Reference change

Updated the article DOI and references to reflect our most up-to-date publication changes
kevin931 · Nov 22, 2023 · fae6887 · fae6887
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diff --git a/README.md b/README.md
@@ -137,18 +137,20 @@ regarding documentations!
 
 ## References
 
-If you are cytomulating in your workflow, citing [our paper](https://doi.org/10.1101/2022.06.14.496200) is appreciated:
+If you are cytomulating in your workflow, citing [our paper](https://doi.org/10.1186/s13059-023-03099-1) is appreciated:
 
 ```
-@article {Yang2022.06.14.496200,
-	author = {Yang, Yuqiu and Wang, Kaiwen and Lu, Zeyu and Wang, Tao and Wang, Xinlei},
-	title = {Cytomulate: Accurate and Efficient Simulation of CyTOF data},
-	elocation-id = {2022.06.14.496200},
-	year = {2022},
-	doi = {10.1101/2022.06.14.496200},
-	publisher = {Cold Spring Harbor Laboratory},
-	URL = {https://www.biorxiv.org/content/early/2022/06/16/2022.06.14.496200},
-	eprint = {https://www.biorxiv.org/content/early/2022/06/16/2022.06.14.496200.full.pdf},
-	journal = {bioRxiv}
+@article{Yang2023,
+	title = {Cytomulate: accurate and efficient simulation of CyTOF data},
+    volume = {24},
+    ISSN = {1474-760X},
+    url = {http://dx.doi.org/10.1186/s13059-023-03099-1},
+    DOI = {10.1186/s13059-023-03099-1},
+  	number = {1},
+	journal = {Genome Biology},
+	publisher = {Springer Science and Business Media LLC},
+	author = {Yang,  Yuqiu and Wang,  Kaiwen and Lu,  Zeyu and Wang,  Tao and Wang,  Xinlei},
+	year = {2023},
+	month = nov 
 }
 ```
diff --git a/cytomulate/__init__.py b/cytomulate/__init__.py
@@ -5,7 +5,7 @@
 """
 
 __version__ = "0.1.1"
-__author__ = "Yuqiu Yang, Kevin Wang, Tao Wang, Sherry Wang"
+__author__ = "Yuqiu Yang, Kevin Wang, Zeyu Lu,  Tao Wang, Sherry Wang"
 
 from cytomulate.creation.cytof_data import CreationCytofData
 from cytomulate.emulation.cytof_data import EmulationCytofData
diff --git a/docs/source/index.rst b/docs/source/index.rst
@@ -68,8 +68,8 @@ For more details, **read our tutorials and documentations linked below!** Or try
    :hidden:
 
    references
-   Our Paper <https://doi.org/10.1101/2022.04.26.489549>
-   Dr. Xinlei (Shery) Wang <https://people.smu.edu/swang/>
+   Our Paper <https://doi.org/10.1186/s13059-023-03099-1>
+   Dr. Xinlei (Sherry) Wang <https://www.uta.edu/academics/faculty/profile?username=wangx9>
    Dr. Tao Wang <https://qbrc.swmed.edu/labs/wanglab/aboutpi.php>
    DBAI <https://dbai.biohpc.swmed.edu/>
    GitHub <https://github.com/kevin931/cytomulate/>
@@ -79,11 +79,11 @@ For more details, **read our tutorials and documentations linked below!** Or try
 Resources
 ***********************
 
-For our paper, read our preprint `here <https://doi.org/10.1101/2022.04.26.489549>`_.
+For our paper, read our preprint `here <https://doi.org/10.1186/s13059-023-03099-1>`_.
 
 For more resources on our labs, collaborators, and related projects, please visit the following:
 
-   * `Dr. Xinlei (Shery) Wang faculty page <https://people.smu.edu/swang/>`_
+   * `Dr. Xinlei (Sherry) Wang faculty page <https://www.uta.edu/academics/faculty/profile?username=wangx9>`_
    * `Dr. Tao Wang Lab <https://qbrc.swmed.edu/labs/wanglab/aboutpi.php>`_
    * `Database for Actionable Immunology (DBAI) for more computational immunology-related tools <https://dbai.biohpc.swmed.edu/>`_
 

diff --git a/docs/source/references.rst b/docs/source/references.rst
@@ -3,7 +3,7 @@ References
 ################
 
 Here, you will find a list of relevant references. For a complete list, you can
-read `our paper <https://doi.org/10.1101/2022.04.26.489549>`_.
+read `our paper <https://doi.org/10.1186/s13059-023-03099-1>`_.
 
 -----------------------
 
@@ -15,16 +15,18 @@ If you decide to cytomulate it in your package, citing our paper is highly appre
 
 .. code-block:: text
 
-    @article {Yang2022.06.14.496200,
-        author = {Yang, Yuqiu and Wang, Kaiwen and Lu, Zeyu and Wang, Tao and Wang, Xinlei},
-        title = {Cytomulate: Accurate and Efficient Simulation of CyTOF data},
-        elocation-id = {2022.06.14.496200},
-        year = {2022},
-        doi = {10.1101/2022.06.14.496200},
-        publisher = {Cold Spring Harbor Laboratory},
-        URL = {https://www.biorxiv.org/content/early/2022/06/16/2022.06.14.496200},
-        eprint = {https://www.biorxiv.org/content/early/2022/06/16/2022.06.14.496200.full.pdf},
-        journal = {bioRxiv}
+    @article{Yang2023,
+        title = {Cytomulate: accurate and efficient simulation of CyTOF data},
+        volume = {24},
+        ISSN = {1474-760X},
+        url = {http://dx.doi.org/10.1186/s13059-023-03099-1},
+        DOI = {10.1186/s13059-023-03099-1},
+        number = {1},
+        journal = {Genome Biology},
+        publisher = {Springer Science and Business Media LLC},
+        author = {Yang,  Yuqiu and Wang,  Kaiwen and Lu,  Zeyu and Wang,  Tao and Wang,  Xinlei},
+        year = {2023},
+        month = nov 
     }
 
 

diff --git a/setup.py b/setup.py
@@ -58,8 +58,8 @@ def run(self):
     name = "cytomulate",
     version = VERSION,
     description = "Accurate and Efficient Simulation of CyTOF data",
-    author = "Yuqiu Yang, Kevin Wang, Tao Wang, Sherry Wang",
-    author_email = "[email protected], [email protected], [email protected], swang@smu.edu",
+    author = "Yuqiu Yang, Kevin Wang, Zeyu Lu, Tao Wang, Sherry Wang",
+    author_email = "[email protected], [email protected], [email protected], [email protected], xinlei.wang@uta.edu",
     long_description_content_type = "text/markdown",
     long_description = open("README.md").read(),
     packages=["cytomulate",