Genomic footprinting uncovers global transcription factor responses to amino acids in Escherichia coli

Escherichia coli Leucine-Responsive Regulatory Protein Bridges DNA In Vivo and Tunably Dissociates in the Presence of Exogenous Leucine

(2023) Christine A. Ziegler et al.   mBio

Shaping bacterial gene expression by physiological and proteome allocation constraints

(2022) Matthew Scott et al.   NATURE REVIEWS MICROBIOLOGY

The leucine-responsive regulatory proteins/feast-famine regulatory proteins: an ancient and complex class of transcriptional regulators in bacteria and archaea

(2021) Christine A. Ziegler et al.   CRITICAL REVIEWS IN BIOCHEMISTRY AND MOLECULAR BIOLOGY

Unraveling the functions of uncharacterized transcription factors in Escherichia coli using ChIP-exo

(2021) Ye Gao et al.   NUCLEIC ACIDS RESEARCH

Dynamic landscape of protein occupancy across the Escherichia coli chromosome

(2021) Peter L. Freddolino et al.   PLOS BIOLOGY

Distinct heterochromatin‐like domains promote transcriptional memory and silence parasitic genetic elements in bacteria

(2021) Haley M Amemiya et al.   EMBO JOURNAL

Persistence and plasticity in bacterial gene regulation

(2021) Leo A. Baumgart et al.   NATURE METHODS

Determination of the two-component systems regulatory network reveals core and accessory regulations across Pseudomonas aeruginosa lineages

(2021) Julian Trouillon et al.   NUCLEIC ACIDS RESEARCH

Philosopher: a versatile toolkit for shotgun proteomics data analysis

(2020) Felipe da Veiga Leprevost et al.   NATURE METHODS

Redefining fundamental concepts of transcription initiation in bacteria

(2020) Citlalli Mejía-Almonte et al.   NATURE REVIEWS GENETICS

iModulonDB: a knowledgebase of microbial transcriptional regulation derived from machine learning

(2020) Kevin Rychel et al.   NUCLEIC ACIDS RESEARCH

Transcription activation in bacteria: ancient and modern

(2019) Stephen J. W. Busby   MICROBIOLOGY-SGM

Bacterial Transcription Factors: Regulation by Pick “N” Mix

(2019) Douglas F. Browning et al.   JOURNAL OF MOLECULAR BIOLOGY

Systematic identification of metabolites controlling gene expression in E. coli

(2019) Martin Lempp et al.   Nature Communications

Species-specific recruitment of transcription factors dictates toxin expression

(2019) Julian Trouillon et al.   NUCLEIC ACIDS RESEARCH

Differential protein-DNA contacts for activation and repression by ArgP, a LysR-type (LTTR) transcriptional regulator in Escherichia coli

(2018) Phu Nguyen Le Minh et al.   MICROBIOLOGICAL RESEARCH

Escherichia coli Lrp Regulates One-Third of the Genome via Direct, Cooperative, and Indirect Routes

(2018) Grace M. Kroner et al.   JOURNAL OF BACTERIOLOGY

Expression of the alaE gene is positively regulated by the global regulator Lrp in response to intracellular accumulation of l -alanine in Escherichia coli

(2017) Kohei Ihara et al.   JOURNAL OF BIOSCIENCE AND BIOENGINEERING

MSFragger: ultrafast and comprehensive peptide identification in mass spectrometry–based proteomics

(2017) Andy T Kong et al.   NATURE METHODS

Mapping genome-wide transcription-factor binding sites using DAP-seq

(2017) Anna Bartlett et al.   Nature Protocols

Global Mapping of Small RNA-Target Interactions in Bacteria

(2016) Sahar Melamed et al.   MOLECULAR CELL

Genome-wide footprinting: ready for prime time?

(2016) Myong-Hee Sung et al.   NATURE METHODS

Genomic footprinting

(2016) Jeff Vierstra et al.   NATURE METHODS

Real-time metabolome profiling of the metabolic switch between starvation and growth

(2015) Hannes Link et al.   NATURE METHODS

The architecture of ArgR-DNA complexes at the genome-scale in Escherichia coli

(2015) Suhyung Cho et al.   NUCLEIC ACIDS RESEARCH

HTSeq--a Python framework to work with high-throughput sequencing data

(2014) S. Anders et al.   BIOINFORMATICS

Coordination of microbial metabolism

(2014) Victor Chubukov et al.   NATURE REVIEWS MICROBIOLOGY

Everything old is new again: An update on current research on the Cpx envelope stress response

(2013) Tracy L. Raivio   BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR CELL RESEARCH

Dissecting specific and global transcriptional regulation of bacterial gene expression

(2013) L. Gerosa et al.   Molecular Systems Biology

Fast gapped-read alignment with Bowtie 2

(2012) Ben Langmead et al.   NATURE METHODS

Role of ArgP (IciA) in Lysine-Mediated Repression in Escherichia coli

(2011) C. N. Marbaniang et al.   JOURNAL OF BACTERIOLOGY

Deciphering the transcriptional regulatory logic of amino acid metabolism

(2011) Byung-Kwan Cho et al.   Nature Chemical Biology

BEDTools: a flexible suite of utilities for comparing genomic features

(2010) Aaron R. Quinlan et al.   BIOINFORMATICS

Genetics and Regulation of the Major Enzymes of Alanine Synthesis in Escherichia coli

(2010) S. H. Kim et al.   JOURNAL OF BACTERIOLOGY

Unexpected Coregulator Range for the Global Regulator Lrp of Escherichia coli and Proteus mirabilis

(2010) B. R. Hart et al.   JOURNAL OF BACTERIOLOGY

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS

Growth Rate-Dependent Global Effects on Gene Expression in Bacteria

(2009) Stefan Klumpp et al.   CELL

Absolute metabolite concentrations and implied enzyme active site occupancy in Escherichia coli

(2009) Bryson D Bennett et al.   Nature Chemical Biology

Genome-scale reconstruction of the Lrp regulatory network in Escherichia coli

(2008) B.-K. Cho et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Model-based Analysis of ChIP-Seq (MACS)

(2008) Yong Zhang et al.   GENOME BIOLOGY