Browsing Bergen Open Research Archive by Author "Zhang, Xiaokang"
Now showing items 1-11 of 11
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Application of quantitative transcriptomics in evaluating the ex vivo effects of per- and polyfluoroalkyl substances on Atlantic cod (Gadus morhua) ovarian physiology
Khan, Essa Ahsan; Zhang, Xiaokang; Hanna, Eileen Marie; Yadetie, Fekadu; Jonassen, Inge; Goksøyr, Anders; Arukwe, Augustine (Journal article; Peer reviewed, 2021)Because of their global consumption and persistence, per- and polyfluoroalkyl substances (PFASs), are ubiquitously distributed in the environment, as well as in wildlife and humans. In the present study, we have employed ... -
Biomarker Discovery Using Statistical and Machine Learning Approaches on Gene Expression Data
Zhang, Xiaokang (Doctoral thesis, 2020-10-30)My PhD is affiliated with the dCod 1.0 project (https://www.uib.no/en/dcod): decoding the systems toxicology of Atlantic cod (Gadus morhua), which aims to better understand how cods adapt and react to the stressors in the ... -
The chemical defensome of five model teleost fish
Eide, Marta; Zhang, Xiaokang; Karlsen, Odd André; Goldstone, Jared V.; Stegeman, John; Jonassen, Inge; Goksøyr, Anders (Journal article; Peer reviewed, 2021)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 ... -
A Comparative Analysis of Feature Selection Methods for Biomarker Discovery in Study of Toxicant-Treated Atlantic Cod (Gadus Morhua) Liver
Zhang, Xiaokang; Jonassen, Inge (Chapter; Conference object; Peer reviewed, 2019)Univariate and multivariate feature selection methods can be used for biomarker discovery in analysis of toxicant exposure. Among the univariate methods, differential expression analysis (DEA) is often applied for its ... -
An Ensemble Feature Selection Framework Integrating Stability
Zhang, Xiaokang; Jonassen, Inge (Chapter; Conference object; Peer reviewed, 2019)Ensemble feature selection has drawn more and more attention in recent years. There are mainly two strategies for ensemble feature selection, namely data perturbation and function perturbation. Data perturbation performs ... -
Machine Learning Approaches for Biomarker Discovery Using Gene Expression Data
Zhang, Xiaokang; Jonassen, Inge; Goksøyr, Anders (Chapter, 2021)Biomarkers are of great importance in many fields, such as cancer research, toxicology, diagnosis and treatment of diseases, and to better understand biological response mechanisms to internal or external intervention. ... -
Proteomics and lipidomics analyses reveal modulation of lipid metabolism by perfluoroalkyl substances in liver of Atlantic cod (Gadus morhua)
Dale, Karina; Yadetie, Fekadu; Müller, Mette Helen Bjørge; Pampanin, Daniela Maria; Gilabert, Alejandra; Zhang, Xiaokang; Tairova, Zhanna; Haarr, Ane; Lille-Langøy, Roger; Lyche, Jan Ludvig; Porte, Cinta; Karlsen, Odd Andre; Goksøyr, Anders (Journal article; Peer reviewed, 2020)The aim of the present study was to investigate effects of defined mixtures of polycyclic aromatic hydrocarbons (PAHs) and perfluoroalkyl substances (PFASs), at low, environmentally relevant (1× = L), or high (20× = H) ... -
Quantitative transcriptomics, and lipidomics in evaluating ovarian developmental effects in Atlantic cod (Gadus morhua) caged at a capped marine waste disposal site
Khan, Essa Ahsan; Zhang, Xiaokang; Hanna, Eileen Marie; Bartosova, Zdenka; Yadetie, Fekadu; Jonassen, Inge; Goksøyr, Anders; Arukwe, Augustine (Journal article; Peer reviewed, 2020)In the present study, a previously capped waste disposal site at Kollevåg (Norway) was selected to study the effects of contaminant leakage on biomarkers associated with Atlantic cod (Gadus morhua) reproductive endocrinology ... -
RASflow: an RNA-Seq analysis workflow with Snakemake
Zhang, Xiaokang; Jonassen, Inge (Journal article; Peer reviewed, 2020)Background With the cost of DNA sequencing decreasing, increasing amounts of RNA-Seq data are being generated giving novel insight into gene expression and regulation. Prior to analysis of gene expression, the RNA-Seq ... -
ReCodLiver0.9: Overcoming Challenges in Genome-Scale Metabolic Reconstruction of a Non-model Species
Hanna, Eileen Marie; Zhang, Xiaokang; Eide, Marta; Fallahi, Shirin; Furmanek, Tomasz; Yadetie, Fekadu; Zielinski, Daniel Craig; Goksøyr, Anders; Jonassen, Inge (Journal article; Peer reviewed, 2020-11)The availability of genome sequences, annotations, and knowledge of the biochemistry underlying metabolic transformations has led to the generation of metabolic network reconstructions for a wide range of organisms in ... -
Single PFAS and PFAS mixtures affect nuclear receptor- and oxidative stress-related pathways in precision-cut liver slices of Atlantic cod (Gadus morhua)
Dale, Karina; Yadetie, Fekadu; Horvli, Torill; Zhang, Xiaokang; Frøysa, Håvard G; Karlsen, Odd André; Goksøyr, Anders (Journal article; Peer reviewed, 2022)The aim of the present study was to investigate effects of per- and polyfluoroalkyl substances (PFAS), both single compounds and a mixture of these, using precision-cut liver slices (PCLS) from Atlantic cod (Gadus morhua). ...