SEEK ID: https://fairdomhub.org/people/853
Location:
Norway
ORCID:
https://orcid.org/0000-0003-4054-9842
Joined: 2nd Feb 2017
Expertise: Not specified
Tools: Not specified
Related items
- Programmes (1)
- Projects (1)
- Institutions (1)
- Investigations (0+1)
- Studies (2+2)
- Assays (4+4)
- Data files (3+2)
- Models (3)
- Publications (5)
- Documents (1)
The goal of the dCod-project is to combine the competencies in environmental toxicology, biology, bioinformatics and mathematics across the traditional department boundaries, to create a deeper understanding of cods' adaptations and reactions to stressors in the environment. Building on the thoroughly studies and mapping of the cod genome at UiO and the long research traditions on cod at the Department of Biology at UiB, the dCod project will expand our knowledge with methods based on genomics; ...
Projects: Systems toxicology of Atlantic cod
Web page: http://dcod.no
Coastal zones and oceans constitute an essential fundament for Norway’s history as well as current economy, providing ecosystem services for fisheries, aquaculture, transport, tourism, and recreation. The petroleum activities in Norwegian waters have been crucial for Norway’s financial growth and in financing the Norwegian welfare state. As the pressure on the oceans continuously increases, both the petroleum industry and the seafood industries have acknowledged that awareness and actions are ...
Programme: dCod 1.0: decoding systems toxicology of cod
Public web page: http://www.uib.no/en/dcod
Organisms: Gadus morhua
Interspecies differences in sensitivity to chemical exposures pose a great challenge in toxicological risk assessments. How an organism copes with chemicals is largely determined by the genes and proteins that collectively function to defend against, detoxify and eliminate chemical stressors. This integrative network includes receptors and transcription factors, biotransformation enzymes, transporters, antioxidants, and metal- and heat-responsive genes, and is collectively known as the chemical ...
Submitter: Sofie Söderström
Investigation: 1 hidden item
Assays: Chemical defensome genes for five fish species, Exposure response of defensome genes, Expression of defensome genes in early development of fish
Snapshots: Snapshot 1
Snapshots: No snapshots
Submitter: Xiaokang Zhang
Biological problem addressed: Metabolic Network
Investigation: 1 hidden item
Study: 1 hidden item
Organisms: Gadus morhua
Models: Draft metabolic reconstruction model of Atlanti..., Draft metabolic reconstruction model of Atlanti..., Draft metabolic reconstruction model of Atlanti...
SOPs: No SOPs
Data files: Draft metabolic reconstruction model of Atlanti..., Draft metabolic reconstruction model of Atlanti..., Draft metabolic reconstruction model of Atlanti..., Visualization of gap filling of subsystem "Meta...
Snapshots: Snapshot 1, Snapshot 2
Build the chemical defensome gene list for 5 fish: Zebrafish (Danio rerio), Atlantic cod (Gadus morhua), medaka (Oryzias latipes), Atlantic killifish (Fundulus heteroclitus) and stickleback (Gasterosteus aculeatus). Source code and relevant files can be found on GitHub: https://github.com/zhxiaokang/fishDefensome/tree/main/defensomeGenes
Submitter: Xiaokang Zhang
Biological problem addressed: Stress response/Adaptation
Investigation: 1 hidden item
Organisms: No organisms
Models: No Models
SOPs: No SOPs
Data files: Chemical defensome genes overview for five fish, Chemical defensome relevant Pfam accession list, Gene pattern to filter defensome relevant genes
Snapshots: No snapshots
To study the defensome genes' expression in early developmental stages of zebrafish and stickleback. Souce code and relevant files can be found on GitHub: https://github.com/zhxiaokang/fishDefensome/tree/main/developmentalStages
Submitter: Xiaokang Zhang
Biological problem addressed: Stress response/Adaptation
Investigation: 1 hidden item
Organisms: No organisms
Models: No Models
SOPs: No SOPs
Data files: Defensome gene expression in early develepmenta..., Defensome gene expression in early develepmenta..., Gene lists for clusters in developmental stages..., Gene lists for clusters in developmental stages...
Snapshots: Snapshot 1, Snapshot 2
Exposing zebrafish to benzo(a)pyrene (B(a)P) (gene counts from NCBI GEO: GSE64198, previously published by Fang, et al. 2015. Souce code and relevant files can be found on GitHub: https://github.com/zhxiaokang/fishDefensome/tree/main/exposureResponse
Submitter: Xiaokang Zhang
Biological problem addressed: Stress response/Adaptation
Investigation: 1 hidden item
Organisms: No organisms
Models: No Models
SOPs: No SOPs
Data files: Exposure response on defensome genes in zebrafi...
Snapshots: No snapshots
Creators: Xiaokang Zhang, Marta Eide, Odd André Karlsen, Inge Jonassen, Anders Goksøyr, Jared V. Goldstone; John Stegeman
Submitter: Xiaokang Zhang
Investigations: 1 hidden item
Studies: The chemical defensome of fish
There are four datasheets in the Excel file: 1. Gene pattern and the corresponding category (the gene list is then divided into the other three datasheets); 2. These gene names (patterns) can be directly followed by either a letter or a number; 3. These gene names (patterns) should be directly followed by a letter; 4. These gene names (patterns) should be directly followed by a number.
Creators: Xiaokang Zhang, Marta Eide, Odd André Karlsen, Inge Jonassen, Anders Goksøyr, Jared V. Goldstone; John Stegeman
Submitter: Xiaokang Zhang
Investigations: 1 hidden item
Studies: The chemical defensome of fish
Creators: Xiaokang Zhang, Marta Eide, Odd André Karlsen, Inge Jonassen, Anders Goksøyr, Jared V. Goldstone; John Stegeman
Submitter: Xiaokang Zhang
Investigations: 1 hidden item
Studies: The chemical defensome of fish
This is an auto-generated model with COBRA Matlab toolbox. This model was deposited in BioModels [1] and assigned the identifier MODEL2010090003.
[1] Malik-Sheriff et al. BioModels — 15 years of sharing computational models in life science. Nucleic Acids Research. 2020 Jan, 48(D1):D407–415
Creators: Xiaokang Zhang, Eileen Marie Hanna, Marta Eide, Shirin Fallahi, Fekadu Yadetie, Anders Goksøyr, Inge Jonassen, Tomasz Furmanek; Daniel Craig Zielinski
Submitter: Xiaokang Zhang
Model type: Metabolic network
Model format: SBML
Environment: Matlab
This is an auto-generated model with COBRA Matlab toolbox. This model was deposited in BioModels [1] and assigned the identifier MODEL2010090002.
[1] Malik-Sheriff et al. BioModels — 15 years of sharing computational models in life science. Nucleic Acids Research. 2020 Jan, 48(D1):D407–415
Creators: Xiaokang Zhang, Eileen Marie Hanna, Marta Eide, Shirin Fallahi, Fekadu Yadetie, Anders Goksøyr, Inge Jonassen, Tomasz Furmanek; Daniel Craig Zielinski
Submitter: Xiaokang Zhang
Model type: Metabolic network
Model format: SBML
Environment: Matlab
This is an auto-generated model with COBRA Matlab toolbox. This model was deposited in BioModels [1] and assigned the identifier MODEL2010090001.
[1] Malik-Sheriff et al. BioModels — 15 years of sharing computational models in life science. Nucleic Acids Research. 2020 Jan, 48(D1):D407–415
Creators: Xiaokang Zhang, Eileen Marie Hanna, Marta Eide, Shirin Fallahi, Fekadu Yadetie, Anders Goksøyr, Inge Jonassen, Tomasz Furmanek; Daniel Craig Zielinski
Submitter: Xiaokang Zhang
Model type: Metabolic network
Model format: SBML
Environment: Matlab
Abstract (Expand)
Authors: Marta Eide, Xiaokang Zhang, Odd André Karlsen, Jared V. Goldstone, John Stegeman, Inge Jonassen, Anders Goksøyr
Date Published: 1st Dec 2021
Publication Type: Journal
DOI: 10.1038/s41598-021-89948-0
Citation: Sci Rep 11(1),10546
Abstract (Expand)
Authors: Eileen Marie Hanna, Xiaokang Zhang, Marta Eide, Shirin Fallahi, Tomasz Furmanek, Fekadu Yadetie, Daniel Craig Zielinski, Anders Goksøyr, Inge Jonassen
Date Published: 26th Nov 2020
Publication Type: Journal
DOI: 10.3389/fmolb.2020.591406
Citation: Front. Mol. Biosci. 7,591406
Abstract (Expand)
Authors: Pål A. Olsvik, Anett Kristin Larsen, Marc H. G. Berntssen, Anders Goksøyr, Odd André Karlsen, Fekadu Yadetie, Monica Sanden, Torstein Kristensen
Date Published: 26th Sep 2019
Publication Type: Journal
Citation: Front. Genet. 10,794
Abstract (Expand)
Authors: E. A. Khan, L. B. Bertotto, K. Dale, R. Lille-Langoy, F. Yadetie, O. A. Karlsen, A. Goksoyr, D. Schlenk, A. Arukwe
Date Published: 18th Jun 2019
Publication Type: Not specified
PubMed ID: 31090407
Citation: Environ Sci Technol. 2019 Jun 18;53(12):7036-7044. doi: 10.1021/acs.est.9b00637. Epub 2019 May 29.
Abstract (Expand)
Authors: K. Dale, M. B. Muller, Z. Tairova, E. A. Khan, K. Hatlen, M. Grung, F. Yadetie, R. Lille-Langoy, N. Blaser, H. J. Skaug, J. L. Lyche, A. Arukwe, K. Hylland, O. A. Karlsen, A. Goksoyr
Date Published: 26th Feb 2019
Publication Type: Not specified
PubMed ID: 30803754
Citation: Mar Environ Res. 2019 Mar;145:39-51. doi: 10.1016/j.marenvres.2019.02.003. Epub 2019 Feb 11.
Supplementary Table1 and Table2 for manuscript "The chemical defensome of fish"
Creators: Xiaokang Zhang, Marta Eide, Inge Jonassen, Anders Goksøyr, Odd André Karlsen, Jared V. Goldstone; John Stegeman
Submitter: Xiaokang Zhang
Investigations: 1 hidden item
Studies: The chemical defensome of fish