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

The single-cell transcriptional landscape of mammalian organogenesis

(2019) Junyue Cao et al.   NATURE

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

High-Throughput Single-Cell Sequencing with Linear Amplification

(2019) Yi Yin et al.   MOLECULAR CELL

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

(2018) Kelly Street et al.   BMC GENOMICS

SLAM-ITseq: sequencing cell type-specific transcriptomes without cell sorting

(2018) Wayo Matsushima et al.   DEVELOPMENT

Highly scalable generation of DNA methylation profiles in single cells

(2018) Ryan M Mulqueen et al.   NATURE BIOTECHNOLOGY

Integrating single-cell transcriptomic data across different conditions, technologies, and species

(2018) Andrew Butler et al.   NATURE BIOTECHNOLOGY

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

(2018) Jeremy A Schofield et al.   NATURE METHODS

SLAM-seq defines direct gene-regulatory functions of the BRD4-MYC axis

(2018) Matthias Muhar et al.   SCIENCE

Single-cell profiling of the developing mouse brain and spinal cord with split-pool barcoding

(2018) Alexander B. Rosenberg et al.   SCIENCE

RNA velocity of single cells

(2018) Gioele La Manno et al.   NATURE

Joint profiling of chromatin accessibility and gene expression in thousands of single cells

(2018) Junyue Cao et al.   SCIENCE

Regulatory crosstalk between the oxidative stress-related transcription factor Nfe2l2/Nrf2 and mitochondria

(2018) In-geun Ryoo et al.   TOXICOLOGY AND APPLIED PHARMACOLOGY

SCENIC: single-cell regulatory network inference and clustering

(2017) Sara Aibar et al.   NATURE METHODS

Sequencing thousands of single-cell genomes with combinatorial indexing

(2017) Sarah A Vitak et al.   NATURE METHODS

Thiol-linked alkylation of RNA to assess expression dynamics

(2017) Veronika A Herzog et al.   NATURE METHODS

Reversed graph embedding resolves complex single-cell trajectories

(2017) Xiaojie Qiu et al.   NATURE METHODS

TRRUST v2: an expanded reference database of human and mouse transcriptional regulatory interactions

(2017) Heonjong Han et al.   NUCLEIC ACIDS RESEARCH

Comprehensive single-cell transcriptional profiling of a multicellular organism

(2017) Junyue Cao et al.   SCIENCE

Mitotic transcription and waves of gene reactivation during mitotic exit

(2017) Katherine C. Palozola et al.   SCIENCE

Direct GR Binding Sites Potentiate Clusters of TF Binding across the Human Genome

(2016) Christopher M. Vockley et al.   CELL

Wishbone identifies bifurcating developmental trajectories from single-cell data

(2016) Manu Setty et al.   NATURE BIOTECHNOLOGY

Diffusion pseudotime robustly reconstructs lineage branching

(2016) Laleh Haghverdi et al.   NATURE METHODS

Transition states and cell fate decisions in epigenetic landscapes

(2016) Naomi Moris et al.   NATURE REVIEWS GENETICS

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

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

TT-seq maps the human transient transcriptome

(2016) Björn Schwalb et al.   SCIENCE

Krüppel-Like Factor 5 Promotes Epithelial Proliferation and DNA Damage Repair in the Intestine of Irradiated Mice

(2015) Ming Li et al.   International Journal of Biological Sciences

Tracking Distinct RNA Populations Using Efficient and Reversible Covalent Chemistry

(2015) Erin E. Duffy et al.   MOLECULAR CELL

Multiplex single-cell profiling of chromatin accessibility by combinatorial cellular indexing

(2015) D. A. Cusanovich et al.   SCIENCE

Cell cycle progression is an essential regulatory component of phospholipid metabolism and membrane homeostasis

(2015) Miguel Sanchez-Alvarez et al.   Open Biology

Regularization Paths for Generalized Linear Models via Coordinate Descent

(2015) Jerome Friedman et al.   Journal of Statistical Software

Identification of functional glucocorticoid response elements in the mouse FoxO1 promoter

(2014) Weiping Qin et al.   BIOCHEMICAL AND BIOPHYSICAL RESEARCH COMMUNICATIONS

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

(2014) Cole Trapnell et al.   NATURE BIOTECHNOLOGY

Clustering by fast search and find of density peaks

(2014) A. Rodriguez et al.   SCIENCE

Mouse TU tagging: a chemical/genetic intersectional method for purifying cell type-specific nascent RNA

(2013) L. Gay et al.   GENES & DEVELOPMENT

STAR: ultrafast universal RNA-seq aligner

(2012) Alexander Dobin et al.   BIOINFORMATICS

VarScan 2: Somatic mutation and copy number alteration discovery in cancer by exome sequencing

(2012) D. C. Koboldt et al.   GENOME RESEARCH

The Hypersensitive Glucocorticoid Response Specifically Regulates Period 1 and Expression of Circadian Genes

(2012) T. E. Reddy et al.   MOLECULAR AND CELLULAR BIOLOGY

Dynamic transcriptome analysis measures rates of mRNA synthesis and decay in yeast

(2011) C. Miller et al.   Molecular Systems Biology

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

(2011) Michal Rabani et al.   NATURE BIOTECHNOLOGY

Chromatin accessibility pre-determines glucocorticoid receptor binding patterns

(2011) Sam John et al.   NATURE GENETICS

A User's Guide to the Encyclopedia of DNA Elements (ENCODE)

(2011)   PLOS BIOLOGY

Jun and JunD-dependent functions in cell proliferation and stress response

(2010) A Meixner et al.   CELL DEATH AND DIFFERENTIATION

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS

Genomic determination of the glucocorticoid response reveals unexpected mechanisms of gene regulation

(2009) T. E. Reddy et al.   GENOME RESEARCH

GATA3 in development and cancer differentiation: Cells GATA have it!

(2009) Jonathan Chou et al.   JOURNAL OF CELLULAR PHYSIOLOGY

TU-tagging: cell type–specific RNA isolation from intact complex tissues

(2009) Michael R Miller et al.   NATURE METHODS

The role of FKBP5, a co-chaperone of the glucocorticoid receptor in the pathogenesis and therapy of affective and anxiety disorders

(2009) Elisabeth B. Binder   PSYCHONEUROENDOCRINOLOGY

Role of Nrf1 in antioxidant response element-mediated gene expression and beyond

(2009) Madhurima Biswas et al.   TOXICOLOGY AND APPLIED PHARMACOLOGY

Identification of an Activator Protein-1-Like Sequence as the Glucocorticoid Response Element in the Rat Tyrosine Hydroxylase Gene

(2008) C. S. S. Rani et al.   MOLECULAR PHARMACOLOGY

High-resolution gene expression profiling for simultaneous kinetic parameter analysis of RNA synthesis and decay

(2008) L. Dolken et al.   RNA

Glucocorticoids: exemplars of multi-tasking

(2006) Julia C Buckingham   BRITISH JOURNAL OF PHARMACOLOGY