A5028674030- Cancer Genomics and Diagnostics
- Single-cell and spatial transcriptomics
- Genetic factors in colorectal cancer
- Intraocular Surgery and Lenses
- Genomics and Phylogenetic Studies
- Connexins and lens biology
- Ophthalmology and Visual Impairment Studies
- Genomics and Chromatin Dynamics
- Cancer Immunotherapy and Biomarkers
- Cancer Cells and Metastasis
- Yersinia bacterium, plague, ectoparasites research
- Gene expression and cancer classification
- Tryptophan and brain disorders
- Epigenetics and DNA Methylation
- Bipolar Disorder and Treatment
- Genetic Associations and Epidemiology
- Pancreatic and Hepatic Oncology Research
- Genomic variations and chromosomal abnormalities
- Corneal surgery and disorders
- Extracellular vesicles in disease
- Cancer-related molecular mechanisms research
- Cell Image Analysis Techniques
- Cancer, Hypoxia, and Metabolism
- Glaucoma and retinal disorders
- Gene Regulatory Network Analysis
Affiliated Eye Hospital of Wenzhou Medical College
2023-2025
Wenzhou Medical University
2023-2025
Columbia University
2018-2024
Second Affiliated Hospital & Yuying Children's Hospital of Wenzhou Medical University
2024
Icahn School of Medicine at Mount Sinai
2020-2023
Allen Institute for Brain Science
2022-2023
New York Proton Center
2022
Center for Neuro-Oncology
2022
Pediatrics and Genetics
2022
Center for Information Technology
2022
The cellular complexity of the human brain is established via dynamic changes in gene expression throughout development that mediated, part, by spatiotemporal activity cis-regulatory elements (CREs). We simultaneously profiled and chromatin accessibility 45,549 cortical nuclei across six broad developmental time points from fetus to adult. identified cell type-specific domains which highly correlated with expression. Differentiation pseudotime trajectory analysis indicates at CREs precedes...
During the last ten years, many research results have been referring to a particular type of cancer-associated fibroblasts associated with poor prognosis, invasiveness, metastasis and resistance therapy in multiple cancer types, characterized by gene expression signature prominent presence genes COL11A1, THBS2 INHBA. Identifying underlying biological mechanisms responsible for their creation may facilitate discovery targets potential pan-cancer therapeutics. Using novel computational...
Abstract Background This study evaluates the impact of corneal power on accuracy 14 newer intraocular lens (IOL) calculation formulas in cataract surgery. The aim is to assess how these perform across different curvature ranges, thereby guiding more precise IOL selection. Methods In this retrospective case series, 336 eyes from patients who underwent surgery were studied. cohort was divided into three groups according preoperative power. Key metrics analyzed included mean prediction error...
Congenital cataracts (CC) are one of the leading causes impaired vision or blindness in children, with approximately 8.3–25% being inherited. The aim this study is to investigate mutation spectrum and frequency 9 cataract-associated genes 19 Chinese families congenital cataracts. To identify gene variants associated This included a total 58 patients from pedigrees All probands were initially screened by whole-exome sequencing(WES), then validated co-segregation analysis using Sanger...
We developed 2DImpute, an imputation method for correcting false zeros (known as dropouts) in single-cell RNA-sequencing (scRNA-seq) data. It features preventing excessive correction by predicting the and imputing their values making use of interrelationships between both genes cells expression matrix. showed that 2DImpute outperforms several leading methods applying it on datasets from various scRNA-seq protocols.The R package is freely available at GitHub...
Abstract Subclonal reconstruction algorithms use bulk DNA sequencing data to quantify parameters of tumor evolution, allowing an assessment how cancers initiate, progress and respond selective pressures. We launched the ICGC–TCGA (International Cancer Genome Consortium–The Atlas) DREAM Somatic Mutation Calling Tumor Heterogeneity Evolution Challenge benchmark existing subclonal algorithms. This 7-year community effort used cloud computing 31 on 51 simulated tumors. Algorithms were scored...
Abstract Tumours evolve through time and space. Computational techniques have been developed to infer their evolutionary dynamics from DNA sequencing data. A growing number of studies used these approaches link molecular cancer evolution clinical progression response therapy. There has not yet a systematic evaluation methods for reconstructing tumour subclonality, in part due the underlying mathematical biological complexity difficulties creating gold-standards. To fill this gap, we...
Tumors are heterogeneous in the sense that they consist of multiple subpopulations cells, referred to as subclones, each which is characterized by a distinct profile genomic variations such somatic mutations. Inferring underlying clonal landscape has become an important topic it can help understanding cancer development and progression, thereby improving treatment. We describe novel state-space model, based on feature allocation framework efficient sequential Monte Carlo (SMC) algorithm,...
Abstract The cellular complexity of the human brain is established via dynamic changes in gene expression throughout development that mediated, part, by spatiotemporal activity cis-regulatory elements. We simultaneously profiled and chromatin accessibility 45,549 cortical nuclei across 6 broad developmental time-points from fetus to adult. identified cell-type specific domains which highly correlated with expression. Differentiation pseudotime trajectory analysis indicates at elements...
Abstract Background Congenital cataracts (CC) are one of the leading causes impaired vision or blindness in children, which approximately 8.3–25% inherited. More than 100 cataract-related genes have been identified globally. Purpose To identify gene variants associated with congenital cataracts. Methods This study included a total 58 patients from 19 pedigrees All probands were initially screened by whole-exome sequencing(WES), and some validated co-segregation analysis using Sanger...
Bulk samples of the same patient are heterogeneous in nature, comprising different subpopulations (subclones) cancer cells. Cells a tumor subclone characterized by unique mutational genotype profile. Resolving heterogeneity estimating genotypes, cellular proportions and number subclones present can help understanding progression treatment. We novel method, ChaClone2, to efficiently deconvolve observed variant allele fractions (VAFs), with consideration for possible effects from copy...
Abstract During the last ten years, many research results have been referring to a particular type of cancer-associated fibroblasts associated with poor prognosis, invasiveness, metastasis and resistance therapy in multiple cancer types, characterized by gene expression signature prominent presence genes COL11A1 , THBS2 INHBA . Identifying underlying biological mechanisms responsible for their creation may facilitate discovery targets potential pan-cancer therapeutics. Using novel...
Abstract Tumours are dynamically evolving populations of cells. Subclonal reconstruction algorithms use bulk DNA sequencing data to quantify parameters tumour evolution, allowing assessment how cancers initiate, progress and respond selective pressures. A plethora subclonal have been created, but their relative performance across the varying biological technical features real-world cancer genomic is unclear. We therefore launched ICGC-TCGA DREAM Somatic Mutation Calling -- Tumour...