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Our research at the Krishnaswamy Lab focuses on applying machine learning methods to high-throughput high dimensional biological data. Our research projects aim to study and develop algorithmic approaches to naturally process data, visualize it, understand progressions, find phenotypic diversity, and infer patterns. Below are our key research areas and priorities, along with some example projects that were developed in the Lab:

  • Unsupervised Deep Learning (e.g SAUCIE)

  • Manifold Learning and Data Geometry (e.g MAGICPHATESAUCIE)

  • Graph Signal Processing and Filtering (e.g Diffusion Maps, MAGICPHATE)

  • Information Theory and Gene Logic (e.g DREMIMAGIC)

  • Single-Cell, High-Throughput, and High-Dimensional Data 

    • Single-cell RNA sequencing (e.g. 10x genomics)

    •  CyTOF

  • Biological Systems

    • Developmental (e.g. Embryoid Bodies, Brain organoids, Mouse Brain, Hematopoiesis)

    • Immunology (e.g. Dengue, Zika, HIV, Cancer Immunotherapy, Lupus, Type 1 Diabetes)

    • Cancer (e.g EMT, Immunotherapy)


Selected Publications



Kevin R. Moon, Jay S. Stanley, Daniel Burkhardt, David van Dijk, Guy Wolf, Smita Krishnaswamy: Manifold learning-based methods for analyzing single-cell RNA-sequencing data. Current Opinion in Systems Biology. Elsevier. February 2018.


Yao Y, Welp T, Liu Q, Niu N, Wang X, Britto CJ, Krishnaswamy S, Chupp GL, Montgomery RR: Multiparameter Single Cell Profiling of Airway Inflammatory Cells. Cytometry B Clin Cytom. 2017 Jan. PMID: 27807928


Lowther DE, Goods BA, Lucca LE, Lerner BA, Raddassi K, van Dijk D, Hernandez AL, Duan X, Gunel M, Coric V, Krishnaswamy S, Love JC, Hafler DA: PD-1 marks dysfunctional regulatory T cells in malignant gliomas. JCI Insight. 2016 Apr 21. PMID: 27182555


Zunder ER, Finck R, Behbehani GK, Amir el-AD, Krishnaswamy S, Gonzalez VD, Lorang CG, Bjornson Z, Spitzer MH, Bodenmiller B, Fantl WJ, Pe'er D, Nolan GP: Palladium-based mass tag cell barcoding with a doublet-filtering scheme and single-cell deconvolution algorithm. Nat Protoc. 2015 Feb; 2015 Jan 22. PMID: 25612231


Krishnaswamy S, Spitzer MH, Mingueneau M, Bendall SC, Litvin O, Stone E, Pe'er D, Nolan GP: Systems biology. Conditional density-based analysis of T cell signaling in single-cell data. Science. 2014 Nov 28; 2014 Oct 23. PMID: 25342659

Mingueneau M, Krishnaswamy S, Spitzer MH, Bendall SC, Stone EL, Hedrick SM, Pe'er D, Mathis D, Nolan GP, Benoist C: Single-cell mass cytometry of TCR signaling: amplification of small initial differences results in low ERK activation in NOD mice. Proc Natl Acad Sci U S A. 2014 Nov 18; 2014 Oct 31. PMID: 25362052

Amir el-AD, Davis KL, Tadmor MD, Simonds EF, Levine JH, Bendall SC, Shenfeld DK, Krishnaswamy S, Nolan GP, Pe'er D: viSNE enables visualization of high dimensional single-cell data and reveals phenotypic heterogeneity of leukemia. Nat Biotechnol. 2013 Jun; 2013 May 19. PMID: 23685480

Finck R, Simonds EF, Jager A, Krishnaswamy S, Sachs K, Fantl W, Pe'er D, Nolan GP, Bendall SC: Normalization of mass cytometry data with bead standards. Cytometry A. 2013 May; 2013 Mar 19. PMID: 23512433



Book Cover.jpg

Design, Analysis and Test of Logic Circuits Under Uncertainty. 2014

Authors: Krishnaswamy, Smita, Markov, Igor L., Hayes, John P.