(Q33559638)

28 July 2017

title

Re-annotation of the Saccharopolyspora erythraea genome using a systems biology approach (English)

1 reference

Saccharopolyspora erythraea

28 July 2017

main subject

object named as

Saccharopolyspora erythraea

1 reference

5

1 reference

Cuauhtémoc Licona-Cassani

28 July 2017

Robin William Palfreyman

object named as

Robin W Palfreyman

series ordinal

4

0 references

series ordinal

2

object named as

Cuauhtemoc Licona-Cassani

1 reference

28 July 2017

Esteban Marcellin

1

1 reference

28 July 2017

Tim R Mercer

series ordinal

3

1 reference

28 July 2017

language of work or name

English

0 references

publication date

11 October 2013

1 reference

28 July 2017

1 reference

28 July 2017

volume

14

1 reference

28 July 2017

page(s)

699

1 reference

https://scigraph.springernature.com/pub.10.1186/1471-2164-14-699

28 July 2017

exact match

0 references

cites work

Saccharopolyspora erythraea's genome is organised in high-order transcriptional regions mediated by targeted degradation at the metabolic switch

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4008361

Pinstripe: a suite of programs for integrating transcriptomic and proteomic datasets identifies novel proteins and improves differentiation of protein-coding and non-coding genes

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4008361

Reconstruction of the Saccharopolyspora erythraea genome-scale model and its use for enhancing erythromycin production

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4008361

The ribosome profiling strategy for monitoring translation in vivo by deep sequencing of ribosome-protected mRNA fragments

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4008361

The anti-Shine-Dalgarno sequence drives translational pausing and codon choice in bacteria

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4008361

The translational landscape of mTOR signalling steers cancer initiation and metastasis

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4008361

High-throughput proteogenomics of Ruegeria pomeroyi: seeding a better genomic annotation for the whole marine Roseobacter clade.

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4008361

High-resolution view of the yeast meiotic program revealed by ribosome profiling

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4008361

Proteogenomic analysis of bacteria and archaea: a 46 organism case study

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4008361

Reorganizing the protein space at the Universal Protein Resource (UniProt)

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4008361

Ribosome profiling of mouse embryonic stem cells reveals the complexity and dynamics of mammalian proteomes

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4008361

SMART 7: recent updates to the protein domain annotation resource

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4008361

PATRIC: the comprehensive bacterial bioinformatics resource with a focus on human pathogenic species

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4008361

The STRING database in 2011: functional interaction networks of proteins, globally integrated and scored

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4008361

Nuclear-localized tiny RNAs are associated with transcription initiation and splice sites in metazoans.

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4008361

Proteogenomics to discover the full coding content of genomes: a computational perspective

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4008361

Structural and operational complexity of the Geobacter sulfurreducens genome.

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4008361

Using comparative genome analysis to identify problems in annotated microbial genomes.

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4008361

Prodigal: prokaryotic gene recognition and translation initiation site identification

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4008361

Proteogenomics and systems biology: quest for the ultimate missing parts

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4008361

The Pfam protein families database

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4008361

The Sequence Alignment/Map format and SAMtools

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4008361

The RAST Server: rapid annotations using subsystems technology

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4008361

MAKER: an easy-to-use annotation pipeline designed for emerging model organism genomes

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4008361

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

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4008361

CPC: assess the protein-coding potential of transcripts using sequence features and support vector machine.

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4008361

Large-scale prokaryotic gene prediction and comparison to genome annotation

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4008361

The tRNAscan-SE, snoscan and snoGPS web servers for the detection of tRNAs and snoRNAs

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4008361

Genome-scale analysis of Streptomyces coelicolor A3(2) metabolism

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4008361

Simple cDNA normalization using kamchatka crab duplex-specific nuclease

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4008361

Reannotation of Shewanella oneidensis Genome

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4008361

FrameD: A flexible program for quality check and gene prediction in prokaryotic genomes and noisy matured eukaryotic sequences

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4008361

AMIGene: Annotation of MIcrobial Genes

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4008361

Occurrence of a putative ancient-like isomerase involved in histidine and tryptophan biosynthesis

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4008361

InterProScan--an integration platform for the signature-recognition methods in InterPro

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4008361

Trypsin-like protease of Streptomyces exfoliatus SMF13, a potential agent in mycelial differentiation

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4008361

GenePRIMP: a gene prediction improvement pipeline for prokaryotic genomes

28 July 2018

1 reference

https://api.crossref.org/works/10.1186%2F1471-2164-14-699

Thoughts and facts about antibiotics: where we are now and where we are heading

21 January 2018

1 reference

https://api.crossref.org/works/10.1186%2F1471-2164-14-699

Complete genome sequence of the erythromycin-producing bacterium Saccharopolyspora erythraea NRRL23338.

21 January 2018

1 reference

https://api.crossref.org/works/10.1186%2F1471-2164-14-699

The endonuclease activity of RNase III is required for the regulation of antibiotic production by Streptomyces coelicolor

21 January 2018

1 reference

https://api.crossref.org/works/10.1186%2F1471-2164-14-699

The Paragon Algorithm, a next generation search engine that uses sequence temperature values and feature probabilities to identify peptides from tandem mass spectra.

21 January 2018

1 reference

https://api.crossref.org/works/10.1186%2F1471-2164-14-699

Ortho-proteogenomics: multiple proteomes investigation through orthology and a new MS-based protocol.

21 January 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4008361

Phosphoproteome analysis of E. coli reveals evolutionary conservation of bacterial Ser/Thr/Tyr phosphorylation

31 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4008361

InterProScan: protein domains identifier

31 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4008361

31 October 2018

Identifiers

DOI

10.1186/1471-2164-14-699

1 reference

Dimensions Publication ID

28 July 2017

1 reference

https://scigraph.springernature.com/pub.10.1186/1471-2164-14-699

9 September 2019

1 reference

28 July 2017

1 reference