A5000868597- Genetic factors in colorectal cancer
- Ferroptosis and cancer prognosis
- Epigenetics and DNA Methylation
- 3D Printing in Biomedical Research
- Cancer Immunotherapy and Biomarkers
- Single-cell and spatial transcriptomics
- Cancer Genomics and Diagnostics
- Cancer Cells and Metastasis
- Mathematical Biology Tumor Growth
- Genomics and Phylogenetic Studies
- CRISPR and Genetic Engineering
- RNA modifications and cancer
- Cancer-related molecular mechanisms research
- Molecular Biology Techniques and Applications
- Cell Image Analysis Techniques
- Advanced Algorithms and Applications
- Maritime Navigation and Safety
- Gene expression and cancer classification
- Advanced Sensor and Control Systems
- Renal and related cancers
- Photocathodes and Microchannel Plates
- Ovarian cancer diagnosis and treatment
- Smart Agriculture and AI
- Photoacoustic and Ultrasonic Imaging
- Stock Market Forecasting Methods
Fuzhou University
2024-2025
Peking University People's Hospital
2024
Peking University
2016-2024
First People's Hospital of Yunnan Province
2023
National Institute of Biological Sciences, Beijing
2018-2022
Tsinghua University
2019-2022
Abstract Motivation To characterize long non-coding RNAs (lncRNAs), both identifying and functionally annotating them are essential to be addressed. Moreover, a comprehensive construction for lncRNA annotation is desired facilitate the research in field. Results We present LncADeep, novel identification functional tool. For identification, LncADeep integrates intrinsic homology features into deep belief network constructs models targeting full- partial-length transcripts. annotation,...
Abstract There is no effective way to detect structure variations (SVs) and extra-chromosomal circular DNAs (ecDNAs) at single-cell whole-genome level. Here, we develop a novel third-generation sequencing platform-based (scWGS) method named SMOOTH-seq (single-molecule real-time of long fragments amplified through transposon insertion). We evaluate the for detecting CNVs, SVs, SNVs in human cancer cell lines colorectal sample show that reliably effectively detects SVs ecDNAs individual cells,...
Abstract Colorectal cancer is a highly heterogeneous disease, with well-characterized subtypes based on genome, DNA methylome, and transcriptome signatures. To chart the epigenetic landscape of colorectal cancers, we generated high-quality single-cell chromatin accessibility atlas epithelial cells for 29 patients. Abnormal states acquired in adenomas were largely retained which tightly accompanied by opposite changes methylation. Unsupervised analysis malignant revealed two subtypes, exactly...
High-grade serous cancer (HGSC) is the most common subtype of ovarian cancer. HGSC highly aggressive with poor patient outcomes, and a deeper understanding tumorigenesis could help guide future treatment development. To systematically characterize underlying pathologic mechanisms intratumoral heterogeneity in human HGSC, we used an optimized single-cell multiomics sequencing technology to simultaneously analyze somatic copy-number alterations (SCNA), DNA methylation, chromatin accessibility,...
Genome assembly has been benefited from long-read sequencing technologies with higher accuracy and continuity. However, most human genome require large amount of DNAs homogeneous cell lines without keeping heterogeneities, since heterogeneity could profoundly affect haplotype results. Herein, using single-cell technology (SMOOTH-seq), we have sequenced K562 HG002 cells on PacBio HiFi Oxford Nanopore Technologies (ONT) platforms conducted de novo assembly. For the first time, completed high...
Identifying agricultural machinery operations is crucial for enhancing productivity and promoting the transition to data-driven agriculture. Current research focuses solely on administrative divisions, overlooking links between movement, natural spatial patterns, spatiotemporal dependencies. The direct clustering of GNSS points inefficient incurs substantial computational costs. In response these challenges, we introduce an unsupervised method based multiscale partitioning, which...
Abstract Single-cell whole-genome sequencing methods have undergone great improvements over the past decade. However, allele dropout, which means inability to detect both alleles simultaneously in an individual diploid cell, largely restricts application of these particularly for medical applications. Here, we develop a new single-cell method based on third-generation (TGS) platform named Refresh-seq (restriction fragment ligation-based genome amplification and TGS). It is restriction...
Although localized haploid phasing can be achieved using long read genome sequencing without parental data, reliable chromosome-scale remains a great challenge. Given that sperm is natural cell, single-sperm provide chromosome-wide phase signal. Due to the limitation of length, current short-read-based methods only achieve SNP haplotyping and come with difficulties in detecting structural variations (SVs) complex genomic regions. To overcome these limitations, we developed long-read-based...
Relevant studies suggest that serum vitamin level is related to the risk of breast cancer, and dietary pattern drug supplementation can significantly affect in body. Therefore, intervention body expected be a potential strategy reduce cancer. However, current epidemiological findings levels cancer are inconsistent, relationship between still controversial. In this study, we compared expression healthy people, benign patients, evaluated B risk.The study used liquid chromatography-tandem mass...
High malignancy is a prominent characteristic of epithelial ovarian cancer (EOC), emphasizing the necessity for further elucidation potential mechanisms underlying progression. Aneuploidy and copy number variation (CNV) partially contribute to heightened observed in EOC; however, precise features aneuploidy their molecular patterns, as well relationship between CNV EOC, remain unclear. In this study, we employed single-cell sequencing data along with The Cancer Genome Atlas (TCGA)...
High-bunch-charge photoemission electron-sources operating in a continuous wave (CW) mode are required for many advanced applications of particle accelerators, such as electron coolers hadron beams, electron-ion colliders, and free-electron lasers. Superconducting RF (SRF) has several advantages over other electron-gun technologies CW it offers higher acceleration rate potentially can generate bunch charges average beam currents. A 112 MHz SRF photoinjector (gun) was developed at Brookhaven...
Abstract In biological systems, genes function in conjunction rather than isolation. However, traditional single-cell RNA-seq (scRNA-seq) analyses heavily rely on the transcriptional similarity of individual genes, ignoring inherent gene-gene interactions. Here, we present SCORE, a network-based method, which incorporates validated molecular network features to infer cellular states. Using real scRNA-seq datasets, SCORE outperforms existing methods accuracy, robustness, scalability, data...
With the rapid development of single-cell sequencing techniques, several large-scale cell atlas projects have been launched across world. However, it is still challenging to integrate RNA-seq (scRNA-seq) datasets with diverse tissue sources, developmental stages and/or few overlaps, due ambiguity in determining batch information, which particularly important for current batch-effect correction methods. Here, we present SCORE, a simple network-based integration methodology, incorporates...
The widespread adoption of social media platforms has led to an influx data that reflects public sentiment, presenting a novel opportunity for market analysis. This research aims quantify the correlation between fleeting sentiments expressed on and measurable fluctuations in stock market. By adapting pre-existing sentiment analysis algorithm, we refined model specifically evaluating tweets associated with financial markets. was trained validated against comprehensive dataset stock-related...
<p>Supplementary Figure 9. Epigenetic regulators of tumor evolution in patient P26.</p>
<p>Supplementary Figure 11. Identification of CIMP subtypes.</p>
<p>Supplementary Figure 4. Dynamics of gene expression along malignant transformation.</p>
<p>Supplementary Figure 10. Chromatin accessibility profiles of intra-tumor heterogeneities.</p>
<p>Supplementary Figure 5. NMF identification of two malignant subtypes consistent with iCMS classification.</p>
<p>Supplementary Figure 3. Validation and TF enrichment of adenoma-related differential peaks.</p>