Bacterial transcriptomics: what is beyond the RNA horiz-ome?

Transcript amplification from single bacterium for transcriptome analysis

(2011) Y. Kang et al.   GENOME RESEARCH

Nascent transcript sequencing visualizes transcription at nucleotide resolution

(2011) L. Stirling Churchman et al.   NATURE

Termination and antitermination: RNA polymerase runs a stop sign

(2011) Thomas J. Santangelo et al.   NATURE REVIEWS MICROBIOLOGY

Subcellular localization of RNA degrading proteins and protein complexes in prokaryotes

(2011) Elena Evguenieva-Hackenberg et al.   RNA Biology

Translation-Independent Localization of mRNA in E. coli

(2011) K. Nevo-Dinur et al.   SCIENCE

A genome-wide survey of sRNAs in the symbiotic nitrogen-fixing alpha-proteobacterium Sinorhizobium meliloti

(2010) Jan-Philip Schlüter et al.   BMC GENOMICS

Structural and operational complexity of the Geobacter sulfurreducens genome

(2010) Y. Qiu et al.   GENOME RESEARCH

Chromosome conformation capture of transcriptional interactions between cytochrome c oxidase genes and genes of glutamatergic synaptic transmission in neurons

(2010) Shilpa S. Dhar et al.   JOURNAL OF NEUROCHEMISTRY

A minimal base-pairing region of a bacterial small RNA SgrS required for translational repression of ptsG mRNA

(2010) Kimika Maki et al.   MOLECULAR MICROBIOLOGY

The SAM-responsive SMK box is a reversible riboswitch

(2010) Angela M. Smith et al.   MOLECULAR MICROBIOLOGY

Recognition of heptameric seed sequence underlies multi-target regulation by RybB small RNA in Salmonella enterica

(2010) Roberto Balbontín et al.   MOLECULAR MICROBIOLOGY

A three-dimensional model of the yeast genome

(2010) Zhijun Duan et al.   NATURE

The primary transcriptome of the major human pathogen Helicobacter pylori

(2010) Cynthia M. Sharma et al.   NATURE

Genome-wide measurement of RNA secondary structure in yeast

(2010) Michael Kertesz et al.   NATURE

Spatial organization of the flow of genetic information in bacteria

(2010) Paula Montero Llopis et al.   NATURE

FragSeq: transcriptome-wide RNA structure probing using high-throughput sequencing

(2010) Jason G Underwood et al.   NATURE METHODS

Direct detection of DNA methylation during single-molecule, real-time sequencing

(2010) Benjamin A Flusberg et al.   NATURE METHODS

Bacterial nucleoid-associated proteins, nucleoid structure and gene expression

(2010) Shane C. Dillon et al.   NATURE REVIEWS MICROBIOLOGY

Microbiome Profiling by Illumina Sequencing of Combinatorial Sequence-Tagged PCR Products

(2010) Gregory B. Gloor et al.   PLoS One

Evidence for an autonomous 5' target recognition domain in an Hfq-associated small RNA

(2010) K. Papenfort et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Quantifying E. coli Proteome and Transcriptome with Single-Molecule Sensitivity in Single Cells

(2010) Y. Taniguchi et al.   SCIENCE

Cooperation Between Translating Ribosomes and RNA Polymerase in Transcription Elongation

(2010) S. Proshkin et al.   SCIENCE

Widespread Antisense Transcription in Escherichia coli

(2010) J. E. Dornenburg et al.   mBio

Bacterial/archaeal/organellar polyadenylation

(2010) Bijoy K. Mohanty et al.   Wiley Interdisciplinary Reviews-RNA

SOAP2: an improved ultrafast tool for short read alignment

(2009) R. Li et al.   BIOINFORMATICS

Fast and accurate short read alignment with Burrows-Wheeler transform

(2009) H. Li et al.   BIOINFORMATICS

Regulatory RNAs in Bacteria

(2009) Lauren S. Waters et al.   CELL

Beyond ribosome rescue: tmRNA and co-translational processes

(2009) Christopher S. Hayes et al.   FEBS LETTERS

A single-base resolution map of an archaeal transcriptome

(2009) O. Wurtzel et al.   GENOME RESEARCH

Structure and Complexity of a Bacterial Transcriptome

(2009) K. D. Passalacqua et al.   JOURNAL OF BACTERIOLOGY

Protein Occupancy Landscape of a Bacterial Genome

(2009) Tiffany Vora et al.   MOLECULAR CELL

The transcriptionally active regions in the genome ofBacillus subtilis

(2009) Simon Rasmussen et al.   MOLECULAR MICROBIOLOGY

Rapid cleavage of RNA by RNase E in the absence of 5′ monophosphate stimulation

(2009) Louise Kime et al.   MOLECULAR MICROBIOLOGY

Bidirectional promoters generate pervasive transcription in yeast

(2009) Zhenyu Xu et al.   NATURE

The Listeria transcriptional landscape from saprophytism to virulence

(2009) Alejandro Toledo-Arana et al.   NATURE

Preferential associations between co-regulated genes reveal a transcriptional interactome in erythroid cells

(2009) Stefan Schoenfelder et al.   NATURE GENETICS

mRNA-Seq whole-transcriptome analysis of a single cell

(2009) Fuchou Tang et al.   NATURE METHODS

Sense from sequence reads: methods for alignment and assembly

(2009) Paul Flicek et al.   NATURE METHODS

Single molecule–sensitive probes for imaging RNA in live cells

(2009) Philip J Santangelo et al.   NATURE METHODS

Continuous base identification for single-molecule nanopore DNA sequencing

(2009) James Clarke et al.   Nature Nanotechnology

Prokaryotic transcriptomics: a new view on regulation, physiology and pathogenicity

(2009) Rotem Sorek et al.   NATURE REVIEWS GENETICS

Mapping the Burkholderia cenocepacia niche response via high-throughput sequencing

(2009) D. R. Yoder-Himes et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Mesoporous silica chips for selective enrichment and stabilization of low molecular weight proteome

(2009) Ali Bouamrani et al.   PROTEOMICS

Proteome Organization in a Genome-Reduced Bacterium

(2009) S. Kuhner et al.   SCIENCE

Transcriptome Complexity in a Genome-Reduced Bacterium

(2009) M. Guell et al.   SCIENCE

Epigenetic Control of Virulence Gene Expression in Pseudomonas aeruginosa by a LysR-Type Transcription Regulator

(2009) Keith H. Turner et al.   PLoS Genetics

A Strand-Specific RNA–Seq Analysis of the Transcriptome of the Typhoid Bacillus Salmonella Typhi

(2009) Timothy T. Perkins et al.   PLoS Genetics

Ultrafast and memory-efficient alignment of short DNA sequences to the human genome

(2009) Ben Langmead et al.   GENOME BIOLOGY

Quorum Sensing in Staphylococci

(2008) Richard P. Novick et al.   Annual Review of Genetics

Quality control of bacterial mRNA decoding and decay

(2008) J RICHARDS et al.   Biochimica et Biophysica Acta-Gene Regulatory Mechanisms

SOAP: short oligonucleotide alignment program

(2008) R. Li et al.   BIOINFORMATICS

Helicobacter pylori single-stranded DNA binding protein - functional characterization and modulation of H. pylori DnaB helicase activity

(2008) Atul Sharma et al.   FEBS Journal

Genome-wide detection and analysis of hippocampus core promoters using DeepCAGE

(2008) E. Valen et al.   GENOME RESEARCH

Mapping short DNA sequencing reads and calling variants using mapping quality scores

(2008) H. Li et al.   GENOME RESEARCH

Establishment of an mRNA Gradient Depends on the Promoter: An Investigation of Polarity in Gene Expression

(2008) Hee Jung Lee et al.   JOURNAL OF MOLECULAR BIOLOGY

The bacterial enzyme RppH triggers messenger RNA degradation by 5′ pyrophosphate removal

(2008) Atilio Deana et al.   NATURE

Evolvability and hierarchy in rewired bacterial gene networks

(2008) Mark Isalan et al.   NATURE

Dynamic repertoire of a eukaryotic transcriptome surveyed at single-nucleotide resolution

(2008) Brian T. Wilhelm et al.   NATURE

RNA-Seq: a revolutionary tool for transcriptomics

(2008) Zhong Wang et al.   NATURE REVIEWS GENETICS

Advances in bacterial promoter recognition and its control by factors that do not bind DNA

(2008) Shanil P. Haugen et al.   NATURE REVIEWS MICROBIOLOGY

S-box and T-box riboswitches and antisense RNA control a sulfur metabolic operon of Clostridium acetobutylicum

(2008) Gaëlle André et al.   NUCLEIC ACIDS RESEARCH

Microbial community gene expression in ocean surface waters

(2008) J. Frias-Lopez et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Ribosomes bind leaderless mRNA in Escherichia coli through recognition of their 5'-terminal AUG

(2008) J. E. Brock et al.   RNA

Real-Time DNA Sequencing from Single Polymerase Molecules

(2008) J. Eid et al.   SCIENCE

Deep Sequencing Analysis of Small Noncoding RNA and mRNA Targets of the Global Post-Transcriptional Regulator, Hfq

(2008) Alexandra Sittka et al.   PLoS Genetics