Single-molecule dynamics and genome-wide transcriptomics reveal that NF-kB (p65)-DNA binding times can be decoupled from transcriptional activation

DNA residence time is a regulatory factor of transcription repression

(2017) Karen Clauß et al.   NUCLEIC ACIDS RESEARCH

Live-cell p53 single-molecule binding is modulated by C-terminal acetylation and correlates with transcriptional activity

(2017) Alessia Loffreda et al.   Nature Communications

A Stringent Systems Approach Uncovers Gene-Specific Mechanisms Regulating Inflammation

(2016) Ann-Jay Tong et al.   CELL

A general method to improve fluorophores for live-cell and single-molecule microscopy

(2015) Jonathan B Grimm et al.   NATURE METHODS

limma powers differential expression analyses for RNA-sequencing and microarray studies

(2015) Matthew E. Ritchie et al.   NUCLEIC ACIDS RESEARCH

Genome-wide predictors of NF-κB recruitment and transcriptional activity

(2015) Marcin Cieślik et al.   BioData Mining

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

(2014) S. Anders et al.   BIOINFORMATICS

Single-Molecule Dynamics of Enhanceosome Assembly in Embryonic Stem Cells

(2014) Jiji Chen et al.   CELL

Single-molecule analysis of transcription factor binding at transcription sites in live cells

(2014) Tatsuya Morisaki et al.   Nature Communications

voom: precision weights unlock linear model analysis tools for RNA-seq read counts

(2014) Charity W Law et al.   GENOME BIOLOGY

Regulation of the NF-κB-Mediated Transcription of Inflammatory Genes

(2014) Dev Bhatt et al.   Frontiers in Immunology

STAR: ultrafast universal RNA-seq aligner

(2012) Alexander Dobin et al.   BIOINFORMATICS

Gene expression induced by Toll-like receptors in macrophages requires the transcription factor NFAT5

(2012) Maria Buxadé et al.   JOURNAL OF EXPERIMENTAL MEDICINE

Genome-wide protein–DNA binding dynamics suggest a molecular clutch for transcription factor function

(2012) Colin R. Lickwar et al.   NATURE

A benchmark for chromatin binding measurements in live cells

(2012) Davide Mazza et al.   NUCLEIC ACIDS RESEARCH

Activated STAT1 Transcription Factors Conduct Distinct Saltatory Movements in the Cell Nucleus

(2011) Jasmin Speil et al.   BIOPHYSICAL JOURNAL

RSEM: accurate transcript quantification from RNA-Seq data with or without a reference genome

(2011) Bo Li et al.   BMC BIOINFORMATICS

Genomic Analysis Reveals a Novel Nuclear Factor-κB (NF-κB)-binding Site in Alu-repetitive Elements

(2011) Athina Antonaki et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Single-cell NF-κB dynamics reveal digital activation and analogue information processing

(2010) Savaş Tay et al.   NATURE

edgeR: a Bioconductor package for differential expression analysis of digital gene expression data

(2009) M. D. Robinson et al.   BIOINFORMATICS

Two Modes of Transcriptional Activation at Native Promoters by NF-κB p65

(2009) Dominic van Essen et al.   PLOS BIOLOGY

HaloTag: A Novel Protein Labeling Technology for Cell Imaging and Protein Analysis

(2008) Georgyi V. Los et al.   ACS Chemical Biology

The enhanceosome

(2008) Daniel Panne   CURRENT OPINION IN STRUCTURAL BIOLOGY

Highly inclined thin illumination enables clear single-molecule imaging in cells

(2008) Makio Tokunaga et al.   NATURE METHODS

Rational vector design and multi-pathway modulation of HEK 293E cells yield recombinant antibody titers exceeding 1 g/l by transient transfection under serum-free conditions

(2008) Gaurav Backliwal et al.   NUCLEIC ACIDS RESEARCH