diff --git a/tools/phenotype_association/beam.xml b/tools/phenotype_association/beam.xml
index c8d3930bd2e..d2700b91a23 100644
--- a/tools/phenotype_association/beam.xml
+++ b/tools/phenotype_association/beam.xml
@@ -134,4 +134,8 @@ Block-based bayesian epistasis association mapping with application to WTCCC typ
 Submitted.
 
   </help>
+  <citations>
+    <citation type="doi">10.1038/ng2110</citation>
+    <citation type="doi">10.1214/11-AOAS469</citation>
+  </citations>
 </tool>
diff --git a/tools/phenotype_association/gpass.xml b/tools/phenotype_association/gpass.xml
index 231a1a54456..0c6edaf1938 100644
--- a/tools/phenotype_association/gpass.xml
+++ b/tools/phenotype_association/gpass.xml
@@ -109,4 +109,7 @@ Fast and accurate significance approximation for genome-wide association studies
 Submitted.
 
   </help>
+  <citations>
+    <citation type="doi">10.1198/jasa.2011.ap10657</citation>
+  </citations>
 </tool>
diff --git a/tools/phenotype_association/ldtools.xml b/tools/phenotype_association/ldtools.xml
index 86f4f3a1247..9fc188ea934 100644
--- a/tools/phenotype_association/ldtools.xml
+++ b/tools/phenotype_association/ldtools.xml
@@ -108,4 +108,7 @@ association analyses using linkage disequilibrium.
 Am J Hum Genet. 74(1):106-20. Epub 2003 Dec 15.
 
   </help>
+  <citations>
+    <citation type="doi">10.1086/381000</citation>
+  </citations>
 </tool>
diff --git a/tools/phenotype_association/linkToDavid.xml b/tools/phenotype_association/linkToDavid.xml
index a9574fb8047..be45114f54f 100644
--- a/tools/phenotype_association/linkToDavid.xml
+++ b/tools/phenotype_association/linkToDavid.xml
@@ -107,4 +107,8 @@ DAVID: database for annotation, visualization, and integrated discovery.
 Genome Biol. 4(5):P3. Epub 2003 Apr 3.
 
   </help>
+  <citations>
+    <citation type="doi">10.1038/nprot.2008.211</citation>
+    <citation type="doi">10.1186/gb-2003-4-5-p3</citation>
+  </citations>
 </tool>
diff --git a/tools/phenotype_association/linkToGProfile.xml b/tools/phenotype_association/linkToGProfile.xml
index b1b9c7cf6bb..a21a00d3c8c 100644
--- a/tools/phenotype_association/linkToGProfile.xml
+++ b/tools/phenotype_association/linkToGProfile.xml
@@ -87,4 +87,7 @@ toolset for functional profiling of gene lists from large-scale experiments.
 Nucleic Acids Res. 35(Web Server issue):W193-200. Epub 2007 May 3.
 
   </help>
+  <citations>
+    <citation type="doi">10.1093/nar/gkm226</citation>
+  </citations>
 </tool>
diff --git a/tools/phenotype_association/lps.xml b/tools/phenotype_association/lps.xml
index 05bf22ef480..94b7dc9e84d 100644
--- a/tools/phenotype_association/lps.xml
+++ b/tools/phenotype_association/lps.xml
@@ -301,4 +301,18 @@ Technical Report. University of Wisconsin. August 10, 2010.
 -->
 
   </help>
+  <citations>
+    <citation type="bibtex">@ARTICLE{Kim07aninterior-point,
+    author = {Seung-jean Kim and Kwangmoo Koh and Michael Lustig and Stephen Boyd and Dimitry Gorinevsky},
+    title = {An interior-point method for large-scale l1-regularized logistic regression},
+    journal = {Journal of Machine Learning Research},
+    year = {2007},
+    volume = {2007}
+}</citation>
+    <citation type="bibtex">@MISC{Shi08lasso-patternsearchalgorithm,
+    author = {Weiliang Shi and Grace Wahba and Stephen Wright and Kristine Lee and Ronald Klein and Barbara Klein},
+    title = { LASSO-Patternsearch Algorithm with Application to Ophthalmology and Genomic Data},
+    year = {2008}
+}</citation>
+  </citations>
 </tool>
diff --git a/tools/phenotype_association/pass.xml b/tools/phenotype_association/pass.xml
index 6d42da95800..00953931352 100644
--- a/tools/phenotype_association/pass.xml
+++ b/tools/phenotype_association/pass.xml
@@ -123,4 +123,8 @@ A varying threshold method for ChIP peak calling using multiple sources of infor
 Submitted.
 
   </help>
+  <citations>
+    <citation type="doi">10.1093/bioinformatics/btn549</citation>
+    <citation type="doi">10.1093/bioinformatics/btq379</citation>
+  </citations>
 </tool>
diff --git a/tools/phenotype_association/sift.xml b/tools/phenotype_association/sift.xml
index b4f3984dd1d..3654c74a053 100644
--- a/tools/phenotype_association/sift.xml
+++ b/tools/phenotype_association/sift.xml
@@ -171,4 +171,10 @@ on protein function using the SIFT algorithm.
 Nat Protoc. 4(7):1073-81. Epub 2009 Jun 25.
 
   </help>
+  <citations>
+    <citation type="doi">10.1101/gr.176601</citation>
+    <citation type="doi">10.1101/gr.212802</citation>
+    <citation type="doi">10.1093/nar/gkg509</citation>
+    <citation type="doi">10.1038/nprot.2009.86</citation>
+  </citations>
 </tool>
diff --git a/tools/plotting/boxplot.xml b/tools/plotting/boxplot.xml
index d34c1259bb6..8a6a77e3109 100644
--- a/tools/plotting/boxplot.xml
+++ b/tools/plotting/boxplot.xml
@@ -105,4 +105,7 @@ If you use this tool, please cite `Blankenberg D, Gordon A, Von Kuster G, Coraor
 
 
   </help>
+  <citations>
+    <citation type="doi">10.1093/bioinformatics/btq281</citation>
+  </citations>
 </tool>