Ubiquitous mRNA decay fragments in E. coli redefine the functional transcriptome

Ribosome Rescue Pathways in Bacteria

(2021) Claudia Müller et al.   Frontiers in Microbiology

Nanopore sequencing of RNA and cDNA molecules in Escherichia coli

(2021) Felix Grünberger et al.   RNA

The Dynamics of Cytoplasmic mRNA Metabolism

(2020) Timothy J. Eisen et al.   MOLECULAR CELL

Regulation of RNA processing and degradation in bacteria

(2020) Aude Trinquier et al.   Biochimica et Biophysica Acta-Gene Regulatory Mechanisms

Growth-Optimized Aminoacyl-tRNA Synthetase Levels Prevent Maximal tRNA Charging

(2020) Darren J. Parker et al.   Cell Systems

Functionally uncoupled transcription–translation in Bacillus subtilis

(2020) Grace E. Johnson et al.   NATURE

Ribosome recycling is not critical for translational coupling in Escherichia coli

(2020) Kazuki Saito et al.   eLife

Regulation of mRNA Stability During Bacterial Stress Responses

(2020) Diego A. Vargas-Blanco et al.   Frontiers in Microbiology

A systematically-revised ribosome profiling method for bacteria reveals pauses at single-codon resolution

(2019) Fuad Mohammad et al.   eLife

Full-length RNA profiling reveals pervasive bidirectional transcription terminators in bacteria

(2019) Xiangwu Ju et al.   Nature Microbiology

Evolutionary Convergence of Pathway-Specific Enzyme Expression Stoichiometry

(2018) Jean-Benoît Lalanne et al.   CELL

Long-read sequencing of nascent RNA reveals coupling among RNA processing events

(2018) Lydia Herzel et al.   GENOME RESEARCH

Extensive reshaping of bacterial operons by programmed mRNA decay

(2018) Daniel Dar et al.   PLoS Genetics

SMRT-Cappable-seq reveals complex operon variants in bacteria

(2018) Bo Yan et al.   Nature Communications

Widespread Accumulation of Ribosome-Associated Isolated 3′ UTRs in Neuronal Cell Populations of the Aging Brain

(2018) Peter H. Sudmant et al.   Cell Reports

In Vivo Cleavage Map Illuminates the Central Role of RNase E in Coding and Non-coding RNA Pathways

(2017) Yanjie Chao et al.   MOLECULAR CELL

Examining tRNA 3′-ends in Escherichia coli : teamwork between CCA-adding enzyme, RNase T, and RNase R

(2017) Karolin Wellner et al.   RNA

Regulation of mRNA Decay in Bacteria

(2016) Bijoy K. Mohanty et al.   Annual Review of Microbiology

Splicing of Nascent RNA Coincides with Intron Exit from RNA Polymerase II

(2016) Fernando Carrillo Oesterreich et al.   CELL

Small RNA interactome of pathogenic E. coli revealed through crosslinking of RNase E

(2016) Shafagh A Waters et al.   EMBO JOURNAL

A ribosome profiling study of mRNA cleavage by the endonuclease RelE

(2016) Jae-Yeon Hwang et al.   NUCLEIC ACIDS RESEARCH

Term-seq reveals abundant ribo-regulation of antibiotics resistance in bacteria

(2016) D. Dar et al.   SCIENCE

Improved Ribosome-Footprint and mRNA Measurements Provide Insights into Dynamics and Regulation of Yeast Translation

(2016) David E. Weinberg et al.   Cell Reports

Spatial organization shapes the turnover of a bacterial transcriptome

(2016) Jeffrey R Moffitt et al.   eLife

NusA-dependent transcription termination prevents misregulation of global gene expression

(2016) Smarajit Mondal et al.   Nature Microbiology

Next generation sequencing analysis reveals that the ribonucleases RNase II, RNase R and PNPase affect bacterial motility and biofilm formation in E. coli

(2015) Vânia Pobre et al.   BMC GENOMICS

Widespread Co-translational RNA Decay Reveals Ribosome Dynamics

(2015) Vicent Pelechano et al.   CELL

Mechanisms of ribosome rescue in bacteria

(2015) Kenneth C. Keiler   NATURE REVIEWS MICROBIOLOGY

Direct observation of processive exoribonuclease motion using optical tweezers

(2015) Furqan M. Fazal et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Polyadenylation inE. coli: a 20 year odyssey

(2015) Sidney R. Kushner   RNA

Messenger RNA Degradation in Bacterial Cells

(2014) Monica P. Hui et al.   Annual Review of Genetics

Direct entry by RNase E is a major pathway for the degradation and processing of RNA in Escherichia coli

(2014) Justin E. Clarke et al.   NUCLEIC ACIDS RESEARCH

A pause sequence enriched at translation start sites drives transcription dynamics in vivo

(2014) M. H. Larson et al.   SCIENCE

Interactions between RNA polymerase and the "core recognition element" counteract pausing

(2014) I. O. Vvedenskaya et al.   SCIENCE

Initiation of mRNA decay in bacteria

(2013) Soumaya Laalami et al.   CELLULAR AND MOLECULAR LIFE SCIENCES

Comparative analysis of RNA sequencing methods for degraded or low-input samples

(2013) Xian Adiconis et al.   NATURE METHODS

Circadian control of mRNA polyadenylation dynamics regulates rhythmic protein expression

(2012) S. Kojima et al.   GENES & DEVELOPMENT

Fiji: an open-source platform for biological-image analysis

(2012) Johannes Schindelin et al.   NATURE METHODS

RNA snap ™: a rapid, quantitative and inexpensive, method for isolating total RNA from bacteria

(2012) Mark B. Stead et al.   NUCLEIC ACIDS RESEARCH

Escherichia coli YaeJ protein mediates a novel ribosome-rescue pathway distinct from SsrA- and ArfA-mediated pathways

(2011) Yuhei Chadani et al.   MOLECULAR MICROBIOLOGY

Nascent transcript sequencing visualizes transcription at nucleotide resolution

(2011) L. Stirling Churchman et al.   NATURE

Integrative genomics viewer

(2011) James T Robinson et al.   NATURE BIOTECHNOLOGY

BEDTools: a flexible suite of utilities for comparing genomic features

(2010) Aaron R. Quinlan et al.   BIOINFORMATICS

MochiView: versatile software for genome browsing and DNA motif analysis

(2010) Oliver R Homann et al.   BMC BIOLOGY

Ribosome rescue by Escherichia coli ArfA (YhdL) in the absence of trans-translation system

(2010) Yuhei Chadani et al.   MOLECULAR MICROBIOLOGY

Nucleases: diversity of structure, function and mechanism

(2010) Wei Yang   QUARTERLY REVIEWS OF BIOPHYSICS

Cooperation Between Translating Ribosomes and RNA Polymerase in Transcription Elongation

(2010) S. Proshkin et al.   SCIENCE

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS

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

(2009) Ben Langmead et al.   GENOME BIOLOGY