Publications of SeekGene
Author: Ruifeng Gao
Time: 105 min
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Updated: 2026-03-02
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Overview
Below is a list of all project publications. You can filter by year, product type, and impact factor range, sort by impact factor or year, and search by keyword. The table can be exported as CSV, and DOIs link directly to the original articles.
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| Year | Title | Journal | Impact factor | Sample type | Product type | DOI | Summary |
|---|---|---|---|---|---|---|---|
| 2023 | Single-cell transcriptome analysis profiles cellular and molecular alterations in submandibular gland and blood in IgG4-related disease | Annals of the Rheumatic Diseases | 27.4 | PBMC and submandibular gland tissue | 3' scRNA-seq | https://doi.org/10.1136/ard-2023-224363 | |
| 2024 | Janus liposozyme for the modulation of redox and immune homeostasis in infected diabetic wounds | Nature Nanotechnology | 38.3 | Mouse skin wound | 3' scRNA-seq, SeekSoul™ Online | https://doi.org/10.1038/s41565-024-01660-y | In May 2024, SeekBio's single-cell transcriptome products assisted a research team from Nankai University in publishing an article entitled "Janus liposozyme for the modulation of redox and immune homeostasis in infected diabetic wounds" in Nat. Nanotechnol. SeekBio provided single-cell transcriptome (scRNA-seq) sequencing and data analysis services based on SeekSoul™ Online. |
| 2024 | Computing cell state discriminates the aberrant hematopoiesis and activated microenvironment in Myelodysplastic syndrome (MDS) through a single cell genomic study | Journal of Translational Medicine | 6.1 | Bone marrow cells | 3' scRNA-seq | https://doi.org/10.1186/s12967-024-05496-x | |
| 2024 | Integrative profiling of untreated primary membranous nephropathy at the single-cell transcriptome level | Clinical Kidney Journal | 3.9 | Blood, kidney and urine from PMN patients | 3' scRNA-seq | https://doi.org/10.1093/ckj/sfae168 | |
| 2024 | Cooperative progression of colitis and leukemia modulated by clonal hematopoiesis via PTX3/IL-1β pro-inflammatory signaling | Genes & Diseases | 6.9 | Cells from mouse colon tissue | other | https://doi.org/10.1101/2023.08.29.555330 | |
| 2024 | A distinct immune landscape in anti-synthetase syndrome profiled by a single-cell genomic study | Frontiers in Immunology | 5.7 | PBMC | 3' scRNA-seq | https://doi.org/10.3389/fimmu.2024.1436114 | |
| 2025 | Utilization of donor CLL-1 CAR-T cells for the treatment of relapsed of acute myeloid leukemia following allogeneic hematopoietic stem cell transplantation | Frontiers in Immunology | 5.7 | Cells from patient 4's CLL-1 CAR-T cell infusion product and peripheral blood mononuclear cells (PBMCs) at peak expansion | 3' scRNA-seq | https://doi.org/10.3389/fimmu.2024.1491341 | |
| 2025 | Single-cell and spatial transcriptomics reveal the pathogenesis of chronic granulomatous disease in a natural model | Cell Reports | 7.5 | Lung tissue | Spatial-seq | https://doi.org/10.1016/j.celrep.2025.115612 | |
| 2025 | Longitudinal Changes in Peripheral and Alveolar Monocyte and Inflammatory Biomarkers are Distinct in Hypercapnia Patients Following Pulmonary Sepsis-Induced ARDS | Journal of Inflammation Research | 4.2 | Peripheral blood | 5' + Immune Profiling | https://doi.org/10.2147/JIR.S508311 | |
| 2025 | Myeloid-lineage-specific membrane protein LRRC25 suppresses immunity in solid tumor and is a potential cancer immunotherapy checkpoint target | Cell Reports | 7.5 | Multiple cancer tissues in mice | other | https://doi.org/10.1016/j.celrep.2025.115631 | |
| 2025 | Single-cell profiling reveals monocyte heterogeneity and association with liver fibrosis in patients with chronic HBV | Hepatology Communications | 5.6 | Peripheral blood | SeekSoul™ Online | https://doi.org/10.1097/HC9.0000000000000672 | |
| 2025 | Cooperative progression of colitis and leukemia modulated by clonal hematopoiesis via PTX3/IL-1β pro-inflammatory signaling | Genes & Diseases | 9.4 | Mouse colon tissue | other | https://doi.org/10.1016/j.gendis.2024.101397 | |
| 2025 | Single-cell atlas reveals heterogeneous response to FcRn blockade in anti-AChR antibody-positive generalised myasthenia gravis | Clinical and Translational Medicine | 6.8 | PBMC | 3' scRNA-seq | https://doi.org/10.1002/ctm2.70436 | |
| 2025 | Nociceptor neurons promote PDAC progression and cancer pain by interaction with cancer-associated fibroblasts and suppression of natural killer cells | Cell Research | 28.1 | Pancreatic ductal adenocarcinoma tissue | 3' scRNA-seq | https://doi.org/10.1038/s41422-025-01098-4 | |
| 2024 | CXCR6 defines therapeutic subtypes of CD4+ cytotoxic T cell lineage for adoptive cell transfer therapy in pediatric B cell acute lymphoblastic leukemia | International Immunopharmacology | 4.8 | Peripheral blood and bone marrow samples | 3' scRNA-seq | https://doi.org/10.1016/j.intimp.2024.111972 | |
| 2025 | Rational Design and Organoid-Based Evaluation of a Cocktail CAR-γδ T Cell Therapy for Heterogeneous Glioblastoma | Advanced Science | 14.3 | Glioblastoma | 3' scRNA-seq | https://doi.org/10.1002/advs.202501772 | |
| 2023 | Efficacy, Mechanism, and Structure−Activity Relationship of 6‑Methoxy Benzofuran Derivatives as a Useful Tool for Senile Osteoporosis | Journal of Medicinal Chemistry | 7.3 | Osteoporosis | 3' scRNA-seq | https://doi.org/10.1021/acs.jmedchem.2c01377 | Institute of Medical Biotechnology, Chinese Academy of Medical Sciences and Peking Union Medical College published an article entitled "Efficacy, Mechanism, and Structure−Activity Relationship of 6‑Methoxy Benzofuran Derivatives as a Useful Tool for Senile Osteoporosis" in the Journal of Medicinal Chemistry. The first author is Zhou Ziying, and the corresponding authors are Researcher Li Zhuorong and Associate Researcher Xue Situ. This study used C57 and SAMP-6 aged mouse models to investigate the therapeutic and preventive effects of 6-methoxybenzofuran derivative 125 on senile osteoporosis (SOP). Single-cell transcriptome analysis revealed that BMP2 upregulation is the mechanism by which 125 accelerates bone turnover and increases the proportion of osteoblasts. This study provides a foundation for the development of SOP drugs. SeekBio provided single-cell transcriptome sequencing and analysis services for this research. SeekOne® MM single-cell transcriptome helped validate that small molecule drug 125 regulates bone formation through the PERK-eIF2α-ATF4 pathway. |
| 2023 | Single-cell RNA sequencing reveals intratumoral heterogeneity and potential mechanisms of malignant progression in prostate cancer with perineural invasion | Frontiers in Genetics | 3.7 | Prostate cancer | 3' scRNA-seq | https://doi.org/10.3389/fgene.2022.1073232 | |
| 2023 | Liver macrophages show an immunotolerance phenotype in nonalcoholic fatty liver combined with Porphyromonas gingivalis-lipopolysaccharide infection | West China Journal of Stomatology | 1.3 | Mouse liver | 3' scRNA-seq | https://doi.org/10.7518/hxkq.2023.2023111 | |
| 2024 | Network-based screening identifies sitagliptin as an antitumor drug targeting dendritic cells | J Immunother Cancer | 10.9 | Control/drug-treated tumors | 5' + Immune Profiling | https://doi.org/10.1136/jitc-2023-008254 | |
| 2024 | BMP2–ERK–ATF4 Axis-Based 6-methoxybenzofuran Compound I-9 Acts as Candidate Drug for Bone Formation and Anti-Osteoporosis | International Journal of Molecular Sciences | 4.9 | Femur | 3' scRNA-seq | https://doi.org/10.3390/ijms25063350 | |
| 2024 | Multi-omic analysis identifies metabolic biomarkers for the early detection of breast cancer and therapeutic response prediction | iScience | 4.6 | Breast cancer and adjacent tissue | 3' scRNA-seq | https://doi.org/10.1016/j.isci.2024.110682 | |
| 2024 | TLR agonists promote formation of Tertiary Lymphoid Structure and improve anti-glioma immunity | Neuro-Oncology | 16.4 | Mouse glioma cells | 5' + Immune Profiling | https://doi.org/10.1093/neuonc/noae167 | |
| 2024 | Immunosuppression and phenotypic plasticity in an atlas of human hepatocholangiocarcinoma | Hepatobiliary Surgery and Nutrition | 6.1 | Liver tumor | 3' scRNA-seq | https://doi.org/10.21037/hbsn-23-400 | |
| 2024 | Neoadjuvant toripalimab plus axitinib for clear cell renal cell carcinoma with inferior vena cava tumor thrombus: NEOTAX, a phase 2 study | Signal Transduct Target Ther | 40.8 | Tumor thrombus | 3' scRNA-seq | https://doi.org/10.1038/s41392-024-01990-2 | |
| 2024 | Cellular and molecular landscape of primary dermatofibrosarcoma protuberans: Insights from single‐cell RNA sequencing analysis | Exp Dermatol | 3.5 | Shoulder tumor nodules | 3' scRNA-seq | https://doi.org/10.1111/exd.15121 | |
| 2024 | PD - L1 protects tumor - associated dendritic cells from ferroptosis during immunogenic chemotherapy | Cell Reports | 7.5 | T cells from draining lymph nodes (dLNs) in mouse tumor models | 5' + Immune Profiling | https://doi.org/10.1016/j.celrep.2024.114868 | |
| 2024 | Lung Single-Cell Transcriptomics Offers Insights into the Pulmonary Interstitial Toxicity Caused by Silica Nanoparticles | Environment & Health | 5.3 | Rat lung tissue | 3' scRNA-seq | https://doi.org/10.1021/envhealth.4c00052 | |
| 2024 | Single - cell transcriptomic analysis reveals regulative mechanisms of follicular selection and atresia in chicken granulosa cells | Food Research International | 7 | Cells from chicken follicular granulosa cell layer | 3' scRNA-seq | https://doi.org/10.1016/j.foodres.2024.115368 | |
| 2025 | Transcriptomic Profiling Unveils EDN3+ Meningeal Fibroblasts as Key Players in Sturge-Weber Syndrome Pathogenesis | Advanced Science | 14.3 | Cells from malformed tissue (SWS samples) and perilesional tissue (control samples) in the brain of Sturge-Weber syndrome (SWS) patients | 3' scRNA-seq | https://doi.org/10.1002/advs.202408888 | Sturge-Weber syndrome (SWS), also known as cerebral facial angioma, is characterized by meningeal vascular malformations, leading to major risks of life-threatening epileptic seizures and strokes. Due to the current lack of specific therapeutic drugs, it is urgently needed to deeply understand the molecular and cellular mechanisms driving SWS progression to provide potential targets for future therapeutic interventions. On February 10, 2025, the team of Luan Guoming and Guan Yuguang from Sanbo Brain Hospital of Capital Medical University collaborated with the team of Ge Wuping from Beijing Institute of Brain Science and Intelligent Technology to publish "Transcriptomic Profiling Unveils EDN3+ Meningeal Fibroblasts as Key Players in Sturge-Weber Syndrome Pathogenesis" in Advanced Science. Based on malformed brain tissue and perilesional tissue from SWS patients, the study analyzed complex cellular heterogeneity, revealed different cell substates associated with disease progression, and identified EDN3+ meningeal fibroblasts and their molecular mechanisms that promote SWS development, providing potential targets for future therapeutic interventions. SeekBio provided professional single-cell transcriptome sequencing services using the SeekOne® MM platform in this project, ensuring that the research team obtained high-quality single-cell transcriptome data. |
| 2025 | Epitope‑focused vaccine immunogens design using tailored horseshoe‑shaped scaffold | Journal of Nanobiotechnology | 10.6 | B cells in spleen of immunized mice | 5' + Immune Profiling | https://doi.org/10.1186/s12951-025-03200-9 | |
| 2025 | Splicing diversity enhances the molecular classification of pituitary neuroendocrine tumors | Nature Communications | 14.4 | Pituitary neuroendocrine tumors (including GH, PG, PRL, TSH, ACTH, GO, NULL subtypes) and normal pituitary tissue | scFAST-seq | https://doi.org/10.1038/s41467-025-56821-x | Pituitary neuroendocrine tumors (PitNETs) are one of the most common intracranial tumors with diverse clinical manifestations. The current pathological classification system mainly relies on histological hormone staining and transcription factor (TFs) expression. Although it can effectively identify three major lineages, molecular features based on hormones and TFs lack sufficient resolution to fully capture complex tumor heterogeneity. On February 11, 2025, researchers from the Beijing Neurosurgical Institute/Tiantan Hospital Xie Weiyan and Li Chuzhong teams, along with the Liu Zhaoqi team from the Computational Biology Department of the National Center for Bioinformation, published the article "Splicing diversity enhances the molecular classification of pituitary neuroendocrine tumors" in Nature Communications. Researchers conducted bulk RNA sequencing on 264 PitNET patients and 4 normal samples, as well as full-length RNA sequencing on 14 PitNET patients and 2 normal samples, comprehensively investigating alternative splicing (AS) dysregulation in all PitNET lineages. This study effectively distinguished the silent corticotropin subtype and defined a unique TPIT lineage subtype, which is associated with poor clinical outcomes and increased splicing abnormalities driven by ESRP1 expression changes. These results characterize subtype-specific AS landscapes in PitNETs and enhance understanding of PitNET subtypes. |
| 2025 | Single-cell transcriptome analysis reveals cellular heterogeneity in the aortas of Takayasu arteritis | Arthritis Research & Therapy | 4.4 | Aortic tissue | 3' scRNA-seq | https://doi.org/10.1186/s13075-025-03523-w | |
| 2025 | Single-cell transcriptome analysis reveals cellular heterogeneity in the aortas of Takayasu arteritis | Arthritis Research & Therapy | 4.4 | Aortic tissue | 3' scRNA-seq | https://doi.org/10.1186/s13075-025-03523-w | |
| 2025 | A skin organoid-based infection platform identifies an inhibitor specific for HFMD | Nature Communications | 14.7 | Skin organoids | 3' scRNA-seq | https://doi.org/10.1038/s41467-025-57610-2 | EV-A71 is the main pathogen of hand, foot, and mouth disease (HFMD), which can spread through direct and indirect skin contact, seriously threatening children's health and even lives. Therefore, there is an urgent need to create new skin models using human cells to study viral biology and pathogenesis and promote drug screening. On March 13, 2025, the team of Leng Ling from Peking Union Medical College Hospital, Chinese Academy of Medical Sciences, published a paper entitled "A skin organoid-based infection platform identifies an inhibitor specific for HFMD" in the journal Nature Communications. This study created a human induced pluripotent stem cell-derived skin organoid (hiPSC-SOs) infection model. Using single-cell transcriptome sequencing and proteomics technologies, the research found that EV-A71 can mediate epidermal cell damage through autophagy and the Integrin/Hippo-YAP/TAZ signaling pathway, thereby promoting excessive proliferation of progenitor cells. Based on this discovery, an autophagy-related protein was identified as a drug target for EV-A71, and an EV-A71 replication inhibitor was found to provide a new beneficial direction for clinical treatment of hand, foot, and mouth disease. |
| 2025 | Microglial MS4A4A Protects against Epileptic Seizures in Alzheimer’s Disease | Advanced Science | 14.3 | Tuberous sclerosis lesion and surrounding brain tissue | 3' scRNA-seq | https://doi.org/10.1002/advs.202417733 | Alzheimer's disease (AD) is one of the most common neurodegenerative diseases worldwide, and epileptic seizures are one of its common complications. Studies have found that seizure episodes can worsen cognitive decline in patients, highlighting the great potential of early therapeutic intervention. However, the underlying mechanisms regulating epileptogenesis in AD remain poorly understood, which hinders the progress of translational research. On May 11, 2025, a collaborative study by Professor Zeng Wenwen's research group from the Institute of Immunology and Basic Medical School of Tsinghua University, together with the team of Cai Lixin/Sun Yu from Peking University First Hospital and Luo Maoguo from Tsinghua University, published a research paper entitled "Microglial MS4A4A Protects against Epileptic Seizures in Alzheimer's Disease" online in the journal Advanced Science. This study first revealed the important role of microglial MS4A4A in epileptic seizures in Alzheimer's disease (AD), providing new targets for AD-related treatments. SeekBio provided professional single-cell transcriptome sequencing services using the SeekOne® DD platform in this project, ensuring that the research team obtained high-quality single-cell transcriptome data. |
| 2025 | Predictive factors for neoadjuvant combined immunotherapy in gastric adenocarcinoma: Focusing on the primitive enterocyte phenotype and PVR | British Journal of Cancer | 6.4 | Gastric adenocarcinoma | FFPE scRNA-seq | https://doi.org/10.1038/s41416-025-03031-3 | |
| 2025 | Reading of Human Acute Immune Dynamics in Omicron SARS-CoV-2 Breakthrough Infection | Emerging Microbes & Infections | 8.4 | Peripheral blood | 5' + Immune Profiling | https://doi.org/10.1080/22221751.2025.2494705 | |
| 2025 | Diverse approaches and sources to derive antitumor T cell for liver cancer: a single-cell sequence based research | Hepatology International | 5.9 | Primary liver cancer | 5' + Immune Profiling | https://doi.org/10.1007/s12072-025-10818-2 | |
| 2025 | Single-cell transcriptomic analysis deciphers the inflammatory microenvironment characterized by CXCL9+ fibroblasts and ACKR1+ endothelial cells in immune-related myocarditis | Journal of Translational Medicine | 6.1 | Endocardial biopsy tissue | 3' scRNA-seq | https://doi.org/10.1186/s12967-025-06551-x | |
| 2025 | FK506 prolongs corneal allograft survival and prevents dendritic cell infiltration in an MDSC-dependent manner | American Journal of Transplantation | 8.2 | Corneal graft | other | https://doi.org/10.1016/j.ajt.2025.05.018 | |
| 2025 | Single-cell transcriptome analysis profiles cellular and molecular alterations in aortic tissue from patients with Behçet’s syndrome | Rheumatology | 4.4 | Aortic tissue specimens | 3' scRNA-seq | https://doi.org/10.1093/rheumatology/keaf252 | |
| 2025 | Dissecting the tumor microenvironment in primary breast angiosarcoma: insights from single‑cell RNA sequencing | Breast Cancer Research | 5.6 | Tumor samples of primary breast angiosarcoma and invasive breast cancer | scFAST-seq | https://doi.org/10.1186/s13058-025-02022-9 | |
| 2025 | Identification of Schwann Cells in Human Intracranial Arteries: Potential Regulatory Role in Atherosclerotic Plaque Progression | Advanced Science | 14.1 | Human intracranial artery | 3' scRNA-seq | https://doi.org/10.1002/advs.202503033 | |
| 2025 | Single-cell transcriptomic analysis deciphers the inflammatory microenvironment characterized by CXCL9+ fibroblasts and ACKR1+ endothelial cells in immune-related myocarditis | Journal of Translational Medicine | 7.5 | Endocardium | 3' scRNA-seq | https://doi.org/10.1186/s12967-025-06551-x | |
| 2025 | Mechanical force‑induced oncostatin M secretion by Jun‑positive neutrophils promotes craniofacial bone regeneration for midface hypoplasia treatment | Stem Cell Research & Therapy | 7.3 | Mouse zygomaticomaxillary suture | 3' scRNA-seq | https://doi.org/10.1186/s13287-025-04458-4 | |
| 2025 | Targeting AKR1B1 inhibits metabolic reprogramming toreverse systemic therapy resistance inhepatocellular carcinoma | Signal Transduction and Targeted Therapy | 52.7 | Drug-sensitive and drug-resistant hepatocellular carcinoma cell lines (HCC cell lines) | scFAST-seq | https://doi.org/10.1038/s41392-025-02321-9. | |
| 2024 | Macro CD5L+ deteriorates CD8+T cells exhaustion and impairs combination of Gemcitabine-Oxaliplatin-Lenvatinib-anti-PD1 therapy in intrahepatic cholangiocarcinoma | Nature Communications | 16.6 | Mouse control/intrahepatic cholangiocarcinoma model | 3' scRNA-seq | https://doi.org/10.1038/s41467-024-44795-1 | On January 20, 2024, Fudan University's Fan Jia, Zhou Jian, Shi Guoming, and Sun Yidi from the Institute of Neuroscience, Chinese Academy of Sciences, co-corresponded in Nature Communications to publish a research paper entitled "Macro CD5L+ deteriorates CD8+T cells exhaustion and impairs combination of Gemcitabine-Oxaliplatin-Lenvatinib-anti-PD1 therapy in intrahepatic cholangiocarcinoma". This study characterized the cellular and molecular dynamics landscape of tumor microenvironment in intrahepatic cholangiocarcinoma (iCCA) patients before and after receiving gemcitabine-oxaliplatin-lenvatinib-anti-PD1 antibody combination therapy (GOLP) through scRNA-seq and T cell receptor (TCR) sequencing. The study found that high proportions of CD8 GZMB+, CD8+, and low proportions of Macro CD5L+ indicate good treatment response. In patients with poor response, CD8 GZMB+ and CD8+ proliferation ratios increased, but CD8 GZMK+ ratio decreased after treatment, and Macro CD5L-CD8 GZMB+ crosstalk elevated CTLA4 in CD8 GZMB+, reducing efficacy. SeekBio mainly provided scRNA-seq using the SeekOne® platform in this study to validate that CTLA4 is a potential target that can reverse GOLP resistance in future clinical settings. |
| 2024 | Unveiling Major Histocompatibility Complex-mediated Pan-Cancer Immune Features by Integrated Single-Cell and Bulk RNA Sequencing | Cancer Letters | 9.1 | Colorectal cancer | 3' scRNA-seq | https://doi.org/10.1016/j.canlet.2024.217062 | |
| 2024 | Single-cell transcriptomic profiling unveils insights into ovarian fibrosis in obese mice | Biology Direct | 5.7 | Mouse ovarian tissue | 3' scRNA-seq | https://doi.org/10.1186/s13062-024-00496-9 | |
| 2024 | Overcoming tyrosine kinase inhibitor resistance in lung cancer brain metastasis with CTLA4 blockade | Cancer Cell | 48.8 | Human lung cancer brain metastasis (LCBM) samples | 3' scRNA-seq | https://doi.org/10.1016/j.ccell.2024.09.012 | |
| 2024 | Activation of NOD1 on tumor - associated macrophages augments CD8 + T cell–mediated antitumor immunity in hepatocellular carcinoma | Science Advances | 11.7 | CD45 immune cells isolated from HCC tumors | other | https://doi.org/10.1126/sciadv.adp8266 | |
| 2025 | Individualized patient tumor organoids faithfully preserve human brain tumor ecosystems and predict patient response to therapy | Cell Stem Cell | 19.8 | Tumor tissues from patients with primary central nervous system tumors and brain metastases of different origins, and human iPSC-derived brain organoid cells co-cultured with tumor tissues | 3' scRNA-seq | https://doi.org/10.1016/j.stem.2025.01.002 | |
| 2025 | Methionine intervention induces PD-L1 expression to enhance the immune checkpoint therapy response in MTAP-deleted osteosarcoma | Cell Reports Medicine | 11.7 | Single cells from fresh osteosarcoma tissues (including primary tumor lesions and metastatic lesions) | 3' scRNA-seq | https://doi.org/10.1016/j.xcrm.2025.101977 | |
| 2025 | nhaled PAMAM-based nano-formulation prolonged lung retention for alleviating pulmonary inflammation of COPD | Materials Today Bio | 8.7 | Mouse lung | 3' scRNA-seq | https://doi.org/10.1016/j.mtbio.2025.101845 | |
| 2025 | Resolving the spatial organization of fetal liver hematopoiesis by SeekSpace | Cell Regeneration | 4 | Mouse fetal liver tissue | Spatial-seq | https://doi.org/10.1186/s13619-025-00234-0 | |
| 2025 | Single-Cell Atlas Reveals Tumorigenic Profiles and Immune Dynamics of Adrenal Incidentalomas | Advanced Science | 14.3 | Adrenocortical adenoma | other | https://doi.org/10.1002/advs.202413493 | In April 2025, the team of Zhang Chao from Shanghai Jiao Tong University, the team of Liu Bing from Eastern Hepatobiliary Surgery Hospital, and the team of Zhao Ruxing from Qilu Hospital of Shandong University collaborated to publish an article "Single-Cell Atlas Reveals Tumorigenic Profiles and Immune Dynamics of Adrenal Incidentalomas" in Advanced Science, constructing a comprehensive, organ-specific adrenal tumor scRNA-seq atlas. This atlas includes samples from 11 primary AI patients. Additionally, publicly available single-cell datasets were incorporated, including 2 fetal adrenal control samples, 15 NB samples, and 4 PCC samples along with their peritumoral tissues. By utilizing these diverse and unbiased samples, patients were stratified, and disease-specific markers for different adrenal tumor subtypes were identified. Furthermore, to further elucidate factors affecting hormone secretion and inter-tumor microenvironment in AI, bulk RNA-seq data and multiplex immunofluorescence data were integrated. Although most AI samples were benign, this study represents the largest-scale single-cell AI sampling work to date, covering a wide range of AI characteristics. |
| 2025 | CLDN4 palmitoylation promotes hepatic-to-biliary lineage transition and lenvatinib resistance in hepatocellular carcinoma | Cell Reports Medicine | 10.6 | Hepatocellular carcinoma | 3' scRNA-seq | https://doi.org/10.1016/j.xcrm.2025.102208 | |
| 2023 | Single-cell dynamics of liver development in postnatal pigs | Science Bulletin | 18.9 | Porcine liver | 3' scRNA-seq | https://doi.org/10.1016/j.scib.2023.09.021 | |
| 2023 | NADase CD38 is a key determinant of ovarian aging | Nature aging | 16.6 | Mouse ovary | 3' scRNA-seq | https://doi.org/10.1038/s43587-023-00532-9 | In December 2023, the team of Sun Yingpu/Yang Qingling from the First Affiliated Hospital of Zhengzhou University published an article entitled "NADase CD38 is a key determinant of ovarian aging" in Nature Aging. This article combined bulk RNA-seq and scRNA-seq with molecular experiments to reveal that ovarian aging precedes other organs, manifested by upregulated inflammatory pathway gene expression. Inflammation induces upregulation of NADase CD38 expression, leading to a significant decrease in nicotinamide adenine dinucleotide (NAD+) levels, regulating ovarian aging. CD38 gene knockout can delay ovarian aging in mice and improve fertility; furthermore, treating middle-aged mice with the CD38 small molecule inhibitor 78c can increase ovarian NAD+ levels, improve oocyte quality, and enhance fertility. SeekBio mainly provided scRNA-seq technology using the SeekOne® DD platform in this study. Let's learn about this article together. |
| 2024 | Single-cell profiling of the pig cecum at various developmental stages | Zoological Research | 4.9 | Porcine cecum | 3' scRNA-seq | https://doi.org/10.24272/j.issn.2095-8137.2023.007 | |
| 2024 | CCDC66 mutations are associated with high myopia through affected cell mitosis | J Med Genet | 3.5 | Retina | other | https://doi.org/10.1136/jmg-2023-109434 | |
| 2024 | High expression of PLA2G2A in fibroblasts plays a crucial role in the early progression of carotid atherosclerosis | Journal of Translational Medicine | 6.1 | Carotid plaque | 3' scRNA-seq | https://doi.org/10.1186/s12967-024-05679-6 | |
| 2025 | Blockade of purine metabolism reverses macrophage immunosuppression and enhances anti-tumor immunity in non-small cell lung cancer | Drug Resistance Updates | 15.8 | Macrophages from lung cancer and adjacent tissues | 5' + Immune Profiling | https://doi.org/10.1016/j.drup.2024.101175 | |
| 2025 | Smad2 Cooperating with TGIF2 Contributes to EMT and Cancer Stem Cells Properties in Pancreatic Cancer via Co-Targeting SOX2 | International Journal of Biological Sciences | 8.2 | Pancreatic cancer | other | https://doi.org/10.7150/ijbs.102381 | |
| 2025 | Novel Lysosomal-Associated Transmembrane Protein 4B-Positive Stem-Like Cell Subpopulation Characterizes High-Risk Colorectal Cancer Subtypes | MedComm | 10.7 | Colorectal cancer and adjacent tissues | 3' scRNA-seq | https://doi.org/10.1002/mco2.70284 | |
| 2023 | Allogenic and autologous anti-CD7 CAR-T cell therapies in relapsed or refractory T-cell malignancies | Blood Cancer Journal | 12.8 | PBMC | 5' + Immune Profiling | https://doi.org/10.1038/s41408-023-00822-w | In April 2023, the team of Mei Heng from the Institute of Hematology at Huazhong University of Science and Technology published an article entitled "Allogenic and autologous anti-CD7 CAR-T cell therapies in relapsed or refractory T-cell malignancies" in Blood Cancer Journal (IF=12.8). This study investigated the safety and efficacy of autologous and allogeneic CAR-T cells in adolescent and adult patients with relapsed or refractory (r/r) T-cell malignancies, and used single-cell sequencing to reveal patient immune reconstitution after CAR-T cell infusion and mechanisms of long-term allogeneic CAR-T cell survival. SeekBio mainly provided 5' single-cell transcriptome sequencing work in this study. Let's learn about this article together. |
| 2023 | Corticotropin-Releasing Hormone: A Novel Stimulator of Somatolactin in Teleost Pituitary Cells | Cells (Zone 2) | 5.1 | Pituitary cells | 3' scRNA-seq | https://doi.org/10.3390/cells12242770 | |
| 2024 | IGFBP1a is a nutrient deficient response factor that can inhibit fish reproduction through the hypothalamus-pituitary-ovary axis | Biology of Reproduction | 3.1 | Pituitary cells | 3' scRNA-seq | https://doi.org/10.1093/biolre/ioae009 | |
| 2024 | Immunoglobin attenuates fulminant myocarditis by inhibiting overactivated innate immune response | British Journal of Pharmacology | 6.8 | CD45⁺ immune cells in heart tissue | 3' scRNA-seq | https://doi.org/10.1111/bph.17372 | |
| 2025 | Single-cell transcriptome reveals three types of adipocytes associated with intramuscular fat content in pigs | Genomics | 3.4 | Adult porcine longissimus dorsi muscle | 3' scRNA-seq | https://doi.org/10.1016/j.ygeno.2025.110998 | |
| 2025 | Cholecystokinin (CCK) Is a Mediator Between Nutritional Intake and Gonadal Development in Teleosts | Cells | 5.1 | Hypothalamic cells and pituitary cells from grass carp | 3' scRNA-seq, SeekSoul™ Online | https://doi.org/10.3390/cells14020078 | |
| 2025 | Hydroxychloroquine cures autoimmune myocarditis by inhibiting the innate immune system via the C-X-C motif chemokine ligand 16 and C-X-C motif receptor 6 axis between macrophages and T cells | British Journal of Pharmacology | 6.8 | Mouse heart | 3' scRNA-seq | https://doi.org/10.1111/bph.70028 | |
| 2025 | CD73 inhibitor AB680 suppresses glioblastoma in mice by inhibiting purine metabolism and promoting P2RY12+ microglia transformation | Acta Pharmacologica Sinica | 8.4 | Intracranial G422 TN-GBM tumor | 3' scRNA-seq | https://doi.org/10.1038/s41401-025-01585-9 | |
| 2025 | CD73 inhibitor AB680 suppresses glioblastoma in mice by inhibiting purine metabolism and promoting P2RY12+ microglia transformation | Acta Pharmacologica Sinica | 8.4 | Intracranial G422 TN-GBM tumor | 3' scRNA-seq | https://doi.org/10.1038/s41401-025-01585-9 | |
| 2025 | OTUD1 exacerbates sepsis-associated encephalopathy by promoting HK2 mitochondrial release to drive microglia pyroptosis | Journal of Neuroinflammation | 10.1 | Single-cell suspension of hippocampal tissue from cecal ligation and puncture (CLP) model mice and sham-operated mice | 3' scRNA-seq | https://doi.org/10.1186/s12974-025-03480-w | |
| 2025 | OTUD1 exacerbates sepsis-associated encephalopathy by promoting HK2 mitochondrial release to drive microglia pyroptosis | Journal of Neuroinflammation | 10.1 | Single-cell suspension of hippocampal tissue from cecal ligation and puncture (CLP) model mice and sham-operated mice | 3' scRNA-seq | https://doi.org/10.1186/s12974-025-03480-w | |
| 2024 | The landscape of RNA-binding proteins in mammalianspermatogenesis | science | 44.7 | Mouse testicular cells | scFAST-seq | https://doi.org/10.1126/science.adj8172 | On August 29, 2024, Zheng Ke, Lin Mingyan, and Guo Xuejiang from Nanjing Medical University co-corresponded to publish a research paper entitled "The landscape of RNA-binding proteins in mammalian spermatogenesis" online in Science. This study revealed the molecular landscape of RNA-binding proteins in mammalian spermatogenesis. This study provides a comprehensive and rich resource for RNA-binding proteins associated with spermatogenesis and male infertility, and demonstrated the functional significance of non-domain elements in regulating RNA and spermatogenesis, highlighting the potentially broad and important value of this resource in decoding the genetic and molecular basis of male fertility. SeekBio's SeekOne® DD single-cell full-length sequencing technology assisted the single-cell related experiments on mouse testes in this study, determining the composition of mitotic germ cells in mouse testes. |
| 2025 | Joint analysis of single-cell RNA sequencing and bulk transcriptome reveals the heterogeneity of the urea cycle of astrocytes in glioblastoma | Neurobiology of Disease | 5.1 | Cells from adjacent and tumor tissues of 3 glioblastoma patients | 3' scRNA-seq | https://doi.org/10.1016/j.nbd.2025.106835 | |
| 2025 | Integrating microbial GWAS and single cell transcriptomics reveals associations between host cell populations and the gut microbiome | Nature Microbiology | 20.5 | Liver, pancreas, lung, intestine, etc. | 3' scRNA-seq | https://doi.org/10.1038/s41564-025-01978-w | On April 7, 2025, the team of Su Jianzhong from the Eye Hospital of Wenzhou Medical University jointly co-corresponded with the team of Chen Weihua from Huazhong University of Science and Technology to publish a research paper entitled "Integrating microbial GWAS and single cell transcriptomics reveals associations between host cell populations and the gut microbiome" in Nature Microbiology. To break through the analytical bottlenecks in host-microbe interaction research, the research team developed an innovative algorithmic framework scBPS, achieving the first integration analysis of microbial GWAS with human multi-organ single-cell transcriptomes. Through systematic screening, the study revealed highly specific interaction relationships between multiple bacterial genera and specific cell populations, particularly pointing out that Collinsella can participate in the regulation of host metabolic diseases by regulating cholesterol metabolism in central venous hepatocytes. SeekBio provided professional single-cell 3'-end transcriptome sequencing services using the SeekOne® DD platform in this project, ensuring that the research team obtained high-quality single-cell transcriptome data. |
| 2025 | Single-cell and spatial RNA sequencing identify divergent microenvironments and progression signatures in early- versus late-onset prostate cancer | Nature Aging | 17 | Prostate cancer | 3' scRNA-seq | https://doi.org/10.1038/s43587-025-00842-0 | |
| 2025 | The Hypoxia-Associated High-Risk Cell Subpopulation Distinctly Enhances the Progression of Glioma | Advanced Science | 14.3 | Glioma | other | https://doi.org/10.1002/advs.202416231 | |
| 2025 | YY1 enhances HIF-1α stability in tumor-associated macrophages to suppress antitumor immunity of prostate cancer in mice | Nature Communications | 15.7 | Single-cell suspension of subcutaneous tumors in mice | 3' scRNA-seq | https://doi.org/10.1038/s41467-025-61560-0 | |
| 2025 | Fibroblast reprogramming in the dura mater of NTG-induced migraine-related chronic hypersensitivity model drives monocyte infiltration via Angptl1-dependent stromal signaling | The Journal of Headache and Pain | 7.3 | Mouse dura mater tissue | 3' scRNA-seq | https://doi.org/10.1186/s10194-025-02058-4 | |
| 2022 | Single-cell profiling of the microenvironment in decidual tissue from women with missed abortions | Fertility and Sterility | 6.7 | Decidual tissue | 3' scRNA-seq | https://doi.org/10.1016/j.fertnstert.2022.12.016 | |
| 2024 | APOE ε4–associated downregulation of the IL-7/IL-7R pathway in effector memory T cells: Implications for Alzheimer's disease | Alzheimers Dement | 13 | PBMC | 3' scRNA-seq | https://doi.org/10.1002/alz.14173 | |
| 2024 | APOE ε4–associated downregulation of the IL-7/IL-7R pathway in effector memory T cells: Implications for Alzheimer's disease | Alzheimers Dement | 13 | PBMC | 3' scRNA-seq | https://doi.org/10.1002/alz.14173 | |
| 2025 | Single-cell profiling reveals a reduced epithelial defense system, decreased immune responses and the immune regulatory roles of different fibroblast subpopulations in chronic atrophic gastritis | Journal of Translational Medicine | 6.1 | Chronic atrophic gastritis | 3' scRNA-seq | https://doi.org/10.1186/s12967-025-06150-w | |
| 2025 | Oxygen/sulfate radicals-generating CaS2 O8 nanosonosensitizers induce PAN‐optosis and calcium overload for enhanced peritoneal metastasis immunotherapy | Science Bulletin | 18.8 | Colon adenocarcinoma/gastric cancer cell lines | 5' + Immune Profiling | https://doi.org/10.1016/j.scib.2025.03.015 | |
| 2025 | Oxygen/sulfate radicals-generating CaS2 O8 nanosonosensitizers induce PAN‐optosis and calcium overload for enhanced peritoneal metastasis immunotherapy | Science Bulletin | 18.8 | Colon adenocarcinoma/gastric cancer cell lines | 5' + Immune Profiling | https://doi.org/10.1016/j.scib.2025.03.015 | |
| 2025 | Single‑cell analysis reveals distinct immune characteristics of hepatocellular carcinoma in HBV‑positive vs. HBV‑negative cases | Molecular and Clinical Oncology | 1.4 | Fresh tumors from HBV-positive and HBV-negative hepatocellular carcinoma patients | 3' scRNA-seq | https://doi.org/10.3892/mco.2025.2871 | |
| 2025 | Glucagon-like peptide-1 receptor signaling activation in alveolar type II cells enhances lung development in neonatal rats exposed to hyperoxia | Redox Biology | 10.7 | Lung tissue from neonatal rats (control group and GLP-1R knockdown group) | 3' scRNA-seq | https://doi.org/10.1016/j.redox.2025.103586 | |
| 2023 | Exploring the global immune landscape of peripheral blood mononuclear cells in H5N6-infected patient with single-cell transcriptomics | BMC Medical Genomics | 2.7 | PBMC | 3' scRNA-seq | https://doi.org/10.1186/s12920-023-01693-7 | |
| 2025 | Single-cell transcriptomics reveals the mechanisms of lung injury induced by Galt gene editing in mouse | Biochemical and Biophysical Research Communications | 2.5 | Mouse lung | 3' scRNA-seq | https://doi.org/10.1016/j.bbrc.2025.151780 | |
| 2024 | Toll-like receptor agonists promote the formation of tertiary lymphoid structure and improve anti-glioma immunity | Neuro-Oncology | 16.4 | Glioblastoma | SeekSoul™ Online | https://doi.org/10.1093/neuonc/noae167 | |
| 2025 | Glucagon-like peptide-1 receptor signaling activation in alveolar type II cells enhances lung development in neonatal rats exposed to hyperoxia | Redox Biology | 10.7 | Lung tissue | SeekSoul™ Online | https://doi.org/10.1016/j.redox.2025.103586 | |
| 2025 | Utilization of donor CLL-1 CAR-T cells for the treatment of relapsed of acute myeloid leukemia following allogeneic hematopoietic stem cell transplantation | Cell Death & Disease | 8.1 | PBMC | SeekSoul™ Online | https://doi.org/10.3389/fimmu.2024.1491341 | |
| 2025 | CD151 Promotes Cancer Progression in Triple-Negative Breast Cancer by Inducing EMT through the MAPK Signaling Pathway | Breast Cancer: Targets and Therapy | 3.3 | Breast cancer | SeekSoul™ Online | https://doi.org/10.2147/bctt.s518760 | |
| 2025 | Inhaled PAMAM-based nano-formulation prolonged lung retention for alleviating pulmonary inflammation of COPD | Mater Today Bio. | 8.7 | Mouse lung | SeekSoul™ Online | https://doi.org/10.1016/j.mtbio.2025.101845 | |
| 2025 | Dissecting the tumor microenvironment in primary breast angiosarcoma: insights from single-cell RNA sequencing | Breast Cancer Research | 5.6 | Breast angiosarcoma, breast cancer | SeekSoul™ Online | https://doi.org/10.1186/s13058-025-02022-9 | |
| 2022 | A Small-Molecule Cocktails-Based Strategy in Culture of Mesenchymal Stem Cells | Front Bioeng Biotechnol | 5.7 | MSC-induced organoids | 3' scRNA-seq | https://doi.org/10.3389/fbioe.2022.819148 | |
| 2023 | Blocking Dectin-1 prevents colorectal tumorigenesis by suppressing prostaglandin E2 production inmyeloid-derived suppressor cells and enhancing IL-22 binding protein expression | Nature Communications | 16.6 | Colon/colorectal cancer model | 3' scRNA-seq | https://doi.org/10.1038/s41467-023-37229-x | Researcher Tang Ce and his team from the Institute of Precision Medicine, the First Affiliated Hospital of Sun Yat-sen University published an article entitled Blocking Dectin-1 prevents colorectal tumorigenesis by suppressing prostaglandin E2 production in myeloid-derived suppressor cells and enhancing IL-22 binding protein expression" in Nature Communications. Combining single-cell transcriptomics and multi-omics technologies |
| 2024 | Tumor cells impair immunological synapse formation via central nervous system-enriched metabolite | Cancer Cell | 50.3 | Breast cancer/adjacent tissue; peripheral blood | 3' scRNA-seq | https://doi.org/10.1016/j.ccell.2024.05.006 | |
| 2024 | Non-invasive determination of gene expression in placental tissue using maternal plasma cell-free DNA fragmentation characters | Gene | 2.6 | Peripheral blood mononuclear cells, chorionic amnion, placental villi, basal decidua | 3' scRNA-seq | https://doi.org/10.1016/j.gene.2024.148789 | |
| 2024 | Single-cell RNA sequencing reveals the role of mitochondrial dysfunction in the cardiogenic toxicity of perfluorooctane sulfonate in human embryonic stem cells | Ecotoxicology and Environmental Safety | 6.2 | Embryonic stem cells during cardiac differentiation | other | https://doi.org/10.1016/j.ecoenv.2024.115945 | |
| 2024 | Gastric Cancer Actively Remodels Mechanical Microenvironment to Promote Chemotherapy Resistance via MSCs-Mediated Mitochondrial Transfer | Advanced Science | 14.3 | Tumor tissues from gastric cancer patients before and after surgery, before and after chemotherapy | 3' scRNA-seq | https://doi.org/10.1002/advs.202404994 | |
| 2024 | Reconstitution of pluripotency from mouse fibroblast through Sall4 overexpression | Nature Communications | 14.4 | Cell samples at different time points (day 0, 4, 7, 10) during reprogramming with SALL4 and SALL4 + OCT4 | 3' scRNA-seq | https://doi.org/10.1038/s41467-024-54924-5 | |
| 2025 | Analysis of the effect of ALA-PDT on macrophages in footpad model of mice infected with Fonsecaea monophora based on single-cell sequencing | Open Medicine | 1.7 | Skin of mouse footpad | 3' scRNA-seq | https://doi.org/10.1515/med-2024-1132 | |
| 2025 | UBE2C mediates follicular thyroid carcinoma invasion and metastasis via K29-Specific vimentin ubiquitination | Cancer Letters | 9.1 | Thyroid cancer | 3' scRNA-seq | https://doi.org/10.1016/j.canlet.2025.217624 | |
| 2025 | Influenza A virus dissemination and infection leads to tissue resident cell injury and dysfunction in viral sepsis | eBioMedicine | 9.7 | Mouse lung and liver tissues | other | https://doi.org/10.1016/j.ebiom.2025.105738 | |
| 2025 | Activation of the NRF2 signaling pathway mitigates arthrofibrosis by suppressing myofibroblast ferroptosis through oxidative stress regulation | Cell Investigation | New Issue | Knee synovial tissue | other | https://doi.org/10.1016/j.clnves.2025.100020 |
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