Publications

Selected Publications

Papers from the predict–mechanism–therapy continuum.
# First author · * Corresponding author. Lab PI's name in bold.

2026
1

AI-driven pathology and blood-based biomarkers: a golden opportunity to democratize precision oncology Cancer Discovery

Danh-Tai Hoang#*, Tian-Gen Chang#*, Cristina R. Ferrone, et al.

Cancer Discovery, 2026 (in press)

In Press
2

AI-Inferred Spatial Transcriptomics Unlocks Large-Scale Breast Cancer Biomarker Discovery from Histopathology Cell

Eldad D. Shulman*, Emma M. Campagnolo*, Roshan Lodha, Amos Stemmer, Thomas Cantore, Beibei Ru, Tian-Gen Chang, et al.

Cell, 2026 (in press)

In Press
3

Mapping Intratumor Heterogeneity Across Layers for Advancing Immunotherapy Cell

Jean-Christophe Marine*, Osnat Bartok, Shira Sagie, Pietro Paolo Vitiello, Alberto Bardelli, Chen Weller, Tian-Gen Chang, et al.

Cell, 2026; 189(8): 2416-2440

DOI →
2025
4

Hypoxia-Induced EGR1 Remodels Neutrophils to Suppress Anti-Tumor Immunity Science Immunology

Tian-Gen Chang#*, Jay Friedman, Paul E. Clavijo, et al.

Science Immunology, 2025; 10(114): eadz2273

DOI →
5

Analysis of RNA translation with a deep learning architecture provides new insight into translation control Nucleic Acids Research

Xiaojuan Fan#*, Tian-Gen Chang#, Chuyun Chen#, et al.

Nucleic Acids Research, 2025; 53(7): gkaf277

DOI →
6

Hallmarks of artificial intelligence contributions to precision oncology Nature Cancer

Tian-Gen Chang#*, Seongyong Park, Alejandro A. Schäffer, et al.

Nature Cancer, 2025; 6, 417–431

DOI →
7

Tumor and blood B cell abundance outperforms established immune checkpoint blockade response prediction signatures in head and neck cancer Annals of Oncology

Tian-Gen Chang#, Aris Spathis#, Alejandro A. Schäffer, et al.

Annals of Oncology, 2025; 36(3): 309–320

DOI → Editorial →
Highlighted in Annals of Oncology Editorial: Is the abundance of B cells the best biomarker to predict immune checkpoint inhibitor response in head and neck squamous cell cancers? 2025; 36(3): 238–239
8

Single-cell-guided identification of logic-gated antigen combinations for designing effective and safe CAR therapy BioRxiv

Sanna Madan#, Tian-Gen Chang#, et al.

BioRxiv, 2025 (In revision)

Preprint →
9

Translation dysregulation in cancer as a source for targetable antigens Cancer Cell

Chen Weller#, Osnat Bartok#, Christopher S. McGinnis#, Heyilimu Palashati, Tian-Gen Chang, et al.

Cancer Cell, 2025; 43(5): 823–840

DOI →
2024
10

Inferring characteristics of the tumor immune microenvironment of patients with HNSCC from single-cell transcriptomics of peripheral blood Cancer Research Communications

Yingying Cao#, Tian-Gen Chang#, Fiorella Schischlik#, et al.

Cancer Research Communications, 2024; 4(9): 2335–2348

DOI →
11

LORIS robustly predicts patient outcomes with immune checkpoint blockade therapy using common clinical, pathologic and genomic features Nature Cancer

Tian-Gen Chang#, Yingying Cao#, Hannah J. Sfreddo#, et al.

Nature Cancer, 2024; 5: 1158–1175

DOI → News & Views → LORIS Tool →
Highlighted in Nature Cancer "News & Views": Enhanced precision in immunotherapy, 2024; 5: 1136–1138 · Featured in Clinical Chemistry, NCI Media Advisory, NCI Podcast "Inside Cancer Careers", and Podcast "Cancer HealthCast"
12

Reusability report: Leveraging supervised learning to uncover phenotype-relevant biology from single-cell RNA sequencing data Nature Machine Intelligence

Yingying Cao#, Tian-Gen Chang#, Sahil Sahni, et al.

Nature Machine Intelligence, 2024; 6: 307–314

DOI →
13

Increased RNA and protein degradation is required for counteracting transcriptional burden and proteotoxic stress in human aneuploid cells Cancer Discovery

Marica Rosaria Ippolito#, Johanna Zerbib#, Yonatan Eliezer, Eli Reuveni, Sonia Viganò, et al., Tian-Gen Chang, et al.

Cancer Discovery, 2024; 14(12): 2532–2553

DOI →
14

Human aneuploid cells depend on the RAF/MEK/ERK pathway for overcoming increased DNA damage Nature Communications

Johanna Zerbib#, Marica Rosaria Ippolito#, Yonatan Eliezer, Giuseppina De Feudis, et al., Tian-Gen Chang, et al.

Nature Communications, 2024; 15(1): 7772

DOI →
15

Microenvironment shapes small-cell lung cancer neuroendocrine states and presents therapeutic opportunities Cell Reports Medicine

Parth Desai#, Nobuyuki Takahashi, Rajesh Kumar, et al., Tian-Gen Chang, et al.

Cell Reports Medicine, 2024; 5(6): 101610

DOI →
2023
16

Optimizing cancer immunotherapy response prediction by tumor aneuploidy score and fraction of copy number alterations npj Precision Oncology

Tian-Gen Chang#*, Yingying Cao, Eldad D. Shulman, et al.

npj Precision Oncology, 2023; 7: 54

DOI →
17

Pan-cancer analysis of patient tumor single-cell transcriptomes identifies promising selective and safe chimeric antigen receptor targets in head and neck cancer Cancers

Sanna Madan#, Sanju Sinha, Tian-Gen Chang, et al.

Cancers, 2023; 15(19): 4885

DOI →

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