Author

Ellie Haber

Carnegie Mellon University

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· 5

Signature Assays, Organisms & Methods

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Organism:mouse· 3 Assay:spatial transcriptomics· 3 Approach:statistical model· 3 Research Focus:clustering· 2 Approach:deep learning· 2 Research Focus:differential expression· 2 Research Focus:dimensionality reduction· 2 Approach:transformer / foundation model· 2

Frequent Co-Authors

Jian MaiD· 5 shared Spencer KriegeriD· 3 shared Shahul AlamiD· 2 shared Ajinkya Deshpande· 1 shared Benjamin ChidesteriD· 1 shared Evan Trop· 1 shared Fei CheniD· 1 shared Kailey HuaiD· 1 shared

Activity by Year

2025-2026 · peak 4/yr

Co-Author Collaboration Network

10 top collaborators · 23 mutual co-author links

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5 shared papersBioinformatics

Jian MaORCID

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Author profile →

5 papers

Recent·Most cited

Uncertainty-aware synthetic lethality prediction with pretrained foundation models

Kailey Hua, Ellie Haber, Jian Ma

This paper predicts synthetic lethal gene pairs using a foundation model-based framework with uncertainty calibration, improving performance without relying on PPI or GO data.

bioRxiv · Feb 27, 2026 · PreprintBioinformatics

Unified integration of spatial transcriptomics across platforms

Ellie Haber, Ajinkya Deshpande, Jian Ma, Spencer Krieger

LO_SCPLOWLOKIC_SCPLOW integrates spatial transcriptomics data across platforms without shared gene panels, improving cross-technology spatial gene program identification and tissue alignment.

Genome Research · Dec 1, 2025Peer-reviewedBioinformatics

HEIMDALL: Disentangling tokenizer design for robust transfer in single-cell foundation models

Ellie Haber, Shahul Alam, Nicholas Ho, Renming Liu, Evan Trop, Shaoheng Liang, Muyu Yang, Spencer Krieger, Jian Ma

This paper introduces HO_SCPLOWEIMDALLC_SCPLOW, a framework to analyze tokenizer design in scFMs, showing that specific tokenization choices improve generalization under distribution shift.

bioRxiv · Nov 9, 2025 · PreprintBioinformatics

EYKTHYR reveals transcriptional regulators of spatial gene programs

Spencer Krieger, Ellie Haber, Jian Ma

EO_SCPLOWYKTHYRC_SCPLOW identifies spatial transcriptional regulators by integrating gene expression and chromatin accessibility in spatial multiome data, outperforming existing methods in mouse brain and tumor datasets.

bioRxiv · May 19, 2025 · PreprintBioinformatics

POPARI: Modeling multisample variation in spatial transcriptomics

Shahul Alam, Tianming Zhou, Ellie Haber, Benjamin Chidester, Sophia Liu, Fei Chen, Jian Ma

This paper introduces a probabilistic model for analyzing multisample spatial transcriptomics data, identifying spatial metagenes and interactions across tissues.

bioRxiv · May 8, 2025 · PreprintBioinformatics