Jay Moore

About Jay Moore:

Systems Biologist specialising in data integration, high-throughput sequence analysis, and evolutionary and comparative analyses.

SEEK ID: https://fairdomhub.org/people/175

Location: United Kingdom

Expertise: Comparative Genomics, Data integration, Database and data warehouse design, High-throughput sequence analysis, Phylogenetics, Systems Biology, Software Engineering, Bioinformatics

Tools: EnsEMBL, BioMart, HTML, XML, R, Perl, Databases, SBML

ORCID: Not specified

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Project positions

Other Projects: STREAM (University of Warwick)

Related items

STREAM

Global metabolic switching in Streptomyces coelicolor

Antibiotics are made during the second phase of growth when there is a transition in metabolism from primary to secondary metabolism. Primary metabolism is growth related and involves all the normal cellular activities associated with cell growth and division. Whereas secondary metabolism is non-growth linked and is non-essential but many important activities occur during this phase which help the bacterium survive.

Programme: SysMO

Public web page: Not specified

Organisms: Streptomyces coelicolor

University of Warwick

Country: United Kingdom

City: Not specified

Web page: Not specified

Metabolism of Streptomyces coelicolor (SysMO STREAM)

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One of these activities is antibiotic production and is widespread in streptomycetes
...

Snapshots: No snapshots

Studies: ScoCyc metabolic pathway curation, Timeseries 1

Assays: Metabolic pathway curation, Online/offline measurements, metabolomics, proteomics, transcriptomics

Created: 26th May 2010 at 15:44, Last updated: 3rd Dec 2016 at 22:28

ScoCyc metabolic pathway curation

STREAM, SYSTERACT

No description specified

Person responsible: Jay Moore

Snapshots: No snapshots

Investigation: Metabolism of Streptomyces coelicolor (SysMO ST...

Assays: Metabolic pathway curation

Created: 4th Nov 2010 at 15:30, Last updated: 2nd Nov 2016 at 09:38

Timeseries 1

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Genotype: Wildtype (M145E)
Medium: Phosphate-limited (F134)

Person responsible: Jay Moore

Snapshots: No snapshots

Investigation: Metabolism of Streptomyces coelicolor (SysMO ST...

Assays: Online/offline measurements, metabolomics, proteomics, transcriptomics

Created: 26th May 2010 at 15:47, Last updated: 2nd Nov 2016 at 09:38

metabolomics

STREAM, SYSTERACT

No description specified

Contributor: Jay Moore

Assay type: Metabolite Profiling

Technology type: Gas Chromatography Mass Spectrometry

Snapshots: No snapshots

Investigation: Metabolism of Streptomyces coelicolor (SysMO ST...

Study: Timeseries 1

Organisms: Streptomyces coelicolor : M145 (wild-type / wild-type) (batch)

SOPs: MCF derivatization, Metabolome extraction, Spore batch generation

Data files: 1 hidden item

Created: 4th Nov 2010 at 14:50, Last updated: 8th Nov 2017 at 15:21

proteomics

STREAM, SYSTERACT

No description specified

Contributor: Jay Moore

Assay type: Proteomics

Technology type: Gas Chromatography Mass Spectrometry

Snapshots: No snapshots

Investigation: Metabolism of Streptomyces coelicolor (SysMO ST...

Study: Timeseries 1

Organisms: Streptomyces coelicolor : M145 (wild-type / wild-type) (batch)

SOPs: No SOPs

Data files: 2 hidden items

Created: 4th Nov 2010 at 14:53, Last updated: 8th Nov 2017 at 15:21

Online/offline measurements

STREAM, SYSTERACT

No description specified

Contributor: Jay Moore

Assay type: Experimental Assay Type

Technology type: Technology Type

Snapshots: No snapshots

Investigation: Metabolism of Streptomyces coelicolor (SysMO ST...

Study: Timeseries 1

Organisms: Streptomyces coelicolor : M145 (wild-type / wild-type) (batch)

SOPs: Cell dry weight (CDW) determination of Streptom..., Contamination test of Streptomyces coelicolor c..., Generation of cell material from Streptomyces c..., Generation of cell material from Streptomyces c..., Generation of cell material from Streptomyces c..., Preparation of inoculum for Streptomyces coelic..., Sampling from Streptomyces coelicolor culture f... and 1 hidden item

Data files: Fermentor 199 cultivation data

Created: 26th May 2010 at 15:59, Last updated: 8th Nov 2017 at 15:21

transcriptomics

STREAM, SYSTERACT

No description specified

Contributor: Jay Moore

Assay type: Transcriptomics

Technology type: Custom Array

Snapshots: No snapshots

Investigation: Metabolism of Streptomyces coelicolor (SysMO ST...

Study: Timeseries 1

Organisms: Streptomyces coelicolor : M145 (wild-type / wild-type) (batch)

SOPs: No SOPs

Data files: Fermentor 199 transcriptomics

Created: 26th May 2010 at 16:23, Last updated: 8th Nov 2017 at 15:21

Metabolic pathway curation

STREAM, SYSTERACT

No description specified

Contributor: Jay Moore

Biological problem addressed: Metabolic Network

Snapshots: No snapshots

Investigation: Metabolism of Streptomyces coelicolor (SysMO ST...

Study: ScoCyc metabolic pathway curation

Organisms: Streptomyces coelicolor : M145 (wild-type / wild-type)

Models: 1 hidden item

SOPs: No SOPs

Data files: No Data files

Created: 4th Nov 2010 at 15:34, Last updated: 8th Nov 2017 at 15:21

A3(2)

Contributor: Jay Moore

Provider Name: Not specified

Provider's strain ID: Not specified

Organism: Streptomyces coelicolor

Genotypes: wild-type

Phenotypes: wild-type

Comment: Not specified

Created: 28th Apr 2010 at 18:21, Last updated: 19th Oct 2012 at 17:57

M145

Contributor: Jay Moore

Provider Name: Not specified

Provider's strain ID: Not specified

Organism: Streptomyces coelicolor

Genotypes: wild-type

Phenotypes: wild-type

Comment: Not specified

Created: 28th Apr 2010 at 18:21, Last updated: 19th Oct 2012 at 17:57

Fermentor 199 cultivation data

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No description specified

Creators: Trond Ellingsen, Øyvind Jakobsen, Per Bruheim, Håvard Sletta, Anders Øverby, Sven Even Borgos, Sunniva Hoel, Alexander Wentzel

Contributor: Jay Moore

Investigations: Metabolism of Streptomyces coelicolor (SysMO ST...

Studies: Timeseries 1

Assays: Online/offline measurements

Created: 4th Nov 2010 at 14:41, Last updated: 5th Dec 2016 at 13:21

Fermentor 199 transcriptomics

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No description specified

Investigations: Metabolism of Streptomyces coelicolor (SysMO ST...

Studies: Timeseries 1

Assays: transcriptomics

Download

Created: 4th Nov 2010 at 14:35, Last updated: 3rd Dec 2016 at 20:37

ScoCyc 14.5 release bundle

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No description specified

Creators: Jay Moore, David Hodgson

Contributor: Jay Moore

Investigations: No Investigations

Studies: No Studies

Assays: No Assays

Download

Created: 15th Nov 2010 at 15:41, Last updated: 15th Nov 2010 at 15:42

ScoCyc 14.6 release bundle

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No description specified

Creators: Jay Moore, David Hodgson

Contributor: Jay Moore

Investigations: No Investigations

Studies: No Studies

Assays: No Assays

Download

Created: 15th Nov 2010 at 15:40, Last updated: 15th Nov 2010 at 15:40

4 hidden items

ScoCyc 14.5 release bundle

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No description specified

Creators: Jay Moore, David Hodgson, Veronica Armendarez, Emma Laing , Govind Chandra, Mervyn Bibb

Contributor: Jay Moore

Model type: Metabolic network

Model format: BioPAX

Environment: Not specified

Organism: Streptomyces coelicolor

Investigations: No Investigations

Studies: No Studies

Modelling analyses: No Modelling analyses

Created: 15th Nov 2010 at 15:43, Last updated: 15th Nov 2010 at 15:49

1 hidden item

Spore batch generation

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No description specified

Creators: Trond Ellingsen, Øyvind Jakobsen, Per Bruheim, Håvard Sletta, Anders Øverby, Sven Even Borgos, Sunniva Hoel, Alexander Wentzel

Contributor: Jay Moore

Investigations: Metabolism of Streptomyces coelicolor (SysMO ST... and 1 hidden item

Studies: Timeseries 1 and 2 hidden items

Assays: metabolomics and 2 hidden items

Download

Created: 4th Nov 2010 at 15:10, Last updated: 4th Nov 2010 at 15:11

Metabolome extraction

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No description specified

Creators: Trond Ellingsen, Øyvind Jakobsen, Per Bruheim, Håvard Sletta, Anders Øverby, Sven Even Borgos, Sunniva Hoel, Alexander Wentzel

Contributor: Jay Moore

Investigations: Metabolism of Streptomyces coelicolor (SysMO ST...

Studies: Timeseries 1

Assays: metabolomics

Download

Created: 4th Nov 2010 at 15:10

MCF derivatization

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No description specified

Creators: Trond Ellingsen, Øyvind Jakobsen, Per Bruheim, Håvard Sletta, Anders Øverby, Sven Even Borgos, Sunniva Hoel, Alexander Wentzel

Contributor: Jay Moore

Investigations: Metabolism of Streptomyces coelicolor (SysMO ST...

Studies: Timeseries 1

Assays: metabolomics

Created: 4th Nov 2010 at 15:08

Proteomic Analysis of the Streptomyces coelicolor Proteome

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No description specified

Creators: Louise Thomas, Maggie Smith

Contributor: Jay Moore

Investigations: No Investigations

Studies: No Studies

Assays: No Assays

Download

Created: 26th May 2010 at 17:30

Total DNA Quantification

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No description specified

Creators: Louise Thomas, Maggie Smith

Contributor: Jay Moore

Investigations: No Investigations

Studies: No Studies

Assays: No Assays

Download

Created: 26th May 2010 at 17:29

Total RNA Quantification

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No description specified

Creators: Louise Thomas, Maggie Smith

Contributor: Jay Moore

Investigations: No Investigations

Studies: No Studies

Assays: No Assays

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Created: 26th May 2010 at 17:29

Total Protein Quantification

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No description specified

Creators: Louise Thomas, Maggie Smith

Contributor: Jay Moore

Investigations: No Investigations

Studies: No Studies

Assays: No Assays

Download

Created: 26th May 2010 at 17:28

Processing Streptomyces coelicolor cell pellets

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No description specified

Creators: Louise Thomas, Maggie Smith

Contributor: Jay Moore

Investigations: No Investigations

Studies: No Studies

Assays: No Assays

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Created: 26th May 2010 at 17:27

Contamination test of Streptomyces coelicolor culture

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No description specified

Creators: Per Bruheim, Trond Ellingsen, Sunniva Hoel, Øyvind Jakobsen, Håvard Sletta, Alexander Wentzel, Anders Øverby, Strøm, A

Contributor: Jay Moore

Investigations: Metabolism of Streptomyces coelicolor (SysMO ST... and 1 hidden item

Studies: Timeseries 1 and 8 hidden items

Assays: Online/offline measurements and 8 hidden items

Download

Created: 26th May 2010 at 17:24, Last updated: 26th May 2010 at 17:24

Generation of cell material from Streptomyces coelicolor culture for metabolome analysis

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No description specified

Creators: Per Bruheim, Trond Ellingsen, Sunniva Hoel, Øyvind Jakobsen, Håvard Sletta, Alexander Wentzel, Anders Øverby, Strøm, A

Contributor: Jay Moore

Investigations: Metabolism of Streptomyces coelicolor (SysMO ST... and 1 hidden item

Studies: Timeseries 1 and 8 hidden items

Assays: Online/offline measurements and 8 hidden items

Download

Created: 26th May 2010 at 17:23

View all 15 items

1 hidden item

An approach to pathway reconstruction using whole genome metabolic models and sensitive sequence searching

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Abstract (Expand)

Metabolic models have the potential to impact on genome annotation and on the interpretation of gene expression and other high throughput genome data. The genome of Streptomyces coelicolor genome has ...

Authors: David Hodgson, David Wild, Saqi Mansoor,Dobson Richard J B,Kraben Preben

Date Published: 13th Nov 2008

Journal: J Integr Bioinform

PubMed ID: 20134075

Citation:

Created: 27th May 2010 at 18:59

Increasing the mass accuracy of high-resolution LC-MS data using background ions: a case study on the LTQ-Orbitrap

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With the advent of a new generation of high-resolution mass spectrometers, the fields of proteomics and metabolomics have gained powerful new tools. In this paper, we demonstrate a novel computational ...

Authors: R Jansen, Rainer Breitling, Scheltema Richard A,Kamleh Anas,Wildridge David,Ebikeme Charles,Watson David G,Barrett Michael P

Date Published: 22nd Oct 2008

Journal: Proteomics

PubMed ID: 18937253

Citation:

Created: 26th May 2010 at 17:08

Probabilistic assignment of formulas to mass peaks in metabolomics experiments

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MOTIVATION: High-accuracy mass spectrometry is a popular technology for high-throughput measurements of cellular metabolites (metabolomics). One of the major challenges is the correct identification ...

Authors: Rainer Breitling, Rogers Simon,Scheltema Richard A,Girolami Mark

Date Published: 18th Dec 2008

Journal: Bioinformatics

PubMed ID: 19095699

Citation:

Created: 26th May 2010 at 17:08

MetaNetter: inference and visualization of high-resolution metabolomic networks

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SUMMARY: We present a Cytoscape plugin for the inference and visualization of networks from high-resolution mass spectrometry metabolomic data. The software also provides access to basic topological ...

Authors: Rainer Breitling, Jourdan Fabien,Barrett Michael P,Gilbert David

Date Published: 14th Nov 2007

Journal: Bioinformatics

PubMed ID: 18003642

Citation:

Created: 26th May 2010 at 16:44

New surveyor tools for charting microbial metabolic maps

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Abstract (Expand)

The computational reconstruction and analysis of cellular models of microbial metabolism is one of the great success stories of systems biology. The extent and quality of metabolic network reconstructions ...

Authors: Rainer Breitling, Vitkup Dennis,Barrett Michael P

Date Published: 21st Nov 2007

Journal: Nat. Rev. Microbiol.

PubMed ID: 18026122

Citation:

Created: 26th May 2010 at 16:43

Chapter 6. Regulation of antibiotic production by bacterial hormones

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Abstract (Expand)

Antibiotic production is regulated by numerous signals, including the so-called bacterial hormones found in antibiotic producing organisms such as Streptomyces. These signals, the gamma-butyrolactones, ...

Authors: Eriko Takano, Hsiao Nai-Hua,Gottelt Marco

Date Published: 21st Apr 2009

Journal: Meth. Enzymol.

PubMed ID: 19374982

Citation:

Created: 26th May 2010 at 16:42

A bistable gene switch for antibiotic biosynthesis: the butyrolactone regulon in Streptomyces coelicolor

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Abstract (Expand)

Many microorganisms, including bacteria of the class Streptomycetes, produce various secondary metabolites including antibiotics to gain a competitive advantage in their natural habitat. The production ...

Authors: Eriko Takano, Mehra Sarika,Charaniya Salim,Hu Wei-Shou

Date Published: 2nd May 2008

Journal: PLoS ONE

PubMed ID: 18628968

Citation:

Created: 26th May 2010 at 15:26

The dynamic architecture of the metabolic switch in Streptomyces coelicolor

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Abstract (Expand)

BACKGROUND: During the lifetime of a fermenter culture, the soil bacterium S. coelicolor undergoes a major metabolic switch from exponential growth to antibiotic production. We have studied gene ...

Authors: Kay Nieselt, Per Bruheim, Alexander Wentzel, Øyvind Jakobsen, Håvard Sletta, M. Tauqeer Alam, Maria Elena Merlo, Jay Moore, Walid Omara, Antonio Rodríguez-García, Louise Thomas, Roxane Legaie, William Gaze, Gregory Challis, R Jansen, Lubbert Dijkhuizen, David Rand, David Wild, Jens Reuther, Wolfgang Wohlleben, Maggie Smith, Nigel Burroughs, Juan-Francisco Martin, David Hodgson, Eriko Takano, Rainer Breitling, Trond Ellingsen, Elizabeth Wellington, Battke Florian,Herbig Alexander,Morrissey Edward R,Juarez-Hermosillo Miguel A,Nentwich Merle,Iqbal Mudassar,Bonin Michael

Date Published: 28th May 2009

Journal: BMC Genomics

PubMed ID: 20053288

Citation:

Created: 26th May 2010 at 15:21

Metabolic modeling and analysis of the metabolic switch in Streptomyces coelicolor

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Abstract (Expand)

Background The transition from exponential to stationary phase in Streptomyces coelicolor is accompanied by a major metabolic switch and results in a strong activation of secondary metabolism. Here we ...

Authors: M. Tauqeer Alam, Maria Elena Merlo, David Hodgson, Elizabeth Wellington, Eriko Takano, Rainer Breitling, (stream) The STREAM Consortium

Date Published: 2010

Journal: BMC Genomics

DOI: 10.1186/1471-2164-11-202

Citation:

Created: 26th May 2010 at 15:17, Last updated: 26th May 2010 at 15:18