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diff --git a/DESCRIPTION b/DESCRIPTION
@@ -1,6 +1,6 @@
 Package: mulea
 Type: Package
-Title: Enrichment Analysis using Multiple Ontologies and False Discovery Rate
+Title: Enrichment Analysis Using Multiple Ontologies and False Discovery Rate
 Version: 1.1.0
 Date: 2024-09-24
 Authors@R: c(

diff --git a/README.Rmd b/README.Rmd
@@ -719,6 +719,6 @@ sessionInfo()
 
 To cite package `mulea` in publications use:
 
-Turek, Cezary, Márton Ölbei, Tamás Stirling, Gergely Fekete, Ervin Tasnádi, Leila Gul, Balázs Bohár, Balázs Papp, Wiktor Jurkowski, and Eszter Ari. 2024. “mulea - an R Package for Enrichment Analysis Using Multiple Ontologies and Empirical FDR Correction.” *bioRxiv*, March. <https://doi.org/10.1101/2024.02.28.582444>.
+Turek, Cezary, Márton Ölbei, Tamás Stirling, Gergely Fekete, Ervin Tasnádi, Leila Gul, Balázs Bohár, Balázs Papp, Wiktor Jurkowski, and Eszter Ari. 2024. “mulea: An R Package for Enrichment Analysis Using Multiple Ontologies and Empirical False Discovery Rate.” *BMC Bioinformatics* 25 (1): 334. <https://doi.org/10.1186/s12859-024-05948-7>.
 
 # References
diff --git a/README.md b/README.md
@@ -388,18 +388,18 @@ ora_results %>%
   filter(eFDR < 0.05)
 ```
 
-| ontology_id | ontology_name | nr_common_with_tested_elements | nr_common_with_background_elements |   p_value |      eFDR |
-|:------------|:--------------|-------------------------------:|-----------------------------------:|----------:|----------:|
-| FNR         | FNR           |                             26 |                                259 | 0.0000003 | 0.0000000 |
-| LexA        | LexA          |                             14 |                                 53 | 0.0000000 | 0.0000000 |
-| SoxS        | SoxS          |                              7 |                                 37 | 0.0001615 | 0.0036667 |
-| Rob         | Rob           |                              5 |                                 21 | 0.0004717 | 0.0051200 |
-| DnaA        | DnaA          |                              4 |                                 13 | 0.0006281 | 0.0052000 |
-| FadR        | FadR          |                              5 |                                 20 | 0.0003692 | 0.0056000 |
-| NsrR        | NsrR          |                              8 |                                 64 | 0.0010478 | 0.0073714 |
-| ArcA        | ArcA          |                             12 |                                148 | 0.0032001 | 0.0197500 |
-| IHF         | IHF           |                             14 |                                205 | 0.0070758 | 0.0458600 |
-| MarA        | MarA          |                              5 |                                 37 | 0.0066068 | 0.0483111 |
+| ontology_id | ontology_name | nr_common_with_tested_elements | nr_common_with_background_elements | p_value | eFDR |
+|:---|:---|---:|---:|---:|---:|
+| FNR | FNR | 26 | 259 | 0.0000003 | 0.0000000 |
+| LexA | LexA | 14 | 53 | 0.0000000 | 0.0000000 |
+| SoxS | SoxS | 7 | 37 | 0.0001615 | 0.0036667 |
+| Rob | Rob | 5 | 21 | 0.0004717 | 0.0051200 |
+| DnaA | DnaA | 4 | 13 | 0.0006281 | 0.0052000 |
+| FadR | FadR | 5 | 20 | 0.0003692 | 0.0056000 |
+| NsrR | NsrR | 8 | 64 | 0.0010478 | 0.0073714 |
+| ArcA | ArcA | 12 | 148 | 0.0032001 | 0.0197500 |
+| IHF | IHF | 14 | 205 | 0.0070758 | 0.0458600 |
+| MarA | MarA | 5 | 37 | 0.0066068 | 0.0483111 |
 
 ### Visualising the ORA Result
 
@@ -572,27 +572,27 @@ merged_results_filtered <- merged_results %>%
          -nr_common_with_background_elements)
 ```
 
-| ontology_name |   p_value |      eFDR | BH_adjusted_p_value | Bonferroni_adjusted_p_value |
-|:--------------|----------:|----------:|--------------------:|----------------------------:|
-| LexA          | 0.0000000 | 0.0000000 |           0.0000001 |                   0.0000001 |
-| FNR           | 0.0000003 | 0.0000000 |           0.0000208 |                   0.0000416 |
-| SoxS          | 0.0001615 | 0.0036667 |           0.0082880 |                   0.0248641 |
-| FadR          | 0.0003692 | 0.0056000 |           0.0142127 |                   0.0568507 |
-| Rob           | 0.0004717 | 0.0051200 |           0.0145296 |                   0.0726479 |
-| DnaA          | 0.0006281 | 0.0052000 |           0.0161218 |                   0.0967306 |
-| NsrR          | 0.0010478 | 0.0073714 |           0.0230517 |                   0.1613622 |
-| ArcA          | 0.0032001 | 0.0197500 |           0.0616014 |                   0.4928114 |
-| MarA          | 0.0066068 | 0.0483111 |           0.1089670 |                   1.0000000 |
-| IHF           | 0.0070758 | 0.0458600 |           0.1089670 |                   1.0000000 |
-| NarL          | 0.0096065 | 0.0534000 |           0.1276532 |                   1.0000000 |
-| NikR          | 0.0099470 | 0.0615833 |           0.1276532 |                   1.0000000 |
-| OxyR          | 0.0174505 | 0.0786923 |           0.2067212 |                   1.0000000 |
-| ExuR          | 0.0261046 | 0.1051867 |           0.2680073 |                   1.0000000 |
-| UxuR          | 0.0261046 | 0.1051867 |           0.2680073 |                   1.0000000 |
-| NrdR          | 0.0328500 | 0.1232750 |           0.3161817 |                   1.0000000 |
-| IscR          | 0.0376038 | 0.1249412 |           0.3406459 |                   1.0000000 |
-| Nac           | 0.0419701 | 0.1487556 |           0.3590774 |                   1.0000000 |
-| Fis           | 0.0457307 | 0.1433053 |           0.3706596 |                   1.0000000 |
+| ontology_name | p_value | eFDR | BH_adjusted_p_value | Bonferroni_adjusted_p_value |
+|:---|---:|---:|---:|---:|
+| LexA | 0.0000000 | 0.0000000 | 0.0000001 | 0.0000001 |
+| FNR | 0.0000003 | 0.0000000 | 0.0000208 | 0.0000416 |
+| SoxS | 0.0001615 | 0.0036667 | 0.0082880 | 0.0248641 |
+| FadR | 0.0003692 | 0.0056000 | 0.0142127 | 0.0568507 |
+| Rob | 0.0004717 | 0.0051200 | 0.0145296 | 0.0726479 |
+| DnaA | 0.0006281 | 0.0052000 | 0.0161218 | 0.0967306 |
+| NsrR | 0.0010478 | 0.0073714 | 0.0230517 | 0.1613622 |
+| ArcA | 0.0032001 | 0.0197500 | 0.0616014 | 0.4928114 |
+| MarA | 0.0066068 | 0.0483111 | 0.1089670 | 1.0000000 |
+| IHF | 0.0070758 | 0.0458600 | 0.1089670 | 1.0000000 |
+| NarL | 0.0096065 | 0.0534000 | 0.1276532 | 1.0000000 |
+| NikR | 0.0099470 | 0.0615833 | 0.1276532 | 1.0000000 |
+| OxyR | 0.0174505 | 0.0786923 | 0.2067212 | 1.0000000 |
+| ExuR | 0.0261046 | 0.1051867 | 0.2680073 | 1.0000000 |
+| UxuR | 0.0261046 | 0.1051867 | 0.2680073 | 1.0000000 |
+| NrdR | 0.0328500 | 0.1232750 | 0.3161817 | 1.0000000 |
+| IscR | 0.0376038 | 0.1249412 | 0.3406459 | 1.0000000 |
+| Nac | 0.0419701 | 0.1487556 | 0.3590774 | 1.0000000 |
+| Fis | 0.0457307 | 0.1433053 | 0.3706596 | 1.0000000 |
 
 A comparison of the significant results revealed that conventional
 *p*-value corrections (Benjamini-Hochberg and Bonferroni) tend to be
@@ -690,7 +690,7 @@ gsea_results %>%
   filter(adjusted_p_value < 0.05) %>% 
   # the number of such rows
   nrow()
-#> [1] 9
+#> [1] 10
 ```
 
 Inspect the significant results:
@@ -703,17 +703,18 @@ gsea_results %>%
   filter(adjusted_p_value < 0.05)
 ```
 
-| ontology_id | ontology_name | nr_common_with_tested_elements |   p_value | adjusted_p_value |
-|:------------|:--------------|-------------------------------:|----------:|-----------------:|
-| LexA        | LexA          |                             53 | 0.0000001 |        0.0000089 |
-| FNR         | FNR           |                            259 | 0.0000379 |        0.0028982 |
-| GlaR        | GlaR          |                              3 | 0.0002188 |        0.0111583 |
-| ArcA        | ArcA          |                            148 | 0.0003258 |        0.0117944 |
-| DnaA        | DnaA          |                             13 | 0.0004397 |        0.0117944 |
-| ModE        | ModE          |                             45 | 0.0004625 |        0.0117944 |
-| SoxS        | SoxS          |                             37 | 0.0007464 |        0.0163152 |
-| PspF        | PspF          |                              7 | 0.0016107 |        0.0308049 |
-| PaaX        | PaaX          |                             14 | 0.0019054 |        0.0323922 |
+| ontology_id | ontology_name | nr_common_with_tested_elements | p_value | adjusted_p_value |
+|:---|:---|---:|---:|---:|
+| LexA | LexA | 53 | 0.0000000 | 0.0000047 |
+| FNR | FNR | 259 | 0.0000660 | 0.0050484 |
+| ArcA | ArcA | 148 | 0.0003076 | 0.0079598 |
+| GlaR | GlaR | 3 | 0.0002188 | 0.0079598 |
+| ModE | ModE | 45 | 0.0003122 | 0.0079598 |
+| SoxS | SoxS | 37 | 0.0002848 | 0.0079598 |
+| DnaA | DnaA | 13 | 0.0010217 | 0.0223306 |
+| PaaX | PaaX | 14 | 0.0017028 | 0.0325652 |
+| PspF | PspF | 7 | 0.0023494 | 0.0399397 |
+| FadR | FadR | 20 | 0.0028304 | 0.0433046 |
 
 ### Visualising the GSEA Results
 
@@ -781,11 +782,11 @@ geo2r_result_tab %>%
   head(3)
 ```
 
-| ID           | adj.P.Val | P.Value |    t |       B | logFC | Gene.symbol                  | Gene.title                                                                                                            |
-|:-------------|----------:|--------:|-----:|--------:|------:|:-----------------------------|:----------------------------------------------------------------------------------------------------------------------|
-| 1765336_s_at |    0.0186 | 2.4e-06 | 21.5 | 4.95769 |  3.70 | gnsB                         | Qin prophage; multicopy suppressor of secG(Cs) and fabA6(Ts)                                                          |
-| 1760422_s_at |    0.0186 | 3.8e-06 | 19.6 | 4.68510 |  3.14 | NA                           | NA                                                                                                                    |
-| 1764904_s_at |    0.0186 | 5.7e-06 | 18.2 | 4.43751 |  2.54 | sulA///sulA///sulA///ECs1042 | SOS cell division inhibitor///SOS cell division inhibitor///SOS cell division inhibitor///SOS cell division inhibitor |
+| ID | adj.P.Val | P.Value | t | B | logFC | Gene.symbol | Gene.title |
+|:---|---:|---:|---:|---:|---:|:---|:---|
+| 1765336_s_at | 0.0186 | 2.4e-06 | 21.5 | 4.95769 | 3.70 | gnsB | Qin prophage; multicopy suppressor of secG(Cs) and fabA6(Ts) |
+| 1760422_s_at | 0.0186 | 3.8e-06 | 19.6 | 4.68510 | 3.14 | NA | NA |
+| 1764904_s_at | 0.0186 | 5.7e-06 | 18.2 | 4.43751 | 2.54 | sulA///sulA///sulA///ECs1042 | SOS cell division inhibitor///SOS cell division inhibitor///SOS cell division inhibitor///SOS cell division inhibitor |
 
 ### **Data Preparation:**
 
@@ -824,11 +825,11 @@ geo2r_result_tab %>%
   head(3)
 ```
 
-| ID           | adj.P.Val |  P.Value |    t |       B | logFC | Gene.symbol | Gene.title                                                                                                                                |
-|:-------------|----------:|---------:|-----:|--------:|------:|:------------|:------------------------------------------------------------------------------------------------------------------------------------------|
-| 1765336_s_at |    0.0186 | 2.40e-06 | 21.5 | 4.95769 |  3.70 | gnsB        | Qin prophage; multicopy suppressor of secG(Cs) and fabA6(Ts)                                                                              |
-| 1764904_s_at |    0.0186 | 5.70e-06 | 18.2 | 4.43751 |  2.54 | sulA        | SOS cell division inhibitor///SOS cell division inhibitor///SOS cell division inhibitor///SOS cell division inhibitor                     |
-| 1761763_s_at |    0.0186 | 1.54e-05 | 15.0 | 3.73568 |  2.16 | recN        | recombination and repair protein///recombination and repair protein///recombination and repair protein///recombination and repair protein |
+| ID | adj.P.Val | P.Value | t | B | logFC | Gene.symbol | Gene.title |
+|:---|---:|---:|---:|---:|---:|:---|:---|
+| 1765336_s_at | 0.0186 | 2.40e-06 | 21.5 | 4.95769 | 3.70 | gnsB | Qin prophage; multicopy suppressor of secG(Cs) and fabA6(Ts) |
+| 1764904_s_at | 0.0186 | 5.70e-06 | 18.2 | 4.43751 | 2.54 | sulA | SOS cell division inhibitor///SOS cell division inhibitor///SOS cell division inhibitor///SOS cell division inhibitor |
+| 1761763_s_at | 0.0186 | 1.54e-05 | 15.0 | 3.73568 | 2.16 | recN | recombination and repair protein///recombination and repair protein///recombination and repair protein///recombination and repair protein |
 
 Following these formatting steps, the data frame is primed for further
 analysis.
@@ -942,7 +943,7 @@ ordered_set %>%
 
 ``` r
 sessionInfo()
-#> R version 4.4.1 (2024-06-14)
+#> R version 4.4.2 (2024-10-31)
 #> Platform: x86_64-pc-linux-gnu
 #> Running under: Ubuntu 22.04.5 LTS
 #> 
@@ -972,18 +973,18 @@ sessionInfo()
 #> loaded via a namespace (and not attached):
 #>  [1] fastmatch_1.1-4     gtable_0.3.5        xfun_0.47          
 #>  [4] ggrepel_0.9.6       lattice_0.22-6      tzdb_0.4.0         
-#>  [7] vctrs_0.6.5         tools_4.4.1         generics_0.1.3     
-#> [10] curl_5.2.2          parallel_4.4.1      fansi_1.0.6        
+#>  [7] vctrs_0.6.5         tools_4.4.2         generics_0.1.3     
+#> [10] curl_5.2.2          parallel_4.4.2      fansi_1.0.6        
 #> [13] highr_0.11          pkgconfig_2.0.3     Matrix_1.7-0       
-#> [16] data.table_1.16.0   lifecycle_1.0.4     compiler_4.4.1     
+#> [16] data.table_1.16.0   lifecycle_1.0.4     compiler_4.4.2     
 #> [19] farver_2.1.2        munsell_0.5.1       ggforce_0.4.2      
-#> [22] fgsea_1.30.0        graphlayouts_1.1.1  codetools_0.2-20   
+#> [22] fgsea_1.30.0        graphlayouts_1.2.0  codetools_0.2-20   
 #> [25] htmltools_0.5.8.1   yaml_2.3.10         crayon_1.5.3       
 #> [28] pillar_1.9.0        MASS_7.3-61         BiocParallel_1.38.0
 #> [31] cachem_1.1.0        viridis_0.6.5       tidyselect_1.2.1   
 #> [34] digest_0.6.37       stringi_1.8.4       labeling_0.4.3     
 #> [37] cowplot_1.1.3       polyclip_1.10-7     fastmap_1.2.0      
-#> [40] grid_4.4.1          colorspace_2.1-1    cli_3.6.3          
+#> [40] grid_4.4.2          colorspace_2.1-1    cli_3.6.3          
 #> [43] magrittr_2.0.3      ggraph_2.2.1        tidygraph_1.3.1    
 #> [46] utf8_1.2.4          withr_3.0.1         scales_1.3.0       
 #> [49] bit64_4.0.5         timechange_0.3.0    rmarkdown_2.28     
@@ -1001,9 +1002,10 @@ To cite package `mulea` in publications use:
 
 Turek, Cezary, Márton Ölbei, Tamás Stirling, Gergely Fekete, Ervin
 Tasnádi, Leila Gul, Balázs Bohár, Balázs Papp, Wiktor Jurkowski, and
-Eszter Ari. 2024. “mulea - an R Package for Enrichment Analysis Using
-Multiple Ontologies and Empirical FDR Correction.” *bioRxiv*, March.
-<https://doi.org/10.1101/2024.02.28.582444>.
+Eszter Ari. 2024. “mulea: An R Package for Enrichment Analysis Using
+Multiple Ontologies and Empirical False Discovery Rate.” *BMC
+Bioinformatics* 25 (1): 334.
+<https://doi.org/10.1186/s12859-024-05948-7>.
 
 # References
 
@@ -1052,9 +1054,10 @@ National Academy of Sciences* 102 (43): 15545–50.
 
 Turek, Cezary, Márton Ölbei, Tamás Stirling, Gergely Fekete, Ervin
 Tasnádi, Leila Gul, Balázs Bohár, Balázs Papp, Wiktor Jurkowski, and
-Eszter Ari. 2024. “Mulea - an R Package for Enrichment Analysis Using
-Multiple Ontologies and Empirical FDR Correction.” *bioRxiv*, March.
-<https://doi.org/10.1101/2024.02.28.582444>.
+Eszter Ari. 2024. “<span class="nocase">mulea</span>: An R Package for
+Enrichment Analysis Using Multiple Ontologies and Empirical False
+Discovery Rate.” *BMC Bioinformatics* 25 (1): 334.
+<https://doi.org/10.1186/s12859-024-05948-7>.
 
 </div>
 

diff --git a/inst/CITATION b/inst/CITATION
@@ -1,4 +1,4 @@
-citHeader("To cite mulea in publications use:")
+citHeader("Please cite the following paper when using the mulea package:")
 
 bibentry(bibtype = "Article",
     author = c(
@@ -14,14 +14,19 @@ bibentry(bibtype = "Article",
         person("Eszter", "Ari")
     ),
     title = "mulea - an R package for enrichment analysis using multiple 
-        ontologies and empirical FDR correction.",
+        ontologies and empirical false discovery rate.",
+    journal = "BMC Bioinformatics",
     year = "2024",
-    publisher = "Cold Spring Harbor Laboratory",
-    URL = "https://doi.org/10.1101/2024.02.28.582444",
-    journal = "bioRxiv",
+    volume = "25",
+    number = "1",
+    pages = "334",
+    URL = "https://doi.org/10.1186/s12859-024-05948-7",
+
     textVersion = paste("C. Turek, M. Olbei, T. Stirling, G. Fekete, E. Tasnadi,
         L. Gul, B. Bohar, B. Papp, W. Jurkowski, E. Ari:",
         "mulea - an R package for enrichment analysis using multiple ontologies
-        and empirical FDR correction.",
-        "bioRxiv (2024), doi:10.1101/2024.02.28.582444v1")
+        and empirical false discovery rate.",
+        "BMC Bioinformatics, 25(1): 334 (2024), doi:10.1186/s12859-024-05948-7")
 )
+
+citFooter("Thank you for using our package!")
diff --git a/man/figures/README-network_plot_gsea-1.png b/man/figures/README-network_plot_gsea-1.png
diff --git a/man/figures/README-network_plot_ora-1.png b/man/figures/README-network_plot_ora-1.png
diff --git a/references.bib b/references.bib
@@ -34,17 +34,21 @@ @article{kuleshov2016
 }
 
 @article{turek,
-	title = {mulea - an {R} package for enrichment analysis using multiple ontologies and empirical {FDR} correction},
-	url = {https://www.biorxiv.org/content/10.1101/2024.02.28.582444v1},
-	doi = {10.1101/2024.02.28.582444},
-	language = {en},
+	title = {{mulea}: {An} {R} package for enrichment analysis using multiple ontologies and empirical false discovery rate},
 	author = {Turek, Cezary and {Ölbei}, {Márton} and Stirling, {Tamás} and Fekete, Gergely and {Tasnádi}, Ervin and Gul, Leila and {Bohár}, {Balázs} and Papp, {Balázs} and Jurkowski, Wiktor and Ari, Eszter},
-	date = {2024-03-01},
-	journal = {bioRxiv}
+	year = {2024},
+	month = {10},
+	date = {2024-10-18},
+	journal = {BMC Bioinformatics},
+	pages = {334},
+	volume = {25},
+	number = {1},
+	doi = {10.1186/s12859-024-05948-7},
+	url = {https://doi.org/10.1186/s12859-024-05948-7}
 }
 
 @article{méhi2014,
-	title = {Perturbation of Iron Homeostasis Promotes the Evolution of Antibiotic Resistance},
+	title = {Perturbation of iron homeostasis promotes the evolution of antibiotic resistance},
 	author = {{Méhi}, Orsolya and Bogos, {Balázs} and {Csörg{{\H o}}}, {Bálint} and {Pál}, Ferenc and Nyerges, {Ákos} and Papp, {Balázs} and {Pál}, Csaba},
 	year = {2014},
 	month = {10},

diff --git a/vignettes/mulea.Rmd b/vignettes/mulea.Rmd
@@ -728,7 +728,7 @@ sessionInfo()
 
 To cite package `mulea` in publications use:
 
-Turek, Cezary, Márton Ölbei, Tamás Stirling, Gergely Fekete, Ervin Tasnádi, Leila Gul, Balázs Bohár, Balázs Papp, Wiktor Jurkowski, and Eszter Ari. 2024. “mulea - an R Package for Enrichment Analysis Using Multiple Ontologies and Empirical FDR Correction.” *bioRxiv*, March. <https://doi.org/10.1101/2024.02.28.582444>.
+Turek, Cezary, Márton Ölbei, Tamás Stirling, Gergely Fekete, Ervin Tasnádi, Leila Gul, Balázs Bohár, Balázs Papp, Wiktor Jurkowski, and Eszter Ari. 2024. “mulea: An R Package for Enrichment Analysis Using Multiple Ontologies and Empirical False Discovery Rate.” *BMC Bioinformatics* 25 (1): 334. <https://doi.org/10.1186/s12859-024-05948-7>.
 
 # References
 
@@ -740,4 +740,4 @@ Méhi, Orsolya, Balázs Bogos, Bálint Csörgő, Ferenc Pál, Ákos Nyerges, Bal
 
 Subramanian, Aravind, Pablo Tamayo, Vamsi K. Mootha, Sayan Mukherjee, Benjamin L. Ebert, Michael A. Gillette, Amanda Paulovich, et al. 2005. “Gene Set Enrichment Analysis: A Knowledge-Based Approach for Interpreting Genome-Wide Expression Profiles.” *Proceedings of the National Academy of Sciences* 102 (43): 15545–50. <https://doi.org/10.1073/pnas.0506580102>.
 
-Turek, Cezary, Márton Ölbei, Tamás Stirling, Gergely Fekete, Ervin Tasnádi, Leila Gul, Balázs Bohár, Balázs Papp, Wiktor Jurkowski, and Eszter Ari. 2024. “Mulea - an R Package for Enrichment Analysis Using Multiple Ontologies and Empirical FDR Correction.” *bioRxiv*, March. <https://doi.org/10.1101/2024.02.28.582444>.
+Turek, Cezary, Márton Ölbei, Tamás Stirling, Gergely Fekete, Ervin Tasnádi, Leila Gul, Balázs Bohár, Balázs Papp, Wiktor Jurkowski, and Eszter Ari. 2024. “mulea: An R Package for Enrichment Analysis Using Multiple Ontologies and Empirical False Discovery Rate.” *BMC Bioinformatics* 25 (1): 334. <https://doi.org/10.1186/s12859-024-05948-7>.