A5027112500- Single-cell and spatial transcriptomics
- Cell Image Analysis Techniques
- Pluripotent Stem Cells Research
- Gene Regulatory Network Analysis
- Acute Myeloid Leukemia Research
- Epigenetics and DNA Methylation
- Cancer Genomics and Diagnostics
- 3D Printing in Biomedical Research
- Immune cells in cancer
- CRISPR and Genetic Engineering
- Hematopoietic Stem Cell Transplantation
- Renal and related cancers
- Cancer Cells and Metastasis
- RNA modifications and cancer
- Immune Cell Function and Interaction
- Genomics and Chromatin Dynamics
- Genomics and Phylogenetic Studies
- Zebrafish Biomedical Research Applications
- T-cell and B-cell Immunology
- Healthcare Systems and Practices
- Cancer-related molecular mechanisms research
- Advanced MRI Techniques and Applications
- Cancer-related gene regulation
- Molecular Biology Techniques and Applications
- Advanced biosensing and bioanalysis techniques
Zhejiang University
2016-2025
First Affiliated Hospital Zhejiang University
2018-2024
Zhejiang Chinese Medical University
2021-2024
Alibaba Group (China)
2022
Zhejiang University-University of Edinburgh Institute
2022
Shenyang Aerospace University
2021-2022
Boston Children's Hospital
2013-2020
Howard Hughes Medical Institute
2016-2020
Dana-Farber/Boston Children's Cancer and Blood Disorders Center
2014-2020
Institut de recherche Saint-Louis
2020
The mouse blastocyst and stem cells derived from its tissue lineages provide a unique genetic system for examining the establishment loss of pluripotency. transcription factor Cdx2 plays central role by repressing pluripotency genes, such as Oct4, promoting extraembryonic trophoblast fate at stage. However, evidence has suggested that does not work alone in lineage. We have used bioinformatic functional genomic strategies to identify Gata3 factor. show be capable inducing embryonic driving...
Significance Characterization of cellular heterogeneity and hierarchy are important tasks in developmental biology may help overcome drug resistance treatment cancer other diseases. Single-cell technologies provide a powerful tool for detecting rare cell types cell-fate transition events, whereas traditional gene expression profiling methods can be used only to measure the average behavior population. However, lack suitable computational single-cell data analysis has become bottleneck. Here...
Objective Hepatocellular carcinoma (HCC) is heterogeneous, especially in multifocal tumours, which decreases the efficacy of clinical treatments. Understanding tumour heterogeneity critical when developing novel treatment strategies. However, a comprehensive investigation HCC lacking, and available evidence regarding has not led to improvements practice. Design We harvested 42 samples from eight patients evaluated using whole-exome sequencing, RNA mass spectrometry-based proteomics...
Recent progress in single-cell technologies has enabled the identification of all major cell types mouse. However, for most types, regulatory mechanism underlying their identity remains poorly understood. By computational analysis recently published mouse atlas data, we have identified 202 regulons whose activities are highly variable across different and more importantly, predicted a small set essential regulators each type Systematic validation by automated literature data mining provides...
Here, we describe that lysine-specific demethylase 1 (Lsd1/KDM1a), which demethylates histone H3 on Lys4 or Lys9 (H3K4/K9), is an indispensible epigenetic governor of hematopoietic differentiation. Integrative genomic analysis, combining global occupancy Lsd1, genome-wide analysis its substrates H3K4 monomethylation and dimethylation, gene expression profiling, reveals Lsd1 represses stem progenitor cell (HSPC) programs during We found acts at transcription start sites, as well enhancer...
Abstract The rapid development of single-cell transcriptomic technologies has helped uncover the cellular heterogeneity within cell populations. However, bulk RNA-seq continues to be main workhorse for quantifying gene expression levels due technical simplicity and low cost. To most effectively extract information from data given new knowledge gained methods, we have developed a novel algorithm estimate cell-type composition RNA-seq-derived signature. Comparison with existing methods using...
Abstract The National Genomics Data Center (NGDC), which is a part of the China for Bioinformation (CNCB), provides family database resources to support global academic and industrial communities. With rapid accumulation multi-omics data at an unprecedented pace, CNCB-NGDC continuously expands updates core through big archiving, integrative analysis value-added curation. Importantly, NGDC collaborates closely with major international databases initiatives ensure seamless exchange...
Abstract Individual cells are basic units of life. Despite extensive efforts to characterize the cellular heterogeneity different organisms, cross-species comparisons landscape dynamics have not been achieved. Here, we applied single-cell RNA sequencing (scRNA-seq) map organism-level cell landscapes at multiple life stages for mice, zebrafish and Drosophila. By integrating comprehensive dataset > 2.6 million single cells, constructed a identified signatures common pathways that...
B lymphocytes are essential mediators of humoral immunity and play multiple roles in human cancer. To decode the functions tumor-infiltrating cells, we generated a cell blueprint encompassing single-cell transcriptome, cell-receptor repertoire, chromatin accessibility data across 20 different cancer types (477 samples, 269 patients). cells harbored extraordinary heterogeneity comprised 15 subsets, which could be grouped into two independent developmental paths (extrafollicular versus...
Abstract Formalin-fixed paraffin-embedded (FFPE) tissues constitute a vast and valuable patient material bank for clinical history follow-up data. It is still challenging to achieve single cell/nucleus RNA (sc/snRNA) profile in FFPE tissues. Here, we develop droplet-based snRNA sequencing technology (snRandom-seq) by capturing full-length total RNAs with random primers. snRandom-seq shows minor doublet rate (0.3%), much higher coverage, detects more non-coding nascent RNAs, compared...
Bacteria colonize almost all parts of the human body and can differ significantly. However, population level transcriptomics measurements only describe average bacteria behaviors, ignoring heterogeneity among bacteria. Here, we report a droplet-based high-throughput single-microbe RNA-seq assay (smRandom-seq), using random primers for in situ cDNA generation, droplets barcoding, CRISPR-based rRNA depletion mRNA enrichment. smRandom-seq showed high species specificity (99%), minor doublet...