Selected publications

Wang, F., Ding, P., Liang, X., Ding, X., Brandt, C. B., Sjöstedt, E., Zhu, J., Bolund, S., Zhang, L., de Rooij, L., Luo, L., Wei, Y., Zhao, W., Lv, Z., Haskó, J., Li, R., Qin, Q., Jia, Y., Wu, W., Yuan, Y., … Luo, Y. (2022). Endothelial cell heterogeneity and microglia regulons revealed by a pig cell landscape at single-cell level. Nature communications13 (1), 3620. doi.org/10.1038/s41467-022-31388-z

Noer JB, Hørsdal OK, Xiang X, Luo Y, Regenberg B. Extrachromosomal circular DNA in cancer: history, current knowledge, and methods. Trends Genet. 2022 Mar 8:S0168-9525(22)00034-8. doi: 10.1016/j.tig.2022.02.007. Epub ahead of print. PMID: 35277298. (This review provides a comprehensive summary of the eccDNA and its roles in cancers.)

Corsi GI, Qu K, Alkan F, Pan X, Luo Y, Gorodkin J. CRISPR/Cas9 gRNA activity depends on free energy changes and on the target PAM context. Nat Commun. 2022 May 30;13(1):3006. doi: 10.1038/s41467-022-30515-0. PMID: 35637227; PMCID: PMC9151727.

Karlsson M, Sjöstedt E, Oksvold P, Sivertsson Å, Huang J, Álvez MB, Arif M, Li X, Lin L, Yu J, Ma T, Xu F, Han P, Jiang H, Mardinoglu A, Zhang C, von Feilitzen K, Xu X, Wang J, Yang H, Bolund L, Zhong W, Fagerberg L, Lindskog C, Pontén F, Mulder J, Luo Y, Uhlen M. Genome-wide annotation of protein-coding genes in pig. BMC Biol. 2022 Jan 25;20(1):25. doi: 10.1186/s12915-022-01229-y. PMID: 35073880; PMCID: PMC8788080. (The first body-wide classification of protein coding gene expression in pig tissues and organs)

Xiang X, Corsi GI, Anthon C, Qu K, Pan X, Liang X, Han P, Dong Z, Liu L, Zhong J, Ma T, Wang J, Zhang X, Jiang H, Xu F, Liu X, Xu X, Wang J, Yang H, Bolund L, Church GM, Lin L, Gorodkin J, Luo Y. Enhancing CRISPR-Cas9 gRNA efficiency prediction by data integration and deep learning. Nat Commun. 2021 May 28;12(1):3238. doi: 10.1038/s41467-021-23576-0. PMID: 34050182; PMCID: PMC8163799. (This study reports the CRISPRTRAP-seq method for high throughput quantification of CRISPR gRNA activity in cells. The study also reported the generation of new deep learning based tool, CRISPRon, for prediction of CRISPR on-target targeting activity.)

Karlsson M, Zhang C, Méar L, Zhong W, Digre A, Katona B, Sjöstedt E, Butler L, Odeberg J, Dusart P, Edfors F, Oksvold P, von Feilitzen K, Zwahlen M, Arif M, Altay O, Li X, Ozcan M, Mardinoglu A, Fagerberg L, Mulder J, Luo Y, Ponten F, Uhlén M, Lindskog C. A single-cell type transcriptomics map of human tissues. Sci Adv. 2021 Jul 28;7(31):eabh2169. doi: 10.1126/sciadv.abh2169. PMID: 34321199; PMCID: PMC8318366. (A single cell type gene expression atlas in human tissues. This study integrate single cell RNA sequencing results to classify the gene expression specificity in single cell type levels)

Sjöstedt E, Zhong W, Fagerberg L, Karlsson M, Mitsios N, Adori C, Oksvold P, Edfors F, Limiszewska A, Hikmet F, Huang J, Du Y, Lin L, Dong Z, Yang L, Liu X, Jiang H, Xu X, Wang J, Yang H, Bolund L, Mardinoglu A, Zhang C, von Feilitzen K, Lindskog C, Pontén F, Luo Y, Hökfelt T, Uhlén M, Mulder J. An atlas of the protein-coding genes in the human, pig, and mouse brain. Science. 2020 Mar 6;367(6482):eaay5947. doi: 10.1126/science.aay5947. PMID: 32139519. (This study reported the first systematic classification of gene expression specificity and distribution of all protein-coding genes in the mouse, pig and human brain.)

Kalucka J, de Rooij LPMH, Goveia J, Rohlenova K, Dumas SJ, Meta E, Conchinha NV, Taverna F, Teuwen LA, Veys K, García-Caballero M, Khan S, Geldhof V, Sokol L, Chen R, Treps L, Borri M, de Zeeuw P, Dubois C, Karakach TK, Falkenberg KD, Parys M, Yin X, Vinckier S, Du Y, Fenton RA, Schoonjans L, Dewerchin M, Eelen G, Thienpont B, Lin L, Bolund L, Li X, Luo Y, Carmeliet P. Single-Cell Transcriptome Atlas of Murine Endothelial Cells. Cell. 2020 Feb 20;180(4):764-779.e20. doi: 10.1016/j.cell.2020.01.015. Epub 2020 Feb 13. PMID: 32059779. (This study reported the first investigation of EC heterogeneity in mouse tissues/organs using single cell transcriptome analysis)

Niu D, Wei HJ, Lin L, George H, Wang T, Lee IH, Zhao HY, Wang Y, Kan Y, Shrock E, Lesha E, Wang G, Luo Y, Qing Y, Jiao D, Zhao H, Zhou X, Wang S, Wei H, Güell M, Church GM, Yang L. Inactivation of porcine endogenous retrovirus in pigs using CRISPR-Cas9. Science. 2017 Sep 22;357(6357):1303-1307. doi: 10.1126/science.aan4187. Epub 2017 Aug 10. PMID: 28798043; PMCID: PMC5813284. (The first PERV inactivated pigs were generated by CRISPR and cloning.)

Full publications

Zeng, Y., Wang, A., Lv, W., Wang, Q., Jiang, S., Pan, X., Wang, F., Yang, H., Bolund, L., Lin, C., Han, P. & Luo, Y. (2023). Recent development of urinary biomarkers for bladder cancer diagnosis and monitoring. Clinical and Translational Discovery, 3(2), Article e183. https://doi.org/10.1002/ctd2.183
Neldeborg, S., Lin, L., Stougaard, M. & Luo, Y. (2019). Rapid and Efficient Gene Deletion by CRISPR/Cas9. In Methods in Molecular Biology: Methods and Protocols (pp. 233-247). Humana Press. https://doi.org/10.1007/978-1-4939-9170-9_14
Cavazza, A., Hendel, A., Bak, R. O., Rio, P., Güell, M., Lainšček, D., Arechavala-Gomeza, V., Peng, L., Hapil, F. Z., Harvey, J., Ortega, F. G., Gonzalez-Martinez, C., Lederer, C. W., Mikkelsen, K., Gasiunas, G., Kalter, N., Gonçalves, M. A. F. V., Petersen, J., Garanto, A. ... COST Action CA21113 (2023). Progress and harmonization of gene editing to treat human diseases: Proceeding of COST Action CA21113 GenE-HumDi. Molecular Therapy Nucleic Acids, 34, 102066. Article 102066. https://doi.org/10.1016/j.omtn.2023.102066, https://doi.org/10.1016/j.omtn.2023.102066
Yuan, H., Song, Z., Sun, X.-Q., Song, C., Guo, L., Zhang, Q., Luo, Y., Yuan, C., Gao, J. & Jia, X. (2025). Profiling the cell diversity and tissue structure of aqueous humor circulatory system in human eyes using spatial single-cell RNA sequencing. Genes & diseases, 12(1), 101304. Article 101304. https://doi.org/10.1016/j.gendis.2024.101304
Luo, Y. & COST Action CA21113 Members (2025). Proceedings of the second annual meeting of GenE-HumDi (COST Action 21113). Frontiers in Genome Editing, 7, Article 1667329. https://doi.org/10.3389/fgeed.2025.1667329
YeYang, S. U., Lin, L., Geng, TIAN., Chen, CHEN., Tao, LIU., XingYa, XU., XinPeng, QI. & XiuQing, ZHANG. (2009). Prepare re-sequencing DNA library of 2 cancer candidate genes using ligation-by-amplification protocol by two PCR reactions. Science in China. Series C: Life Sciences, 52(5), 483-491. https://doi.org/10.1007/s11427-009-0066-8
Gostinčar, C., Sun, X., Zajc, J., Fang, C., Hou, Y., Luo, Y., Gunde-Cimerman, N. & Song, Z. (2019). Population Genomics of an Obligately Halophilic Basidiomycete Wallemia ichthyophaga. Frontiers in Microbiology, 10. https://doi.org/10.3389/fmicb.2019.02019
Xu, Z., He, J., Han, P., Dai, P., Lv, W., Liu, N., Liu, L., Liu, L., Pan, X., Xiang, X., Li, H., Ge, F., Gao, S., Liao, Z., Luo, Y. & Li, Y. (2023). Plasma extrachromosomal circular DNA is a pathophysiological hallmark of short-term intensive insulin therapy for type 2 diabetes. Clinical and Translational Medicine, 13(10), Article e1437. https://doi.org/10.1002/ctm2.1437
Zhou, M., Lv, W., Han, P., Sun, K., Hao, Z., Gao, L., Xu, Y., Xu, Z., Shao, S., Ma, S., Guo, Q., Zhang, H., Liu, K., Yang, F., Yuan, Z., Wu, G., Yu, C., Luo, Y., Yao, Z. & Zhao, J. (2024). Plasma extrachromosomal circular DNA as a potential diagnostic biomarker for nodular thyroid disease. Clinical and Translational Medicine, 14(6), e1740. https://doi.org/10.1002/ctm2.1740
Han, P., Zhang, C., Ge, F., Liu, C., Fu, J., Lv, W., Jin, X., Zhang, J., Zhao, L., Luo, Y., Su, X. & Lan, X. (2025). Plasma cell-free extrachromosomal circular DNA is a molecular hallmark of preeclampsia. Computational and Structural Biotechnology Journal, 27, 2602-2613. https://doi.org/10.1016/j.csbj.2025.06.020
Fan N, Chen J, Shang Z, Dou H, Ji G, Zou Q, Wu L, He L, Wang F, Liu K, Liu N, Han J, Zhou Q, Pan D, Yang D, Zhao B, Ouyang Z, Liu Z, Zhao Y, Lin L, Zhong C, Wang Q, Wang S, Xu Y, Luan J, Liang Y, Yang Z, Li J, Lu C, Vajta G, Li Z, Ouyang H, Wang H, Wang Y, Yang Y, Liu Z, Wei H, Luan Z, Esteban MA, Deng H, Yang H, Pei D, Li N, Pei G, Liu L, Du Y, Xiao L, Lai L. (2013). Piglets cloned from induced pluripotent stem cells. Cell Research, 23(1), 162-6.
Dumas, S. J., Meta, E., Borri, M., Luo, Y., Li, X., Rabelink, T. J. & Carmeliet, P. (2021). Phenotypic diversity and metabolic specialization of renal endothelial cells. Nature Reviews. Nephrology, 17(7), 441-464. https://doi.org/10.1038/s41581-021-00411-9
Zhang, Y., Schmid, B., Nikolaisen, N. K., Rasmussen, M. A., Aldana, B. I., Agger, M., Calloe, K., Stummann, T. C., Larsen, H. M., Nielsen, T. T., Huang, J., Xu, F., Liu, X., Bolund, L., Meyer, M., Bak, L. K., Waagepetersen, H. S., Luo, Y., Nielsen, J. E. ... FReJA Consortium (2017). Patient iPSC-Derived Neurons for Disease Modeling of Frontotemporal Dementia with Mutation in CHMP2B. Stem Cell Reports, 8(3), 648-658. https://doi.org/10.1016/j.stemcr.2017.01.012
Madan, E., Palma, A. M., Vudatha, V., Kumar, A., Bhoopathi, P., Wilhelm, J., Bernas, T., Martin, P. C., Bilolikar, G., Gogna, A., Peixoto, M. L., Dreier, I., Araujo, T. F., Garre, E., Gustafsson, A., Dorayappan, K. D. P., Mamidi, N., Sun, Z., Yekelchyk, M. ... Gogna, R. (2025). Ovarian tumor cells gain competitive advantage by actively reducing the cellular fitness of microenvironment cells. Nature Biotechnology, 43(11), 1833-1847. Article e13714. https://doi.org/10.1038/s41587-024-02453-3
Li, Z., Sun, C., Wang, F., Wang, X., Zhu, J., Luo, L., Ding, X., Zhang, Y., Ding, P., Wang, H., Pu, M., Li, Y., Wang, S., Qin, Q., Wei, Y., Sun, J., Wang, X., Luo, Y., Chen, D. & Qiu, W. (2022). Molecular mechanisms governing circulating immune cell heterogeneity across different species revealed by single-cell sequencing. Clinical and Translational Medicine, 12(1), Article e689. https://doi.org/10.1002/ctm2.689
Nelson, S. R., Zhang, C., Roche, S., O'Neill, F., Swan, N., Luo, Y., Larkin, A., Crown, J. & Walsh, N. (2020). Modelling of pancreatic cancer biology: transcriptomic signature for 3D PDX-derived organoids and primary cell line organoid development. Scientific Reports, 10(1), Article 2778. https://doi.org/10.1038/s41598-020-59368-7
Schmidt M, Winter KD, Dantzer V, Li J, Kragh PM, Du Y, Lin L, Liu Y, Vajta G, Sangild PT, Callesen H, Agerholm JS (2011). Maternal endometrial oedema may increase perinatal mortality of cloned and transgenic piglets. Reproduction, Fertility and Development, 645-53.
Pan, X., Qu, K., Yuan, H., Xiang, X., Anthon, C., Pashkova, L., Liang, X., Han, P., Corsi, G. I., Xu, F., Liu, P., Zhong, J., Zhou, Y., Ma, T., Jiang, H., Liu, J., Wang, J., Jessen, N., Bolund, L. ... Luo, Y. (2022). Massively targeted evaluation of therapeutic CRISPR off-targets in cells. Nature Communications, 13(1), Article 4049. https://doi.org/10.1038/s41467-022-31543-6
Zeng, Y., Lv, W., Tao, H., Li, C., Jiang, S., Liang, Y., Chen, C., Yu, T., Li, Y., Wu, S., Cui, X., Liang, N., Wang, P., Xu, H., Dong, J., Teng, H., Chen, K., Mu, K., Fan, T. ... Han, P. (2025). Mapping the chromothripsis landscape in urothelial carcinoma unravels great intratumoral and intertumoral heterogeneity. iScience, 28(1), 111510. Article 111510. https://doi.org/10.1016/j.isci.2024.111510
Liu, T., Li, J., Dou, H., Xiang, X., Chen, W., Zhang, T., Li, L., Zhang, X., Dong, X., Chen, L., Lin, X., Li, J., Sun, H.-X., Gu, Y. & Lin, L. (2020). Low-Concentration Essential Amino Acids in PZM-3 Improve the Developmental Competence of Porcine Embryos Produced by Handmade Cloning. Cellular reprogramming, 22(6), 282-290. https://doi.org/10.1089/cell.2020.0036
Xiang, X., Luo, L., Nodzyński, M., Li, C., Han, P., Dou, H., Petersen, T. S., Liang, X., Pan, X., Qu, K., Yang, L., Dang, Y., Liu, X., Bolund, L., Zhang, X., Tong, G., Xing, Y., Luo, Y. & Lin, L. (2019). LION: a simple and rapid method to achieve CRISPR gene editing. Cellular and Molecular Life Sciences, 76(13), 2633-2645. https://doi.org/10.1007/s00018-019-03064-x
Li, C., Lv, W., He, Z., Pan, X., Zeng, Y., Mulder, J., Sjöstedt, E., Huang, Z., Liu, W., Xu, L., Eisenberg, E., Lin, L., Hansen, J. B., Huang, J. & Luo, Y. (2025). Landscape of A-I RNA editing in mouse, pig, macaque, and human brains. Nucleic Acids Research, 53(11), Article gkaf534. https://doi.org/10.1093/nar/gkaf534
Ogurlu, B., van Furth, L. A., Zuo, Y., Hamelink, T. L., van Klinken, J. B., Pamplona, C. C., Bennedsgaard, S. S., van Leeuwen, L. L., Lantinga, V. A., Qi, H., Pool, M. B. F., Vendrell, I., Kessler, B. M., Fischer, R., Lin, L., Luo, Y., Jespersen, B., van Dijk, K. W., Bakker, B. M. ... Moers, C. (2026). Kidney Metabolism During Normothermic Machine Perfusion Differs Substantially From In Vivo Conditions. Transplantation, 110(2), e405-e415. https://doi.org/10.1097/TP.0000000000005586
Lebas, M., Chinigò, G., Courmont, E., Bettaieb, L., Machmouchi, A., Goveia, J., Beatovic, A., Van Kerckhove, J., Robil, C., Angulo, F. S., Vedelago, M., Errerd, A., Treps, L., Gao, V., Delgado De la Herrán, H. C., Mayeuf-Louchart, A., L'homme, L., Chamlali, M., Dejos, C. ... Cantelmo, A. R. (2024). Integrated single-cell RNA-seq analysis reveals mitochondrial calcium signaling as a modulator of endothelial-to-mesenchymal transition. Science Advances, 10(32), eadp6182. Article adp6182. https://doi.org/10.1126/sciadv.adp6182
Niu, D., Wei, H.-J., Lin, L., George, H., Wang, T., Lee, I.-H., Zhao, H.-Y., Kan, Y., Shrock, E., Lesha, E., Wang, G., Luo, Y., Qing, Y., Jiao, D., Zhao, H., Zhou, X., Wang, S., Wei, H., Güell, M. ... Yang, L. (2017). Inactivation of porcine endogenous retrovirus in pigs using CRISPR-Cas9. Science, 357(6357), 1303-1307. https://doi.org/10.1126/science.aan4187