| IBS: an illustrator for the presentation and visualization of biological sequences W Liu, Y Xie, J Ma, X Luo, P Nie, Z Zuo, U Lahrmann, Q Zhao, Y Zheng, ... Bioinformatics 31 (20), 3359-3361, 2015 | 861 | 2015 |
| GPS-SUMO: a tool for the prediction of sumoylation sites and SUMO-interaction motifs Q Zhao, Y Xie, Y Zheng, S Jiang, W Liu, W Mu, Z Liu, Y Zhao, Y Xue, ... Nucleic acids research 42 (W1), W325-W330, 2014 | 536 | 2014 |
| N6-Methyladenosine Modulates Nonsense-Mediated mRNA Decay in Human Glioblastoma F Li, Y Yi, Y Miao, W Long, T Long, S Chen, W Cheng, C Zou, Y Zheng, ... Cancer research 79 (22), 5785-5798, 2019 | 198 | 2019 |
| m6AVar: a database of functional variants involved in m6A modification Y Zheng, P Nie, D Peng, Z He, M Liu, Y Xie, Y Miao, Z Zuo, J Ren Nucleic acids research 46 (D1), D139-D145, 2018 | 178 | 2018 |
| GPS-Lipid: a robust tool for the prediction of multiple lipid modification sites Y Xie, Y Zheng, H Li, X Luo, Z He, S Cao, Y Shi, Q Zhao, Y Xue, Z Zuo, ... Scientific reports 6 (1), 28249, 2016 | 148 | 2016 |
| TP63, SOX2, and KLF5 establish a core regulatory circuitry that controls epigenetic and transcription patterns in esophageal squamous cell carcinoma cell lines YY Jiang, Y Jiang, CQ Li, Y Zhang, P Dakle, H Kaur, JW Deng, RYT Lin, ... Gastroenterology 159 (4), 1311-1327. e19, 2020 | 103 | 2020 |
| lnCAR: a comprehensive resource for lncRNAs from cancer arrays Y Zheng, Q Xu, M Liu, H Hu, Y Xie, Z Zuo, J Ren Cancer research 79 (8), 2076-2083, 2019 | 53 | 2019 |
| m6ASNP: a tool for annotating genetic variants by m6A function S Jiang, Y Xie, Z He, Y Zhang, Y Zhao, L Chen, Y Zheng, Y Miao, Z Zuo, ... Gigascience 7 (5), giy035, 2018 | 30 | 2018 |
| Pan-cancer analysis reveals the functional importance of protein lysine modification in cancer development L Chen, Y Miao, M Liu, Y Zeng, Z Gao, D Peng, B Hu, X Li, Y Zheng, ... Frontiers in genetics 9, 254, 2018 | 27 | 2018 |
| A pan-cancer analysis of CpG Island gene regulation reveals extensive plasticity within Polycomb target genes Y Zheng, G Huang, TC Silva, Q Yang, YY Jiang, HP Koeffler, DC Lin, ... Nature communications 12 (1), 2485, 2021 | 25 | 2021 |
| EWS-FLI1 regulates and cooperates with core regulatory circuitry in Ewing sarcoma X Shi, Y Zheng, L Jiang, B Zhou, W Yang, L Li, L Ding, M Huang, S Gery, ... Nucleic Acids Research 48 (20), 11434-11451, 2020 | 20 | 2020 |
| Generation and multiomic profiling of a TP53/CDKN2A double-knockout gastroesophageal junction organoid model H Zhao, Y Cheng, A Kalra, K Ma, Y Zheng, B Ziman, C Tressler, K Glunde, ... Science translational medicine 14 (673), eabq6146, 2022 | 19 | 2022 |
| Activation of bivalent factor DLX5 cooperates with master regulator TP63 to promote squamous cell carcinoma Y Huang, Q Yang, Y Zheng, L Lin, X Xu, XE Xu, TC Silva, M Hazawa, ... Nucleic Acids Research 49 (16), 9246-9263, 2021 | 13 | 2021 |
| An integrated overview of spatiotemporal organization and regulation in mitosis in terms of the proteins in the functional supercomplexes Y Zheng, J Guo, X Li, Y Xie, M Hou, X Fu, S Dai, R Diao, Y Miao, J Ren Frontiers in Microbiology 5, 573, 2014 | 7 | 2014 |
| VirusMap: A visualization database for the influenza A virus Y Xie, X Luo, Z He, Y Zheng, Z Zuo, Q Zhao, Y Miao, J Ren Journal of genetics and genomics= Yi chuan xue bao 44 (5), 281-284, 2017 | 4 | 2017 |
| Comprehensive analyses of partially methylated domains and differentially methylated regions in esophageal cancer reveal both cell-type-and cancer-specific epigenetic regulation Y Zheng, B Ziman, AS Ho, UK Sinha, LY Xu, EM Li, HP Koeffler, ... Genome Biology 24 (1), 193, 2023 | 3 | 2023 |
| Treatment for ovarian clear cell carcinoma with combined inhibition of WEE1 and ATR W Chien, JW Tyner, S Gery, Y Zheng, LY Li, MS Gopinatha Pillai, C Nam, ... Journal of Ovarian Research 16 (1), 80, 2023 | 2 | 2023 |
| A local sequence signature defines a subset of heterochromatin-associated CpGs with minimal loss of methylation in healthy tissues but extensive loss in cancer D Bar, L Fishman, Y Zheng, I Unterman, D Schlesinger, A Eden, DC Lin, ... BioRxiv, 2022.08. 16.504069, 2022 | 2 | 2022 |
| Novel tumorigenic FOXM1-PTAFR-PTAF axis revealed by multi-omic profiling in TP53/CDKN2A-double knockout human gastroesophageal junction organoid model H Zhao, Y Cheng, A Kalra, K Ma, Y Zheng, B Ziman, C Tressler, K Glunde, ... bioRxiv, 2022.05. 10.491356, 2022 | 2 | 2022 |
| Epigenomic analyses identify FOXM1 as a key regulator of anti-tumor immune response in esophageal adenocarcinoma B Ziman, Q Yang, Y Zheng, M Sheth, C Nam, H Zhao, L Zhang, B Hu, ... Cell Death & Disease 15 (2), 1-12, 2024 | | 2024 |
