Shuai Cheng Li
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View article: Targeting TET3 suppresses group 3 medulloblastoma stemness and progression via impairing hypomethylation of Otx2 super-enhancer
Targeting TET3 suppresses group 3 medulloblastoma stemness and progression via impairing hypomethylation of Otx2 super-enhancer Open
View article: MicrobialScope: an integrated genomic resource with rich annotations across bacteria, archaea, fungi, and viruses
MicrobialScope: an integrated genomic resource with rich annotations across bacteria, archaea, fungi, and viruses Open
Microorganisms, including bacteria, archaea, fungi, and viruses, are the most taxonomically diverse and ecologically dominant life forms on Earth, playing critical roles in ecosystems, human health, and industrial applications. While exist…
View article: GeneFamily: a comprehensive mammalian gene family database with extensive annotation and interactive visualization
GeneFamily: a comprehensive mammalian gene family database with extensive annotation and interactive visualization Open
Gene families underlie genetic innovation and phenotypic diversification. However, the identification, analysis, and interpretation of gene families depend on custom bioinformatics and visualization workflows that are mainly unattainable f…
View article: One-year restoration of vaginal health: synergistic dynamics of microbiome and metabolome following the elimination of high-grade cervical intraepithelial neoplasia
One-year restoration of vaginal health: synergistic dynamics of microbiome and metabolome following the elimination of high-grade cervical intraepithelial neoplasia Open
Therapeutic elimination of high-grade cervical intraepithelial neoplasia (CIN) is widely implemented for cervical cancer prevention. Despite the demonstrated dysbiosis of vaginal microenvironment in high-grade CIN, its post-therapy restora…
View article: Anti-PD-L1 plus chemoradiotherapy for limited-stage small-cell lung cancer: a retrospective cohort evaluating efficacy, safety, T-cell subsets and tumor markers
Anti-PD-L1 plus chemoradiotherapy for limited-stage small-cell lung cancer: a retrospective cohort evaluating efficacy, safety, T-cell subsets and tumor markers Open
Background Evidence for immune checkpoint blockade with chemoradiotherapy (CRT) in limited-stage small-cell lung cancer (LS-SCLC) remains limited. We evaluated anti-PD-L1 plus CRT versus CRT alone in routine practice. Methods We retrospect…
View article: MGDA: A provenance graph-based framework for threat detection and attack scenario reconstruction
MGDA: A provenance graph-based framework for threat detection and attack scenario reconstruction Open
View article: EditMark: Watermarking Large Language Models based on Model Editing
EditMark: Watermarking Large Language Models based on Model Editing Open
Large Language Models (LLMs) have demonstrated remarkable capabilities, but their training requires extensive data and computational resources, rendering them valuable digital assets. Therefore, it is essential to watermark LLMs to protect…
View article: Shared and distinct molecular pathways in eutopic endometrium of endometriosis and adenomyosis patients: a transcriptomic study in Chinese women
Shared and distinct molecular pathways in eutopic endometrium of endometriosis and adenomyosis patients: a transcriptomic study in Chinese women Open
View article: Reinforcement Learning on Pre-Training Data
Reinforcement Learning on Pre-Training Data Open
The growing disparity between the exponential scaling of computational resources and the finite growth of high-quality text data now constrains conventional scaling approaches for large language models (LLMs). To address this challenge, we…
View article: A Novel PHyLiC Model Using Dynamic Circulating Biomarkers to Predict Efficacy in Radioimmunotherapy for Advanced Solid Tumors
A Novel PHyLiC Model Using Dynamic Circulating Biomarkers to Predict Efficacy in Radioimmunotherapy for Advanced Solid Tumors Open
View article: Structural basis of peptide recognition and modulation for neuropeptide FF receptors
Structural basis of peptide recognition and modulation for neuropeptide FF receptors Open
Neuropeptide FF receptors 1 and 2 (NPFFR1 and NPFFR2) are RF-amide peptide receptors that couple to Gi/o proteins and regulate pain, opioid tolerance, and metabolism. Despite their physiological significance, their ligand select…
View article: An Ultra‐Selective and Humidity‐Resistant Room‐Temperature‐Operated NO <sub>2</sub> Sensor Based on Black TiO <sub>2</sub>
An Ultra‐Selective and Humidity‐Resistant Room‐Temperature‐Operated NO <sub>2</sub> Sensor Based on Black TiO <sub>2</sub> Open
As a common gas‐sensing material, TiO 2 is limited by poor gas selectivity and humidity immunity like many other metal oxides. Here, an ultra‐selective and humidity‐resistant room temperature‐operated NO 2 sensor is developed using black T…
View article: Inferring causal trajectories from spatial transcriptomics using CASCAT
Inferring causal trajectories from spatial transcriptomics using CASCAT Open
Spatial trajectory inference models cell differentiation and state dynamics within tissues by integrating spatial information. Existing spatial trajectory inference methods depend on similarity-based cell graphs constructed from spatial pr…
View article: Consolidative thoracic radiotherapy improves the prognosis of extensive stage small-cell lung cancer patients in the chemoimmunotherapy era: a multicenter retrospective analysis
Consolidative thoracic radiotherapy improves the prognosis of extensive stage small-cell lung cancer patients in the chemoimmunotherapy era: a multicenter retrospective analysis Open
This study suggests that the addition of cTRT to first-line chemo-immunotherapy significantly improves survival in ES-SCLC with well-tolerated toxicity.
View article: Interpretable spatial multi-omics data integration and dimension reduction with SpaMV
Interpretable spatial multi-omics data integration and dimension reduction with SpaMV Open
Spatial multi-omics technologies have revolutionized our understanding of biological systems by providing spatially resolved molecular profiles from multiple perspectives. Existing spatial multi-omics integration methods often assume that …
View article: Adar contributes to genome integrity by regulating R-loop homeostasis in Drosophila
Adar contributes to genome integrity by regulating R-loop homeostasis in Drosophila Open
View article: AffMB: affinity maturation analysis with SHM-guided B-cell lineage trees
AffMB: affinity maturation analysis with SHM-guided B-cell lineage trees Open
Motivation B-cell lineage trees describe the evolutionary process of immunoglobulin genes during affinity maturation. Existing methods for building B-cell lineage trees generally do not guarantee the parent-to-child inheritance and accumul…
View article: Addressing osteoblast senescence: Molecular pathways and the frontier of anti‐ageing treatments
Addressing osteoblast senescence: Molecular pathways and the frontier of anti‐ageing treatments Open
Background Osteoblast senescence is a central driverof age‐related osteoporosis. Accumulating evidence shows that counteractingthis senescence can substantially mitigate bone loss. In this review, we summarize the hallmarks of osteoblast s…
View article: Ring-lite: Scalable Reasoning via C3PO-Stabilized Reinforcement Learning for LLMs
Ring-lite: Scalable Reasoning via C3PO-Stabilized Reinforcement Learning for LLMs Open
We present Ring-lite, a Mixture-of-Experts (MoE)-based large language model optimized via reinforcement learning (RL) to achieve efficient and robust reasoning capabilities. Built upon the publicly available Ling-lite model, a 16.8 billion…
View article: Controlling risks of AI in chemical science with agents
Controlling risks of AI in chemical science with agents Open
View article: Anomalous Traffic Filtering Algorithm for Power Wireless Sensor Networks Based on Feature Clustering
Anomalous Traffic Filtering Algorithm for Power Wireless Sensor Networks Based on Feature Clustering Open
Conventional power wireless sensor network anomalous traffic filtering algorithm measurement structure is generally set as a unidirectional structure, the filtering efficiency is low, resulting in an increase in the absolute error of the f…
View article: Dual-Priority Delayed Deep Double Q-Network (DPD3QN): A Dueling Double Deep Q-Network with Dual-Priority Experience Replay for Autonomous Driving Behavior Decision-Making
Dual-Priority Delayed Deep Double Q-Network (DPD3QN): A Dueling Double Deep Q-Network with Dual-Priority Experience Replay for Autonomous Driving Behavior Decision-Making Open
The behavior decision control of autonomous vehicles is a critical aspect of advancing autonomous driving technology. However, current behavior decision algorithms based on deep reinforcement learning still face several challenges, such as…
View article: Spatial Correlation of Non-Agriculturalization and Non-Grain Utilization Transformation of Cultivated Land in China and Its Implications
Spatial Correlation of Non-Agriculturalization and Non-Grain Utilization Transformation of Cultivated Land in China and Its Implications Open
China’s rapid urbanization and evolving agricultural practices have driven significant changes in cultivated land utilization, characterized by non-agriculturalization (NA) and non-grain utilization (NGU) transformation. Understanding the …
View article: Salinity and drought suppress C4 and induce CAM photosynthesis in two Portulaca species
Salinity and drought suppress C4 and induce CAM photosynthesis in two Portulaca species Open
View article: CeiTEA: Adaptive Hierarchy of Single Cells with Topological Entropy
CeiTEA: Adaptive Hierarchy of Single Cells with Topological Entropy Open
Advances in single‐cell RNA sequencing (scRNA‐seq) enable detailed analysis of cellular heterogeneity, but existing clustering methods often fail to capture the complex hierarchical structures of cell types and subtypes. CeiTEA is introduc…
View article: Conditional Diffusion Models Based Conditional Independence Testing
Conditional Diffusion Models Based Conditional Independence Testing Open
Conditional independence (CI) testing is a fundamental task in modern statistics and machine learning. The conditional randomization test (CRT) was recently introduced to test whether two random variables, X and Y, are conditionally indepe…
View article: TransHLA: A Hybrid Transformer Model for HLA-Presented Epitope Detection
TransHLA: A Hybrid Transformer Model for HLA-Presented Epitope Detection Open
Background Precise prediction of epitope presentation on human leukocyte antigen (HLA) molecules is crucial for advancing vaccine development and immunotherapy. Conventional HLA-peptide binding affinity prediction tools often focus on spec…
View article: MEGA-GO: functions prediction of diverse protein sequence length using Multi-scalE Graph Adaptive neural network
MEGA-GO: functions prediction of diverse protein sequence length using Multi-scalE Graph Adaptive neural network Open
Motivation The increasing accessibility of large-scale protein sequences through advanced sequencing technologies has necessitated the development of efficient and accurate methods for predicting protein function. Computational prediction …
View article: High cellular plasticity state of medulloblastoma local recurrence and distant dissemination
High cellular plasticity state of medulloblastoma local recurrence and distant dissemination Open
Medulloblastoma (MB), a heterogeneous pediatric brain tumor, poses challenges in the treatment of tumor recurrence and dissemination. To characterize cellular diversity and genetic features, we comprehensively analyzed single-cell/nucleus …
View article: Mgda: A Provenance Graph-Based Framework for Threat Detection and Attack Scenario Reconstruction
Mgda: A Provenance Graph-Based Framework for Threat Detection and Attack Scenario Reconstruction Open