Mingbo Cheng
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View article: Developmental factors drive the compartmentalised and discontinuous maturation of the small intestinal epithelium during the early postnatal period
Developmental factors drive the compartmentalised and discontinuous maturation of the small intestinal epithelium during the early postnatal period Open
The temporal, spatial and cellular diversity of the small intestinal epithelium during the postnatal period, a critical time window that accompanies the transition from placental energy supply to enteral feeding, the establishment of the e…
View article: Deciphering the complex clonal heterogeneity of polycythemia vera and the response to interferon alfa
Deciphering the complex clonal heterogeneity of polycythemia vera and the response to interferon alfa Open
Interferon alfa (IFN-α) is approved for the therapy of patients with polycythemia vera (PV), a subtype of myeloproliferative neoplasm (MPN). Some patients achieve molecular responses (MRs), but clonal factors sensitizing for MRs remain elu…
View article: PHLOWER - Single cell trajectory analysis using Hodge Decomposition
PHLOWER - Single cell trajectory analysis using Hodge Decomposition Open
Multi-modal single-cell sequencing, which captures changes in chromatin and gene expression in the same cells, is a game changer in the study of gene regulation in cellular differentiation processes. Computational trajectory analysis is a …
View article: Lineage tracing reveals transient phenotypic adaptation of tubular cells during acute kidney injury
Lineage tracing reveals transient phenotypic adaptation of tubular cells during acute kidney injury Open
Tubular injury is the hallmark of acute kidney injury (AKI) with a tremendous impact on patients and health-care systems. During injury, any differentiated proximal tubular cell (PT) may transition into a specific injured phenotype, so-cal…
View article: Mapping cardiac remodeling in chronic kidney disease
Mapping cardiac remodeling in chronic kidney disease Open
Patients with advanced chronic kidney disease (CKD) mostly die from sudden cardiac death and recurrent heart failure. The mechanisms of cardiac remodeling are largely unclear. To dissect molecular and cellular mechanisms of cardiac remodel…
View article: <b>Mapping cardiac remodeling in chronic kidney disease</b>
<b>Mapping cardiac remodeling in chronic kidney disease</b> Open
Patients with advanced chronic kidney disease (CKD) mostly die from sudden cardiac death and recurrent heart failure. The mechanisms of cardiac remodeling in these patients are largely unclear. To dissect molecular and cellular mechanisms …
View article: Detection of PatIent-Level distances from single cell genomics and pathomics data with Optimal Transport (PILOT)
Detection of PatIent-Level distances from single cell genomics and pathomics data with Optimal Transport (PILOT) Open
Although clinical applications represent the next challenge in single-cell genomics and digital pathology, we still lack computational methods to analyze single-cell and pathomics data to find sample level trajectories or clusters associat…
View article: Processed Data 2 : Spatial multi-omic map of human myocardial infarction
Processed Data 2 : Spatial multi-omic map of human myocardial infarction Open
We provide here the sub-clustering results for each major cell type for the manuscript: Kuppe, Ramirez Flores, Li et al. "Spatial multi-omic map of human myocardial infarction", 2022. The cells from snRNA-seq and snATAC-seq were first inte…
View article: Raw Data - Part 3 : Spatial multi-omic map of human myocardial infarction
Raw Data - Part 3 : Spatial multi-omic map of human myocardial infarction Open
We provide here the raw data of visium for the manuscript: Kuppe, Ramirez Flores, Li et al. "Spatial multi-omic map of human myocardial infarction", 2022
View article: Processed Data 1 : Spatial multi-omic map of human myocardial infarction
Processed Data 1 : Spatial multi-omic map of human myocardial infarction Open
We provide here the processed snRNA-seq, snATAC-seq, and visium data for the manuscript: Kuppe, Ramirez Flores, Li et al. "Spatial multi-omic map of human myocardial infarction", 2022
View article: Processed Data 1 : Spatial multi-omic map of human myocardial infarction
Processed Data 1 : Spatial multi-omic map of human myocardial infarction Open
We provide here the processed snRNA-seq, snATAC-seq, and visium data for the manuscript: Kuppe, Ramirez Flores, Li et al. "Spatial multi-omic map of human myocardial infarction", 2022
View article: Raw Data - Part 2 : Spatial multi-omic map of human myocardial infarction
Raw Data - Part 2 : Spatial multi-omic map of human myocardial infarction Open
We provide here the raw data of snATAC-seq and snRNA-seq for the manuscript: Kuppe, Ramirez Flores, Li et al. "Spatial multi-omic map of human myocardial infarction", 2022
View article: Raw Data - Part 1 : Spatial multi-omic map of human myocardial infarction
Raw Data - Part 1 : Spatial multi-omic map of human myocardial infarction Open
We provide here the raw data of snATAC-seq for the manuscript: Kuppe, Ramirez Flores, Li et al. "Spatial multi-omic map of human myocardial infarction", 2022
View article: Raw Data - Part 2 : Spatial multi-omic map of human myocardial infarction
Raw Data - Part 2 : Spatial multi-omic map of human myocardial infarction Open
We provide here the raw data of snATAC-seq and snRNA-seq for the manuscript: Kuppe, Ramirez Flores, Li et al. "Spatial multi-omic map of human myocardial infarction", 2022
View article: Raw Data - Part 1 : Spatial multi-omic map of human myocardial infarction
Raw Data - Part 1 : Spatial multi-omic map of human myocardial infarction Open
We provide here the raw data of snATAC-seq for the manuscript: Kuppe, Ramirez Flores, Li et al. "Spatial multi-omic map of human myocardial infarction", 2022
View article: Next-Generation Morphometry for pathomics-data mining in histopathology
Next-Generation Morphometry for pathomics-data mining in histopathology Open
Pathology diagnostics relies on the assessment of morphological features by trained experts, which remains subjective and qualitative. Modern image analysis techniques, particularly deep learning, provide a possible solution, sometimes exc…
View article: MOJITOO: a fast and universal method for integration of multimodal single-cell data
MOJITOO: a fast and universal method for integration of multimodal single-cell data Open
Motivation The advent of multi-modal single-cell sequencing techniques have shed new light on molecular mechanisms by simultaneously inspecting transcriptomes, epigenomes and proteomes of the same cell. However, to date, the existing compu…
View article: MOJITOO: a fast and universal method for integration of multimodal single cell data
MOJITOO: a fast and universal method for integration of multimodal single cell data Open
MOJITOO benchmarking seurat Robjects.
View article: MOJITOO: a fast and universal method for integration of multimodal single cell data
MOJITOO: a fast and universal method for integration of multimodal single cell data Open
MOJITOO benchmarking seurat Robjects.
View article: Single Nucleus ATAC Sequencing Reveals Epigenomic Regulation After Myocardial Infarction
Single Nucleus ATAC Sequencing Reveals Epigenomic Regulation After Myocardial Infarction Open
SeuratObject, we used snATAC product from 10x Genomics to profile myocardial infarction (MI) at Day 0, 3 and 10.
View article: Single Nucleus ATAC Sequencing Reveals Epigenomic Regulation After Myocardial Infarction
Single Nucleus ATAC Sequencing Reveals Epigenomic Regulation After Myocardial Infarction Open
SeuratObject, we used snATAC product from 10x Genomics to profile myocardial infarction (MI) at Day 0, 3 and 10.
View article: MOJITOO: a fast and universal method for integration of multimodal single cell data
MOJITOO: a fast and universal method for integration of multimodal single cell data Open
The advent of multi-modal single cell sequencing techniques have shed new light on molecular mechanisms by simultaneously inspecting transcriptomes, epigenomes and proteomes of the same cell. However, to date, the existing computational ap…
View article: Chromatin-accessibility estimation from single-cell ATAC-seq data with scOpen
Chromatin-accessibility estimation from single-cell ATAC-seq data with scOpen Open
A major drawback of single-cell ATAC-seq (scATAC-seq) is its sparsity, i.e., open chromatin regions with no reads due to loss of DNA material during the scATAC-seq protocol. Here, we propose scOpen, a computational method based on regulari…
View article: Single cell ATAC-seq Mouse Kidney Data: Chromatin-accessibility estimation from single-cell ATAC data with scOpen
Single cell ATAC-seq Mouse Kidney Data: Chromatin-accessibility estimation from single-cell ATAC data with scOpen Open
We provide results regarding the bioinformatic analysis of scATAC-seq from mouse UUO kidney at different time points.
View article: Single cell ATAC-seq Mouse Kidney Data: Chromatin-accessibility estimation from single-cell ATAC data with scOpen
Single cell ATAC-seq Mouse Kidney Data: Chromatin-accessibility estimation from single-cell ATAC data with scOpen Open
We provide results regarding the bioinformatic analysis of scATAC-seq from mouse UUO kidney at different time points.