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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.)