(Q34882378)

5 August 2017

title

Bacterial regulatory networks are extremely flexible in evolution (English)

1 reference

5 August 2017

1 reference

2

Sarath Chandra Janga

0 references

Julio Collado-Vides

object named as

Julio Collado-Vides

series ordinal

3

0 references

Irma Lozada-Chávez

series ordinal

1

object named as

Irma Lozada-Chávez

1 reference

5 August 2017

language of work or name

English

0 references

publication date

13 July 2006

1 reference

5 August 2017

published in

Nucleic Acids Research

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5 August 2017

volume

34

1 reference

5 August 2017

issue

12

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5 August 2017

page(s)

3434-3445

1 reference

An evolutionary and functional assessment of regulatory network motifs

5 August 2017

cites work

1 reference

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8 July 2018

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8 July 2018

1 reference

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Phylogeny determined by protein domain content

8 July 2018

1 reference

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Differences in LexA regulon structure among Proteobacteria through in vivo assisted comparative genomics

8 July 2018

1 reference

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Conservation of adjacency as evidence of paralogous operons

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1524901

Structure and evolution of transcriptional regulatory networks

8 July 2018

1 reference

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Annotation transfer between genomes: protein-protein interologs and protein-DNA regulogs

8 July 2018

1 reference

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Reconstruction of microbial transcriptional regulatory networks

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1524901

Network motifs in integrated cellular networks of transcription-regulation and protein-protein interaction

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1524901

Upstream plasticity and downstream robustness in evolution of molecular networks

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1524901

Global analysis of bacterial transcription factors to predict cellular target processes

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1524901

Open source clustering software

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1524901

RegulonDB (version 4.0): transcriptional regulation, operon organization and growth conditions in Escherichia coli K-12

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1524901

The KEGG resource for deciphering the genome

8 July 2018

1 reference

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DBTBS: database of transcriptional regulation in Bacillus subtilis and its contribution to comparative genomics

8 July 2018

1 reference

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Identifying global regulators in transcriptional regulatory networks in bacteria

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1524901

Discovery of uncharacterized cellular systems by genome-wide analysis of functional linkages

8 July 2018

1 reference

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WU-Blast2 server at the European Bioinformatics Institute

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1524901

Evolution of the protein repertoire

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1524901

The Lrp family of transcriptional regulators

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1524901

Ontologies for proteomics: towards a systematic definition of structure and function that scales to the genome level

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1524901

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

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1524901

Acceleration of genomic evolution caused by enhanced mutation rate in endocellular symbionts.

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1524901

Network motifs in the transcriptional regulation network of Escherichia coli

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1524901

Annotation transfer for genomics: measuring functional divergence in multi-domain proteins

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1524901

Universal trees based on large combined protein sequence data sets.

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1524901

Determination of protein function, evolution and interactions by structural genomics.

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1524901

Global versus local regulatory roles for Lrp-related proteins: Haemophilus influenzae as a case study

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1524901

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

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1524901

Domain size distributions can predict domain boundaries

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1524901

The large-scale organization of metabolic networks

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1524901

Global properties of the metabolic map of Escherichia coli

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1524901

The Pfam protein families database.

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1524901

Fundamentally different logic of gene regulation in eukaryotes and prokaryotes

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1524901

Predicting function: from genes to genomes and back

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1524901

Measuring genome evolution

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1524901

A genomic perspective on protein families

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1524901

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1524901

Accelerated evolution and Muller's rachet in endosymbiotic bacteria

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1524901

Distinguishing Homologous from Analogous Proteins

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1524901

Evolutionary dynamics of prokaryotic transcriptional regulatory networks

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1524901

Gene regulatory network growth by duplication

26 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1524901

Consequences of reductive evolution for gene expression in an obligate endosymbiont

26 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1524901

Tolerating some redundancy significantly speeds up clustering of large protein databases

26 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1524901

Transcription-associated protein families are primarily taxon-specific

26 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1524901

The small world of metabolism.

26 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1524901

Assessing annotation transfer for genomics: quantifying the relations between protein sequence, structure and function through traditional and probabilistic scores.

26 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1524901

Reductive evolution of resident genomes.

26 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1524901

From specific gene regulation to genomic networks: a global analysis of transcriptional regulation in Escherichia coli

26 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1524901

Orthology, paralogy and proposed classification for paralog subtypes

26 October 2018

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/16840530

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Transcription regulation and environmental adaptation in bacteria

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/16840530

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Identifiers

DOI

10.1093/NAR/GKL423

1 reference

5 August 2017

1 reference

5 August 2017

1 reference