Mapping transcriptomic vector fields of single cells

Deciphering transcriptional and functional heterogeneity in hematopoiesis with single-cell genomics

(2021) Jorge D. Martin-Rufino et al.   CURRENT OPINION IN HEMATOLOGY

HLF Expression Defines the Human Hematopoietic Stem Cell State.

(2021) Bernhard Lehnertz et al.   BLOOD

RNA velocity—current challenges and future perspectives

(2021) Volker Bergen et al.   Molecular Systems Biology

Spatio-temporal mRNA tracking in the early zebrafish embryo

(2021) Karoline Holler et al.   Nature Communications

SciPy 1.0: fundamental algorithms for scientific computing in Python

(2020) Pauli Virtanen et al.   NATURE METHODS

Lineage tracing on transcriptional landscapes links state to fate during differentiation

(2020) Caleb Weinreb et al.   SCIENCE

Sequencing metabolically labeled transcripts in single cells reveals mRNA turnover strategies

(2020) Nico Battich et al.   SCIENCE

Inferring Causal Gene Regulatory Networks from Coupled Single-Cell Expression Dynamics Using Scribe

(2020) Xiaojie Qiu et al.   Cell Systems

Sci-fate characterizes the dynamics of gene expression in single cells

(2020) Junyue Cao et al.   NATURE BIOTECHNOLOGY

A single-cell transcriptomic atlas characterizes ageing tissues in the mouse

(2020)   NATURE

Generalizing RNA velocity to transient cell states through dynamical modeling

(2020) Volker Bergen et al.   NATURE BIOTECHNOLOGY

Chromatin Potential Identified by Shared Single-Cell Profiling of RNA and Chromatin

(2020) Sai Ma et al.   CELL

RNA timestamps identify the age of single molecules in RNA sequencing

(2020) Samuel G. Rodriques et al.   NATURE BIOTECHNOLOGY

Massively parallel and time-resolved RNA sequencing in single cells with scNT-seq

(2020) Qi Qiu et al.   NATURE METHODS

Species-specific segmentation clock periods are due to differential biochemical reaction speeds

(2020) Mitsuhiro Matsuda et al.   SCIENCE

Species-specific pace of development is associated with differences in protein stability

(2020) Teresa Rayon et al.   SCIENCE

High-Spatial-Resolution Multi-Omics Sequencing via Deterministic Barcoding in Tissue

(2020) Yang Liu et al.   CELL

Tracking development at the cellular level

(2020) Junyue Cao   SCIENCE

Slide-seq: A scalable technology for measuring genome-wide expression at high spatial resolution

(2019) Samuel G. Rodriques et al.   SCIENCE

Molecular recording of mammalian embryogenesis

(2019) Michelle M. Chan et al.   NATURE

A comparison of single-cell trajectory inference methods

(2019) Wouter Saelens et al.   NATURE BIOTECHNOLOGY

scSLAM-seq reveals core features of transcription dynamics in single cells

(2019) Florian Erhard et al.   NATURE

A comprehensive single cell transcriptional landscape of human hematopoietic progenitors

(2019) Danilo Pellin et al.   Nature Communications

NASC-seq monitors RNA synthesis in single cells

(2019) Gert-Jan Hendriks et al.   Nature Communications

Identification of two distinct pathways of human myelopoiesis

(2019) Roy Drissen et al.   Science Immunology

Dissecting newly transcribed and old RNA using GRAND-SLAM

(2018) Christopher Jürges et al.   BIOINFORMATICS

TimeLapse-seq: adding a temporal dimension to RNA sequencing through nucleoside recoding

(2018) Jeremy A Schofield 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

RNA velocity of single cells

(2018) Gioele La Manno et al.   NATURE

DNA-based memory devices for recording cellular events

(2018) Ravi U. Sheth et al.   NATURE REVIEWS GENETICS

Expanding the Nucleoside Recoding Toolkit: Revealing RNA Population Dynamics with 6-Thioguanosine

(2018) Lea Kiefer et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Genomic encoding of transcriptional burst kinetics

(2018) Anton J. M. Larsson et al.   NATURE

Molecular, spatial, and functional single-cell profiling of the hypothalamic preoptic region

(2018) Jeffrey R. Moffitt et al.   SCIENCE

Synthetic recording and in situ readout of lineage information in single cells

(2017) Kirsten L. Frieda et al.   NATURE

Potential landscape of high dimensional nonlinear stochastic dynamics with large noise

(2017) Ying Tang et al.   Scientific Reports

Transcriptional Heterogeneity and Lineage Commitment in Myeloid Progenitors

(2016) Franziska Paul et al.   CELL

Perturb-Seq: Dissecting Molecular Circuits with Scalable Single-Cell RNA Profiling of Pooled Genetic Screens

(2016) Atray Dixit et al.   CELL

A Multiplexed Single-Cell CRISPR Screening Platform Enables Systematic Dissection of the Unfolded Protein Response

(2016) Britt Adamson et al.   CELL

A predictive computational framework for direct reprogramming between human cell types

(2016) Owen J L Rackham et al.   NATURE GENETICS

Distinct myeloid progenitor–differentiation pathways identified through single-cell RNA sequencing

(2016) Roy Drissen et al.   NATURE IMMUNOLOGY

Diffusion pseudotime robustly reconstructs lineage branching

(2016) Laleh Haghverdi et al.   NATURE METHODS

Comprehensive population-based genome sequencing provides insight into hematopoietic regulatory mechanisms

(2016) Michael H. Guo et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Whole-organism lineage tracing by combinatorial and cumulative genome editing

(2016) Aaron McKenna et al.   SCIENCE

A microfluidic platform enabling single-cell RNA-seq of multigenerational lineages

(2016) Robert J. Kimmerling et al.   Nature Communications

Defining the Minimal Factors Required for Erythropoiesis through Direct Lineage Conversion

(2016) Sandra Capellera-Garcia et al.   Cell Reports

Intrinsic Noise Profoundly Alters the Dynamics and Steady State of Morphogen-Controlled Bistable Genetic Switches

(2016) Ruben Perez-Carrasco et al.   PLoS Computational Biology

The BioMart community portal: an innovative alternative to large, centralized data repositories

(2015) Damian Smedley et al.   NUCLEIC ACIDS RESEARCH

Dissecting Engineered Cell Types and Enhancing Cell Fate Conversion via CellNet

(2014) Samantha A. Morris et al.   CELL

CellNet: Network Biology Applied to Stem Cell Engineering

(2014) Patrick Cahan et al.   CELL

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

(2014) Sean C. Bendall et al.   CELL

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

(2014) Cole Trapnell et al.   NATURE BIOTECHNOLOGY

Validation of noise models for single-cell transcriptomics

(2014) Dominic Grün et al.   NATURE METHODS

Epigenetic state network approach for describing cell phenotypic transitions

(2014) P. Wang et al.   Interface Focus

Clonal Analysis Unveils Self-Renewing Lineage-Restricted Progenitors Generated Directly from Hematopoietic Stem Cells

(2013) Ryo Yamamoto et al.   CELL

Platelet-biased stem cells reside at the apex of the haematopoietic stem-cell hierarchy

(2013) Alejandra Sanjuan-Pla et al.   NATURE

Regularized vector field learning with sparse approximation for mismatch removal

(2013) Jiayi Ma et al.   PATTERN RECOGNITION

Efficient Generation of Rat Induced Pluripotent Stem Cells Using a Non-Viral Inducible Vector

(2013) Claudia Merkl et al.   PLoS One

A Whole-Cell Computational Model Predicts Phenotype from Genotype

(2012) Jonathan R. Karr et al.   CELL

From Understanding the Development Landscape of the Canonical Fate-Switch Pair to Constructing a Dynamic Landscape for Two-Step Neural Differentiation

(2012) Xiaojie Qiu et al.   PLoS One

The multifunctional role of EKLF/KLF1 during erythropoiesis

(2011) M. Siatecka et al.   BLOOD

Hierarchical Differentiation of Myeloid Progenitors Is Encoded in the Transcription Factor Network

(2011) Jan Krumsiek et al.   PLoS One

Quantifying the Waddington landscape and biological paths for development and differentiation

(2011) J. Wang et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

The Potential Landscape of Genetic Circuits Imposes the Arrow of Time in Stem Cell Differentiation

(2010) Jin Wang et al.   BIOPHYSICAL JOURNAL

Taking a long, hard look

(2010) Monya Baker   NATURE

Understanding gene circuits at cell-fate branch points for rational cell reprogramming

(2010) Joseph X. Zhou et al.   TRENDS IN GENETICS

Forcing cells to change lineages

(2009) Thomas Graf et al.   NATURE

Hematopoiesis: An Evolving Paradigm for Stem Cell Biology

(2008) Stuart H. Orkin et al.   CELL