(* Corresponding author, # Co-first author)
1. Qiu Y, Liu Y, Zheng W, Chen W, Yang W, He X, Lin C, Ke R*. Visualization of Protein–Protein Interaction In Situ Using Hybridization-Enhanced Proximity Ligation Assay. Anal Chem. (Accepted)
2. Liu Y, Chen J, Lin C, Ke R*. Multiplexed in situ RNA imaging by combFISH. Anal Bioanal Chem. 2024, 416(16):3765-3774. （Selected for cover）
3. Qiu Y, Wei K, Lin H, Liu Y, Lin C, Ke R*. Combined amplification-based single-molecule fluorescence in situ hybridization with immunofluorescence for simultaneous in situ detection of RNAs and proteins. Biochem Biophys Res Commun. 2024, 696:149508.
4. Chen J, Ke R*. Spatial analysis toolkits for RNA in situ sequencing. Wiley Interdiscip Rev RNA. 2024, 15(2):e1842.
5. Chen Y, Zhang L, Shi X, Han J, Chen J, Zhang X, Xie D, Li Z, Niu X, Chen L, Yang C, Sun X, Zhou T, Su P, Li N, Greenblatt MB, Ke R*, Huang J*, Chen ZS*, Xu R*. Characterization of the Nucleus Pulposus Progenitor Cells via Spatial Transcriptomics. Adv Sci (Weinh). 2024, 4:e2303752.
6. Chen G, Yu D, Yang Y, Li X, Wang X, Sun D, Lu Y, Ke R, Zhang G, Cui J, Feng S. Adaptive expansion of ERVK solo-LTRs is associated with Passeriformes speciation events. Nat Commun. 2024, 15(1):3151.
7. Tang L, Xu D, Luo L, Ma W, He X, Diao Y, Ke R, Kapranov P. A novel human protein-coding locus identified using a targeted RNA enrichment technique. BMC Biol. 2024, 26;22(1):273.
1. Jiang M, Wei K, Li M, Lin C,Ke R*. Single-molecule RNA in situ detection in clinical FFPE tissue sections by vsmCISH. RNA. 2023, 29(6):836-846.
2. Rao X, Zheng L, Wei K, Li M, Jiang M, Qiu J, Zhou Y, Ke R* , Lin C. Novel In Situ Hybridization Assay for Chromogenic Single-Molecule Detection of Human Papillomavirus E6/E7 mRNA. Microbiology Spectrum. 2023, 11(2):e0389622.
3. Tang X, Chen J, Zhang X, Liu X, Xie Z, Wei K, Qiu J, Ma W, Lin C, Ke R*. Improved in situ sequencing for high-resolution targeted spatial transcriptomic analysis in tissue sections. Journal of Genetics and Genomics. 2023, 50(9):652-660.
4. Zhang HX, Zhou YL, Xu WY, Chen XL, Jiang JY, Zhou XM, Wang ZG, Ke RQ, Guo QW. Polymerase chain reaction-based assays facilitate the breeding and study of mouse models of Klinefelter syndrome. Asian J Androl. 2023;53(1):76-80.
5. Zhang Q, Xia K, Jiang M, Li Q, Chen W, Han M, Li W, Ke R, Wang F, Zhao Y, Liu Y, Fan C, Gu H. Catalytic DNA-Assisted Mass Production of Arbitrary Single-Stranded DNA. Angew Chem Int Ed Engl. 2023, 62(5): e202212011.
6. Wang W, Li X, Ding X, Xiong S, Hu Z, Lu X, Zhang K, Zhang H, Hu Q, Lai KS, Chen Z, Yang J, Song H, Wang Y, Wei L, Xia Z, Zhou B, He Y, Pu J, Liu X, Ke R, Wu T, Huang C, Baldini A, Zhang M, Zhang Z. Lymphatic endothelial transcription factor Tbx1 promotes an immunosuppressive microenvironment to facilitate post-myocardial infarction repair. Immunity. 2023, 56(10):2342-2357.e10.
7. Huang R, Liu K, Yue C, Wang Y, Zeng Z, Xiao L, Dong L, Ke R*, Yang C*, Liu D*. Chromogenic Visualization of Single RNA Molecules In Situ with Duplex Capability by Rolling Circle Amplification with Alkaline Phosphatase. Anal Chem, 95(32):12161-12168.
8. Zhu L, Ke R*. High-throughput single-cell genomic analysis for archival tissue blocks. The Innovation Life. 2023, 3: 10034.
1. Li Q, Zhang X, Ke R*. Spatial Transcriptomics for Tumor Heterogeneity Analysis. Frontiers in Genetics. 2022, 13:906158.
1. Yin J, Lin C, Jiang M, Tang X, Xie D, Chen J, Ke R*. CENPL, ISG20L2, LSM4, MRPL3 are four novel hub genes and may serve as diagnostic and prognostic markers in breast cancer. Sci Rep. 2021, 2, 11(1):15610.
2. Lin C, Liu X, Zheng B, Ke R*, Tzeng CM*. Liquid Biopsy, ctDNA Diagnosis through NGS. Life, 2021, 11(9):890.
3. Lin C, Jiang M, Liu L, Chen X, Zhao Y, Chen L, Hong Y, Wang X, Hong C, Yao X, Ke R*. Imaging of individual transcripts by amplification-based single-molecule fluorescence in situ hybridization. New Biotechnology. 2021, 61:116-123.
4. Yu Y, Zeng Z, Xie D, Chen R, Sha Y, Huang S, Cai W, Chen W, Li W, Ke R, Sun T. Interneuron origin and molecular diversity in the human fetal brain. Nat Neurosci. 2021, 24(12):1745-1756.
5. Liu Q, Li J, Zhang W, Xiao C, Zhang S, Nian C, Li J, Su D, Chen L, Zhao Q, Shao H, Zhao H, Chen Q, Li Y, Geng J, Hong L, Lin S, Wu Q, Deng X, Ke R, Ding J, Johnson RL, Liu X, Chen L, Zhou D. Glycogen accumulation and phase separation drives liver tumor initiation. Cell. 2021, 184(22):5559-5576.e19.
1. Zhao Y, Lin C, Wu P, Chen X, Zhao Y, Li Y, Chen L, Nilsson M, Ke R*. Single Cell RNA Expression Analysis Using Flow Cytometry Based on Specific Probe Ligation and Rolling Circle Amplification. ACS Sensors. 2020, 5, 10:3031–3036.
2. Lin C, Jiang M, Duan S, Qiu J, Hong Y, Wang X, Chen X, Ke R*. Visualization of individual microRNA molecules in fixed cells and tissues using target-primed padlock probe assay. Biochem Biophys Res Commun. 2020. 526(3):607-611.
3. Jiang M, Lin C, Ke R*. Detection of Individual RNA in Fixed Cells and Tissues by Chromogenic ISH. Bio Protoc. 2020,10(3): e3510.
1. Jiang M, Liu L, Hong C, Chen D, Yao X, Chen X, Lin C, Ke R*. Single molecule chromogenic in situ hybridization assay for RNA visualization in fixed cells and tissues. RNA. 2019 25(8):1038-1046.
2. Zeng F, Ma X, Zhu L, Xu Q, Zeng Y, Gao Y, Li G, Guo T, Zhang H, Tang X, Wang Z, Ye Z, Zheng L, Zhang H, Zheng Q, Li K, Lu J, Qi X, Luo H, Zhang X, Wang Z, Zhou Y, Yao Y, Ke R, Zhou Y, Liu Y, Sun H, Huang T, Shao Z, Xu H, Wang X. The deubiquitinase USP6 affects memory and synaptic plasticity through modulating NMDA receptor stability. PLoS Biol. 2019. 17(12): e3000525.
1. Ke R#, Mignardi M, Hauling T, Nilsson M. Fourth Generation of Next-Generation Sequencing Technologies: Promise and Consequences. Human Mutation. 2016, 37(12):1363-1367.
2. Ke R#, Mignardi M#, Botling J, Wählby C, and Nilsson M. In situ sequencing for RNA analysis in preserved cells and tissue. Nature Methods. 2013, 10: 857–860.
3. Ke R#, Nong RY#, Fredriksson S, Landegren U, Nilsson M. Improving precision of proximity ligation assay by amplified single molecule detection. PLoS One. 2013, 8(7): e69813.
4. Gómez de la Torre TZ#, Ke R#, Mezger A, Svedlindh P, Strømme M, Nilsson M. Sensitive detection of spores using volume-amplified magnetic nanobeads. Small. 2012, 8:2174-7.
5. Ke R, Zorzet A, Göransson J, Lindegren G, Sharifi-Mood B, Chinikar S, Mardani M, Mirazimi A, Nilsson M. Colorimetric nucleic acid testing assay for RNA virus detection based on circle-to-circle amplification of padlock probes. Journal of Clinical Microbiology. 2011, 49:4279-85.
6. Ke R#, Yang W#, Xia X, Xu Y, Li Q. Tandem conjugation of enzyme and antibody on silica nanoparticle for enzyme immunoassay. Analytical Biochemistry. 2010, 406:8-13. (selected for cover) （封面文章）
7. New technologies for DNA analysis--a review of the READNA Project. New Biotechnology. 2016, 33:311-330.
8. Sun S, Ke R, Hughes D, Nilsson M, Andersson DI. Genome-Wide Detection of Spontaneous Chromosomal Rearrangements in Bacteria. PLoS One. 2012, 7: e42639.
9. Göransson J, Ke R, Nong RY, Howell WM, Karman A, Grawé J, Stenberg J, Granberg M, Elgh M, Herthnek D, Wikström P, Jarvius J, Nilsson M. Rapid identification of bio-molecules applied for detection of biosecurity agents using rolling circle amplification. PLoS One. 2012, 7: e31068.
10. Barišić I, Schoenthaler S, Ke R, Nilsson M, Noehammer C, Wiesinger-Mayr H, Multiplex detection of antibiotic resistance genes using padlock probes. Diagnostic microbiology and infectious disease. 2013, 77: 118-125.
11. Xia X, Xu Y, Ke R, Zhang H, Zou M, Yang W, Li Q, A highly sensitive europium nanoparticle-based lateral flow immunoassay for detection of chloramphenicol residue. Analytical Bioanalytical Chemistry. 2013, 45: 7541-7544.
12. Pacureanu A, Ke R, Mignardi M, Nilsson M, Wählby C, Image based in situ sequencing for RNA analysis in tissue. Biomedical Imaging (ISBI), IEEE 11th International Symposium on, 2014: 286-289.
