(Q29346669)

11 April 2017

Comparative genomic reconstruction of transcriptional networks controlling central metabolism in the Shewanella genus (English)

1 reference

11 April 2017

Dmitry A Ravcheev

7

0 references

Marat D. Kazanov

Marat D Kazanov

6

0 references

Margaret F Romine

Margaret F Romine

14

0 references

Dmitry Rodionov

Dmitry A Rodionov

1

0 references

Adam Arkin

Adam P Arkin

16

0 references

Mikhail Gelfand

Mikhail S Gelfand

19

0 references

Ross Overbeek

13

Ross Overbeek

1 reference

11 April 2017

2

Pavel S Novichkov

1 reference

11 April 2017

11

Elizabeth A Permina

1 reference

11 April 2017

12

Olga N Laikova

1 reference

11 April 2017

17

Inna Dubchak

1 reference

11 April 2017

Elena D Stavrovskaya

3

1 reference

11 April 2017

Irina A Rodionova

4

1 reference

11 April 2017

Xiaoqing Li

5

1 reference

11 April 2017

Anna V Gerasimova

8

1 reference

11 April 2017

Alexey E Kazakov

9

1 reference

11 April 2017

Galina Yu Kovaleva

10

1 reference

11 April 2017

James K Fredrickson

15

1 reference

11 April 2017

Andrei L Osterman

18

1 reference

11 April 2017

language of work or name

English

0 references

publication date

15 June 2011

1 reference

11 April 2017

1 reference

11 April 2017

12 Suppl 1

1 reference

11 April 2017

S3

1 reference

https://scigraph.springernature.com/pub.10.1186/1471-2164-12-s1-s3

11 April 2017

0 references

cites work

Constraint-based model of Shewanella oneidensis MR-1 metabolism: a tool for data analysis and hypothesis generation

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3223726

The Pfam protein families database

11 April 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3223726

Rfam: updates to the RNA families database

11 April 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3223726

InterPro: the integrative protein signature database

11 April 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3223726

Probing regulon of ArcA in Shewanella oneidensis MR-1 by integrated genomic analyses.

11 April 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3223726

DBD--taxonomically broad transcription factor predictions: new content and functionality

11 April 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3223726

Whole proteome analysis of post-translational modifications: applications of mass-spectrometry for proteogenomic annotation

11 April 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3223726

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

11 April 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3223726

Dissimilatory metabolism of nitrogen oxides in bacteria: comparative reconstruction of transcriptional networks

11 April 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3223726

The subsystems approach to genome annotation and its use in the project to annotate 1000 genomes

11 April 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3223726

Transcriptomic and proteomic characterization of the Fur modulon in the metal-reducing bacterium Shewanella oneidensis

11 April 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3223726

The homogentisate pathway: a central catabolic pathway involved in the degradation of L-phenylalanine, L-tyrosine, and 3-hydroxyphenylacetate in Pseudomonas putida

11 April 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3223726

Genes regulated by TorR, the trimethylamine oxide response regulator of Shewanella oneidensis.

11 April 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3223726

Divergent structure and regulatory mechanism of proline catabolic systems: characterization of the putAP proline catabolic operon of Pseudomonas aeruginosa PAO1 and its regulation by PruR, an AraC/XylS family protein

11 April 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3223726

Analysis of Relative Gene Expression Data Using Real-Time Quantitative PCR and the 2−ΔΔCT Method

11 April 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3223726

Conservation of the binding site for the arginine repressor in all bacterial lineages

11 April 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3223726

Information content of binding sites on nucleotide sequences

11 April 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3223726

Genomic encyclopedia of sugar utilization pathways in the Shewanella genus

11 April 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3223726

RegPredict: an integrated system for regulon inference in prokaryotes by comparative genomics approach

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3223726

Characterization of the Pseudomonas aeruginosa transcriptional response to phenylalanine and tyrosine

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3223726

MicrobesOnline: an integrated portal for comparative and functional genomics

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3223726

RegPrecise: a database of curated genomic inferences of transcriptional regulatory interactions in prokaryotes

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3223726

Comparative systems biology across an evolutionary gradient within the Shewanella genus.

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3223726

Direct methods for studying transcription regulatory proteins and RNA polymerase in bacteria.

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3223726

Genomic reconstruction of Shewanella oneidensis MR-1 metabolism reveals a previously uncharacterized machinery for lactate utilization

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3223726

Analysis of mechanisms of activation and repression at bacterial promoters.

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3223726

Comparative genomics of regulation of fatty acid and branched-chain amino acid utilization in proteobacteria.

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3223726

The cis-regulatory map of Shewanella genomes

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3223726

Towards environmental systems biology of Shewanella

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3223726

Impact of Transcription Units rearrangement on the evolution of the regulatory network of gamma-proteobacteria.

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3223726

Characterization of the Shewanella oneidensis Fur gene: roles in iron and acid tolerance response

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3223726

Transcriptional regulation of NAD metabolism in bacteria: NrtR family of Nudix-related regulators.

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3223726

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

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3223726

Ecology and biotechnology of the genus Shewanella

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3223726

Comparative genomic reconstruction of transcriptional regulatory networks in bacteria

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3223726

Comparative genomic analysis of regulation of anaerobic respiration in ten genomes from three families of gamma-proteobacteria (Enterobacteriaceae, Pasteurellaceae, Vibrionaceae).

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3223726

Integration of regulatory signals through involvement of multiple global regulators: control of the Escherichia coli gltBDF operon by Lrp, IHF, Crp, and ArgR.

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3223726

Comparative genomics of regulation of heavy metal resistance in Eubacteria

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3223726

Involvement of cyclic AMP (cAMP) and cAMP receptor protein in anaerobic respiration of Shewanella oneidensis

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3223726

Purine regulon of gamma-proteobacteria: a detailed description

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3223726

Conservation of the biotin regulon and the BirA regulatory signal in Eubacteria and Archaea.

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3223726

Microarray transcription profiling of a Shewanella oneidensis etrA mutant

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3223726

Comparative analysis of FUR regulons in gamma-proteobacteria

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3223726

Computational analysis of the transcriptional regulation of pentose utilization systems in the gamma subdivision of Proteobacteria

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3223726

Regulation of aromatic amino acid biosynthesis in gamma-proteobacteria.

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3223726

Transcriptional regulation of transport and utilization systems for hexuronides, hexuronates and hexonates in gamma purple bacteria

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3223726

Prediction of transcription regulatory sites in Archaea by a comparative genomic approach

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3223726

Computer analysis of transcription regulatory patterns in completely sequenced bacterial genomes

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3223726

Regulation of acetate metabolism by protein phosphorylation in enteric bacteria

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3223726

Domain Organization and a Protease-Sensitive Loop in Eukaryotic Ornithine Decarboxylase

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3223726

Identification of a bacterial regulatory system for ribonucleotide reductases by phylogenetic profiling.

3 June 2018

1 reference

https://api.crossref.org/works/10.1186%2F1471-2164-12-S1-S3

Anaerobic regulation by an atypical Arc system in Shewanella oneidensis.

21 January 2018

1 reference

https://api.crossref.org/works/10.1186%2F1471-2164-12-S1-S3

Comparative genomics and experimental characterization of N-acetylglucosamine utilization pathway of Shewanella oneidensis

21 January 2018

1 reference

https://api.crossref.org/works/10.1186%2F1471-2164-12-S1-S3

Accurate taxonomy assignments from 16S rRNA sequences produced by highly parallel pyrosequencers

21 January 2018

1 reference

https://api.crossref.org/works/10.1186%2F1471-2164-12-S1-S3

Coactivation of Vibrio vulnificus putAP operon by cAMP receptor protein and PutR through cooperative binding to overlapping sites.

21 January 2018

1 reference

https://api.crossref.org/works/10.1186%2F1471-2164-12-S1-S3

Attenuation regulation of amino acid biosynthetic operons in proteobacteria: comparative genomics analysis.

21 January 2018

1 reference

https://api.crossref.org/works/10.1186%2F1471-2164-12-S1-S3

A protein-DNA docking benchmark

21 January 2018

1 reference

https://api.crossref.org/works/10.1186%2F1471-2164-12-S1-S3

Automated purification of recombinant proteins: combining high-throughput with high yield.

21 January 2018

1 reference

https://api.crossref.org/works/10.1186%2F1471-2164-12-S1-S3

Identification of diverse carbon utilization pathways in Shewanella oneidensis MR-1 via expression profiling.

21 January 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3223726

26 November 2018

1 reference

https://pubmed.ncbi.nlm.nih.gov/21810205

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Identifiers

DOI

10.1186/1471-2164-12-S1-S3

1 reference

Dimensions Publication ID

11 April 2017

1 reference

https://scigraph.springernature.com/pub.10.1186/1471-2164-12-s1-s3

9 September 2019

0 references

1 reference