See the Google Scholar page for updated & more collaborative publications.

Preprint

• Robust analysis of allele-specific copy number variations from scRNA-seq data with XClone.
  Huang Rongting^, Huang Xianjie^, Stegle Oliver and Huang Yuanhua#.
  bioRxiv 535352 (2023) | Python package
• Reliable imputation of spatial transcriptome with uncertainty estimation and spatial regularization.
  Qiao Chen and Huang Yuanhua#
  bioRxiv 524992 (2023) | Python package
• CellContrast: reconstructing spatial relationships in single-cell RNA sequencing data via deep contrastive learning.
  Li Shumin^, Ma Jiajun^, Zhao Tianyi, Jia Yuran, Liu Bo, Luo Ruibang#, Huang Yuanhua#
  bioRxiv 562026 (2023) | Python package

2023

• CamoTSS: analysis of alternative transcription start sites for cellular phenotypes and regulatory patterns from 5’ scRNA-seq data.
  Hou Ruiyan, Hon Chung-Chau and Huang Yuanhua#
  Nature Communications in print | Python package | bioRxiv
• SpatialDM: Rapid identification of spatially co-expressed ligand-receptor reveals cell-cell communication patterns.
  Li Zhuoxuan, Wang Tianjie, Liu Pengtao# and Huang Yuanhua#
  Nature Communications 14, 3935 | Python package | bioRxiv
• DCATS: differential composition analysis for complex single-cell experimental designs.
  Lin, X., Chau, C., Huang, Y.#, & Ho, J.W.K.#
  Genome Biology in print | R package | bioRxiv

2022

• UniTVelo: temporally unified RNA velocity reinforces single-cell trajectory inference.
  Gao Mingze, Qiao Chen and Huang Yuanhua
  Nature Communications 13, 6586 (2022) | Python package | bioRxiv
• Genomic sequences and RNA binding proteins predict RNA splicing kinetics in various single-cell contexts.
  Hou Ruiyan and Huang Yuanhua
  Bioinformatics, btac321 (2022) | Scripts | bioRxiv
• MQuad enables clonal substructure discovery using single cell mitochondrial variants.
  Kwok A.W.C., Qiao C, Huang R, Sham M.H., Ho J.W.K.#, Huang Y#.
  Nature Communications 13, 1205 (2022) | Python package | bioRxiv

2021

• Representation learning of RNA velocity reveals robust cell transitions.
  Qiao Chen and Huang Yuanhua
  Proc. Natl. Acad. Sci. U.S.A. 118(49), e2105859118 (2021) | Python package | bioRxiv
• BRIE2: computational identification of splicing phenotypes from single-cell transcriptomic experiments.
  Huang Y, Sanguinetti G.
  Genome Biology 22, 251 (2021) | Python package | Manual | Tutorials
• Uncertainty vs variability: Bayesian methods for analysis of scRNA-seq data.
  Huang Y, Sanguinetti G.
  Current Opinion in Systems Biology 100375 (2021) | review paper
• Cellsnp-lite: an efficient tool for genotyping single cells.
  Huang Xianjie and Huang Yuanhua
  Bioinformatics, 37(23), 4569-4571 (2021) | bioRxiv | software

Before joining HKU

• Naive pluripotent stem cells exhibit phenotypic variability that is driven by genetic variation.
  Ortmann D., Brown S., Czechanski A., Aydin S., Muraro D., Huang Y., Tomaz R.A., Osnato A., Canu G., Wesley B.T., Skelly D., Stegle O., …, Reinholdt L.G., Vallier L.
  Cell Stem Cell, 2020, 7(3), pp.470-481.
• Cardelino: computational integration of somatic clonal substructure and single-cell transcriptomes.
  McCarthy DJ * , Rostom R * , Huang Y * , Kunz DJ, Danecek P, Bonder MJ, Hagai T, Lyu R., Wang W, Gaffney DJ, Simons BD, Stegle O, Teichmann SA. (*: Joint first author)
  Nature Methods Volume 17 (2020) p.414–421 | R package | Usage examples
• Vireo: Bayesian demultiplexing of pooled single-cell RNA-seq data without genotype reference.
  Huang Y, McCarthy DJ, Stegle O.
  Genome Biology Volume 20 (2019) p273 | Python package | Manual
• Using BRIE to Detect and Analyze Splicing Isoforms in scRNA-Seq Data.
  Huang Y, Sanguinetti G.
  Methods Mol Biol Volume 1935 (2019) p.175-185
• Systematic characterization and prediction of post-translational modification cross-talk between proteins.
  Huang R, Huang Y, Guo Y, Ji S, Lu M, Li T.
  Bioinformatics Volume 35 (2019) p.2626-2633
• Transcription rate strongly affects splicing fidelity and cotranscriptionality in budding yeast.
  Aslanzadeh V, Huang Y, Sanguinetti G, Beggs JD.
  Genome Research Volume 28 (2018) p.203-213
• BRIE: transcriptome-wide splicing quantification in single cells.
  Huang Y, Sanguinetti G.
  Genome Biololgy Volume 18 (2017) p.123 | Python package | Manual
• Statistical modeling of isoform splicing dynamics from RNA-seq time series data.
  Huang Y, Sanguinetti G.
  Bioinformatics Volume 32 (2016) p.2965-2972
• Transcriptome-wide RNA processing kinetics revealed using extremely short 4tU labeling.
  Barrass JD, Reid JE, Huang Y, Hector RD, Sanguinetti G, Beggs JD, Granneman S. (*: Joint first author)
  Genome Biology Volume 16 (2015) p.282
• Systematic characterization and prediction of post-translational modification cross-talk.
  Huang Y, Xu B, Zhou X, Li Y, Lu M, Jiang R, Li T.
  Mol Cell Proteomics Volume 14 (2015) p.761-770