As a computational biologist, I am keen in translating data science to medical research. I completed my Ph.D. in Medical Systems Biology at the University of Helsinki in 2016 and defended my thesis with distinction. During my doctoral research, I developed several computational tools and comprehensively studied alternative splicing dynamics in mammalian evolution and treatment resistance in cancer. In 2012, I joined Massachusetts Institute of Technology (USA) as a visiting scholar and studied the regulation of RNA splicing in Professor Christopher Burge's research group.
I moved to Stockholm in 2017 for postdoc research training in Professor Rickard Sandberg's group at the Integrated Cardiometabolic Center, Karolinska Institutet, where I collaborated with different research groups and worked on single-cell data analysis of human metabolic tissues. In addition, I developed the isoform reconstruction procedure for the Smart-seq3 single-cell RNA-seq protocol (Nature Biotechnology, 2020). After working on multiple human metabolic tissues, I became very interested in the field of metabolism and eager to continue my research on human metabolic diseases. In 2020, I joined Dr. Myriam Aouadi's group to deepen my knowledge of human immunometabolism further. Since 2021, I have been Assistant Professor and am currently starting my independent research group in the Division of Clinical Chemistry at KI LABMED, focusing on data-driven research in human cardiometabolic diseases.
My data-driven research aims to dissect the cellular and molecular mechanisms driving human disease pathogenesis and develop new precise diagnosis and treatment strategies for patients. In close collaboration with multidisciplinary researchers, we integrate longitudinal patient data, multi-omics technologies as well as novel computational and experimental approaches in our research.
We study human obesity and associated metabolic diseases, such as non-alcoholic fatty liver disease (NAFLD) and diabetes. I am particularly interested in the role of immune cells and RNA splicing-centric transcriptional regulation in these diseases.
One funded postdoc position is currently available (Apply here). We welcome curious and motivated candidates with wet-lab or dry-lab experiences to join our team.
- Co-organiser of the Karolinska Basic Bioinformatics course for doctoral students (2022--); Frequent teacher in Basic Bioinformatics courses (2019-2022)
- Co-supervisor of two ongoing PhD students at KI MedH (2021--)
- Karolinska professional pedagogy training (equivalent to five weeks of academic studies) (2020)
PhD in medicine (Medical System Biology), 2016
Faculty of Medicine, University of Helsinki, Finland
MSc in Bioinformatics, 2009
Faculty of Computer Science, University of Helsinki, Finland
BSc in Biology & Bioinformatics, 2007
Department of Biology and Basic Medical Sciences, Soochow University, China
Academic honours, awards and prizes
My research has received funding from CIMED, Jeanssons Stiftelser and Karolinska Institutet.
Commission of trust
- Associate Editor of Journal of Translational Medicine (2020--)
- Secretary of the Junior Faculty Steering Group leadership at Karolinska Institutet (2022--); Member of the JF Communication Focus Group (2021--)
- Organization committee member of Karolinska Liver Academy kick-off meeting (2022)
- Junior Faculty representative for evaluating KI new Research Information Management System (2022)
- Organization committee member of Karolinska Discovers seminar series (2021-2022)
1) Barreby E, Chen P, Aouadi M. Macrophage functional diversity in NAFLD - more than inflammation. Nat Rev Endocrinol. 2022 May 9. doi: 10.1038/s41574-022-00675-6.
2) Azzimato V, Chen P, Barreby E, Morgantini C, Levi L, Vankova A, Jager J, Sulen A, Diotallevi M, Shen JX, Miller A, Ellis E, Ryd.n M, N.slund E, Thorell A, Lauschke VM, Channon KM, Crabtree MJ, Haschemi A, Craige SM, Mori M, Spallotta F and Aouad M. miR-144 drives fumarase activity preventing NRF2 activation in obese livers. Gastroenterology. 2021 Dec;161(6):1982-1997.e11.
3) Li Q, Hagberg CE, Cascales HS, Lang S, Hyvönen MT, Salehzadeh F, Chen P, Alexandersson I, Terezaki E, Harms MJ, Kutschke M, Arifen N, Krämer N, Aouadi M, Knibbe C, Boucher J, Thorell A, Spalding KL. Obesity and hyperinsulinemia drive adipocytes to activate a cell cycle program and senesce. Nature Medicine. 2021 Nov;27(11):1941-1953.
4) He B*, Chen P* (*shared first authorship), Zambrano S, Dabaghie D, Hu Y, Jeansson M, Bintanel M, Wernerson A, Ernfors P, Betsholtz C, Lal M, Sandberg R, Patrakka J. Single-cell RNA sequencing reveals the mesangial identity and species diversity of glomerular cell transcriptomes. Nature Communication. 2021. Apr 9;12(1):2141.
5) Hagemann-Jensen M, Ziegenhain C, Chen P, Ramsköld D, Hendriks GJ, Larsson A, Faridani O, Sandberg R. Single-cell RNA counting at allele- and isoform-resolution using Smart-seq3. Nat Biotechnol. 2020 May 4.
6) Azzimato V*, Jager J*, Chen P* (*shared first authorship), Morgantini C, Levi L, Barreby E, Sulen A, Oses C, Willerbrords J, Xu C, Li X, Shen JX, Akbar N, Haag L, Ellis E, Wålhen K, Näslund E, Thorell A, Choudhury RP, Lauschke VM, Rydén M, Craige SM, Aouadi M. Liver macrophages inhibit the endogenous antioxidant response in obesity-associated insulin resistance. Sci Transl Med. 2020 Feb 26;12(532).
7) Chen P, Huhtinen K, Kaipio K, Mikkonen P, Aittomäki V, Lindell R, Hynninen J, Auranen A, Grénman S, Lehtonen R, Carpén O, Hautaniemi S. Identification of Prognostic Groups in High-Grade Serous Ovarian Cancer Treated with Platinum-Taxane Chemotherapy. Cancer Res. 2015 Aug 1;75(15):2987-98.
8) Merkin JJ*, Chen P* (*shared first authorship), Alexis MS, Hautaniemi SK, Burge CB. Origins and impacts of new mammalian exons. Cell Rep. 2015 Mar 31;10(12):1992-2005.
9) Merkin J, Russell C, Chen P, Burge CB. Evolutionary dynamics of gene and isoform regulation in Mammalian tissues. Science. 2012 Dec 21;338(6114):1593-9.
10) Chen P, Lepikhova T, Hu Y, Monni O, Hautaniemi S. Comprehensive exon array data processing method for quantitative analysis of alternative spliced variants. Nucleic Acids Res. 2011 Oct;39(18):e123.