Grad-seq shines light on unrecognized RNA and protein complexes in the model bacterium Escherichia coli

Overexpressed L20 Rescues 50S Ribosomal Subunit Assembly Defects of bipA-Deletion in Escherichia coli

(2020) Eunsil Choi et al.   Frontiers in Microbiology

Grad‐seq in a Gram‐positive bacterium reveals exonucleolytic sRNA activation in competence control

(2020) Jens Hör et al.   EMBO JOURNAL

Lag phase – a dynamic, organized, adaptive, and evolvable period that prepares bacteria for cell division

(2019) Robert L. Bertrand   JOURNAL OF BACTERIOLOGY

The Major RNA-Binding Protein ProQ Impacts Virulence Gene Expression in Salmonella enterica Serovar Typhimurium

(2019) Alexander J. Westermann et al.   mBio

Identifying Small Proteins by Ribosome Profiling with Stalled Initiation Complexes

(2019) Jeremy Weaver et al.   mBio

Does Functional Specialization of Ribosomes Really Exist?

(2019) Max B Ferretti et al.   RNA

Profiling the E. coli membrane interactome captured in peptidisc libraries

(2019) Michael Luke Carlson et al.   eLife

RNA-RNA Interactomes of ProQ and Hfq Reveal Overlapping and Competing Roles

(2019) Sahar Melamed et al.   MOLECULAR CELL

Evolutionary classification of CRISPR–Cas systems: a burst of class 2 and derived variants

(2019) Kira S. Makarova et al.   NATURE REVIEWS MICROBIOLOGY

New aspects of RNA-based regulation by Hfq and its partner sRNAs

(2018) Kumari Kavita et al.   CURRENT OPINION IN MICROBIOLOGY

Toxins, Targets, and Triggers: An Overview of Toxin-Antitoxin Biology

(2018) Alexander Harms et al.   MOLECULAR CELL

Global Maps of ProQ Binding In Vivo Reveal Target Recognition via RNA Structure and Stability Control at mRNA 3′ Ends

(2018) Erik Holmqvist et al.   MOLECULAR CELL

RNA-binding proteins in bacteria

(2018) Erik Holmqvist et al.   NATURE REVIEWS MICROBIOLOGY

ANNOgesic: a Swiss army knife for the RNA-seq based annotation of bacterial/archaeal genomes

(2018) Sung-Huan Yu et al.   GigaScience

UniProt: a worldwide hub of protein knowledge

(2018)   NUCLEIC ACIDS RESEARCH

The PRIDE database and related tools and resources in 2019: improving support for quantification data

(2018) Yasset Perez-Riverol et al.   NUCLEIC ACIDS RESEARCH

The Gene Ontology Resource: 20 years and still GOing strong

(2018)   NUCLEIC ACIDS RESEARCH

The Pfam protein families database in 2019

(2018) Sara El-Gebali et al.   NUCLEIC ACIDS RESEARCH

The small RNA, SdsR, acts as a novel type of toxin in Escherichia coli

(2018) Jee Soo Choi et al.   RNA Biology

Hfq links translation repression to stress-induced mutagenesis in E. coli

(2017) Jiandong Chen et al.   GENES & DEVELOPMENT

Alternative pathways for Escherichia coli biofilm formation revealed by sRNA overproduction

(2017) Ashley Parker et al.   MOLECULAR MICROBIOLOGY

Global landscape of cell envelope protein complexes in Escherichia coli

(2017) Mohan Babu et al.   NATURE BIOTECHNOLOGY

Structure and dynamics of bacterial ribosome biogenesis

(2017) Joseph H. Davis et al.   PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

Increasing intracellular magnesium levels with the 31-amino acid MgtS protein

(2017) Hanbo Wang et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Global role of the bacterial post-transcriptional regulator CsrA revealed by integrated transcriptomics

(2017) Anastasia H. Potts et al.   Nature Communications

Staphylococcus aureusRNAIII and Its Regulon Link Quorum Sensing, Stress Responses, Metabolic Adaptation, and Regulation of Virulence Gene Expression

(2016) Delphine Bronesky et al.   Annual Review of Microbiology

Hfq: the flexible RNA matchmaker

(2016) Taylor B Updegrove et al.   CURRENT OPINION IN MICROBIOLOGY

Global RNA recognition patterns of post‐transcriptional regulators Hfq and CsrA revealed by UV crosslinkingin vivo

(2016) Erik Holmqvist et al.   EMBO JOURNAL

Dual RNA-seq unveils noncoding RNA functions in host–pathogen interactions

(2016) Alexander J. Westermann et al.   NATURE

The EcoCyc database: reflecting new knowledge aboutEscherichia coliK-12

(2016) Ingrid M. Keseler et al.   NUCLEIC ACIDS RESEARCH

Grad-seq guides the discovery of ProQ as a major small RNA-binding protein

(2016) Alexandre Smirnov et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

The Escherichia coli Cryptic Prophage Protein YfdR Binds to DnaA and Initiation of Chromosomal Replication Is Inhibited by Overexpression of the Gene Cluster yfdQ-yfdR-yfdS-yfdT

(2016) Yasunori Noguchi et al.   Frontiers in Microbiology

Structure of Bacterial Regulatory RNAs Determines Their Performance in Competition for the Chaperone Protein Hfq

(2015) Ewelina M. Małecka et al.   BIOCHEMISTRY

Efficient Assembly of Ribosomes Is Inhibited by Deletion ofbipAin Escherichia coli

(2015) Promisree Choudhury et al.   JOURNAL OF BACTERIOLOGY

Functional analysis of CedA based on its structure: residues important in binding of DNA and RNA polymerase and in the cell division regulation

(2015) Yoshito Abe et al.   JOURNAL OF BIOCHEMISTRY

The quantitative and condition-dependent Escherichia coli proteome

(2015) Alexander Schmidt et al.   NATURE BIOTECHNOLOGY

Mechanisms of ribosome rescue in bacteria

(2015) Kenneth C. Keiler   NATURE REVIEWS MICROBIOLOGY

eggNOG 4.5: a hierarchical orthology framework with improved functional annotations for eukaryotic, prokaryotic and viral sequences

(2015) Jaime Huerta-Cepas et al.   NUCLEIC ACIDS RESEARCH

Identification of novel sRNAs involved in biofilm formation, motility and fimbriae formation in Escherichia coli

(2015) Geunu Bak et al.   Scientific Reports

READemption--a tool for the computational analysis of deep-sequencing-based transcriptome data

(2014) K. U. Forstner et al.   BIOINFORMATICS

High resolution clear native electrophoresis is a good alternative to blue native electrophoresis for the characterization of the Escherichia coli membrane complexes

(2014) Ernesto Diéguez-Casal et al.   JOURNAL OF MICROBIOLOGICAL METHODS

Accurate Proteome-wide Label-free Quantification by Delayed Normalization and Maximal Peptide Ratio Extraction, Termed MaxLFQ

(2014) Jürgen Cox et al.   MOLECULAR & CELLULAR PROTEOMICS

Identification of Bacteriophage-Encoded Anti-sRNAs in Pathogenic Escherichia coli

(2014) Jai J. Tree et al.   MOLECULAR CELL

Optimization of lag time underlies antibiotic tolerance in evolved bacterial populations

(2014) Ofer Fridman et al.   NATURE

The binary protein-protein interaction landscape of Escherichia coli

(2014) Seesandra V Rajagopala et al.   NATURE BIOTECHNOLOGY

A multi-split mapping algorithm for circular RNA, splicing, trans-splicing and fusion detection

(2014) Steve Hoffmann et al.   GENOME BIOLOGY

Signal Recognition Particle: An Essential Protein-Targeting Machine

(2013) David Akopian et al.   Annual Review of Biochemistry

Structural Studies of RNase P

(2013) Alfonso Mondragón   Annual Review of Biophysics

An Infection-Relevant Transcriptomic Compendium for Salmonella enterica Serovar Typhimurium

(2013) Carsten Kröger et al.   Cell Host & Microbe

A small RNA activates CFA synthase by isoform-specific mRNA stabilization

(2013) Kathrin Sophie Fröhlich et al.   EMBO JOURNAL

Analysis and Expansion of the Role of the Escherichia coli Protein ProQ

(2013) Daniel T. Sheidy et al.   PLoS One

DEAD-Box RNA Helicases in Bacillus subtilis Have Multiple Functions and Act Independently from Each Other

(2012) M. Lehnik-Habrink et al.   JOURNAL OF BACTERIOLOGY

Characterization of the Ribosome Biogenesis Landscape in E. coli Using Quantitative Mass Spectrometry

(2012) Stephen S. Chen et al.   JOURNAL OF MOLECULAR BIOLOGY

RsfA (YbeB) Proteins Are Conserved Ribosomal Silencing Factors

(2012) Roman Häuser et al.   PLoS Genetics

ViennaRNA Package 2.0

(2011) Ronny Lorenz et al.   Algorithms for Molecular Biology

Characterization of Zn(II)-responsive ribosomal proteins YkgM and L31 in E. coli

(2011) M. Patrick Hensley et al.   JOURNAL OF INORGANIC BIOCHEMISTRY

Complexome of Escherichia coli cytosolic proteins under normal native conditions

(2011) Jian-Yi Pan et al.   Molecular BioSystems

Integrating anaerobic/aerobic sensing and the general stress response through the ArcZ small RNA

(2010) Pierre Mandin et al.   EMBO JOURNAL

Complexome ofEscherichia coliEnvelope Proteins under Normal Physiological Conditions

(2010) Jian-Yi Pan et al.   JOURNAL OF PROTEOME RESEARCH

Cryptic prophages help bacteria cope with adverse environments

(2010) Xiaoxue Wang et al.   Nature Communications

Differential expression analysis for sequence count data

(2010) Simon Anders et al.   GENOME BIOLOGY

VARNA: Interactive drawing and editing of the RNA secondary structure

(2009) Kévin Darty et al.   BIOINFORMATICS

Size and Shape of Protein Molecules at the Nanometer Level Determined by Sedimentation, Gel Filtration, and Electron Microscopy

(2009) Harold P. Erickson   BIOLOGICAL PROCEDURES ONLINE

Global Functional Atlas of Escherichia coli Encompassing Previously Uncharacterized Proteins

(2009) Pingzhao Hu et al.   PLOS BIOLOGY

Feedback Inhibition in the PhoQ/PhoP Signaling System by a Membrane Peptide

(2009) Andrew M. Lippa et al.   PLoS Genetics

Role of HPF (Hibernation Promoting Factor) in Translational Activity in Escherichia coli

(2008) Masami Ueta et al.   JOURNAL OF BIOCHEMISTRY

Recycling of Aborted Ribosomal 50S Subunit-Nascent Chain-tRNA Complexes by the Heat Shock Protein Hsp15

(2008) Linhua Jiang et al.   JOURNAL OF MOLECULAR BIOLOGY

MaxQuant enables high peptide identification rates, individualized p.p.b.-range mass accuracies and proteome-wide protein quantification

(2008) Jürgen Cox et al.   NATURE BIOTECHNOLOGY