add research briefing (#784)

* add research briefing * manuscript link updates * notebook update --------- Co-authored-by: ArinaDanilina <[email protected]> Co-authored-by: Arina Danilina <[email protected]>
theislab · Jan 22, 2025 · 0b25aa8 · 0b25aa8
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diff --git a/docs/_static/img/dark_mode_concept.png b/docs/_static/img/dark_mode_concept.png
diff --git a/docs/_static/img/light_mode_concept.png b/docs/_static/img/light_mode_concept.png
diff --git a/docs/index.rst b/docs/index.rst
@@ -33,11 +33,12 @@ Getting started
 - Read the :doc:`user guide <user_guide>` to get a high-level overview of :mod:`moscot`.
 - Take a look at our :doc:`tutorials <notebooks/tutorials/index>` to learn how to use :mod:`moscot` for data analysis.
 - For more technical examples and specific use cases, check out the :doc:`examples <notebooks/examples/index>` section.
-- To see :mod:`moscot` in action, read our `Klein et al., 2023`_ manuscript.
+- To see :mod:`moscot` in action, read our `Klein et al., 2025`_ manuscript.
+- For a high-level introduction of moscot, check out our `research briefing <https://doi.org/10.1038/d41586-025-00107-1>`_.
 
 Citing moscot
 -------------
-If you find a model useful for your research, please consider citing the `Klein et al., 2023`_ manuscript as
+If you find a model useful for your research, please consider citing the `Klein et al., 2025`_ manuscript as
 well as the publication introducing the model, which can be found in the corresponding documentation.
 
 Important resources
@@ -77,7 +78,7 @@ Important resources
 
     .. grid-item-card:: Manuscript
 
-        Please have a look at `Klein et al., 2023`_ to learn more.
+        Please have a look at `Klein et al., 2025`_ to learn more.
 
 .. toctree::
     :maxdepth: 2
@@ -118,4 +119,4 @@ Important resources
     :target: https://pepy.tech/project/moscot
     :alt: Downloads
 
-.. _Klein et al., 2023: https://www.biorxiv.org/content/10.1101/2023.05.11.540374v2
+.. _Klein et al., 2025: https://www.nature.com/articles/s41586-024-08453-2
diff --git a/docs/notebooks b/docs/notebooks
diff --git a/docs/references.bib b/docs/references.bib
@@ -432,13 +432,17 @@ @article{demetci-scot:22
   year      = {2022},
 }
 
-@article{klein:23,
-  author    = {Klein, Dominik and Palla, Giovanni and Lange, Marius and Klein, Michal and Piran, Zoe and Gander, Manuel and Meng-Papaxanthos Laetitia and Sterr, Michael and Bastidas-Ponce Aimee and Tarquis-Medina, Marta and Lickert, Heiko and Bakhti, Mostafa and Nitzan, Mor and Cuturi, Marco and Theis, Fabian J.},
-  publisher = {Cold Spring Harbor Laboratory},
-  url       = {https://www.biorxiv.org/content/10.1101/2023.05.11.540374v2},
-  journal   = {bioRxiv},
-  title     = {Mapping cells through time and space with moscot},
-  year      = {2023},
+
+ @article{klein:25,
+  title={Mapping cells through time and space with moscot},
+  url={https://www.nature.com/articles/s41586-024-08453-2},
+  DOI={https://doi.org/10.1038/s41586-024-08453-2},
+  journal={Nature},
+  publisher={Nature Publishing Group},
+  author={Klein, Dominik and Palla, Giovanni and Lange, Marius and Klein, Michal and Piran, Zoe and Gander, Manuel and Meng-Papaxanthos, Laetitia and Sterr, Michael and Saber, Lama and Jing, Changying and Bastidas-Ponce, Aimée and Cota, Perla and Tarquis-Medina, Marta and Parikh, Shrey and Gold, Ilan and Lickert, Heiko and Bakhti, Mostafa and Nitzan, Mor and Cuturi, Marco and Theis, Fabian J},
+  year={2025},
+  month={Jan},
+  pages={1–11}
 }
 
 @misc{huguet:23,

diff --git a/src/moscot/datasets.py b/src/moscot/datasets.py
@@ -282,7 +282,7 @@ def pancreas_multiome(
     force_download: bool = True,
     **kwargs: Any,
 ) -> Union[mu.MuData, ad.AnnData]:  # pragma: no cover
-    """Pancreatic endocrinogenesis dataset published with the moscot manuscript :cite:`klein:23`.
+    """Pancreatic endocrinogenesis dataset published with the moscot manuscript :cite:`klein:25`.
 
     The dataset contains paired scRNA-seq and scATAC-seq data of pancreatic cells at embryonic days 14.5, 15.5, and
     16.5. The data was preprocessed and filtered as described in the manuscript, the raw data and the full processed