142 results on '"Yang, Pengyi"'
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2. Evaluating spatially variable gene detection methods for spatial transcriptomics data
3. The current landscape and emerging challenges of benchmarking single-cell methods
4. Thinking process templates for constructing data stories with SCDNEY
5. Evaluation of deep learning-based feature selection for single-cell RNA sequencing data analysis
6. Gene regulatory network reconstruction: harnessing the power of single-cell multi-omic data
7. SnapKin: a snapshot deep learning ensemble for kinase-substrate prediction from phosphoproteomics data
8. The impact of similarity metrics on cell type clustering in highly multiplexed in situ imaging cytometry data
9. Vascular senescence and leak are features of the early breakdown of the blood–brain barrier in Alzheimer’s disease models
10. PAD2: interactive exploration of transcription factor genomic colocalization using ChIP-seq data
11. Benchmarking of analytical combinations for COVID-19 outcome prediction using single-cell RNA sequencing data
12. Multi-task learning from multimodal single-cell omics with Matilda
13. Thinking process templates for constructing data stories with SCDNEY
14. Spatial analysis for highly multiplexed imaging data to identify tissue microenvironments
15. Ensemble deep learning of embeddings for clustering multimodal single-cell omics data
16. Phosphoproteomics reveals rewiring of the insulin signaling network and multi-nodal defects in insulin resistance
17. Ensemble of similarity metrics with a multiview self-organizing map improves cell clustering in highly multiplexed imaging cytometry data
18. Benchmarking of analytical combinations for COVID-19 outcome prediction using single-cell RNA sequencing data
19. Comprehensive characterization of fetal and mature retinal cell identity to assess the fidelity of retinal organoids
20. Evaluating spatially variable gene detection methods for spatial transcriptomics data
21. Phosphoproteomics of three exercise modalities identifies canonical signaling and C18ORF25 as an AMPK substrate regulating skeletal muscle function
22. Integrative analysis reveals histone demethylase LSD1 promotes RNA polymerase II pausing
23. scFeatures: multi-view representations of single-cell and spatial data for disease outcome prediction
24. Comprehensive Characterisation of Fetal and Mature Retinal Cell Identity to Assess the Fidelity of Retinal Organoids
25. Trafficking regulator of GLUT4-1 (TRARG1) is a GSK3 substrate
26. Multi-task learning from single-cell multimodal omics with Matilda
27. Differentiation of brain and retinal organoids from confluent cultures of pluripotent stem cells connected by nerve-like axonal projections of optic origin
28. Time-resolved phosphoproteome and proteome analysis reveals kinase signaling on master transcription factors during myogenesis
29. Computational systems approach towards phosphoproteomics and their downstream regulation
30. Phosphoproteomics reveals rewiring of the insulin signaling network and multi-nodal defects in insulin resistance
31. Mouse organogenesis atlas at single-cell resolution
32. Computational approaches for direct cell reprogramming: from the bulk omics era to the single cell era
33. Benchmarking clustering algorithms on estimating the number of cell types from single-cell RNA-sequencing data
34. scFeatures: Multi-view representations of single-cell and spatial data for disease outcome prediction
35. scREMOTE: Using multimodal single cell data to predict regulatory gene relationships and to build a computational cell reprogramming model
36. Functional analysis of the stable phosphoproteome reveals cancer vulnerabilities
37. Single‐Cell Transcriptome Profiling Reveals Multicellular Ecosystem of Nucleus Pulposus during Degeneration Progression (Adv. Sci. 3/2022)
38. Uncovering cell identity through differential stability with Cepo
39. Feature selection revisited in the single-cell era
40. Single‐Cell Transcriptome Profiling Reveals Multicellular Ecosystem of Nucleus Pulposus during Degeneration Progression
41. A benchmark study of simulation methods for single-cell RNA sequencing data
42. Decoding the function of bivalent chromatin in development and cancer
43. scREMOTE: Using multimodal single cell data to predict regulatory gene relationships and to build a computational cell reprogramming model
44. A hierarchical approach to removal of unwanted variation for large-scale metabolomics data
45. Spatial analysis for highly multiplexed imaging data to identify tissue microenvironments
46. Akt phosphorylates insulin receptor substrate to limit PI3K-mediated PIP3 synthesis
47. A benchmark study of simulation methods for single-cell RNA sequencing data
48. Protocol for the processing and downstream analysis of phosphoproteomic data with PhosR
49. Single-cell transcriptome profiling reveals multicellular ecosystem of nucleus pulposus during degeneration progression
50. Author response: Akt phosphorylates insulin receptor substrate to limit PI3K-mediated PIP3 synthesis
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