Deciphering the regulatory codes in bacterial genomes (Q37918500)

25 August 2017

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title

Deciphering the regulatory codes in bacterial genomes (English)

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25 August 2017

2

Bernhard Palsson

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25 August 2017

Byung-Kwan Cho

1

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25 August 2017

Karsten Zengler

series ordinal

3

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25 August 2017

language of work or name

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15 August 2011

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25 August 2017

published in

Biotechnology Journal

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25 August 2017

volume

6

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25 August 2017

issue

9

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25 August 2017

page(s)

1052-1063

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

25 August 2017

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Large-scale mapping and validation of Escherichia coli transcriptional regulation from a compendium of expression profiles

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Integrating high-throughput and computational data elucidates bacterial networks

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High-throughput identification of transcription start sites, conserved promoter motifs and predicted regulons.

21 January 2018

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Genomic analysis of protein-DNA interactions in bacteria: insights into transcription and chromosome organization

21 January 2018

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The primary transcriptome of the major human pathogen Helicobacter pylori

21 January 2018

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The complete genome sequence of Escherichia coli K-12

21 January 2018

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Whole-genome random sequencing and assembly of Haemophilus influenzae Rd

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21 January 2018

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Strand-specific deep sequencing of the transcriptome

21 January 2018

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Deep sequencing reveals highly complex dynamics of human cytomegalovirus genotypes in transplant patients over time

21 January 2018

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A practical comparison of de novo genome assembly software tools for next-generation sequencing technologies

21 January 2018

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RNA expression analysis using a 30 base pair resolution Escherichia coli genome array

21 January 2018

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Structural and operational complexity of the Geobacter sulfurreducens genome.

21 January 2018

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Degradation of stable RNA in bacteria

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Widespread antisense transcription in Escherichia coli.

21 January 2018

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The impact of next-generation sequencing technology on genetics

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Mapping of transcription factor binding regions in mammalian cells by ChIP: comparison of array- and sequencing-based technologies

21 January 2018

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Immobilization of Escherichia coli RNA polymerase and location of binding sites by use of chromatin immunoprecipitation and microarrays

21 January 2018

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RNA polymerase mutants found through adaptive evolution reprogram Escherichia coli for optimal growth in minimal media

21 January 2018

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Functional modulation of Escherichia coli RNA polymerase

21 January 2018

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https://api.crossref.org/works/10.1002%2FBIOT.201000349

The transition between transcriptional initiation and elongation in E. coli is highly variable and often rate limiting.

21 January 2018

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Identification of mycobacterial sigma factor binding sites by chromatin immunoprecipitation assays

21 January 2018

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Consensus statement. Global burden of tuberculosis: estimated incidence, prevalence, and mortality by country. WHO Global Surveillance and Monitoring Project

21 January 2018

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The complete genome sequence of Mycobacterium bovis

21 January 2018

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Borrelia burgdorferi sigma54 is required for mammalian infection and vector transmission but not for tick colonization

21 January 2018

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https://api.crossref.org/works/10.1002%2FBIOT.201000349

Identifying global regulators in transcriptional regulatory networks in bacteria

21 January 2018

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Global analysis of gene transcription regulation in prokaryotes.

21 January 2018

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The repertoire of DNA-binding transcriptional regulators in Escherichia coli K-12.

21 January 2018

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Integrated genomic and proteomic analyses of a systematically perturbed metabolic network

21 January 2018

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Genes directly controlled by CtrA, a master regulator of the Caulobacter cell cycle.

21 January 2018

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Genomic studies with Escherichia coli MelR protein: applications of chromatin immunoprecipitation and microarrays.

21 January 2018

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Transcription factor distribution in Escherichia coli: studies with FNR protein.

21 January 2018

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https://api.crossref.org/works/10.1002%2FBIOT.201000349

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

21 January 2018

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Genome-wide identification of binding sites for the nitric oxide-sensitive transcriptional regulator NsrR.

21 January 2018

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Functional characterization in vitro of all two-component signal transduction systems from Escherichia coli

21 January 2018

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https://api.crossref.org/works/10.1002%2FBIOT.201000349

Genomic analysis of LexA binding reveals the permissive nature of the Escherichia coli genome and identifies unconventional target sites

21 January 2018

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The PurR regulon in Escherichia coli K-12 MG1655.

21 January 2018

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Genome-wide analysis of Fis binding in Escherichia coli indicates a causative role for A-/AT-tracts

21 January 2018

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https://api.crossref.org/works/10.1002%2FBIOT.201000349

Global gene expression profiling in Escherichia coli K12. The effects of oxygen availability and FNR.

21 January 2018

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https://api.crossref.org/works/10.1002%2FBIOT.201000349

Genome-wide expression analysis indicates that FNR of Escherichia coli K-12 regulates a large number of genes of unknown function

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FBIOT.201000349

A reassessment of the FNR regulon and transcriptomic analysis of the effects of nitrate, nitrite, NarXL, and NarQP as Escherichia coli K12 adapts from aerobic to anaerobic growth

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FBIOT.201000349

Reprogramming of anaerobic metabolism by the FnrS small RNA

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FBIOT.201000349

Transcriptome analysis of Crp-dependent catabolite control of gene expression in Escherichia coli

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FBIOT.201000349

Functional interactions between the carbon and iron utilization regulators, Crp and Fur, in Escherichia coli

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FBIOT.201000349

Identification of the CRP regulon using in vitro and in vivo transcriptional profiling

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FBIOT.201000349

In vivo dissection of the Helicobacter pylori Fur regulatory circuit by genome-wide location analysis

21 January 2018

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https://api.crossref.org/works/10.1002%2FBIOT.201000349

Additional targets of the Bacillus subtilis global regulator CodY identified by chromatin immunoprecipitation and genome-wide transcript analysis

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FBIOT.201000349

The Spo0A regulon of Bacillus subtilis

21 January 2018

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https://api.crossref.org/works/10.1002%2FBIOT.201000349

The program of gene transcription for a single differentiating cell type during sporulation in Bacillus subtilis

21 January 2018

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https://api.crossref.org/works/10.1002%2FBIOT.201000349

Genome-wide regulon and crystal structure of BlaI (Rv1846c) from Mycobacterium tuberculosis

21 January 2018

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https://api.crossref.org/works/10.1002%2FBIOT.201000349

The role of nucleoid-associated proteins in the organization and compaction of bacterial chromatin

21 January 2018

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https://api.crossref.org/works/10.1002%2FBIOT.201000349

Regulation of gene expression by histone-like proteins in bacteria.

21 January 2018

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https://api.crossref.org/works/10.1002%2FBIOT.201000349

Escherichia coli histone-like protein H-NS preferentially binds to horizontally acquired DNA in association with RNA polymerase

21 January 2018

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https://api.crossref.org/works/10.1002%2FBIOT.201000349

Selective silencing of foreign DNA with low GC content by the H-NS protein in Salmonella

21 January 2018

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https://api.crossref.org/works/10.1002%2FBIOT.201000349

H-NS mediates the silencing of laterally acquired genes in bacteria

21 January 2018

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https://api.crossref.org/works/10.1002%2FBIOT.201000349

Direct and indirect effects of H-NS and Fis on global gene expression control in Escherichia coli

21 January 2018

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https://api.crossref.org/works/10.1002%2FBIOT.201000349

The bacterial Sm-like protein Hfq: a key player in RNA transactions

21 January 2018

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https://api.crossref.org/works/10.1002%2FBIOT.201000349

RIP-Chip: the isolation and identification of mRNAs, microRNAs and protein components of ribonucleoprotein complexes from cell extracts.

21 January 2018

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https://api.crossref.org/works/10.1002%2FBIOT.201000349

Global analysis of small RNA and mRNA targets of Hfq

21 January 2018

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https://api.crossref.org/works/10.1002%2FBIOT.201000349

Identification of small Hfq-binding RNAs in Listeria monocytogenes

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FBIOT.201000349

A small bacterial RNA regulates a putative ABC transporter

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FBIOT.201000349

Deep sequencing analysis of small noncoding RNA and mRNA targets of the global post-transcriptional regulator, Hfq

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FBIOT.201000349

Towards multidimensional genome annotation

21 January 2018

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https://api.crossref.org/works/10.1002%2FBIOT.201000349

The model organism as a system: integrating 'omics' data sets

21 January 2018

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https://api.crossref.org/works/10.1002%2FBIOT.201000349

A systems approach to mapping DNA damage response pathways

21 January 2018

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https://api.crossref.org/works/10.1002%2FBIOT.201000349

The global transcriptional regulatory network for metabolism in Escherichia coli exhibits few dominant functional states.

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FBIOT.201000349

Hierarchical structure and modules in the Escherichia coli transcriptional regulatory network revealed by a new top-down approach

21 January 2018

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https://api.crossref.org/works/10.1002%2FBIOT.201000349

An extended transcriptional regulatory network of Escherichia coli and analysis of its hierarchical structure and network motifs

21 January 2018

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https://api.crossref.org/works/10.1002%2FBIOT.201000349

Reconciling Gene Expression Data With Known Genome-Scale Regulatory Network Structures

21 January 2018

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https://api.crossref.org/works/10.1002%2FBIOT.201000349

Network biology: understanding the cell's functional organization

21 January 2018

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https://api.crossref.org/works/10.1002%2FBIOT.201000349

RegulonDB (version 6.0): gene regulation model of Escherichia coli K-12 beyond transcription, active (experimental) annotated promoters and Textpresso navigation.

21 January 2018

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https://api.crossref.org/works/10.1002%2FBIOT.201000349

EcoCyc: a comprehensive database resource for Escherichia coli

21 January 2018

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https://api.crossref.org/works/10.1002%2FBIOT.201000349

Network motifs in the transcriptional regulation network of Escherichia coli

21 January 2018

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https://api.crossref.org/works/10.1002%2FBIOT.201000349

Matrix formalism to describe functional states of transcriptional regulatory systems

21 January 2018

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https://api.crossref.org/works/10.1002%2FBIOT.201000349

Integrated analysis of regulatory and metabolic networks reveals novel regulatory mechanisms in Saccharomyces cerevisiae

21 January 2018

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https://api.crossref.org/works/10.1002%2FBIOT.201000349

Epigenetic gene regulation in the bacterial world

21 January 2018

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Capturing chromosome conformation

21 January 2018

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Gene regulation in the third dimension

21 January 2018

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High-throughput, quantitative analyses of genetic interactions in E. coli

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Bacterial small RNA regulators

21 January 2018

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Dynamic distribution of seqa protein across the chromosome of escherichia coli K-12.

21 January 2018

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DNA methylation modulates Salmonella enterica serovar Typhimurium virulence in Caenorhabditis elegans

21 January 2018

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Transcriptome Complexity in a Genome-Reduced Bacterium

21 January 2018

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21 January 2018

Identifiers

DOI

10.1002/BIOT.201000349

1 reference

25 August 2017

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