Merge pull request #8 from CSOgroup/update-citation-nature-genetics

Update citation nature genetics

Author: Arvindiyer

.gitignore

@@ -12,4 +12,7 @@ src/*.so
 src/*.o
 .*
 !/.gitignore
-!/.github
+!/.githubsrc/*.o
+src/*.so
+src/*.dll
+src/*.dylib

NEWS.md

@@ -10,6 +10,7 @@
 * Expanded test coverage with `test-gam_utils.R`.
 * Repository migrated: development moved from personal branches to [CSOgroup/SelectSim](https://github.com/CSOgroup/SelectSim); `dev` branch merged into `main` for initial public release.
 * Bumped version to 0.1.6 across all source files
+* Updated citation (`inst/CITATION`, `README`) to the published Nature Genetics article: Iyer A, Petrovic M, Sesia D, Nanni L, Mina M, Ciriello G (2026). Evolving patterns of co-mutations from tumor initiation to metastatic progression. *Nature Genetics*. doi:10.1038/s41588-026-02661-4
 
 # SelectSim 0.0.1.3
 

README.Rmd

@@ -28,7 +28,7 @@ The method accounts for heterogeneous tumor types, tissue specificities, and dis
 
 This package accompanies the manuscript:
 
-> Iyer A, Mina M, Petrovic M, Ciriello G (2026). Evolving patterns of co-mutations from tumor initiation to metastatic progression. *TBD*. doi: *TBD*
+> Iyer A, Petrovic M, Sesia D, Nanni L, Mina M, Ciriello G (2026). Evolving patterns of co-mutations from tumor initiation to metastatic progression. *Nature Genetics*. doi: [10.1038/s41588-026-02661-4](https://doi.org/10.1038/s41588-026-02661-4)
 
 ## Installation
 
@@ -78,7 +78,7 @@ Full documentation and vignettes are available at <https://csogroup.github.io/Se
 
 If you use SelectSim in your research, please cite:
 
-> Iyer A, Mina M, Petrovic M, Ciriello G (2026). Evolving patterns of co-mutations from tumor initiation to metastatic progression. *TBD*. doi: *TBD*
+> Iyer A, Petrovic M, Sesia D, Nanni L, Mina M, Ciriello G (2026). Evolving patterns of co-mutations from tumor initiation to metastatic progression. *Nature Genetics*. doi: [10.1038/s41588-026-02661-4](https://doi.org/10.1038/s41588-026-02661-4)
 
 You can also run `citation("SelectSim")` inside R for a formatted reference.
 

README.md

@@ -28,9 +28,10 @@ frequency-stratified FDR control generated via simulation.
 
 This package accompanies the manuscript:
 
-> Iyer A, Mina M, Petrovic M, Ciriello G (2026). Evolving patterns of
-> co-mutations from tumor initiation to metastatic progression. *TBD*.
-> doi: *TBD*
+> Iyer A, Petrovic M, Sesia D, Nanni L, Mina M, Ciriello G (2026).
+> Evolving patterns of co-mutations from tumor initiation to metastatic
+> progression. *Nature Genetics*. doi:
+> [10.1038/s41588-026-02661-4](https://doi.org/10.1038/s41588-026-02661-4)
 
 ## Installation
 
@@ -83,9 +84,10 @@ Full documentation and vignettes are available at
 
 If you use SelectSim in your research, please cite:
 
-> Iyer A, Mina M, Petrovic M, Ciriello G (2026). Evolving patterns of
-> co-mutations from tumor initiation to metastatic progression. *TBD*.
-> doi: *TBD*
+> Iyer A, Petrovic M, Sesia D, Nanni L, Mina M, Ciriello G (2026).
+> Evolving patterns of co-mutations from tumor initiation to metastatic
+> progression. *Nature Genetics*. doi:
+> [10.1038/s41588-026-02661-4](https://doi.org/10.1038/s41588-026-02661-4)
 
 You can also run `citation("SelectSim")` inside R for a formatted
 reference.

inst/CITATION

@@ -5,16 +5,19 @@ bibentry(
   title    = "Evolving patterns of co-mutations from tumor initiation to metastatic progression",
   author   = c(
     person("Arvind",  "Iyer"),
-    person("Marco",   "Mina"),
     person("Miljan",  "Petrovic"),
+    person("Debora",  "Sesia"),
+    person("Luca",    "Nanni"),
+    person("Marco",   "Mina"),
     person("Giovanni","Ciriello")
   ),
-  journal  = "TBD",
+  journal  = "Nature Genetics",
   year     = "2026",
-  doi      = "",   # fill in DOI once assigned
-  url      = "https://github.com/CSOgroup/SelectSim",
+  doi      = "10.1038/s41588-026-02661-4",
+  url      = "https://doi.org/10.1038/s41588-026-02661-4",
   textVersion = paste(
-    "Iyer A, Mina M, Petrovic M, Ciriello G (2026).",
-    "Evolving patterns of co-mutations from tumor initiation to metastatic progression."
+    "Iyer A, Petrovic M, Sesia D, Nanni L, Mina M, Ciriello G (2026).",
+    "Evolving patterns of co-mutations from tumor initiation to metastatic progression.",
+    "Nature Genetics. doi:10.1038/s41588-026-02661-4"
   )
 )