References
==========

Citing ProteoPy
---------------

If you use ProteoPy in your research, please cite:

.. bibliography::
   :filter: key == "fichtner-2026"

.. code-block:: bibtex

    @article{fichtner2026proteopy,
        title={ProteoPy: an AnnData-based framework for integrated proteomics analysis},
        author={Fichtner, Ian Dirk and Sahm, Felix and Gerstung, Moritz and Bludau, Isabell},
        journal={UNPUBLISHED},
        year={2026}
    }

COPF algorithm
--------------

If you use the COPF proteoform inference functionality, please also cite:

.. bibliography::
   :filter: key == "bludau-2021"

.. code-block:: bibtex

    @article{bludau2021systematic,
        title={Systematic detection of functional proteoform groups from bottom-up proteomic datasets},
        author={Bludau, Isabell and Frank, Max and D{\"o}rig, Christian and Cai, Yujia and Heusel, Moritz and Rosenberger, George and Picotti, Paola and Collins, Ben C. and R{\"o}st, Hannes and Aebersold, Ruedi},
        journal={Nature Communications},
        volume={12},
        pages={3810},
        year={2021},
        doi={10.1038/s41467-021-24030-x}
    }

Related Publications
--------------------

AnnData Ecosystem
^^^^^^^^^^^^^^^^^

.. bibliography::
   :filter: key in {"virshup-2024", "wolf-2018", "bredikhin-2022"}

Data Processing Software
^^^^^^^^^^^^^^^^^^^^^^^^

.. bibliography::
   :filter: key in {"demichev-2020", "cox-2008"}

Datasets
^^^^^^^^

.. bibliography::
   :filter: key in {"karayel-2020"}