Krishnaswamy, Smita

Recovering Gene Interactions from Single-Cell Data Using Data Diffusion

van Dijk, D., Sharma, R., Nainys, J., Yim, K., Kathail, P., Carr, A. J., Burdziak, C., Moon, K. R., Chaffer, C. L., Pattabiraman, D., et al. (2018) · Cell

Single-cell and spatial transcriptomicsGene expression and cancer classification

Cited by 1,829

viSNE enables visualization of high dimensional single-cell data and reveals phenotypic heterogeneity of leukemia

Amir, E.-A. D., Davis, K. L., Tadmor, M. D., Simonds, E. F., Levine, J. H., Bendall, S. C., Shenfeld, D. K., Krishnaswamy, S., Nolan, G. P., & Pe'er, D. (2013) · Nature Biotechnology

Single-cell and spatial transcriptomicsData Visualization and Analytics

Cited by 1,550

Visualizing 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

Single-cell and spatial transcriptomicsTopological and Geometric Data Analysis

Cited by 1,065

Palladium-based mass tag cell barcoding with a doublet-filtering scheme and single-cell deconvolution algorithm

Zunder, E. R., Finck, R., Behbehani, G. K., Amir, E.-A. D., Krishnaswamy, S., Gonzalez, V. D., Lorang, C. G., Bjornson, Z., Spitzer, M. H., Bodenmiller, B., et al. (2015) · Nature Protocols

Single-cell and spatial transcriptomicsAdvanced Proteomics Techniques and Applications

Cited by 596

Quantifying the effect of experimental perturbations at single-cell resolution

Burkhardt, D. B., Stanley, J. S., Tong, A., Perdigoto, A. L., Gigante, S. A., Herold, K. C., Wolf, G., Giraldez, A. J., van Dijk, D., & Krishnaswamy, S. (2021) · Nature Biotechnology

Single-cell and spatial transcriptomicsGene expression and cancer classification

Cited by 226

Conditional density-based analysis of T cell signaling in single-cell data

Krishnaswamy, S., Spitzer, M. H., Mingueneau, M., Bendall, S. C., Litvin, O., Stone, E., Pe’er, D., & Nolan, G. P. (2014) · Science

Gene Regulatory Network AnalysisSingle-cell and spatial transcriptomics

Cited by 225

Endocrine-Exocrine Signaling Drives Obesity-Associated Pancreatic Ductal Adenocarcinoma

Chung, K. M., Singh, J., Lawres, L., Dorans, K. J., Garcia, C., Burkhardt, D. B., Robbins, R., Bhutkar, A., Cardone, R., Zhao, X., et al. (2020) · Cell

Pancreatic and Hepatic Oncology ResearchCancer, Lipids, and Metabolism

Cited by 150

Multimodal 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) · bioRxiv (Cold Spring Harbor Laboratory)

Single-cell and spatial transcriptomicsBioinformatics and Genomic Networks

Cited by 81

Multiscale PHATE identifies multimodal signatures of COVID-19

Kuchroo, M., Huang, J., Wong, P., Grenier, J.-C., Shung, D., Tong, A., Lucas, C., Klein, J., Burkhardt, D. B., Gigante, S., et al. (2022) · Nature Biotechnology

Single-cell and spatial transcriptomicsTopological and Geometric Data Analysis

Cited by 72

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

Cancer Cells and MetastasisSingle-cell and spatial transcriptomics

Cited by 72

MLL-AF9 initiates transformation from fast-proliferating myeloid progenitors

Chen, X., Burkhardt, D. B., Hartman, A. A., Hu, X., Eastman, A. E., Sun, C., Wang, X., Zhong, M., Krishnaswamy, S., & Guo, S. (2019) · Nature Communications

Acute Myeloid Leukemia ResearchRetinoids in leukemia and cellular processes

Cited by 58

Uncovering axes of variation among single-cell cancer specimens

Chen, W. S., Zivanovic, N., van Dijk, D., Wolf, G., Bodenmiller, B., & Krishnaswamy, S. (2020) · Nature Methods

Single-cell and spatial transcriptomicsGene expression and cancer classification

Cited by 48