Optimal transport for single-cell and spatial omics
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Optimal transport-based methods' applicability has been limited by strong assumptions and poor scalability.
“Optimal transport (OT)-based methods that map unperturbed to perturbed populations have also been proposed, but their applicability has been limited by strong assumptions and poor scalability.”
From Predicting cellular responses to perturbation across diverse contexts with State (2026) · cites this paper as [30]
Cites
Harris, C. R., Millman, K. J., van der Walt, S. J., Gommers, R., Virtanen, P., Cournapeau, D., Wieser, E., Taylor, J., Berg, S., Smith, N. J., et al. (2020) · Nature · doi:10.1038/s41586-020-2649-2 · Cited by 23,826 · see citing works
Raissi, M., Perdikaris, P., & Karniadakis, G. E. (2019) · Journal of Computational Physics · doi:10.1016/j.jcp.2018.10.045 · Cited by 20,384 · see citing works
UMAP: Uniform Manifold Approximation and Projection
McInnes, L., Healy, J., Saul, N., & Großberger, L. (2018) · Journal of Open Source Software · doi:10.21105/joss.00861 · Cited by 9,826 · cited 1× · see citing works
“Owing to the curse of dimensionality, approaches use Euclidean or Manhattan distances on principal component analysis, uniform manifold approximation and projection 85 or t -distributed stochastic neighbour embeddings 86,87 or run Pearson correlation analysis on high-dimensional data 88 .”
Deep generative modeling for single-cell transcriptomics
Lopez, R., Regier, J., Cole, M. B., Jordan, M. I., & Yosef, N. (2018) · Nature Methods · doi:10.1038/s41592-018-0229-2 · Cited by 2,530 · see citing works
Batch effects in single-cell RNA-sequencing data are corrected by matching mutual nearest neighbors
Haghverdi, L., Lun, A. T. L., Morgan, M. D., & Marioni, J. C. (2018) · Nature Biotechnology · doi:10.1038/nbt.4091 · Cited by 2,416 · see citing works
Semiparametric Difference-in-Differences Estimators
Abadie, A. (2005) · The Review of Economic Studies · doi:10.1111/0034-6527.00321 · Cited by 2,286 · see citing works
Regev, A., Teichmann, S. A., Lander, E. S., Amit, I., Benoist, C., Birney, E., Bodenmiller, B., Campbell, P., Carninci, P., Clatworthy, M., et al. (2017) · eLife · doi:10.7554/elife.27041 · Cited by 2,232 · see citing works
Self-citationScore-Based Generative Modeling through Stochastic Differential Equations
Song, Y., Sohl-Dickstein, J., Kingma, D. P., Kumar, A., Ermon, S., & Poole, B. (2020) · arXiv · doi:10.48550/arxiv.2011.13456 · Cited by 1,953 · see citing works
Dixit, A., Parnas, O., Li, B., Chen, J., Fulco, C. P., Jerby-Arnon, L., Marjanovic, N. D., Dionne, D., Burks, T., Raychowdhury, R., et al. (2016) · Cell · doi:10.1016/j.cell.2016.11.038 · Cited by 1,863 · see citing works
Self-citationSpatiotemporal 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 · doi:10.1016/j.cell.2022.04.003 · Cited by 1,784 · see citing works
Benchmarking atlas-level data integration in single-cell genomics
Luecken, M. D., Büttner, M., Chaichoompu, K., Danese, A., Interlandi, M., Mueller, M. F., Strobl, D. C., Zappia, L., Dugas, M., Colomé-Tatché, M., et al. (2022) · Nature Methods · doi:10.1038/s41592-021-01336-8 · Cited by 1,438 · see citing works
scGPT: Towards Building a Foundation Model for Single-Cell Multi-omics Using Generative AI
Cui, H., Wang, C., Maan, H., Pang, K., Luo, F., & Wang, B. (2023) · doi:10.1101/2023.04.30.538439 · Cited by 1,383 · see citing works
Multiplexed droplet single-cell RNA-sequencing using natural genetic variation
Kang, H. M., Subramaniam, M., Targ, S., Nguyen, M., Maliskova, L., McCarthy, E., Wan, E., Wong, S., Byrnes, L., Lanata, C. M., et al. (2018) · Nature Biotechnology · doi:10.1038/nbt.4042 · Cited by 1,339 · see citing works
Chromatin Potential Identified by Shared Single-Cell Profiling of RNA and Chromatin
Ma, S., Zhang, B., LaFave, L. M., Earl, A. S., Chiang, Z., Hu, Y., Ding, J., Brack, A., Kartha, V. K., Tay, T., et al. (2020) · Cell · doi:10.1016/j.cell.2020.09.056 · Cited by 1,146 · see citing works
Self-citationVisualizing structure and transitions in high-dimensional biological data
Moon, K. R., van Dijk, D., Wang, Z., Gigante, S., Burkhardt, D. B., Chen, W. S., Yim, K., Elzen, A. V. D., Hirn, M. J., Coifman, R. R., et al. (2019) · Nature Biotechnology · doi:10.1038/s41587-019-0336-3 · Cited by 1,065 · see citing works
Densely Interconnected Transcriptional Circuits Control Cell States in Human Hematopoiesis
Novershtern, N., Subramanian, A., Lawton, L. N., Mak, R. H., Haining, W. N., McConkey, M. E., Habib, N., Yosef, N., Chang, C. Y., Shay, T., et al. (2011) · Cell · doi:10.1016/j.cell.2011.01.004 · Cited by 942 · see citing works
Self-citationSingle-cell reconstruction of developmental trajectories during zebrafish embryogenesis
Farrell, J. A., Wang, Y., Riesenfeld, S. J., Shekhar, K., Regev, A., & Schier, A. F. (2018) · Science · doi:10.1126/science.aar3131 · Cited by 876 · see citing works
Self-citationFundamental properties of unperturbed haematopoiesis from stem cells in vivo
Busch, K., Klapproth, K., Barile, M., Flossdorf, M., Holland-Letz, T., Schlenner, S. M., Reth, M., Höfer, T., & Rodewald, H.-R. (2015) · Nature · doi:10.1038/nature14242 · Cited by 769 · see citing works
Mapping information-rich genotype-phenotype landscapes with genome-scale Perturb-seq
Replogle, J. M., Saunders, R. A., Pogson, A. N., Hussmann, J. A., Lenail, A., Guna, A., Mascibroda, L., Wagner, E. J., Adelman, K., Lithwick-Yanai, G., et al. (2022) · Cell · doi:10.1016/j.cell.2022.05.013 · Cited by 751 · cited 2× · see citing works
“Similarly, this has fruitful applications for predicting the effect of unseen (combinations of) genetic perturbations, in particular with the rise of Perturb-seq screens that allow to simultaneously profile the effect of a perturbation on individual cells 71,72,74 .”
Lineage tracing on transcriptional landscapes links state to fate during differentiation
Weinreb, C., Rodriguez-Fraticelli, A., Camargo, F. D., & Klein, A. M. (2020) · Science · doi:10.1126/science.aaw3381 · Cited by 730 · cited 2× · see citing works
“Cell differentiation processes have been captured by clonally connecting cells and their progenitors through barcodes 107 .”
Single-cell methylomes identify neuronal subtypes and regulatory elements in mammalian cortex
Luo, C., Keown, C. L., Kurihara, L., Zhou, J., He, Y., Li, J., Castanon, R., Lucero, J., Nery, J. R., Sandoval, J. P., et al. (2017) · Science · doi:10.1126/science.aan3351 · Cited by 545 · see citing works
Wilson, N. K., Kent, D. G., Buettner, F., Shehata, M., Macaulay, I. C., Calero-Nieto, F. J., Sánchez Castillo, M., Oedekoven, C. A., Diamanti, E., Schulte, R., et al. (2015) · Cell Stem Cell · doi:10.1016/j.stem.2015.04.004 · Cited by 466 · see citing works
Massively multiplex chemical transcriptomics at single-cell resolution
Srivatsan, S. R., McFaline-Figueroa, J. L., Ramani, V., Saunders, L., Cao, J., Packer, J., Pliner, H. A., Jackson, D. L., Daza, R. M., Christiansen, L., et al. (2020) · Science · doi:10.1126/science.aax6234 · Cited by 401 · see citing works
Predicting transcriptional outcomes of novel multigene perturbations with GEARS
Roohani, Y., Huang, K., & Leskovec, J. (2024) · Nature Biotechnology · doi:10.1038/s41587-023-01905-6 · Cited by 355 · see citing works
Frangieh, C. J., Melms, J. C., Thakore, P. I., Geiger-Schuller, K. R., Ho, P., Luoma, A. M., Cleary, B., Jerby-Arnon, L., Malu, S., Cuoco, M. S., et al. (2021) · Nature Genetics · doi:10.1038/s41588-021-00779-1 · Cited by 276 · see citing works
Self-citationImpact of the Human Cell Atlas on medicine
Rood, J. E., Maartens, A., Hupalowska, A., Teichmann, S. A., & Regev, A. (2022) · Nature Medicine · doi:10.1038/s41591-022-02104-7 · Cited by 222 · see citing works
Self-citationA single-embryo, single-cell time-resolved model for mouse gastrulation
Mittnenzweig, M., Mayshar, Y., Cheng, S., Ben-Yair, R., Hadas, R., Rais, Y., Chomsky, E., Reines, N., Uzonyi, A., Lumerman, L., et al. (2021) · Cell · doi:10.1016/j.cell.2021.04.004 · Cited by 214 · see citing works
Program, C. S.-C. B., Abdulla, S., Aevermann, B., Assis, P., Badajoz, S., Bell, S. M., Bezzi, E., Cakir, B., Chaffer, J., Chambers, S., et al. (2023) · doi:10.1101/2023.10.30.563174 · Cited by 142 · see citing works
Machine learning for perturbational single-cell omics
Ji, Y., Lotfollahi, M., Wolf, F. A., & Theis, F. J. (2021) · Cell Systems · doi:10.1016/j.cels.2021.05.016 · Cited by 137 · see citing works
Conditional out-of-distribution generation for unpaired data using transfer VAE
Lotfollahi, M., Naghipourfar, M., Theis, F. J., & Wolf, F. A. (2020) · Bioinformatics · doi:10.1093/bioinformatics/btaa800 · Cited by 130 · see citing works
Prediction of single-cell RNA expression profiles in live cells by Raman microscopy with Raman2RNA
Kobayashi-Kirschvink, K. J., Comiter, C. S., Gaddam, S., Joren, T., Grody, E. I., Ounadjela, J. R., Zhang, K., Ge, B., Kang, J. W., Xavier, R. J., et al. (2024) · Nature Biotechnology · doi:10.1038/s41587-023-02082-2 · Cited by 93 · see citing works
Self-citationMultimodal single cell data integration challenge: results and lessons learned
Lance, C., Luecken, M. D., Burkhardt, D. B., Cannoodt, R., Rautenstrauch, P., Laddach, A., Ubingazhibov, A., Cao, Z.-J., Deng, K., Khan, S., et al. (2022) · doi:10.1101/2022.04.11.487796 · Cited by 81 · see citing works
Trellis tree-based analysis reveals stromal regulation of patient-derived organoid drug responses
Ramos Zapatero, M., Tong, A., Opzoomer, J. W., O’Sullivan, R., Cardoso Rodriguez, F., Sufi, J., Vlckova, P., Nattress, C., Qin, X., Claus, J., et al. (2023) · Cell · doi:10.1016/j.cell.2023.11.005 · Cited by 72 · see citing works
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Predicting cellular responses to perturbation across diverse contexts with State
Adduri, A. K., Gautam, D., Bevilacqua, B., Naghipourfar, M., Imran, A., Shah, R., Teyssier, N., Verma, R., Carpenter, C., Eraslan, B., et al. (2026) · Cell · doi:10.1016/j.cell.2026.07.052 · Cited by 100 · see citing works
- Authors
- Bunne, C., Schiebinger, G., Krause, A., Regev, A., & Cuturi, M.
- Affiliations
- Genentech (US)
- University of British Columbia (CA)
- ETH Zurich (CH)
- Apple (United States) (US)
- Corresponding author
- Bunne, Charlotte
- Cuturi, Marco
- Venue
- Nature Reviews Methods Primers
- Published
- 2024-08-14
- Volume
- 4
- Issue
- 1
- ISSN
- 2662-8449 (ISSN-L)
- OpenAlex
- W4401586123
- Cited by
- 71
- References
- 33
- Citations by year
- 2026: 44 · 2025: 26 · 2024: 1
- FWCI
- 2.90
- Type
- journal article
- Language
- en
- Open access
- closed
- Licence
- Locations
- Nature Reviews Methods Primers (publishedVersion)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Single-cell and spatial transcriptomics
- Physical Sciences › Computer Science › Computational Theory and Mathematics › Topological and Geometric Data Analysis
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Gene Regulatory Network Analysis
- Keywords
- optimal transport, single-cell omics, spatial omics, cell trajectory inference, deep learning, personalized medicine, computational biology
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