The structural code of cyanobacterial genomes. (Q34044460)

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:25056315%20AND%20SRC:MED&resulttype=core&format=json

10 March 2020

title

The structural code of cyanobacterial genomes (English)

1 reference

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10 March 2020

1 reference

Rainer Machné

1 reference

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10 March 2020

language of work or name

English

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publication date

23 July 2014

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https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:25056315%20AND%20SRC:MED&resulttype=core&format=json

10 March 2020

published in

Nucleic Acids Research

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10 March 2020

volume

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10 March 2020

issue

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10 March 2020

page(s)

8873-8883

1 reference

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Creative Commons Attribution 4.0 International

10 March 2020

start time

4 October 2016

1 reference

April 2022 Public Data File from Crossref

copyrighted

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cites work

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5 July 2018

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5 July 2018

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5 July 2018

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Spatial ordering of chromosomes enhances the fidelity of chromosome partitioning in cyanobacteria

5 July 2018

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5 July 2018

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5 July 2018

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5 July 2018

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DNA information: from digital code to analogue structure

5 July 2018

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5 July 2018

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5 July 2018

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Gene order and chromosome dynamics coordinate spatiotemporal gene expression during the bacterial growth cycle

5 July 2018

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5 July 2018

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The 3-base periodicity and codon usage of coding sequences are correlated with gene expression at the level of transcription elongation

5 July 2018

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Structural basis for recognition of AT-rich DNA by unrelated xenogeneic silencing proteins

5 July 2018

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Learning to live together: mutualism between self-splicing introns and their hosts

5 July 2018

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The origin of multicellularity in cyanobacteria

5 July 2018

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A simple topological filter in a eukaryotic transposon as a mechanism to suppress genome instability

5 July 2018

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https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4132750

Comparative analysis of sequence periodicity among prokaryotic genomes points to differences in nucleoid structure and a relationship to gene expression

5 July 2018

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Oscillations in supercoiling drive circadian gene expression in cyanobacteria

5 July 2018

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The role of DNA shape in protein-DNA recognition

5 July 2018

1 reference

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Timing of morphological and ecological innovations in the cyanobacteria--a key to understanding the rise in atmospheric oxygen

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4132750

A systematic molecular dynamics study of nearest-neighbor effects on base pair and base pair step conformations and fluctuations in B-DNA.

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4132750

Stretches of alternating pyrimidine/purines and purines are respectively linked with pathogenicity and growth temperature in prokaryotes

5 July 2018

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flowClust: a Bioconductor package for automated gating of flow cytometry data

5 July 2018

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Choreography of the transcriptome, photophysiology, and cell cycle of a minimal photoautotroph, prochlorococcus

5 July 2018

1 reference

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Factors acting on Mos1 transposition efficiency

5 July 2018

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uShuffle: a useful tool for shuffling biological sequences while preserving the k-let counts

5 July 2018

1 reference

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SILVA: a comprehensive online resource for quality checked and aligned ribosomal RNA sequence data compatible with ARB

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4132750

Fluorescence staining of live cyanobacterial cells suggest non-stringent chromosome segregation and absence of a connection between cytoplasmic and thylakoid membranes

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4132750

In vitro transposition of ISY100, a bacterial insertion sequence belonging to the Tc1/mariner family.

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4132750

Silencing of xenogeneic DNA by H-NS-facilitation of lateral gene transfer in bacteria by a defense system that recognizes foreign DNA.

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4132750

No promoter left behind: global circadian gene expression in cyanobacteria

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4132750

Specific selection pressure at the third codon positions: contribution to 10- to 11-base periodicity in prokaryotic genomes

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4132750

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

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4132750

A periodic pattern of mRNA secondary structure created by the genetic code

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4132750

Involvement of DNA curvature in intergenic regions of prokaryotes

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4132750

Cell Cycle Regulation in Marine Synechococcus sp. Strains

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4132750

A-tract clusters may facilitate DNA packaging in bacterial nucleoid

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4132750

The GC-rich transposon Bytmar1 from the deep-sea hydrothermal crab, Bythograea thermydron, may encode three transposase isoforms from a single ORF.

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4132750

Genomic transcriptional response to loss of chromosomal supercoiling in Escherichia coli

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4132750

Structure and segregation of the bacterial nucleoid

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4132750

DNA analysis servers: plot.it, bend.it, model.it and IS.

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4132750

Transposition of cyanobacterium insertion element ISY100 in Escherichia coli

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4132750

A DNA structural atlas for Escherichia coli

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4132750

Structural analysis of DNA sequence: evidence for lateral gene transfer in Thermotoga maritima

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4132750

Investigating deep phylogenetic relationships among cyanobacteria and plastids by small subunit rRNA sequence analysis

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4132750

10-11 bp periodicities in complete genomes reflect protein structure and DNA folding

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4132750

Prochlorococcus, a marine photosynthetic prokaryote of global significance

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4132750

IHF modulation of Tn10 transposition: sensory transduction of supercoiling status via a proposed protein/DNA molecular spring

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4132750

Correlations in protein sequences and property codes.

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4132750

Supercoiling-dependent flexibility of adenosine-tract-containing DNA detected by a topological method.

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4132750

VMD: visual molecular dynamics

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4132750

DNA length, bending, and twisting constraints on IS50 transposition

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4132750

Periodicity in DNA primary structure is defined by secondary structure of the coded protein

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4132750

Codon preference and its use in identifying protein coding regions in long DNA sequences

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4132750

The pitch of chromatin DNA is reflected in its nucleotide sequence

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4132750

Relationship between Cell Size and Time of Initiation of DNA Replication

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4132750

Sequence periodicities in chicken nucleosome core DNA.

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4132750

The codon Adaptation Index--a measure of directional synonymous codon usage bias, and its potential applications

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4132750

Curved helix segments can uniquely orient the topology of supertwisted DNA.

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4132750

A protein factor which reduces the negative supercoiling requirement in the Mu DNA strand transfer reaction is Escherichia coli integration host factor.

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4132750

Curved DNA without A-A: experimental estimation of all 16 DNA wedge angles

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4132750

The apical localization of transcribing RNA polymerases on supercoiled DNA prevents their rotation around the template

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4132750

The chromatin-associated protein H-NS interacts with curved DNA to influence DNA topology and gene expression

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4132750

Patterns of growth and development in pleurocapsalean cyanobacteria

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4132750

Periodicities of 10-11bp as indicators of the supercoiled state of genomic DNA.

5 July 2018

1 reference

https://api.crossref.org/works/10.1093%2FNAR%2FGKU641

Sequence periodicity in complete genomes of archaea suggests positive supercoiling

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FNAR%2FGKU641

A systematic in vitro study of nucleoprotein complexes formed by bacterial nucleoid-associated proteins revealing novel types of DNA organization.

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FNAR%2FGKU641

Mode of binding of RNA polymerase α subunit to the phased A-tracts upstream of the phospholipase C gene promoter of Clostridium perfringens

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FNAR%2FGKU641

Upstream curved sequences in E. coli are related to the regulation of transcription initiation.

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FNAR%2FGKU641

Generic Assignments, Strain Histories and Properties of Pure Cultures of Cyanobacteria

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FNAR%2FGKU641

Physical properties of DNA components affecting the transposition efficiency of the mariner Mos1 element.

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FNAR%2FGKU641

A global analysis of adaptive evolution of operons in cyanobacteria

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FNAR%2FGKU641

Assessing diversity of DNA structure-related sequence features in prokaryotic genomes

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FNAR%2FGKU641

21 January 2018

Ploidy in cyanobacteria.

1 reference

https://api.crossref.org/works/10.1093%2FNAR%2FGKU641

Expression of Genes in Cyanobacteria: Adaptation of Endogenous Plasmids as Platforms for High-Level Gene Expression in Synechococcus sp. PCC 7002

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FNAR%2FGKU641

Light-dependent and asynchronous replication of cyanobacterial multi-copy chromosomes.

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FNAR%2FGKU641

RpoD Promoters in Campylobacter jejuni Exhibit a Strong Periodic Signal Instead of a −35 Box

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FNAR%2FGKU641

Growth of prochlorococcus, a photosynthetic prokaryote, in the equatorial pacific ocean

21 January 2018

1 reference

12 December 2020

Supercoiling-induced DNA bending

1 reference

12 December 2020

ApA dinucleotide periodicity in prokaryote, eukaryote, and organelle genomes

1 reference

12 December 2020

DNA supercoiling regulates the stress-inducible expression of genes in the cyanobacterium Synechocystis

1 reference

12 December 2020

Identifiers

DOI

10.1093/NAR/GKU641

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:25056315%20AND%20SRC:MED&resulttype=core&format=json

10 March 2020

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:25056315%20AND%20SRC:MED&resulttype=core&format=json

10 March 2020

PubMed publication ID

25056315

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:25056315%20AND%20SRC:MED&resulttype=core&format=json