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 communications, 13 (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

2019

Contribution to journal

Mikkelsen, R. B., Frederiksen, H. R. S., Gjerris, M., Holst, B., Hyttel, P., Luo, Y., Freude, K. & Sandøe, P. (2019). Genetic Protection Modifications: Moving Beyond the Binary Distinction Between Therapy and Enhancement for Human Genome Editing. The CRISPR Journal, 2(6), 362-369. https://doi.org/10.1089/crispr.2019.0024

Fløe, L. & Luo, Y. (2016). Precision Epigenome Editing – Promise and Challenge. Biozoom, (4).

Nissen, P. & Heilesen, L. (2014). Brian Clark has died - marking the end of an era: Professor Brian Frederic Carl Clark, founder of Structural Biology Research at Aarhus University, died on Monday, October 6, 2014. Aged 78 years. IUBMB Life, 66(10), 655-656. https://doi.org/10.1002/iub.1325

2025

Working Paper

AlZaim, I., Hassan, M. N., Schröter, M., Mannino, L., Dragicevic, K., Sjogaard, M. B., Festa, J., Dokshokova, L., Weinbrenner, S., Tardajos Ayllon, B., Hansen, B., Rasmussen, R. K., Christensen, J. N., Wagman, O., Schipper, R., Cai, M., Dheedene, W., Bohn, A. B., Farup, J. ... Kalucka, J. (2025). Defining the vascular niche of human adipose tissue across metabolic states. bioRxiv. https://doi.org/10.1101/2024.09.22.610444

Ma, W., Huang, J., Cai, B., Shao, M., Yu, X., Kjær, M. B., Lv, M., Zhong, X., Xu, S., Zhan, B., Li, Q., Huang, Q., Ma, M., Cheng, L., Luo, Y., Grønbæk, H., Zhou, X. & Lin, L. (2024). A gene-based clustering approach reveals QSOX1/IL1RAP as promising biomarkers for the severity of non-alcoholic fatty liver disease. https://doi.org/10.1101/2023.07.26.23293038

Ma, W., Zhong, X., Cai, B., Shao, M., Yu, X., Lv, M., Xu, S., Zhan, B., Li, Q., Ma, M., Kjær, M. B., Huang, J., Luo, Y., Grønbæk, H. & Lin, L. (2023). Unveiling the pathogenesis of non-alcoholic fatty liver disease by decoding biomarkers through integrated single-cell and single-nucleus profiles. https://doi.org/10.1101/2023.10.05.23296635

Andersen, O. M., Bøgh, N., Landau, A., Pløen, G. G., Jensen, A. M. G., Monti, G., Ulhøi, B. P., Nyengaard, J. R., Jacobsen, K. R., Jørgensen, M. M., Holm, I. E., Kristensen, M. L., Søvsø Szocska Hansen, E., Teunissen, C. E., Breidenbach, L., Droescher, M., Liu, Y., Pedersen, H. S., Callesen, H. ... Sørensen, C. B. (2021). In vivo evidence that SORL1, encoding the endosomal recycling receptor SORLA, can function as a causal gene in Alzheimer´s Disease. http://biorxiv.org/content/early/2021/07/13/2021.07.13.452149

2012

Thesis

Luo, Y. (2012). Development of BRCA1 Knockout Pigs and Transcriptome Studies of Disease Progression.

Lin, L. (2011). Effects of physicochemical stress om developmental competence of porcine embryos and their tolerance to vitrification. Aarhus Universitet.

2016

Patent

Luo, Y. & Bolund, L. (2016). Pig model for diabetes.

2023

Contribution to conference

Zhou, X., Rahimi, K., Kjems, J. & Lin, L. (2023). High-resolution RNA isoform variation analysis by combining the advantages of single-cell RNA and nanopore sequencing. 44. Abstract from Neuroscience Day, Aarhus, Denmark.

Berthelsen, M. F., Møller, S., Callesen, H., Dagnæs-Hansen, F., Luo, Y., Jakobsen, J. E. & Thomsen, M. K. (2016). The CRISPR-Cas9 Minipig.

Lin, L., Liu, Y., Kragh, P., Li, J., Bolund, L., Yang, H., Zhang, X., Du, Y., Kuwayama, M., Callesen, H. & Vajta, G. (2008). Osmotic pre-treatment of porcine oocytes improves their cryotolerance and developmental competence. Abstract from Scientific Meeting og the AETE Conference, Pau, France.

Liu, Y., Østrup, O., Li, J., Vajta, G., Lin, L., Kragh, P. M., Purup, S. & Callesen, H. (2010). Effect of Xenopus egg extract treatment of donor cells on porcine somatic cell nuclear transfer. Poster session presented at Annual Conference of the International Embryo Transfer Society, Cordoba, Argentina.

2008

Contribution to book anthology

Li, J., Liu, Y., Lin, L., Kragh, P. M., Jacobsen, J. E., Jørgensen, A. L., Purup, S., Bolund, L., Callesen, H. & Vajta, G. (2008). Production of porcine chimeric embryos with aggregation of embryos or blastomeres. In 24th Annual Meeting AETE Proceedings (pp. 192)

Xiang, X., Li, C., Chen, X., Dou, H., Li, Y., Zhang, X. & Luo, Y. (2019). CRISPR/Cas9-Mediated Gene Tagging: A Step-by-Step Protocol. In Y. Luo (Ed.), Methods in Molecular Biology (pp. 255-269). Humana Press. https://doi.org/10.1007/978-1-4939-9170-9_16

Lin, L. & Luo, Y. (2019). Functional Evaluation of CRISPR Activity by the Dual-Fluorescent Surrogate System: C-Check. In Y. Luo (Ed.), Methods in Molecular Biology: Methods and Protocols (pp. 67-77). Springer Science+Business Media. https://doi.org/10.1007/978-1-4939-9170-9_5

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

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

Berthelsen, M. F., Thomsen, M. K. & Luo, Y. (2018). Genetically Engineered Pig Models for Human Diseases using ZFNs, TALENs and CRISPR/Cas9. In Genome Editing and Engineering: From TALENs, ZFNs and CRISPRs to Molecular Surgery (pp. 110-131). Cambridge University Press. https://doi.org/10.1017/9781316756300.010

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.

2012

Contribution to journal

Schmidt, M., Winter, K. D., Li, J., Kragh, P., Du, Y., Lin, L., Liu, Y., Li, R., Vajta, G. & Callesen, H. (2012). Malformations found by autopsy of cloned and transgenic piglets of different breeds. Reproduction, Fertility and Development, 24(1), 123-123.

Bentzon, J. F., Sørensen, C. B., Al-Mashhadi, R. H., Kragh, P. M., Nielsen, L. B., Li, J., Lin, L., Liu, Y., Moldt, B., Schmidt, M., Thim, T., Vajta, G., Purup, S., Bolund, L., Callesen, H., Mikkelsen, J. G. & Falk, E. (2012). Hypercholesterolemic minipigs created by liver-specific expression of a PCSK9 gain-of-function mutant. Transgenic Research, 21(4), 910-911. https://doi.org/10.1007/s11248-011-9570-2

Dantzer, V., Schmidt, M., Callesen, H., Winter, K. D., Kragh, P. M., Li, J., Du, Y., Lin, L., Liu, Y., Vajta, G. & Agerholm, J. S. (2011). Placental morphology near term after transfer of cloned and transgenic embyoes: miscarriage showed endometrial oedema and blood extravasation. Placenta, 2011(32), A23.

Liu, Y., Østrup, O., Li, J., Vajta, G., Lin, L., Kragh, P. M., Purup, S. & Callesen, H. (2010). Effect of Xenopus egg extract treatment of donor cells on porcine somatic cell nuclear transfer. Reproduction, Fertility and Development, (1), 192.

Schmidt, M., Kragh, P. M., Li, J., Lin, L., Liu, Y., Vajta, G. & Callesen, H. (2010). Establishment of Pregnancies in Large White Sow Recipients after Transfer of Cloned Embryos of Different Pig Breeds. Reproduction, Fertility and Development, (1), 197-198.

Du, Y., Yang, Z., Lin, L., Lv, B., Kragh, P. M., Zhang, X., Vajta, G., Yang, H. & Bolund, L. (2010). Simplified activation method to improve the in vitro development of handmade cloned (HMC) porcine embryos. Reproduction, Fertility and Development, (1), 114. http://www.publish.csiro.au/nid/45/issue/4842.htm

Lin, L., Kragh, P. M., Purup, S., Du, Y., Zhang, X., Bolund, L., Callesen, H. & Vajta, G. (2009). Comparison of the effects of pre-treatment with sodium chloride, sucrose and trehalose on developmental competence porcine oocytes. Reproduction, Fertility and Development, (1), 121. https://doi.org/10.1071/RDv21n1Ab43

Gao, P., Li, S., Dong, Z., Luo, Y., Zhang, X., Han, L., Peng, S., Shen, J., Xu, F. & Deng, Z. (2024). A plasma-derived exosomal microRNA signature by small RNA sequencing for early detection of postmenopausal osteoporosis. Clinical and Translational Medicine, 14(4), Article e1637. https://doi.org/10.1002/ctm2.1637

Wang, F., Ding, P., Liang, X., Ding, X., Brandt, C. B., Sjöstedt, E., Zhu, J., Bolund, S., Zhang, L., de Rooij, L. P. M. H., Luo, L., Wei, Y., Zhao, W., Lv, Z., Haskó, J., Li, R., Qin, Q., Jia, Y., Wu, W. ... Luo, Y. (2022). Author Correction: Endothelial cell heterogeneity and microglia regulons revealed by a pig cell landscape at single-cell level (Nature Communications, (2022), 13, 1, (3620), 10.1038/s41467-022-31388-z). Nature Communications, 13(1), Article 6748. https://doi.org/10.1038/s41467-022-34498-w

Wang, F., Xu, Q., Zhuang, Z., Li, Z., Gao, Q., Huang, Y., Luo, Y., Zhang, X., Zhu, L. & Chao, C.-C. (2021). A single-cell approach to engineer CD8+ T cells targeting cytomegalovirus. Cellular & molecular immunology, 18, 1326-1328. https://doi.org/10.1038/s41423-020-0466-z

Olagnier, D., Farahani, E., Thyrsted, J., Blay-Cadanet, J., Herengt, A., Idorn, M., Hait, A., Hernaez, B., Knudsen, A., Iversen, M. B., Schilling, M., Jørgensen, S. E., Thomsen, M., Reinert, L. S., Lappe, M., Hoang, H.-D., Gilchrist, V. H., Hansen, A. L., Ottosen, R. ... Holm, C. K. (2020). Author Correction: SARS-CoV2-mediated suppression of NRF2-signaling reveals potent antiviral and anti-inflammatory activity of 4-octyl-itaconate and dimethyl fumarate. Nature Communications, 11(1), Article 5419. https://doi.org/10.1038/s41467-020-19363-y

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

Chen, D., Luo, Y. & Cheng, G. (2023). Single cell and immunity: Better understanding immune cell heterogeneities with single cell sequencing. Clinical and Translational Medicine, 13(1), Article e1159. https://doi.org/10.1002/ctm2.1159

Luo, Y. (2019). Refining CRISPR-based genome and epigenome editing off-targets. Cell Biology and Toxicology, 35(4), 281-283. https://doi.org/10.1007/s10565-019-09482-8

Ortiz-Bueno, M., Zinghirino, F., Serra, P. P., Paschoudi, K., Montoliu, L., Atilla, E., Luo, Y., Cavazza, A., Lederer, C. W. & Benabdellah, K. (2026). From Bench to Bedside: Ethical and Clinical Best Practices for Genome Editing Applications. International Journal of Molecular Sciences , 27(3), Article 1484. https://doi.org/10.3390/ijms27031484

Cavazza, A., Molina-Estévez, F. J., Reyes, Á. P., Ronco, V., Naseem, A., Malenšek, Š., Pečan, P., Santini, A., Heredia, P., Aguilar-González, A., Boulaiz, H., Ni, Q., Cortijo-Gutierrez, M., Pavlovic, K., Herrera, I., de la Cerda, B., Garcia-Tenorio, E. M., Richard, E., Granados-Principal, S. ... Benabdellah, K. (2025). Advanced delivery systems for gene editing: A comprehensive review from the GenE-HumDi COST Action Working Group. Molecular Therapy Nucleic Acids, 36(1), Article 102457. https://doi.org/10.1016/j.omtn.2025.102457

Yuan, H., Song, C., Xu, H., Sun, Y., Anthon, C., Bolund, L., Lin, L., Benabdellah, K., Lee, C., Hou, Y., Gorodkin, J. & Luo, Y. (2025). An Overview and Comparative Analysis of CRISPR-SpCas9 gRNA Activity Prediction Tools. The CRISPR Journal, 8(2), 89-104. https://doi.org/10.1089/crispr.2024.0058

Nadukkandy, A. S., Kalaiselvan, S., Lin, L. & Luo, Y. (2025). Clinical application of single-cell RNA sequencing in disease and therapy. Clinical and Translational Medicine, 15(11), Article e70512. https://doi.org/10.1002/ctm2.70512

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

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

Berggreen, A. H., Petersen, J. L., Lin, L., Benabdellah, K. & Luo, Y. (2023). CRISPR delivery with extracellular vesicles: Promises and challenges. Journal of Extracellular Biology, 2(9), e111. Article e111. https://doi.org/10.1002/jex2.111

Noer, J. B., Hørsdal, O. K., Xiang, X., Luo, Y. & Regenberg, B. (2022). Extrachromosomal circular DNA in cancer: history, current knowledge, and methods. Trends in Genetics, 38(7), 766-781. https://doi.org/10.1016/j.tig.2022.02.007

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

Jovic, D., Yu, Y., Wang, D., Wang, K., Li, H., Xu, F., Liu, C., Liu, J. & Luo, Y. (2022). A Brief Overview of Global Trends in MSC-Based Cell Therapy. Stem Cell Reviews and Reports, 18(5), 1525-1545. https://doi.org/10.1007/s12015-022-10369-1

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

Wang, J., Zhang, X., Cheng, L. & Luo, Y. (2020). An overview and metanalysis of Machine and Deep Learning-Based CRISPR gRNA Design Tools. RNA Biology, 17(1), 13-22. https://doi.org/10.1080/15476286.2019.1669406

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

Holm, I. E., Alstrup, A. K. O. & Luo, Y. (2016). Genetically modified pig models for neurodegenerative disorders. Journal of Pathology, 238(2), 267-287. https://doi.org/10.1002/path.4654

Luo, Y., Lin, L., Bolund, L., Jensen, T. G. & Sørensen, C. B. (2012). Genetically modified pigs for biomedical research. Journal of Inherited Metabolic Disease, 35(4), 695-713. https://doi.org/10.1007/s10545-012-9475-0

Displaying results 1 to 50 out of 217

Link to full publications at PURE

https://pure.au.dk/portal/en/persons/alun%40biomed.au.dk

Revised 11.09.2025

Yonglun Luo