A5101606192- Single-cell and spatial transcriptomics
- Cell Image Analysis Techniques
- Gene Regulatory Network Analysis
- Cancer Cells and Metastasis
- RNA modifications and cancer
- Digestive system and related health
- Extracellular vesicles in disease
- MicroRNA in disease regulation
- Peptidase Inhibition and Analysis
- Neonatal Respiratory Health Research
- Viral-associated cancers and disorders
- Tissue Engineering and Regenerative Medicine
- Circular RNAs in diseases
- Cancer-related molecular mechanisms research
- Genomics and Chromatin Dynamics
- Cancer-related gene regulation
- Advanced Fluorescence Microscopy Techniques
- Circadian rhythm and melatonin
- Electrolyte and hormonal disorders
- Molecular Biology Techniques and Applications
- DNA Repair Mechanisms
- Cell Adhesion Molecules Research
- Neuroendocrine regulation and behavior
- Genetic factors in colorectal cancer
- Epigenetics and DNA Methylation
Helmholtz Zentrum München
2021-2024
Technical University of Munich
2021-2024
Qilu Hospital of Shandong University
2023
Xiamen University
2021-2022
Center for Environmental Health
2021
Shandong University
2020-2021
Single-cell technologies have transformed our understanding of human tissues. Yet, studies typically capture only a limited number donors and disagree on cell type definitions. Integrating many single-cell datasets can address these limitations individual the variability present in population. Here we integrated Human Lung Cell Atlas (HLCA), combining 49 respiratory system into single atlas spanning over 2.4 million cells from 486 individuals. The HLCA presents consensus re-annotation with...
Abstract Recent advances in multiplexed single‐cell transcriptomics experiments facilitate the high‐throughput study of drug and genetic perturbations. However, an exhaustive exploration combinatorial perturbation space is experimentally unfeasible. Therefore, computational methods are needed to predict, interpret, prioritize Here, we present compositional autoencoder (CPA), which combines interpretability linear models with flexibility deep‐learning approaches for response modeling. CPA...
Abstract Phenotypic polarization of macrophages is regulated by a milieu cues in the local tissue microenvironment. Currently, little known about how intrinsic regulators modulate proinflammatory (M1) versus prohealing (M2) activation. Here, it observed that insulin‐like growth factor 2 messenger RNA (mRNA)‐binding protein (IGF2BP2)‐deleted exhibit enhanced M1 phenotype and promote dextran sulfate sodium induced colitis development. However, IGF2BP2 −/− are refractory to interleukin‐4 (IL‐4)...
Tumor metastasis is a hallmark of colorectal cancer (CRC), in which exosome plays crucial role with its function intercellular communication. Plasma exosomes were collected from healthy control (HC) donors, localized primary CRC and liver-metastatic patients. We performed proximity barcoding assay (PBA) for single-exosome analysis, enabled us to identify the alteration subpopulations associated progression. By vitro vivo experiments, biological impact these on proliferation, migration,...
Abstract With the growing number of single-cell analysis tools, benchmarks are increasingly important to guide and method development. However, a lack standardisation extensibility in current limits their usability, longevity, relevance community. We present Open Problems, living, extensible, community-guided benchmarking platform including 10 tasks that we envision will raise standards for selection, evaluation, development methods analysis.
Abstract Recent advances in multiplexed single-cell transcriptomics experiments are facilitating the high-throughput study of drug and genetic perturbations. However, an exhaustive exploration combinatorial perturbation space is experimentally unfeasible, so computational methods needed to predict, interpret, prioritize Here, we present compositional autoencoder (CPA), which combines interpretability linear models with flexibility deep-learning approaches for response modeling. CPA encodes...
Advances in single-cell technology have enabled the measurement of cell-resolved molecular states across a variety cell lines and tissues under plethora genetic, chemical, environmental, or disease perturbations. Current methods focus on differential comparison are specific to particular task multi-condition setting with purely statistical perspectives. The quickly growing number, size, complexity such studies requires scalable analysis framework that takes existing biological context into...
Research shows a higher incidence of colorectal cancer in men. However, the molecular mechanisms for this gender disparity remain unknown. We report roles androgen proliferation and differentiation intestinal stem cells via targeting receptor (AR) on stromal by negatively regulating BMP signaling. Orchidectomy (ORX) or AR antagonist promotes expansion epithelium but suppresses cell (ISC) proliferation. Conversely, agonist inhibits ISC augments ovariectomized mice. Mechanistically, activation...
Biological systems can be understood by perturbing individual components and studying the system’s response. Cell biology experiments are defined applied treatment, cellular state, assayed phenotype. Given vast number of possible combinations, testing every scenario is impractical. We present Prophet, a transformer-based computational model for phenotype prediction. Prophet learns representation cell experiment space, enabling it to predict outcomes untested small molecule or genetic...
Abstract In single-cell data workflows and modeling, distance metrics are commonly used in loss functions, model evaluation, subpopulation analysis. However, these behave differently depending on the source of variation, conditions subpopulations expression profiles due to sparsity high dimensionality. Thus, for downstream tasks this domain should be carefully selected. We establish a set benchmarks with three evaluation measures, capturing desirable facets absolute relative behavior. Based...
Recent studies have highlighted the biological significance of exosomes and m6A modifications in immunity. Nonetheless, it remains unclear whether modification gene body fluid has potential roles tumor microenvironment (TME). Herein, we identified three different m6A-related exosomal patterns based on 59 genes, which instructed distinguishing characteristics TME colon cancer (CC). We demonstrated that these could predict stage inflammation, subtypes, genetic variation, patient prognosis....
Abstract Background Gradually, more researches pay attention to the potential relationship between N6-methyladenosine (m 6 A) modification of RNA and immunity in tumor microenvironment (TME). Therefore, they developed unique scoring modes through detecting level m A various tumors learn immune phenotypes. Nevertheless, direct detection always is harmful even fatal patients. Recent studies demonstrated that exosomes body fluid would deliver with from tumors. Methods Through analyzing datasets...