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

Cham, L. B., Gunst, J. D., Schleimann, M. H., Frattari, G. S., Rosas-Umbert, M., Vibholm, L. K., van der Sluis, R. M., Jakobsen, M. R., Olesen, R., Lin, L., Tolstrup, M. & Søgaard, O. S. (2023). Single cell analysis reveals a subset of cytotoxic-like plasmacytoid dendritic cells in people with HIV-1. iScience, 26(9), Article 107628. https://doi.org/10.1016/j.isci.2023.107628

Cham, L. B., Lin, L., Tolstrup, M. & Søgaard, O. S. (2024). Development of single-cell transcriptomic atlas of human plasmacytoid dendritic cells from people with HIV-1. STAR Protocols, 5(1), 102777. Article 102777. https://doi.org/10.1016/j.xpro.2023.102777

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

Chai, C., Liang, L., Mikkelsen, N. S., Wang, W., Zhao, W., Sun, C., Bak, R. O., Li, H., Lin, L., Wang, F. & Luo, Y. (2024). Single-cell transcriptome analysis of epithelial, immune, and stromal signatures and interactions in human ovarian cancer. Communications Biology, 7(1), 131. Article 131. https://doi.org/10.1038/s42003-024-05826-1

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

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

Cai, Y., Laustsen, A., Zhou, Y., Sun, C., Anderson, M. V., Li, S., Uldbjerg, N., Luo, Y., Jakobsen, M. R. & Mikkelsen, J. G. (2016). Targeted, homology-driven gene insertion in stem cells by ZFN-loaded 'all-in-one' lentiviral vectors. eLife, 5(JUN2016), Article e12213. https://doi.org/10.7554/eLife.12213

Brorson, J., Lin, L., Wang, J., Bæk, A., Billeskov, T. B., Thybo, F. F., Just, J., Haskó, J., Ravn, C., Hansen, R. L., Bue, M., Jørgensen, J. O. L., Luo, Y., Jessen, N. & Farup, J. (2025). Complementing muscle regeneration-fibro-adipogenic progenitor and macrophage-mediated repair of elderly human skeletal muscle. Nature Communications, 16(1), Article 5233. https://doi.org/10.1038/s41467-025-60627-2

Brix, J., Zhou, Y. & Luo, Y. (2015). The Epigenetic Reprogramming Roadmap in Generation of iPSCs from Somatic Cells. Journal of Genetics and Genomics.

Brandt, C. B., Fonager, S. V., Haskó, J., Helmig, R. B., Degn, S., Bolund, L., Jessen, N., Lin, L. & Luo, Y. (2023). HIF1A Knockout by Biallelic and Selection-Free CRISPR Gene Editing in Human Primary Endothelial Cells with Ribonucleoprotein Complexes. Biomolecules, 13(1), Article 23. https://doi.org/10.3390/biom13010023

Blechingberg, J., Luo, Y., Bolund, L., Damgaard, C. K. & Nielsen, A. L. (2012). Gene Expression Responses to FUS, EWS, and TAF15 Reduction and Stress Granule Sequestration Analyses Identifies FET-Protein Non-Redundant Functions. PLoS One, 7(9), e46251. https://doi.org/10.1371/journal.pone.0046251

Björkman, A., Johansen, S. L., Lin, L., Schertzer, M., Kanellis, D. C., Katsori, A.-M., Christensen, S. T., Luo, Y., Andersen, J. S., Elsässer, S. J., Londono-Vallejo, A., Bartek, J. & Schou, K. B. (2020). Human RTEL1 associates with Poldip3 to facilitate responses to replication stress and R-loop resolution. Genes & Development, 34(15-16), 1065-1074. https://doi.org/10.1101/gad.330050.119

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

Berthelsen, M. F., Riedel, M., Cai, H., Skaarup, S. H., Alstrup, A. K. O., Dagnæs-Hansen, F., Luo, Y., Jensen, U. B., Hager, H., Liu, Y., Callesen, H., Vendelbo, M. H., Jakobsen, J. E. & Thomsen, M. K. (2021). The CRISPR/Cas9 Minipig—A Transgenic Minipig to Produce Specific Mutations in Designated Tissues. Cancers, 13(12), Article 3024. https://doi.org/10.3390/cancers13123024

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

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

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

Banerjee, S., Zhang, X., Kuang, S., Wang, J., Li, L., Fan, G., Luo, Y., Sun, S., Han, P., Wu, Q., Yang, S., Ji, X., Li, Y., Deng, L., Tian, X., Wang, Z., Zhang, Y., Wu, K., Zhu, S. ... Liu, X. (2021). Comparative analysis of clonal evolution among patients with right- and left-sided colon and rectal cancer. iScience, 24(7), Article 102718. https://doi.org/10.1016/j.isci.2021.102718

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

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

Andersen, O. M., Bøgh, N., Landau, A. M., 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., Alstrup, A. K. O., Hansen, E. S. S., Teunissen, C. E., Breidenbach, L., Droescher, M., Liu, Y., Pedersen, H. S. ... Sørensen, C. B. (2022). A genetically modified minipig model for Alzheimer's disease with SORL1 haploinsufficiency. Cell Reports Medicine, 3(9), Article 100740. https://doi.org/10.1016/j.xcrm.2022.100740

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

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. (2026). Defining the vascular niche of human adipose tissue across metabolic states. Nature Metabolism, 8(3), 722-740. https://doi.org/10.1038/s42255-026-01475-2

Almeida Ferreira, S. R., Li, C., Klæstrup, I. H., Vitic, Z., Rasmussen, R. K., Kirkegaard, A., Toft, G. U., Betzer, C., Svendsen, P., Jensen, P. H., Luo, Y., Etzerodt, A., Moestrup, S. K. & Romero-Ramos, M. (2023). Sex-dimorphic neuroprotective effect of CD163 in an α-synuclein mouse model of Parkinson's disease. npj Parkinson's Disease , 9(1), 164. Article 164. https://doi.org/10.1038/s41531-023-00606-w

Ahlgreen, O. A., Hansen, M. W., Baake, J., Hybel, T. E., Rossi, R., Lai, X., Sankaranarayanan, I., Pold, J. A., Lin, L., Reinert, L., Paludan, S. R., Price, T. J., Pallesen, L. T. & Vægter, C. B. (2026). Mapping Satellite Glial Cell Heterogeneity Reveals Distinct Spatial Organization and Implies Functional Diversity in the Dorsal Root Ganglion. Advanced Science, 13(1), Article e11569. https://doi.org/10.1002/advs.202511569

Displaying results 201 to 225 out of 225

Link to full publications at PURE

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

Revised 11.09.2025

Yonglun Luo