Live-seq enables temporal transcriptomic recording of single cells

Variability within rare cell states enables multiple paths toward drug resistance

(2021) Benjamin L. Emert et al.   NATURE BIOTECHNOLOGY

Lineage tracing on transcriptional landscapes links state to fate during differentiation

(2020) Caleb Weinreb et al.   SCIENCE

Single-cell RNA counting at allele and isoform resolution using Smart-seq3

(2020) Michael Hagemann-Jensen et al.   NATURE BIOTECHNOLOGY

Benchmarking single-cell RNA-sequencing protocols for cell atlas projects

(2020) Elisabetta Mereu et al.   NATURE BIOTECHNOLOGY

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

(2020) Junyue Cao et al.   NATURE BIOTECHNOLOGY

The emergence and promise of single-cell temporal-omics approaches

(2020) Alex R Lederer et al.   CURRENT OPINION IN BIOTECHNOLOGY

A comparison of single-cell trajectory inference methods

(2019) Wouter Saelens et al.   NATURE BIOTECHNOLOGY

Challenges in measuring and understanding biological noise

(2019) Nils Eling et al.   NATURE REVIEWS GENETICS

Comprehensive Integration of Single-Cell Data

(2019) Tim Stuart et al.   CELL

Concepts and limitations for learning developmental trajectories from single cell genomics

(2019) Sophie Tritschler et al.   DEVELOPMENT

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

(2019) Florian Erhard et al.   NATURE

NASC-seq monitors RNA synthesis in single cells

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

NF-κB Signaling in Macrophages: Dynamics, Crosstalk, and Signal Integration

(2019) Michael G. Dorrington et al.   Frontiers in Immunology

Unravelling cellular relationships during development and regeneration using genetic lineage tracing

(2019) Chloé S. Baron et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

Slingshot: cell lineage and pseudotime inference for single-cell transcriptomics

(2018) Kelly Street et al.   BMC GENOMICS

Single-Cell Transcriptomics Meets Lineage Tracing

(2018) Lennart Kester et al.   Cell Stem Cell

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

Rewritable multi-event analog recording in bacterial and mammalian cells

(2018) Weixin Tang et al.   SCIENCE

A Single-Cell Transcriptional Atlas of the Developing Murine Cerebellum

(2018) Robert A. Carter et al.   CURRENT BIOLOGY

The Transcription Factor ZEB2 Is Required to Maintain the Tissue-Specific Identities of Macrophages

(2018) Charlotte L. Scott et al.   IMMUNITY

RNA velocity of single cells

(2018) Gioele La Manno et al.   NATURE

A stromal cell population that inhibits adipogenesis in mammalian fat depots

(2018) Petra C. Schwalie et al.   NATURE

Transcriptional recording by CRISPR spacer acquisition from RNA

(2018) Florian Schmidt et al.   NATURE

Comparative Analysis of Single-Cell RNA Sequencing Methods

(2017) Christoph Ziegenhain et al.   MOLECULAR CELL

Rare cell variability and drug-induced reprogramming as a mode of cancer drug resistance

(2017) Sydney M. Shaffer et al.   NATURE

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

(2017) Kirsten L. Frieda et al.   NATURE

Dissecting the brown adipogenic regulatory network using integrative genomics

(2017) Rachana N. Pradhan et al.   Scientific Reports

Tunable Single-Cell Extraction for Molecular Analyses

(2016) Orane Guillaume-Gentil et al.   CELL

Early myeloid lineage choice is not initiated by random PU.1 to GATA1 protein ratios

(2016) Philipp S. Hoppe et al.   NATURE

Transition states and cell fate decisions in epigenetic landscapes

(2016) Naomi Moris et al.   NATURE REVIEWS GENETICS

Transcription–replication conflicts: how they occur and how they are resolved

(2016) Tatiana García-Muse et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

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

(2016) Zhicheng Ji et al.   NUCLEIC ACIDS RESEARCH

Enrichr: a comprehensive gene set enrichment analysis web server 2016 update

(2016) Maxim V. Kuleshov et al.   NUCLEIC ACIDS RESEARCH

Bright monomeric near-infrared fluorescent proteins as tags and biosensors for multiscale imaging

(2016) Daria M. Shcherbakova et al.   Nature Communications

Single-cell RNA-seq reveals changes in cell cycle and differentiation programs upon aging of hematopoietic stem cells

(2015) Monika S. Kowalczyk et al.   GENOME RESEARCH

The Technology and Biology of Single-Cell RNA Sequencing

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

Dynamic profiling of the protein life cycle in response to pathogens

(2015) M. Jovanovic et al.   SCIENCE

Cancer stem cells and cell size: A causal link?

(2015) Qiuhui Li et al.   SEMINARS IN CANCER BIOLOGY

HTSeq--a Python framework to work with high-throughput sequencing data

(2014) S. Anders et al.   BIOINFORMATICS

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

(2014) Cole Trapnell et al.   NATURE BIOTECHNOLOGY

Genomically encoded analog memory with precise in vivo DNA writing in living cell populations

(2014) F. Farzadfard et al.   SCIENCE

Switching of the Relative Dominance Between Feedback Mechanisms in Lipopolysaccharide-Induced NF- B Signaling

(2014) M.-H. Sung et al.   Science Signaling

Force-controlled manipulation of single cells: from AFM to FluidFM

(2014) Orane Guillaume-Gentil et al.   TRENDS IN BIOTECHNOLOGY

Smart-seq2 for sensitive full-length transcriptome profiling in single cells

(2013) Simone Picelli et al.   NATURE METHODS

Amplifying Genetic Logic Gates

(2013) J. Bonnet et al.   SCIENCE

STAR: ultrafast universal RNA-seq aligner

(2012) Alexander Dobin et al.   BIOINFORMATICS

Highly multiplexed and strand-specific single-cell RNA 5′ end sequencing

(2012) Saiful Islam et al.   Nature Protocols

Differential expression analysis of multifactor RNA-Seq experiments with respect to biological variation

(2012) Davis J. McCarthy et al.   NUCLEIC ACIDS RESEARCH

clusterProfiler: an R Package for Comparing Biological Themes Among Gene Clusters

(2012) Guangchuang Yu et al.   OMICS-A JOURNAL OF INTEGRATIVE BIOLOGY

Stochastic State Transitions Give Rise to Phenotypic Equilibrium in Populations of Cancer Cells

(2011) Piyush B. Gupta et al.   CELL

Metabolic labeling of RNA uncovers principles of RNA production and degradation dynamics in mammalian cells

(2011) Michal Rabani et al.   NATURE BIOTECHNOLOGY

Incorporation of non-natural nucleotides into template-switching oligonucleotides reduces background and improves cDNA synthesis from very small RNA samples

(2010) Jeremy Kapteyn et al.   BMC GENOMICS

BioMart – biological queries made easy

(2009) Damian Smedley et al.   BMC GENOMICS

FluidFM: Combining Atomic Force Microscopy and Nanofluidics in a Universal Liquid Delivery System for Single Cell Applications and Beyond

(2009) André Meister et al.   NANO LETTERS

Cell Growth and Size Homeostasis in Proliferating Animal Cells

(2009) A. Tzur et al.   SCIENCE

Synthetic Gene Networks That Count

(2009) A. E. Friedland et al.   SCIENCE