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

Koning, M., Dumas, S. J., Avramut, M. C., Koning, R. I., Meta, E., Lievers, E., Wiersma, L. E., Borri, M., Liang, X., Xie, L., Liu, P., Chen, F., Lin, L., Luo, Y., Mulder, J., Spijker, H. S., Jaffredo, T., van den Berg, B. M., Carmeliet, P. ... Rabelink, T. J. (2022). Vasculogenesis in kidney organoids upon transplantation. npj Regenerative Medicine, 7(1), Article 40. https://doi.org/10.1038/s41536-022-00237-4
Arslanova, A., Shafaattalab, S., Ye, K., Asghari, P., Lin, L., Kim, B. R., Roston, T. M., Hove-Madsen, L., Van Petegem, F., Sanatani, S., Moore, E., Lynn, F., Søndergaard, M., Luo, Y., Chen, S. R. W. & Tibbits, G. F. (2021). Using hiPSC-CMs to Examine Mechanisms of Catecholaminergic Polymorphic Ventricular Tachycardia. Current Protocols, 1(12), Article e320. https://doi.org/10.1002/cpz1.320
Song, Q., Datta, S., Liang, X., Xu, X., Pavicic, P., Zhang, X., Zhao, Y., Liu, S., Zhao, J., Xu, Y., Xu, J., Wu, L., Wu, Z., Zhang, M., Zhao, Z., Lin, C., Wang, Y., Han, P., Jiang, P. ... Yang, J. (2023). Type I interferon signaling facilitates resolution of acute liver injury by priming macrophage polarization. Cellular & molecular immunology, 20(2), 143-157. https://doi.org/10.1038/s41423-022-00966-y
Teuwen, L. A., De Rooij, L. P. M. H., Cuypers, A., Rohlenova, K., Dumas, S. J., García-Caballero, M., Meta, E., Amersfoort, J., Taverna, F., Becker, L. M., Veiga, N., Cantelmo, A. R., Geldhof, V., Conchinha, N. V., Kalucka, J., Treps, L., Conradi, L. C., Khan, S., Karakach, T. K. ... Carmeliet, P. (2021). Tumor vessel co-option probed by single-cell analysis. Cell Reports, 35(11), Article 109253. https://doi.org/10.1016/j.celrep.2021.109253
Luo, Y., Ceasar, S. A. & Benabdellah, K. (2025). Trajectory of genome editing technology. BMC Biology, 23(1), 351. Article 351. https://doi.org/10.1186/s12915-025-02450-1
Lin, L. & Luo, Y. (2019). Tracking CRISPR's Footprints. In Y. Luo (Ed.), Methods in Molecular Biology: Methods and Protocols (pp. 13-28). Springer Science+Business Media. https://doi.org/10.1007/978-1-4939-9170-9_2
Kostanjšek, R., Diderichsen, B., Recknagel, H., Gunde-Cimerman, N., Gostinčar, C., Fan, G., Kordiš, D., Trontelj, P., Jiang, H., Bolund, L. & Luo, Y. (2022). Toward the massive genome of Proteus anguinus-illuminating longevity, regeneration, convergent evolution, and metabolic disorders. Annals of the New York Academy of Sciences, 1507(1), 5-11. https://doi.org/10.1111/nyas.14686
Li, C., Zhang, Y., Leng, L., Pan, X., Zhao, D., Li, X., Huang, J., Bolund, L., Lin, G., Luo, Y. & Xu, F. (2022). The single-cell expression profile of transposable elements and transcription factors in human early biparental and uniparental embryonic development. Frontiers in Cell and Developmental Biology, 10, Article 1020490. https://doi.org/10.3389/fcell.2022.1020490
Falkenberg, K. D., Rohlenova, K., Luo, Y. & Carmeliet, P. (2019). The metabolic engine of endothelial cells. Nature Metabolism, 1(10), 937-946. https://doi.org/10.1038/s42255-019-0117-9
FarmGTEx Consortium (2025). The Farm Animal Genotype-Tissue Expression (FarmGTEx) Project. Nature Genetics, 57(4), 786-796. Article 604. https://doi.org/10.1038/s41588-025-02121-5
Zhang, C., Li, C., Yang, L., Leng, L., Jovic, D., Wang, J., Fang, F., Li, G., Zhao, D., Li, X., Lin, L., Luo, Y., Bolund, L., Huang, J., Lin, G. & Xu, F. (2021). The Dynamic Changes of Transcription Factors During the Development Processes of Human Biparental and Uniparental Embryos. Frontiers in Cell and Developmental Biology, 9, Article 709498. https://doi.org/10.3389/fcell.2021.709498
Luo, Y., Lin, L., Golas, M. M., Sørensen, C. B. & Bolund, L. (2015). Targeted Porcine Genome Engineering with TALENs. In Somatic Genome Manipulation : Advances, Methods and Applications (pp. 17-33). Springer.
Secher, J. O., Ceylan, A., Mazzoni, G., Mashayekhi, K., Li, T., Muenthaisong, S., Nielsen, T. T., Li, D., Li, S., Petkov, S., Cirera, S., Luo, Y., Thombs, L., Kadarmideen, H. N., Dinnyes, A., Bolund, L., Roelen, B. A. J., Schmidt, M., Callesen, H. ... Freude, K. K. (2017). Systematic in vitro and in vivo characterization of Leukemia-inhibiting factor- and Fibroblast growth factor-derived porcine induced pluripotent stem cells. Molecular Reproduction and Development, 84(3), 229-245. https://doi.org/10.1002/mrd.22771
Zheng, T., Huang, J., Xiang, X., Li, S., Yu, J., Qu, K., Xu, Z., Han, P., Dong, Z., Liu, Y., Xu, F., Yang, H., Jäättelä, M., Luo, Y. & Liu, B. (2021). Systematical analysis reveals a strong cancer relevance of CREB1-regulated genes. Cancer Cell International, 21(1), Article 530. https://doi.org/10.1186/s12935-021-02224-z
Gultom, M., Lin, L., Brandt, C. B., Milusev, A., Despont, A., Shaw, J., Döring, Y., Luo, Y. & Rieben, R. (2025). Sustained Vascular Inflammatory Effects of SARS-CoV-2 Spike Protein on Human Endothelial Cells. Inflammation, 48(4), 2531–2547. https://doi.org/10.1007/s10753-024-02208-x
Pribenszky, C., Vajta, G., Molnár, M., Du, Y., Lin, L., Bolund, L. & Yovich, J. (2010). Stress for Stress Tolerance? A Fundamentally New Approach in Mammalian Embryology. Biology of Reproduction, 83(5), 690-697. https://doi.org/10.1095/biolreprod.110.083386
Liu, B., Palmfeldt, J., Lin, L., Colaço, A., Clemmensen, K. K. B., Huang, J., Xu, F., Liu, X., Maeda, K., Luo, Y. & Jäättelä, M. (2018). STAT3 associates with vacuolar H+-ATPase and regulates cytosolic and lysosomal pH. Cell Research, 28(10), 996–1012. https://doi.org/10.1038/s41422-018-0080-0
Lv, W., Zeng, Y., Li, C., Liang, Y., Tao, H., Zhu, Y., Sui, X., Li, Y., Jiang, S., Gao, Q., Rodriguez-Fos, E., Prasad, G., Wang, Y., Zhou, R., Xu, Z., Pan, X., Chen, L., Xiang, X., Teng, H. ... Han, P. (2025). Spatial-Temporal Diversity of Extrachromosomal DNA Shapes Urothelial Carcinoma Evolution and the Tumor Immune Microenvironment. Cancer Discovery, 15(6), 1225-1246. https://doi.org/10.1158/2159-8290.CD-24-1532
Yang, S., Lan, T., Wei, R., Lin, L., Du, H., Huang, Y., Zhang, G., Huang, S., Shi, M., Wang, C., Li, R., Han, L., Tang, D., Li, H., Zhang, H., Cui, J., Lu, H., Huang, J., Luo, Y. ... Fang, S.-G. (2023). Single-nucleus transcriptome inventory of giant panda reveals cellular basis for fitness optimization under low metabolism. BMC Biology, 21(1), 222. Article 222. https://doi.org/10.1186/s12915-023-01691-2
Koning, M., Dumas, S. J., Meta, E., Lievers, E., de Graaf, A. M. A., Borri, M., Nai Chung Tong, L. J., Liang, X., Liu, P., Chen, F., Lin, L., Luo, Y., Carmeliet, P., van den Berg, C. W. & Rabelink, T. J. (2025). Single cell transcriptomics of human kidney organoid endothelium reveals vessel growth processes and arterial maturation upon transplantation. npj Regenerative Medicine, 10(1), Article 32. https://doi.org/10.1038/s41536-025-00418-x
Kalucka, J., de Rooij, L. P. M. H., Goveia, J., Rohlenova, K., Dumas, S. J., Meta, E., Conchinha, N. V., Taverna, F., Teuwen, L.-A., Veys, K., García-Caballero, M., Khan, S., Geldhof, V., Sokol, L., Chen, R., Treps, L., Borri, M., de Zeeuw, P., Dubois, C. ... Carmeliet, P. (2020). Single-Cell Transcriptome Atlas of Murine Endothelial Cells. Cell, 180(4), 764-779.e20. https://doi.org/10.1016/j.cell.2020.01.015
Leng, L., Sun, J., Huang, J., Gong, F., Yang, L., Zhang, S., Yuan, X., Fang, F., Xu, X., Luo, Y., Bolund, L., Peters, B. A., Lu, G., Jiang, T., Xu, F. & Lin, G. (2019). Single-Cell Transcriptome Analysis of Uniparental Embryos Reveals Parent-of-Origin Effects on Human Preimplantation Development. Cell Stem Cell, 25(5), 697-712.e6. https://doi.org/10.1016/j.stem.2019.09.004
Jovic, D., Liang, X., Zeng, H., Lin, L., Xu, F. & Luo, Y. (2022). Single-cell RNA sequencing technologies and applications: A brief overview. Clinical and Translational Medicine, 12(3), Article e694. https://doi.org/10.1002/ctm2.694
Dumas, S. J., Meta, E., Borri, M., Goveia, J., Rohlenova, K., Conchinha, N. V., Falkenberg, K., Teuwen, L.-A., de Rooij, L., Kalucka, J., Chen, R., Khan, S., Taverna, F., Lu, W., Parys, M., De Legher, C., Vinckier, S., Karakach, T. K., Schoonjans, L. ... Carmeliet, P. (2020). Single-Cell RNA Sequencing Reveals Renal Endothelium Heterogeneity and Metabolic Adaptation to Water Deprivation. Journal of the American Society of Nephrology : JASN, 31(1), 118-138. https://doi.org/10.1681/ASN.2019080832
Rohlenova, K., Goveia, J., García-Caballero, M., Subramanian, A., Kalucka, J., Treps, L., Falkenberg, K. D., de Rooij, L. P. M. H., Zheng, Y., Lin, L., Sokol, L., Teuwen, L.-A., Geldhof, V., Taverna, F., Pircher, A., Conradi, L.-C., Khan, S., Stegen, S., Panovska, D. ... Carmeliet, P. (2020). Single-Cell RNA Sequencing Maps Endothelial Metabolic Plasticity in Pathological Angiogenesis. Cell Metabolism, 31(4), 862-877.e14. https://doi.org/10.1016/j.cmet.2020.03.009
Geldhof, V., de Rooij, L. P. M. H., Sokol, L., Amersfoort, J., De Schepper, M., Rohlenova, K., Hoste, G., Vanderstichele, A., Delsupehe, A. M., Isnaldi, E., Dai, N., Taverna, F., Khan, S., Truong, A. C. K., Teuwen, L. A., Richard, F., Treps, L., Smeets, A., Nevelsteen, I. ... Carmeliet, P. (2022). Single cell atlas identifies lipid-processing and immunomodulatory endothelial cells in healthy and malignant breast. Nature Communications, 13, Article 5511. https://doi.org/10.1038/s41467-022-33052-y
Cham, L. B., Rosas-Umbert, M., Lin, L., Tolstrup, M. & Søgaard, O. S. (2024). Single-Cell Analysis Reveals That CD47 mRNA Expression Correlates with Immune Cell Activation, Antiviral Isgs, and Cytotoxicity. Cellular physiology and biochemistry : international journal of experimental cellular physiology, biochemistry, and pharmacology, 58(4), 322-335. https://doi.org/10.33594/000000715
Zhang, J., Li, H., Teng, H., Zhang, T., Luo, Y., Zhao, M., Li, Y.-Q. & Sun, Z. S. (2012). Regulation of Peripheral Clock to Oscillation of Substance P Contributes to Circadian Inflammatory Pain. Anesthesiology News, 117(1). https://doi.org/10.1097/ALN.0b013e31825b4fc1