diff --git a/CITATION.cff b/CITATION.cff
index 863ca7a9..b691b44e 100644
--- a/CITATION.cff
+++ b/CITATION.cff
@@ -88,4 +88,14 @@ title: "Reproducible image-based profiling with Pycytominer"
 version: "1.1.0"
 license: BSD 3-Clause License
 repository-code: "https://github.com/cytomining/pycytominer"
-doi: 10.48550/arXiv.2311.13417
+doi: 10.1038/s41592-025-02611-8
+identifiers:
+  - description: Nature.com article
+    type: doi
+    value: "10.1038/s41592-025-02611-8"
+  - description: arXiv.org preprint
+    type: doi
+    value: "10.48550/arXiv.2311.13417"
+  - description: Zenodo software DOI
+    type: doi
+    value: "10.5281/zenodo.14194368"
diff --git a/README.md b/README.md
index c621c4c0..fe571e13 100644
--- a/README.md
+++ b/README.md
@@ -6,7 +6,7 @@
 [![Coverage Status](https://codecov.io/gh/cytomining/pycytominer/branch/main/graph/badge.svg)](https://codecov.io/github/cytomining/pycytominer?branch=main)
 [![Ruff](https://img.shields.io/endpoint?url=https://raw.githubusercontent.com/astral-sh/ruff/main/assets/badge/v2.json)](https://github.com/astral-sh/ruff)
 [![RTD](https://readthedocs.org/projects/pycytominer/badge/?version=latest&style=flat)](https://pycytominer.readthedocs.io/)
-[![DOI](https://img.shields.io/badge/DOI-10.48550/arXiv.2311.13417-blue)](https://doi.org/10.48550/arXiv.2311.13417)
+[![DOI](https://img.shields.io/badge/DOI-10.1038/s41592--025--02611--8-blue)](https://doi.org/10.1038/s41592-025-02611-8)
 
 Pycytominer is a suite of common functions used to process high dimensional readouts from high-throughput cell experiments.
 The tool is most often used for processing data through the following pipeline: