4. Information Theory and Gene Logic


3. Manifold Learning and Data Geometry


5. Single-Cell, High-Throughput, and High-Dimensional Data

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

6. 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.