Tissue regeneration is an orchestrated progression of cells from an immature state to a mature one, conventionally represented as distinctive cell subsets. A continuum of transitional cell states exists between these discrete stages. We combine the depth of single-cell mass cytometry and an algorithm developed to leverage this continuum by aligning single cells of a given lineage onto a unified trajectory that accurately predicts the developmental path de novo. Applied to human B cell lymphopoiesis, the algorithm (termed Wanderlust) constructed trajectories spanning from hematopoietic stem cells through to naive B cells. This trajectory revealed nascent fractions of B cell progenitors and aligned them with developmentally cued regulatory signaling including IL-7/STAT5 and cellular events such as immunoglobulin rearrangement, highlighting checkpoints across which regulatory signals are rewired paralleling changes in cellular state. This study provides a comprehensive analysis of human B lymphopoiesis, laying a foundation to apply this approach to other tissues and "corrupted" developmental processes including cancer.
Role of STAT5 in controlling cell survival and immunoglobulin gene recombination during pro-B cell development
Ordering human CD34+CD10-CD19+ pre/pro-B-cell and CD19- common lymphoid progenitor stages in two pro-B-cell development pathways
Single-cell mass cytometry of differential immune and drug responses across a human hematopoietic continuum
The many roles of IL-7 in B cell development; mediator of survival, proliferation and differentiation
viSNE enables visualization of high dimensional single-cell data and reveals phenotypic heterogeneity of leukemia
Computational and experimental single cell biology techniques for the definition of cell type heterogeneity, interplay and intracellular dynamics
High-dimensional immune profiling of total and rotavirus VP6-specific intestinal and circulating B cells by mass cytometry
Metal Stable Isotope Tagging: Renaissance of Radioimmunoassay for Multiplex and Absolute Quantification of Biomolecules
Laser Ablation Inductively Coupled Plasma Mass Spectrometry: An Emerging Technology for Multiparametric Analysis of Tissue Antigens
Sincell: an R/Bioconductor package for statistical assessment of cell-state hierarchies from single-cell RNA-seq
Multiparameter analysis of stimulated human peripheral blood mononuclear cells: A comparison of mass and fluorescence cytometry
Cytometry by time-of-flight immunophenotyping identifies a blood Sjögren's signature correlating with disease activity and glandular inflammation
Reconstructing and analysing cellular states, space and time from gene expression profiles of many cells and single cells
Gene expression kinetics in individual plasmodial cells reveal alternative programs of differential regulation during commitment and differentiation
Emerging proteomic technologies for elucidating context-dependent cellular signaling events: A big challenge of tiny proportions
Data-Driven Phenotypic Dissection of AML Reveals Progenitor-like Cells that Correlate with Prognosis
Mapping the Diversity of Follicular Helper T Cells in Human Blood and Tonsils Using High-Dimensional Mass Cytometry Analysis
SCOUP: a probabilistic model based on the Ornstein-Uhlenbeck process to analyze single-cell expression data during differentiation
Measuring and sorting cell populations expressing isospectral fluorescent proteins with different fluorescence lifetimes
Cell surface profiling using high-throughput flow cytometry: a platform for biomarker discovery and analysis of cellular heterogeneity
Single-cell genome-wide studies give new insight into nongenetic cell-to-cell variability in animals
Single-cell RNA-seq reveals novel regulators of human embryonic stem cell differentiation to definitive endoderm
Integrated live imaging and molecular profiling of embryoid bodies reveals a synchronized progression of early differentiation
CellTree: an R/bioconductor package to infer the hierarchical structure of cell populations from single-cell RNA-seq data
Novel Strategy for Phenotypic Characterization of Human B Lymphocytes from Precursors to Effector Cells by Flow Cytometry
CXCR4 identifies transitional bone marrow premonocytes that replenish the mature monocyte pool for peripheral responses
Single-Cell-Based Analysis Highlights a Surge in Cell-to-Cell Molecular Variability Preceding Irreversible Commitment in a Differentiation Process
Exploring Glucocorticoid Receptor Agonists Mechanism of Action Through Mass Cytometry and Radial Visualizations
Mass Cytometry of Follicular Lymphoma Tumors Reveals Intrinsic Heterogeneity in Proteins Including HLA-DR and a Deficit in Nonmalignant Plasmablast and Germinal Center B-Cell Populations
Single cell proteomics in biomedicine: High-dimensional data acquisition, visualization, and analysis
Order Under Uncertainty: Robust Differential Expression Analysis Using Probabilistic Models for Pseudotime Inference
Single-cell topological RNA-seq analysis reveals insights into cellular differentiation and development
Single-cell RNA-seq and computational analysis using temporal mixture modelling resolves Th1/Tfh fate bifurcation in malaria
Quantitative stability of hematopoietic stem and progenitor cell clonal output in rhesus macaques receiving transplants.
Emerging Proteomic Technologies Provide Enormous and Underutilized Potential for Brain Cancer Research.
Dr.seq2: A quality control and analysis pipeline for parallel single cell transcriptome and epigenome data
Single-cell developmental classification of B cell precursor acute lymphoblastic leukemia at diagnosis reveals predictors of relapse
A Bayesian framework for the inference of gene regulatory networks from time and pseudo-time series data
Pseudotime Dynamics in Melanoma Single-Cell Transcriptomes Reveals Different Mechanisms of Tumor Progression
Inference of differentiation time for single cell transcriptomes using cell population reference data
Reverse-engineering of gene networks for regulating early blood development from single-cell measurements
Reconstructing differentiation networks and their regulation from time series single-cell expression data
Creating Lineage Trajectory Maps Via Integration of Single-Cell RNA-Sequencing and Lineage Tracing: Integrating transgenic lineage tracing and single-cell RNA-sequencing is a robust approach for mapping developmental lineage trajectories and cell fate changes
RNA-seq analysis identifies different transcriptomic types and developmental trajectories of primary melanomas
Surface Immobilization of Redox-Labile Fluorescent Probes: Enabling Single-Cell Co-Profiling of Aerobic Glycolysis and Oncogenic Protein Signaling Activities
Single-cell RNA-seq analysis identifies markers of resistance to targeted BRAF inhibitors in melanoma cell populations
T Cell-Dependent Affinity Maturation and Innate Immune Pathways Differentially Drive Autoreactive B Cell Responses in Rheumatoid Arthritis
Mbd3/NuRD controls lymphoid cell fate and inhibits tumorigenesis by repressing a B cell transcriptional program
A new experimental platform facilitates assessment of the transcriptional and chromatin landscapes of aging yeast
DensityPath: an algorithm to visualize and reconstruct cell state-transition path on density landscape for single-cell RNA sequencing data
Beyond the message: advantages of snapshot proteomics with single-cell mass cytometry in solid tumors
Connecting the dots across time: reconstruction of single-cell signalling trajectories using time-stamped data
Cytometry-based single-cell analysis of intact epithelial signaling reveals MAPK activation divergent from TNF-α-induced apoptosis in vivo
Quantifying pluripotency landscape of cell differentiation from scRNA-seq data by continuous birth-death process
FLOW-MAP: a graph-based, force-directed layout algorithm for trajectory mapping in single-cell time course datasets.
Discrete roles and bifurcation of PTEN signaling and mTORC1-mediated anabolic metabolism underlie IL-7-driven B lymphopoiesis
CellTagging: combinatorial indexing to simultaneously map lineage and identity at single-cell resolution.
Molecular natural history of breast cancer: Leveraging transcriptomics to predict breast cancer progression and aggressiveness
Meta-analysis of Caenorhabditis elegans single-cell developmental data reveals multi-frequency oscillation in gene activation
Mapping lung cancer epithelial-mesenchymal transition states and trajectories with single-cell resolution
Training Novices in Generation and Analysis of High-Dimensional Human Cell Phospho-Flow Cytometry Data.
Towards multi-omics characterization of tumor heterogeneity: a comprehensive review of statistical and machine learning approaches
Identification of Vaccine-Altered Circulating B Cell Phenotypes Using Mass Cytometry and a Two-Step Clustering Analysis
Human B-cell and progenitor stages as determined by probability state modeling of multidimensional cytometry data
Scater: pre-processing, quality control, normalization and visualization of single-cell RNA-seq data in R
Using transfer learning from prior reference knowledge to improve the clustering of single-cell RNA-Seq data
Identification of the immune checkpoint signature of multiple myeloma using mass cytometry-based single-cell analysis
An atlas of transcriptional, chromatin accessibility, and surface marker changes in human mesoderm development
scFTD-seq: freeze-thaw lysis based, portable approach toward highly distributed single-cell 3' mRNA profiling
Cellular network modeling and single cell gene expression analysis reveals novel hepatic stellate cell phenotypes controlling liver regeneration dynamics
Quantifying the Dynamics of Hematopoiesis by In Vivo IdU Pulse-Chase, Mass Cytometry, and Mathematical Modeling
Single-cell analysis of bone marrow-derived CD34+ cells from children with sickle cell disease and thalassemia.
From Bivariate to Multivariate Analysis of Cytometric Data: Overview of Computational Methods and Their Application in Vaccination Studies
HopLand: single-cell pseudotime recovery using continuous Hopfield network-based modeling of Waddington's epigenetic landscape
PAGA: graph abstraction reconciles clustering with trajectory inference through a topology preserving map of single cells
Circular Trajectory Reconstruction Uncovers Cell-Cycle Progression and Regulatory Dynamics from Single-Cell Hi-C Maps
Multi-omic single-cell snapshots reveal multiple independent trajectories to drug tolerance in a melanoma cell line
DTWscore: differential expression and cell clustering analysis for time-series single-cell RNA-seq data
SINCERITIES: Inferring gene regulatory networks from time-stamped single cell transcriptional expression profiles
Killer-like receptors and GPR56 progressive expression defines cytokine production of human CD4+ memory T cells
Mass Cytometry for the Assessment of Immune Reconstitution After Hematopoietic Stem Cell Transplantation
Mass cytometry-based single-cell analysis of human stem cell reprogramming uncovers differential regulation of specific pluripotency markers
Single-cell gene expression analysis reveals regulators of distinct cell subpopulations among developing human neurons
The impact of single-cell RNA sequencing on understanding the functional organization of the immune system
Data analysis to modeling to building theory in NK cell biology and beyond: How can computational modeling contribute?
Reconstructing temporal and spatial dynamics from single-cell pseudotime using prior knowledge of real scale cell densities
Single-cell transcriptomics uncover distinct innate and adaptive cell subsets during tissue homeostasis and regeneration.
Sequencing dropout-and-batch effect normalization for single-cell mRNA profiles: a survey and comparative analysis
A pseudo-temporal causality approach to identifying miRNA-mRNA interactions during biological processes
Kidney Single-cell Transcriptomes Predict Spatial Corticomedullary Gene Expression and Tissue Osmolality Gradients.
Key steps and methods in the experimental design and data analysis of highly multi-parametric flow and mass cytometry
Immune cell profiles associated with measured exposure to phthalates in the Norwegian EuroMix biomonitoring study - A mass cytometry approach in toxicology
Regulatory Dynamics of Cell Differentiation Revealed by True Time Series From Multinucleate Single Cells.
Multidimensional Proteomic Approach of Endothelial Progenitors Demonstrate Expression of KDR Restricted to CD19 Cells
Disentangling a complex response in cell reprogramming and probing the Waddington landscape by automatic construction of Petri nets
Toward Therapeutic Targeting of Bone Marrow Leukemic Niche Protective Signals in B-Cell Acute Lymphoblastic Leukemia.
Transient phases of OXPHOS inhibitor resistance reveal underlying metabolic heterogeneity in single cells.
Cell Checkpoints & Regulators
Cell cycle checkpoints are a series of complex checkpoint mechanisms that detect DNA abnormalities and ensure that DNA replication and repair are complete before cell division. They are primarily regulated by cyclins, cyclin-dependent kinases, and the anaphase-promoting complex/cyclosome. Here is the latest research.
Cell is a scientific journal publishing research across a broad range of disciplines within the life sciences field. Discover the latest research from Cell here.
Apoptosis is a specific process that leads to programmed cell death through the activation of an evolutionary conserved intracellular pathway leading to pathognomic cellular changes distinct from cellular necrosis
Blood And Marrow Transplantation
The use of hematopoietic stem cell transplantation or blood and marrow transplantation (bmt) is on the increase worldwide. BMT is used to replace damaged or destroyed bone marrow with healthy bone marrow stem cells. Here is the latest research on bone and marrow transplantation.
Adult Stem Cells
Adult stem cells reside in unique niches that provide vital cues for their survival, self-renewal, and differentiation. They hold great promise for use in tissue repair and regeneration as a novel therapeutic strategies. Here is the latest research.
CZI Human Cell Atlas Seed Network
The aim of the Human Cell Atlas (HCA) is to build reference maps of all human cells in order to enhance our understanding of health and disease. The Seed Networks for the HCA project aims to bring together collaborators with different areas of expertise in order to facilitate the development of the HCA. Find the latest research from members of the HCA Seed Networks here.