Publications
============

This page contains publications that used the CASPULE pipeline or its associated analysis tooling.

If you used CASPULE in your work, please cite the following `paper <https://www.biorxiv.org/content/10.1101/2025.11.09.687447v1/>`__.

If you want to list your paper in the website, please open a pull reques on our `github <https://github.com/caspule/caspule>`__ with the citation and link.

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Articles
----------------------

2025
^^^^

- **CASPULE: A computational tool to study sticker–spacer polymer condensates.**
  (*bioRxiv*, 2025).  
  Chattaraj, A.; Kanovich, D. S.; Ranganathan, S.; Shakhnovich, E. I.  
  `bioRxiv <https://www.biorxiv.org/content/10.1101/2025.11.09.687447v1/>`__ ·
  `PDF <https://www.biorxiv.org/content/10.1101/2025.11.09.687447v1.full.pdf>`__

- **Separation of sticker–spacer energetics governs the coalescence of metastable condensates.**
  (*Biophysical Journal*, 2025).  
  Chattaraj, A.; Shakhnovich, E. I.  
  `DOI <https://doi.org/10.1016/j.bpj.2024.12.017>`__ 

2024
^^^^

- **Multi-condensate state as a functional strategy to optimize the cell signaling output.**
  (*Nature Communications*, 2024).  
  Chattaraj, A.; Shakhnovich, E. I.  
  `DOI <https://doi.org/10.1038/s41467-024-50489-5>`__ 

2020
^^^^

- **Dynamic metastable long-living droplets formed by sticker-spacer proteins.**
  (*eLife*, 2020).  
  Ranganathan, S.; Shakhnovich, E. I.  
  `DOI <https://doi.org/10.7554/eLife.56159>`__ 

For general background on sticker-spacer polymers 
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^

- **Physical Principles Underlying the Complex Biology of Intracellular Phase Transitions.**
  (*Annual Review of Biophysics*, 2020).  
  Choi, J-M.; Holehouse A. S.; Pappu R. V.   
  `DOI <https://doi.org/10.1146/annurev-biophys-121219-081629>`__