Selected publications

2025

GUANACO: A Unified Web-Based Platform for Single-Cell Multi-Omics Data Visualization

Zhang X, Kuddus M, Xia Q, Hu Y#, Chen P#.

bioRxiv [Preprint]. 2025. doi: https://doi.org/10.1101/2025.09.18.677070.

  

Single-cell MultiOmics and spatial transcriptomics demonstrate neuroblastoma developmental plasticity

Xu Y*, Lou D*, Chen P*, Li G, Usoskin D, Pan J, Li F, Huang S, Hess C, Tang R, Hu X, Yu J, Arceo M, de Krijger RR, Tischler AS, Schlisio S, Ernfors P, Hu Y, Wang J. 

Dev Cell. 2025 Sep 8;60(17):2248-2263.e11. doi: 10.1016/j.devcel.2025.04.013. Epub 2025 May 9.

  

Induced somatic mutation accumulation during skeletal muscle regeneration reduces muscle strength

Vrtačnik P, Merino LG, Subhash S, Helgadóttir HT, Bardin M, Stefani F, Wang D, Chen P, Franco I, Revêchon G, Eriksson M. 

Nat Aging. 2025 Sep;5(9):1739-1749. doi: 10.1038/s43587-025-00941-y. Epub 2025 Aug 20. 

  

Epithelial cell shape changes contribute to regulation of ureteric bud branching morphogenesis

Kurtzeborn K, Iaroshenko V, Zárybnický T, Koivula J, Anttonen H, Mäkelä OJM, Bridgewater D, Krishnan R, Chen P, Kuure S. 

FEBS J. 2025 Jun 15. doi: 10.1111/febs.70156. Epub ahead of print.

  

2023

Human resident liver myeloid cells protect against metabolic stress in obesity

Barreby E, Strunz B, Nock S, Naudet L, Shen JX, Johansson H, Sönnerborg I, Ma J, Urgard E, Pallett LJ, Hu Y, Fardellas A, Azzimato V, Vankova A, Levi L, Morgantini C, Maini MK, Stål P, Rosshart SP, Coquet JM, Nowak G, Näslund E, Lauschke VM, Ellis E, Björkström NK, Chen P#, Aouadi M#.

Nat Metab. 2023 Jul;5(7):1188-1203. doi: 10.1038/s42255-023-00834-7. Epub 2023 Jul 6.

  

Cholinergic regulation of vascular endothelial function by human ChAT+ T cells

Tarnawski L, Shavva VS, Kort EJ, Zhuge Z, Nilsson I, Gallina AL, Martínez-Enguita D, Heller Sahlgren B, Weiland M, Caravaca AS, Schmidt S, Chen P, Abbas K, Wang FH, Ahmed O, Eberhardson M, Färnert A, Weitzberg E, Gustafsson M, Kehr J, Malin SG, Hult H, Carlström M, Jovinge S, Olofsson PS.

Proc Natl Acad Sci U S A. 2023 Apr 4;120(14):e2212476120. doi: 10.1073/pnas.2212476120. Epub 2023 Mar 29.

  

2022

Macrophage functional diversity in NAFLD - more than inflammation

Barreby E, Chen P, Aouadi M. 

Nat Rev Endocrinol. 2022 Aug;18(8):461-472. doi: 10.1038/s41574-022-00675-6. Epub 2022 May 9.

  

2021

Obesity and hyperinsulinemia drive adipocytes to activate a cell cycle program and senesce

Li Q, Hagberg CE, Silva Cascales H, 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.

Nat Med. 2021 Nov;27(11):1941-1953. doi: 10.1038/s41591-021-01501-8. Epub 2021 Oct 4. 

  

A subset of Kupffer cells regulates metabolism through the expression of CD36

Blériot 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.

Immunity. 2021 Sep 14;54(9):2101-2116.e6. doi: 10.1016/j.immuni.2021.08.006. Epub 2021 Aug 31.

  

Single-cell RNA sequencing reveals the mesangial identity and species diversity of glomerular cell transcriptomes

He B*, Chen P*, Zambrano S, Dabaghie D, Hu Y, Möller-Hackbarth K, Unnersjö-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.

Nat Commun. 2021 Apr 9;12(1):2141. doi: 10.1038/s41467-021-22331-9. 

  

2020

Single-cell RNA counting at allele- and isoform-resolution using Smart-seq3

Hagemann-Jensen M, Ziegenhain C, Chen P, Ramsköld D, Hendriks GJ, Larsson AJM, Faridani OR, Sandberg R.

Nat Biotechnol. 2020 Jun;38(6):708-714. doi: 10.1038/s41587-020-0497-0. Epub 2020 May 4. 

  

Liver macrophages inhibit the endogenous antioxidant response in obesity-associated insulin resistance

Azzimato 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, Wålhen K, Näslund E, Thorell A, Choudhury RP, Lauschke VM, Rydén M, Craige SM, Aouadi M.

Sci Transl Med. 2020 Feb 26;12(532):eaaw9709. doi: 10.1126/scitranslmed.aaw9709. 

  

2015

Origins and impacts of new mammalian exons

Merkin JJ*, Chen P*, Alexis MS, Hautaniemi SK, Burge CB. 

Cell Rep. 2015 Mar 31;10(12):1992-2005. doi: 10.1016/j.celrep.2015.02.058. Epub 2015 Mar 19.

  

Identification of Prognostic Groups in High-Grade Serous Ovarian Cancer Treated with Platinum-Taxane Chemotherapy

Chen P, Huhtinen K, Kaipio K, Mikkonen P, Aittomäki V, Lindell R, Hynninen J, Auranen A, Grénman S, Lehtonen R, Carpén O, Hautaniemi S.

Cancer Res. 2015 Aug 1;75(15):2987-98. doi: 10.1158/0008-5472.CAN-14-3242. Epub 2015 Jun 29.

  

2012

Evolutionary dynamics of gene and isoform regulation in Mammalian tissues

Merkin J, Russell C, Chen P, Burge CB. 

Science. 2012 Dec 21;338(6114):1593-9. doi: 10.1126/science.1228186.

  

2011

Comprehensive exon array data processing method for quantitative analysis of alternative spliced variants

Chen P, Lepikhova T, Hu Y, Monni O, Hautaniemi S.

Nucleic Acids Res. 2011 Oct;39(18):e123. doi: 10.1093/nar/gkr513. Epub 2011 Jul 10.