Publications

Publications

Publications

Publications

CellNEST reveals cell–cell relay networks using attention mechanisms on spatial transcriptomics

Nature Methods, 2025

Zohora FT*, Paliwal D*, Flores-Figueroa E, Li J, Gao T, Notta F & Schwartz GW

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

GigaScience, 2024

Klamann C*, Lau CJ*, Ruiz-Ramírez J, 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^.

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.

CellNEST reveals cell–cell relay networks using attention mechanisms on spatial transcriptomics

Nature Methods 2025

Zohora FT*, Paliwal D*, Flores-Figueroa E, Li J, Gao T, Notta F & Schwartz GW

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.

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.

Classes of ITD predict outcomes in AML patients treated with FLT3 inhibitors.

Clin. Cancer Res. 2019

Schwartz GW, Manning BS, Zhou Y, Velu PD, Bigdeli A, Astles R, Lehman AW, Morrissette JJD, Perl AE, Li M, Carroll M, and Faryabi RB.

Differential integration of transcriptome and proteome identifies pan-cancer prognostic biomarkers.

Front. Genet. 2018

Schwartz GW, Petrovic J, Zhou Y, and Faryabi RB.

An atlas of B cell clonal distribution in the human body.

Nat. Biotechnol. 2017

Meng W*, Zhang B*, Schwartz GW, Rosenfeld AM, Ren D, Thome J JC, Carpenter DJ, Matsuoka N, Lerner H, Friedman AL, Granot T, Farber DL, Shlomchik MJ, Hershberg U and Luning Prak ET.

Utilization of HIV-1 envelope V3 to identify X4- and R5-specific Tat and LTR sequence signatures.

Retrovirology 2016

Antell GC, Dampier W, Aiamkitsumrit B, Nonnemacher MR, Jacobson JM, Pirrone V, Zhong W, Kercher K, and Passic S, Williams JW, Schwartz G, Hershberg U, Krebs FC, and Wigdahl B.

Trials and Tribulations with VH Replacement.

Front. Immunol. 2014

Meng W, Jayaraman S, Zhang B, Schwartz GW, Daber RD, Hershberg U, Garfall AL, Carlson CS, Luning Prak ET.