Author

Doris Fu

Broad InstituteORCID 0009-0004-7331-6927Unclaimed ORCID profile · follow to get notified of new preprints

Biology Disciplines

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Signature Assays, Organisms & Methods

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Organism:human· 4 Research Focus:cell type annotation· 3 Research Focus:differential expression· 3 Research Focus:gene regulatory network inference· 3 Approach:benchmark study· 2 Research Focus:benchmarking· 2 Assay:bulk RNA-seq· 2 Approach:deep learning· 2

Frequent Co-Authors

Manolis KellisiD· 3 shared Amy Y. HuangiD· 2 shared Cassia Wang· 2 shared David LiuiD· 2 shared Emily J. RobitschekiD· 2 shared Genevieve Marie BolandiD· 2 shared Jiekun YangiD· 2 shared Kelly P. BurkeiD· 2 shared

Activity by Year

2024-2026 · peak 2/yr

Co-Author Collaboration Network

10 top collaborators · 37 mutual co-author links

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3 shared papersCancer Biology

Manolis KellisORCID

Mutual co-authors in cluster

Author profile →

4 papers

Recent·Most cited

Evaluating agentic AI for biological discovery in autonomous and copilot settings

Shreya Johri, Erica Maria Pimenta, Josephine Yates, Jingxin Fu, Erik L. Bao, Hyeji Jun, Brendan Michael Reardon, Sasha Bacot, Maha Shady, Doris Fu, Wenbin Mei, Sabrina Yvonne Camp, J Park, Eliezer M. Van Allen

This study evaluates agentic AI's ability to support biological discovery in autonomous and human-AI copilot settings using multi-omic cancer datasets.

bioRxiv · Jun 9, 2026 · PreprintCancer Biology

A chromatin fiber model explains cell-free DNA fragmentation signatures of active regulatory elements

Alexis Yang, Garyoung Gary Lee, Surya B. Chhetri, Razane El Hajj Chehade, Gunsagar Singh Gulati, Medha Pandey, Doris Fu, Yoo-Na Kim, Shahabeddin Sotudian, Hunter Savignano, Sadia D. Shahbazi, Chelsea Philpot, Taylor A. Hoggood, D. Gulhan, M Kellis, , Sylvan C. Baca

The paper infers enhancer activity from cfDNA fragmentation patterns and proposes a chromatin fiber model to explain these signatures.

bioRxiv · Nov 6, 2025 · PreprintGenomics

Mature and migratory dendritic cells promote immune infiltration and response to anti-PD-1 checkpoint blockade in metastatic melanoma

Jiekun Yang, Cassia Wang, Doris Fu, Li‐Lun Ho, Kyriakitsa Galani, Lee Chen, Jose Gonzalez, Jolene Yin Ling Fu, Amy Y. Huang, Dennie Tompers Frederick, Liang He, Mukta Asnani, Rahul Tacke, Emily J. Robitschek, Sandeep K. Yadav, , Manolis Kellis

The paper identifies a mature dendritic cell subtype associated with improved immune response and prognosis in melanoma patients treated with anti-PD-1 checkpoint inhibitors.

Nature Communications · Sep 1, 2025Peer-reviewedCancer Biology

Stratified analysis identifies HIF-2α as a therapeutic target for highly immune-infiltrated melanomas

Amy Y. Huang, Kelly P. Burke, Ryan M. Porter, Lynn Meiger, Peter R. Fatouros, Jiekun Yang, Emily J. Robitschek, Natalie I. Vokes, Cora A. Ricker, Valeria Rosado, Giuseppe Tarantino, Jiajia Chen, Tyler J. Aprati, Marc Glettig, Yiwen He, , David Liu

The paper identifies HIF-2α as a therapeutic target for immune-infiltrated melanomas through stratified analysis of clinical and molecular data.

bioRxiv · Oct 29, 2024 · PreprintCancer Biology