Marijn Berg


Bioinformatics PhD Candidate, Department of Pathology and Medical Biology, University Medical Center Groningen (UMCG),  The Netherlands, 2019

Bioinformatics analysist, Department of Pathology and Medical Biology, University Medical Center Groningen (UMCG),  The Netherlands,  2017 2019

BSc Bioinformatics, Hanze University of Applied Sciences, The Netherlands, 2017



I’m interested in the differences in the cellular landscape of the airway epithelium between healthy, asthmatic and asthma remission populations. To look at those differences I analyze single cell RNA-sequencing data from bronchial biopsies. These data can be used to computationally identify cell types and states based on their transcriptional profile and those can be compared between the groups.
The first results of this have already been published in Nature Medicine where we showed some interesting differences in the relative cell populations and cell type interactions in asthmatic individuals compared to controls.
We’re currently adding more samples to our data which also includes asthma remission groups. Now that we have more data, improved methods to analyze them and an increasing expertise in interpreting these results and placing them into the broader context of the fields of scRNA-sequencing technologies and airway diseases there are doubtless interesting results coming in the future.

Berg, M, Petoukhov, I, van den Ende, I, Meyer, KB, Guryev, V, Vonk, JM et al.. FastCAR: fast correction for ambient RNA to facilitate differential gene expression analysis in single-cell RNA-sequencing datasets. BMC Genomics. 2023;24 (1):722. doi: 10.1186/s12864-023-09822-3. PubMed PMID:38030970 PubMed Central PMC10687889.

Sikkema, L, Ramírez-Suástegui, C, Strobl, DC, Gillett, TE, Zappia, L, Madissoon, E et al.. An integrated cell atlas of the lung in health and disease. Nat Med. 2023;29 (6):1563-1577. doi: 10.1038/s41591-023-02327-2. PubMed PMID:37291214 PubMed Central PMC10287567.

Faiz, A, Pavlidis, S, Kuo, CH, Rowe, A, Hiemstra, PS, Timens, W et al.. Th2 high and mast cell gene signatures are associated with corticosteroid sensitivity in COPD. Thorax. 2023;78 (4):335-343. doi: 10.1136/thorax-2021-217736. PubMed PMID:36598042 PubMed Central PMC10086461.

van Breugel, M, Qi, C, Xu, Z, Pedersen, CT, Petoukhov, I, Vonk, JM et al.. Nasal DNA methylation at three CpG sites predicts childhood allergic disease. Nat Commun. 2022;13 (1):7415. doi: 10.1038/s41467-022-35088-6. PubMed PMID:36456559 PubMed Central PMC9715628.

Qi, C, Berg, M, Chu, X, Timens, W, Kole, T, van den Berge, M et al.. Cell-type eQTL deconvolution of bronchial epithelium through integration of single-cell and bulk RNA-seq. Allergy. 2022;77 (12):3663-3666. doi: 10.1111/all.15410. PubMed PMID:35708915 .

Luecken, MD, Zaragosi, LE, Madissoon, E, Sikkema, L, Firsova, AB, De Domenico, E et al.. The discovAIR project: a roadmap towards the Human Lung Cell Atlas. Eur Respir J. 2022;60 (2):. doi: 10.1183/13993003.02057-2021. PubMed PMID:35086829 PubMed Central PMC9386332.

van de Wetering, C, Elko, E, Berg, M, Schiffers, CHJ, Stylianidis, V, van den Berge, M et al.. Glutathione S-transferases and their implications in the lung diseases asthma and chronic obstructive pulmonary disease: Early life susceptibility?. Redox Biol. 2021;43 :101995. doi: 10.1016/j.redox.2021.101995. PubMed PMID:33979767 PubMed Central PMC8131726.

Dwyer, DF, Ordovas-Montanes, J, Allon, SJ, Buchheit, KM, Vukovic, M, Derakhshan, T et al.. Human airway mast cells proliferate and acquire distinct inflammation-driven phenotypes during type 2 inflammation. Sci Immunol. 2021;6 (56):. doi: 10.1126/sciimmunol.abb7221. PubMed PMID:33637594 PubMed Central PMC8362933.

Pouwels, SD, Wiersma, VR, Fokkema, IE, Berg, M, Ten Hacken, NHT, van den Berge, M et al.. Acute cigarette smoke-induced eQTL affects formyl peptide receptor expression and lung function. Respirology. 2021;26 (3):233-240. doi: 10.1111/resp.13960. PubMed PMID:33078507 PubMed Central PMC7983955.

Jiang, J, Faiz, A, Berg, M, Carpaij, OA, Vermeulen, CJ, Brouwer, S et al.. Gene signatures from scRNA-seq accurately quantify mast cells in biopsies in asthma. Clin Exp Allergy. 2020;50 (12):1428-1431. doi: 10.1111/cea.13732. PubMed PMID:32935368 PubMed Central PMC7756890.

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