Isolation of the protein and RNA content of active sites of transcription from mammalian cells

Native Elongating Transcript Sequencing Reveals Human Transcriptional Activity at Nucleotide Resolution

(2015) Andreas Mayer et al.   CELL

Mammalian NET-Seq Reveals Genome-wide Nascent Transcription Coupled to RNA Processing

(2015) Takayuki Nojima et al.   CELL

Analysis of intronic and exonic reads in RNA-seq data characterizes transcriptional and post-transcriptional regulation

(2015) Dimos Gaidatzis et al.   NATURE BIOTECHNOLOGY

iRNA-seq: computational method for genome-wide assessment of acute transcriptional regulation from total RNA-seq data

(2015) Jesper Grud Skat Madsen et al.   NUCLEIC ACIDS RESEARCH

Dissecting the nascent human transcriptome by analysing the RNA content of transcription factories

(2015) Maïwen Caudron-Herger et al.   NUCLEIC ACIDS RESEARCH

Transcription Factories: Genome Organization and Gene Regulation

(2013) Argyris Papantonis et al.   CHEMICAL REVIEWS

Novel proteomic approach (PUNCH-P) reveals cell cycle-specific fluctuations in mRNA translation

(2013) R. Aviner et al.   GENES & DEVELOPMENT

Remodeling of the Enhancer Landscape during Macrophage Activation Is Coupled to Enhancer Transcription

(2013) Minna U. Kaikkonen et al.   MOLECULAR CELL

Revisiting Global Gene Expression Analysis

(2012) Jakob Lovén et al.   CELL

Transcript Dynamics of Proinflammatory Genes Revealed by Sequence Analysis of Subcellular RNA Fractions

(2012) Dev M. Bhatt et al.   CELL

Ultrashort and progressive 4sU-tagging reveals key characteristics of RNA processing at nucleotide resolution

(2012) L. Windhager et al.   GENOME RESEARCH

Fast gapped-read alignment with Bowtie 2

(2012) Ben Langmead et al.   NATURE METHODS

Nascent-seq indicates widespread cotranscriptional pre-mRNA splicing in Drosophila

(2011) Y. L. Khodor et al.   GENES & DEVELOPMENT

iProphet: Multi-level Integrative Analysis of Shotgun Proteomic Data Improves Peptide and Protein Identification Rates and Error Estimates

(2011) David Shteynberg et al.   MOLECULAR & CELLULAR PROTEOMICS

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

(2011) Michal Rabani et al.   NATURE BIOTECHNOLOGY

The proteomes of transcription factories containing RNA polymerases I, II or III

(2011) Svitlana Melnik et al.   NATURE METHODS

Total RNA sequencing reveals nascent transcription and widespread co-transcriptional splicing in the human brain

(2011) Adam Ameur et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Proteomic-Based Identification of CD4-Interacting Proteins in Human Primary Macrophages

(2011) Rui André Saraiva Raposo et al.   PLoS One

CPFP: a central proteomics facilities pipeline

(2010) D. C. Trudgian et al.   BIOINFORMATICS

Widespread transcription at neuronal activity-regulated enhancers

(2010) Tae-Kyung Kim et al.   NATURE

Organization of Transcription

(2010) L. Chakalova et al.   Cold Spring Harbor Perspectives in Biology

Molecular Architecture of the Human Pre-mRNA 3′ Processing Complex

(2009) Yongsheng Shi et al.   MOLECULAR CELL

A practical guide to the MaxQuant computational platform for SILAC-based quantitative proteomics

(2009) Jürgen Cox et al.   Nature Protocols

Transcription factories: gene expression in unions?

(2009) Heidi Sutherland et al.   NATURE REVIEWS GENETICS

Structure of Eukaryotic RNA Polymerases

(2008) P. Cramer et al.   Annual Review of Biophysics

NOPdb: Nucleolar Proteome Database--2008 update

(2008) Y. Ahmad et al.   NUCLEIC ACIDS RESEARCH

Nascent RNA Sequencing Reveals Widespread Pausing and Divergent Initiation at Human Promoters

(2008) Leighton J. Core et al.   SCIENCE