Ping Chen
- Institutionen för laboratoriemedicin
- Avdelningen för Klinisk kemi vid Labmed
- Kardiometabola sjukdomar – Ping Chen forskargrupp
Om mig
As a computational biologist, I am dedicated to bridging the gap between data science and medical research. I earned my Ph.D. in Medical Systems Biology from the University of Helsinki in 2016, where my doctoral dissertation focused on the ‘Quantitative Study of Transcriptome Dynamics during Evolution and Treatment Resistance in Cancer’. Following my Phd, I pursued received postdoctoral research training on Smart-seq2/3 single cell methodology in Rickard Sandberg’s group, and on immunometabolism in Myriam Aouadi’s group at Karolinska Institutet, Sweden. Since 2022, I have been leading my independent research group at the Division of Clinical Chemistry in KI LABMED. Our team is deeply engaged in data-driven research on human cardiometabolic diseases, encompassing both computational method development and in-depth mechanistic studies. Additionally, since September 2023, I have started my second lab at the University of Helsinki in Finland. This lab is dedicated to investigating the regulation of alternative splicing in human metabolic diseases and cancers.
*Research funding*
My research has received funding from Swedish Research Council, CIMED, Jeanssons Stiftelser, SRP Diabetes, Karolinska Institutet, Research Council of Finland, Sigrid Jusélius Foundation and iCAN – Digital Precision Cancer Medicine Flagship.
*Commission of trust*- KI Liver Academy steering group member (2025--)
- Member of master thesis evaluation committee and member of doctoral student half-time review committee at Karolinska Institutet (2023--)
- Doctoral education board member at the Department of Laboratory Medicine, Karolinska Institutet (2022--)
- Associate Editor of Journal of Translational Medicine (2020-2024)
- Secretary of the Junior Faculty Steering Group leadership at Karolinska Institutet (2022-2023) and vice chair (2024)
- Organization committee member of Karolinska Discovers seminar series (2021-2022)
Forskningsbeskrivning
We study human obesity and related metabolic disorders, such as non-alcoholic fatty liver disease (NAFLD) and diabetes. I am particularly enthusiastic about developing AI-driven tools to enhance our insights on disease diagnostics. Additionally, my focus includes advancing data-driven methodologies to explore the roles of immune cells and transcriptional regulation, with a special emphasis on RNA splicing, in these diseases.
Since 2022, I have been leading my independent research group at the Division of Clinical Chemistry in KI LABMED. Our team is deeply engaged in data-driven research on human cardiometabolic diseases, encompassing both computational method development and in-depth mechanistic studies. Our data-driven research aims to develop new precise diagnosis and treatment strategies for patients and further dissect the cellular and molecular mechanisms driving disease pathogenesis . 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. Since September 2023, I have started a second lab in the University of Helsinki in Finland. This lab is dedicated to investigating the role of alternative splicing in human metabolic diseases and cancers.
Undervisning
* Co-organiser of the Karolinska Basic Bioinformatics course for doctoral students (2022-2024)
* Teaching in Basic Bioinformatics courses (2019-2022)
* Teaching in LABMED courses (2022--)
* Co-supervisor of two ongoing PhD students at KI MedH (2021--) and main supervisor of my lab members (2023--)
Artiklar
- Article: NATURE METABOLISM. 2023;5(7):1188-1203Barreby E; Strunz B; Nock S; Naudet L; Shen JX; Johansson H; Soennerborg I; Ma J; Urgard E; Pallett LJ; Hu Y; Fardellas A; Azzimato V; Vankova A; Levi L; Morgantini C; Maini MK; Stal P; Rosshart SP; Coquet JM; Nowak G; Naeslund E; Lauschke VM; Ellis E; Bjoerkstroem NK; Chen P; Aouadi M
- Article: AGING-US. 2023;15(12):5240-5265Salignon J; Faridani OR; Miliotis T; Janssens GE; Chen P; Zarrouki B; Sandberg R; Davidsson P; Riedel CG
- Article: PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA. 2023;120(14):e2212476120Tarnawski L; Shavva VS; Kort EJ; Zhuge Z; Nilsson I; Gallina AL; Martinez-Enguita D; Sahlgren BH; Weiland M; Caravaca AS; Schmidt S; Chen P; Abbas K; Wang F-H; Ahmed O; Eberhardson M; Farnert A; Weitzberg E; Gustafsson M; Kehr J; Malin SG; Hult H; Carlstrom M; Jovinge S; Olofsson PS
- Article: SCIENTIFIC REPORTS. 2022;12(1):20519Holmer M; Hagstrom H; Chen P; Danielsson O; Aouadi M; Ryden M; Stal P
- Article: GASTROENTEROLOGY. 2021;161(6):1982-1997.e11Azzimato V; Chen P; Barreby E; Morgantini C; Levi L; Vankova A; Jager J; Sulen A; Diotallevi M; Shen JX; Miller A; Ellis E; Ryden M; Naslund E; Thorell A; Lauschke VM; Channon KM; Crabtree MJ; Haschemi A; Craige SM; Mori M; Spallotta F; Aouadi M
- Article: NATURE MEDICINE. 2021;27(11):1941-1953Li Q; Hagberg CE; Silva Cascales H; Lang S; Hyvonen MT; Salehzadeh F; Chen P; Alexandersson I; Terezaki E; Harms MJ; Kutschke M; Arifen N; Kramer N; Aouadi M; Knibbe C; Boucher J; Thorell A; Spalding KL
- Article: IMMUNITY. 2021;54(9):2101-2116.e6Bleriot C; Barreby E; Dunsmore G; Ballaire R; Chakarov S; Ficht X; De Simone G; Andreata F; Fumagalli V; Guo W; Wan G; Gessain G; Khalilnezhad A; Zhang XM; Ang N; Chen P; Morgantini C; Azzimato V; Kong WT; Liu Z; Pai R; Lum J; Shihui F; Low I; Xu C; Malleret B; Kairi MFM; Balachander A; Cexus O; Larbi A; Lee B; Newell EW; Ng LG; Phoo WW; Sobota RM; Sharma A; Howland SW; Chen J; Bajenoff M; Yvan-Charvet L; Venteclef N; Iannacone M; Aouadi M; Ginhoux F
- Article: NATURE COMMUNICATIONS. 2021;12(1):2141He B; Chen P; Zambrano S; Dabaghie D; Hu Y; Moller-Hackbarth K; Unnersjoe-Jess D; Korkut GG; Charrin E; Jeansson M; Bintanel-Morcillo M; Witasp A; Wennberg L; Wernerson A; Schermer B; Benzing T; Ernfors P; Betsholtz C; Lal M; Sandberg R; Patrakka J
- Article: NATURE BIOTECHNOLOGY. 2020;38(6):708-714Hagemann-Jensen M; Ziegenhain C; Chen P; Ramskold D; Hendriks G-J; Larsson AJM; Faridani OR; Sandberg R
- Article: SCIENCE TRANSLATIONAL MEDICINE. 2020;12(532):eaaw9709Azzimato V; Jager J; Chen P; Morgantini C; Levi L; Barreby E; Sulen A; Oses C; Willerbrords J; Xu C; Li X; Shen JX; Akbar N; Haag L; Ellis E; Walhen K; Naslund E; Thorell A; Choudhury RP; Lauschke VM; Ryden M; Craige SM; Aouadi M
- Article: JOURNAL OF PATHOLOGY. 2020;250(2):159-169Kaipio K; Chen P; Roering P; Huhtinen K; Mikkonen P; Ostling P; Lehtinen L; Mansuri N; Korpela T; Potdar S; Hynninen J; Auranen A; Grenman S; Wennerberg K; Hautaniemi S; Carpen O
- Article: TRANSLATIONAL ONCOLOGY. 2019;12(1):170-179Aakko S; Straume AH; Birkeland EE; Chen P; Qiao X; Lonning PE; Kallio MJ
- Article: BIODATA MINING. 2016;9:20Icay K; Chen P; Cervera A; Rantanen V; Lehtonen R; Hautaniemi S
- Article: ONCOTARGET. 2016;7(11):12267-12285Tambe M; Pruikkonen S; Maki-Jouppila J; Chen P; Elgaaen BV; Straume AH; Huhtinen K; Carpen O; Lonning PE; Davidson B; Hautaniemi S; Kallio MJ
- Article: ONCOGENE. 2016;35(7):867-877Wang L; Yang H; Lei Z; Zhao J; Chen Y; Chen P; Li C; Zeng Y; Liu Z; Liu X; Zhang H-T
- Article: CANCER RESEARCH. 2015;75(15):2987-2998Chen P; Huhtinen K; Kaipio K; Mikkonen P; Aittomaki V; Lindell R; Hynninen J; Auranen A; Grenman S; Lehtonen R; Carpen O; Hautaniemi S
- Article: CELL REPORTS. 2015;10(12):1992-2005Merkin JJ; Chen P; Alexis MS; Hautaniemi SK; Burge CB
- Article: PLOS ONE. 2014;9(3):e91031Taskinen M; Louhimo R; Koivula S; Chen P; Rantanen V; Holte H; Delabie J; Karjalainen-Lindsberg M-L; Bjorkholm M; Fluge O; Pedersen LM; Fjorden K; Jerkeman M; Eriksson M; Hautaniemi S; Leppa S
- Article: PLOS ONE. 2013;8(11):e80363Li L; Hu Y; Ylivinkka I; Li H; Chen P; Keski-Oja J; Hyytiainen M
- Article: JOURNAL OF CELL SCIENCE. 2013;126(11):2459-2469Ylivinkka I; Hu Y; Chen P; Rantanen V; Hautaniemi S; Nyman TA; Keski-Oja J; Hyytiainen M
- Article: PLOS ONE. 2013;8(4):e60930Haapa-Paananen S; Chen P; Hellstrom K; Kohonen P; Hautaniemi S; Kallioniemi O; Perala M
- Article: SCIENCE. 2012;338(6114):1593-1599Merkin J; Russell C; Chen P; Burge CB
- Article: EXPERIMENTAL AND THERAPEUTIC MEDICINE. 2012;3(4):655-664Liu R-Y; Song X; Chen P; Lei Z; Miao J; Yi N; Zhang K; Pasche B; Zhang H-T
- Article: NEOPLASIA. 2012;14(3):219-227Hu Y; Ylivinkka I; Chen P; Li L; Hautaniemi S; Nyman TA; Keski-Oja J; Hyytiainen M
- Article: NUCLEIC ACIDS RESEARCH. 2011;39(18):e123Chen P; Lepikhova T; Hu Y; Monni O; Hautaniemi S
- Article: GENOME MEDICINE. 2010;2(9):65Ovaska K; Laakso M; Haapa-Paananen S; Louhimo R; Chen P; Aittomaki V; Valo E; Nunez-Fontarnau J; Rantanen V; Karinen S; Nousiainen K; Lahesmaa-Korpinen A-M; Miettinen M; Saarinen L; Kohonen P; Wu J; Westermarck J; Hautaniemi S
- Article: CYTOTECHNOLOGY. 2009;60(1-3):85-94Zheng F; Qiu Y; Chen Y; Chen P; Zhu Y; Xie W; Zhu H; Zhu J
- Article: BMC GENOMICS. 2008;9:304Liu F; Chen P; Cui S-J; Wang Z-Q; Han Z-G
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Alla övriga publikationer
- Review: NATURE REVIEWS ENDOCRINOLOGY. 2022;18(8):461-472Barreby E; Chen P; Aouadi M
Forskningsbidrag
- Swedish Research Council1 January 2025 - 31 December 2027Non-Alcoholic Steatohepatitis (NASH) is on the verge of becoming the leading cause of liver-related morbidity and mortality in the foreseeable future. The FDA´s approval of the inaugural medication for NASH treatment in March 2024 brought a glimmer of hope to those afflicted by this condition. Yet, the limited treatment options highlight an urgent need for a deeper grasp of the intricate mechanisms underlying NASH to identify alterative treatment strategies. This project is dedicated to exploring the role of alternative splicing in NASH, specifically concentrating on human liver myeloid cells, and circulating monocytes. Our objective is to unravel how alternative splicing shapes the diverse phenotypes of human myeloid cells during NASH progression. To achieve this, we will develop innovative computational tools to characterize alternative splicing and single nucleotide variants at both single cell and subpopulation levels. Further, we will investigate the impact of SNVs and the tissue microenvironment on RNA splicing in cells disrupted by NASH. By integrating spatial and single-cell omics data, our research will illuminate the intricate inter- and intracellular regulatory networks of alternative splicing dynamics during NASH progression. Crucial findings will be validated experimentally using established pre-clinical models, aiming to discover novel splicing-centric biomarkers and therapeutic targets for NASH patients.
Anställningar
- Senior Forskare, Laboratoriemedicin, Karolinska Institutet, 2025-
- Biträdande Lektor, Laboratoriemedicin, Karolinska Institutet, 2023-2024
Examina och utbildning
- PhD, Faculty of Medicine, University of Helsinki, 2016
- MSc, Faculty of Computer Science, University of Helsinki, 2009
- BSc, Biology and Bioinformatics, Department of Biology and Basic Medical Sciences, Soochow University, 2007