In context of Neuro-SysMed, the Jonassen group is working with Tzoulis and colleagues on development and application of methods to analyze omics data for PD patients and controls. The work has benefited from earlier work in the Jonassen group developing novel methods for gene expression deconvolution resulting in the method Deblender, developed in collaboration with the Akslen and Wik groups at the Centre for Cancer Biomarkers (CCBIO), UiB, published in BMC Bioinformatics in 2018. In a later publication in collaboration with Tzoulis and colleagues, the group showed the importance of taking tissue composition into account in analysis of gene expression data, showing that previous expression signatures developed for Parkinson’s disease to a large extent were driven by alterations in cell composition (published in Acta Neuro Comm in 2020).
Further work involve co-analysis of proteomics and transcriptomics level data from the same patients – work that is on-going and not yet published. Jonassen is planning recruitment of a post-doctoral researcher to work between Jonassen/CBU and the Tzoulis group on applying methods for multi-omics analysis on data from PD patients and controls, and an internal proposal for work in this direction has been authored by Jonassen and Kjell Petersen at CBU.
Through his engagement in the pan-European bioinformatics infrastructure ELIXIR and as Head of ELIXIR Norway, Jonassen has also worked to establish infrastructure for controlled sharing of molecular level and clinical data supporting medical biomedical research findings. As one of the first in Europe, ELIXIR Norway is ready to operate a node of the federated European Genome-phenome Archive – enabling controlled sharing of data that due to consent or other legal constraints cannot be deposited in international repositories. Through ELIXIR Norway, the Jonassen group has also worked to provide solutions for analyzing human molecular level data as well as phenotypic data in secure environments and to establish better support for data management and
FAIR data sharing for Norwegian life science research projects.
Selected Key Publications
1. X Zhang, I Jonassen, RASflow: an RNA-Seq analysis workflow with Snakemake, BMC bioinformatics 21 (1), 1-9
2. Gonzalo S Nido, Fiona Dick, Lilah Toker, Kjell Petersen, Guido Alves, Ole-Bjørn Tysnes, Inge Jonassen, Kristoffer Haugarvoll, Charalampos Tzoulis, Common gene expression signatures in Parkinson’s disease are driven by changes in cell composition, Acta neuropathologica communications 8, 1-14
3. Mitra Parissa Barzine, Karlis Freivalds, James C Wright, Mārtiņš Opmanis, Darta Rituma, Fatemeh Zamanzad Ghavidel, Andrew F Jarnuczak, Edgars Celms, Kārlis Čerāns, Inge Jonassen, Lelde Lace, Juan Antonio Vizcaíno, Jyoti Sharma Choudhary, Alvis Brazma, Juris Viksna, Using Deep Learning to Extrapolate Protein Expression Measurements, Proteomics 20 (21-22)
4. Xiaokang Zhang, Inge Jonassen, An Ensemble Feature Selection Framework Integrating Stability, 2019 IEEE International Conference on Bioinformatics and Biomedicine (BIBM), 2792-2798