Publications

Publications

Publications

Publications

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TooManyCellsInteractive: A visualization tool for dynamic exploration of single-cell data

GigaScience, 2024

Klamann C*, Lau, CJ*, Ruiz-Ramírez J, and Schwartz GW

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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.

An inflammatory state defines a high-risk T-lineage acute lymphoblastic leukemia subgroup

Science Translational Medicine 2025

Gower M, Li X, Aguilar-Navarro AG, Lin B, Fernandez M, Edun G, Nader M, Rondeau V, Arruda A, Tierens A, Eames Seffernick A, Pölönen P, Durocher J, Wagenblast E, Yang L, Lee HS, Mullighan CG, Teachey D, Rashkovan M, Tremblay CS, Herranz D, Itkin T, Loghavi S, Dick JE, Schwartz G, Perusini MA, Sibai H, Hitzler J, Gruber TA, Minden M, Jones CL, Dolgalev I, Jahangiri S & Tikhonova AN

Enhancer-promoter hubs organize transcriptional networks promoting oncogenesis and drug resistance

Nature Communications 2024

Perlman BS, Burget N, Zhou Y, Schwartz GW, Petrovic J, Modrusan Z & Faryabi RB

TooManyCellsInteractive: A visualization tool for dynamic exploration of single-cell data

GigaScience 2024

Klamann C*, Lau, CJ*, Ruiz-Ramírez J, and Schwartz GW

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.