Institutionen för biovetenskap
I'm an associate senior lecturer in bioinformatics at the University of Skövde, Sweden, and part of the Translational Bioinformatics research group. I obtained a MSc degree in Molecular Biology at University of Skövde 2008 and my PhD degree in Medical Science at Örebro University in 2016. During my PhD I worked on developing bioinformatics tools for discovery of biomarkers, including a machine learning algorithm and a database for miRNAs in endometrial cancer. After I obtained my PhD degree I became post doc in bioinformatics at University of Skövde and worked on analysis of high-throughput data from stem cell cultures undergoing differentiation towards functional cell types.
My main research interests are in developing bioinformatics algorithms integration of multi-omics data, data mining and biomarker discovery. I'm currently PI of a research project on data integration, and invovled in serveral ongoing projects in the Translational Bioinformatics research group. Common for several of these projects is that we are analyzing multiple types of omics data, e.g. transcriptomics, proteomics and epigenomics, and we want to combine these to perform integrative analysis. The purpose of this effort is to better understand the stem cell differentiation process and identify biomarkers for e.g. drug toxicity and diease modeling. A pre-print of my latest work is available in bioRxiv: https://www.biorxiv.org/content/10.1101/431429v2.
Univariate and classification analysis reveals potential diagnostic biomarkers for early stage ovarian cancer Type 1 and Type 2Marcišauskas Simonas, Ulfenborg Benjamin, Kristjansdottir Björg et al.Journal of Proteomics, 2019, 196, 57-68.
Novel human iPSC-derived hepatocytes with advanced functionality and long-term 2D cultures of human primary hepatocytes for metabolic disease studiesKüppers-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).
Comparative transcriptomics of hepatic differentiation of human pluripotent stem cells and adult human liver tissue
Ghosheh Nidal, Küppers-Munther Barbara, Asplund Annika et al.Physiological Genomics, 2017, 49(8), 430-446.
Bioinformatics tools for discovery and evaluation of biomarkers: Applications in clinical assessment of cancerUlfenborg BenjaminDoktorsavhandling: Örebro University, 2016.
Genome-wide discovery of miRNAs using ensembles of machine learning algorithms and logistic regressionUlfenborg Benjamin, Klinga-Levan Karin, Olsson BjörnInternational Journal of Data Mining and Bioinformatics, 2015, 13(4), 338-359.
miREC: a database of miRNAs involved in the development of endometrial cancer
Ulfenborg Benjamin, Jurcevic Sanja, Lindelöf Angelica et al.BMC Research Notes, 2015, 8(1).
GenoScan: Genomic Scanner for Putative miRNA PrecursorsUlfenborg Benjamin, Klinga-Levan Karin, Olsson BjörnBioinformatics Research and Applications: 10th International Symposium, ISBRA 2014, Zhangjiajie, China, June 28-30, 2014. Proceedings (266-277). Springer, 2014.
Classification of tumor samples from expression data using decision trunksUlfenborg Benjamin, Klinga-Levan Karin, Olsson BjörnCancer Informatics, 2013, 12, 53-66.