Lineage tracing on transcriptional landscapes links state to fate during differentiation

Optimal-Transport Analysis of Single-Cell Gene Expression Identifies Developmental Trajectories in Reprogramming

(2019) Geoffrey Schiebinger et al.   CELL

Molecular recording of mammalian embryogenesis

(2019) Michelle M. Chan et al.   NATURE

Single-Cell Transcriptomics Meets Lineage Tracing

(2018) Lennart Kester et al.   Cell Stem Cell

Simultaneous lineage tracing and cell-type identification using CRISPR–Cas9-induced genetic scars

(2018) Bastiaan Spanjaard et al.   NATURE BIOTECHNOLOGY

FateID infers cell fate bias in multipotent progenitors from single-cell RNA-seq data

(2018) Josip S Herman et al.   NATURE METHODS

Fundamental limits on dynamic inference from single-cell snapshots

(2018) Caleb Weinreb et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Single-cell mapping of gene expression landscapes and lineage in the zebrafish embryo

(2018) Daniel E. Wagner et al.   SCIENCE

DiSNE Movie Visualization and Assessment of Clonal Kinetics Reveal Multiple Trajectories of Dendritic Cell Development

(2018) Dawn S. Lin et al.   Cell Reports

A single-cell atlas of the airway epithelium reveals the CFTR-rich pulmonary ionocyte

(2018) Lindsey W. Plasschaert et al.   NATURE

RNA velocity of single cells

(2018) Gioele La Manno et al.   NATURE

Population snapshots predict early haematopoietic and erythroid hierarchies

(2018) Betsabeh Khoramian Tusi et al.   NATURE

A revised airway epithelial hierarchy includes CFTR-expressing ionocytes

(2018) Daniel T. Montoro et al.   NATURE

Single-cell mapping of lineage and identity in direct reprogramming

(2018) Brent A. Biddy et al.   NATURE

Granulocyte-Monocyte Progenitors and Monocyte-Dendritic Cell Progenitors Independently Produce Functionally Distinct Monocytes

(2017) Alberto Yáñez et al.   IMMUNITY

Human haematopoietic stem cell lineage commitment is a continuous process

(2017) Lars Velten et al.   NATURE CELL BIOLOGY

Building a lineage from single cells: genetic techniques for cell lineage tracking

(2017) Mollie B. Woodworth et al.   NATURE REVIEWS GENETICS

A single-cell resolution map of mouse hematopoietic stem and progenitor cell differentiation

(2016) S. Nestorowa et al.   BLOOD

The Branching Point in Erythro-Myeloid Differentiation

(2015) Leïla Perié et al.   CELL

Droplet Barcoding for Single-Cell Transcriptomics Applied to Embryonic Stem Cells

(2015) Allon M. Klein et al.   CELL

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

(2015) F. Notta et al.   SCIENCE

Cellular barcoding: A technical appraisal

(2014) Shalin H. Naik et al.   EXPERIMENTAL HEMATOLOGY

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

Equitability, mutual information, and the maximal information coefficient

(2014) Justin B. Kinney et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

PANTHER in 2013: modeling the evolution of gene function, and other gene attributes, in the context of phylogenetic trees

(2012) Huaiyu Mi et al.   NUCLEIC ACIDS RESEARCH

Tracking single hematopoietic stem cells in vivo using high-throughput sequencing in conjunction with viral genetic barcoding

(2011) Rong Lu et al.   NATURE BIOTECHNOLOGY

Cellular barcoding tool for clonal analysis in the hematopoietic system

(2010) A. Gerrits et al.   BLOOD