*,^# Equal contribution

Theory & Methods

Wang S, Al-Radhawi MA, Lauffenburger DA^#, Sontag ED^#. Recovering biomolecular network dynamics from single-cell omics data requires three time points. npj syst bio. 2024 Aug 27;10, 97. https://doi.org/10.1038/s41540-024-00424-7

Wang S, Sontag ED^#, Lauffenburger DA^#. What cannot be seen correctly in 2D visualizations of single-cell ‘omics data? Cell Syst. 2023 Sep 20;14(9):723-731. https://doi.org/10.1016/j.cels.2023.07.00

Sritharan D*, Wang S*, Hormoz S. Computing the Riemannian curvature of image patch and single-cell RNA sequencing data manifolds using extrinsic differential geometry. Proc Natl Acad Sci U S A. 2021 Jul 20;118(29):e2100473118. https://doi.org/10.1073/pnas.2100473118

Wang S, Lin JR, Sontag ED, Sorger PK. Inferring reaction network structure from single-cell, multiplex data, using toric systems theory. PLoS Comput Biol. 2019 Dec 6;15(12):e1007311. https://doi.org/10.1371/journal.pcbi.1007311

Applications

Wang S*, Myers AJ*, Irvine EB, Wang C, Maiello P, Rodgers MA, Tomko J, Kracinovsky K, Borish HJ, Chao MC, Mugahid D, Darrah PA, Seder RA, Roederer M, Scanga CA, Lin PL, Alter G, Fortune SM, Flynn JL, Lauffenburger DA. Markov Field network model of multi-modal data predicts effects of immune system perturbations on intravenous BCG vaccination in macaques. Cell Syst. 2024 Apr 16. https://doi.org/10.1016/j.cels.2024.10.001
https://www.biorxiv.org/content/10.1101/2024.04.13.589359v1

Irvine EB, Darrah PA, Wang S, Wang C, McNamara RP, Roederer M, Seder RA, Lauffenburger DA, Flynn JL, Fortune SM, Alter G. Humoral correlates of protection against Mycobacterium tuberculosis following intravenous Bacille Calmette-Guerin vaccination in rhesus macaques. iScience. 2024 Oct 15. https://doi.org/10.1016/j.isci.2024.111128

Lin JR*, Wang S*, Coy S*, Chen YA, Yapp C, Tyler M, Nariya MK, Heiser CN, Lau KS, Santagata S^#, Sorger PK^#. Multiplexed 3D atlas of state transitions and immune interaction in colorectal cancer. Cell. 2023 Jan 19;186(2):363-381.e19. https://doi.org/10.1016/j.cell.2022.12.028

Coy S, Wang S, Stopka SA, Lin JR, Yapp C, Ritch CC, Salhi L, Baker GJ, Rashid R, Baquer G, Regan M, Khadka P, Cole KA, Hwang J, Wen PY, Bandopadhayay P, Santi M, De Raedt T, Ligon KL, Agar NYR, Sorger PK, Touat M, Santagata S. Single cell spatial analysis reveals the topology of immunomodulatory purinergic signaling in glioblastoma. Nat Commun. 2022 Aug 16;13(1):4814. https://doi.org/10.1038/s41467-022-32430-w

Gaglia G, Kabraji S, Rammos D, Dai Y, Verma A, Wang S, Mills CE, Chung M, Bergholz JS, Coy S, Lin JR, Jeselsohn R, Metzger O, Winer EP, Dillon DA, Zhao JJ, Sorger PK, Santagata S. Temporal and spatial topography of cell proliferation in cancer. Nat Cell Biol. 2022 Mar;24(3):316-326. https://doi.org/10.1038/s41556-022-00860-9

Liu D*, Lin JR*, Robitschek EJ, Kasumova GG, Heyde A, Shi A, Kraya A, Zhang G, Moll T, Frederick DT, Chen YA, Wang S, Schapiro D, Ho LL, Bi K, Sahu A, Mei S, Miao B, Sharova T, Alvarez-Breckenridge C, Stocking JH, Kim T, Fadden R, Lawrence D, Hoang MP, Cahill DP, Malehmir M, Nowak MA, Brastianos PK, Lian CG, Ruppin E, Izar B, Herlyn M, Van Allen EM, Nathanson K, Flaherty KT, Sullivan RJ, Kellis M, Sorger PK, Boland GM. Evolution of delayed resistance to immunotherapy in a melanoma responder. Nat Med. 2021 Jun;27(6):985-992. https://doi.org/10.1038/s41591-021-01331-8

Du Z*, Lin JR*, Rashid R*, Maliga Z, Wang S, Aster JC, Izar B, Sorger PK, Santagata S. Qualifying antibodies for image-based immune profiling and multiplexed tissue imaging. Nat Protoc. 2019 Oct;14(10):2900-2930. https://doi.org/10.1038/s41596-019-0206-y

Lin JR*, Izar B*, Wang S, Yapp C, Mei S, Shah PM, Santagata S, Sorger PK. Highly multiplexed immunofluorescence imaging of human tissues and tumors using t-CyCIF and conventional optical microscopes. Elife. 2018 Jul 11;7:e31657. https://doi.org/10.7554/eLife.31657

Jerby-Arnon L, Shah P, Cuoco MS, Rodman C, Su MJ, Melms JC, Leeson R, Kanodia A, Mei S, Lin JR, Wang S, Rabasha B, Liu D, Zhang G, Margolais C, Ashenberg O, Ott PA, Buchbinder EI, Haq R, Hodi FS, Boland GM, Sullivan RJ, Frederick DT, Miao B, Moll T, Flaherty KT, Herlyn M, Jenkins RW, Thummalapalli R, Kowalczyk MS, Cañadas I, Schilling B, Cartwright ANR, Luoma AM, Malu S, Hwu P, Bernatchez C, Forget MA, Barbie DA, Shalek AK, Tirosh I, Sorger PK, Wucherpfennig K, Van Allen EM, Schadendorf D, Johnson BE, Rotem A, Rozenblatt-Rosen O, Garraway LA, Yoon CH, Izar B, Regev A. A Cancer Cell Program Promotes T Cell Exclusion and Resistance to Checkpoint Blockade. Cell. 2018 Nov 1;175(4):984-997.e24. https://doi.org/10.1016/j.cell.2018.09.006