Computational methods for trajectory inference from single-cell transcriptomics

SCOUP: a probabilistic model based on the Ornstein–Uhlenbeck process to analyze single-cell expression data during differentiation

(2016) Hirotaka Matsumoto et al.   BMC BIOINFORMATICS

Transcriptional Heterogeneity and Lineage Commitment in Myeloid Progenitors

(2016) Franziska Paul et al.   CELL

Single-Cell RNA-Seq Reveals Lineage and X Chromosome Dynamics in Human Preimplantation Embryos

(2016) Sophie Petropoulos et al.   CELL

Heterogeneity in Oct4 and Sox2 Targets Biases Cell Fate in 4-Cell Mouse Embryos

(2016) Mubeen Goolam et al.   CELL

Dynamic Gene Regulatory Networks Drive Hematopoietic Specification and Differentiation

(2016) Debbie K. Goode et al.   DEVELOPMENTAL CELL

Challenges: Crowdsourced solutions

(2016) Eric Bender   NATURE

Tracing haematopoietic stem cell formation at single-cell resolution

(2016) Fan Zhou et al.   NATURE

Dissecting direct reprogramming from fibroblast to neuron using single-cell RNA-seq

(2016) Barbara Treutlein et al.   NATURE

Wishbone identifies bifurcating developmental trajectories from single-cell data

(2016) Manu Setty et al.   NATURE BIOTECHNOLOGY

Single-cell analysis defines the divergence between the innate lymphoid cell lineage and lymphoid tissue–inducer cell lineage

(2016) Isabel E Ishizuka et al.   NATURE IMMUNOLOGY

Characterizing transcriptional heterogeneity through pathway and gene set overdispersion analysis

(2016) Jean Fan et al.   NATURE METHODS

Single-cell genome sequencing: current state of the science

(2016) Charles Gawad et al.   NATURE REVIEWS GENETICS

TSCAN: Pseudo-time reconstruction and evaluation in single-cell RNA-seq analysis

(2016) Zhicheng Ji et al.   NUCLEIC ACIDS RESEARCH

Single-Cell Transcript Profiles Reveal Multilineage Priming in Early Progenitors Derived from Lgr5 + Intestinal Stem Cells

(2016) Tae-Hee Kim et al.   Cell Reports

Reconstructing gene regulatory dynamics from high-dimensional single-cell snapshot data

(2015) Andrea Ocone et al.   BIOINFORMATICS

Diffusion maps for high-dimensional single-cell analysis of differentiation data

(2015) Laleh Haghverdi et al.   BIOINFORMATICS

The Branching Point in Erythro-Myeloid Differentiation

(2015) Leïla Perié et al.   CELL

Single-Cell RNA-Seq with Waterfall Reveals Molecular Cascades underlying Adult Neurogenesis

(2015) Jaehoon Shin et al.   Cell Stem Cell

FlowSOM: Using self-organizing maps for visualization and interpretation of cytometry data

(2015) Sofie Van Gassen et al.   CYTOMETRY PART A

The end of gating? An introduction to automated analysis of high dimensional cytometry data

(2015) Florian Mair et al.   EUROPEAN JOURNAL OF IMMUNOLOGY

Defining cell types and states with single-cell genomics

(2015) Cole Trapnell   GENOME RESEARCH

The Technology and Biology of Single-Cell RNA Sequencing

(2015) Aleksandra A. Kolodziejczyk et al.   MOLECULAR CELL

Advances and Applications of Single-Cell Sequencing Technologies

(2015) Yong Wang et al.   MOLECULAR CELL

Single-cell messenger RNA sequencing reveals rare intestinal cell types

(2015) Dominic Grün et al.   NATURE

Single-cell chromatin accessibility reveals principles of regulatory variation

(2015) Jason D. Buenrostro et al.   NATURE

Computational analysis of cell-to-cell heterogeneity in single-cell RNA-sequencing data reveals hidden subpopulations of cells

(2015) Florian Buettner et al.   NATURE BIOTECHNOLOGY

Decoding the regulatory network of early blood development from single-cell gene expression measurements

(2015) Victoria Moignard et al.   NATURE BIOTECHNOLOGY

Single-cell ChIP-seq reveals cell subpopulations defined by chromatin state

(2015) Assaf Rotem et al.   NATURE BIOTECHNOLOGY

Identification of cDC1- and cDC2-committed DC progenitors reveals early lineage priming at the common DC progenitor stage in the bone marrow

(2015) Andreas Schlitzer et al.   NATURE IMMUNOLOGY

Computational and analytical challenges in single-cell transcriptomics

(2015) Oliver Stegle et al.   NATURE REVIEWS GENETICS

Flow cytometry strikes gold

(2015) J. Paul Robinson et al.   SCIENCE

Cell types in the mouse cortex and hippocampus revealed by single-cell RNA-seq

(2015) A. Zeisel et al.   SCIENCE

Distinct routes of lineage development reshape the human blood hierarchy across ontogeny

(2015) F. Notta et al.   SCIENCE

Single-Cell Network Analysis Identifies DDIT3 as a Nodal Lineage Regulator in Hematopoiesis

(2015) Cristina Pina et al.   Cell Reports

Single-Cell DNA Methylome Sequencing and Bioinformatic Inference of Epigenomic Cell-State Dynamics

(2015) Matthias Farlik et al.   Cell Reports

Single-cell transcriptional analysis to uncover regulatory circuits driving cell fate decisions in early mouse development

(2014) Haifen Chen et al.   BIOINFORMATICS

Single-Cell Trajectory Detection Uncovers Progression and Regulatory Coordination in Human B Cell Development

(2014) Sean C. Bendall et al.   CELL

Quantitative Single-Cell Approaches to Stem Cell Research

(2014) Martin Etzrodt et al.   Cell Stem Cell

An animated landscape representation of CD4+T-cell differentiation, variability, and plasticity: Insights into the behavior of populations versus cells

(2014) Jonathan A. Rebhahn et al.   EUROPEAN JOURNAL OF IMMUNOLOGY

T Follicular Helper Cell Differentiation, Function, and Roles in Disease

(2014) Shane Crotty   IMMUNITY

Clonal dynamics of native haematopoiesis

(2014) Jianlong Sun et al.   NATURE

The dynamics and regulators of cell fate decisions are revealed by pseudotemporal ordering of single cells

(2014) Cole Trapnell et al.   NATURE BIOTECHNOLOGY

Early specification of CD8+ T lymphocyte fates during adaptive immunity revealed by single-cell gene-expression analyses

(2014) Janilyn Arsenio et al.   NATURE IMMUNOLOGY

High-dimensional analysis of the murine myeloid cell system

(2014) Burkhard Becher et al.   NATURE IMMUNOLOGY

Multiplexed ion beam imaging of human breast tumors

(2014) Michael Angelo et al.   NATURE MEDICINE

Single-cell genome-wide bisulfite sequencing for assessing epigenetic heterogeneity

(2014) Sébastien A Smallwood et al.   NATURE METHODS

Highly multiplexed imaging of tumor tissues with subcellular resolution by mass cytometry

(2014) Charlotte Giesen et al.   NATURE METHODS

Molecular ties between the cell cycle and differentiation in embryonic stem cells

(2014) Victor C. Li et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Bifurcation analysis of single-cell gene expression data reveals epigenetic landscape

(2014) Eugenio Marco et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Mapping Cellular Hierarchy by Single-Cell Analysis of the Cell Surface Repertoire

(2013) Guoji Guo et al.   Cell Stem Cell

Dynamic Analysis of Gene Expression and Genome-wide Transcription Factor Binding during Lineage Specification of Multipotent Progenitors

(2013) Gillian May et al.   Cell Stem Cell

Haematopoietic stem cells and early lymphoid progenitors occupy distinct bone marrow niches

(2013) Lei Ding et al.   NATURE

Single-cell transcriptomics reveals bimodality in expression and splicing in immune cells

(2013) Alex K. Shalek et al.   NATURE

viSNE enables visualization of high dimensional single-cell data and reveals phenotypic heterogeneity of leukemia

(2013) El-ad David Amir et al.   NATURE BIOTECHNOLOGY

Characterization of transcriptional networks in blood stem and progenitor cells using high-throughput single-cell gene expression analysis

(2013) Victoria Moignard et al.   NATURE CELL BIOLOGY

Identification of transcriptional regulators in the mouse immune system

(2013) Vladimir Jojic et al.   NATURE IMMUNOLOGY

Eukaryotic transcriptional dynamics: from single molecules to cell populations

(2013) Antoine Coulon et al.   NATURE REVIEWS GENETICS

Positive Feedback Between PU.1 and the Cell Cycle Controls Myeloid Differentiation

(2013) H. Y. Kueh et al.   SCIENCE

Single-Cell Metabolomics: Analytical and Biological Perspectives

(2013) R. Zenobi   SCIENCE

Temporal dynamics and transcriptional control using single-cell gene expression analysis

(2013) Tsukasa Kouno et al.   GENOME BIOLOGY

Single-Cell Expression Analyses during Cellular Reprogramming Reveal an Early Stochastic and a Late Hierarchic Phase

(2012) Yosef Buganim et al.   CELL

Bistability, Bifurcations, and Waddington's Epigenetic Landscape

(2012) James E. Ferrell   CURRENT BIOLOGY

Studying and modelling dynamic biological processes using time-series gene expression data

(2012) Ziv Bar-Joseph et al.   NATURE REVIEWS GENETICS

Densely Interconnected Transcriptional Circuits Control Cell States in Human Hematopoiesis

(2011) Noa Novershtern et al.   CELL

Extracting a cellular hierarchy from high-dimensional cytometry data with SPADE

(2011) Peng Qiu et al.   NATURE BIOTECHNOLOGY

Single-Cell Mass Cytometry of Differential Immune and Drug Responses Across a Human Hematopoietic Continuum

(2011) S. C. Bendall et al.   SCIENCE

Resolution of Cell Fate Decisions Revealed by Single-Cell Gene Expression Analysis from Zygote to Blastocyst

(2010) Guoji Guo et al.   DEVELOPMENTAL CELL

Clinical consequences of defects in B-cell development

(2010) Andre M. Vale et al.   JOURNAL OF ALLERGY AND CLINICAL IMMUNOLOGY

Mass Cytometry: Technique for Real Time Single Cell Multitarget Immunoassay Based on Inductively Coupled Plasma Time-of-Flight Mass Spectrometry

(2009) Dmitry R. Bandura et al.   ANALYTICAL CHEMISTRY

Stem Cell States, Fates, and the Rules of Attraction

(2009) Tariq Enver et al.   Cell Stem Cell

Inference of Gene Regulatory Networks Using Time-Series Data: A Survey

(2009) Chao Sima et al.   CURRENT GENOMICS

Myeloproliferative disorders

(2008) R. L. Levine et al.   BLOOD