fixed citations + wording

README.md

@@ -14,10 +14,9 @@ should also be useful more generally.
 
 The methods are based on a new model for sparse multiple regression,
 which we call the "Sum of Single Effects" (SuSiE) model.  This model,
-which will be described in a manuscript in preparation (Wang et al),
-lends itself to a particularly simple and intuitive fitting procedure
--- effectively a Bayesian modification of simple forward selection,
-which we call "Iterative Bayesian Step-wise Selection".
+which is described in [Wang et al. (2020)](https://doi.org/10.1111/rssb.12388), lends itself to a particularly simple and intuitive fitting 
+procedure -- effectively a Bayesian modification of simple forward 
+selection, which we call "Iterative Bayesian Step-wise Selection".
 
 The output of the fitting procedure is a number of "Credible Sets"
 (CSs), which are each designed to have high probability to contain a
@@ -27,10 +26,12 @@ correlated" variables that are each associated with the response: you
 can be confident that one of the variables has a non-zero coefficient,
 but they are too correlated to be sure which one.
 
-The package is developed by Gao Wang, Peter Carbonetto, Yuxin Zou,
-Kaiqian Zhang, and Matthew Stephens from the
+The package was initially developed by Gao Wang, Peter Carbonetto,
+Yuxin Zou, Kaiqian Zhang, and Matthew Stephens from the
 [Stephens Lab](https://stephenslab.uchicago.edu) at the University of
-Chicago.
+Chicago. It was later extended with new methods and implementations by
+Alexander McCreight from the [StatFunGen Lab](https://wanggroup.org/) at
+Columbia University.
 
 Please
 [post issues](https://github.com/stephenslab/susieR/issues) to ask
@@ -61,21 +62,42 @@ please visit https://stephenslab.github.io/susieR
 ## Citing this work
 
 If you find the `susieR` package or any of the source code in this
-repository useful for your work, please cite:
+repository useful for your work, please cite both:
 
-> G. Wang, G., Sarkar, A., Carbonetto, P. & Stephens, M. (2020). A
+> Wang, G., Sarkar, A., Carbonetto, P. & Stephens, M. (2020). A
 > simple new approach to variable selection in regression, with
 > application to genetic fine mapping. *Journal of the Royal
 > Statistical Society, Series B* **82**, 1273–1300.
 > https://doi.org/10.1111/rssb.12388
 
-If you use any of the summary data methods such as `susie_suff_stat`
-or `susie_rss`, please also cite:
+> McCreight, A., Cho, Y., Nachun, D., Li, R., Gan, H-Y., Stephens,
+> M., Carbonetto, P., Denault, W.R.P. & Wang, G. (2025). SuSiE 2.0:
+> improved methods and implementations for genetic fine-mapping and
+> phenotype prediction. Submitting to *Genome Biology*.
+
+If you use any of the summary data methods such as `susie_ss` or 
+`susie_rss`, please also cite:
 
 > Zou, Y., Carbonetto, P., Wang, G. & Stephens, M. (2022). Fine-mapping
 > from summary data with the "Sum of Single Effects" model. *PLoS
 > Genetics* **18**, e1010299. https://doi.org/10.1371/journal.pgen.1010299
 
+If you use the Servin-Stephens prior on residual variance estimates
+(`estimate_residual_method = "Servin_Stephens"`), please also cite:
+
+> Denault, W.R.P., Carbonetto, P., Li, R., Consortium, A.D.F.G., Wang,
+> G. & Stephens, M. (2025). Accounting for uncertainty in residual
+> variances improves calibration of the "Sum of Single Effects" model
+> for small sample sizes. *bioRxiv*, 2025-05. Under review for *Nature
+> Methods*.
+
+If you use infinitesimal effects modeling (`unmappable_effects = "inf"`), 
+please also cite:
+
+> Cui, R., Elzur, R.A., Kanai, M. et al. (2024). Improving fine-mapping
+> by modeling infinitesimal effects. *Nature Genetics* **56**, 162–169.
+> https://doi.org/10.1038/s41588-023-01597-3
+
 ## Developer notes
 
 

inst/CITATION

@@ -1,40 +1,101 @@
-citHeader("To cite the susieR package, please use:")
+citHeader("To cite the susieR package, please use both:")
 
 bibentry(bibtype = "Article",
          title = paste("A simple new approach to variable selection in",
                        "regression, with application to genetic fine",
                        "mapping"),
          author = c(person("Gao","Wang"),
                     person("Abhishek","Sarkar"),
-                    person("Peter","Carbonetto"),             
+                    person("Peter","Carbonetto"),
                     person("Matthew","Stephens")),
          journal = "Journal of the Royal Statistical Society, Series B",
          year    = "2020",
          volume  = "82",
          pages   = "1273-1300",
-         doi     = "10.1101/501114",
-         textVersion = 
-           paste("Gao Wang, Abhishek Sarkar, Peter Carbonetto and Matthew",
-                 "Stephens (2020). A simple new approach to variable",
-                 "selection in regression, with application to genetic",
-                 "fine mapping. Journal of the Royal Statistical Society,",
-                 "Series B, 82, 1273-1300, doi:10.1101/501114"))
+         doi     = "10.1111/rssb.12388",
+         textVersion =
+           paste("Wang, G., Sarkar, A., Carbonetto, P. & Stephens, M. (2020).",
+                 "A simple new approach to variable selection in regression,",
+                 "with application to genetic fine mapping. Journal of the",
+                 "Royal Statistical Society, Series B 82, 1273-1300.",
+                 "https://doi.org/10.1111/rssb.12388"))
+
+bibentry(bibtype = "Article",
+         title = paste("SuSiE 2.0: improved methods and implementations for",
+                "genetic fine-mapping and phenotype prediction"),
+         author = c(person("Alexander", "McCreight"),
+                    person("Yanghyeon", "Cho"),
+                    person("Daniel", "Nachun"),
+                    person("Ruixi", "Li"),
+                    person("Hao-Yu", "Gan"),
+                    person("Matthew", "Stephens"),
+                    person("Peter", "Carbonetto"),
+                    person("William", "R.P. Denault"),
+                    person("Gao", "Wang")),
+         journal = "Submitting to Genome Biology",
+         year = "2025",
+         textVersion =
+           paste("McCreight, A., Cho, Y., Nachun, D., Li, R., Gan, H-Y., Stephens,",
+                 "M., Carbonetto, P., Denault, W.R.P. & Wang, G. (2025). SuSiE 2.0:",
+                 "improved methods and implementations for genetic fine-mapping and",
+                 "phenotype prediction. Submitting to Genome Biology."))
 
 bibentry(header = "If susie_suff_stat or susie_rss is used, please also cite:",
          bibtype = "Article",
          title = paste('Fine-mapping from summary data with the',
                        '"Sum of Single Effects" model'),
          author = c(person("Yuxin","Zou"),
-                    person("Peter","Carbonetto"),             
+                    person("Peter","Carbonetto"),
                     person("Gao","Wang"),
                     person("Matthew","Stephens")),
          journal = "PLoS Genetics",
          volume  = "18",
          year    = "2022",
          pages   = "e1010299",
          doi     = "10.1371/journal.pgen.1010299",
-         textVersion = 
-           paste('Yuxin Zou, Peter Carbonetto, Gao Wang and Matthew Stephens',
-                 '(2022). Fine-mapping from summary data with the "Sum of',
-                 'Single Effects" model. PLoS Genetics 18, e1010299',
-                 'doi:10.1371/journal.pgen.1010299'))
+         textVersion =
+           paste('Zou, Y., Carbonetto, P., Wang, G. & Stephens, M. (2022).',
+                 'Fine-mapping from summary data with the "Sum of Single',
+                 'Effects" model. PLoS Genetics 18, e1010299.',
+                 'https://doi.org/10.1371/journal.pgen.1010299'))
+
+bibentry(header = paste("If estimate_residual_method = 'Servin_Stephens' is used,",
+                        "please also cite:"),
+         bibtype = "Article",
+         title = paste("Accounting for uncertainty in residual variances",
+                       "improves calibration of the 'Sum of Single Effects'",
+                       "model for small sample sizes"),
+         author = c(person("William", "R.P. Denault"),
+                    person("Peter", "Carbonetto"),
+                    person("Ruixi", "Li"),
+                    person("A.D.F.G.", "Consortium"),
+                    person("Gao", "Wang"),
+                    person("Matthew", "Stephens")),
+         journal = "bioRxiv",
+         year    = "2025",
+         note    = "Under review for Nature Methods",
+         textVersion =
+           paste("Denault, W.R.P., Carbonetto, P., Li, R., Consortium, A.D.F.G.,",
+                 "Wang, G. & Stephens, M. (2025). Accounting for uncertainty in",
+                 "residual variances improves calibration of the 'Sum of Single",
+                 "Effects' model for small sample sizes. bioRxiv, 2025-05.",
+                 "Under review for Nature Methods."))
+
+bibentry(header = paste("If unmappable_effects = 'inf' is used,",
+                        "please also cite:"),
+         bibtype = "Article",
+         title = "Improving fine-mapping by modeling infinitesimal effects",
+         author = c(person("Rui", "Cui"),
+                    person("R.A.", "Elzur"),
+                    person("M.", "Kanai"),
+                    person(c("et", "al."))),
+         journal = "Nature Genetics",
+         volume  = "56",
+         year    = "2024",
+         pages   = "162-169",
+         doi     = "10.1038/s41588-023-01597-3",
+         textVersion =
+           paste("Cui, R., Elzur, R.A., Kanai, M. et al. (2024).",
+                 "Improving fine-mapping by modeling infinitesimal effects.",
+                 "Nature Genetics 56, 162-169.",
+                 "https://doi.org/10.1038/s41588-023-01597-3"))