Institutionen för biovetenskap
I am Associate Professor in bioinformatics at the University of Skövde, Sweden, and Head of the Translational Bioinformatics research group consisting of a group of 19 researchers with a dedicated interest in bioinformatics. I have a background in Data Science and received my MSc in Computer Sciences from the University of Skövde in 2003. During my graduate studies I developed my expertise in bioinformatics and large-scale omics data analysis and received my PhD from the University of Gothenburg in 2010.
My research is focused on analysis methods for identification of biomarkers and integration of multiple types of omics data. I am PI for several research projects specialized in stem cell differentiation, toxicity testing and disease modeling using stem cell based in vitro systems. I am also leading projects particularly focused on advanced analysis of big data, biomarker identification, and data integration with particular interest in machine-learning methods.
Working in close collaboration with the stem cell industry and the pharmaceutical industry we perform global expression studies including transcriptomics, proteomics, epigenomics, and metabolomics of human pluripotent stem cells during their differentiation towards functional cell types. The results from these studies have revealed mechanistic highlights during the early phases of stem cell differentiation and identified biomarkers with potential importance for applications in toxicity testing, drug development, and disease modeling.
Characterization of Human Induced Pluripotent Stem Cell-Derived Hepatocytes with Mature Features and Potential for Modeling Metabolic DiseasesHolmgren Gustav, Ulfenborg Benjamin, Asplund Annika et al.International Journal of Molecular Sciences, 2020, 21(2).
Diabetic Cardiomyopathy Modelling Using Induced Pluripotent Stem Cell Derived Cardiomyocytes: Recent Advances and Emerging ModelsGranéli Cecilia, Hicks Ryan, Brolén Gabriella et al.Stem Cell Reviews, 2019, 15(1), 13-22.
Enhanced xeno-free differentiation of hiPSC-derived astroglia applied in a blood-brain barrier model
Delsing Louise, Kallur Therese, Zetterberg Henrik et al.Fluids and Barriers of the CNS, 2019, 16(1).
Barrier properties and transcriptome expression in human iPSC-derived models of the blood-brain barrierDelsing Louise, Dönnes Pierre, Sánchez José et al.Stem Cells, 2018, 36(12), 1816-1827.
Current Perspectives on Multi-Omics Data Integration With Application on Toxicity Biomarkers Discovery
Synnergren Jane, Dönnes PierreOpen Access journal of Toxicology, 2018, 2(5), 1-2.
Expression profiling of human pluripotent stem cell-derived cardiomyocytes exposed to doxorubicin - integration and visualization of multi omics data
Holmgren Gustav, Sartipy Peter, Andersson Christian X. et al.Toxicological Sciences, 2018, 163(1), 182-195.
Human iPS-Derived Astroglia from a Stable Neural Precursor State Show Improved Functionality Compared with Conventional Astrocytic Models
Lundin Anders, Delsing Louise, Clausen Maryam et al.Stem Cell Reports, 2018, 10(3), 1030-1045.
Integration of Biomedical Big Data Requires Efficient Batch Effect Reduction
Synnergren Jane, Ghosheh Nidal, Dönnes Pierre10th International Conference on Bioinformatics and Computational Biology (BICOB): Las Vegas, Nevada, USA 19 – 21 March 2018 (76-82). 2018.
Novel human iPSC-derived hepatocytes with advanced functionality and long-term 2D cultures of human primary hepatocytes for metabolic disease studies
Küppers-Munther Barbara, Asplund A., Ulfenborg Benjamin et al.Human Gene Therapy, 2018, 29(12), A146-A146.
A data analysis framework for biomedical big data: Application on mesoderm differentiation of human pluripotent stem cellsUlfenborg Benjamin, Karlsson Alexander, Riveiro Maria et al.PLoS ONE, 2017, 12(6).