Skelly DA, Czechanski A, Byers C, Aydin S, Spruce C, Olivier C, Choi KB, Gatti DM, Raghupathy N, Stanton A, Vincent M, Dion S, Greenstein I, Pankratz M, Porter DK, Martin W, Qi W, Harrill AH, Choi T, Churchill GA§, Munger SC§, Baker CL§, and Reinholdt LA§. Genetic variation influences pluripotent ground state stability in mouse embryonic stem cells through a hierarchy of molecular phenotypes. bioRxiv:  §Corresponding authors.  [Link]

Ortmann D, Brown S, Czechanski A, Aydin S, Tomaz RA, Osnato A, Skelly DA, Choi T, Churchill GA, Baker CL, Munger SC, Reinholdt LG, and Vallier L. Genetic background impacts on variability of ground state pluripotent stem cell lines. In Review.

Ruthig VA, Friedersdorf MB, Garness JA, Munger SC, Bunce C, Keene JD, and Capel B. The RNA-binding protein DND1 acts sequentially as a negative regulator of pluripotency and a positive regulator of epigenetic modifiers required for germ cell reprogramming. bioRxiv:  [Link]


Raghupathy N, Choi K, Vincent MJ, Beane GL, Sheppard KS, Munger SC, Korstanje R, Pardo-Manual de Villena F, and Churchill GA. Hierarchical analysis of RNA-seq reads improves the accuracy of allele-specific expression. Bioinformatics 2018, 34(13):2177-2184.   [Link] ​


Tyler AL, Ji B, Munger SC, Churchill GA, Svenson KL, and Carter GW. Epistatic networks jointly influence phenotypes related to Metabolic Disease and gene expression in Diversity Outbred mice. Genetics 2017, 206(2): 621-639.  [Link]


Chick JM*, Munger SC*, Simecek P, Huttlin EL, Choi KB, Gatti DM, Raghupathy N, Svenson KL, Churchill GA§, and Gygi SP§. Defining the consequences of genetic variation on a proteome-wide scale. Nature 2016, doi:10.1038/nature18270 

*Equal contributors. §Corresponding authors. [Link]  [Data]

Morton NM, Beltram J, Carter RE, Michailidou Z, Gorjanc G, McFadden C, Barrios-Llerena M, Rodriguez-Cuenca S, Gibbins M, Aird R, Moreno-Navarrete JM, Munger SC, Svenson KL, Gastaldello A, Ramage L, Naredo, G, Zeyda M, Wang ZV, Howie AF, Saari A, Sipila P, Stulnig TM, Gudnasson V, Kenyon CJ, Seckl JR, Walker BR, Webster SP, Dunbar DR, Churchill GA, Vidal-Puig A, Fernandez-Real JM, Emilsson V, and Horvat S. Genetic identification of an adipocyte expressed anti-diabetic target in mice selected for resistance to diet-induced obesity. Nature Medicine 2016, doi: 10.1038/nm.4115  [Link]   [Data]


Munger SC, Raghupathy N, Choi K, Simons AK, Gatti DM, Hinerfeld DA, Svenson KL, Keller MP, Attie AD, Hibbs MA, Graber JH, Chesler EJ, and Churchill GA. RNA-seq alignment to individualized genomes improves transcript abundance estimates in multiparent populations. Genetics 2014, 198(1): 59-73.  [Link]   [Data]

French JE, Gatti DM, Morgan DL, Kissling GE, Shockley KR, Knudsen GA, Shepard KG, Price HC, King D, Witt KL, Pedersen LC, Munger SC, Svenson KL, and Churchill GA. Diversity Outbred mice identify population-based exposure thresholds and genetic factors that influence benzene-induced genotoxicity. Environmental Health Perspectives 2014, DOI:10.1289/ehp.1408202.  [Link]


Munger SC*, Natarajan A*, Looger LL, Ohler U, and Capel B. Fine timecourse expression analysis reveals cascades of activation and repression and maps a regulator of mammalian sex determination.  PLoS Genetics 2013, 9(7): e1003630. 

* Equal contributors.  [Link]   [Data]

Musser MA*, Munger SC*, and Gunn TM. Meeting report of the 26th International Mammalian Genome Conference.

Mammalian Genome 2013, 24(5-6): 179-89.

Meeting Report.  * Equal contributors.  [Link]


Churchill GA, Gatti DM, Munger SC, and Svenson KL. The diversity outbred mouse population.

Mammalian Genome 2012, 23(9-10): 713-718.  [Link]

Jameson SA, Natarajan A, Maatouk DM, DeFalco T, Cool J, Mork L, Munger SC, and Capel B. Temporal transcriptional profiling of somatic and germ cells reveals lineage priming of sexual fate in the fetal mouse gonad.

PLoS Genetics 2012, 8 (3): e1002575.  [Link]   [Data]

Munger SC and Capel B. Sex and the circuitry: Progress toward a systems-level understanding of vertebrate sex determination. Wiley Interdisciplinary Reviews – Systems Biology and Medicine 2012, doi: 10.1002/wsbm. 1172.

Review article.   [Link]


Cook MS, Munger SC, Nadeau JH, and Capel B. (2011) Regulation of male germ cell cycle arrest and differentiation by DND1 is modulated by genetic background. Development 2011, 138 (1): 23-32.  [Link]   [Data]


Munger SC, Aylor DL, Syed HA, Magwene PM, Threadgill DW, and Capel B. Elucidation of the transcription network governing mammalian sex determination by exploiting strain-specific susceptibility to sex reversal.

Genes & Development 2009, 23: 2521-2536.  [Link]   [Data]


Ross A, Munger SC, and Capel B. Bmp7 regulates germ cell proliferation in mouse fetal gonads.

Sexual Development 2007, 1 (2): 127-137.  [Link]