Author

Qiyu Gong

Broad Institute

Listed by name: these papers carry no ORCID for this author, so different people with the same name may be mixed together.

Biology Disciplines

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Bioinformatics· 4 Cancer Biology· 1 Genomics· 1 Immunology· 1 Molecular Biology· 1

Signature Assays, Organisms & Methods

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Assay:spatial transcriptomics· 5 Organism:human· 4 Approach:deep learning· 3 Research Focus:gene regulatory network inference· 3 Research Focus:cell type annotation· 2 Research Focus:cell-cell communication· 2 Approach:experimental assay· 2 Assay:imaging· 2

Frequent Co-Authors

Fei CheniD· 6 shared Kai CaoiD· 3 shared Orr AshenbergiD· 2 shared Qitian WuiD· 2 shared Ramnik J. XavieriD· 2 shared Sophia LiuiD· 2 shared Xi Dawn CheniD· 2 shared Aditi SahuiD· 1 shared

Activity by Year

2020-2026 · peak 5/yr

Co-Author Collaboration Network

10 top collaborators · 22 mutual co-author links

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6 shared papersBioinformatics

Fei ChenORCID

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Author profile →

8 papers

Recent·Most cited

Multi-modal foundation model with whole-slide attention enables transferrable digital pathology at single-cell resolution

Qitian Wu, Qiyu Gong, Luezhen Yuan, Zhiyi Li, Orr Ashenberg, Fei Chen, Ramnik J. Xavier, Caroline Uhler

TissueFormer is a foundation model that predicts spatial gene expression from histology images at single-cell resolution and scales to diagnostic tasks.

bioRxiv · Aug 6, 2026 · PreprintBioinformatics

Generative Design of Cell Type-Specific RNA Splicing Elements for Programmable Gene Regulation

Xi Dawn Chen, Manson Jim, Mounica Vallurupalli, Kai Cao, Andrea Navarro Torres, Jing Wesley Leong, Yifan Zhang, David Wollensak, Qiyu Gong, Jing Sun, Mehdi Borji, Gail Schor, Sofia Mrowka, Margaret Hu, Anisha Laumas, , Fei Chen

The paper introduces SPICE, a framework that uses splicing assays and generative design to create cell-specific gene regulation elements for research and therapy.

bioRxiv · Nov 5, 2025 · PreprintMolecular Biology

Craters on the melanoma surface facilitate tumor-immune interactions and demonstrate pathologic response to checkpoint blockade in humans

Aya Ludin, Georgia L. Stirtz, Asaf Tal, Ajit J. Nirmal, Kathleen Lindahl Pfaff, Michael P. Manos, Naomi R. Besson, Nebiyat Eskndir, Billie A. Porter, Stephanie M. Jones, Hannah Mae Faulkner, Qiyu Gong, Sophia Liu, Irving Barrera, Lijian Wu, , Leonard Ira Zon

The paper identifies crater-shaped structures in melanoma that enhance immune response to checkpoint blockade therapy in humans and zebrafish.

Cell · Oct 17, 2025Peer-reviewedCancer Biology

Energy-Regularized Graph Learning for Multiscale Spatial Representation

Qiyu Gong, Kai Cao, Jackson A. Weir, Qitian Wu, Dongshunyi Li, Fei Chen

Glimmer improves spatial representation learning by adaptively learning graphs that balance molecular similarity and spatial proximity across scales, outperforming existing methods in clustering and spatial conservation.

bioRxiv · Aug 22, 2025 · PreprintBioinformatics

Tissue architecture dynamics underlying immune development and decline in the thymus

Sophia Liu, Mirco Friedrich, Ruth Raichur, Dennis H. Gong, Niklas Kehl, Qiyu Gong, Bingxian Chen, Karin Gustafsson, L. Larissa, David T. Scadden, Rhiannon K. Macrae, Feng Zhang, Fei Chen

This study uses spatial transcriptomics and TCR sequencing in mice to analyze thymus changes across lifespan, revealing structural and transcriptional alterations linked to immune decline.

bioRxiv · Jun 28, 2025 · PreprintImmunology

Sensitive Transcriptomics and Genotyping reveals function of genetic variants in immunity

Kai Liu, Anders W. Rasmussen, Wenkai Han, Qiyu Gong, Seneca Bohley, Xi Dawn Chen, Masahiro Kanai, Regan Maronick, Zhangyuan Yin, Chenlei Hu, T.S. Jain, Jorge Diego Martin-Rufino, Vijay G. Sankaran, Orr Ashenberg, Mark J. Daly, , Ramnik J. Xavier

This study introduces STAG-seq, a method combining transcriptomics and genotyping to functionally analyze genetic variants in immune cells, revealing their impact on gene expression and disease mechanisms.

bioRxiv · Mar 12, 2025 · PreprintGenomics

uniPort: a unified computational framework for single-cell data integration with optimal transport

Kai Cao, Qiyu Gong, Yiguang Hong, Lin Wan

uniPort integrates single-cell multi-omics datasets using a coupled-VAE and Minibatch-UOT, enabling shared latent space embedding and reference atlas construction.

Nature Communications · Dec 1, 2022Peer-reviewedBioinformatics

Meta-transcriptomic analysis reveals the gene expression and novel conserved sub-genomic RNAs in SARS-CoV-2 and MERS-CoV.

Lin Lyu, Ru Feng, Mingnan Zhang, Qiyu Gong, Yinjing Liao, Yanjiao Zhou, Xiaokui Guo, Bing Su, Yair Dorsett, Lei Chen

The paper analyzes meta-transcriptomic data to identify gene expression and novel conserved sub-genomic RNAs in SARS-CoV-2 and MERS-CoV, revealing new peptides with potential functional roles in viral virulence.

bioRxiv · Apr 16, 2020 · PreprintBioinformatics