The genome-scale DNA-binding profile of BarR, a β-alanine responsive transcription factor in the archaeon Sulfolobus acidocaldarius

Genome-wide binding analysis of the transcriptional regulator TrmBL1 in Pyrococcus furiosus

(2016) Robert Reichelt et al.   BMC GENOMICS

Role of intragenic binding of cAMP responsive protein (CRP) in regulation of the succinate dehydrogenase genes Rv0249c-Rv0247c in TB complex mycobacteria

(2015) G. S. Knapp et al.   NUCLEIC ACIDS RESEARCH

Characterization of a cAMP responsive transcription factor, Cmr (Rv1675c), in TB complex mycobacteria reveals overlap with the DosR (DevR) dormancy regulon

(2015) Sridevi Ranganathan et al.   NUCLEIC ACIDS RESEARCH

ChIP-seq reveals the global regulator AlgR mediating cyclic di-GMP synthesis inPseudomonas aeruginosa

(2015) Weina Kong et al.   NUCLEIC ACIDS RESEARCH

The DNA-binding network of Mycobacterium tuberculosis

(2015) Kyle J. Minch et al.   Nature Communications

Evolution of context dependent regulation by expansion of feast/famine regulatory proteins

(2014) Christopher L Plaisier et al.   BMC Systems Biology

The Transcription Factor Titration Effect Dictates Level of Gene Expression

(2014) Robert C. Brewster et al.   CELL

Lies and deception in bacterial gene regulation: the roles of nucleic acid decoys

(2014) Yvonne Göpel et al.   MOLECULAR MICROBIOLOGY

BarR, an Lrp-type transcription factor inSulfolobus acidocaldarius, regulates an aminotransferase gene in a β-alanine responsive manner

(2014) Han Liu et al.   MOLECULAR MICROBIOLOGY

Inference of Expanded Lrp-Like Feast/Famine Transcription Factor Targets in a Non-Model Organism Using Protein Structure-Based Prediction

(2014) Justin Ashworth et al.   PLoS One

Comprehensive Mapping of the Escherichia coli Flagellar Regulatory Network

(2014) Devon M. Fitzgerald et al.   PLoS Genetics

Cis-regulatory logic in archaeal transcription

(2013) Eveline Peeters et al.   BIOCHEMICAL SOCIETY TRANSACTIONS

The genome-wide binding profile of the Sulfolobus solfataricus transcription factor Ss-LrpB shows binding events beyond direct transcription regulation

(2013) Trong Nguyen-Duc et al.   BMC GENOMICS

A thermodynamic model of the cooperative interaction between the archaeal transcription factor Ss-LrpB and its tripartite operator DNA

(2013) Eveline Peeters et al.   GENE

Genome-Scale Analyses of Escherichia coli and Salmonella enterica AraC Reveal Noncanonical Targets and an Expanded Core Regulon

(2013) A. M. Stringer et al.   JOURNAL OF BACTERIOLOGY

Expanded target and cofactor repertoire for the transcriptional activator LysM from Sulfolobus

(2013) Ningning Song et al.   NUCLEIC ACIDS RESEARCH

Global Analysis of the Regulon of the Transcriptional Repressor LexA, a Key Component of SOS Response inMycobacterium tuberculosis

(2012) Katherine L. Smollett et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Nanobody®-based chromatin immunoprecipitation/micro-array analysis for genome-wide identification of transcription factor DNA binding sites

(2012) Trong Nguyen-Duc et al.   NUCLEIC ACIDS RESEARCH

A workflow for genome-wide mapping of archaeal transcription factors with ChIP-seq

(2012) Elizabeth G. Wilbanks et al.   NUCLEIC ACIDS RESEARCH

Versatile Genetic Tool Box for the Crenarchaeote Sulfolobus acidocaldarius

(2012) Michaela Wagner et al.   Frontiers in Microbiology

Sa-Lrp fromSulfolobus acidocaldariusis a versatile, glutamine-responsive, and architectural transcriptional regulator

(2012) Amelia Vassart et al.   MicrobiologyOpen

Integrative genomics viewer

(2011) James T Robinson et al.   NATURE BIOTECHNOLOGY

Deciphering the transcriptional regulatory logic of amino acid metabolism

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

Genome-wide transcription factor binding: beyond direct target regulation

(2011) Kyle L. MacQuarrie et al.   TRENDS IN GENETICS

Fast and accurate long-read alignment with Burrows–Wheeler transform

(2010) Heng Li et al.   BIOINFORMATICS

BEDTools: a flexible suite of utilities for comparing genomic features

(2010) Aaron R. Quinlan et al.   BIOINFORMATICS

Transcriptional control by two leucine-responsive regulatory proteins in Halobacterium salinarum R1

(2010) Rita Schwaiger et al.   BMC MOLECULAR BIOLOGY

Two transcription factors are necessary for iron homeostasis in a salt-dwelling archaeon

(2010) Amy K. Schmid et al.   NUCLEIC ACIDS RESEARCH

Abduction and asylum in the lives of transcription factors

(2010) A. Burger et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

The Lrp Family of Transcription Regulators in Archaea

(2010) Eveline Peeters et al.   ARCHAEA-AN INTERNATIONAL MICROBIOLOGICAL JOURNAL

A single transcription factor regulates evolutionarily diverse but functionally linked metabolic pathways in response to nutrient availability

(2009) Amy K Schmid et al.   Molecular Systems Biology

The DNA-recognition mode shared by archaeal feast/famine-regulatory proteins revealed by the DNA-binding specificities of TvFL3, FL10, FL11 and Ss-LrpB

(2009) K. Yokoyama et al.   NUCLEIC ACIDS RESEARCH

MEME SUITE: tools for motif discovery and searching

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

Transcription Regulation by Feast/Famine Regulatory Proteins, FFRPs, in Archaea and Eubacteria

(2008) Tsuyoshi Kawashima et al.   BIOLOGICAL & PHARMACEUTICAL BULLETIN

Ss-LrpB, a transcriptional regulator fromSulfolobus solfataricus, regulates a gene cluster with a pyruvate ferredoxin oxidoreductase-encoding operon and permease genes

(2008) Eveline Peeters et al.   MOLECULAR MICROBIOLOGY

The Escherichia coli RutR transcription factor binds at targets within genes as well as intergenic regions

(2008) Tomohiro Shimada et al.   NUCLEIC ACIDS RESEARCH

Model-based Analysis of ChIP-Seq (MACS)

(2008) Yong Zhang et al.   GENOME BIOLOGY