Biology subjects

Inoue, Y.

Publications and source records attributed to Inoue, Y..

At least 19 recordsLinked to original sources

bioRxiv2026

Can carcasses cause environmental nucleic acid pollution? Implications for interpreting environmental RNA/DNA survey results

Environmental nucleic acid (eRNA and eDNA) metabarcoding is a promising tool for biodiversity assessment as it supports low-cost, noninvasive biological surveys. A critical challenge for eRNA/eDNA analyses is accounting for nucleic acid contamination that can compromise the accuracy of biomonitoring results. The primary aim of the current study was to examine carcasses as potential sources of eRNA/eDNA contamination, a contribution that remains poorly understood. Using Japanese medaka (Oryzias latipes), we quantified the detectability and persistence of carcass-derived eRNA/eDNA in water through two complementary experiments: (i) a shedding study comparing eRNA/eDNA release from live and dead individuals and (ii) a decay experiment measuring temperature-dependent degradation from 4 to 34 {degrees}C. Dead fish released detectable amounts of both eDNA and eRNA, indicating that eRNA-based surveys cannot fully eliminate carcass-derived signals. Arrhenius-based analysis showed that eRNA degradation was more temperature-dependent than eDNA degradation. These results suggest that eRNA may improve temporal resolution for recent organismal presence under warm conditions, whereas carcass-derived eRNA may persist under cold conditions and complicate interpretation of positive detections. Overall, eRNA may help reduce carcass-related false positives, particularly in warm conditions, but should be paired with temperature-aware sampling strategies and temporal replication during colder periods.

ecology↗

bioRxiv2026

Dynamic Schlafen 11 (SLFN11) expression revealed by single-cell RNA sequencing of clonal human cancer cells

Schlafen 11 (SLFN11) is a key determinant of sensitivity to DNA-damaging therapies in multiple cancers including leukemia, Ewing sarcoma, head and neck cancers, mesothelioma and small cell lung cancer (SCLC). Here, utilizing immunofluorescence microscopy and single-cell RNA sequencing we characterized SLFN11 expression across eight different human cancer cell lines and found cell-to-cell heterogenous expression both at the protein and RNA levels. Gene set enrichment and pathway analyses show that SLFN11 is coexpressed with a distinct stress-response state and enhanced genome maintenance programs while being inversely correlated with protein translation pathways. Publicly available single-cell RNA-sequencing datasets of human SCLC tumors confirmed the heterogeneous distribution of SLFN11 expression and confirmed its association with replication-related transcriptional programs. These findings indicate that heterogeneous SLFN11 expression reflects dynamic regulation at the single-cell level. They also underscore the limitations of bulk proteomic and transcriptome profiling and point to a potential reservoir of intrinsic chemotherapy resistance.

cancer biology↗

bioRxiv2026

Stigmatic papilla cells recover nonself pollen acceptance after self-pollen recognition

In Brassicaceae, self-incompatibility is initiated when the pollen ligand SP11/SCR activates the cognate stigma receptor kinase SRK. Although this interaction is usually considered at a single pollen-papilla interface, individual papilla cells encounter mixed pollen loads. Here, using a self-incompatibility-reconstituted Arabidopsis thaliana system, we show that self-pollen recognition transiently delays the hydration and germination of neighboring nonself pollen. The delay was stronger when two self-pollen grains were present but largely disappeared when nonself pollen was applied 2 h after self pollen. Repollination after removal of a self-pollen grain nevertheless revealed persistent inhibition at the original contact site. Live imaging with Lifeact-tdTomato showed that self-pollination transiently broadened F-actin orientations throughout the papilla cell, followed by recovery toward the longitudinal organization of unpollinated cells. Upon self- and non-self-dual pollination, actin-bundle orientation returned toward the papilla long axis prior to the delayed hydration of the non-self-pollen. These observations support the view that the nature of the self-recognition signaling produces a reversible, papilla-wide state that temporarily reduces compatible-pollen acceptance, while local self-rejection persists at the original contact site.

plant biology↗

bioRxiv2026

Therapeutic Potential of the Novel Monoclonal Antibody 7-4G against HBsAg in a Mouse Model of Chronic Hepatitis B Virus Infection

Chronic hepatitis B virus (HBV) infection remains a major global health challenge because current antiviral therapies rarely achieve complete viral clearance. We evaluated the antiviral activity of a newly developed monoclonal antibody, 7-4G mAb, directed against the hepatitis B surface antigen (HBsAg). The antibody showed specific binding to the p27 component of HBsAg and efficiently removed HBV-related particles from patient serum in vitro. Significant HBV neutralizing activity of 7-4G mAb was observed in primary human hepatocytes and in humanized mouse models. In persistently HBV-infected PXB mice, a single administration of 7-4G mAb, either alone or in combination with another monoclonal antibody, reduced serum HBsAg levels and HBV DNA levels by two orders magnitude for two weeks after the treatment. In half of the treated mice, suppression of both viral markers was maintained through the study period, whereas rebound occurred within three to four weeks in the remaining animals. In addition, 7-4G mAb enhanced the HBV DNA-lowering effect of entecavir, a known anti-HBV drug. These findings support the further development of 7-4G mAb as part of an innovative HBV treatment strategy, addressing limitations of existing therapies and advancing toward a more effective HBV management solution.

immunology↗

bioRxiv2026

Tumor Microenvironment Modulates Lineage Plasticity in Lung Squamous Cell Carcinoma

Lung squamous cell carcinoma (LUSC) is the second most common type of lung cancer, yet therapeutic options remain limited. A deeper understanding of its biology and molecular pathogenesis is essential for developing new treatment strategies. Here, we investigated the mechanisms of phenotypic plasticity in LUSC by comparing organoid-derived orthotopic lung models (ODOLs) and subcutaneous xenograft models (ODXs). ODXs showed greater tumor growth, squamous differentiation, and extracellular matrix (ECM) organization compared to ODOLs. Transcriptomic analyses revealed upregulation of multiple HIF1 and SOX2 target genes together with enhanced hypoxia signaling in ODXs. CRISPR/Cas9-mediated HIF1-knockout ODXs showed reduced SOX2 expression, tumor growth, and ECM organization, whereas SOX2-knockout ODXs reduced tumor growth without affecting HIF1 and ECM organization. These results indicate that HIF1 regulates squamous lineage maintenance through SOX2 and ECM remodeling. Spatial transcriptomics revealed enrichment of basal cell-like and squamous-differentiated tumor states in ODXs, whereas ODOLs displayed less differentiated phenotypes. These findings identify the tumor microenvironment as a critical determinant of lineage plasticity in LUSC and provide mechanistic insight into how hypoxia shapes tumor differentiation.

Cancer Biology↗

bioRxiv2025

Morphogenesis of the Carapace from Phyllosoma to Puerulus in Spiny Lobsters

Molting in exoskeleton-bearing organisms can result in dramatic body shape transformations. While this phenomenon has been well-studied in insects, limited knowledge exists for other taxa, including crustaceans. Among crustaceans, achelatan lobsters, such as Palinuridae and Scyllaridae, exhibit a unique metamorphic transition from a flattened phyllosoma larva to a three-dimensional puerulus or nisto larva in a single molt. This study investigates the mechanisms underlying this transformation, focusing on carapace deformation through histological analysis, live imaging, and computational modeling. Three-dimensional micro-computed tomography revealed a significant reduction in body length during metamorphosis. Live imaging captured dynamic morphological changes, including epithelial contraction and subsequent reshaping. Scanning electron microscopy identified a distinctive furrow structure on the carapace surface, absent in post-molt puerulus larvae, suggesting a role in the transformation process. To explore the formation of this furrow pattern, a computational model was developed based on differential shrinkage rates in vertical and horizontal directions. The model successfully reproduced similar patterns observed in natural specimens, implying that controlled anisotropic contraction could contribute to morphogenesis. Furthermore, three-dimensional shrinkage simulations demonstrated that local contraction with constrained out-of-plane deformation can generate folds, which later expand to form curved structures. This study provides novel insights into the biomechanics of arthropod molting, highlighting a previously unrecognized mechanism of two-dimensional-to-three-dimensional transformation. The findings enhance our understanding of achelatan lobster development and offer broader implications for exoskeletal morphogenesis across arthropods.

developmental biology↗

bioRxiv2025

Environmental RNA/DNA Metabarcoding for Ecological Risk Assessment of Chemicals Based on Response of Benthic Communities in Natural Environments

To achieve the current Nature Positive goals, it is important to identify the effects of chemicals on ecosystems and strategically reduce their risks. We therefore estimated the safe concentration (SC) of linear alkylbenzene sulfonate (LAS) by investigating the relationship between benthic communities detected via environmental RNA (eRNA) and environmental DNA (eDNA) metabarcoding and the water quality in a river contaminated with LAS. Non-metric multidimensional scaling of benthic communities detected via eRNA indicated significant differences between contaminated and non-contaminated sites, and redundancy analysis showed significant correlation between the benthic communities and LAS concentration. These results demonstrate that eRNA is more sensitive than eDNA for capturing the community changes that result from LAS contamination. No significant differences were observed in biodiversity indices between the highest LAS concentration site and non-contaminated site; thus, the SC was estimated at >47 {micro}g/L. The results suggest that, although hazard assessment using the assessment factor (AF) leads to conservative estimation of the effects of chemicals because the predicted no-effect concentration in previous studies is lower than the SC, hazard assessment based on the response of biological communities using eRNA metabarcoding can refine such ecological assessments, developing the environmental management standards to achieve nature-positive goals.

ecology↗

bioRxiv2025

Extracellular stiffness regulates cell fate determination and drives the emergence of evolutionary novelty in teleost heart

The diversification of life is driven by the acquisition of new phenotypic traits, known as evolutionary novelties. While some genetic mechanisms underlying such traits have been identified, the role of physical properties of cellular and extracellular components remains largely unexplored. Here, we show that the evolution and development of the bulbus arteriosus (BA)-a teleost-specific, smooth muscle-rich heart outflow tract-is regulated by the mechanical properties of its extracellular environment. Specifically, we demonstrate that the teleost-specific extracellular matrix gene elastin b confers the uniquely low stiffness of the BA. In contrast to the BA, the homologous organ in non-teleost actinopterygians, the conus arteriosus (CA), and the ventricle are predominantly composed of cardiomyocytes, and exhibit higher extracellular stiffness. Loss of elastin b function by knockdown or knockout leads to ectopic cardiomyocyte formation in the BA, accompanied by increased extracellular stiffness comparable to that of the ventricle. Furthermore, artificial stiffening of the BA extracellular environment is sufficient to induce ectopic cardiomyocyte differentiation. Taken together, these findings demonstrate that extracellular stiffness governs cell fate determination and highlight its role in the emergence of evolutionary novelties in the teleost heart. Significant StatementThe acquisition of new phenotypic traits is a key driver for a diversification of life. While genetic underpinnings of such traits have been well studied, the contribution of physical properties remains elusive. Here, we show that extracellular stiffness plays a key role in the evolution and development of the bulbus arteriosus (BA), a smooth muscle-based cardiac outflow tract unique to teleost hearts. We demonstrate that elastin b, a teleost-specific gene, confers characteristically low stiffness to the BA, which is required for proper cell fate determination. Notably, such low stiffness is absent in non-teleost fishes and in teleosts with impaired elastin b function, and artificial stiffening alters cell fate. Our findings highlight the importance of physical properties in driving evolutionary novelties.

developmental biology↗

bioRxiv2025

Class I myosins direct circumferential F-actin flows to define cell chirality

Eukaryotic cells possess intrinsic chirality in their structure, motility, and intracellular dynamics, which are designated cell chirality. Cell chirality participates in the left-right asymmetric morphogenesis and tissue integrity. However, the mechanisms of cell chirality formation remain elusive. In Drosophila, two evolutionarily conserved myosin I genes, Myosin 1D (Myo1D) and Myosin 1C (Myo1C), respectively, dictate the dextral and sinistral chirality of the cells and body. Here, we reported that Myo1D and Myo1C respectively directed the clockwise and counterclockwise circumferential flow of F-actin in Drosophila macrophages. Both induced the corresponding circular cytoplasm flows and depended on Myosin2 (Myo2). In a modified in vitro motility assay using near-physiological actin concentrations, Myo1D triggered the self-organization of the F-actin ring (chiral F-actin ring) that rotated clockwise; conversely, Myo1C induced the random flow of F-actin. The chiral F-actin ring implied that the F-actin bundle was parallelly and annularly polarized concerning its barbed pointed end. Considering that Myo1D and Myo1C are localized to the dorsal plasma membrane of macrophages, Myo1D and Myo1C might organize the parallelly polarized F-actin in macrophages. Our results suggest that Myo2 might drive the clockwise circumferential flow of F-actin along its parallel and annular polarity induced by Myo1D, which may be a molecular basis of cell and organ chirality.

cell biology↗

bioRxiv2025

Elucidating Chiral Myosin-Induced Actin Dynamics: From Single Filament Behavior to Collective Structures

The myosin superfamily comprises over 70 classes, each with multiple subclasses, and shows substantial diversity in properties such as velocity, ATPase activity, duty ratio, and directionality. This functional diversity enables the specialized roles of each myosin in various organisms, organs, and cell types. Recent studies have revealed that certain myosins induce chiral curved motions of actin filaments. However, this newly identified property remains largely unexplored. Here, we investigated this chiral motion in vitro using Chara corallina myosin XI (CcXI), which drives fast counterclockwise (CCW) movement of actin filaments. This chiral motion arises from asymmetric displacement at the filaments leading tip, and its curvature depends on the surface density of myosin. Surprisingly, at near-physiological actin concentrations, actin filaments exhibiting chiral curved motion undergo collective motion, spontaneously forming a novel structure--termed the actin chiral ring (ACR)--that exhibits persistent CCW rotation. ACRs display remarkable stability, continuing to rotate at their formation site until ATP is depleted, while maintaining their structure even after rotation ceases. This stability is unprecedented among reported collective motions of cytoskeletal proteins driven by various motors. Our findings demonstrate that myosins with chiral activity can autonomously organize actin filaments into stable, chiral structures through collective motion, providing new insights into actin self-organization by unconventional myosins. This study advances our understanding of the diverse functional roles of unconventional myosins and introduces a new paradigm for cytoskeletal organization. Significance StatementMyosins are motor proteins that move along actin filaments and support various intracellular functions. Recently, some myosins have been found to drive actin filaments along chiral curved paths, but the mechanisms and significance of this behavior remain poorly understood. Here, we analyzed this activity and discovered that it not only drives chiral curved motion of single actin filaments, but also organizes them into stable, unidirectionally rotating ring structures through collective motion. These rings, termed actin chiral rings (ACRs), spontaneously emerge at near-physiological actin concentrations. Our findings uncover a previously unrecognized organizing principle of actin self-assembly driven by myosin with chiral activity and provide a new framework for understanding how cytoskeletal chirality is made.

cell biology↗

bioRxiv2025

Bulk sample testing by real-time PCR for detecting Diaporthe destruens-infected seedlings of sweet potatoes

Foot rot disease of sweet potato is a fungal disease that causes serious damage to sweet potato production. It is especially important to check the health of seedlings as there is a risk that if the seed tubers or stem seedlings infected with foot rot pathogen are introduced into the production fields, it will rapidly spread throughout the fields. We have already developed a real-time PCR method to diagnose sweet potatoes contaminated with foot rot pathogen. In this study, to apply this method to the bulk sample testing, we provided examples on estimating the "probability of detection (POD)" for detecting bulk samples, and determining the number of subgroups and the number of samples in each subgroup for the bulk sample testing. Our results indicate that, for tubers, when testing between 100 and 1200 fragments per bulk sample, the lowest detection rate was approximately 81% at 800 fragments. For stems, when testing between 100 and 600 fragments, the lowest detection rate was approximately 83% at 500 fragments. Based on the estimated POD, the required sample size for bulk testing was calculated as follows: for the impermissible threshold proportion of contamination of infected plants (p) of 1%, between 390 and 624 samples are needed, while for p of 0.1%, between 3,840 and 6,228 samples are required. The bulk sample testing method using real-time PCR demonstrated in this study will become a powerful quality testing method for checking the health of sweet potato seedlings, and will make a significant contribution to sweet potato production.

plant biology↗

bioRxiv2025

Evaluation of real-time PCR performance for detecting Diaporthe destruens in sweet potatoes

Sweet potato foot rot disease caused by Diaporthe destruens is a major threat to sweet potato production. Rapid and accurate detection in advance is essential to secure healthy plants or to implement effective control. In this study, we evaluated the detection performance of a real-time PCR method previously developed by our research group. The evaluation was conducted using sweet potato samples collected in the field, including those naturally infected with D. destruens. Based on the real-time PCR results and the actual occurrence of the disease, a receiver operating characteristic (ROC) curve was generated, and the area under the curve (AUC) was calculated. The AUC values ranged from 0.7041571 to 0.9204286, confirming that this real-time PCR method is a well-balanced detection method for both tubers and stems. Furthermore, to minimize the occurrence of false negatives, the cycle threshold (Ct) cutoff was set at 35, and detection performance (sensitivity, specificity, accuracy, etc.) was analyzed. Then, by considering abnormal melting temperature (Tm) values as negative, high accuracy was achieved, with values of 0.871212 for tubers and 0.715447 for stems. This study not only evaluated the detection performance of the real-time PCR for foot rot pathogens but also contributes to providing information on the methodology and significance of performance evaluation in various real-time PCR genetic detection methods.

plant biology↗

bioRxiv2025

The dominant lineage of Phakopsora pachyrhizi in the United States of America does not have a Brazilian origin

O_LIAsian soybean rust (ASR), caused by the obligate biotrophic fungus, Phakopsora pachyrhizi, was first reported in the continental United States of America (USA) in 2004 and over the years has been of concern to soybean production in the USA. The prevailing hypothesis is that P. pachyrhizi spores were introduced into the USA via hurricanes originating from South America, particularly Hurricane Ivan. C_LIO_LITo investigate the genetic diversity and global population structure of P. pachyrhizi, we employed exome-capture based sequencing on 84 field isolates collected from different geographic regions worldwide. We compared the gene-encoding regions from all these field isolates and found that four major haplotypes are prevalent worldwide. Here, we provide genetic evidence supporting multiple incursions that have led to the currently established P. pachyrhizi population of the USA. Phylogenetic analysis of mitochondrial genes further supports this hypothesis. C_LIO_LINotably, we observed limited genetic diversity in P. pachyrhizi populations in Brazil, suggesting a clonal population structure in that country that contrasts to populations from the USA and Africa. C_LIO_LIThis study provides the first comprehensive characterization of P. pachyrhizi population structures defined by genetic evidence from populations across major soybean growing regions. C_LI

evolutionary biology↗

bioRxiv2024

Improvement of D-lactic acid production from methanol by metabolically engineered Komagataella phaffii via ultra-violet mutagenesis

Methanol has attracted attention as an alternative carbon source to petroleum. Komagataella phaffii, a methanol-assimilating yeast, is a useful host for the chemical production from methanol. A previous study successfully constructed a metabolically engineered K. phaffii GS115/S8/Z3 strain capable of producing D-lactic acid from methanol. In this study, we aimed to develop a strain with improved D-lactic acid production by applying ultra-violet mutagenesis to the D-lactic acid-producing strain, GS115/S8/Z3. The resulting mutant strain DLac_Mut2_221 produced 5.38 g/L of D-lactic acid from methanol, a 1.52-fold increase compared to the parent strain GS115/S8/Z3. Transcriptome analysis revealed 167 differentially expressed genes in DLac_Mut2_221, comprising 104 upregulated and 63 downregulated genes. These results suggest that the improvement in D-lactic acid production from methanol in the mutant strain involves three important mechanisms: (1) avoiding excessive formaldehyde accumulation, (2) activating the glyoxylate pathway, and (3) reducing the expression of O-glycosylated proteins required for cell wall stability. Metabolic engineering strategies for K. phaffii based on the knowledge gained from this study will contribute to improving the productivity of various useful chemicals from methanol.

bioengineering↗

bioRxiv2024

Fish environmental RNA sequencing sensitively captures accumulative stress responses through short-term aquarium sampling

The utility of environmental RNA (eRNA) in capturing biological responses to stresses has been discussed previously; however, the limited number of genes detected remains a significant hindrance to its widespread implementation. Here, we investigated the potential of eRNA to assess the health status of Japanese medaka fish exposed to linear alkylbenzene sulfonate. Analyzing eRNA and organismal RNA (oRNA) in aquarium water for > 12 h, we achieved high mapping rates and 10 times more differentially expressed genes than previously reported. This advancement has facilitated the previously unattainable capability of gene ontology (GO) analysis. In GO analysis, it was found that eRNA could detect nuclear genes in cellular component, and oRNA provided gene expression signatures in the short term, whereas eRNA demonstrated the potential to reflect cumulative gene expression signatures over a period of time in biological process. Moreover, eRNA exhibited high sensitivity in responding to genes associated with sphingolipid and ceramide biosynthesis, which are involved in inflammatory responses possibly originating from impaired cells. This finding aligns with the observations made in oRNA. Conclusively, eRNA-sequencing (eRNA-seq) using aquarium water emerges as a valuable high sensitivity tool for analyzing physiological stress. The findings of this study lay the foundation for further development of eRNA-seq technologies.

ecology↗

bioRxiv2024

Biregional division angles generate sharp apex and concave joints in leaves

Leaf apex, the distal end of the leaf blade, exhibits enormous shape variations across plant species. Among these variations, the sharp apex, characterized by its pointed tip, is important in species identification and environmental adaptation. Despite its taxonomic and ecological importance, the developmental mechanisms underlying the formation of a sharp apex remain unknown. The present study aims to investigate the curvature patterns and morphogenesis of the sharp apex to uncover these mechanisms using Triadica sebifera leaves. Our research revealed that the sharp apex marks the maximum positive curvature, and is flanked by concave joints with negative curvatures, suggestive of differential tissue growth and spatially regulated cellular behavior. Through a combination of wet experiments and numerical simulations, we demonstrated that biregional cell division angles, rather than locally differing cell expansion or division frequency, play a determining role in shaping distinct leaf morphology. Our study highlights the importance of spatiotemporal regulation of cell division angles during leaf development, suggesting that a biregional growth pattern and cellular behavior contribute to diversity in leaf apex morphology.

plant biology↗

bioRxiv2024

Development of a noninvasive olfactory stimulation fMRI system in marmosets

Olfactory dysfunction is associated with aging and the earliest stages of neurodegenerative diseases, such as Alzheimers and Parkinsons diseases; it is thought to be an early biomarker of cognitive decline. In marmosets, a small non-human primate model used in brain research, olfactory pathway activity during olfactory stimulation has not been well studied because of the difficulty in clearly switching olfactory stimuli inside a narrow MRI. Here, we developed an olfactory-stimulated fMRI system using a small-aperture MRI machine. The olfactory presentation system consisted of two tubes, one for supply and one for suction of olfactory stimulants and a balloon valve. A balloon valve installed in the air supply tube controlled the presentation of the olfactory stimulant, which enabled sharp olfactory stimulation within MRI, such as 30 seconds of stimulation repeated five times at five-minute intervals. The olfactory stimulation system was validated in vivo and in a simulated system. fMRI analysis showed a rapid increase in signal values within 30 s of olfactory stimulation in eight regions related to the sense of smell. As these regions include those associated with Alzheimers and Parkinsons diseases, olfactory stimulation fMRI may be useful in clarifying the relationship between olfactory dysfunction and dementia in non-human primates.

physiology↗

bioRxiv2024

BiGCN: Leveraging Cell and Gene Similarities for Single-cell Transcriptome Imputation with Bi-Graph Convolutional Networks

MotivationRNA profiling at the single-cell level is essential for characterizing the molecular activities and functions of individual cells. The current technical limitations of single-cell RNA sequencing (scRNA-seq) technologies can lead to a phenomenon known as "dropout", where a significant portion of gene expression is not captured. Dropout is particularly prominent in genes with low or sparse expression, greatly impacting the reliability and interpretability of scRNA-seq data. Consequently, various techniques have been developed to estimate missing gene expression using imputation, often by either modeling similarities in gene expression among cells or using gene co-expression, but rarely both. ResultsIn this study, we introduce a Bi-Graph Convolutional Network (BiGCN), a deep learning method that leverages both cell similarities and gene co-expression to capture cell-type-specific gene co-expression patterns for imputing scRNA-seq data. BiGCN constructs both a cell similarity graph and a gene co-expression graph, and employs them for convolutional smoothing in a dual two-layer Graph Convolutional Networks (GCNs). The embeddings from the two GCNs can subsequently be combined to facilitate the final imputation. BiGCN demonstrates superior performance compared to state-of-the-art imputation methods on both real and simulated scRNA-seq data. Additionally, BiGCN outperforms existing methods when tasked with clustering cells into cell types. We also perform a novel validation using a PBMC scRNA-seq dataset, and this experiment supports that BiGCNs imputations are more realistic than competing imputation methods. In both the imputation and the cluster tasks, BiGCN consistently outperformed two variants of BiGCN that solely relied on either the gene co-expression graph or cell similarity graph. This indicates that the two graphs offer complimentary information for imputation and cell clustering, underscoring the importance of incorporating both types of information. Code Availabilityhttps://github.com/inoue0426/scBiGCN. Contactkuang@umn.edu

bioinformatics↗