From 42f7955c8619ba43766a3b13626d554c2f3d8399 Mon Sep 17 00:00:00 2001
From: Pjotr Prins
Date: Sun, 29 May 2016 16:57:28 +0000
Subject: JOSS: add MQM citation and fix typo

---
 doc/joss/2016/paper.bib | 14 ++++++++++++++
 doc/joss/2016/paper.md  |  8 ++++----
 2 files changed, 18 insertions(+), 4 deletions(-)

(limited to 'doc/joss')

diff --git a/doc/joss/2016/paper.bib b/doc/joss/2016/paper.bib
index 73a88227..34c0fd05 100644
--- a/doc/joss/2016/paper.bib
+++ b/doc/joss/2016/paper.bib
@@ -34,3 +34,17 @@
   url          = {http://www.ncbi.nlm.nih.gov/pubmed/21892150},
   abstract     = {We describe factored spectrally transformed linear mixed models (FaST-LMM), an algorithm for genome-wide association studies (GWAS) that scales linearly with cohort size in both run time and memory use. On Wellcome Trust data for 15,000 individuals, FaST-LMM ran an order of magnitude faster than current efficient algorithms. Our algorithm can analyze data for 120,000 individuals in just a few hours, whereas current algorithms fail on data for even 20,000 individuals (http://mscompbio.codeplex.com/).}
 }
+
+@article{Arends:2010,
+  author       = {Arends, D. and Prins, P. and Jansen, R. C. and Broman, K. W.},
+  title        = {{R/qtl: high-throughput multiple QTL mapping}},
+  journal      = {Bioinformatics},
+  year         = {2010},
+  volume       = {26},
+  number       = {23},
+  pages        = {2990-2992},
+  doi          = {10.1093/bioinformatics/btq565},
+  url          = {http://www.ncbi.nlm.nih.gov/pubmed/20966004},
+  abstract     = {MOTIVATION: R/qtl is free and powerful software for mapping and exploring quantitative trait loci (QTL). R/qtl provides a fully comprehensive range of methods for a wide range of experimental cross types. We recently added multiple QTL mapping (MQM) to R/qtl. MQM adds higher statistical power to detect and disentangle the effects of multiple linked and unlinked QTL compared with many other methods. MQM for R/qtl adds many new features including improved handling of missing data, analysis of 10,000 s of molecular traits, permutation for determining significance thresholds for QTL and QTL hot spots, and visualizations for cis-trans and QTL interaction effects. MQM for R/qtl is the first free and open source implementation of MQM that is multi-platform, scalable and suitable for automated procedures and large genetical genomics datasets. AVAILABILITY: R/qtl is free and open source multi-platform software for the statistical language R, and is made available under the GPLv3 license. R/qtl can be installed from http://www.rqtl.org/. R/qtl queries should be directed at the mailing list, see http://www.rqtl.org/list/. CONTACT: kbroman@biostat.wisc.edu.},
+
+}
diff --git a/doc/joss/2016/paper.md b/doc/joss/2016/paper.md
index 81ec2b72..42fcd500 100644
--- a/doc/joss/2016/paper.md
+++ b/doc/joss/2016/paper.md
@@ -41,10 +41,10 @@ bibliography: paper.bib
 
 # Summary
 
-GeneNetwork (GN) is a free and open source (FOSS) framework for web
-based genetics that can be deployed anywhere. GN allows biologists to
-upload experimental data and map phenotypes interactively against
-genotypes using tools, such as R/QTL [@mqm paper] mapping, interval
+GeneNetwork (GN) is a free and open source (FOSS) framework for
+web-based genetics that can be deployed anywhere. GN allows biologists
+to upload experimental data and map phenotypes interactively against
+genotypes using tools, such as R/QTL [@Arends:2010] mapping, interval
 mapping for model organisms and pylmm; an implementation of FaST-LMM
 [@Lippert:2011] which is suitable for human populations and outbred
 crosses, such as the mouse diversity outcross. Interactive D3 graphics
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