From 6d024becec4b7d1655a29b021f37006e487505f4 Mon Sep 17 00:00:00 2001
From: Mariia Bilous <38460599+mariiabilous@users.noreply.github.com>
Date: Thu, 18 Jun 2026 16:02:04 +0200
Subject: [PATCH 1/5] Enhance README with links to SPLIT resources

Updated README to include links to the original SPLIT repository and publication.
---
 README.md | 13 ++++++++++---
 1 file changed, 10 insertions(+), 3 deletions(-)

diff --git a/README.md b/README.md
index 0a9e411..585edce 100644
--- a/README.md
+++ b/README.md
@@ -21,7 +21,7 @@
 
 # SPLIT-ST
 
-A **pure-Python re-implementation of SPLIT** for spatial transcriptomics purification.
+A **pure-Python re-implementation of [SPLIT](https://github.com/bdsc-tds/SPLIT)** for spatial transcriptomics purification.
 
 - AnnData-native — works directly with cell x gene spatial matrices
 - No `rpy2`, no R install, no RCTD/Seurat object dependency
@@ -235,8 +235,15 @@ from splitst import (
 
 ## Citation
 
-If you use this package, please cite the original SPLIT work and acknowledge this repository for the Python port.
+This package is a Python re-implementation of the original SPLIT method. If you use this package, please cite the original SPLIT publication:
 
+Bilous, M., Buszta, D., Bac, J., Kang, S., Dong, Y., Tissot, S., Andre, S., Alexandre-Gaveta, M., Voize, C., Peters, S., Homicsko, K. & Gottardo, R.
+Resolving sensitivity, specificity and signal contamination in Xenium spatial transcriptomics.
+Nature Methods (2026). https://doi.org/10.1038/s41592-026-03089-8
+
+Original SPLIT R package: https://github.com/bdsc-tds/SPLIT
+
+Please also acknowledge this repository when using the Python port.
 ## License
 
-GNU GPLv3 — matching the upstream SPLIT license.
+GNU GPLv3 — matching the upstream [SPLIT](https://github.com/bdsc-tds/SPLIT) license.

From 08e6605b3cbbc443dfbe70c557b6ac8e16b76003 Mon Sep 17 00:00:00 2001
From: Mariia Bilous <38460599+mariiabilous@users.noreply.github.com>
Date: Thu, 18 Jun 2026 16:03:11 +0200
Subject: [PATCH 2/5] Add upstream and paper URLs to project metadata

---
 pyproject.toml | 2 ++
 1 file changed, 2 insertions(+)

diff --git a/pyproject.toml b/pyproject.toml
index cf8cbac..f570add 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -43,6 +43,8 @@ dev = [
 Homepage = "https://github.com/omicverse/py-SPLIT"
 Repository = "https://github.com/omicverse/py-SPLIT"
 Issues = "https://github.com/omicverse/py-SPLIT/issues"
+Upstream = "https://github.com/bdsc-tds/SPLIT"
+Paper = "https://doi.org/10.1038/s41592-026-03089-8"
 
 [tool.setuptools.packages.find]
 include = ["splitst*"]

From 30c39a7067d1cb76f94eb8ebce286955d37b83be Mon Sep 17 00:00:00 2001
From: Mariia Bilous <38460599+mariiabilous@users.noreply.github.com>
Date: Thu, 18 Jun 2026 16:04:29 +0200
Subject: [PATCH 3/5] Update DISCOVERY.md with upstream citation

Added upstream citation for SPLIT R package.
---
 DISCOVERY.md | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/DISCOVERY.md b/DISCOVERY.md
index 308ccff..be65f76 100644
--- a/DISCOVERY.md
+++ b/DISCOVERY.md
@@ -6,7 +6,8 @@
 - **Description**: Spatial transcript purification for contamination-aware spatial transcriptomics workflows
 - **License**: GPL-3
 - **Repository**: https://github.com/bdsc-tds/SPLIT
-
+- **Upstream citation**: Bilous et al., *Nature Methods* (2026), https://doi.org/10.1038/s41592-026-03089-8
+  
 ## Existing py- Mirror Check
 
 - **py-SPLIT exists in omicverse?**: No - this is a new port.

From 66262db7cf907ebcd4a6f20ba76da18d731bd4c1 Mon Sep 17 00:00:00 2001
From: Mariia Bilous <38460599+mariiabilous@users.noreply.github.com>
Date: Thu, 18 Jun 2026 16:06:00 +0200
Subject: [PATCH 4/5] Update SPLIT-ST workflow notebook with citations

Added citation and references for SPLIT-ST workflow.
---
 examples/split_workflow.ipynb | 4 ++++
 1 file changed, 4 insertions(+)

diff --git a/examples/split_workflow.ipynb b/examples/split_workflow.ipynb
index d9c602f..23f9fcd 100644
--- a/examples/split_workflow.ipynb
+++ b/examples/split_workflow.ipynb
@@ -8,6 +8,10 @@
     "# SPLIT-ST workflow\n",
     "\n",
     "This notebook runs the standalone Python SPLIT workflow on a deterministic AnnData fixture."
+
+   Please cite: Bilous et al., **Resolving sensitivity, specificity and signal contamination in Xenium spatial transcriptomics**, *Nature Methods* (2026), https://doi.org/10.1038/s41592-026-03089-8.
+
+   Original SPLIT R package: https://github.com/bdsc-tds/SPLIT
    ]
   },
   {

From 8bfad6746d6ee6bf4dabf3d07f6dd15f2fa077a9 Mon Sep 17 00:00:00 2001
From: Mariia Bilous <38460599+mariiabilous@users.noreply.github.com>
Date: Thu, 18 Jun 2026 16:07:31 +0200
Subject: [PATCH 5/5] Format citation for SPLIT publication in README

---
 README.md | 5 +++--
 1 file changed, 3 insertions(+), 2 deletions(-)

diff --git a/README.md b/README.md
index 585edce..b23d540 100644
--- a/README.md
+++ b/README.md
@@ -238,12 +238,13 @@ from splitst import (
 This package is a Python re-implementation of the original SPLIT method. If you use this package, please cite the original SPLIT publication:
 
 Bilous, M., Buszta, D., Bac, J., Kang, S., Dong, Y., Tissot, S., Andre, S., Alexandre-Gaveta, M., Voize, C., Peters, S., Homicsko, K. & Gottardo, R.
-Resolving sensitivity, specificity and signal contamination in Xenium spatial transcriptomics.
-Nature Methods (2026). https://doi.org/10.1038/s41592-026-03089-8
+**Resolving sensitivity, specificity and signal contamination in Xenium spatial transcriptomics.**
+*Nature Methods* (2026). https://doi.org/10.1038/s41592-026-03089-8
 
 Original SPLIT R package: https://github.com/bdsc-tds/SPLIT
 
 Please also acknowledge this repository when using the Python port.
+
 ## License
 
 GNU GPLv3 — matching the upstream [SPLIT](https://github.com/bdsc-tds/SPLIT) license.