A5036176693- Gene expression and cancer classification
- Bioinformatics and Genomic Networks
- RNA modifications and cancer
- Single-cell and spatial transcriptomics
- Genomics and Chromatin Dynamics
- Machine Learning in Bioinformatics
- Cancer-related molecular mechanisms research
- Epigenetics and DNA Methylation
- Genomics and Phylogenetic Studies
- Cancer Immunotherapy and Biomarkers
- Cancer Genomics and Diagnostics
- Ferroptosis and cancer prognosis
- RNA and protein synthesis mechanisms
- Immune Cell Function and Interaction
- Cell Image Analysis Techniques
- RNA Research and Splicing
- Computational Drug Discovery Methods
- Higher Education and Teaching Methods
- Antibiotic Resistance in Bacteria
- Nanoplatforms for cancer theranostics
- Cardiac Imaging and Diagnostics
- Advanced Graph Neural Networks
- Gene Regulatory Network Analysis
- Extracellular vesicles in disease
- Radiomics and Machine Learning in Medical Imaging
Shandong University
2009-2025
Lanzhou University Second Hospital
2019-2024
Case Western Reserve University
2018-2024
City University of Hong Kong, Shenzhen Research Institute
2024
Northwest A&F University
2015-2024
Wenzhou Medical University
2022-2024
First Affiliated Hospital of Wenzhou Medical University
2022-2024
Xi'an Jiaotong University
2024
Shanxi Medical University
2024
Lanzhou University
2019-2024
Pse-in-One 2.0 is a package of web-servers evolved from (Liu, B., Liu, F., Wang, X., Chen, J. Fang, L. & Chou, K.C. Nucleic Acids Research, 2015, 43:W65-W71). In order to make it more flexible and comprehensive as suggested by many users, the updated has incorporated 23 new pseudo component modes well series feature analysis approaches. It available at http://bioinformatics.hitsz.edu.cn/Pse-in-One2.0/. Moreover, maximize convenience provided also stand-alone version called...
Abstract Cell membrane–based nanosystems with desirable characteristics have been studied extensively for many therapeutic applications. However, current research has focused on single cell membrane, and multifunctional fused membrane materials from different types are still rare. Herein, a platelet–cancer stem (CSC) hybrid membrane‐coated iron oxide magnetic nanoparticle (MN) {[CSC‐P]MN} is presented the first time enhanced photothermal therapy of head neck squamous carcinoma (HNSCC)....
Abstract Immunosuppression is common in head and neck squamous cell carcinoma (HNSCC). In previous studies, the TIGIT/CD155 pathway was identified as an immune-checkpoint signaling that contributes to “exhaustion” state of infiltrating T cells. Here, we sought explore clinical significance HNSCC identify therapeutic effect a transgenic mouse model. TIGIT overexpressed on tumor-infiltrating CD8+ CD4+ cells both patients models, correlated with molecules (PD-1, TIM-3, LAG-3). also expressed...
Abstract A major challenge for traditional cancer therapy, including surgical resection, chemoradiotherapy, and immunotherapy, is how to induce tumor cell death leverage the host immune system at same time. Here, a myeloid‐derived suppressor (MDSC) membrane‐coated iron oxide magnetic nanoparticle (MNP@MDSC) overcome this conundrum therapy developed. In study, MNP@MDSC demonstrates its superior performance in evasion, active tumor‐targeting, resonance imaging, photothermal (PTT)‐induced...
Owing to the abuse of antibiotics, drug resistance pathogenic bacteria becomes more and serious. Therefore, it is interesting develop a reasonable way solve this issue. Because they can destroy bacterial cell structure then kill infectious bacterium, wall lyases are suitable candidates antibacteria sources. Thus, urgent an accurate efficient computational method predict lyases. Based on consideration, in paper, set objective rigorous data was collected by searching through Universal Protein...
To expedite the pace in conducting genome/proteome analysis, we have developed a Python package called Pse-Analysis. The powerful can automatically complete following five procedures: (1) sample feature extraction, (2) optimal parameter selection, (3) model training, (4) cross validation, and (5) evaluating prediction quality. All work user needs to do is input benchmark dataset along with query biological sequences concerned. Based on dataset, Pse-Analysis will construct an ideal predictor,...
The biology function of antisense intronic long noncoding RNA (Ai-lncRNA) is still unknown. Meanwhile, cancer patients with paclitaxel resistance have limited therapeutic options in the clinic. However, potential involvement Ai-lncRNA sensitivity remains unclear human cancer. Whole transcriptome sequencing 33 breast specimens was performed to identify EGOT. Next, role EGOT regulation investigated. Moreover, mechanism enhancing autophagy sensitizes cytotoxicity via upregulation ITPR1...
Abstract Promoters are consensus DNA sequences located near the transcription start sites and they play an important role in initiation. Due to their importance biological processes, identification of promoters is significantly for characterizing expression genes. Numerous computational methods have been proposed predict promoters. However, it difficult these achieve satisfactory performance multiple species. In this study, we propose a novel weighted average ensemble learning model, termed...
Abstract Motivation Three-dimensional (3D) genome organization is of vital importance in gene regulation and disease mechanisms. Previous studies have shown that CTCF-mediated chromatin loops are crucial to studying the 3D structure cells. Although various experimental techniques been developed detect loops, they found be time-consuming costly. Nowadays, sequence-based computational methods can capture significant features help predict loops. However, these low performance poor...
Identification of chromatin interactions is crucial for advancing our knowledge gene regulation. However, due to the limitations high-throughput experimental techniques, there an urgent need develop computational methods predicting interactions. In this study, we propose a novel attention-based deep learning model, termed IChrom-Deep, identify using sequence features and genomic features. The results based on datasets three cell lines demonstrate that IChrom-Deep achieves satisfactory...
Abstract Whole-heart coronary calcium Agatston score is a well-established predictor of major adverse cardiovascular events (MACE), but it does not account for individual calcification features related to the pathophysiology disease (e.g., multiple-vessel disease, spread along vessel, stable calcifications, numbers lesions, and density). We used novel, hand-crafted (calcium-omics); Cox time-to-event modeling; elastic net; up down synthetic sampling methods imbalanced data, assess MACE risk....
Abstract Iron is an essential metal ion in the human body and usually dysregulated cancers. However, a comprehensive overview of iron‐related genes their clinical relevance cancer lacking. In this study, we utilized expression profiling, proteomics, epigenetics from Cancer Genome Atlas database to systematically characterized alterations genes. There were multiple with dysregulation across 14 cancers some these ectopic changes may be associated aberrant DNA methylation. Meanwhile, variety...
Abstract Advances in the molecular characteristics of cancers have facilitated classification system from morphology to characteristic-based subtypes. Cancer profiling has expanded its focus protein-coding genes noncoding RNAs, with advances depth and quality transcriptome sequencing. Here, we examined profiles long RNAs (lncRNAs) according breast cancer subtype categories The Genome Atlas (TCGA) database identify a cohort cancer- oestrogen receptor (ER)-negative-associated lncRNAs....
Abstract Enhancers, noncoding DNA fragments, play a pivotal role in gene regulation, facilitating transcription. Identifying enhancers is crucial for understanding genomic regulatory mechanisms, pinpointing key elements and investigating networks governing expression disease-related mechanisms. Existing enhancer identification methods exhibit limitations, prompting the development of our novel multi-input deep learning framework, termed Enhancer-MDLF. Experimental results illustrate that...
The emergence of single-cell Hi-C (scHi-C) technology has provided unprecedented opportunities for investigating the intricate relationship between cell cycle phases and three-dimensional (3D) structure chromatin. However, accurately predicting based on scHi-C data remains a formidable challenge. Here, we present scHiCyclePred, prediction model that integrates multiple feature sets to leverage phases. scHiCyclePred extracts 3D chromatin features by incorporating multi-scale interaction...
In this paper, we present a novel rough-fuzzy clustering (RFC) method to detect overlapping protein complexes in protein-protein interaction (PPI) networks. RFC focuses on fuzzy relation model rather than graph by integrating sets and rough sets, employs the upper lower approximations of deal with complexes, calculates number automatically. Fuzzy between proteins is established then transformed into equivalence relation. Non-overlapping correspond classes satisfying certain To obtain...
Recent studies have highlighted the critical roles of long non-coding RNAs (lncRNAs) in various biological processes, including but not limited to dosage compensation, epigenetic regulation, cell cycle and differentiation regulation. Consequently, lncRNAs emerged as a central focus genetic studies. The identification subcellular localization is essential for gaining insights into crucial information about lncRNA interaction partners, post- or co-transcriptional regulatory modifications,...
Abnormally expressed long noncoding RNAs (lncRNAs) have been reported to affect the occurrence and progression of hepatocellular carcinoma (HCC) by modulating autophagy axis. However, none studies has explored clinical significance these autophagy-related lncRNAs in HCC comprehensively. In this study, RNA-seq, miRNA-seq, data normal patients from TCGA database genes Human Autophagy Database were extracted. Subsequently, we screened out 78 differentially lncRNAs, four prognostic-related...