Author

Zijian Niu

Massachusetts Institute of TechnologyORCID 0009-0002-4301-0789Unclaimed ORCID profile · follow to get notified of new preprints

Biology Disciplines

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Systems Biology· 2 Bioinformatics· 1 Immunology· 1

Signature Assays, Organisms & Methods

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Organism:human· 3 Assay:bulk RNA-seq· 2 Research Focus:cell type annotation· 2 Research Focus:differential expression· 2 Approach:statistical model· 2 Research Focus:benchmarking· 1 Research Focus:clustering· 1 Approach:deep learning· 1

Frequent Co-Authors

Aoife O’FarrelliD· 3 shared Arjun RajiD· 3 shared Jingxin LiiD· 2 shared Kavitha SarmaiD· 2 shared Naveen JainiD· 2 shared Yogesh GoyaliD· 2 shared Abhyudai SinghiD· 1 shared Ashani T. WeeraratnaiD· 1 shared

Activity by Year

2023-2025 · peak 2/yr

Co-Author Collaboration Network

10 top collaborators · 21 mutual co-author links

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3 shared papersBioinformatics

Aoife O’FarrellORCID

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4 papers

Recent·Most cited

Piscis: a novel loss estimator of the F1 score enables accurate spot detection in fluorescence microscopy images via deep learning

Zijian Niu, Aoife O’Farrell, Jingxin Li, Sam Reffsin, Naveen Jain, Ian P. Dardani, Yogesh Goyal, Arjun Raj

Piscis uses a novel loss function to improve spot detection in RNA FISH images, outperforming existing methods without manual parameter tuning.

Cell Systems · Nov 1, 2025Peer-reviewedBioinformatics

Innate Immune Memory is Stimulus Specific

Aoife O’Farrell, Zijian Niu, Jingxin Li, Laura C. Van Eyndhoven, Kavitha Sarma, Arjun Raj

This study shows that innate immune memory in macrophages is stimulus-specific, with distinct phenotypic and epigenetic responses depending on the initial training stimulus.

bioRxiv · Jan 22, 2025 · PreprintImmunology

AP-1 Mediates Cellular Adaptation and Memory Formation During Therapy Resistance

Jingxin Li, Pavithran T. Ravindran, Aoife O’Farrell, Gianna T. Busch, Ryan H. Boe, Zijian Niu, Sean Woo, Margaret C. Dunagin, Naveen Jain, Yogesh Goyal, Kavitha Sarma, Meenhard Herlyn, Arjun Raj

The paper shows melanoma cells develop therapy resistance through AP-1-mediated cellular memories that encode transient gene expression and chromatin changes.

bioRxiv · Jul 25, 2024 · PreprintSystems Biology

Disrupting cellular memory to overcome drug resistance

Guillaume Harmange, Raúl A. Reyes Hueros, Dylan L. Schaff, Benjamin L. Emert, Michael Saint-Antoine, Laura C. Kim, Zijian Niu, Shivani Nellore, Mitchell E. Fane, Gretchen Marie Alicea, Ashani T. Weeraratna, Marie Celeste Simon, Abhyudai Singh, Sydney M. Shaffer

The paper develops a method to quantify gene expression memory and identify regulators of cell state transitions, showing that modulating PI3K and TGF-β pathways can reduce drug resistance in melanoma.

Nature Communications · Nov 6, 2023Peer-reviewedSystems Biology