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Citation

How to cite ChimeraLM in your research.

BibTeX

If you use ChimeraLM in your research, please cite:

@software{chimeralm2025,
  title={ChimeraLM: A genomic language model to identify chimera artifacts},
  author={Li, Yangyang and Guo, Qingxiang and Yang, Rendong},
  year={2025},
  url={https://github.com/ylab-hi/ChimeraLM},
  version={0.1.0}
}

APA Style

Li, Y., Guo, Q., & Yang, R. (2025). ChimeraLM: A genomic language model to identify chimera artifacts (Version 0.1.0) [Computer software]. https://github.com/ylab-hi/ChimeraLM

MLA Style

Li, Yangyang, Qingxiang Guo, and Rendong Yang. ChimeraLM: A Genomic Language Model to Identify Chimera Artifacts. Version 0.1.0, 2025, https://github.com/ylab-hi/ChimeraLM.

Chicago Style

Li, Yangyang, Qingxiang Guo, and Rendong Yang. 2025. "ChimeraLM: A Genomic Language Model to Identify Chimera Artifacts." Version 0.1.0. https://github.com/ylab-hi/ChimeraLM.

Plain Text

ChimeraLM: A genomic language model to identify chimera artifacts
Yangyang Li, Qingxiang Guo, Rendong Yang
2025
https://github.com/ylab-hi/ChimeraLM

Citing Specific Version

To cite a specific version of ChimeraLM:

@software{chimeralm2025,
  title={ChimeraLM: A genomic language model to identify chimera artifacts},
  author={Li, Yangyang and Guo, Qingxiang and Yang, Rendong},
  year={2025},
  url={https://github.com/ylab-hi/ChimeraLM},
  version={0.1.0},
  doi={10.5281/zenodo.XXXXXXX}  # Replace with actual DOI when available
}

If you use the HyenaDNA backbone, please also cite:

@article{hyenadna2023,
  title={HyenaDNA: Long-Range Genomic Sequence Modeling at Single Nucleotide Resolution},
  author={Nguyen, Eric and others},
  journal={NeurIPS},
  year={2023}
}

Acknowledgments

ChimeraLM builds upon several open-source projects:

  • PyTorch & PyTorch Lightning: Deep learning framework
  • HyenaDNA: Genomic language model backbone
  • pysam: BAM/SAM file processing
  • Hydra: Configuration management

Questions?

For citation-related questions, contact: