publications | Nicholas Ho

See Google Scholar for the latest publications. * indicates equal contribution.

2026

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, and Jian Ma

Cell Systems, 2026

Bib HTML

@article{haber2025heimdall,
  title = {{HEIMDALL: Disentangling Tokenizer Design for Robust Transfer in Single-Cell Foundation Models}},
  author = {Haber, Ellie and Alam, Shahul and Ho, Nicholas and Liu, Renming and Trop, Evan and Liang, Shaoheng and Yang, Muyu and Krieger, Spencer and Ma, Jian},
  year = {2026},
  journal = {Cell Systems},
  url = {https://www.biorxiv.org/content/10.1101/2025.11.09.687403v3},
}

Foundation Models Improve Perturbation Response Prediction

Elijah Cole, Geert-Jan Huizing, Sohan Addagudi, Nicholas Ho, Euxhen Hasanaj, Merel Kuijs, Toby Johnstone, Maria Carilli, Alec Davi, Caleb Ellington, Christoph Feinauer, Pan Li, Romain Menegaux, Shahin Mohammadi, Yanjun Shao, Josiah Zhang, Emma Lundberg, Le Song, Ziv Bar-Joseph, and Eric P. Xing

bioRxiv, 2026

Bib HTML

@article{cole2026perturbation,
  title = {{Foundation Models Improve Perturbation Response Prediction}},
  author = {Cole, Elijah and Huizing, Geert-Jan and Addagudi, Sohan and Ho, Nicholas and Hasanaj, Euxhen and Kuijs, Merel and Johnstone, Toby and Carilli, Maria and Davi, Alec and Ellington, Caleb and Feinauer, Christoph and Li, Pan and Menegaux, Romain and Mohammadi, Shahin and Shao, Yanjun and Zhang, Josiah and Lundberg, Emma and Song, Le and Bar-Joseph, Ziv and Xing, Eric P.},
  year = {2026},
  journal = {bioRxiv},
  url = {https://www.biorxiv.org/content/10.64898/2026.02.18.706454v2},
}

2025

AIDO.Tissue: Spatial Cell-Guided Pretraining for Scalable Spatial Transcriptomics Foundation Model

Jing Gong^*, Yixuan Wang^*, Nicholas Ho, Xingyi Cheng, Le Song, and Eric Xing

In ICML 2025 Generative AI and Biology (GenBio) Workshop, 2025

Bib HTML

@inproceedings{gong2025aidotissue,
  title = {{AIDO.Tissue: Spatial Cell-Guided Pretraining for Scalable Spatial Transcriptomics Foundation Model}},
  author = {Gong, Jing and Wang, Yixuan and Ho, Nicholas and Cheng, Xingyi and Song, Le and Xing, Eric},
  year = {2025},
  booktitle = {ICML 2025 Generative AI and Biology (GenBio) Workshop},
  url = {https://www.biorxiv.org/content/10.1101/2025.07.04.663102v1},
}

2024

Scaling Dense Representations for Single Cell with Transcriptome-Scale Context

Nicholas Ho, Caleb N. Ellington, Jinyu Hou, Sohan Addagudi, Shentong Mo, Tianhua Tao, Dian Li, Yonghao Zhuang, Hongyi Wang, Xingyi Cheng, Le Song, and Eric P. Xing

In NeurIPS Workshop on AI for New Drug Modalities, 2024

Bib HTML

@inproceedings{ho2024aidocell,
  title = {{Scaling Dense Representations for Single Cell with Transcriptome-Scale Context}},
  author = {Ho, Nicholas and Ellington, Caleb N. and Hou, Jinyu and Addagudi, Sohan and Mo, Shentong and Tao, Tianhua and Li, Dian and Zhuang, Yonghao and Wang, Hongyi and Cheng, Xingyi and Song, Le and Xing, Eric P.},
  year = {2024},
  booktitle = {NeurIPS Workshop on AI for New Drug Modalities},
  url = {https://www.biorxiv.org/content/10.1101/2024.11.28.625303v1},
}

Accurate and General DNA Representations Emerge from Genome Foundation Models at Scale

Caleb N. Ellington, Ning Sun, Nicholas Ho, Tianhua Tao, Sazan Mahbub, Dian Li, Yonghao Zhuang, Hongyi Wang, Le Song, and Eric P. Xing

In NeurIPS Workshop on AI for New Drug Modalities, 2024

Bib HTML

@inproceedings{ellington2024aidodna,
  title = {{Accurate and General DNA Representations Emerge from Genome Foundation Models at Scale}},
  author = {Ellington, Caleb N. and Sun, Ning and Ho, Nicholas and Tao, Tianhua and Mahbub, Sazan and Li, Dian and Zhuang, Yonghao and Wang, Hongyi and Song, Le and Xing, Eric P.},
  year = {2024},
  booktitle = {NeurIPS Workshop on AI for New Drug Modalities},
  url = {https://www.biorxiv.org/content/10.1101/2024.12.01.625444v1},
}

2022

Learning Free Energy Pathways through Reinforcement Learning of Adaptive Steered Molecular Dynamics

Nicholas Ho, John Kevin Cava, John Vant, Ankita Shukla, Jacob Miratsky, Pavan Turaga, Ross Maciejewski, and Abhishek Singharoy

In Machine Learning In Structural Biology (MLSB) Workshop at the 36th Conference on Neural Information Processing Systems, 2022

Bib HTML

@inproceedings{ho2022pathways,
  title = {{Learning Free Energy Pathways through Reinforcement Learning of Adaptive Steered Molecular Dynamics}},
  author = {Ho, Nicholas and Cava, John Kevin and Vant, John and Shukla, Ankita and Miratsky, Jacob and Turaga, Pavan and Maciejewski, Ross and Singharoy, Abhishek},
  year = {2022},
  booktitle = {Machine Learning In Structural Biology (MLSB) Workshop at the 36th Conference on Neural Information Processing Systems},
  url = {https://www.biorxiv.org/content/10.1101/2022.10.04.510845v1},
}

2021

Towards Conditional Generation of Minimal Action Potential Pathways for Molecular Dynamics

John Kevin Cava, John Vant, Nicholas Ho, Ankita Shukla, Pavan Turaga, Ross Maciejewski, and Abhishek Singharoy

In ELLIS ML4Molecules Workshop, 2021

Bib HTML Code

@inproceedings{cava2021generation,
  title = {{Towards Conditional Generation of Minimal Action Potential Pathways for Molecular Dynamics}},
  author = {Cava, John Kevin and Vant, John and Ho, Nicholas and Shukla, Ankita and Turaga, Pavan and Maciejewski, Ross and Singharoy, Abhishek},
  year = {2021},
  booktitle = {ELLIS ML4Molecules Workshop},
  url = {https://arxiv.org/pdf/2111.14053.pdf},
}

CyanoPATH: a knowledgebase of genome-scale functional repertoire for toxic cyanobacterial blooms

Wei Du, Gaoyang Li, Nicholas Ho, Landon Jenkins, Drew Hockaday, Jiankang Tan, and Huansheng Cao

Briefings in Bioinformatics, 2021

Bib HTML

@article{du2021cyanopath,
  title = {{CyanoPATH: a knowledgebase of genome-scale functional repertoire for toxic cyanobacterial blooms}},
  author = {Du, Wei and Li, Gaoyang and Ho, Nicholas and Jenkins, Landon and Hockaday, Drew and Tan, Jiankang and Cao, Huansheng},
  year = {2021},
  journal = {Briefings in Bioinformatics},
  url = {https://academic.oup.com/bib/article/22/4/bbaa375/6035272},
}