by author Publications by date highlights


  • Chick JM, Munger SC, Simecek P, Huttlin EL, Choi K, Gatti DM, Raghupathy N, Svenson KL, Churchill GA, Gygi SG
    Author Correction: Defining the consequences of genetic variation on a proteome-wide scale
    Nature . 2022 Jun;606(7915):E16. doi: 10.1038/s41586-022-04920-w.
  • Crouse WL, Keele GR, Gastonguay MS, Churchill GA, Valdar W.
    A Bayesian model selection approach to mediation analysis
    PLoS Genet . 2022 May 9;18(5):e1010184. doi: 10.1371/journal.pgen.1010184. eCollection 2022 May
  • Gerdes Gyuricza I, Chick JM, Keele GR, Deighan AG, Munger SC, Korstanje R, Gygi SP, Churchill GA.
    Genome-wide transcript and protein analysis highlights the role of protein homeostasis in the aging mouse heart
    Genome Res . 2022 May;32(5):838-852. doi: 10.1101/gr.275672.121. Epub 2022 Mar 11.
  • Ouellette AR, Hadad N, Deighan A, Robinson L, O'Connell KO, Freund A, Churchill GA, Kaczorowski CC
    Life-long dietary restrictions have negligible or damaging effects on late-life cognitive performance: A key role for genetics in outcomes
    Neurobiol Aging . 2022 Jul 11;118:108-116. doi: 10.1016/j.neurobiolaging.2022.07.004. Online ahead of print.
  • Perez BC, Bink MCAM, Svenson KL, Churchill GA, Calus MPL.
    Prediction performance of linear models and gradient boosting machine on complex phenotypes in outbred mice
    G3 (Bethesda) . 2022 Apr 4;12(4):jkac039. doi: 10.1093/g3journal/jkac039.
  • Vincent M, Gerdes Gyuricza I, Keele GR, Gatti DM, Keller MP, Broman KW, Churchill GA
    QTLViewer: an interactive webtool for genetic analysis in the Collaborative Cross and Diversity Outbred mouse populations
    G3 (Bethesda) . 2022 Jul 29;12(8):jkac146. doi: 10.1093/g3journal/jkac146.
  • Wright KM, Deighan AG, Di Francesco A, Freund A, Jojic V, Churchill GA, Raj A
    Age and diet shape the genetic architecture of body weight in diversity outbred mice
    Elife . 2022 Jul 15;11:e64329. doi: 10.7554/eLife.64329.
  • Zhang G, Deighan A, Raj A, Robinson L, Donato HJ, Garland G, Leland M, Martin-McNulty B, Kolumam GA, Riegler J, Freund A, Wright KM, Churchill GA.
    Intermittent fasting and caloric restriction interact with genetics to shape physiological health in mice
    Genetics . 2022 Jan 4;220(1):iyab157. doi: 10.1093/genetics/iyab157.


  • Dong C, Simonett SP, Shin S, Stapleton DS, Schueler KL, Churchill GA, Lu L, Liu X, Jin F, Li Y, Attie AD, Keller MP, Keleş S.
    INFIMA leverages multi-omics model organism data to identify effector genes of human GWAS variants
    enome Biol . 2021 Aug 23;22(1):241. doi: 10.1186/s13059-021-02450-8.
  • Gould RL, Craig SW, McClatchy S, Churchill GA, Pazdro R.
    Genetic mapping of renal glutathione suggests a novel regulatory locus on the murine X chromosome and overlap with hepatic glutathione regulation
    Free Radic Biol Med . 2021 Oct;174:28-39. doi: 10.1016/j.freeradbiomed.2021.07.035. Epub 2021 Jul 26.
  • Gould RL, Craig SW, McClatchy S, Churchill GA, Pazdro R.
    Quantitative trait mapping in Diversity Outbred mice identifies novel genomic regions associated with the hepatic glutathione redox system
    Redox Biol . 2021 Oct;46:102093. doi: 10.1016/j.redox.2021.102093. Epub 2021 Aug 5.
  • Keele GR, Zhang T, Pham DT, Vincent M, Bell TA, Hock P, Shaw GD, Paulo JA, Munger SC, Pardo-Manuel de Villena F, Ferris MT, Gygi SP, Churchill GA.
    Regulation of protein abundance in genetically diverse mouse populations
    Cell Genomics. 2021 August; 1(1). doi: 10.1101/2020.09.18.296657.
  • Keenan BT, Webster JC, Wiemken AS, Lavi-Romer N, Nguyen T, Svenson KL, Galante RJ, Churchill GA, Pickup S, Pack AI, Schwab RJ.
    Heritability of fat distributions in male mice from the founder strains of the Diversity Outbred mouse population
    G3 (Bethesda) . 2021 May 7;11(5):jkab079. doi: 10.1093/g3journal/jkab079.
  • Keenan BT, Galante RJ, Lian K, Zhang L, Guo X, Veatch OJ, Chesler EJ, O'Brien WT, Svenson KL, Churchill GA, Pack AI
    The dihydropyrimidine dehydrogenase gene contributes to heritable differences in sleep in mice
    Curr Biol . 2021 Dec 6;31(23):5238-5248.e7. doi: 10.1016/j.cub.2021.09.049. Epub 2021 Oct 14.
  • Korstanje R, Peters LL, Robinson LL, Krasinski SD, Churchill GA.
    The Jackson Laboratory Nathan Shock Center: impact of genetic diversity on aging
    Geroscience . 2021 Oct;43(5):2129-2137. doi: 10.1007/s11357-021-00421-2. Epub 2021 Jul 23.
  • Palliyaguru DL, Shiroma EJ, Nam JK, Duregon E, Vieira Ligo Teixeira C, Price NL, Bernier M, Camandola S, Vaughan KL, Colman RJ, Deighan A, Korstanje R, Peters LL, Dickinson SL, Ejima K, Simonsick EM, Launer LJ, Chia CW, Egan J, Allison DB, Churchill GA, Anderson RM, Ferrucci L, Mattison JA, de Cabo R.
    Fasting blood glucose as a predictor of mortality: Lost in translation
    Cell Metab . 2021 Nov 2;33(11):2189-2200.e3. doi: 10.1016/j.cmet.2021.08.013. Epub 2021 Sep 10.
  • Starcher AE, Peissig K, Stanton JB, Churchill GA, Cai D, Maxwell JT, Grider A, Love K, Chen SY, Coleman AE, Strauss E, Pazdro R
    A systems approach using Diversity Outbred mice distinguishes the cardiovascular effects and genetics of circulating GDF11 from those of its homolog, myostatin
    G3 (Bethesda) . 2021 Oct 19;11(11):jkab293. doi: 10.1093/g3journal/jkab293.
  • Takemon Y, Chick JM, Gerdes Gyuricza I, Skelly DA, Devuyst O, Gygi SP, Churchill GA, Korstanje R.
    Proteomic and transcriptomic profiling reveal different aspects of aging in the kidney
    Elife . 2021 Mar 9;10:e62585. doi: 10.7554/eLife.62585.
  • Zhang G, Deighan A, Raj A, Robinson L, Donato HJ, Garland G, Leland M, Martin-McNulty B, Kolumam GA, Riegler J, Freund A, Wright KM, Churchill GA.
    Intermittent fasting and caloric restriction interact with genetics to shape physiological health in mice
    Genetics . 2021 Sep 25;220(1):iyab157. doi: 10.1093/genetics/iyab157. Online ahead of print.
  • Zhang T, Keele GR, Churchill GA, Gygi SP, Paulo JA.
    Strain-Specific Peptide (SSP) Interference Reference Sample: A Genetically Encoded Quality Control for Isobaric Tagging Strategies
    Anal Chem . 2021 Mar 30;93(12):5241-5247. doi: 10.1021/acs.analchem.0c05483. Epub 2021 Mar 18.


  • Choi K, Chen Y, Skelly DA, Churchill GA.
    Bayesian model selection reveals biological origins of zero inflation in single-cell transcriptomics
    Genome Biol . 2020 Jul 27;21(1):183. doi: 10.1186/s13059-020-02103-2.
  • Keenan BT, Galante RJ, Lian J, Simecek P, Gatti DM, Zhang L, Lim DC, Svenson KL, Churchill GA, Pack AI.
    High-throughput sleep phenotyping produces robust and heritable traits in Diversity Outbred mice and their founder strains. 
    Sleep. 2020 May 12;43(5). doi: 10.1093/sleep/zsz278. PubMed PMID: 32074270; PubMed Central PMCID: PMC7215270.
  • Linke V, Overmyer KA, Miller IJ, Brademan DR, Hutchins PD, Trujillo EA, Reddy TR, Russell JD, Cushing EM, Schueler KL, Stapleton DS, Rabaglia ME, Keller MP, Gatti DM, Keele GR, Pham D, Broman KW, Churchill GA, Attie AD, Coon JJ
    A large-scale genome-lipid association map guides lipid identification
    Nat Metab . 2020 Oct;2(10):1149-1162. doi: 10.1038/s42255-020-00278-3. Epub 2020 Sep 21.
  • McClatchy S, Bass KM, Gatti DM, Moylan A, Churchill G
    Nine quick tips for efficient bioinformatics curriculum development and training.
    PLoS Comput Biol. 2020;16(7):e1008007. Published 2020 Jul 23. doi:10.1371/journal.pcbi.1008007
  • Ortmann D, Brown S, Czechanski A, Aydin S, Muraro D, Huang Y, Tomaz RA, Osnato A, Canu G, Wesley BT, Skelly DA, Stegle O, Choi T, Churchill GA, Baker CL, Rugg-Gunn PJ, Munger SC, Reinholdt LG, Vallier L.
    Naive Pluripotent Stem Cells Exhibit Phenotypic Variability that Is Driven by Genetic Variation
    Cell Stem Cell. 2020 Aug 11;. doi: 10.1016/j.stem.2020.07.019. [Epub ahead of print]
  • Ouellette AR, Neuner SM, Dumitrescu L, Anderson LC, Gatti DM, Mahoney ER, Bubier JA, Churchill G, Peters L, Huentelman MJ, Herskowitz JH, Yang HS, Smith AN, Reitz C, Kunkle BW, White CC, De Jager PL, Schneider JA, Bennett DA, Seyfried NT
    Cross-Species Analyses Identify Dlgap2 as a Regulator of Age-Related Cognitive Decline and Alzheimer's Dementia
    ll Rep . 2020 Sep 1;32(9):108091. doi: 10.1016/j.celrep.2020.108091.
  • Skelly DA, Czechanski A, Byers C, Aydin S, Spruce C, Olivier C, Choi K, Gatti DM, Raghupathy N, Keele GR, Stanton A, Vincent M, Dion S, Greenstein I, Pankratz M, Porter DK, Martin W, O'Connor C, Qin W, Harrill AH, Choi T, Churchill GA, Munger SC, Baker CL, Reinholdt LG.
    Mapping the Effects of Genetic Variation on Chromatin State and Gene Expression Reveals Loci That Control Ground State Pluripotency
    Cell Stem Cell. 2020 Aug 7;. doi: 10.1016/j.stem.2020.07.005. [Epub ahead of print]


  • Broman KW, Gatti DM, Svenson KL, Sen Ś, Churchill GA.
    Cleaning Genotype Data from Diversity Outbred Mice.
    G3 (Bethesda). 2019 Mar 15. pii: g3.400165.2019. doi: 10.1534/g3.119.400165. [Epub ahead of print]
  • Broman KW, Gatti DM, Simecek P, Furlotte NA, Prins P, Sen Ś, Yandell BS, Churchill GA
    R/qtl2: Software for Mapping Quantitative Trait Loci with High-Dimensional Data and Multiparent Populations
    Genetics. 2019 Feb;211(2):495-502. doi: 10.1534/genetics.118.301595. Epub 2018 Dec 27.
  • Broman KW, Gatti DM, Svenson KL, Sen Ś, Churchill GA
    Cleaning Genotype Data from Diversity Outbred Mice
    G3 (Bethesda). 2019 May 7;9(5):1571-1579. doi: 10.1534/g3.119.400165. PubMed PMID: 30877082; PubMed Central PMCID: PMC6505173.
  • Choi K, Raghupathy N, Churchill GA.
    A Bayesian mixture model for the analysis of allelic expression in single cells. 
    Nat Commun. 2019 Nov 15;10(1):5188. doi: 10.1038/s41467-019-13099-0. PubMed PMID: 31729374; PubMed Central PMCID: PMC6858378.
  • Choi K, Raghupathy N, Churchill GA.
    A Bayesian mixture model for the analysis of allelic expression in single cells.
    Nat Commun. 2019 Nov 15;10(1):5188. doi: 10.1038/s41467-019-13099-0.
  • Keller MP, Rabaglia ME, Schueler KL, Stapleton DS, Gatti DM, Vincent M, Mitok KA, Wang Z, Ishimura T, Simonett SP, Emfinger CH, Das R, Beck T, Kendziorski C, Broman KW, Yandell BS, Churchill GA, Attie AD
    Gene loci associated with insulin secretion in islets from non-diabetic mice
    J Clin Invest. 2019 Jul 25;130. doi: 10.1172/JCI129143
  • Kemis JH, Linke V, Barrett KL, Boehm FJ, Traeger LL, Keller MP, Rabaglia ME, Schueler KL, Stapleton DS, Gatti DM, Churchill GA, Amador-Noguez D, Russell JD, Yandell BS, Broman KW, Coon JJ, Attie AD, Rey FE.
    Genetic determinants of gut microbiota composition and bile acid profiles in mice. 
    PLoS Genet. 2019 Aug;15(8):e1008073. doi: 10.1371/journal.pgen.1008073. eCollection 2019 Aug. PubMed PMID: 31465442; PubMed Central PMCID: PMC6715156.
  • Kemis JH, Linke V, Barrett KL, Boehm FJ, Traeger LL, Keller MP, Rabaglia ME, Schueler KL, Stapleton DS, Gatti DM, Churchill GA, Amador-Noguez D, Russell JD, Yandell BS, Broman KW, Coon JJ, Attie AD, Rey FE.
    Genetic determinants of gut microbiota composition and bile acid profiles in mice.
    PLoS Genet. 2019 Aug;15(8):e1008073. doi: 10.1371/journal.pgen.1008073. eCollection 2019 Aug.
  • Mesner LD, Calabrese GM, Al-Barghouthi B, Gatti DM, Sundberg JP, Churchill GA, Godfrey DA, Ackert-Bicknell CL, Farber CR
    Mouse genome-wide association and systems genetics identifies Lhfp as a regulator of bone mass.
    PLoS Genet. 2019 May;15(5):e1008123. doi: 10.1371/journal.pgen.1008123. eCollection 2019 May
  • Recla JM, Bubier JA, Gatti DM, Ryan JL, Long KH, Robledo RF, Glidden NC, Hou G, Churchill GA, Maser RS, Zhang ZW, Young EE, Chesler EJ, Bult CJ.
    Genetic mapping in Diversity Outbred mice identifies a Trpa1 variant influencing late-phase formalin response.
    Pain. 2019 Mar 27. doi: 10.1097/j.pain.0000000000001571. [Epub ahead of print]
  • Sarsani VK, Raghupathy N, Fiddes IT, Armstrong J, Thibaud-Nissen F, Zinder O, Bolisetty M, Howe K, Hinerfeld D, Ruan X, Rowe L, Barter M, Ananda G, Paten B, Weinstock GM, Churchill GA, Wiles MV, Schneider VA, Srivastava A, Reinholdt LG.
    The Genome of C57BL/6J "Eve", the Mother of the Laboratory Mouse Genome Reference Strain.
    G3 (Bethesda). 2019 Jun 5;9(6):1795-1805. doi: 10.1534/g3.119.400071. PubMed PMID: 30996023
  • Zeiss CJ, Gatti DM, Toro-Salazar O, Davis C, Lutz CM, Spinale F, Stearns T, Furtado MB, Churchill GA.
    Doxorubicin-Induced Cardiotoxicity in Collaborative Cross (CC) Mice Recapitulates Individual Cardiotoxicity in Humans. 
    G3 (Bethesda). 2019 Aug 8;9(8):2637-2646. doi: 10.1534/g3.119.400232. PubMed PMID: 31263061; PubMed Central PMCID: PMC6686936.


  • 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, Churchill GA.
    Erratum: "Diversity Outbred Mice Identify Population-Based Exposure Thresholds and Genetic Factors that Influence Benzene-Induced Genotoxicity".
    Environ Health Perspect. 2018 Jun 27;126(6):069003. doi: 10.1289/EHP3950. eCollection 2018 Jun.
  • Gatti DM, Weber SN, Goodwin NC, Lammert F, Churchill GA.
    Genetic background influences susceptibility to chemotherapy-induced hematotoxicity.
    Pharmacogenomics J. 2018 Apr;18(2):319-330. doi: 10.1038/tpj.2017.23. Epub 2017 Jun 13.
  • Keller MP, Simecek P, Schueler KL, Rabaglia ME, Stapleton DS, Broman AT, Gatti DM, Vincent M, Allen S, Bacher R, Kendziorski C, Broman KW, Yandell BS, Churchill GA, Attie AD
    Genetic Drivers of Pancreatic Islet Function
    Genetics. 2018 May;209(1):335-356. doi: 10.1534/genetics.118.300864. Epub 2018 Mar 22.
  • Raghupathy N, Choi K, Vincent MJ, Beane GL, Sheppard KS, Munger SC, Korstanje R, Pardo-Manual de Villena F, Churchill GA.
    Hierarchical analysis of RNA-seq reads improves the accuracy of allele-specific expression.
    Bioinformatics. 2018 Jul 1;34(13):2177-2184. doi: 10.1093/bioinformatics/bty078
  • Thompson MJ, Chwiałkowska K, Rubbi L, Lusis AJ, Davis RC, Srivastava A, Korstanje R, Churchill GA, Horvath S, Pellegrini M.
    A multi-tissue full lifespan epigenetic clock for mice.
    Aging (Albany NY). 2018 Oct 21;10(10):2832-2854. doi: 10.18632/aging.101590.


  • Attie AD, Churchill GA, Nadeau JH
    How mice are indispensable for understanding obesity and diabetes genetics.
    Curr Opin Endocrinol Diabetes Obes. 2017 Apr;24(2):83-91. doi: 10.1097/MED.0000000000000321
  • Gatti DM, Weber SN, Goodwin NC, Lammert F, Churchill GA
    Genetic Background Influences Susceptibility to Chemotherapy-Induced Hematotoxicity
    Pharmacogenomics J. 2017 Jun 13. doi: 10.1038/tpj.2017.23
  • Morgan AP, Gatti DM, Najarian ML, Keane TM, Galante RJ, Pack AI, Mott R, Churchill GA, de Villena FP.
    Structural Variation Shapes the Landscape of Recombination in Mouse.
    Genetics. 2017 Jun;206(2):603-619. doi: 10.1534/genetics.116.197988
  • Percival CJ, Green R, Roseman CC, Gatti DM, Morgan JL, Murray SA, Donahue LR, Mayeux J, Pollard M, Pomp D, Marcucio R, Hallgrímsson B
    Developmental constraint through negative pleiotropy in the zygomatic arch



  • Simecek P, Forejt J, Williams RW, Shiroishi T, Takada T, Lu L, Johnson TE, Bennett B, Deschepper CF, Scott-Boyer MP, Pardo-Manuel de Villena F, Churchill GA.
    High-Resolution Maps of Mouse Reference Populations.
    G3 (Bethesda). 2017 Oct 5;7(10):3427-3434. doi: 10.1534/g3.117.300188.
  • Srivastava A, Morgan AP, Najarian ML, Sarsani VK, Sigmon JS, Shorter JR, Kashfeen A, McMullan RC, Williams LH, Giusti-Rodríguez P, Ferris MT, Sullivan P, Hock P, Miller DR, Bell TA, McMillan L, Churchill GA, de Villena FP.
    Genomes of the Mouse Collaborative Cross
    Genetics. 2017 Jun;206(2):537-556. doi: 10.1534/genetics.116.198838.
  • Tyler AL, Ji B, Gatti DM, Munger SC, Churchill GA, Svenson KL, Carter GW.
    Epistatic Networks Jointly Influence Phenotypes Related to Metabolic Disease and Gene Expression in Diversity Outbred Mice.
    Genetics. 2017 Jun;206(2):621-639. doi: 10.1534/genetics.116.198051.
  • Winter JM, Gildea DE, Andreas JP, Gatti DM, Williams KA, Lee M, Hu Y, Zhang S; NISC Comparative Sequencing Program., Mullikin JC, Wolfsberg TG, McDonnell SK, Fogarty ZC, Larson MC, French AJ, Schaid DJ, Thibodeau SN, Churchill GA, Crawford NP.
    Mapping Complex Traits in a Diversity Outbred F1 Mouse Population Identifies Germline Modifiers of Metastasis in Human Prostate Cancer.
    Cell Syst. 2017 Jan 25;4(1):31-45.e6. doi: 10.1016/j.cels.2016.10.018. Epub 2016 Dec 1


  • Chesler EJ, Gatti DM, Morgan AP, Strobel M, Trepanier L, Oberbeck D, McWeeney S, Hitzemann R, Ferris M, McMullan R, Clayshultle A, Bell TA, Pardo-Manuel de Villena F, Churchill GA
    Diversity Outbred Mice at 21: Maintaining allelic variation in the face of selection
    G3 (Bethesda). 2016 Dec 7;6(12):3893-3902. doi: 10.1534/g3.116.035527.
  • Chick JM, Munger SC, Simecek P, Huttlin EL, Choi K, Gatti DM, Raghupathy N, Svenson KL, Churchill GA, Gygi SP
    Defining the consequences of genetic variation on a proteome-wide scale
    Nature. 2016 Jun 23;534(7608):500-5. doi: 10.1038/nature18270. Epub 2016 Jun 15
  • Churchill GA
    Eric Lander and David Botstein on Mapping Quantitative Traits
    Genetics. 2016 May;203(1):1-3. doi: 10.1534/genetics.116.189803. Epub 2016 May 5
  • Didion JP, Morgan AP, Yadgary L, Bell TA, McMullan RC, Ortiz de Solorzano L, Britton-Davidian J, Bult CJ, Campbell KJ, Castiglia R, Ching YH, Chunco AJ, Crowley JJ, Chesler EJ, Forster DW, French JE, Gabriel SI, Gatti DM, Garland T, Giagia-Athanasopoulou EB, Gimenez MD, Grize SA, Gunduz I, Holmes A, Hauffe HC, Herman JS, Holt JM, Hua K, Jolley WJ, Lindholm AK, Lopez-Fuster MJ, Mitsainas G, da Luz Mathias M, McMillan L, Ramalhinho Mda G, Rehermann B, Rosshart SP, Searle JB, Shiao MS, Solano E, Svenson KL, Thomas-Laemont P, Threadgill DW, Ventura J, Weinstock GM, Pomp D, Churchill GA, Pardo-Manuel de Villena F
    R2d2 Drives Selfish Sweeps in the House Mouse
    Mol Biol Evol. 2016 Jun;33(6):1381-95. doi: 10.1093/molbev/msw036. Epub 2016 Feb 15
  • Gu T, Gatti DM, Srivastava A, Snyder EM, Raghupathy N, Simecek P, Svenson KL, Dotu I, Chuang JH, Keller MP, Attie AD, Braun RE, Churchill GA
    Genetic Architectures of Quantitative Variation in RNA Editing Pathways
    Genetics. 2016 Feb;202(2):787-98. doi: 10.1534/genetics.115.179481. Epub 2015 Nov 27
  • Jiang Z, Harrison DE, Parsons ME, McClatchy S, Jacobs L, Pazdro R
    Heritability of in vitro phenotypes exhibited by murine adipose-derived stromal cells
    Mamm Genome. 2016 Jul 8
  • Morgan AP, Fu CP, Kao CY, Welsh CE, Didion JP, Yadgary L, Hyacinth L, Ferris MT, Bell TA, Miller DR, Giusti-Rodriguez P, Nonneman RJ, Cook KD, Whitmire JK, Gralinski LE, Keller M, Attie AD, Churchill GA, Petkov P, Sullivan PF, Brennan JR, McMillan L, Pardo-Manuel de Villena F
    The Mouse Universal Genotyping Array: From Substrains to Subspecies
    G3 (Bethesda). 2015 Dec 18;6(2):263-79. doi: 10.1534/g3.115.022087
  • Morton NM, Beltram J, Carter RN, Michailidou Z, Gorjanc G, McFadden C, Barrios-Llerena ME, Rodriguez-Cuenca S, Gibbins MT, Aird RE, 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, Gudnason V, Kenyon CJ, Seckl JR, Walker BR, Webster SP, Dunbar DR, Churchill GA, Vidal-Puig A, Fernandez-Real JM, Emilsson V, Horvat S
    Genetic identification of thiosulfate sulfurtransferase as an adipocyte-expressed antidiabetic target in mice selected for leanness
    Nat Med. 2016 Jul;22(7):771-9. doi: 10.1038/nm.4115. Epub 2016 Jun 6
  • Nair KS, Cosma M, Raghupathy N, Sellarole MA, Tolman NG, de Vries W, Smith RS, John SW
    YBR/EiJ mice: a new model of glaucoma caused by genes on chromosomes 4 and 17
    Dis Model Mech. 2016 Aug 1;9(8):863-71. doi: 10.1242/dmm.024307. Epub 2016 Jun 9
  • Tyler AL, Donahue LR, Churchill GA, Carter GW
    Weak Epistasis Generally Stabilizes Phenotypes in a Mouse Intercross
    PLoS Genet. 2016 Feb 1;12(2):e1005805. doi: 10.1371/journal.pgen.1005805. eCollection 2016 Feb


  • Ackert-Bicknell CL, Anderson LC, Sheehan S, Hill WG, Chang B, Churchill GA,. Chesler EJ, Korstanje R, Peters LL
    Aging Research Using Mouse Models
    Curr Protoc Mouse Biol. 2015 Jun 1;5(2):95-133. doi: 10.1002/9780470942390.mo140195
  • Baker CL, Kajita S, Walker M, Saxl RL, Raghupathy N, Choi K, Petkov PM and Paigen K
    PRDM9 drives evolutionary erosion of hotspots in Mus musculus through haplotype-specific initiation of meiotic recombination
    PLoS Genetics. 2015;11(1):e1004916
  • Bogue MA, Churchill GA, Chesler EJ
    Collaborative Cross and Diversity Outbred data resources in the Mouse Phenome Database
    Mamm Genome. 2015 Oct;26(9-10):511-20. doi: 10.1007/s00335-015-9595-6. Epub 2015 Aug 19
  • Carmody RN, Gerber GK, Luevano JM, Gatti DM, Somes L, Svenson KL, Turnbaugh PJ
    Diet dominates host genotype in shaping the murine gut microbiota
    Cell Host Microbe. 2015 Jan 14;17(1):72-84. doi: 10.1016/j.chom.2014.11.010. Epub 2014 Dec 18
  • Church RJ, Gatti DM, Urban TJ, Long N, Yang X, Shi Q, Eaddy JS, Mosedale M, Ballard S, Churchill GA, Navarro V, Watkins PB, Threadgill DW, Harrill AH
    Sensitivity to hepatotoxicity due to epigallocatechin gallate is affected by genetic background in diversity outbred mice
    Food Chem Toxicol 2015;76:19-26
  • Dell'Acqua M, Gatti DM, Pea G, Cattonaro F, Coppens F, Magris G, Hlaing AL, Aung HH, Nelissen H, Baute J, Frascaroli E, Churchill GA, Inze D, Morgante M, Pe ME
    Genetic properties of the MAGIC maize population: a new platform for high definition QTL mapping in Zea mays
    Genome Biol. 2015 Sep 11;16:167. doi: 10.1186/s13059-015-0716-z
  • Didion JP, Morgan AP, Clayshulte AM, McMullan RC, Yadgary L, Petkov PM, Bell TA, Gatti DM, Crowley JJ, Hua K, Aylor DL, Bai L, Calaway M, Chesler EJ, French JE, Geiger TR, Gooch TJ, Garland T. Jr, Harrill AH, Hunter K, McMillan L, Holt M, Miller DR, O'Brien DA, Paigen K, Pan W, Rowe LB, Shaw GD, Simecek P, Sullivan PF, Svenson KL, Weinstock GM, Threadgill DW, Pomp D, Churchill GA, Pardo-Manuel de Villena F
    A multi-megabase copy number gain causes maternal transmission ratio distortion on mouse chromosome 2
    PLoS Genetics. 2015;11(2):e1004850
  • 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, Churchill GA
    Diversity Outbred Mice Identify Population Based Exposure Thresholds and Genetic Factors that Influence Benzene-Induced Genotoxicity
    Env. Health Persp., 2015;123(3):237-45
  • Gralinski LE, Ferris MT, Aylor DL, Whitmore AC, Green R, Frieman MB, Deming D, Menachery VD, Miller DR, Buus RJ, Bell TA, Churchill GA, Threadgill DW, Katze MG, McMillan L, Valdar W, Heise MT, Pardo-Manuel de Villena F, Baric RS
    Genome Wide Identification of SARS-CoV Susceptibility Loci Using the Collaborative Cross
    PLoS Genet. 2015 Oct 9;11(10):e1005504. doi: 10.1371/journal.pgen.1005504. eCollection 2015 Oct
  • Niazi MK, Dhulekar N, Schmidt D, Major S, Cooper R, Abeijon C, Gatti DM, Kramnik I, Yener B, Gurcan M, Beamer G
    Lung necrosis and neutrophils reflect common pathways of susceptibility to Mycobacterium tuberculosis in genetically diverse, immune-competent mice
    Dis Model Mech. 2015 Sep;8(9):1141-53. doi: 10.1242/dmm.020867. Epub 2015 Jul 23
  • Rau CD, Parks B, Wang Y, Eskin E, Simecek P, Churchill GA, Lusis AJ
    High-Density Genotypes of Inbred Mouse Strains: Improved Power and Precision of Association Mapping
    G3 (Bethesda). 2015 Jul 28;5(10):2021-6. doi: 10.1534/g3.115.020784
  • Rutledge H, Baran-Gale J, de Villena FP, Chesler EJ, Churchill GA, Sethupathy P, Kelada SN
    Identification of microRNAs associated with allergic airway disease using a genetically diverse mouse population
    BMC Genomics. 2015 Aug 25;16:633. doi: 10.1186/s12864-015-1732-9
  • Simecek P, Churchill GA, Yang H, Rowe LB, Herberg L, Serreze DV, Leiter EH
    Genetic Analysis of Substrain Divergence in NOD Mice
    G3. 2015
  • Walker M, Billings T, Baker CL, Powers N, Tian H, Saxl RL, Choi K, Hibbs MA, Carter GW, Handel MA, Paigen K, Petkov PM
    Affinity-seq detects genome-wide PRDM9 binding sites and reveals the impact of prior chromatin modifications on mammalian recombination hotspot usage
    Epigenetics Chromatin. 2015 Sep 7;8:31. doi: 10.1186/s13072-015-0024-6. eCollection 2015.


  • Bogue MA, Peters LL, Paigen B, Korstanje R, Yuan R, Ackert-Bicknell C, Grubb SC, Churchill GA, Chesler EJ
    Accessing Data Resources in the Mouse Phenome Database for Genetic Analysis of Murine Life Span and Health Span
    J Gerontol A Biol Sci Med Sci. 2014
  • Churchill GA
    Misleading results: don't blame the mice
    Science. 2014;343(6169):370
  • Churchill GA
    When are results too good to be true?
    Genetics. 2014;198(2):447-8
  • Gatti DM, Svenson KL, Shabalin A, Wu LY, Valdar W, Simecek P, Goodwin N, Cheng R, Pomp D, Palmer A, Chesler EJ, Broman KW and Churchill GA
    Quantitative trait locus mapping methods for diversity outbred mice
    G3. 2014;4(9):1623-33
  • Kelada SN, Carpenter DE, Aylor DL, Chines P, Rutledge H, Chesler EJ, Churchill GA, Pardo-Manuel de Villena F, Schwartz DA and Collins FS
    Integrative genetic analysis of allergic inflammation in the murine lung
    Am J Respir Cell Mol Biol. 2014 Sep;51(3):436-45. doi: 10.1165/rcmb.2013-0501OC
  • Liu EY, Morgan AP, Chesler EJ, Wang W, Churchill GA, Pardo-Manuel de Villena F
    High-Resolution Sex-Specific Linkage Maps of the Mouse Reveal Polarized Distribution of Crossovers in Male Germline
    Genetics. 2014 Feb 27. doi: 10.1534/genetics.114.161653
  • 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
  • Ram R, Mehta M, Balmer L, Gatti DM, Morahan G
    Rapid identification of major-effect genes using the collaborative cross
    Genetics. 2014 Sep;198(1):75-86. doi: 10.1534/genetics.114.163014
  • Recla JM, Robledo RF, Gatti DM, Bult CJ, Churchill GA, Chesler EJ
    Precise genetic mapping and integrative bioinformatics in Diversity Outbred mice reveals Hydin as a novel pain gene
    Mamm Genome. 2014 Jun;25(5-6):211-22
  • Rutledge H, Aylor DL, Carpenter DE, Peck BC, Chines P, Ostrowski LE, Chesler EJ, Churchill GA, de Villena FP and Kelada SN
    Genetic regulation of Zfp30, CXCL1, and neutrophilic inflammation in murine lung
    Genetics. 2014;198(2):735-45
  • Smallwood TL, Gatti DM, Quizon P, Weinstock GM, Jung KC, Zhao L, Hua K, Pomp D, Bennett BJ
    High-resolution genetic mapping in the diversity outbred mouse population identifies Apobec1 as a candidate gene for atherosclerosis
    G3 (Bethesda). 2014 Oct 23;4(12):2353-63. doi: 10.1534/g3.114.014704
  • Yu W, Ackert-Bicknell C, Larigakis JD, MacIver B, Steers WD, Churchill GA, Hill WG, Zeidel, ML
    Spontaneous voiding by mice reveals strain-specific lower urinary tract function to be a quantitative genetic trait
    Am J Physiol Renal Physiol. 2014 Jun 1;306(11):F1296-307
  • Yuan R, Gatti DM, Krier R, Malay E, Schultz D, Peters LL, Churchill GA, Harrison, DE, Paigen B
    Genetic Regulation of Female Sexual Maturation and Longevity Through Circulating IGF1
    J Gerontol A Biol Sci Med Sci 2014 July 28


  • Brockmann GA, Schäfer N, Hesse C, Heise S, Neuschl C, Wagener A, Churchill GA, Li
    Relationship between obesity phenotypes and genetic determinants in a mouse model for juvenile obesity
    Physiol Genomics. 2013 Sep 16;45(18):817-26. doi: 10.1152/physiolgenomics.00058.2013
  • Ferris MT, Aylor DL, Bottomly D, Whitmore AC, Aicher LD, Bell TA, Bradel-Tretheway B, Bryan JT, Buus RJ, Gralinski LE, Haagmans BL, McMillan L, Miller DR, Rosenzweig E, Valdar W, Wang J, Churchill GA, Threadgill DW, McWeeney SK, Katze MG, Pardo-Manuel de Villena F, Baric RS, Heise MT
    Modeling host genetic regulation of influenza pathogenesis in the collaborative cross
    PLoS Pathog. 2013 Feb;9(2):e1003196
  • Himes BE, Sheppard K, Berndt A, Leme AS, Myers RA, Gignoux CR, Levin AM, Gauderman WJ, Yang JJ, Mathias RA, Romieu I, Torgerson DG, Roth LA, Huntsman S, Eng C, Klanderman B, Ziniti J, Senter-Sylvia J, Szefler SJ, Lemanske RF Jr, Zeiger RS, Strunk RC, Martinez FD, Boushey H, Chinchilli VM, Israel E, Mauger D, Koppelman GH, Postma DS, Nieuwenhuis MA, Vonk JM, Lima JJ, Irvin CG, Peters SP, Kubo M, Tamari M, Nakamura Y, Litonjua AA, Tantisira KG, Raby BA, Bleecker ER, Meyers DA, London SJ, Barnes KC, Gilliland FD, Williams LK, Burchard EG, Nicolae DL, Ober C, Demeo DL, Silverman EK, Paigen B, Churchill G, Shapiro SD, Weiss ST
    Integration of Mouse and Human Genome-Wide Association Data Identifies KCNIP4 as an Asthma Gene
    PLoS One. 2013;8(2):e56179. doi: 10.1371/journal.pone.0056179
  • Kumar V, Kim K, Joseph C, Kourrich S, Yoo SH, Huang HC, Vitaterna MH, de Villena FP, Churchill GA, Bonci A, Takahashi JS
    C57BL/6N Mutation in Cytoplasmic FMRP interacting protein 2 Regulates Cocaine Response
    Science. 2013 Dec 20;342(6165):1508-12. doi: 10.1126/science.1245503.
  • Logan RW, Robledo RF, Recla JM, Philip VM, Bubier JA, Jay JJ, Harwood C, Wilcox T, Gatti DM, Bult CJ, Churchill GA, Chesler EJ
    High-precision genetic mapping of behavioral traits in the diversity outbred mouse population
    Genes Brain Behav. 2013 Feb 21. doi: 10.1111/gbb.12029
  • McClatchy S, McGann D, Gotwals R, Baskett A, Churchill G
    Students as collaborators in systems biology research
    Science. 2013 May 31;340(6136):1061-2. doi: 10.1126/science.1229906


  • Aljakna A, Choi S, Savage H, Hageman Blair R, Gu T, Svenson KL, Churchill GA, Hibbs M, Korstanje R
    Pla2g12b and Hpn Are Genes Identified by Mouse ENU Mutagenesis That Affect HDL Cholesterol
    PLoS One. 2012;7(8):e43139
  • Andrus BM, Blizinsky K, Vedell PT, Dennis K, Shukla PK, Schaffer DJ, Radulovic J, Churchill GA, Redei EE
    Gene expression patterns in the hippocampus and amygdala of endogenous depression and chronic stress models
    Mol Psychiatry. 2012 Jan;17(1):49-61
  • Blair RH, Kliebenstein DJ, Churchill GA
    What Can Causal Networks Tell Us about Metabolic Pathways?
    PLoS Comput Biol. 2012 Apr;8(4):e1002458
  • Churchill GA, Gatti DM, Munger SC, Svenson KL
    The Diversity Outbred Mouse Population
    Mamm Genome. 2012 Oct;23(9-10):713-8
  • Collaborative Cross Consortium
    The Genome Architecture of the Collaborative Cross Mouse Genetic Reference Population
    Genetics. 2012 Feb;190(2):389-401
  • Didion JP, Yang H, Sheppard K, Fu CP, McMillan L, Pardo-Manuel de Villena F, Churchill GA
    Discovery of novel variants in genotyping arrays improves genotype retention and reduces ascertainment bias
    BMC Genomics. 2012 Jan 19;13(1):34
  • Kelada SNP, Aylor DL, Peck BCE, Ryan JF, Tavarez U, Buus RJ, Miller DR, Chesler EJ, Threadgill DW, Churchill GA, Pardo-Manuel de Villena F, Collins FS
    Genetic Analysis of Hematologic Parameters in Incipient Lines of the Collaborative Cross
    G3 (Bethesda). 2012 Feb;2(2):157-65
  • Leduc MS, Blair RH, Verdugo RA, Tsaih SW, Walsh K, Churchill GA, Paigen B
    Using bioinformatics and systems genetics to dissect HDL cholesterol levels in an MRL/MpJ x SM/J intercross
    J Lipid Res. 2012 Jun;53(6):1163-75
  • Lenarcic AB, Svenson KL, Churchill GA, Valdar W
    A General Bayesian Approach to Analyzing Diallel Crosses of Inbred Strains
    Genetics. 2012 Feb;190(2):413-35
  • Pajer K, Andrus BM, Gardner W, Lourie A, Strange B, Campo J, Bridge J, Blizinsky K, Dennis K, Vedell P, Churchill GA, Redei EE
    Discovery of blood transcriptomic markers for depression in animal models and pilot validation in subjects with early-onset major depression
    Transl Psychiatry. 2012 Apr 17;2:e101. doi: 10.1038/tp.2012.26
  • Phifer-Rixey M, Bonhomme F, Boursot P, Churchill GA, Piálek J, Tucker P, Nachman M
    Adaptive evolution and effective population size in wild house mice
    Mol Biol Evol. 2012 Oct;29(10):2949-55
  • Svenson KL, Gatti DM, Valdar W, Welsh CE, Cheng R, Chesler EJ, Palmer AA, McMillan L, Churchill GA
    High-Resolution Genetic Mapping Using the Mouse Diversity Outbred Population
    Genetics. 2012 Feb;190(2):437-47
  • Thaisz J, Tsaih SW, Feng M, Philip V, Zhang Y, Yanas L, Sheehan S, Xu L, Miller DR, Paigen B, Chesler EJ, Churchill GA, Dipetrillo KJ
    Genetic analysis of albuminuria in Collaborative Cross and multiple mouse intercross populations
    Am J Physiol Renal Physiol. 2012 Oct;303(7):F972-81
  • Threadgill DW, Churchill GA
    Ten Years of the Collaborative Cross
    Genetics. 2012 Feb;190(2):291-4
  • Wang JR, Pardo-Manuel de Villena F, Lawson HA, Cheverud JM, Churchill GA, McMillan L
    Imputation of single-nucleotide polymorphisms in inbred mice using local phylogeny
    Genetics. 2012 Feb;190(2):449-58
  • Zhang W, Korstanje R, Thaisz J, Staedtler F, Harttman N, Xu L, Feng M, Yanas L, Yang H, Valdar W, Churchill GA, DiPetrillo K
    Genome-Wide Association Mapping of Quantitative Traits in Outbred Mice
    G3 (Bethesda). 2012 Feb;2(2):167-74


  • Aitman TJ, Boone C, Churchill GA, Hengartner MO, Mackay TFC, Stemple DL
    The future of model organisms in human disease research
    Nat Rev Genet. 2011 Jul 18;12(8):575-82. doi: 10.1038/nrg3047
  • Aylor DL, Valdar W, Foulds-Mathes W, Buus RJ, Verdugo RA, Baric RS, Ferris MT, Frelinger JA, Heise M, Frieman MB, Gralinski LE, Bell TA, Didion JD, Hua K, Nehrenberg DL, Powell CL, Steigerwalt J, Xie Y, Kelada SN, Collins FS, Yang IV, Schwartz DA, Branstetter LA, Chesler EJ, Miller DR, Spence J, Liu EY, McMillan L, Sarkar A, Wang J, Wang W, Zhang Q, Broman KW, Korstanje R, Durrant C, Mott R, Iraqi FA, Pomp D, Threadgill D, Pardo-Manuel de Villena F, Churchill GA
    Genetic analysis of complex traits in the emerging collaborative cross
    Genome Res. 2011 Aug;21(8):1223-38
  • Berndt A, Leme AS, Williams LK, Von Smith R, Savage HS, Stearns T, Tsaih SW, Shapiro SD, Peters LL, Paigen BJ, Svenson KL
    Comparison of unrestrained plethysmography and forced oscillation for identifying genetic variability of airway responsiveness in inbred mice
    Physiol Genomics. 2011 Jan 11; 43: 1-11
  • Hageman RS, Leduc MS, Korstanje R, Paigen B, Churchill GA
    A Bayesian Framework for Inference of the Genotype-Phenotype Map for Segregating Populations
    Genetics. 2011 Apr;187(4):1163-70
  • Hageman RS, Leduc MS, Caputo CR, Tsaih SW, Churchill GA, Korstanje R
    Uncovering Genes and Regulatory Pathways Related to Urinary Albumin Excretion
    J Am Soc Nephrol. 2011 Jan;22(1):73-81
  • Leduc MS, Hageman RS, Verdugo RA, Tsaih SW, Walsh K, Churchill GA, Paigen B
    Integration of QTL and bioinformatic tools to identify candidate genes for triglycerides in mice
    J Lipid Res. 2011 Sep;52(9):1672-82
  • Mathes WF, Aylor DL, Miller DR, Churchill GA, Chesler EJ, Pardo Manuel de Villena F, Threadgill DW, Pomp D
    Architecture of energy balance traits in emerging lines of the Collaborative Cross
    Am J Physiol Endocrinol Metab. 2011 Jun;300(6):E1124-34
  • Philip VM, Sokoloff G, Ackert-Bicknell CL, Striz M, Branstetter L, Beckmann MA, Spence JS, Jackson BL, Galloway LD, Barker P, Wymore AM, Hunsicker PR, Durtschi DC, Shaw GS, Shinpock S, Manly KF, Miller DR, Donohue KD, Culiat CT, Churchill GA, Lariviere WR, Palmer AA, O'Hara BF, Voy BH, Chesler EJ
    Genetic analysis in the Collaborative Cross breeding population
    Genome Res. 2011 Aug;21(8):1223-38
  • Threadgill DW, Pardo-Manuel de Villena F, Miller DR, Miller DR, Churchill GA
    The collaborative cross: a recombinant inbred mouse population for the systems genetic era
    ILAR J. 2011 Feb 8;52(1):24-31
  • Vedell PT, Svenson KL, Churchill GA
    Stochastic Variation of Transcript Abundance in C57BL/6J mice
    BMC Genomics. 2011 Mar 30;12(1):167
  • Yang H, Wang JR, Didion JP, Buus RJ, Bell TA, Welsh CE, Bonhomme F, Yu AH, Nachman MW, Piálek J, Tucker P, Boursot P, McMillan L, Churchill GA, Pardo-Manuel de Villena F
    Subspecific origin and haplotype diversity in the laboratory mouse
    Nat Genet. 2011 May 29;43(7):648-55


  • Ackert-Bicknell CL, Karasik D, Li Q, Smith RV, Hsu YH, Churchill GA, Paigen BJ, Tsaih SW
    Mouse BMD quantitative trait loci show improved concordance with human genome wide association loci when recalculated on a new, common mouse genetic map
    J Bone Miner Res. 2010 Aug;25(8):1808-20
  • Hageman RS, Wagener A, Hantschel C, Svenson KL, Churchill GA, Brockmann GA
    High fat diet leads to tissue specific changes reflecting risk factors for diseases in DBA/2J mice
    Physiol Genomics. 2010 Jun;42(1):55-66
  • Hutchins LN, Ding Y, Szatkiewicz JP, Smith RV, Yang H, de Villena FP, Churchill GA, Graber JH
    CGDSNPdb: a database resource for error-checked and imputed mouse SNPs
    Database (Oxford). 2010 Jul 6;2010:baq008. Print 2010
  • Leduc MS, Hageman RS, Meng Q, Verdugo RA, Tsaih SW, Churchill GA, Paigen B, Yuan R
    Identification of genetic determinants of IGF-1 levels and longevity among mouse inbred strains
    Aging Cell. 2010 Oct;9(5):823-36. doi: 10.1111/j.1474-9726.2010.00612.x
  • Li R, Churchill GA
    Epistasis contributes to the genetic buffering of plasma HDL cholesterol in mice
    Physiol Genomics. 2010 Nov 29;42A(4):228-34
  • Li Y, Tesson BM, Churchill GA, Jansen RC
    Critical reasoning on causal inference in genome-wide linkage and association studies
    Trends Genet. 2010 Dec;26(12):493-8. doi: 10.1016/j.tig.2010.09.002. Epub 2010 Oct 15
  • Peters LL, Shavit JA, Lambert AJ, Tsaih SW, Li Q, Su Z, Leduc MS, Paigen B, Churchill GA, Ginsburg D, Brugnara C
    Sequence variation at multiple loci influences red cell hemoglobin concentration
    Blood. 2010 Dec 16;116(25):e139-49
  • Tsaih SW, Pezzolesi MG, Yuan R, Warram JH, Krolewski AS, Korstanje R
    Genetic analysis of albuminuria in aging mice and concordance with loci for human diabetic nephropathy found in a genome-wide association scan
    Kidney Int. 2010 Feb;77(3):201-10
  • Woo YH, Walker M, Churchill GA
    Coordinated expression domains in Mammalian genomes
    PLoS One. 2010 Aug 18;5(8). pii: e12158


  • Ackert-Bicknell CL, Shockley KR, Horton LG, Lecka-Czernik B, Churchill GA, Rosen CJ
    Strain-specific effects of rosiglitazone on bone mass, body composition, and serum insulin-like growth factor-I
    Endocrinology. 2009 Mar;150(3):1330-40
  • Brockmann GA, Tsaih SW, Neuschl C, Churchill GA, Li R
    Genetic factors contributing to obesity and body weight can act through mechanisms affecting muscle weight, fat weight, or both
    Physiol Genomics 2009 Jan 8;36(2):114-126
  • Cox A, Ackert-Bicknell C, Dumont BL, Ding Y, Tzenova Bell J, Brockmann GA, Wergedal JE, Bult C, Paigen B, Flint J, Tsaih SW, Churchill GA, Broman KW
    A New Standard Genetic Map for the Mouse
    Genetics. 2009 Aug;182(4):1335-44
  • Feng M, Deerhake ME, Keating R, Thaisz J, Xu L, Tsaih SW, Smith R, Ishige T, Sugiyama F, Churchill GA, Dipetrillo K
    Genetic Analysis of Blood Pressure in 8 Mouse Intercross Populations
    Hypertension. 2009 Oct;54(4):802-9
  • Leiter EH, Reifsnyder PC, Wallace R, Li R, King B, Churchill GC
    NOD x 129.H2g7 Backcross Delineates 129S1/SvImJ-Derived Genomic Regions Modulating Type 1 Diabetes (T1D) Development In Mice
    Diabetes. 2009 Jul;58(7):1700-3
  • Llamas B, Verdugo RA, Churchill GA, Deschepper CF
    Chromosome Y variants from different inbred mouse strains are linked to differences in the morphologic and molecular responses of cardiac cells to postpubertal testosterone
    BMC Genomics. 2009 Apr 7;10:150
  • Mackiewicz M, Zimmerman JE, Shockley KR, Churchill GA, Pack AI
    What are microarrays teaching us about sleep?
    Trends Mol Med. 2009 Feb;15(2):79-87
  • Rodriguez MR, Lundgren A, Sabastian P, Li Q, Churchill G, Brown MG
    A Cmv2 QTL on chromosome X affects MCMV resistance in New Zealand male mice
    Mamm Genome. 2009 Jul;20(7):414-23
  • Shockley KR, Lazarenko OP, Czernik PJ, Rosen CJ, Churchill GA, Lecka-Czernik B
    PPARgamma2 nuclear receptor controls multiple regulatory pathways of osteoblast differentiation from marrow mesenchymal stem cells
    J Cell Biochem. 2009 Feb 1;106(2):232-46
  • Shockley KR, Witmer D, Burgess-Herbert SL, Paigen B, Churchill GA
    The Effects of Atherogenic Diet on Hepatic Gene Expression Across Mouse Strains
    Physiol Genomics. 2009 Nov 6;39(3):172-82
  • Smith R, McGann D, Gotwals R, Symonds R, Hageman R, Vedell P, Churchill G
    Independent Studies in Computational Biology
    NCSSSMST Journal. Fall 2009:10-16
  • Smith R, Sheppard K, Dipetrillo K, Churchill G
    Quantitative Trait Locus Analysis Using J/qtl
    Methods Mol Biol. 2009;573:175-88
  • Solberg Woods LC, Ahmadiyeh N, Baum A, Shimomura K, Li Q, Steiner DF, Turek FW, Takahashi JS, Churchill GA, Redei EE
    Identification of genetic loci involved in diabetes using a rat model of depression
    Mamm Genome. 2009 Aug;20(8):486-97
  • Su Z, Wang X, Tsaih SW, Zhang A, Cox A, Sheehan S, Paigen B
    Genetic basis of HDL variation in 129/SvImJ and C57BL/6J mice: importance of testing candidate genes in targeted mutant mice
    J Lipid Res. 2009 Jan;50(1):116-25
  • Su Z, Ishimori N, Chen Y, Leiter EH, Churchill GA, Paigen B, Stylianou IM
    Four additional mouse crosses improve the lipid QTL landscape and identify Lipg as a QTL gene
    J Lipid Res. 2009 Oct;50(10):2083-94
  • Tsaih SW, Korstanje R
    Haplotype association mapping in mice
    Methods Mol Biol. 2009;573:213-22
  • Verdugo RA, Deschepper CF, Muñoz G, Pomp D, Churchill GA
    Importance of randomization in microarray experimental designs with Illumina platforms
    Nucleic Acids Res. 2009 Sep;37(17):5610-8
  • Xing S, Tsaih SW, Yuan R, Svenson KL, Jorgenson LM, So M, Paigen BJ, Korstanje R
    Genetic influence on electrocardiogram time intervals and heart rate in aging mice
    Am J Physiol Heart Circ Physiol. 2009 Jun;296(6):H1907-13
  • Yang H, Ding Y, Hutchins LN, Szatkiewicz J, Bell TA, Paigen BJ, Graber JH, Pardo-Manuel de Villena F, Churchill GA
    A customized and versatile high-density genotyping array for the mouse
    Nat Methods. 2009 Sep;6(9):663-6
  • Yuan R, Tsaih SW, Petkova SB, Marin de Evsikova C, Xing S, Marion MA, Bogue MA, Mills KD, Peters LL, Bult CJ, Rosen CJ, Sundberg JP, Harrison DE, Churchill GA, Paigen B
    Aging in inbred strains of mice: study design and interim report on median lifespans and circulating IGF1 levels
    Aging Cell. 2009 June; 8(3):277-87


  • Ackert-Bicknell CL, Demissie S, Marin de Evsikova C, Hsu YH, DeMambro VE, Karasik D, Cupples LA, Ordovas JM, Tucker KL, Cho K, Canalis E, Paigen B, Churchill GA, Forejt J, Beamer WG, Ferrari S, Bouxsein ML, Kiel DP, Rosen CJ
    PPARG by dietary fat interaction influences bone mass in mice and humans
    J Bone Miner Res. 2008 Sep; 23(9):1398-408
  • Bailey JS, Grabowski-Boase L, Steffy BM, Wiltshire T, Churchill GA, Tarantino LM
    Identification of QTL for locomotor activation and anxiety using closely-related inbred strains
    Genes Brain Behav. 2008 Oct;7(7):761-9
  • Burgess-Herbert SL, Cox A, Tsaih SW, Paigen B
    Practical Applications of the Bioinformatics Toolbox for Narrowing Quantitative Trait Loci
    Genetics. 2008 Dec;180(4):2227-35
  • Chen YG, Scheuplein F, Osborne MA, Tsaih SW, Chapman HD, Serreze DV
    Idd9/11 genetic locus regulates diabetogenic activity of CD4 T-cells in nonobese diabetic (NOD) mice
    Diabetes. 2008 Dec;57(12):3273-80
  • Chesler EJ, Miller DR, Branstetter LR, Galloway LD, Jackson BL, Philip VM, Voy BH, Culiat CT, Threadgill DW, Williams RW, Churchill GA, Johnson DK, Manly KF
    The Collaborative Cross at Oak Ridge National Laboratory: developing a powerful resource for systems genetics
    Mamm Genome. 2008 Jun;19(6):382-9
  • Churchill GA, Doerge RW
    Naive application of permutation testing leads to inflated type I error rates
    Genetics. 2008 Jan;178(1):609-10
  • Doorenbos C, Tsaih SW, Sheehan S, Ishimori N, Navis G, Churchill G, Dipetrillo K, Korstanje R
    Quantitative trait loci for urinary albumin in crosses between C57BL/6J and A/J inbred mice in the presence and absence of Apoe
    Genetics. 2008 May;179(1):693-9
  • Iraqi FA, Churchill G, Mott R
    The Collaborative Cross, developing a resource for mammalian systems genetics: a status report of the Wellcome Trust cohort
    Mamm Genome. 2008 Jun;19(6):379-81
  • Ishimori N, Stylianou IM, Korstanje R, Marion MA, Li R, Donahue LR, Rosen CJ, Beamer WG, Paigen B, Churchill GA
    Quantitative trait loci for BMD in an SM/J by NZB/BlNJ intercross population and identification of Trps1 as a probable candidate gene
    J Bone Miner Res. 2008 Sep;23(9):1529-37
  • Kumar KG, Byerley LO, Volaufova J, Drucker DJ, Churchill GA, Li R, York B, Zuberi A, Richards BK
    Genetic variation in Glp1r expression influences the rate of gastric emptying in mice
    Am J Physiol Regul Integr Comp Physiol. 2008 Feb;294(2):R362-71
  • Li R, Svenson KL, Donahue LR, Peters LL, Churchill GA
    Relationships of dietary fat, body composition, and bone mineral density in inbred mouse strain panels
    Physiol Genomics. 2008 Mar 14;33(1):26-32
  • Mrug M, Zhou J, Woo Y, Cui X, Szalai AJ, Novak J, Churchill GA, Guay-Woodford LM
    Overexpression of innate immune response genes in a model of recessive polycystic kidney disease
    Kidney Int. 2008 Jan;73(1):63-76
  • Petkova SB, Yuan R, Tsaih SW, Schott W, Roopenian DC, Paigen B
    Genetic influence on immune phenotype revealed strain-specific variations in peripheral blood lineages
    Physiol Genomics. 2008 Aug 15;34(3):304-14
  • Stylianou IM, Affourtit JP, Shockley KR, Wilpan RY, Abdi FA, Bhardwaj S, Rollins J, Churchill GA, Paigen B
    Applying gene expression, proteomics and single-nucleotide polymorphism analysis for complex trait gene identification
    Genetics. 2008 Mar;178(3):1795-805
  • Su Z, Tsaih SW, Szatkiewicz J, Shen Y, Paigen B
    Candidate genes for plasma triglyceride, FFA, and glucose revealed from an intercross between inbred mouse strains NZB/B1NJ and NZW/LacJ
    J Lipid Res. 2008 Jul;49(7):1500-10
  • Su Z, Korstanje R, Tsaih SW, Paigen B
    Candidate genes for obesity revealed from a C57BL/6J x 129S1/SvImJ intercross
    Int J Obes (Lond). 2008 Jul;32(7):1180-9
  • Szatkiewicz JP, Beane GL, Ding Y, Hutchins L, Pardo-Manuel de Villena F, Churchill GA
    An imputed genotype resource for the laboratory mouse
    Mamm Genome. 2008 Mar;19(3):199-208
  • Yang H, Harrington CA, Vartanian K, Coldren CD, Hall R, Churchill GA
    Randomization in laboratory procedure is key to obtaining reproducible microarray results
    PLoS ONE. 2008;3(11):e3724


  • Churchill GA
    Recombinant inbred strain panels: a tool for systems genetics
    Physiol Genomics. 2007 Oct 22;31(2):174-5
  • Davidson CE, Li Q, Churchill GA, Osborne LR, McDermid HE
    Modifier locus for exencephaly in Cecr2 mutant mice is syntenic to the 10q25.3 region associated with neural tube defects in humans
    Physiol Genomics. 2007 Oct 22;31(2):244-51
  • Herschkowitz JI, Simin K, Weigman VJ, Mikaelian I, Usary J, Hu Z, Rasmussen KE, Jones LP, Assefnia S, Chandrasekharan S, Backlund MG, Yin Y, Khramtsov AI, Bastein R, Quackenbush J, Glazer RI, Brown PH, Green JE, Kopelovich L, Furth PA, Palazzo JP, Olopade OI, Bernard PS, Churchill GA, Van Dyke T, Perou CM
    Identification of conserved gene expression features between murine mammary carcinoma models and human breast tumors
    Genome Biol. 2007;8(5):R76
  • Kiernan AE, Li R, Hawes NL, Churchill GA, Gridley T
    Genetic background modifies inner ear and eye phenotypes of jag1 heterozygous mice
    Genetics. 2007 Sep;177(1):307-11
  • Lecka-Czernik B, Ackert-Bicknell C, Adamo ML, Marmolejos V, Churchill GA, Shockley KR, Reid IR, Grey A, Rosen CJ
    Activation of peroxisome proliferator-activated receptor gamma (PPARgamma) by rosiglitazone suppresses components of the insulin-like growth factor regulatory system in vitro and in vivo
    Endocrinology. 2007 Feb;148(2):903-11
  • Mackiewicz M, Shockley KR, Romer MA, Galante RJ, Zimmerman JE, Naidoo N, Baldwin DA, Jensen ST, Churchill GA, Pack AI
    Macromolecule biosynthesis: a key function of sleep
    Physiol Genomics. 2007 Nov 14;31(3):441-57
  • Nishihara E, Tsaih SW, Tsukahara C, Langley S, Sheehan S, Dipetrillo K, Kunita S, Yagami K, Churchill GA, Paigen B, Sugiyama F
    Quantitative trait loci associated with blood pressure of metabolic syndrome in the progeny of NZO/HILtJ x C3H/HeJ intercrosses
    Mamm Genome. 2007 Aug;18(8):573-83
  • Peters LL, Robledo RF, Bult CJ, Churchill GA, Paigen BJ, Svenson KL
    The mouse as a model for human biology: a resource guide for complex trait analysis
    Nat Rev Genet. 2007 Jan;8(1):58-69
  • Petkov PM, Graber JH, Churchill GA, DiPetrillo K, King BL, Paigen K
    Evidence of a large-scale functional organization of mammalian chromosomes
    PLoS Biol. 2007 May;5(5):e127; author reply e128
  • Satagopan JM, Sen S, Churchill GA
    Sequential Quantitative Trait Locus Mapping in Experimental Crosses
    Stat Appl Genet Mol Biol. 2007;6:Article12
  • Sen S, Satagopan JM, Broman KW, Churchill GA
    R/qtlDesign: inbred line cross experimental design
    Mamm Genome. 2007 Feb;18(2):87-93
  • Sheehan S, Tsaih SW, King BL, Stanton C, Churchill GA, Paigen B, DiPetrillo K
    Genetic analysis of albuminuria in a cross between C57BL/6J and DBA/2J mice
    Am J Physiol Renal Physiol 2007 Nov;293(5):F1649-56
  • Shockley KR, Rosen CJ, Churchill GA, Lecka-Czernik B
    PPARgamma2 Regulates a Molecular Signature of Marrow Mesenchymal Stem Cells
    PPAR Res. 2007;2007:81219
  • Svenson KL, Von Smith R, Magnani PA, Suetin HR, Paigen B, Naggert JK, Li R, Churchill GA, Peters LL
    Multiple trait measurements in 43 inbred mouse strains capture the phenotypic diversity characteristic of human populations
    J Appl Physiol. 2007 Jun;102(6):2369-78
  • The International Stem Cell Initiative
    Characterization of human embryonic stem cell lines by the International Stem Cell Initiative
    Nat Biotechnol. 2007 Jul;25(7):803-16
  • Yang H, Bell TA, Churchill GA, Pardo-Manuel de Villena F
    On the subspecific origin of the laboratory mouse
    Nat Genet. 2007 Sep;39(9):1100-7
  • Yang H, Churchill G
    Estimating p-values in small microarray experiments
    Bioinformatics. 2007 Jan 1;23(1):38-43


  • Baum AE, Solberg LC, Churchill GA, Ahmadiyeh N, Takahashi JS, Redei EE
    Test- and behavior-specific genetic factors affect WKY hypoactivity in tests of emotionality
    Behav Brain Res. 2006 May 15;169(2):220-30
  • Broman KW, Sen S, Owens SE, Manichaikul A, Southard-Smith EM, Churchill GA
    The X chromosome in quantitative trait locus mapping
    Genetics. 2006 Dec;174(4):2151-8
  • Churchill GA
    The genetics of gene expression
    Mamm Genome. 2006 Jun;17(6):465
  • Cui X, Affourtit J, Shockley KR, Woo Y, Churchill GA
    Inheritance patterns of transcript levels in f1 hybrid mice
    Genetics. 2006 Oct;174(2):627-37
  • Graber JH, Churchill GA, Dipetrillo KJ, King BL, Petkov PM, Paigen K
    Patterns and mechanisms of genome organization in the mouse
    J Exp Zoolog A Comp Exp Biol. 2006 Sep 1;305(9):683-8
  • Ishimori N, Li R, Walsh KA, Korstanje R, Rollins JA, Petkov P, Pletcher MT, Wiltshire T, Donahue LR, Rosen CJ, Beamer WG, Churchill GA, Paigen B
    Quantitative trait loci that determine BMD in C57BL/6J and 129S1/SvImJ inbred mice
    J Bone Miner Res. 2006 Jan;21(1):105-12
  • Li R, Tsaih SW, Shockley K, Stylianou IM, Wergedal J, Paigen B, Churchill GA
    Structural model analysis of multiple quantitative traits
    PLoS Genet. 2006 Jul;2(7):e114
  • Peters LL, Lambert AJ, Zhang W, Churchill GA, Brugnara C, Platt OS
    Quantitative trait loci for baseline erythroid traits
    Mamm Genome. 2006 Apr;17(4):298-309
  • Reifsnyder PC, Li R, Silveira PA, Churchill G, Serreze DV, Leiter EH
    Conditioning the genome identifies additional diabetes resistance loci in Type 1 diabetes-resistant NOR/Lt mice
    Genes Immun. 2006 Mar;7(2):184
  • Shockley KR, Churchill GA
    Gene expression analysis of mouse chromosome substitution strains
    Mamm Genome. 2006 Jun;17(6):598-614
  • Solberg LC, Baum AE, Ahmadiyeh N, Shimomura K, Li R, Turek FW, Takahashi JS, Churchill GA, Redei EE
    Genetic analysis of the stress-responsive adrenocortical axis
    Physiol Genomics. 2006 Nov 27;27(3):362-9
  • Stylianou IM, Tsaih SW, Dipetrillo K, Ishimori N, Li R, Paigen B, Churchill G
    Complex genetic architecture revealed by analysis of high-density lipoprotein cholesterol in chromosome substitution strains and f2 crosses
    Genetics. 2006 Oct;174(2):999-1007
  • Stylianou IM, Korstanje R, Li R, Sheehan S, Paigen B, Churchill GA
    Quantitative trait locus analysis for obesity reveals multiple networks of interacting loci
    Mamm Genome. 2006 Jan;17(1):22-36
  • Wergedal JE, Ackert-Bicknell CL, Tsaih S-W, Sheng M H-C, Li R, Mohan S, Beamer WG, Churchill GA, Baylink DJ
    Femur mechanical properties in the F2 Progeny of an NZB/B1NJ x RF/J cross are regulated predominantly by genetic loci that regulate bone geometry
    J Bone Miner Res. 2006 Aug;21(8):1256-66
  • Wittenburg H, Lyons MA, Li R, Kurtz U, Wang X, Mossner J, Churchill GA, Carey MC, Paigen B
    QTL mapping for genetic determinants of lipoprotein cholesterol levels in combined crosses of inbred mouse strains
    J Lipid Res. 2006 Aug;47(8):1780-90
  • Zimmerman JE, Rizzo W, Shockley KR, Raizen DM, Naidoo N, Mackiewicz M, Churchill GA, Pack AI
    Multiple mechanisms limit the duration of wakefulness in Drosophila brain
    Physiol Genomics. 2006 Nov 27;27(3):337-50


  • Ackerman KG, Huang H, Grasemann H, Puma C, Singer JB, Hill AE, Lander E, Nadeau JH, Churchill GA, Drazen JM, Beier DR
    Interacting genetic loci cause airway hyperresponsiveness
    Physiol Genomics. 2005 Mar 21;21(1):105-11
  • Ahmadiyeh N, Churchill GA, Solberg LC, Baum AE, Shimomura K, Takahashi JS, Redei EE
    Lineage is an epigenetic modifier of QTL influencing behavioral coping with stress
    Behav Genet. 2005 Mar;35(2):189-98
  • Baum AE, Solberg LC, Kopp P, Ahmadiyeh N, Churchill G, Takahashi JS, Jameson JL, Redei EE
    Quantitative trait loci associated with elevated thyroid-stimulating hormone in the Wistar-Kyoto rat
    Endocrinology. 2005 Feb;146(2):870-8
  • Beamer WG, Shultz KL, Donahue LR, Churchill GA, Sen S, Wergedal JR, Baylink DJ, Rosen CJ
    Quantitative trait loci for femoral and lumbar vertebral bone mineral density in C57BL/6J and C3h/HeJ inbred strains of mice. (2001).
    J Bone Miner Res. 2005 Sep;20(9):1701-12; discussion 1700
  • Bouma GJ, Albrecht KH, Washburn LL, Recknagel AK, Churchill GA, Eicher EM
    Gonadal sex reversal in mutant Dax1 XY mice: a failure to upregulate Sox9 in pre-Sertoli cells
    Development. 2005 Jul;132(13):3045-54
  • Cui X, Hwang JT, Qiu J, Blades NJ, Churchill GA
    Improved statistical tests for differential gene expression by shrinking variance components estimates
    Biostatistics. 2005 Jan;6(1):59-75
  • Dorward AM, Shultz KL, Horton LG, Li R, Churchill GA, Beamer WG
    Distal Chr 4 harbors a genetic locus (Gct1) fundamental for spontaneous ovarian granulosa cell tumorigenesis in a mouse model
    Cancer Res. 2005 Feb 15;65(4):1259-64
  • Li R, Lyons MA, Wittenburg H, Paigen B, Churchill GA
    Combining data from multiple inbred line crosses improves the power and resolution of quantitative trait loci mapping
    Genetics. 2005 Mar;169(3):1699-709
  • Lyons MA, Korstanje R, Li R, Sheehan SM, Walsh KA, Rollins JA, Carey MC, Paigen B, Churchill GA
    Single and interacting QTLs for cholesterol gallstones revealed in an intercross between mouse strains NZB and SM
    Mamm Genome. 2005 Mar;16(3):152-63
  • Mrug M, Li R, Cui X, Schoeb TR, Churchill GA, Guay-Woodford LM
    Kinesin family member 12 is a candidate polycystic kidney disease modifier in the cpk mouse
    J Am Soc Nephrol. 2005 Apr;16(4):905-16
  • Peters LL, Zhang W, Lambert AJ, Brugnara C, Churchill GA, Platt OS
    Quantitative trait loci for baseline white blood cell count, platelet count, and mean platelet volume
    Mamm Genome. 2005 Oct;16(10):749-63
  • Petkov PM, Graber JH, Churchill GA, DiPetrillo K, King BL, Paigen K
    Evidence of a large-scale functional organization of mammalian chromosomes
    PLoS Genet. 2005 Sep;1(3):e33
  • Reifsnyder PC, Li R, Silveira PA, Churchill G, Serreze DV, Leiter EH
    Conditioning the genome identifies additional diabetes resistance loci in Type I diabetes resistant NOR/Lt mice
    Genes Immun. 2005 Sep;6(6):528-38
  • Sen S, Satagopan JM, Churchill GA
    Quantitative trait locus study design from an information perspective
    Genetics. 2005 May;170(1):447-64
  • Tsaih SW, Lu L, Airey DC, Williams RW, Churchill GA
    Quantitative trait mapping in a diallel cross of recombinant inbred lines
    Mamm Genome. 2005 May;16(5):344-55
  • Wittenburg H, Lyons MA, Li R, Kurtz U, Mossner J, Churchill GA, Carey MC, Paigen B
    Association of a lithogenic Abcg5/Abcg8 allele on Chromosome 17 (Lith9) with cholesterol gallstone formation in PERA/EiJ mice
    Mamm Genome. 2005 Jul;16(7):495-504
  • Woo Y, Krueger W, Kaur A, Churchill G
    Experimental design for three-color and four-color gene expression microarrays
    Bioinformatics. 2005 Jun;21 Suppl 1:i459-67
  • Yi N, Yandell BS, Churchill GA, Allison DB, Eisen EJ, Pomp D
    Bayesian model selection for genome-wide epistatic quantitative trait loci analysis
    Genetics. 2005 Jul;170(3):1333-44


  • Bouxsein ML, Uchiyama T, Rosen CJ, Shultz KL, Donahue LR, Turner CH, Sen S, Churchill GA, Muller R, Beamer WG
    Mapping quantitative trait loci for vertebral trabecular bone volume fraction and microarchitecture in mice
    J Bone Miner Res. 2004 Apr;19(4):587-99
  • Churchill GA
    Using ANOVA to analyze microarray data
    Biotechniques. 2004 Aug;37(2):173-5, 177
  • Churchill GA, Airey DC, Allayee H, Angel JM, Attie AD, Beatty J, Beavis WD, Belknap JK, Bennett B, Berrettini W, Bleich A, Bogue M, Broman KW, Buck KJ, Buckler E, Burmeister M, Chesler EJ, Cheverud JM, Clapcote S, Cook MN, Cox RD, Crabbe JC, Crusio WE, Darvasi A, Deschepper CF, Doerge RW, Farber CR, Forejt J, Gaile D, Garlow SJ, Geiger H, Gershenfeld H, Gordon T, Gu J, Gu W, de Haan G, Hayes NL, Heller C, Himmelbauer H, Hitzemann R, Hunter K, Hsu HC, Iraqi FA, Ivandic B, Jacob HJ, Jansen RC, Jepsen KJ, Johnson DK, Johnson TE, Kempermann G, Kendziorski C, Kotb M, Kooy RF, Llamas B, Lammert F, Lassalle JM, Lowenstein PR, Lu L, Lusis A, Manly KF, Marcucio R, Matthews D, Medrano JF, Miller DR, Mittleman G, Mock BA, Mogil JS, Montagutelli X, Morahan G, Morris DG, Mott R, Nadeau JH, Nagase H, Nowakowski RS, O'Hara BF, Osadchuk AV, Page GP, Paigen B, Paigen K, Palmer AA, Pan HJ, Peltonen-Palotie L, Peirce J, Pomp D, Pravenec M, Prows DR, Qi Z, Reeves RH, Roder J, Rosen GD, Schadt EE, Schalkwyk LC, Seltzer Z, Shimomura K, Shou S, Sillanpää MJ, Siracusa LD, Snoeck HW, Spearow JL, Svenson K, Tarantino LM, Threadgill D, Toth LA, Valdar W, de Villena FP, Warden C, Whatley S, Williams RW, Wiltshire T, Yi N, Zhang D, Zhang M, Zou F; Complex Trait Consortium
    The Collaborative Cross, a community resource for the genetic analysis of complex traits
    Nat Genet. 2004 Nov;36(11):1133-7
  • Complex Trait Consortium
    The Collaborative Cross, a community resource for the genetic analysis of complex traits
    Nat Genet. 2004 Nov;36(11):1133-7
  • DiPetrillo K, Tsaih SW, Sheehan S, Johns C, Kelmenson P, Gavras H, Churchill GA, Paigen B
    Genetic analysis of blood pressure in C3H/HeJ and SWR/J mice
    Physiol Genomics. 2004 Apr 13;17(2):215-20
  • Grubb SC, Churchill GA, Bogue MA
    A collaborative database of inbred mouse strain characteristics
    Bioinformatics. 2004 Nov 1;20(16):2857-9
  • Ishimori N, Li R, Kelmenson PM, Korstanje R, Walsh KA, Churchill GA, Forsman-Semb K, Paigen B
    Quantitative trait loci that determine plasma lipids and obesity in C57BL/6J and 129S1/SvImJ inbred mice
    J Lipid Res 2004 Sep;45(9):1624-1632
  • Ishimori N, Li R, Kelmenson PM, Korstanje R, Walsh KA, Churchill GA, Forsman-Semb K, Paigen B
    Quantitative trait loci analysis for plasma HDL-cholesterol concentrations and atherosclerosis susceptibility between inbred mouse strains C57BL/6J and 129S1/SvIm
    J. Arterioscler Thromb Vasc Biol 2004 Jan;24(1):161-6
  • Jin C, Lan H, Attie AD, Churchill GA, Bulutuglo D, Yandell BS
    Selective phenotyping for increased efficiency in genetic mapping studies
    Genetics. 2004 Dec;168(4):2285-93
  • Korstanje R, Eriksson P, Samnegard A, Olsson PG, Forsman-Semb K, Sen S, Churchill GA, Rollins J, Harris S, Hamsten A, Paigen B
    Locating Ath8, a locus for murine atherosclerosis susceptibility and testing several of its candidate genes in mice and humans
    Atherosclerosis. 2004 Dec;177(2):443-50
  • Korstanje R, Albers JJ, Wolfbauer G, Li R, Tu AY, Churchill GA, Paigen BJ
    Quantitative trait locus mapping of genes that regulate phospholipid transfer activity in SM/J and NZB/BlNJ inbred mice
    Arterioscler Thromb Vasc Biol. 2004 Jan;24(1):155-60
  • Korstanje R, Li R, Howard T, Kelmenson P, Marshall J, Paigen B, Churchill G
    Influence of sex and diet on quantitative trait loci for HDL cholesterol levels in an SM/J by NZB/BlNJ intercross population
    J Lipid Res. 2004 May;45(5):881-8
  • Lobenhofer EK, Cui X, Bennett L, Cable PL, Merrick BA, Churchill GA, Afshari CA
    Exploration of low-dose estrogen effects: identification of No Observed Transcriptional Effect Level (NOTEL)
    Toxicol Pathol. 2004 Jul-Aug;32(4):482-92
  • Lyons MA, Wittenburg H, Li R, Walsh KA, Korstanje R, Churchill GA, Carey MC, Paigen B
    Quantitative trait loci that determine lipoprotein cholesterol levels in an intercross of 129S1/SvImJ and CAST/Ei inbred mice
    Physiol Genomics. 2004 Mar 12;17(1):60-8
  • Lyons MA, Korstanje R, Li R, Walsh KA, Churchill GA, Carey MC, Paigen B
    Genetic contributors to lipoprotein cholesterol levels in an intercross of 129S1/SvImJ and RIIIS/J inbred mice
    Physiol Genomics. 2004 Apr 13;17(2):114-21
  • Mikaelian I, Blades N, Churchill GA, Fancher K, Knowles BB, Eppig JT, Sundberg JP
    Proteotypic classification of spontaneous and transgenic mammary neoplasms
    Breast Cancer Res. 2004;6(6):R668-79
  • Peters LL, Swearingen RA, Andersen SG, Gwynn B, Lambert AJ, Li R, Lux SE, Churchill GA
    Identification of quantitative trait loci that modify the severity of hereditary spherocytosis in wan, a new mouse model of band-3 deficiency
    Blood. 2004 Apr 15;103(8):3233-40
  • Solberg LC, Baum AE, Ahmadiyeh N, Shimomura K, Li R, Turek FW, Churchill GA, Takahashi JS, Redei EE
    Sex- and lineage-specific inheritance of depression-like behavior in the rat
    Mamm Genome. 2004 Aug;15(8):648-62
  • Woo Y, Affourtit J, Daigle S, Viale A, Johnson K, Naggert J, Churchill G
    A comparison of cDNA, oligonucleotide, and Affymetrix GeneChip gene expression microarray platforms
    J Biomol Tech 2004 Dec;15:276-284


  • Ahmadiyeh N, Churchill GA, Shimomura K, Solberg LC, Takahashi JS, Redei EE
    X-linked and lineage-dependent inheritance of coping responses to stress
    Mamm Genome. 2003 Nov;14(11):748-57
  • Brich J, Shie FS, Howell BW, Li R, Tus K, Wakeland EK, Jin LW, Mumby M, Churchill G, Herz J, Cooper JA
    Genetic modulation of tau phosphorylation in the mouse
    J Neurosci. 2003 Jan 1;23(1):187-92
  • Broman KW, Wu H, Sen S, Churchill GA
    R/qtl: QTL mapping in experimental crosses
    Bioinformatics. 2003 May 1;19(7):889-90
  • Complex Trait Consortium
    The nature and identification of quantitative trait loci: a community's view
    Nat Rev Genet. 2003 Nov;4(11):911-6
  • Cui XQ, Kerr MK, Churchill GA
    Transformations for cDNA microarray data
    Stat Appl Genet Mol Biol. 2003;2:Article4
  • Cui XQ, Churchill GA
    Statistical tests for differential expression in cDNA microarray experiments
    Genome Biol. 2003;4(4):210
  • Cui XQ, Churchill GA
    How many mice and how many arrays? Replication in mouse cDNA microarray experiments
    In: Methods of Microarray Data Analysis III, Kimberly F. Johnson and Simon M. Lin (eds). Kluwer Academic Publishers, Norwell, MA. 139-154.
  • Lyons MA, Wittenburg H, Li R, Walsh KA, Leonard MR, Korstanje R, Churchill GA, Carey MC, Paigen B
    Lith6: a new QTL for cholesterol gallstones from an intercross of CAST/Ei and DBA/2J inbred mouse strains
    J Lipid Res. 2003 Sep;44(9):1763-71
  • Lyons MA, Wittenburg H, Li R, Walsh KA, Leonard MR, Churchill GA, Carey MC, Paigen B
    New quantitative trait loci that contribute to cholesterol gallstone formation detected in an intercross of CAST/Ei and 129S1/SvImJ inbred mice
    Physiol Genomics. 2003 Aug 15;14(3):225-39
  • Lyons MA, Wittenburg H, Li R, Walsh KA, Churchill GA, Carey MC, Paigen B
    Quantitative trait loci that determine lipoprotein cholesterol levels in DBA/2J and CAST/Ei inbred mice
    J Lipid Res. 2003 May;44(5):953-67
  • Mathews CE, Graser RT, Bagley RJ, Caldwell JW, Li R, Churchill GA, Serreze DV, Leiter EH
    Genetic analysis of resistance to Type-1 Diabetes in ALR/Lt mice, a NOD-related strain with defenses against autoimmune-mediated diabetogenic stress
    Immunogenetics. 2003 Oct;55(7):491-6
  • Nadeau JH, Burrage LC, Restivo J, Pao YH, Churchill G, Hoit BD
    Pleiotropy, homeostasis, and functional networks based on assays of cardiovascular traits in genetically randomized populations
    Genome Res. 2003 Sep;13(9):2082-91
  • Sundberg JP, Boggess D, Silva KA, McElwee KJ, King LE, Li R, Churchill G, Cox GA
    Major locus on mouse chromosome 17 and minor locus on chromosome 9 are linked with alopecia areata in C3H/HeJ mice
    J Invest Dermatol. 2003 May;120(5):771-5
  • Wang X, Le Roy I, Nicodeme E, Li R, Wagner R, Petros C, Churchill GA, Harris S, Darvasi A, Kirilovsky J, Roubertoux PL, Paigen B
    Using advanced intercross lines for high-resolution mapping of HDL cholesterol quantitative trait loci
    Genome Res. 2003 Jul;13(7):1654-64
  • Wittenburg H, Lyons MA, Li R, Churchill GA, Carey MC, Paigen B
    FXR and ABCG5/ABCG8 as determinants of cholesterol gallstone formation from quantitative trait locus mapping in mice
    Gastroenterology. 2003 Sep;125(3):868-81
  • Wu H, Kerr MK, Cui XQ, Churchill GA
    MAANOVA: A software package for the analysis of spotted cDNA microarray experiments in the analysis of gene expression data: an overview of methods and software
    Parmgiani G, Garret ES, Irizarry RA, Zeger SL, (eds), Springer, NY.


  • Bouxsein ML, Rosen CJ, Turner CH, Ackert CL, Shultz KL, Donahue LR, Churchill G, Adamo ML, Powell DR, Turner RT, Muller R, Beamer WG
    Generation of a new congenic mouse strain to test the relationships among serum insulin-like growth factor I, bone mineral density, and skeletal morphology in vivo
    J Bone Miner Res. 2002 Apr;17(4):570-9
  • Broman KW, Rowe LB, Churchill GA, Paigen K
    Crossover interference in the mouse
    Genetics. 2002 Mar;160(3):1123-31
  • Churchill GA
    Fundamentals of experimental design for cDNA microarrays
    Nat Genet. 2002 Dec;32 Suppl:490-5
  • Kerr MK, Afsharie CA, Bennett L, Bushel P, Martinez J, Walker N, Churchill GA
    Statistical analysis of a gene expression microarray experiment with replication
    Statistica Sinica 2002;12:203-218
  • Kerr MK, Leiter EH, Picard L, Churchill GA
    Sources of Variation in Microarray Experiments
    In: Computational and Statistical Approaches to Genomics, Wei Zhang and Ilya Shmulevich (eds). Kluwer Academic Publishers 41-51.
  • Mahler M, Most C, Schmidtke S, Sundberg JP, Li R, Hedrich HJ, Churchill GA
    Genetics of colitis susceptibility in IL-10-deficient mice: backcross versus F2 results contrasted by principal component analysis
    Genomics. 2002 Sep;80(3):274-82
  • Oleksiak MF, Churchill GA, Crawford DL
    Variation in gene expression within and among natural populations
    Nat Genet. 2002 Oct;32(2):261-6
  • Pitman WA, Korstanje R, Churchill GA, Nicodeme E, Albers JJ, Cheung MC, Staton MA, Sampson SS, Harris S, Paigen B
    Quantitative trait locus mapping of genes that regulate HDL cholesterol in SM/J and NZB/B1NJ inbred mice
    Physiol Genomics. 2002;9(2):93-102
  • Smith Richards BK, Belton BN, Poole AC, Mancuso JJ, Churchill GA, Li R, Volaufova J, Zuberi A, York B
    QTL analysis of self-selected macronutrient diet intake: fat, carbohydrate, and total kilocalories
    Physiol Genomics. 2002 Dec 3;11(3):205-17
  • Sugiyama F, Churchill GA, Li R, Libby LJ, Carver T, Yagami K, John SW, Paigen B
    QTL associated with blood pressure, heart rate, and heart weight in CBA/CaJ and BALB/cJ mice
    Physiol Genomics. 2002 Jul 12;10(1):5-12
  • Wittenburg H, Lammert F, Wang DQ, Churchill GA, Li R, Bouchard G, Carey MC, Paigen B
    Interacting QTLs for cholesterol gallstones and gallbladder mucin in AKR and SWR strains of mice
    Physiol Genomics. 2002 Feb 11;8(1):67-77


  • Beamer WG, Shultz KL, Donahue LR, Churchill GA, Sen S, Wergedal JR, Baylink DJ, Rosen CJ
    Quantitative trait loci for femoral and lumbar vertebral bone mineral density in C57BL/6J and C3H/HeJ inbred strains of mice
    J Bone Miner Res. 2001 Jul;16(7):1195-206
  • Churchill GA
    In: Encyclopedia of Genetics. Academic Press, New York
  • Churchill GA
    Inferring ancestral character states
    In: Limits to Knowledge in Evolutionary Genetics, Clegg M (ed). Plenum Press
  • Churchill GA, Oliver B
    Sex, flies and microarrays
    Nat Genet. 2001 Dec;29(4):355-6
  • Farmer MA, Sundberg JP, Bristol IJ, Churchill GA, Li R, Elson CO, Leiter EH
    A major quantitative trait locus on chromosome 3 controls colitis severity in IL-10-deficient mice
    Proc Natl Acad Sci U S A 2001 Nov 20;98:13820-13825
  • Kerr MK, Churchill GA
    Statistical design and the analysis of gene expression microarray data
    Genet Res. 2001 Apr;77(2):123-8
  • Kerr MK, Churchill GA
    Bootstrapping cluster analysis: assessing the reliability of conclusions from microarray experiments
    Proc Natl Acad Sci U S A 2001 Jul 31;98:8961-8965
  • Kerr MK, Churchill GA
    Experimental design for gene expression microarrays
    Biostatistics. 2001 Jun;2(2):183-201
  • Kim JH, Sen S, Avery CS, Simpson E, Chandler P, Nishina PM, Churchill GA, Naggert JK
    Genetic analysis of a new mouse model for non-insulin-dependent diabetes
    Genomics. 2001 Jun 15;74(3):273-86
  • Reeb-Whitaker CK, Paigen B, Beamer WG, Bronson RT, Churchill GA, Schweitzer IB, Myers DD
    The impact of reduced frequency of cage changes on the health of mice housed in ventilated cages
    Lab Anim. 2001 Jan;35(1):58-73
  • Sen S, Churchill GA
    A statistical framework for quantitative trait mapping
    Genetics. 2001 Sep;159(1):371-87
  • Shimomura K, Low-Zeddies SS, King DP, Steeves TDL, Whiteley A, Kushla J, Zemenides PD, Lin A, Vitaterna MH, Churchill GA, Takahashi JS
    Genome-wide epistatic interaction analysis reveals complex genetic determinants of circadian behavior in mice
    Genome Res. 2001 Jun;11(6):959-80
  • Sugiyama F, Churchill GA, Higgins DC, Johns C, Makaritsis KP, Gavras H, Paigen B
    Concordance of murine quantitative trait loci for salt-induced hypertension with rat and human loci
    Genomics. 2001 Jan 1;71(1):70-7


  • Churchill GA
    Complexity and uncertainty in genetics
    Sig Bio Newsletter 19:3-8
  • Clemens KE, Churchill G, Bhatt N, Richardson K, Noonan FP
    Genetic control of susceptibility to UV-induced immunosuppression by interacting quantitative trait loci
    Genes Immun. 2000;1(4):251-9
  • Guay-Woodford LM, Wright CJ, Walz G, Churchill GA
    Quantitative trait loci modulate renal cystic disease severity in the mouse bpk model
    J Am Soc Nephrol. 2000 Jul;11(7):1253-60
  • Kerr MK, Martin M, Churchill GA
    Analysis of variance for gene expression microarray data
    J Comput Biol. 2000;7(6):819-37
  • Livingstone KD, Churchill G, Jahn MK
    Linkage mapping in populations with karyotypic rearrangements
    J Hered. 2000 Nov-Dec;91(6):423-8
  • Morozov P, Sitnikova T, Churchill G, Ayala FJ, Rzhetsky A
    A new method for characterizing replacement rate variation in molecular sequences. Application of the Fourier and wavelet models to Drosophila and mammalian proteins
    Genetics. 2000 Jan;154(1):381-95
  • Reifsnyder PC, Churchill G, Leiter EH
    Maternal environment and genotype interact to establish diabesity in mice
    Genome Res 2000 Oct;10:1568-1578
  • Rosen CJ, Churchill GA, Donahue LR, Shultz KL, Burgess JK, Powell DR, Beamer WG
    Mapping quantitative trait loci for serum insulin-like growth factor-1 levels in mice
    Bone. 2000 Oct;27(4):521-8
  • Shpak M, Churchill GA
    The information content of a character under a Markov model of evolution
    Mol Phylogenet Evol. 2000 Nov;17(2):231-43


  • Beamer WG, Shultz KL, Churchill GA, Frankel WN, Baylink DJ, Rosen CJ, Donahue LR
    Quantitative trait loci for bone density in C57BL/6J and CAST/EiJ inbred mice
    Mamm Genome. 1999 Nov;10(11):1043-9
  • Blauth SL, Steffens JC, Churchill GA, Mutschler MA
    Identification of QTL's controlling acylsugar fatty acid composition in an intraspecific population of Lycopersicon pennellii (Corr.) D'Arcy
    Theor Appl Genetics 1999 99(1-2):373-381
  • Churchill GA, Lazareva B
    Bayesian restoration of a hidden Markov chain with applications to DNA sequencing
    J Comput Biol. 1999 Summer;6(2):261-77
  • Mahler M, Bristol IJ, Sundberg JP, Churchill GA, Birkenmeier EH, Elson CO, Leiter EH
    Genetic analysis of susceptibility to dextran sulfate sodium-induced colitis in mice
    Genomics. 1999 Jan 15;55(2):147-56
  • Ripol MI, Churchill GA, da Silva JAG, Sorrells M
    Statistical aspects of genetic mapping in autopolyploids
    Gene. 1999 Jul 22;235(1-2):31-41
  • Schultz TR, Churchill GA
    The role of subjectivity in reconstructing ancestral character states: A Bayesian approach to unknown rates, states and transformation asymmetries
    Syst Biol 1999;48:651-664
  • Upadhya P, Churchill G, Birkenmeier EH, Barker JE, Frankel WN
    Genetic modifiers of polycystic kidney disease in intersubspecific KAT2J mutants
    Genomics. 1999 Jun 1;58(2):129-37


  • Beamer WG, Shultz KL, Tennent BJ, Nadeau JH, Churchill GA, Eicher EM
    Multigenic and imprinting control of ovarian granulosa cell tumorigenesis in mice
    Cancer Res. 1998 Aug 15;58(16):3694-9
  • Blauth SL, Churchill GA, Mutschler MA
    Identification of quantitative trait loci associated with acylsugar accumulation using intraspecific populations of the wild tomato, Lycopersicon pennellii
    Theor Appl Genet 1998 Mar;96(3-4):458-467
  • Churchill GA, Doerge RW
    Mapping quantitative trait loci in experimental populations
    In: Molecular Dissection of Complex Traits, Paterson AH (ed). CRC Press 31-41.
  • Churchill GA
    Hidden Markov models
    In: Encyclopedia of Biostatistics. John Wiley & Sons, Ltd 3:1908-1916.


  • Simonsen KL, Churchill GA
    A Markov chain model of coalescence with recombination
    Theor Popul Biol. 1997 Aug;52(1):43-59


  • Doerge RW, Churchill GA
    Permutation tests for multiple loci affecting a quantitative character
    Genetics. 1996 Jan;142(1):285-94
  • Felsenstein J, Churchill GA
    A hidden Markov model approach to variation among sites in rate of evolution
    Mol Biol Evol. 1996 Jan;13(1):93-104
  • Kelly C, Churchill GA
    Biases in amino acid replacement matrices and alignment scores due to rate heterogeneity
    J Comput Biol. 1996 Summer;3(2):307-18
  • Nachman MW, Churchill GA
    Heterogeneity in rates of recombination across the mouse genome
    Genetics. 1996 Feb;142(2):537-48
  • Schultz TR, Cocroft RB, Churchill GA
    The reconstruction of ancestral character states
    Evolution 1996 50:504-511


  • Churchill GA
    Accurate restoration of DNA sequences
    In: Case Studies in Bayesian Statistics 2, Gatsonis C, Hodges JS, Kass RE, Singpurwalla ND (eds).
  • Simonsen KL, Churchill GA, Aquadro CF
    Properties of statistical tests of neutrality for DNA polymorphism data
    Genetics. 1995 Sep;141(1):413-29
  • Thorne JL, Churchill GA
    Estimation and reliability of molecular sequence alignments
    Biometrics 1995 Mar; 51:100-113



  • Anderson JA, Churchil GA, Atrique JE, Tanksley SD, Sorrells ME
    Opimizing parental selection for genetic linkage maps
    Genome. 1993 Feb;36(1):181-6
  • Churchill GA, Giovannoni JJ, Tanksley SD
    Pooled-sampling makes high-resolution mapping practical with DNA markers
    Proc Natl Acad Sci U S A. 1993 Jan 1;90(1):16-20
  • Navidi WC, Churchill GA, von Haeseler A
    Phylogenetic inference: linear invariants and maximum likelihood
    Biometrics. 1993 Jun;49(2):543-55
  • von Haeseler A, Churchill GA
    Network models for sequence evolution
    J Mol Evol. 1993 Jul;37(1):77-85


  • Churchill GA, von Haeseler A, Navidi WC
    Sample size for a phylogenetic inference
    Mol Biol Evol. 1992 Jul;9(4):753-69
  • Churchill GA, Waterman MS
    The accuracy of DNA sequences: estimating sequence quality
    Genomics. 1992 Sep;14(1):89-98
  • Churchill GA
    Hidden Markov chains and the analysis of genome structure
    Comput Chem 1992;16:107-115


  • Navidi WC, Churchill GA, von Haeseler A
    Methods for inferring phylogenies from nucleic acid sequence data by using maximum likelihood and linear invariants
    Mol Biol Evol. 1991 Jan;8(1):128-43


  • Churchill GA, Daniels DL, Waterman MS
    The distribution of restriction enzyme sites in Escherichia coli
    Nucleic Acids Res. 1990 Feb 11;18(3):589-97


  • Churchill GA
    Stochastic models for heterogeneous DNA sequences
    Bull Math Biol. 1989;51(1):79-94
  • Fangman WL, Henly JW, Churchill G, Brewer BJ
    Stable maintenance of a 35-base-pair yeast mitochondrial genome
    Mol Cell Biol. 1989 May;9(5):1917-21


  • Breslow NE, Churchill G, Nesmith B, Thomas PR, Beckwith JB, Othersen HB, D'Angio GJ
    Clinicopathologic features and prognosis for Wilms' tumor patients with metastases at diagnosis
    Cancer. 1986 Dec 1;58(11):2501-11


  • Breslow N, Churchill G, Beckwith JB, Fernbach DJ, Otherson HB, Tefft M, D'Angio GJ
    Prognosis for Wilms' tumor patients with nonmetastatic disease at diagnosis--results of the second National Wilms' Tumor Study
    J Clin Oncol. 1985 Apr;3(4):521-31