Papers - by author

  

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A

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. [ Full Text ] [ datasets ]

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. PMCID: PMC3153351 [ Full Text ] [ datasets 1 ] [ datasets 2 ] [ datasets 3 ] [ datasets 4 ]

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. PMCID: PMC2654751 [ Full Text ] [ datasets (login required)]

Ackert-Bicknell CL, Demissie S, Marín 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. PMCID: PMC2683155 [ Full Text ] [ datasets ]

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. [ datasets ]

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. [ datasets ]

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.

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. PMCID: PMC3422231 [ Full Text ]

Anderson JA, Churchil GA, Atrique JE, Tanksley SD, Sorrells ME.
Opimizing parental selection for genetic linkage maps
Genome. 1993 Feb;36(1):181-6.

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. PMCID: PMC3117129 [ Full Text ] [ datasets ]

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. PMCID: PMC3149489 [ Full Text ] [ Highlight in Nature Reviews Genetics ] [ datasets ]

B

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. PMCID: PMC2888940 [ Full Text ] [ datasets ]

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. PMCID: PMC4287450 [ Full Text ]

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. [ datasets ]

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. [ Full Text ] [ datasets ]

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. [ datasets ]

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.

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. [ datasets ]

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. [ Full Text ]

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. PMCID: PMC3026348 [ Full Text ] [ datasets ]

Blair RH, Kliebenstein DJ, Churchill GA.
What Can Causal Networks Tell Us about Metabolic Pathways?
PLoS Comput Biol. 2012 Apr;8(4):e1002458. PMCID: PMC3320578 [ Full Text ] [ software ]

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.

Blauth SL, Steffens JC, Churchill GA, Mutschler MA.
Identification of QTLs controlling acylsugar fatty acid composition in an intraspecific population of Lycopersicon pennellii (Corr.) D'Arcy
Theor Appl Genetics 1999 99(1-2):373-381.

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. [ Full Text ]

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. [ datasets ]

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. [ Full Text ] [ datasets ]

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.

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.

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.

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. [ Full Text ] [ datasets ]

Brockmann GA, Schäfer N, Hesse C, Heise S, Neuschl C, Wagener A, Churchill GA, Li R.
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.

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. PMCID: PMC2636925 [ Full Text ] [ dataset 1 ] [ dataset 2 ]

Broman KW, Rowe LB, Churchill GA, Paigen K.
Crossover interference in the mouse
Genetics. 2002 Mar;160(3):1123-31. PMCID: PMC1462020. [ Full Text ] [ datasets ]

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. PMCID: PMC1698653. [ Full Text ] [ datasets ]

Broman KW, Wu H, Sen S, Churchill GA.
R/qtl: QTL mapping in experimental crosses
Bioinformatics. 2003 May 1;19(7):889-90. [ Full Text ]

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. PMCID: PMC2600954 [ Full Text ]

C

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. PMCID: PMC2584133 [ Full Text ]

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. PMCID: PMC2745091 [ Full Text ]

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. PMCID: PMC4324012 [ Full Text ]

Churchill GA.
When are results too good to be true?
Genetics. 2014;198(2):447-8. PMCID: PMC4196601. [ Full Text ]

Churchill GA.
Misleading results: don't blame the mice
Science. 2014;343(6169):370. [ Full Text ]

Churchill GA.
Recombinant inbred strain panels: a tool for systems genetics
Physiol Genomics. 2007 Oct 22;31(2):174-5. [ Full Text ]

Churchill GA.
The genetics of gene expression
Mamm Genome. 2006 Jun;17(6):465.

Churchill GA.
Using ANOVA to analyze microarray data
Biotechniques. 2004 Aug;37(2):173-5, 177.

Churchill GA.
Fundamentals of experimental design for cDNA microarrays
Nat Genet. 2002 Dec;32 Suppl:490-5.

Churchill GA.
Hidden Markov chains and the analysis of genome structure
Comput Chem. 1992.16:107-115.

Churchill GA.
Stochastic models for heterogeneous DNA sequences
Bull Math Biol. 1989;51(1):79-94.

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. PMCID: PMC333466. [ Full Text ]

Churchill GA, Doerge RW.
Naive application of permutation testing leads to inflated type I error rates
Genetics. 2008 Jan;178(1):609-10. PMCID: PMC2206111 [ Full Text ]

Churchill GA, Doerge RW.
Empirical threshold values for quantitative trait mapping
Genetics. 1994 Nov;138(3):963-71. PMCID: PMC1206241. [ Full Text ]

Churchill GA, Gatti DM, Munger SC, Svenson KL
The Diversity Outbred Mouse Population
Mamm Genome. 2012 Oct;23(9-10):713-8. PMCID: PMC3524832 [ datasets ]

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. PMCID: PMC45590. [ Full Text ]

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.

Churchill GA, Oliver B.
Sex, flies and microarrays
Nat Genet. 2001 Dec;29(4):355-6.

Churchill GA, von Haeseler A, Navidi WC.
Sample size for a phylogenetic inference
Mol Biol Evol. 1992 Jul;9(4):753-69. [ Full Text ]

Churchill GA, Waterman MS.
The accuracy of DNA sequences: estimating sequence quality
Genomics. 1992 Sep;14(1):89-98.

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. [ Full Text ] [ datasets ]

Collaborative Cross Consortium
The Genome Architecture of the Collaborative Cross Mouse Genetic Reference Population
Genetics. 2012 Feb;190(2):389-401. PMCID: PMC3276630 [ Full Text ] [ datasets ]

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 nature and identification of quantitative trait loci: a community's view
Nat Rev Genet. 2003 Nov;4(11):911-6. PMCID: PMC2063446. [ Full Text ]

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. PMCID: PMC2728870 [ Full Text ]

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. PMCID: PMC1602077. [ Full Text ] [ datasets ]

Cui XQ, Churchill GA.
Statistical tests for differential expression in cDNA microarray experiments
Genome Biol. 2003;4(4):210. PMCID: PMC154570. [ Full Text ]

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. [ Full Text ]

Cui XQ, Kerr MK, Churchill GA.
Transformations for cDNA microarray data
Stat Appl Genet Mol Biol. 2003;2:Article4.

D

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. [ Full Text ] [ datasets ]

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. PMCID: PMC4334553 [ Full Text ]

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. PMCID: PMC3305361 [ Full Text ] [ software ] [ datasets 1 ] [ datasets 2 ]

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. [ datasets ]

Doerge RW, Churchill GA.
Permutation tests for multiple loci affecting a quantitative character
Genetics. 1996 Jan;142(1):285-94. PMCID: PMC1206957. [ Full Text ]

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. PMCID: PMC2390645 [ Full Text ] [ datasets 1 ] [ datasets 2 ]

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. [ Full Text ] [ datasets ]

F

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. PMCID: PMC362982. [ Full Text ]

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. PMCID: PMC61125. [ Full Text ] [ datasets ]

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. [ Full Text ]

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. PMCID: PMC2854560 [ Full Text ]
[ dataset 1 ] [ dataset 2 ] [ dataset 3 ] [ dataset 4 ] [ dataset 5 ] [ dataset 6 ] [ dataset 7 ] [ dataset 8 ]

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. [ Full Text ]

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. [ Full Text ]

G

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. PMCID: PMC4169154. [ Full Text ] [ datasets ]

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.

Grubb SC, Churchill GA, Bogue MA.
A collaborative database of inbred mouse strain characteristics
Bioinformatics. 2004 Nov 1;20(16):2857-9. [ Full Text ]

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. [ Full Text ] [ datasets ]

H

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. PMCID: PMC3014036 [ Full Text ] [ datasets 1 ] [ datasets 2 ]

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. PMCID: PMC3070524 [ Full Text ] [ datasets 1 ] [ datasets 2 ]

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. PMCID: PMC2888560 [ Full Text ] [ datasets ]

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. PMCID: PMC1929138 [ Full Text ] [ datasets ]

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. PMCID: PMC3572953 [ Full Text ]

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. PMCID: PMC2911843 [ Full Text ] [ database ]

I

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, 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. [ Full Text ] [ datasets ]

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 Sept;45(9):1624-1632. [ Full Text ] [ datasets ]

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. [ datasets ]

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. PMCID: PMC2586053. [ Full Text ]

J

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. PMCID: PMC1448737. [ Full Text ]

K

Kelada SN, 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. PMCID: PMC3284323 [ Full Text ] [ datasets ]

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
American Journal of Respiratory Cell and Molecular Biology. 2014;51(3):436-45. PMCID: PMC4189492.

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.

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. [ Full Text ] [ datasets ]

Kerr MK, Churchill GA.
Experimental design for gene expression microarrays
Biostatistics. 2001 Jun;2(2):183-201. [ Full Text ]

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. PMCID: PMC55356. [ Full Text ]

Kerr MK, Churchill GA.
Statistical design and the analysis of gene expression microarray data
Genet Res. 2001 Apr;77(2):123-8.

Kerr MK, Martin M, Churchill GA.
Analysis of variance for gene expression microarray data
J Comput Biol. 2000;7(6):819-37. [ datasets ]

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. PMCID: PMC2013712 [ Full Text ] [ datasets ]

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. [ datasets ]

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. [ Full Text ]

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, 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. [ Full Text ]

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. [ Full Text ] [ datasets 1 ] [ datasets 2 ]

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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. PMCID: PMC1851001 [ Full Text ] [ datasets ]

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. PMCID: PMC3351823 [Available on 2013/6/1]

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. PMCID: PMC3025299 [ Full Text ] [ datasets ]

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. PMCID: PMC3151687 [ Full Text ]

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. PMCID: PMC2699846 [ Full Text ] [ datasets ]

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. PMCID: PMC3276624 [ Full Text ] [ datasets ] [ software ]

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. PMCID: PMC3008368 [ Full Text ] [ datasets ]

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. PMCID: PMC1449540 [ Full Text ] [ datasets 1 ] [ datasets 2 ] [ datasets 3 ] [ datasets 4 ]

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. [ Full Text ] [ datasets ]

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. PMCID: PMC2991400 [ Full Text ]

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. PMCID: PMC1513264. [ Full Text ] [ datasets ]

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. PMCID: PMC4012503. [ Full Text ]

Livingstone KD, Churchill G, Jahn MK.
Linkage mapping in populations with karyotypic rearrangements
J Hered. 2000 Nov-Dec;91(6):423-8. [ Full Text ]

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. PMCID: PMC2679052 [ Full Text ] [ datasets ]

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. [ datasets ]

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.

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.

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. [ datasets ]

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. [ Full Text ] [ datasets ]

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. [ datasets ]

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. [ Full Text ] [ datasets ]

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. [ datasets ]

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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. [ Full Text ] [ datasets ]

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. PMCID: PMC2942088 [ Full Text ]

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.

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. [ datasets 1 ] [ datasets 2 ]

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. PMCID: PMC3118585 [ Full Text ] [ datasets ]

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. [ datasets ]

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. [ Full Text ]

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. PMCID: PMC1064077. [ Full Text ]

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. PMCID: PMC1460898. [ Full Text ]

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. [ Full Text ] [ datasets ]

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. [ datasets ]

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. PMCID: PMC4174954 [ Full Text ]

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Nachman MW, Churchill GA.
Heterogeneity in rates of recombination across the mouse genome
Genetics. 1996 Feb;142(2):537-48. PMCID: PMC1206986. [ Full Text ]

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. PMCID: PMC403692. [ Full Text ] [ datasets ]

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. [ datasets ]

Navidi WC, Churchill GA, von Haeseler A.
Phylogenetic inference: linear invariants and maximum likelihood
Biometrics. 1993 Jun;49(2):543-55.

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. [ Full Text ]

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Oleksiak MF, Churchill GA, Crawford DL.
Variation in gene expression within and among natural populations
Nat Genet. 2002 Oct;32(2):261-6.

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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. PMCID: PMC3337072 [ Full Text ]

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.

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.

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. PMCID: PMC3031420 [ Full Text ]

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. [ Full Text ] [ datasets ]

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 Biol. 2007 May;5(5):e127; author reply e128. PMCID: PMC1868061 [ Full Text ]

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. PMCID: PMC1201368 [ Full Text ] [ datasets ]

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. PMCID: PMC2519960 [ Full Text ] [ datasets ]

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. PMCID: PMC3457769 [Available on 2013/10/1] [ datasets ]

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. PMCID: PMC3149490 [ Full Text ] [ datasets ]

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. [ Full Text ] [ datasets ]

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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. PMCID: PMC4032469. [ Full Text ]

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. [ Full Text ]

Reifsnyder PC, Churchill G, Leiter EH.
Maternal environment and genotype interact to establish diabesity in mice
Genome Res 2000 Oct;10:1568-1578. PMCID: PMC310941. [ Full Text ] [ datasets ]

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. 2005 Sep;6(6):528-38. [ datasets ]

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. [ datasets ]

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.

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. PMCID: PMC2767104 [ Full Text ] [ datasets ]

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. [ datasets ]

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. PMCID: PMC4196624 [ Full Text ]

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Satagopan JM, Sen S, Churchill GA.
Sequential Quantitative Trait Locus Mapping in Experimental Crosses
Stat Appl Genet Mol Biol. 2007;6:Article12.

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.

Schultz TR, Cocroft RB, Churchill GA.
The reconstruction of ancestral character states
Evolution 1996 50:504-511.

Sen S, Churchill GA.
A statistical framework for quantitative trait mapping
Genetics. 2001 Sep;159(1):371-887. PMCID: PMC1461799 [ Full Text ] [ datasets ]

Sen S, Satagopan JM, Broman KW, Churchill GA.
R/qtlDesign: inbred line cross experimental design
Mamm Genome. 2007 Feb;18(2):87-93. PMCID: PMC2366108 [ Full Text ]

Sen S, Satagopan JM, Churchill GA.
Quantitative trait locus study design from an information perspective
Genetics. 2005 May;170(1):447-64. PMCID: PMC1449722. [ Full Text ]

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. [ Full Text ] [ datasets ]

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. [ Full Text ] [ datasets ]

Shockley KR, Churchill GA.
Gene expression analysis of mouse chromosome substitution strains
Mamm Genome. 2006 Jun;17(6):598-614. [ datasets ]

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. PMCID: PMC2745312 [ Full Text ] [ datasets ]

Shockley KR, Rosen CJ, Churchill GA, Lecka-Czernik B.
PPARgamma2 Regulates a Molecular Signature of Marrow Mesenchymal Stem Cells
PPAR Res. 2007;2007:81219. PMCID: PMC2234088 [ Full Text ] [ datasets ]

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. PMCID: PMC2789673 [ Full Text ] [ datasets ] [ Commentary ]

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.

Simecek P, Churchill GA, Yang H, Rowe LB, Herberg L, Serreze DV, Leiter EH.
Genetic Analysis of Substrain Divergence in NOD Mice
G3. 2015. [ Full Text ]

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

Simonsen KL, Churchill GA, Aquadro CF.
Properties of statistical tests of neutrality for DNA polymorphism data
Genetics. 1995 Sep;141(1):413-29. PMCID: PMC1206737. [ Full Text ]

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. [ Full Text ] [ datasets ]

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. [ Full Text ]

Smith R, Sheppard K, Dipetrillo K, Churchill G.
Quantitative Trait Locus Analysis Using J/qtl
Methods Mol Biol. 2009;573:175-88.

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. [ datasets ]

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. [ Full Text ] [ datasets ]

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. PMCID: PMC2775460 [ Full Text ] [ datasets ]

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. PMCID: PMC2278051 [ Full Text ] [ datasets ]

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.

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. PMCID: PMC1602087 [ Full Text ] [ datasets 1 ] [ datasets 2 ] [ datasets 3 ] [ datasets 4 ]

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. PMCID: PMC2739753 [ Full Text ] [ datasets 1 ] [ datasets 2 ]

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. PMCID: PMC2782629 [ Full Text ]

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. PMCID: PMC2431102 [ Full Text ]

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. PMCID: PMC2602865 [ Full Text ]

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. [ datasets ]

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. [ datasets ]

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. [ datasets ]

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. [ Full Text ] [ datasets ]

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. PMCID: PMC3276626 [ Full Text ] [ datasets ]

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. [ Full Text ] [ datasets ]

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. PMCID: PMC2725522. [ Full Text ] [ datasets ]

T

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. PMCID: PMC3469684 [Available on 2013/10/1]

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.

Thorne JL, Churchill GA.
Estimation and reliability of molecular sequence alignments
Biometrics 1995 Mar;51:100-113.

Threadgill DW, Churchill GA.
Ten Years of the Collaborative Cross
Genetics. 2012 Feb;190(2):291-4. PMCID: PMC3276648 [ Full Text ]

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.

Tsaih SW, Korstanje R.
Haplotype association mapping in mice
Methods Mol Biol. 2009;573:213-22.

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. PMCID: PMC2807478 [ Full Text ] [ Commentary ] [ datasets ]

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. [ datasets ]

U

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.

V

Vedell PT, Svenson KL, Churchill GA.
Stochastic Variation of Transcript Abundance in C57BL/6J mice
BMC Genomics. 2011 Mar 30;12(1):167. PMCID: PMC3082245 [ Full Text ] [ datasets ]

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. PMCID: PMC2761262 [ Full Text ] [ datasets ]

von Haeseler A, Churchill GA.
Network models for sequence evolution
J Mol Evol. 1993 Jul;37(1):77-85.

W

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. PMCID: PMC403739. [ Full Text ] [ datasets 1 ] [ datasets 2 ]

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. PMCID: PMC3276610 [ Full Text ] [ datasets ] [ software ]

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. [ datasets ]

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. [ datasets ]

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. [ datasets ]

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. [ datasets ]

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. [ Full Text ] [ datasets 1 ] [ datasets 2 ]

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. PMCID: PMC2291701. [ Full Text ] [ datasets ]

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. [ Full Text ] [ datasets ]

Woo YH, Walker M, Churchill GA.
Coordinated expression domains in Mammalian genomes
PLoS One. 2010 Aug 18;5(8). pii: e12158. PMCID: PMC2923606 [ Full Text ] [ datasets ]

X

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. PMCID: PMC2716104 [ Full Text ] [ datasets ]

Y

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. [ Full Text ] [ datasets ]

Yang H, Ding Y, Hutchins LN, Szatkiewicz J, Bell TA, Paigen BJ, Graber JH, de Villena FP, Churchill GA.
A customized and versatile high-density genotyping array for the mouse
Nat Methods. 2009 Sep;6(9):663-6. PMCID: PMC2735580 [ Full Text ] [ datasets ]

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. PMCID: PMC2579585 [ Full Text ]

Yang H, Wang JR, Didion JP, Buus RJ, Bell TA, Welsh CE, Bonhomme F, Yu AH, Nachman MW, Pialek J, Tucker P, Boursot P, McMillan L, Churchill GA, de Villena FP.
Subspecific origin and haplotype diversity in the laboratory mouse
Nat Genet. 2011 May 29;43(7):648-55. PMCID: PMC3125408 [ Full Text ] [ News Article ] [ datasets ]

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. PMCID: PMC1451197. [ Full Text ] [ datasets ]

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. PMCID: PMC4042106[ Full Text ]

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.[ Full Text ]

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. PMCID: PMC2768517 [ Full Text ] [ datasets 1 ] [ datasets 2 ]

Z

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. PMCID: PMC3284324 [ Full Text ] [ datasets ]

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. [ Full Text ] [ datasets ]