PUBLICATIONS

2022

Zhang T, Keele GR, Gyuricza IG, Vincent M, Brunton C, Bell TA, Hock P, Shaw GD, Munger SC, de Villena FPM, Ferris M, Paulo JA, Gygi SP, Churchill GA. Multi-omics analysis identifies drivers of protein phosphorylation. BioRxiv 2022. https://doi.org/10.1101/2022.06.03.494740 [Link}

Aydin S, Pham DT, Zhang T, Keele G, Skelly DA, Pankratz M, Choi T, Gygi SP, Reinholdt LG§, Baker CL§, Churchill GA§, Munger SC§. Genetic dissection of the pluripotent proteome through multi-omics data integration. BioRxiv. 2022. https://doi.org/10.1101/2022.04.22.489216 [Link

Gyuricza IG, Chick JM, Keele GR, Deighan AG, Munger SC, Korstanje R, Gygi SP, Churchill GA. Genome-wide transcript and protein analysis reveals distinct features of aging in the mouse heart. Genome Research 2022 fr.275672.121. https://doi.org/10.1101/gr.275672.121. [Link]

 

Kuffler L, Skelly DA, Czechanski A, Munger SC, Baker CL, Reinholdt LG, Carter GW. Imputation of 3D genome structure by genetic-epigenetic interaction modeling in mice. BioRxiv 2022. https://doi.org/10.1101/2022.02.07.479436. [Link]

 

Byers C, Spruce C, Fortin HJ, Hartig EI, Czechanski A, Munger SC, Reinholdt LG, Skelly DA, Baker CL. Genetic control of pluripotency epigenome determines differentiation bias in mouse embryonic stem cells. The EMBO Journal 2022 41:e109445. https://doi.org/10.15252/embj.2021109445. [Link]

2021

Keele GR, Zhang T, Pham DT, Vincent M, Bell TA, Hock P, Shaw GD, Paulo JA, Munger SC, de Villena FPM, Ferris MT, Gygi SP, Churchill GA. Regulation of protein abundance in genetically diverse mouse populations. Cell Genomics 2021 1(1) 100003. https://doi.org/10.1016/j.xgen.2021.100003. [Link] [CC Proteomics Data] [QTL Viewer]

Robertson SJ, Bedard O, McNally KL, Lewis M, Clancy C, Shaia C, Broeckel RM, Chiramel AI, Sturdevant GL, Forte E, Preuss C, Baker CN, Brunton C, Munger SC, Martens C, Holland SM, Rosenthal NA, Best SM. Genetically diverse mouse models of SARS-CoV-2 infection model clinical variation and cytokine responses in COVID-19. BioRxiv 2021. https://doi.org/10.1101/2021.09.17.460664. [Link]

2020

Wells AE, Raghupathy N, Robledo RF, Gatti DM, Munger SC, Phillips C, Ndukum J, Wilcox J, Graber JH, Hibbs M, Langston MA, Churchill GA, Carter GW, Chesler EJ. Natural genetic variation alters Alzheimer’s-related gene expression modules in mice: Development of new models and analysis methods/novel assays and technologies. Alzheimer’s & Dementia 2020 Dec: e042019. https://doi.org/10.1002/alz.042019. [Link]

 

Choi KB, He H, Gatti DM, Philip VM, Raghupathy N, Gyuricza IG, Munger SC, Chesler EJ, Churchill GA. Genotype-free individual genome reconstruction of Multiparental Population Models by RNA sequencing data. BioRxiv 2020. https://doi.org/10.1101/2020.10.11.335323. [Link]

 

Liang ZS, Cimino I, Yalcin B, Raghupathy N, Vancollie VE, Ibarra-Soria X, Firth HV, Rimmington D, Farooqi S, Lelliott CJ, Munger SC, O’Rahilly S, Ferguson-Smith AC, Coll AP, and Logan DW. Trappc9 deficiency causes parent-of-origin dependent microcephaly and obesity. PLoS Genetics 2020 Sep 2;16(9)e1008916 https://doi.org/10.1371/journal.pgen.1008916. [Link]

 

Katz DC, Aponte D, Liu W, Green RM, Mayeux JM, Pollard KM, Pomp D, Munger SC, Murray SA, Roseman CC, Percival CJ, Cheverud J, Marcucio RS, and Hallgrimsson B. Facial shape and allometry quantitative trait locus intervals in the Diversity Outbred mouse are enriched for known skeletal and facial development genes. PLoS One 2020 Jun 5;15(6):e0233377. https://doi.org/10.1371/journal.pone.0233377. [Link]

 

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. Cell Stem Cell 2020 Sep 3;27(3):459-469.e8. https://doi.org/10.1016/j.stem.2020.07.005. §Corresponding authors.  [Link]  [Data]          

 

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. Cell Stem Cell 2020 Sep 3;27(3):470-481.e6. https://doi.org/10.1016/j.stem.2020.07.019. [Link]

2019

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: https://doi.org/10.1101/552059.  §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: https://doi.org/10.1101/402008.  [Link]

2018

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] ​

2017

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]

2016

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]  [DO RNA-Seq Data] [DO Proteomics Data] [QTL Viewer]

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]

2014

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]

2013

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]

2012

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]   [Expression Viewer]

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]

2011

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]

2009

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]

2007

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

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