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- Katy Wolstencroft
I am a Research Fellow at the University of Manchester, working in Bioinformatics and Computer Science. I am also a guest researcher at the Vrije Universiteit.My research interests include scientific workflows, semantic discovery, and applying ontology technologies to biological data
SEEK ID: https://demo.fairdomhub.org/people/132
Locations:
Netherlands
,
United Kingdom
Expertise: Biochemistry, Bioinformatics, Data Management
Tools: Data Management, Transcriptomics, Databases, Workflows, Web services, Taverna, Ontologies
ORCID: Not specified
Related items
- Projects (2)
- Institutions (2)
- Investigations (4)
- Studies (4+2)
- Assays (9+1)
- Data files (6+2)
- Models (2)
- SOPs (1+2)
- Publications (9)
- Presentations (1+1)
The main objectives of SysMO-DB are to: facilitate the web-based exchange of data between research groups within- and inter- consortia, and to provide an integrated platform for the dissemination of the results of the SysMO projects to the scientific community. We aim to devise a progressive and scalable solution to the data management needs of the SysMO initiative, that:
* facilitates and maximises the potential for data exchange between SysMO research groups;
* maximises the ‘shelf life’ and
...
Programme: SysMO
Public web page: http://www.sysmo-db.org/
Organisms: Saccharomyces cerevisiae, Lactic Acid Bacteria
Silicon cell model for the central carbohydrate metabolism of the archaeon Sulfolobus solfataricus under temperature variation
Programme: SysMO
Public web page: http://sulfosys.com/
Organisms: Sulfolobus solfataricus
Cell growth underlies many key cellular and developmental processes, yet a limited number of studies have been carried out on cell-growth regulation. Comprehensive studies at the transcriptional, proteomic and metabolic levels under defined controlled conditions are currently lacking.
This investigation shows public data taken from the BioInvestigation Index. (http://www.ebi.ac.uk/bioinvindex/study.seam?studyId=BII-S-1)
Organism: Saccharomyces Cerevisiae
Snapshots: Snapshot 1
Studies: A time course analysis of transcription response in yeast treated with ..., Can yeast glycolysis be understood in terms of in vitro kinetics of the ...
Assays: Changes in flux on the metabolome, Changes in flux on the proteome, Changes in flux on the transcriptome, Glycolysis in Saccharomyces cerevisiae, Time course analysis of transcription
Scales: Not specified
This Investigation was performed by SySMO DB team together with PALS in order to crete methods and best practices for capturing experimental data.
Snapshots: No snapshots
Studies: No Studies
Assays: Computer Practicals "Data management in practice" Advanced Lecture Cours..., Transcriptional profiling
Scales: Not specified
An investigation into the control mechanisms of glycolytic flux in Lactococcus lactis.
This investigation represents the data and models published by Hoefnagel et al in JWS Online and in M.H.N. Hoefnagel, J. Hugenholtz and J.L. SnoepMol. Biol. Reports 29, 157-161 (2002)
Snapshots: No snapshots
Scales: Not specified
Glycerol, a major by-product of ethanol fermentation by Saccharomyces cerevisiae, is of significant importance to the wine, beer, and ethanol production industries. This investigation aims to gain a clearer understanding of and to quantify the extent to which parameters of the pathway affect glycerol flux in S. cerevisiae.
This investigation represents the data and models submitted to JWS online by Cronwright et al
(http://jjj.biochem.sun.ac.za/cgi-bin/getMoreInfo.py?modeldir=cronwright) and
...
Snapshots: No snapshots
Scales: Not specified
Comprehensive high-throughput analyses at the levels of mRNAs, proteins, and metabolites, and studies on gene expression patterns are required for systems biology studies of cell growth [4,26-29]. Although such comprehensive data sets are lacking, many studies have pointed to a central role for the target-of-rapamycin (TOR) signal transduction pathway in growth control. TOR is a serine/threonine kinase that has been conserved from yeasts to mammals; it integrates signals from nutrients or growth
...
Person responsible: Katy Wolstencroft
Snapshots: No snapshots
Investigation: Growth control of the eukaryote cell: a systems...
Scales: Not specified
This study examines whether the in vivo behavior of yeast glycolysis can be understood in terms of the in vitro kinetic properties of the constituent enzymes.
Person responsible: Jacky Snoep
Snapshots: No snapshots
Investigation: Growth control of the eukaryote cell: a systems...
Scales: Not specified
A study which combines mathematical modelling and experimental measurements to determine the effects of redox charge on glycolytic flux
Person responsible: Jacky Snoep
Snapshots: No snapshots
Scales: Not specified
This is a study of the glycerol synthesis pathway, using model predictions and experimental measurements
Person responsible: Katy Wolstencroft
Snapshots: No snapshots
Scales: Not specified
Assay to measure gene expression of Saccharomyces cerevisiae (yeast) under different nutrient limitations
Limiting Nutrients:
ethanol, nitrogen, glucose, phosphorus, carbon, sulfur, sulphur
This data is public data taken from the BioInvestigation Index.
(http://www.ebi.ac.uk/bioinvindex/study.seam?studyId=BII-S-1)
Submitter: Katy Wolstencroft
Assay type: Transcriptional Profiling
Technology type: Microarray
Snapshots: No snapshots
Investigation: Growth control of the eukaryote cell: a systems...
Study: 1 hidden item
Organisms: Saccharomyces cerevisiae
SOPs: 1 hidden item
Data files: a_transcriptome from BII-S-1
Scales: Not specified
Assay to measure metabolites of yeast saccharomyces cerevisiae under different nutrient limitations
Limiting Nutrients:
ethanol, nitrogen, glucose, phosphorus, carbon, sulfur, sulphur
This data is public data taken from the BioInvestigation Index. (http://www.ebi.ac.uk/bioinvindex/study.seam?studyId=BII-S-1)
Submitter: Katy Wolstencroft
Assay type: Metabolite Profiling
Technology type: Mass Spectrometry
Snapshots: No snapshots
Investigation: Growth control of the eukaryote cell: a systems...
Study: 1 hidden item
Organisms: Saccharomyces cerevisiae
SOPs: No SOPs
Data files: a_metabolome_BII-S-1
Scales: Not specified
Assay to measure protein expression in yeast saccharomyces cerevisiae under different nutrient limitations
Limiting Nutrients:
ethanol, nitrogen, glucose, phosphorus, carbon, sulfur, sulphur
This data is public data taken from the BioInvestigation Index. (http://www.ebi.ac.uk/bioinvindex/study.seam?studyId=BII-S-1)
Submitter: Katy Wolstencroft
Assay type: Protein Expression Profiling
Technology type: Mass Spectrometry
Snapshots: No snapshots
Investigation: Growth control of the eukaryote cell: a systems...
Study: 1 hidden item
Organisms: Saccharomyces cerevisiae
SOPs: No SOPs
Data files: a_proteome from BII-S-1
Scales: Not specified
Assay for transcriptional profiling time course in yeast treated with rapamycin
This is public data from the BioInvestigation Index (http://www.ebi.ac.uk/bioinvindex/study.seam?studyId=BII-S-2)
Submitter: Katy Wolstencroft
Assay type: Transcriptional Profiling
Technology type: Microarray
Snapshots: No snapshots
Investigation: Growth control of the eukaryote cell: a systems...
Study: A time course analysis of transcription respon...
Organisms: Saccharomyces cerevisiae
SOPs: Nutrient_limited_stationary
Data files: a_microarray from BII-S-2
Scales: Not specified
Investigation: Glycolitic Flux in Lactococcus lactis
Study: The effects of Redox Charge on Glycolytic Flux
Organisms: Escherichia coli
SOPs: No SOPs
Data files: No Data files
Scales: Not specified
Creator: Jacky Snoep
Submitter: Katy Wolstencroft
Investigations: Glycolitic Flux in Lactococcus lactis
Scales: Not specified
Intracellular metabolite measurements used for validation of the gycerol synthesis pathway model
Creator: Jacky Snoep
Submitter: Katy Wolstencroft
Investigations: Glycerol Synthesis in Saccharomyces cerevisiae
Studies: Glycerol Synthesis Pathway
Assays: Glycerol Synthesis Model construction, Intracellular Metabolites
Scales: Not specified
Results of transcriptional profile in Saccharomyces cerevisiae after rapamycin treatment
Creator: Katy Wolstencroft
Submitter: Katy Wolstencroft
Investigations: Growth control of the eukaryote cell: a systems...
Scales: Not specified
Results of proteomics profile in Saccharomyces cerevisiae under different experimental conditions
Creator: Katy Wolstencroft
Submitter: Katy Wolstencroft
Investigations: Growth control of the eukaryote cell: a systems...
Studies: 1 hidden item
Assays: Changes in flux on the proteome
Scales: Not specified
results of metabolic profiling of Saccharomyces cerevisiae in different conditions
Creator: Katy Wolstencroft
Submitter: Katy Wolstencroft
Investigations: Growth control of the eukaryote cell: a systems...
Studies: 1 hidden item
Scales: Not specified
Detailed kinetic model for glycolysis of L. lactis. The model is basically the same model as that published by Hoefnagel et al 2002 (Mol. Biol. Reports 29, 157-161). The change made to the model is to make external glucose a variable such that a glucose pulse can be simulated.
Creators: Jacky Snoep, Ana Rute Neves
Submitter: Katy Wolstencroft
Model type: Ordinary differential equations (ODE)
Model format: SBML
Environment: Not specified
Organism: Lactococcus lactis
Investigations: Glycolitic Flux in Lactococcus lactis
Studies: The effects of Redox Charge on Glycolytic Flux
Modelling analyses: Time dependent responses of glycolytic intermed...
Scales: Not specified
MCA of Glycerol Synthesis in Saccharomyces cerevisiae
Creators: Jacky Snoep, Garth R. Cronwright, Johann M. Rohwer, and Bernard A. Prior
Submitter: Katy Wolstencroft
Model type: Ordinary differential equations (ODE)
Model format: SBML
Environment: Not specified
Organism: Saccharomyces cerevisiae
Investigations: Glycerol Synthesis in Saccharomyces cerevisiae
Studies: Glycerol Synthesis Pathway
Modelling analyses: Glycerol Synthesis Model construction
Scales: Not specified
A stationary-phase culture (10ml) was used to inoculate the fermenter vessel.
Taken from ArrayExpress:
http://www.ebi.ac.uk/microarray-as/ae/browse.html?keywords=E-MEXP-115
Creator: Katy Wolstencroft
Submitter: Katy Wolstencroft
Investigations: Growth control of the eukaryote cell: a systems...
Scales: Not specified
Abstract (Expand)
Authors: Firstname Lastname, Jannis Uhlendorf, Timo Lubitz, Marvin Schulz, Edda Klipp, Wolfram Liebermeister
Date Published: 17th Nov 2009
Publication Type: Not specified
PubMed ID: 19933161
Citation:
Scales: Not specified
Abstract (Expand)
Authors: Kay Nieselt, Florian Battke, Alexander Herbig, Per Bruheim, Alexander Wentzel, Øyvind M Jakobsen, Håvard Sletta, Mohammad T Alam, Maria E Merlo, Firstname Lastname, Firstname Lastname, Edward R Morrissey, Miguel A Juarez-Hermosillo, Antonio Rodríguez-García, Merle Nentwich, Louise Thomas, Mudassar Iqbal, Roxane Legaie, William H Gaze, Gregory L Challis, Ritsert C Jansen, Lubbert Dijkhuizen, David A Rand, David L Wild, Michael Bonin, Jens Reuther, Wolfgang Wohlleben, Margaret C M Smith, Nigel J Burroughs, Juan F Martín, David A Hodgson, Eriko Takano, Rainer Breitling, Trond E Ellingsen, Elizabeth M H Wellington
Date Published: 28th May 2009
Publication Type: Not specified
PubMed ID: 20053288
Citation:
Scales: Not specified
Abstract (Expand)
Authors: Damian Smedley, Morris A Swertz, Firstname Lastname, Glenn Proctor, Michael Zouberakis, Jonathan Bard, John M Hancock, Paul Schofield
Date Published: 30th Dec 2008
Publication Type: Not specified
PubMed ID: 19112082
Citation:
Scales: Not specified
Abstract (Expand)
Authors: Firstname Lastname, Martin Golebiewski, Renate Kania, Firstname Lastname, Saqib Mir, Andreas Weidemann, Ulrike Wittig
Date Published: 14th Sep 2007
Publication Type: Not specified
PubMed ID: 17822389
Citation:
Scales: Not specified

Abstract (Expand)
Authors: Paul Fisher, Cornelia Hedeler, Firstname Lastname, Helen Hulme, Harry Noyes, Stephen Kemp, Robert Stevens, Andrew Brass
Date Published: 20th Aug 2007
Publication Type: Not specified
PubMed ID: 17709344
Citation:
Scales: Not specified
Creator: Katy Wolstencroft
Submitter: Katy Wolstencroft
Scales: Not specified