Qiu, Xiaojie

Reversed graph embedding resolves complex single-cell trajectories

Qiu, X., Mao, Q., Tang, Y., Wang, L., Chawla, R., Pliner, H. A., & Trapnell, C. (2017) · Nature Methods

Single-cell and spatial transcriptomicsGene Regulatory Network Analysis

Cited by 5,070

The single-cell transcriptional landscape of mammalian organogenesis

Cao, J., Spielmann, M., Qiu, X., Huang, X., Ibrahim, D. M., Hill, A. J., Zhang, F., Mundlos, S., Christiansen, L., Steemers, F. J., et al. (2019) · Nature

Single-cell and spatial transcriptomicsDevelopmental Biology and Gene Regulation

Cited by 4,490

Spatiotemporal transcriptomic atlas of mouse organogenesis using DNA nanoball-patterned arrays

Chen, A., Liao, S., Cheng, M., Ma, K., Wu, L., Lai, Y., Qiu, X., Yang, J., Xu, J., Hao, S., et al. (2022) · Cell

Single-cell and spatial transcriptomicsDevelopmental Biology and Gene Regulation

Cited by 1,784

Comprehensive single cell transcriptional profiling of a multicellular organism by combinatorial indexing

Cao, J., Packer, J. S., Ramani, V., Cusanovich, D. A., Huynh, C., Daza, R., Qiu, X., Lee, C., Furlan, S. N., Steemers, F. J., et al. (2017) · Science

Single-cell and spatial transcriptomicsGenomics and Phylogenetic Studies

Cited by 1,402

Cicero predicts cis-regulatory DNA interactions from single-cell chromatin accessibility data

Pliner, H. A., Packer, J. S., McFaline-Figueroa, J. L., Cusanovich, D. A., Daza, R. M., Aghamirzaie, D., Srivatsan, S., Qiu, X., Jackson, D., Minkina, A., et al. (2018) · Molecular Cell

Genomics and Chromatin DynamicsSingle-cell and spatial transcriptomics

Cited by 789

The cis-regulatory dynamics of embryonic development at single-cell resolution

Cusanovich, D. A., Reddington, J. P., Garfield, D. A., Daza, R. M., Aghamirzaie, D., Marco-Ferreres, R., Pliner, H. A., Christiansen, L., Qiu, X., Steemers, F. J., et al. (2018) · Nature

Genomics and Chromatin DynamicsSingle-cell and spatial transcriptomics

Cited by 363

Single-cell Stereo-seq reveals induced progenitor cells involved in axolotl brain regeneration

Wei, X., Fu, S., Li, H., Liu, Y., Wang, S., Feng, W., Yang, Y., Liu, X., Zeng, Y.-Y., Cheng, M., et al. (2022) · Science

Neurogenesis and neuroplasticity mechanismsSingle-cell and spatial transcriptomics

Cited by 311

Inferring Causal Gene Regulatory Networks from Coupled Single-Cell Expression Dynamics Using Scribe

Qiu, X., Rahimzamani, A., Wang, L., Ren, B., Mao, Q., Durham, T., McFaline-Figueroa, J. L., Saunders, L., Trapnell, C., & Kannan, S. (2020) · Cell Systems

Gene Regulatory Network AnalysisSingle-cell and spatial transcriptomics

Cited by 185

Thyroid hormone regulates distinct paths to maturation in pigment cell lineages

Saunders, L. M., Mishra, A. K., Aman, A. J., Lewis, V. M., Toomey, M. B., Packer, J. S., Qiu, X., McFaline-Figueroa, J. L., Corbo, J. C., Trapnell, C., et al. (2019) · eLife

Developmental Biology and Gene Regulationmelanin and skin pigmentation

Cited by 170

Spatiotemporally resolved transcriptomics reveals the subcellular RNA kinetic landscape

Ren, J., Zhou, H., Zeng, H., Wang, C. K., Huang, J., Qiu, X., Sui, X., Li, Q., Wu, X., Lin, Z., et al. (2023) · Nature Methods

Single-cell and spatial transcriptomicsRNA Research and Splicing

Cited by 79

Spatiotemporally resolved transcriptomics reveals subcellular RNA kinetic landscape

Ren, J., Zhou, H., Zeng, H., Wang, C. K., Huang, J., Qiu, X., Maher, K., Lin, Z., He, Y., Tang, X., et al. (2022) · Nature Methods

Single-cell and spatial transcriptomicsRNA Research and Splicing

Cited by 78

Chromatin accessibility dynamics of myogenesis at single cell resolution

Pliner, H. A., Packer, J., McFaline-Figueroa, J. L., Cusanovich, D. A., Daza, R., Srivatsan, S., Qiu, X., Jackson, D., Minkina, A., Adey, A., et al. (2017) · bioRxiv (Cold Spring Harbor Laboratory)

Genomics and Chromatin DynamicsChromatin Remodeling and Cancer

Cited by 16