Publications

Publications

Publications

Publications

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NEST: Spatially-mapped cell-cell communication patterns using a deep learning-based attention mechanism

bioRxiv, 2024

Zohora FT, Flores-Figueroa E, Li J, Paliwal D, Notta F, and Schwartz GW

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AnnoSpat annotates cell types and quantifies cellular arrangements from spatial proteomics

Nature Communications, 2024

Mongia A, Zohora FT, Burget NG, Zhou Y, Saunders DC, Wang YJ, Brissova M, Powers AC, Kaestner KH, Vahedi G, Naji A, Schwartz GW^, and Faryabi RB^.

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Single-cell multi-omics analysis of human pancreatic islets reveals novel cellular states in type 1 diabetes.

Nat Metab, 2022

Fasolino M*, Schwartz GW*, Patil AR, Mongia A, Golson ML, Wang YJ, Morgan A, Liu C, Schug J, Liu J, Wu M, Traum D, Kondo A, May CL, Goldman N, Wang W, Feldman M, Moore JH, Japp AS, Betts MR; HPAP Consortium, Faryabi RB, Naji A, Kaestner KH, Vahedi G.

NEST: Spatially-mapped cell-cell communication patterns using a deep learning-based attention mechanism

bioRxiv 2024

Zohora FT, Flores-Figueroa E, Li J, Paliwal D, Notta F, and Schwartz GW

AnnoSpat annotates cell types and quantifies cellular arrangements from spatial proteomics

Nature Communications 2024

Mongia A, Zohora FT, Burget NG, Zhou Y, Saunders DC, Wang YJ, Brissova M, Powers AC, Kaestner KH, Vahedi G, Naji A, Schwartz GW^, and Faryabi RB^.

AnnoSpat annotates cell types and quantifies cellular arrangements from spatial proteomics

bioRxiv 2023

Mongia A, Saunders DC, Wang YJ, Brissova M, Powers AC, Kaestner KH, Vahedi G, Naji A, Schwartz GW^, Faryabi RB^.

Single-cell multi-omics analysis of human pancreatic islets reveals novel cellular states in type 1 diabetes.

Nat Metab 2022

Fasolino M*, Schwartz GW*, Patil AR, Mongia A, Golson ML, Wang YJ, Morgan A, Liu C, Schug J, Liu J, Wu M, Traum D, Kondo A, May CL, Goldman N, Wang W, Feldman M, Moore JH, Japp AS, Betts MR; HPAP Consortium, Faryabi RB, Naji A, Kaestner KH, Vahedi G.

TooManyCells identifies and visualizes relationships of single-cell clades.

Nat. Methods 2020

Schwartz GW, Petrovic J, Fasolino M, Zhou Y, Cai S, Xu L, Pear WS, Vahedi G, and Faryabi RB.

Trib1 regulates T cell differentiation during chronic infection by restraining the effector program.

J. Exp. Med. 2020

Rome KS, Stein, SJ, Kurachi M, Petrovic J, Schwartz GW, Mack EA, Uljon S, Wu WW, DeHart AG, McClory SE, Xu L, Gimotty PA, Blacklow SC, Faryabi RB, Wherry EJ, Jordan MS, Pear WS.

Oncogenic Notch Promotes Long-Range Regulatory Interactions within Hyperconnected 3D Cliques.

Mol. Cell. 2019

Petrovic J, Zhou Y, Fasolino M, Goldman N, Schwartz GW, Mumbach MR, Nguyen SC, Rome KS, Sela Y, Zapataro Z, Blacklow SC, Kruhlak MJ, Shi J, Aster JC, Joyce EF, Little SC, Vahedi G, Pear WS, Faryabi RB.