Add ref to new paper

Author: mass-a

README.md

@@ -1,4 +1,4 @@
-# pyUCell: Robust and scalable single-cell signature scoring 
+# pyUCell: Robust and scalable single-cell signature scoring
 
 [![PyPI](https://img.shields.io/pypi/v/pyucell.svg)](https://pypi.org/project/pyucell/)
 [![Tests][badge-tests]][tests]
@@ -67,9 +67,10 @@ Please address your questions and bug reports at: [UCell issues](https://github.
 
 ### Citation
 
-* UCell and pyUCell: single-cell gene signature scoring for R and Python. Massimo Andreatta & Santiago J Carmona **(2026)** *Bioinformatics* https://doi.org/10.1093/bioinformatics/btag055
+* UCell and pyUCell: single-cell gene signature scoring for R and Python. Massimo Andreatta & Santiago J Carmona (2026) *Bioinformatics* - [doi.org/10.1093/bioinformatics/btag055](https://doi.org/10.1093/bioinformatics/btag055)
+
+* UCell: robust and scalable single-cell gene signature scoring. Massimo Andreatta & Santiago J Carmona (2021) *CSBJ* - [doi.org/10.1016/j.csbj.2021.06.043](https://doi.org/10.1016/j.csbj.2021.06.043)
 
-* UCell: robust and scalable single-cell gene signature scoring. Massimo Andreatta & Santiago J Carmona **(2021)** *CSBJ* https://doi.org/10.1016/j.csbj.2021.06.043
 
 
 ### Developer guide for scverse tools

docs/notebooks/basic.ipynb

@@ -344,7 +344,10 @@
    "source": [
     "If you used UCell in your research, please cite:\n",
     "\n",
-    "**UCell: robust and scalable single-cell gene signature scoring.** Massimo Andreatta & Santiago J Carmona (2021) CSBJ - [doi.org/10.1016/j.csbj.2021.06.043](https://doi.org/10.1016/j.csbj.2021.06.043)"
+    "**UCell and pyUCell: single-cell gene signature scoring for R and Python.** Massimo Andreatta & Santiago J Carmona (2026) *Bioinformatics* - [doi.org/10.1093/bioinformatics/btag055](https://doi.org/10.1093/bioinformatics/btag055)\n",
+    "\n",
+    "**UCell: robust and scalable single-cell gene signature scoring.** Massimo Andreatta & Santiago J Carmona (2021) *CSBJ* - [doi.org/10.1016/j.csbj.2021.06.043](https://doi.org/10.1016/j.csbj.2021.06.043)\n",
+    "\n"
    ]
   }
  ],
@@ -355,16 +358,7 @@
    "name": "python3"
   },
   "language_info": {
-   "codemirror_mode": {
-    "name": "ipython",
-    "version": 3
-   },
-   "file_extension": ".py",
-   "mimetype": "text/x-python",
-   "name": "python",
-   "nbconvert_exporter": "python",
-   "pygments_lexer": "ipython3",
-   "version": "3.11.11"
+   "name": "python"
   }
  },
  "nbformat": 4,

docs/notebooks/knn.ipynb

@@ -422,7 +422,9 @@
    "source": [
     "If you used UCell in your research, please cite:\n",
     "\n",
-    "**UCell: robust and scalable single-cell gene signature scoring.** Massimo Andreatta & Santiago J Carmona (2021) CSBJ - [doi.org/10.1016/j.csbj.2021.06.043](https://doi.org/10.1016/j.csbj.2021.06.043)"
+    "**UCell and pyUCell: single-cell gene signature scoring for R and Python.** Massimo Andreatta & Santiago J Carmona (2026) *Bioinformatics* - [doi.org/10.1093/bioinformatics/btag055](https://doi.org/10.1093/bioinformatics/btag055)\n",
+    "\n",
+    "**UCell: robust and scalable single-cell gene signature scoring.** Massimo Andreatta & Santiago J Carmona (2021) *CSBJ* - [doi.org/10.1016/j.csbj.2021.06.043](https://doi.org/10.1016/j.csbj.2021.06.043)"
    ]
   },
   {
@@ -441,16 +443,7 @@
    "name": "python3"
   },
   "language_info": {
-   "codemirror_mode": {
-    "name": "ipython",
-    "version": 3
-   },
-   "file_extension": ".py",
-   "mimetype": "text/x-python",
-   "name": "python",
-   "nbconvert_exporter": "python",
-   "pygments_lexer": "ipython3",
-   "version": "3.11.11"
+   "name": "python"
   }
  },
  "nbformat": 4,

docs/notebooks/parameters.ipynb

@@ -659,8 +659,9 @@
    "source": [
     "If you used UCell in your research, please cite:\n",
     "\n",
-    "**UCell: robust and scalable single-cell gene signature scoring.** Massimo Andreatta & Santiago J Carmona (2021) \n",
-    "CSBJ - [doi.org/10.1016/j.csbj.2021.06.043](https://doi.org/10.1016/j.csbj.2021.06.043)"
+    "**UCell and pyUCell: single-cell gene signature scoring for R and Python.** Massimo Andreatta & Santiago J Carmona (2026) *Bioinformatics* - [doi.org/10.1093/bioinformatics/btag055](https://doi.org/10.1093/bioinformatics/btag055)\n",
+    "\n",
+    "**UCell: robust and scalable single-cell gene signature scoring.** Massimo Andreatta & Santiago J Carmona (2021) *CSBJ* - [doi.org/10.1016/j.csbj.2021.06.043](https://doi.org/10.1016/j.csbj.2021.06.043)\n"
    ]
   }
  ],
@@ -671,16 +672,7 @@
    "name": "python3"
   },
   "language_info": {
-   "codemirror_mode": {
-    "name": "ipython",
-    "version": 3
-   },
-   "file_extension": ".py",
-   "mimetype": "text/x-python",
-   "name": "python",
-   "nbconvert_exporter": "python",
-   "pygments_lexer": "ipython3",
-   "version": "3.11.11"
+   "name": "python"
   }
  },
  "nbformat": 4,

docs/references.bib

@@ -1,3 +1,13 @@
+@article{andreatta2026ucell,
+    author = {Andreatta, Massimo and Carmona, Santiago J},
+    title = {UCell and pyUCell: single-cell gene signature scoring for R and python},
+    journal = {Bioinformatics},
+    pages = {btag055},
+    year = {2026},
+    month = {02},
+    doi = {10.1093/bioinformatics/btag055},
+    url = {https://doi.org/10.1093/bioinformatics/btag055}
+}
 @article{andreatta2021ucell,
   title={UCell: Robust and scalable single-cell gene signature scoring},
   author={Andreatta, Massimo and Carmona, Santiago J},