| Vireo: Bayesian demultiplexing of pooled single-cell RNA-seq data without genotype reference Y Huang, DJ McCarthy, O Stegle Genome biology 20 (1), 273, 2019 | 338 | 2019 |
| Cellsnp-lite: an efficient tool for genotyping single cells X Huang, Y Huang Bioinformatics 37 (23), 4569-4571, 2021 | 186 | 2021 |
| Transcription rate strongly affects splicing fidelity and cotranscriptionality in budding yeast V Aslanzadeh, Y Huang, G Sanguinetti, JD Beggs Genome research 28 (2), 203-213, 2018 | 137 | 2018 |
| UniTVelo: temporally unified RNA velocity reinforces single-cell trajectory inference M Gao, C Qiao, Y Huang Nature Communications 13 (1), 6586, 2022 | 112 | 2022 |
| BRIE: transcriptome-wide splicing quantification in single cells Y Huang, G Sanguinetti Genome biology 18 (1), 123, 2017 | 108 | 2017 |
| SpatialDM for rapid identification of spatially co-expressed ligand–receptor and revealing cell–cell communication patterns Z Li, T Wang, P Liu, Y Huang Nature communications 14 (1), 3995, 2023 | 103 | 2023 |
| Transcriptome-wide RNA processing kinetics revealed using extremely short 4tU labeling JD Barrass, JEA Reid, Y Huang, RD Hector, G Sanguinetti, JD Beggs, ... Genome biology 16 (1), 282, 2015 | 91 | 2015 |
| Chronic type I interferon signaling promotes lipid-peroxidation-driven terminal CD8+ T cell exhaustion and curtails anti-PD-1 efficacy W Chen, JMN Teo, SW Yau, MYM Wong, CN Lok, CM Che, A Javed, ... Cell reports 41 (7), 2022 | 90 | 2022 |
| Cardelino: computational integration of somatic clonal substructure and single-cell transcriptomes DJ McCarthy, R Rostom, Y Huang, DJ Kunz, P Danecek, MJ Bonder, ... Nature methods 17 (4), 414-421, 2020 | 86* | 2020 |
| Representation learning of RNA velocity reveals robust cell transitions C Qiao, Y Huang Proceedings of the National Academy of Sciences 118 (49), e2105859118, 2021 | 64 | 2021 |
| Naive pluripotent stem cells exhibit phenotypic variability that is driven by genetic variation D Ortmann, S Brown, A Czechanski, S Aydin, D Muraro, Y Huang, ... Cell stem cell 27 (3), 470-481. e6, 2020 | 55 | 2020 |
| Systematic characterization and prediction of post-translational modification cross-talk Y Huang, B Xu, X Zhou, Y Li, M Lu, R Jiang, T Li Molecular & Cellular Proteomics 14 (3), 761-770, 2015 | 48 | 2015 |
| BRIE2: computational identification of splicing phenotypes from single-cell transcriptomic experiments Y Huang, G Sanguinetti Genome biology 22 (1), 251, 2021 | 46 | 2021 |
| MQuad enables clonal substructure discovery using single cell mitochondrial variants AWC Kwok, C Qiao, R Huang, MH Sham, JWK Ho, Y Huang Nature communications 13 (1), 1205, 2022 | 43 | 2022 |
| A combinatorial CRISPR–Cas9 screen identifies ifenprodil as an adjunct to sorafenib for liver cancer treatment F Xu, M Tong, CSW Tong, BKC Chan, HY Chu, TL Wong, JHC Fong, ... Cancer Research 81 (24), 6219-6232, 2021 | 33 | 2021 |
| Systematic characterization and prediction of post-translational modification cross-talk between proteins R Huang, Y Huang, Y Guo, S Ji, M Lu, T Li Bioinformatics 35 (15), 2626-2633, 2019 | 23 | 2019 |
| Time-series single-cell transcriptomic profiling of luteal-phase endometrium uncovers dynamic characteristics and its dysregulation in recurrent implantation failures D Cao, Y Liu, Y Cheng, J Wang, B Zhang, Y Zhai, K Zhu, Y Liu, Y Shang, ... Nature Communications 16 (1), 137, 2025 | 22 | 2025 |
| PD-L1 regulates inflammatory programs of macrophages from human pluripotent stem cells H Cao, Y Xiang, S Zhang, Y Chao, J Guo, T Aurich, JWK Ho, Y Huang, ... Life Science Alliance 7 (2), 2024 | 19 | 2024 |
| DCATS: differential composition analysis for flexible single-cell experimental designs X Lin, C Chau, K Ma, Y Huang, JWK Ho Genome biology 24 (1), 151, 2023 | 18 | 2023 |
| Organoid-based single-cell spatiotemporal gene expression landscape of human embryonic development and hematopoiesis Y Chao, Y Xiang, J Xiao, W Zheng, MR Ebrahimkhani, C Yang, AR Wu, ... Signal transduction and targeted therapy 8 (1), 230, 2023 | 18 | 2023 |
Guido SanguinettiReader in Informatics, University of EdinburghVerified email at inf.ed.ac.uk
