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

Dissecting newly transcribed and old RNA using GRAND-SLAM

(2018) Christopher Jürges et al.   BIOINFORMATICS

Two-phase differential expression analysis for single cell RNA-seq

(2018) Zhijin Wu et al.   BIOINFORMATICS

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

(2018) Andrew Butler et al.   NATURE BIOTECHNOLOGY

Analysis of DNA methylation in cancer: location revisited

(2018) Alexander Koch et al.   Nature Reviews Clinical Oncology

RNA velocity of single cells

(2018) Gioele La Manno et al.   NATURE

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

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

Thiol-linked alkylation of RNA to assess expression dynamics

(2017) Veronika A Herzog et al.   NATURE METHODS

Reconstructing cell cycle pseudo time-series via single-cell transcriptome data

(2017) Zehua Liu et al.   Nature Communications

cGAS-STING Signaling Regulates Initial Innate Control of Cytomegalovirus Infection

(2016) Chan-Wang J. Lio et al.   JOURNAL OF VIROLOGY

Revealing the vectors of cellular identity with single-cell genomics

(2016) Allon Wagner et al.   NATURE BIOTECHNOLOGY

Characterizing transcriptional heterogeneity through pathway and gene set overdispersion analysis

(2016) Jean Fan et al.   NATURE METHODS

A single-molecule view of transcription reveals convoys of RNA polymerases and multi-scale bursting

(2016) Katjana Tantale et al.   Nature Communications

Structure of silent transcription intervals and noise characteristics of mammalian genes

(2015) B. Zoller et al.   Molecular Systems Biology

Transient acquisition of pluripotency during somatic cell transdifferentiation with iPSC reprogramming factors

(2015) Itay Maza et al.   NATURE BIOTECHNOLOGY

Random monoallelic expression of autosomal genes: stochastic transcription and allele-level regulation

(2015) Björn Reinius et al.   NATURE REVIEWS GENETICS

Murine Cytomegalovirus Virion-Associated Protein M45 Mediates Rapid NF- B Activation after Infection

(2014) E. Krause et al.   JOURNAL OF VIROLOGY

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

(2013) Alex K. Shalek et al.   NATURE

Accounting for technical noise in single-cell RNA-seq experiments

(2013) Philip Brennecke et al.   NATURE METHODS

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

(2013) Simone Picelli et al.   NATURE METHODS

Multi-layered stochasticity and paracrine signal propagation shape the type-I interferon response

(2012) Ulfert Rand et al.   Molecular Systems Biology

SwissRegulon, a database of genome-wide annotations of regulatory sites: recent updates

(2012) Mikhail Pachkov et al.   NUCLEIC ACIDS RESEARCH

Real-time Transcriptional Profiling of Cellular and Viral Gene Expression during Lytic Cytomegalovirus Infection

(2012) Lisa Marcinowski et al.   PLoS Pathogens

Global quantification of mammalian gene expression control

(2011) Björn Schwanhäusser et al.   NATURE

Nucleosomal Fluctuations Govern the Transcription Dynamics of RNA Polymerase II

(2009) C. Hodges et al.   SCIENCE

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

(2008) L. Dolken et al.   RNA