update pypi readme

Author: VolkerBergen

pypi.rst

@@ -1,4 +1,4 @@
-|PyPI| |PyPIDownloads| |travis|
+|PyPI| |PyPIDownloads| |CI|
 
 scVelo - RNA velocity generalized through dynamical modeling
 ============================================================
@@ -7,37 +7,54 @@ scVelo - RNA velocity generalized through dynamical modeling
    :width: 300px
    :align: left
 
-**scVelo** is a scalable toolkit for RNA velocity analysis in single cells.
-The methods are based on our preprint
-`Bergen et al. (2019) <https://doi.org/10.1101/820936>`_.
+**scVelo** is a scalable toolkit for RNA velocity analysis in single cells, based on
+`Bergen et al. (Nature Biotech, 2020) <https://doi.org/10.1038/s41587-020-0591-3>`_.
 
-RNA velocity enables the recovery of directed dynamic information by leveraging splicing information.
-scVelo generalizes the concept of RNA velocity (`La Manno et al., 2018 <https://doi.org/10.1038/s41586-018-0414-6>`_)
+RNA velocity enables the recovery of directed dynamic information by leveraging splicing kinetics.
+scVelo generalizes the concept of RNA velocity
+(`La Manno et al., Nature, 2018 <https://doi.org/10.1038/s41586-018-0414-6>`_)
 by relaxing previously made assumptions with a stochastic and a dynamical model that solves the full
 transcriptional dynamics. It thereby adapts RNA velocity to widely varying specifications such as non-stationary populations.
 
 scVelo is compatible with scanpy_ and hosts efficient implementations of all RNA velocity models.
 
-See `<https://scvelo.org>`_ for documentation and tutorials.
-
 scVelo's key applications
--------------------------
+^^^^^^^^^^^^^^^^^^^^^^^^^
 - estimate RNA velocity to study cellular dynamics.
 - identify putative driver genes and regimes of regulatory changes.
 - infer a latent time to reconstruct the temporal sequence of transcriptomic events.
 - estimate reaction rates of transcription, splicing and degradation.
 - use statistical tests, e.g., to detect different kinetics regimes.
 
+scVelo has, for instance, recently been used to study immune response in COVID-19
+patients and dynamic processes in human lung regeneration. Find out more in this list of
+`application examples <https://scholar.google.com/scholar?cites=18195185735875895912>`_.
+
+Latest news
+^^^^^^^^^^^
+- Feb/2021: scVelo goes multi-core
+- Dec/2020: Cover of `Nature Biotechnology <https://www.nature.com/nbt/volumes/38>`_
+- Nov/2020: Talk at `Single Cell Biology <https://coursesandconferences.wellcomegenomecampus.org/our-events/single-cell-biology-2020/>`_
+- Oct/2020: `Helmholtz Best Paper Award <https://twitter.com/ICBmunich/status/1318611467722199041>`_
+- Oct/2020: Map cell fates with `CellRank <https://cellrank.org>`_
+- Sep/2020: Talk at `Single Cell Omics <https://twitter.com/fabian_theis/status/1305621028056465412>`_
+- Aug/2020: `scVelo out in Nature Biotech <https://www.helmholtz-muenchen.de/en/aktuelles/latest-news/press-information-news/article/48658/index.html>`_
+
 Reference
----------
-Bergen et al. (2019), *Generalizing RNA velocity to transient cell states through dynamical modeling*,
-`biorxiv <https://doi.org/10.1101/820936>`_.
+^^^^^^^^^
+Bergen *et al.* (2020), Generalizing RNA velocity to transient cell states through dynamical modeling,
+`Nature Biotech <https://doi.org/10.1038/s41587-020-0591-3>`_.
+|dim|
 
 Support
--------
-Feel free to submit an `issue <https://github.com/theislab/scvelo/issues/new/choose>`_
-or send us an `email <mailto:mail@scvelo.org>`_.
+^^^^^^^
+Found a bug or would like to see a feature implemented? Feel free to submit an
+`issue <https://github.com/theislab/scvelo/issues/new/choose>`_.
+Have a question or would like to start a new discussion? Head over to
+`GitHub discussions <https://github.com/theislab/scvelo/discussions>`_.
+In either case, you can also always send us an `email <mailto:mail@scvelo.org>`_.
 Your help to improve scVelo is highly appreciated.
+For further information visit `scvelo.org <https://scvelo.org>`_.
 
 
 .. |PyPI| image:: https://img.shields.io/pypi/v/scvelo.svg
@@ -49,7 +66,16 @@ Your help to improve scVelo is highly appreciated.
 .. |Docs| image:: https://readthedocs.org/projects/scvelo/badge/?version=latest
    :target: https://scvelo.readthedocs.io
 
-.. |travis| image:: https://travis-ci.org/theislab/scvelo.svg?branch=master
-   :target: https://travis-ci.org/theislab/scvelo
+.. |CI| image:: https://img.shields.io/github/workflow/status/theislab/scvelo/CI/master
+   :target: https://github.com/theislab/scvelo/actions?query=workflow%3ACI
+
+.. _scanpy: https://scanpy.readthedocs.io
+
+.. |br| raw:: html
+
+  <br/>
+
+.. |dim| raw:: html
 
-.. _scanpy: https://scanpy.readthedocs.io
+   <span class="__dimensions_badge_embed__" data-id="pub.1129830274" data-style="small_rectangle"></span>
+   <script async src="https://badge.dimensions.ai/badge.js" charset="utf-8"></script>