach for Epigenomic Profiling in Tissue Sections

Spatial profiling of protein-DNA interactions is essential for understanding gene regulatory processes, but current methods suffer from low sensitivity, limited resolution, and complex workflows. Here we introduce Super-CUT&Tag (Solid-phase interface embedded with an Ultra-dense DNA barcode array to Profile Epigenomic landscapes for spatially Resolved CUT&Tag), a robust spatial epigenomic method that directly transfers in situ protein-DNA interactions from tissue sections onto a pre-fabricated spatially barcoded array. Incorporating 3D polyamidoamine (PAMAM) dendrimers markedly improves chromatin capture efficiency, achieving several-fold higher sensitivity compared to current spatial CUT&Tag approaches. Using Super-CUT&Tag, we profile H3K27ac spatial landscape and uncover previously hidden active-chromatin heterogeneity across mouse embryonic tissues and stages. Integration with spatial transcriptomics further reveals spatiotemporal enhancer regulation dynamics of Neurod2 during corticogenesis. By overcoming key bottlenecks in sensitivity, resolution and usability, Super-CUT&Tag establishes a powerful platform for spatial epigenomic profiling in complex tissues.

genetics↗

bioRxiv2025

Context-aware simulation enables systematic optimization of long-read mapping parameters

The performance of long-read mapping is critical yet highly sensitive to parameter choices. We present CycSim, a context-aware simulator that models sequence-context-dependent errors from empirical sequencing data, coupled with a Bayesian optimization framework for systematic parameter tuning. CycSim more accurately reproduces real error profiles than existing simulators, enabling reliable simulation-based optimization. The framework identified parameter configurations that achieved 2.78-fold faster mapping for data from the newly developed Cyclone platform, and consistently improved both mapping efficiency (8.14-32.65% faster) and structural variant calling accuracy (0.75-1.70% higher F1) across ONT, HiFi, and Cyclone datasets, providing a robust and generalizable foundation for analysis-goal-driven parameter refinement.

bioinformatics↗

bioRxiv2025

AlphaFold3 for Structure-guided Ligand Discovery

Deep-learning methods for protein structure prediction, such as AlphaFold2 (AF2) and RosettaFold (RF), have transformed structural biology and accelerated downstream biological discovery. More recent models, including AlphaFold3 (AF3) and RosettaFold All-Atom (RFAA), extend this capability to protein-ligand co-folding, enabling direct prediction of bound complexes from sequence and ligand inputs. This advance has raised the possibility that such models could function not only as structure predictors but also as AI-based molecular docking engines for virtual screening. Yet their true impact on ligand discovery remains unclear and, in many cases, controversial. Here, we systematically assess AF3 co-folding across tasks central to small-molecule discovery compared to conventional molecular docking. First, retrospective enrichment of actives over decoys showed that AF3 outperforms the physics-based docking program DOCK3 across 43 drug targets in DUDE-Z; however, this advantage is largely driven by hidden ligand-only biases inherent to computational decoy sets. In contrast, in three large experimental datasets (the sigma-2 receptor ({sigma}2), the D4 dopamine receptor (D4), AmpC {beta}-lactamase (AmpC)) with over 2,500 tested molecules that lack such biases, DOCK3 achieved stronger overall enrichment, while AF3 contributed mainly to early enrichment. Second, out-of-sample pose reproduction on >8,000 protein-ligand complexes deposited after the AF3 training and validation cutoff showed that AF3 accuracy is strongly dependent on training-set similarity, indicating that the model memorizes atomic positions more than learning general principles of molecular recognition. Finally, in the first prospective head-to-head screen against the {sigma}2 receptor, novel to AF3s training set, AF3 achieved a 13% hit rate and identified a 13 nM binder directly from the screen. However, compared with the parallel DOCK3 campaign, AF3 delivered a two-fold lower hit rate, despite yielding a similar affinity distribution among the top five hits. A crystal structure of the {sigma}2 receptor bound to the most potent AF3-derived hit confirmed that AF3 produced a near-native ligand pose. AF3 therefore represents the beginning of deep-learning-based structure-guided ligand discovery: a complementary tool rather than a replacement for conventional docking, with practical applications both as a screening engine and as a post-docking filter that improves hit rates. More broadly, this work establishes a framework for evaluating next-generation deep-learning co-folding models and quantifying their impact on small-molecule discovery.

pharmacology and toxicology↗

bioRxiv2025

Dynamic alterations of DNA methylation and transcriptome in adaptation to and recovery from the space environment

Space exploration presents tremendous health challenges. Here, we report time series of multi-omic and phenotypic profiles of seventeen astronauts from six China Manned Space missions with continuous spaceflight durations ranging from 13 to 180 days. We revealed a key role of DNA methylation regulation in reshaping gene expression patterns to adapt to the space environment. Long-duration spaceflight showed more alterations in epigenetic modifications correlated with alternative splicing and protein acetylation. During recovery, an "overrange rebound" phenomenon was observed, furthermore, a mathematical model was established to describe this implying important phenomenon. Moreover, we revealed the correlations between molecular alterations and phenotypic changes such as coagulation activation and bone intensity loss. Additionally, we performed ground-based simulation experiments to estimate the impacts of individual stressors in the space environment on DNA methylation. In summary, our study highlights the importance and complexity of epigenetic regulation in adaptation to and recovery from the space environment.

genomics↗

bioRxiv2025

YibaoGaussian: Generate dynamic 3D models from text using Gaussian splatting as the explicit representation

In recent years, the latest advances in the field of 3D content creation have been primarily based on neural radiation fields (NeRF). Despite significant research achievements, these methods often suffer from slow optimization speeds and high memory consumption. More importantly, these studies still mainly focus on static modeling, with very limited research on dynamic models, which restricts their practical applications. This paper proposes a method Yibaogaussian for generating dynamic 3D models from text descriptions, which can generate dynamic 3D models while ensuring efficiency and quality. Our key insight is on constructing canonical space and temporal deformation field . We build static 3D Gaussian fields in canonical space to capture the overall geometry and appearance features of a scene. By dynamically mapping the parameters of the Gaussian field to the temporal deformation field, we achieve continuous changes and natural motion of the static 3D model over time. Extensive experiments demonstrate that our proposed method offers higher efficiency and highly competitive generated quality. Notably, YibaoGaussian can generate high-quality dynamic 3D models from text descriptions in just 3 minutes, approximately 3 times faster than existing methods. This study verifies the feasibility of combining Gaussian representation and temporal deformation field in regular space, providing a new solution for text-driven dynamic 3D model generation and laying the technical foundation for multimodal applications such as digital humans, virtual reality (VR/AR), and film and television special effects.

bioengineering↗

bioRxiv2025

Phosphorus stress and spatial confinement lower the threshold for quorum-sensing activation of redox-active metabolite production in Pseudomonas synxantha

Bacteria often coordinate collective behaviors such as biofilm formation and secondary metabolite production through quorum sensing (QS), a regulatory system traditionally linked to high cell density. However, in environments like soil, where microbial populations are spatially fragmented, sparse, nutrient-limited, and subject to mass transport, the mechanisms that enable QS-dependent processes remain incompletely understood. Here, we investigate the regulation of a secreted redox-active metabolite, phenazine-1-carboxylic acid (PCA), in Pseudomonas synxantha 2-79, a model rhizobacterium, under phosphorus (P) limitation, a persistent stress in many soils. Using a combination of microscopy and molecular genetic approaches, we show that P limitation sensitizes the QS activation threshold by an order of magnitude, enabling phenazine induction at relatively low population densities in comparison to P replete conditions. This induction is abolished in QS-deficient mutants and restored by the addition of exogenous acyl-homoserine lactone (AHL), demonstrating that quorum sensing remains essential but its threshold becomes environmentally tuned. Under P limitation, spatial confinement and pore saturation levels further shape the timing and location of induction, illustrating how physical structure and nutrient stress can modulate bacterial activities. Moreover, phosphorus stress confers both collaborative and competitive advantages, enabling P. synxantha to undergo low-cell density AHL cross-talk between related Pseudomonas spp. and to suppress other rhizobacteria. Lastly, on plant roots, PCA genes are more predominantly induced under P limitation. These findings illustrate how the nutrient status of an environment can modulate the onset of quorum sensing, enabling quorum-regulated behaviors to activate at lower thresholds.

microbiology↗

bioRxiv2025

Using the simple telegraph model to decipher transcriptional burst regulation across genome-wide data

Gene transcription is a stochastic bursting process, with burst frequency and burst size as core parameters. Deciphering its genome-wide regulation is challenging, as complex models (capturing detailed biology) are impractical for large-scale use due to unstable inference and high computation. We proposed a simple telegraph model-based framework to analyze genome-wide scRNA-seq and smFISH datasets, addressing these limitations. When sample size [≥] 500 and burst parameter change [≥] 3-fold, its inferred burst frequency- and size-dominated variations reliably proxy true regulation. Analyses across mouse cells (CAST/C57 alleles, fibroblasts vs. embryonic stem cells) and healthy/hypertrophic cardiomyopathy (HCM) human heart tissues revealed key rules: 1) Burst frequency- or size-dominated regulation was primary (over 70% of variable genes), with more bursty-regulated genes in HCM; 2) TATA-initiator synergy (enhancing burst size-dominated regulation) was lost in HCM; 3) Burst frequency-dominated genes enriched in genome stability/cell cycle/apoptosis (via TFs like Foxo4/Mcm2), while burst size-dominated ones in signaling/metabolism/proteostasis (via TFs like Zfp322a/Smchd1/Ppargc1a), and their interdependent dysregulation accelerated HCM. This study establishes the simple telegraph model as a scalable framework linking transcriptional burst dynamics to cell fate and pathology.

molecular biology↗

bioRxiv2025

Complete and haplotype-resolved maps of genomic and epigenetic discordance in monozygotic twins

Telomere-to-telomere (T2T) genome assemblies are indispensable for accurate detection of genetic variation and for resolving complex repetitive regions. Monozygotic (MZ) twin pedigrees provide a powerful model to investigate de novo mutations (DNMs), however, comprehensive, haplotype-resolved analyses of structural variation (SV), allele-specific inheritance in complex regions, and DNA methylation in diploid human genomes remain limited. Here, we generated complete, haplotype-resolved T2T assemblies for two female twins (C33 and C35) from a Han Chinese pedigree by integrating complementary, state-of-the-art sequencing technologies. The resulting T2T-C33 and T2T-C35 assemblies are highly contiguous and complete, with Genome Continuity Inspector (GCI) scores of 74.94 (maternal) and 77.94 (paternal), and consensus quality values (QV) >75 (k = 21). We comprehensively cataloged 62 inter-twin single-nucleotide variants (SNVs), 15 small indels, and identified both shared and private DNMs, revealing nascent genomic divergence between the MZ twins. Focused interrogation of complex regions uncovered pronounced haplotype-specific length polymorphisms and structural heterogeneity within centromeric higher-order repeat (HOR) arrays. Notably, we observed extensive HOR copy-number variation between haplotypes, including a large copy-number difference on maternal chromosome 18, underscoring dynamic HOR array evolution even among genetically identical individuals. Concurrently, genome-wide DNA methylation profiling delineated allele-specific epigenetic variation that may contribute to phenotypic discordance. Together, these high-quality, diploid T2T genomes from a Han Chinese pedigree provide a valuable resource for population-aware genomics and reveal fine-scale, haplotype-specific divergence in MZ twins. Our results advance understanding of repeat dynamics, centromeric architecture, epigenetic variation and the spectrum of human genomic variation at single-base and structural scales.

genomics↗

bioRxiv2025

IS110 transposon utilizes two mechanistically distinct RNA-guided transposition pathways

The recently discovered IS110 elements employ RNA-guided transposases that use bridge-RNA to coordinate donor and target DNA recognition and integration via donor- and target-binding loops, offering promise for precise, DSB-free genome editing. However, their transposition mechanism remains unclear, with prior inconsistent observations. Using a IS110 element from Caloranaerobacter azorensis, we show that IS110 transposons utilize two independent transposition pathways. The first depends on bridge-RNA and excises the element via copy-out to form a circular intermediate, revisiting the earlier cut-out model. Integration occurs predominantly through top-strand insertion, suggesting an alternative to the earlier Holliday junction-mediated dual-strand mechanism. The second involves cooperation between a truncated target-binding loop RNA and bridge-RNA, enabling direct top-strand transfer to a new target via two sequential reactions, bypassing circular intermediates. Both pathways preserve the original transposon copy. These findings redefine the mechanistic understanding of IS110 transposition and reconcile prior discrepancies, offering insight into programmable, RNA-guided genome modification.

molecular biology↗

bioRxiv2025

A simplified MiMe for producing clonal gametes to enable synthetic apomixis in allotetraploid Brassica napus

Synthetic apomixis has been established in Arabidopsis and rice by combining MiMe that produces clonal unreduced gametes with the factors inducing parthenogenesis or haploids. The MiMe requires the simultaneous inactivation of three genes, which imposes challenges for its application in polyploids harbouring multiple copies for each gene. Here, we demonstrate that mutating two genes in the allotetraploid oil crop Brassica napus effectively converts meiosis into mitosis-like division, producing over 95% viable clonal gametes and thus establishing a simplified MiMe system in polyploids.

plant biology↗

bioRxiv2025

CTDP: Identifying cell types associated with disease phenotypes using scRNA-seq data

Single-cell RNA sequencing enables transcriptome-wide analysis at single-cell resolution, offering unprecedented insights into cellular heterogeneity across biological conditions. However, accurately comparing transcriptomic distributions of cells from distinct biological states, such as healthy versus diseased individuals, remains challenging. To address this, we developed CTDP, a robust and interpretable computational framework that identifies disease phenotype-associated cell types of interest by integrating Lasso-regularized logistic regression with permutation testing. Through comprehensive evaluations on both simulated and real-world datasets, including melanoma immunotherapy, COVID-19 severity, and liver cirrhosis, CTDP consistently outperformed existing methods such as DA-seq, scDist, and PENCIL in both accuracy and robustness. In melanoma, CTDP uncovered immune-responsive clusters and revealed transcriptional regulators like PTPRC, CREM, and JUNB linked to immunotherapy efficacy. In COVID-19, it identified critical severity-associated cell types, such as B cells, NK cells, epithelial cells, and macrophages, which contribute to dysregulated immune responses and inflammation in severe cases. These results highlight CTDPs power in uncovering disease-relevant cell populations and its potential to advance precision medicine through single-cell analysis.

bioinformatics↗