Biology subjects

Shi, G.

Publications and source records attributed to Shi, G..

At least 19 recordsLinked to original sources

bioRxiv2026

FLASH X-rays preserve neutrophil chromatin to boost antitumor immunity

Ultrahigh dose-rate FLASH radiotherapy spares normal tissue while preserving antitumor activity, positioning it as a promising technology in radiation oncology, but its immunomodulatory mechanisms remain elusive. Here, using a bilateral subcutaneous tumor model in mice, we show that 8-Gy FLASH X-rays, versus an equal dose of conventional dose-rate (CONV) X-rays, elicit a robust abscopal antitumor effect with anti-PD-1 therapy. Single-cell transcriptome and T cell receptor (TCR) profiling reveal that FLASH X-rays plus anti-PD-1 enhance antitumor immune infiltration and TCR clonal expansion in both irradiated and abscopal tumor lesions. Mechanistically, the ultrashort temporal continuity of FLASH dose delivery conserves chromatin compaction in neutrophils during exposure and inhibits neutrophil extracellular trap (NET) formation, thereby dismantling NET-mediated CD8+ T-cell exclusion within primary tumors. Conversely, CONV or split-dose FLASH X-rays induce marked chromatin modifications prior to dose completion, leading to chromatin hyper-relaxation which promotes NETosis and consequently abrogates systemic antitumor immunity. Notably, this detrimental effect can be reversed by pharmacologically suppressing PARylation-mediated chromatin modification and decondensation in neutrophils. These findings identify radiation-induced aberrant chromatin relaxation in neutrophils as a critical determinant of radioimmunotherapy outcomes, providing a rationale for redefining the FLASH effect and advancing its clinical translation.

cancer biology↗

bioRxiv2026

Distinct Temporal Responses to Xanthomonas translucens Strains Shape Bacterial Leaf Streak Development in Triticale

Bacterial leaf streak caused by Xanthomonas translucens threatens cereal production, however, the temporal coordination of host transcriptional responses during resistant and susceptible interactions in polyploid crops remains partially understood. Here, we used time-resolved transcriptomics to characterize responses of synthetic hexaploid triticale to two X. translucens pv. undulosa strains that produce contrasting disease outcomes. The resistant interaction with non-virulent LB10 showed a strong early transcriptional response that subsequently declined, whereas responses to the virulent strain P3 progressively intensified as water-soaking symptoms developed. Analysis of syntenic A-, B-, and R-subgenome homoeologs revealed extensive regulatory asymmetry, with R-subgenome homoeologs disproportionately represented among transcriptionally suppressed genes. Despite their conserved coding sequences, homoeologs often showed divergent transcriptional responses during infection, whereas greater similarity in upstream regulatory regions was associated with more coordinated responsive trajectories. We next examined pathogen-mediated transcriptional regulation through transcription activator-like (TAL) effectors. Among eight TAL effector templates identified in LB10 and P3, TAL5-associated predicted targets showed the strongest preferential induction during P3 infection. Disruption of TAL5 in P3 predominantly reduced host gene expression, including genes involved in immune signaling, cell wall-associated defense and photosynthetic function, accompanied by reduced maximum photosystem II quantum efficiency at 72 h post-inoculation. Together, our results show that bacterial leaf streak outcomes are shaped by temporally distinct host responses and pathogen effector-associated transcriptional reprogramming, providing insight into the dynamic regulation underlying cereal-Xanthomonas interactions.

plant biology↗

bioRxiv2026

The common evolution of fungicide persistence in cryptococcosis patients

Fungicide persistence, the ability of dormant fungal cells to survive lethal drug exposure, undermines treatment efficacy, yet its clinical evolution remains largely unexplored. We assembled a nationwide collection of clinical Cryptococcus neoformans isolates from China and revealed extensive inter strain variation in amphotericin B (AmB) persistence. This variation can arise from common evolutionary events in patients, generating previously undescribed high persistence cryptococcal variants refractory to AmB clearance. Genome wide fitness landscape analysis shows that persistence associated mutations generally impose minimal fitness costs, facilitating persistence evolution even in fungistatic resistant and hypervirulent genetic backgrounds. Machine learning identified deficient ACO2 expression as a key predictor of high persistence clinical isolates. ACO2 deficiency reproduces the high persistence phenotype by promoting POPC accumulation, which competes with AmB for its target. Moreover, the clinical stage antifungal T-2307 effectively eliminates high persistence strains across diverse genetic backgrounds. Collectively, our findings unveil common evolution of fungicide persistence in cryptococcosis patients, representing a previously overlooked clinical concern.

microbiology↗

bioRxiv2026

X-Gutor: a high-fidelity in vitro platform for long-term gut microbiome recovery

In vitro gut microbiome-culturing models are essential for studying host-microbe interactions, yet achieving high microbial recovery and long-term stability remains a long-standing challenge. Here we devise X-Gutor, an ecologically designed in vitro platform that recapitulates the monogastric digestive system with precise control of pH, redox potential, and a mucin-based biofilm matrix. Using an integrated assessment framework, microbial source tracking, a curated gut metabolism database (GutDB), and short-chain fatty acid profiling, we benchmarked gut community recovery. Building on this platform, HanGutor and PigGutor were developed to recover 96.27{+/-}4.92% and 90.48{+/-}5.95% of human and swine gut microbiota, respectively. Ecological fine-tuning revealed that redox potential drives the Prevotella-Bacteroides trade-off and that spatial biofilm structure suppresses cheater (Succinivibrio) growth. The X-Gutor provides a scalable, modular platform for gut microbiome engineering, dietary intervention, and microbiota-targeted therapy development.

microbiology↗

bioRxiv2026

Loop Extrusion Reversal by Condensin Motor is Mediated by Catch Bonds

Structural Maintenance Complexes (SMC) are energy consuming motors that are important in folding the genome by loop extrusion (LE) in all stages of the cell cycle. Single molecule magnetic tweezer pulling experiments have revealed that condensin, a member of the SMC family involved in mitosis, takes occasional backward steps, thus coughing up the gains in the length of the extruded loop. To reveal the mechanism of the forward and backward steps simultaneously, we developed a theory using the stochastic kinetic model and the scrunching mechanism for LE. The calculations quantitatively account for the measured force-dependent step size and dwell time distributions in both the directions. By postulating the existence of an intermediate state in the ATP-driven cycle that is poised to take a forward or a backward step, we predict that its lifetime increases as the external mechanical force increases till a critical value and subsequently decreases at higher forces. The surprising finding of lifetime increase in an active motor, at sub-piconewton forces, is the characteristic of catch bonds, known in force-induced rupture of several passive protein complexes. The identification of catch bond-like states in condensin not only expands our understanding of LE but also highlights the significance of mechanical forces in regulating genome organization.

biophysics↗

bioRxiv2026

PARP1-mediated 5' flap dynamics facilitate Okazaki fragment maturation

Abstract/SummaryPrecise regulation of enzyme recruitment during Okazaki fragment maturation (OFM) is essential for faithful and efficient lagging-strand DNA synthesis. Emerging evidence suggests that PARP1 contributes to OFM yet its specific functions remain unclear. Here, we define context-dependent functions of PARP1 during OFM. Under physiological conditions, PARP1 co-localizes with PCNA in early S phase and restrains Pol {delta}-PCNA- mediated strand-displacement DNA synthesis, thereby preventing the formation of long 5' flaps, which is refractory to FEN1 cleavage. On the other hand, in LIG1-deficient cells, in which DNA nicks and unexpectedly long 5' flaps accumulate, PARP1 promotes the recruitment of LIG3 to catalyze OF ligation and DNA2 to facilitate long 5' flap processing. Collectively, our findings uncover previously unrecognized roles of PARP1 in regulating 5' flap dynamics to ensure efficient OFM and cell viability. HighlightsO_LIPARP1 plays context-dependent regulatory functions in Okazaki fragment maturation (OFM). C_LIO_LIPARP1 controls strand displacement DNA synthesis by the PCNA-Pol{delta} complex to dictate generation of short over long RNA-DNA flaps during canonic OFM. C_LIO_LIPARP1 senses unligated Okazaki fragments in DNA Ligase 1 deficient cells and suppresses unwanted conversion of DNA nicks into 5 flaps. C_LIO_LIProcessing of unligated nicks or flaps by DNA ligase 3 or DNA2, respectively in LIG1 deficient cells depends on PARP1. C_LIO_LIPARP1 inhibitors induce synthetic lethality with DNA ligase 1 or DNA2 inhibition. C_LI

molecular biology↗

bioRxiv2026

Connecting multiway enhancer-promoter interactions to changes in gene expression in cancer

Hi-C, and more recently Micro-C, experiments suggest that genome organization is altered as normal cells become cancerous, often resulting in aberrant gene expression. In prostate cancer, there is evidence that large topologically associating domains in normal cells split and are accompanied by shifts in the epigenetic marks from inactive to active states. However, it is unclear whether changes in genome organization alone can account for the gene expression increase in cancer cells. By combining polymer physics concepts and data-driven modeling, we first calculated an ensemble of three-dimensional (3D) chromatin structures using only the 2D contact map as input. The enhancer-promoter (E-P) distance distributions for the overexpressed Androgen Receptor (AR) and Forkhead Box Protein A1 (FOXA1) are broad, with mean values exceeding the threshold for direct E-P contact. Importantly, the average E-P distances decrease in the cancer cells, compared to normal cells in the AR locus, whereas in FOXA1 they are roughly constant or increase modestly. Similarly, the number of multiway contacts increases as cancer progresses across cancer cell lines in the AR locus. In contrast, the number of multiway contacts in FOXA1 is similar in normal and cancer cells. Because the 3D characteristics do not explain the enhanced gene expression in cancer cells, we developed Activity-by-Multiway-Contact (AMC) Model that integrates the multiway contacts with enhancer biochemical activity. The AMC model provides a plausible mechanism for the overexpression of both AR and FOXA1 in prostate cancer. Moreover, using Micro-C data for breast cancer, we show that the number of multiway enhancer-promoter contacts increases in four of five genes studied. When multiway contacts are combined with biochemical activity, changes in gene expression found in the experiment, positively correlate with the AMC score. The predictions of the AMC model not only account for overexpression of genes in prostate and breast cancer but also provide a basis for understanding gene expression variations in other genes as well.

genomics↗

bioRxiv2026

CellChem: Cellular transcriptional responses reshape molecular representation space for efficient and multi-scale drug discovery

Despite decades of progress in computational drug discovery, deep learning-based molecular representation models remain largely structure-centric, assuming that chemical similarity approximates functional similarity. However, drug effects in cells are shaped not only by chemical similarity but also by molecular interactions in the cellular context. To capture this complexity, we introduce CellChem, a cellular-chemical representation-learning framework that learns cell-guided molecular representations of small-molecule actions within cells. By incorporating large-scale cellular transcriptional profiles during pretraining, CellChem reshapes molecular representation space from structure-centric to a balanced integration of structure and function. The learned CellChem molecular representations exhibit biologically meaningful geometric organization, such that distances between molecules encode not only structural similarity but also similarity in the cellular responses they elicit, independent of downstream tasks. Using downstream derivative models such as cell-guided compound-protein interaction prediction and drug-induced transcriptional response profile generation, CellChem supports highly efficient, multi-scale drug discovery, achieving significantly better performance than traditional models.

molecular biology↗

bioRxiv2025

Epigenetic state encodes locus-specific chromatin mechanics

Chromatin is repeatedly deformed in vivo during transcription, nuclear remodeling, and confined migration - yet how mechanical response varies from locus to locus, and how it relates to epigenetic state, remains unclear. We develop a theory to infer locus-specific viscoelasticity from three-dimensional genome organization. Using chromatin structures derived from contact maps, we calculate frequency-dependent storage and loss moduli for individual loci and establish that the mechanical properties are determined both by chromatin epigenetic marks and organization. On large length scales, chromatin exhibits Rouse-like viscoelastic scaling, but this coarse behavior masks extensive heterogeneity at the single-locus level. Loci segregate into two mechanical subpopulations with distinct longest relaxation times: one characterized by single-timescale and another by multitimescale relaxation. The multi-timescale loci are strongly enriched in active marks, and the longest relaxation time for individual loci correlates inversely with effective local stiffness. Pull-release simulations further predict a time-dependent susceptibility: H3K27ac-rich loci deform more under sustained forcing yet can resist brief, large impulses. At finer genomic scales, promoters, enhancers, and gene bodies emerge as "viscoelastic islands" aligned with their focal interactions. Together, these results suggest that chromatin viscoelasticity is an organized, epigenetically coupled property of the 3D genome, providing a mechanistic layer that may influence enhancer-promoter communication, condensate-mediated organization, and response to cellular mechanical stress. The prediction that locus-specific mechanics in chromatin are controlled by 3D structures as well as the epigenetic states is amenable to experimental test.

biophysics↗

bioRxiv2025

Substrates Coupling and Inhibition of the human Na+- dependent Cl-/HCO3-exchanger

Maintaining pH homeostasis is essential for neuronal excitability and for regulating cerebrospinal fluid (CSF). The Na+-dependent Cl-/HCO3- exchanger, NCBE (SLC4A10), abundant in the choroid plexus, contributes to CSF pH control by mediating bicarbonate flux, yet its molecular mechanism has remained unclear. Here we report cryo-EM structures of human NCBE in multiple functional states, revealing conserved binding sites for Na+, Cl-, and HCO3-, as well as an unexpected K+ site indicating relaxed cation selectivity. The inhibitor DIDS binds above the substrate cavity, locking NCBE in an outward-facing conformation and defining a subfamily-selective inhibitory mechanism. Functional assays and molecular dynamics simulations validate ion coordination and inhibitor effects. Comparison of cryo-EM structures with an AlphaFold3 inward-facing model supports an elevator-like mechanism and completes the conformational cycle of Na+-coupled HCO3- transporters. Together, these findings define the structural basis of NCBE and provide a framework for understanding ion coupling and pharmacological modulation within the SLC4 family.

biophysics↗

bioRxiv2025

Gut microbial interaction networks control autoimmunity to neuroretina

The gut microbiome influences the development of immune-mediated inflammatory diseases, including autoimmune uveitis, a sight-threatening ocular inflammation driven by retina-specific T cells1. Using a model of spontaneous autoimmune uveitis (sEAU) we showed that gut commensals provide immune stimuli that trigger disease2. Here we report that uveitis-promoting microbes are present in human gut flora and that colonization of germ-free (GF) mice with commensals from healthy human donors was sufficient to provoke disease. Severity of sEAU correlated with expansion of Akkermansia and contraction of short-chain fatty acid (SCFA)-producing Firmicutes, followed by decreased SCFA levels and a dominant gut Th1 effector response. Mechanistic gain-of-function experiments, enriching GF sEAU mice with Akkermansia, reproduced these microbiome, metabolite and immune phenotype shifts, and exacerbated disease, suggesting that Akkermansia promotes autoimmunity by outcompeting SCFA-producers and enhancing Th1-type responses. An inverse correlation between Akkermansia (Verrucomicrobia) and Firmicutes was also present in patients with uveitis, multiple sclerosis and Crohns disease. These findings reveal a stereotypic gut microbial interaction network that regulates systemic immune balance, and may represent an ecologically conserved mechanism through which the gut microbiome modulates autoimmune and inflammatory diseases.

immunology↗

bioRxiv2025

ERAD Activity Distinguishes the Functional Heterogeneity of Hematopoietic Stem Cells

Hematopoietic stem cells (HSCs) rely on precisely controlled proteostasis to sustain lifelong self-renewal, yet whether intrinsic proteostatic characteristics can prospectively define functional diversity within the HSC pool remains unknown. In this study, we developed a dual-fluorescence reporter system to visualize endoplasmic reticulum-associated degradation (ERAD) activity in vivo and discovered that ERAD activity can prospectively predicts the long-term reconstitution potential of HSCs. Remarkably, ERAD states were maintained through self-renewal, revealing an inheritable "proteostatic memory" within the HSC pool. Transcriptomic and functional analyses identified SOCS2 as a key regulator of this process: SOCS2 inhibits JAK2 signaling to sustain ERAD activity, whereas hyperactive JAK2 interacts with the ERAD E3 ligase Hrd1 and suppresses VCP-mediated misfolded substrate. These findings define a SOCS2-JAK2-ERAD axis that connects cytokine signaling to intrinsic proteostasis remodeling, establishing ERAD activity as a predictive and heritable marker of HSC function and providing a conceptual framework for understanding hematopoietic stem cell heterogeneity.

cell biology↗

bioRxiv2025

A subset of world barley collection was used in the identification of sources of resistance and marker-trait association for resistance for bacterial leaf streak

The bacterial leaf streak (BLS) disease of barley, caused by Xanthomonas translucens pv. translucens (Xtt), has become increasingly important worldwide in recent years. Inefficacy of chemical control methods leaves deployment of host resistance to be the only option to manage this disease. However, current commercial varieties are mainly susceptible to BLS. Therefore, our goal was to identify sources of resistance from diverse barley germplasms and map associated genetic factors. To do so, we evaluated a subset of the World Barley Core Collection (BCC), consisting of 198 accessions, on their reaction to BLS from 2013 to 2016 under natural or artificially inoculated disease pressures. Ten accessions exhibited consistently low disease severities over four years of evaluations. Using genotype data from the T3/Barley database, genome-wide association studies were conducted to identify marker-trait associations (MTAs) in this barley mini-core panel for BLS resistance. Utilizing four mixed-model analyses (MLM, MLMM, FarmCPU, BLINK), five significant MTAs were consistently identified from at least two mixed model analyses including two in chromosome 2H, and one each in chromosomes 5H, and 7H. Associations in chromosomes 2H and 5H appear to be in the same region with loci identified in a previous association study, reinforcing their potential relevance. The identified resistant barley accessions and associated markers will be valuable inbreeding BLS-resistant barley varieties. Core ideas- A subset of world barley collection was used in the identification of sources of resistance and marker-trait association for resistance for bacterial leaf streak. - Ten accessions consistently showed low disease severity across different years, highlighting their value in BLS resistance breeding. - Five MTAs were consistently identified using different models, with two aligning with previously identified resistance QTLs.

plant biology↗

bioRxiv2025

XPF mediates 3' flap processing for FEN1-independent Okazaki fragment maturation

Okazaki fragment maturation (OFM), the process that removes RNA-DNA primers, is a major source of DNA replication stress and mutations. It involves Pol{delta}-mediated DNA strand displacement synthesis that produces 5 flaps, FEN1-mediated 5 flap cleavage, and LIG1-catalyzed nick ligation. Recently, we discovered that under stress conditions, yeast cells convert 5 flaps into 3 flaps, which are degraded by 3 flap nucleases to produce ligatable DNA nicks. However, little is known about this stress-induced, 3 flap-based OFM in human cells. Here, we report that 3 flaps frequently form in various human cancer cells, and that FEN1 deficiency significantly enhances 3 flap levels. XPF1 is recruited to the replication forks in FEN1 mutant or FEN1-chemically inhibited cells. Notably, XPF deficiency or inhibition in those defective cells leads to accumulation of 3 flaps, replication-related DNA strand breaks, and unique mutation signatures. Furthermore, XPF and FEN1 inhibitors show synergistic effects in killing human cancer cells. In summary, we demonstrate that 3 flap-based OFM is an important alternative of 5 flap-based OFM in mammalian cells. XPF is a key nuclease to degrade 3 flaps and complete OFM for survival. Targeting this compensatory mechanism could provide new therapeutic strategies to selectively impair cancer cell survival under pre-existed replication stress. HighlightsO_LIXPF is recruited to DNA replication forks in mouse or human cells of functional deficiency of FEN1 due to genetic mutations or chemical inhibition. C_LIO_LIXPF gene deficiency or chemical inhibition results in accumulation of 3 flaps and replicative DNA single-stranded breaks. C_LIO_LIFunctional deficiency of XPF and FEN1 displays a synergy in inducing genome instability and cell death in human cancer cells. C_LI

cell biology↗

bioRxiv2025

JMJD1B-mediated FEN1 demethylation allows timely switching of Okazaki fragment maturation core enzymes to avoid mutagenic flap ligation by PARP1-LIG3

Efficient and faithful Okazaki fragment maturation (OFM) depends on the PCNA-coordinated actions of core enzymes Pol{delta}, FEN1, and LIG1. We demonstrate that Pol{delta}, FEN1, and LIG1 sequentially but not simultaneously bind to PCNA in mammalian cells. The association of FEN1 with PCNA, which lies at the center of this orderly program, is mediated by FEN1 R192 methylation, which is also crucial for preventing premature loading of LIG1. Conversely, FEN1 demethylation by the recently identified arginine demethylase JMJD1B promotes FEN1 dissociation from PCNA and LIG1 recruitment. Disruption of the sequential PCNA binding program in R192Q or Jmjd1b-/- cells results in unprocessed 5 flaps that prevent OFM and induction of PARP1-dependent recruitment of LIG3, which has flap ligation activity to join incompletely processed OFs. This alternative OFM process supports cell survival but causes duplications and other DNA mutations. Our findings define fundamental and alternative DNA replication processes underlying mutagenesis and cell survival. HighlightsO_LIThe core enzymes involved in Okazaki fragment maturation (OFM), DNA polymerase {delta} (Pol{delta}), flap endonuclease 1 (FEN1), and ligase 1 (LIG1), sequentially bind to the scaffold protein PCNA for their concerted actions C_LIO_LIFEN1 R192 methylation enables FEN1 binding to PCNA; JMJD1B-mediated FEN1 arginine demethylation provokes FEN1 exit from PCNA and LIG1 recruitment C_LIO_LIFEN1 R192Q mutation and JMJD1B deficiency oppositely alter dynamic PCNA interactions with FEN1 and LIG1 and result in distinct OFM DNA intermediate structures C_LIO_LIActivation of PARP1 at replication forks due to disruption of the sequential PCNA binding program induces LIG3-mediated alternative mutagenic 5 flap ligation for survival. C_LI

cell biology↗

bioRxiv2025

IFITM1 and IFITM3 cooperate to restrict virus entry in endolysosomes

Interferon-induced transmembrane (IFITM) proteins are potent innate immune factors that restrict an array of viruses at the entry stage of infection. We previously characterized a GxxxG motif in the CD225 domain of human IFITM3 that mediates its multimerization, which is essential for the reduction of membrane fluidity by IFITM3 and for its antiviral activity against Influenza A virus. Here, using an unbiased approach coupling immunoprecipitation with mass spectrometry, we show that the GxxxG motif is also important for the interaction of IFITM3 with other proteins, including IFITM1. While IFITM1 is primarily regarded as a cell surface protein that restricts the entry of viruses fusing at the plasma membrane, this model is based mostly on overexpression studies and is at odds with some studies showing that it can restrict endocytic viruses. Here, we show that endogenous IFITM1 and IFITM3 co-reside in membranes of acidic late endosomes and lysosomes (endolysosomes) and form a protein-protein complex as determined by co-immunoprecipitation and proximity ligation assay. Knockdown of endogenous IFITM3 resulted in enhanced localization of IFITM1 at the plasma membrane, indicating that IFITM3 promotes IFITM1 localization to endolysosomes. To assess the antiviral protection conferred by endogenous IFITM1 and IFITM3 against viruses fusing at endolysosomal membranes, we measured cell entry mediated by the Influenza A fusogen hemagglutinin (HA). While knockdown of IFITM3 significantly boosted HA-mediated entry, combined knockdown of both IFITM3 and IFITM1 boosted entry even further. These results suggest that endogenous IFITM1 restricts Influenza A virus entry in a manner that is non-redundant with IFITM3, and that IFITM1 and IFITM3 inhibit virus entry in a cooperative manner.

microbiology↗

bioRxiv2025

Chromosome-scale genome assembly of B10.RIII, an autoimmune susceptible mouse strain

BackgroundA vast majority of potential drug candidates are initially tested in mice before human trials, resulting in life-saving treatments and preventive measures. Hundreds of autoimmune disorders, including arthritis, lupus etc., affect millions of people all over the world. Studying those disorders using mouse models is crucial for understanding the disease mechanisms. Knowing the genome sequence of these mouse models would help with those vital studies. B10.RIII is one of the most susceptible mouse strains used as a model to understand autoimmune diseases but did not have its genome sequenced until now. FindingsIn this study, we generated the first, high-quality chromosome level genome sequence of B10.RIII, using a combination of long read, short read and optical mapping techniques. The B10.RIII genome sequence scored higher than the reference mouse genome both in assembly completeness and assembly quality. The B10.RIII genome annotation based on the reference genome identified about 98% of the known reference genes. ConclusionsWe believe the availability of B10.RIII genome sequence will help advance the understanding of autoimmune diseases, giving the researchers a better idea on its unique genetic makeup. Comparative studies of B10.RIII with other mouse models could also significantly enhance the power of these models towards their clinical applications.

immunology↗

bioRxiv2025

SCassist: An AI Based Workflow Assistant for Single-Cell Analysis

SummarySingle-cell RNA sequencing (scRNA-seq) data analysis often involves complex iterative workflow, requiring significant expertise and time. To navigate this complexity, we have developed SCassist, an R package that leverages the power of the large language models (LLMs) to guide and enhance scRNA-seq analysis. SCassist integrates LLMs into key workflow steps, to analyze user data and provide relevant recommendations for filtering, normalization and clustering parameters. It also provides LLM guided insightful interpretations of variable features and principal components, along with cell type annotations and enrichment analysis. SCassist provides intelligent assistance using popular LLMs like Googles Gemini, OpenAIs GPT and Metas Llama3, making scRNA-seq analysis accessible to researchers at all levels. Availability and implementationThe SCassist package, along with the detailed tutorials, is available at GitHub. https://github.com/NIH-NEI/SCassist

bioinformatics↗