A novel enrichment strategy reveals unprecedented number of novel transcription start sites at single base resolution in a model prokaryote and the gut microbiome

Leaderless Transcripts and Small Proteins Are Common Features of the Mycobacterial Translational Landscape

(2015) Scarlet S. Shell et al.   PLoS Genetics

Primary transcriptome map of the hyperthermophilic archaeon Thermococcus kodakarensis

(2014) Dominik Jäger et al.   BMC GENOMICS

Differential RNA-seq: the approach behind and the biological insight gained

(2014) Cynthia M Sharma et al.   CURRENT OPINION IN MICROBIOLOGY

RNA Sequencing and Proteogenomics Reveal the Importance of Leaderless mRNAs in the Radiation-Tolerant Bacterium Deinococcus deserti

(2014) Arjan de Groot et al.   Genome Biology and Evolution

Global Transcriptional Start Site Mapping Using Differential RNA Sequencing Reveals Novel Antisense RNAs in Escherichia coli

(2014) Maureen K. Thomason et al.   JOURNAL OF BACTERIOLOGY

A comparison of key aspects of gene regulation inStreptomyces coelicolorandEscherichia coliusing nucleotide-resolution transcription maps produced in parallel by global and differential RNA sequencing

(2014) David A. Romero et al.   MOLECULAR MICROBIOLOGY

Integrative Genomics Viewer (IGV): high-performance genomics data visualization and exploration

(2012) H. Thorvaldsdottir et al.   BRIEFINGS IN BIOINFORMATICS

CapSeq and CIP-TAP Identify Pol II Start Sites and Reveal Capped Small RNAs as C. elegans piRNA Precursors

(2012) Weifeng Gu et al.   CELL

Fast gapped-read alignment with Bowtie 2

(2012) Ben Langmead et al.   NATURE METHODS

RegulonDB v8.0: omics data sets, evolutionary conservation, regulatory phrases, cross-validated gold standards and more

(2012) Heladia Salgado et al.   NUCLEIC ACIDS RESEARCH

An Improved Protection-Free One-Pot Chemical Synthesis of 2′-Deoxynucleoside-5′-Triphosphates

(2012) Anilkumar R. Kore et al.   NUCLEOSIDES NUCLEOTIDES & NUCLEIC ACIDS

The Primary Transcriptome of Barley Chloroplasts: Numerous Noncoding RNAs and the Dominating Role of the Plastid-Encoded RNA Polymerase

(2012) P. Zhelyazkova et al.   PLANT CELL

Efficient and robust RNA-seq process for cultured bacteria and complex community transcriptomes

(2012) Georgia Giannoukos et al.   GENOME BIOLOGY

Leaderless genes in bacteria: clue to the evolution of translation initiation mechanisms in prokaryotes

(2011) Xiaobin Zheng et al.   BMC GENOMICS

Integrative genomics viewer

(2011) James T Robinson et al.   NATURE BIOTECHNOLOGY

The UCSC Archaeal Genome Browser: 2012 update

(2011) P. P. Chan et al.   NUCLEIC ACIDS RESEARCH

The primary transcriptome of the major human pathogen Helicobacter pylori

(2010) Cynthia M. Sharma et al.   NATURE

Nucleosome rotational setting is associated with transcriptional regulation in promoters of tissue-specific human genes

(2010) Charles Hebert et al.   GENOME BIOLOGY

Analysis and Optimization of Copper-Catalyzed Azide–Alkyne Cycloaddition for Bioconjugation

(2009) Vu Hong et al.   ANGEWANDTE CHEMIE-INTERNATIONAL EDITION

MEME SUITE: tools for motif discovery and searching

(2009) T. L. Bailey et al.   NUCLEIC ACIDS RESEARCH