Papers - by topic (2006 - Present)


Microarray Design & Analysis

PPARG by dietary fat interaction influences bone mass in mice and humans
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.
J Bone Miner Res. 2008 Sep; 23(9):1398-408. PMCID: PMC2683155 [ Full Text ] [ datasets ]

Strain-specific effects of rosiglitazone on bone mass, body composition, and serum insulin-like growth factor-I
Ackert-Bicknell CL, Shockley KR, Horton LG, Lecka-Czernik B, Churchill GA, Rosen CJ.
Endocrinology. 2009 Mar;150(3):1330-40. PMCID: PMC2654751 [ Full Text ] [ datasets (login required)]

Gene expression patterns in the hippocampus and amygdala of endogenous depression and chronic stress models
Andrus BM, Blizinsky K, Vedell PT, Dennis K, Shukla PK, Schaffer DJ, Radulovic J, Churchill GA, Redei EE.
Mol Psychiatry. 2012 Jan;17(1):49-61. PMCID: PMC3117129 [ Full Text ] [ datasets ]

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

Inheritance patterns of transcript levels in f1 hybrid mice
Cui X, Affourtit J, Shockley KR, Woo Y, Churchill GA.
Genetics. 2006 Oct;174(2):627-37. PMCID: PMC1602077. [ Full Text ] [ datasets ]

Identification of conserved gene expression features between murine mammary carcinoma models and human breast tumors
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.
Genome Biol. 2007;8(5):R76. PMCID: PMC1929138 [ Full Text ] [ datasets ]

Characterization of human embryonic stem cell lines by the International Stem Cell Initiative
The International Stem Cell Initiative.
Nat Biotechnol. 2007 Jul;25(7):803-16.

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
Lecka-Czernik B, Ackert-Bicknell C, Adamo ML, Marmolejos V, Churchill GA, Shockley KR, Reid IR, Grey A, Rosen CJ.
Endocrinology. 2007 Feb;148(2):903-11. PMCID: PMC1851001 [ Full Text ] [ datasets ]

Chromosome Y variants from different inbred mouse strains are linked to differences in the morphologic and molecular responses of cardiac cells to postpubertal testosterone
Llamas B, Verdugo RA, Churchill GA, Deschepper CF.
BMC Genomics. 2009 Apr 7;10:150. PMCID: PMC2679052 [ Full Text ] [ datasets ]

Macromolecule biosynthesis: a key function of sleep
Mackiewicz M, Shockley KR, Romer MA, Galante RJ, Zimmerman JE, Naidoo N, Baldwin DA, Jensen ST, Churchill GA, Pack AI.
Physiol Genomics. 2007 Nov 14;31(3):441-57. [ Full Text ] [ datasets ]

What are microarrays teaching us about sleep?
Mackiewicz M, Zimmerman JE, Shockley KR, Churchill GA, Pack AI.
Trends Mol Med. 2009 Feb;15(2):79-87.

Overexpression of innate immune response genes in a model of recessive polycystic kidney disease
Mrug M, Zhou J, Woo Y, Cui X, Szalai AJ, Novak J, Churchill GA, Guay-Woodford LM.
Kidney Int. 2008 Jan;73(1):63-76. [ datasets ]

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

PPARgamma2 nuclear receptor controls multiple regulatory pathways of osteoblast differentiation from marrow mesenchymal stem cells
Shockley KR, Lazarenko OP, Czernik PJ, Rosen CJ, Churchill GA, Lecka-Czernik B.
J Cell Biochem. 2009 Feb 1;106(2):232-46. PMCID: PMC2745312 [ Full Text ] [ datasets ]

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

The Effects of Atherogenic Diet on Hepatic Gene Expression Across Mouse Strains
Shockley KR, Witmer D, Burgess-Herbert SL, Paigen B, Churchill GA.
Physiol Genomics. 2009 Nov 6;39(3):172-82. PMCID: PMC2789673 [ Full Text ] [ datasets ] [ Commentary ]

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

Importance of randomization in microarray experimental designs with Illumina platforms
Verdugo RA, Deschepper CF, Muñoz G, Pomp D, Churchill GA.
Nucleic Acids Res. 2009 Sep;37(17):5610-8. PMCID: PMC2761262 [ Full Text ] [ datasets ]

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

Estimating p-values in small microarray experiments
Yang H, Churchill G.
Bioinformatics. 2007 Jan 1;23(1):38-43. [ Full Text ] [ datasets ]

Randomization in laboratory procedure is key to obtaining reproducible microarray results
Yang H, Harrington CA, Vartanian K, Coldren CD, Hall R, Churchill GA.
PLoS ONE. 2008;3(11):e3724. PMCID: PMC2579585 [ Full Text ]

Multiple mechanisms limit the duration of wakefulness in Drosophila brain
Zimmerman JE, Rizzo W, Shockley KR, Raizen DM, Naidoo N, Mackiewicz M, Churchill GA, Pack AI.
Physiol Genomics. 2006 Nov 27;27(3):337-50. [ Full Text ] [ datasets ]

Quantitative Trait Loci (QTL) Methods & Applications

Mouse BMD quantitative trait loci show improved concordance with human genome wide association loci when recalculated on a new, common mouse genetic map
Ackert-Bicknell CL, Karasik D, Li Q, Smith RV, Hsu YH, Churchill GA, Paigen BJ, Tsaih SW.
J Bone Miner Res. 2010 Aug;25(8):1808-20. [ Full Text ] [ datasets 1 ] [ datasets 2 ] [ datasets 3 ] [ datasets 4 ]

Identification of QTL for locomotor activation and anxiety using closely-related inbred strains
Bailey JS, Grabowski-Boase L, Steffy BM, Wiltshire T, Churchill GA, Tarantino LM.
Genes Brain Behav. 2008 Oct;7(7):761-9. PMCID: PMC2888940 [ Full Text ] [ datasets ]

Test- and behavior-specific genetic factors affect WKY hypoactivity in tests of emotionality
Baum AE, Solberg LC, Churchill GA, Ahmadiyeh N, Takahashi JS, Redei EE.
Behav Brain Res. 2006 May 15;169(2):220-30. [ datasets ]

Comparison of unrestrained plethysmography and forced oscillation for identifying genetic variability of airway responsiveness in inbred mice
Berndt A, Leme AS, Williams LK, Von Smith R, Savage HS, Stearns T, Tsaih SW, Shapiro SD, Peters LL, Paigen BJ, Svenson KL.
Physiol Genomics. 2011 Jan 11; 43: 1-11. PMCID: PMC3026348 [ Full Text ] [ datasets ]

Relationship between obesity phenotypes and genetic determinants in a mouse model for juvenile obesity
Brockmann GA, Schäfer N, Hesse C, Heise S, Neuschl C, Wagener A, Churchill GA, Li R.
Physiol Genomics. 2013 Sep 16;45(18):817-26. doi: 10.1152/physiolgenomics.00058.2013.

Genetic factors contributing to obesity and body weight can act through mechanisms affecting muscle weight, fat weight, or both
Brockmann GA, Tsaih SW, Neuschl C, Churchill GA, Li R.
Physiol Genomics 2009 Jan 8;36(2):114-126. PMCID: PMC2636925 [ Full Text ] [ dataset 1 ] [ dataset 2 ]

The X chromosome in quantitative trait locus mapping
Broman KW, Sen S, Owens SE, Manichaikul A, Southard-Smith EM, Churchill GA.
Genetics. 2006 Dec;174(4):2151-8. PMCID: PMC1698653. [ Full Text ] [ datasets ]

Practical Applications of the Bioinformatics Toolbox for Narrowing Quantitative Trait Loci
Burgess-Herbert SL, Cox A, Tsaih SW, Paigen B.
Genetics. 2008 Dec;180(4):2227-35. PMCID: PMC2600954 [ Full Text ]

Idd9/11 genetic locus regulates diabetogenic activity of CD4 T-cells in nonobese diabetic (NOD) mice
Chen YG, Scheuplein F, Osborne MA, Tsaih SW, Chapman HD, Serreze DV.
Diabetes. 2008 Dec;57(12):3273-80. PMCID: PMC2584133 [ Full Text ]

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

A New Standard Genetic Map for the Mouse
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.
Genetics. 2009 Aug;182(4):1335-44. PMCID: PMC2728870 [ Full Text ]

Modifier locus for exencephaly in Cecr2 mutant mice is syntenic to the 10q25.3 region associated with neural tube defects in humans
Davidson CE, Li Q, Churchill GA, Osborne LR, McDermid HE.
Physiol Genomics. 2007 Oct 22;31(2):244-51. [ Full Text ] [ datasets ]

Quantitative trait loci for urinary albumin in crosses between C57BL/6J and A/J inbred mice in the presence and absence of Apoe
Doorenbos C, Tsaih SW, Sheehan S, Ishimori N, Navis G, Churchill G, Dipetrillo K, Korstanje R.
Genetics. 2008 May;179(1):693-9. PMCID: PMC2390645. [ Full Text ] [ datasets 1 ] [ datasets 2 ]

Genetic Analysis of Blood Pressure in 8 Mouse Intercross Populations
Feng M, Deerhake ME, Keating R, Thaisz J, Xu L, Tsaih SW, Smith R, Ishige T, Sugiyama F, Churchill GA, Dipetrillo K.
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 ]

Uncovering Genes and Regulatory Pathways Related to Urinary Albumin Excretion
Hageman RS, Leduc MS, Caputo CR, Tsaih SW, Churchill GA, Korstanje R.
J Am Soc Nephrol. 2011 Jan;22(1):73-81. PMCID: PMC3014036 [ Full Text ] [ datasets 1 ] [ datasets 2 ]

A Bayesian Framework for Inference of the Genotype-Phenotype Map for Segregating Populations
Hageman RS, Leduc MS, Korstanje R, Paigen B, Churchill GA.
Genetics. 2011 Apr;187(4):1163-70. PMCID: PMC3070524 [ Full Text ] [ datasets 1 ] [ datasets 2 ]

High fat diet leads to tissue specific changes reflecting risk factors for diseases in DBA/2J mice
Hageman RS, Wagener A, Hantschel C, Svenson KL, Churchill GA, Brockmann GA.
Physiol Genomics. 2010 Jun;42(1):55-66. PMCID: PMC2888560 [ Full Text ] [ datasets ]

Quantitative trait loci that determine BMD in C57BL/6J and 129S1/SvImJ inbred mice
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.
J Bone Miner Res. 2006 Jan;21(1):105-12. [ datasets ]

Quantitative trait loci for BMD in an SM/J by NZB/BlNJ intercross population and identification of Trps1 as a probable candidate gene
Ishimori N, Stylianou IM, Korstanje R, Marion MA, Li R, Donahue LR, Rosen CJ, Beamer WG, Paigen B, Churchill GA.
J Bone Miner Res. 2008 Sep;23(9):1529-37. PMCID: PMC2586053. [ Full Text ]

Genetic background modifies inner ear and eye phenotypes of jag1 heterozygous mice
Kiernan AE, Li R, Hawes NL, Churchill GA, Gridley T.
Genetics. 2007 Sep;177(1):307-11. PMCID: PMC2013712 [ Full Text ] [ datasets ]

Genetic variation in Glp1r expression influences the rate of gastric emptying in mice
Kumar KG, Byerley LO, Volaufova J, Drucker DJ, Churchill GA, Li R, York B, Zuberi A, Richards BK.
Am J Physiol Regul Integr Comp Physiol. 2008 Feb;294(2):R362-71. [ Full Text ] [ datasets 1 ] [ datasets 2 ]

Using bioinformatics and systems genetics to dissect HDL cholesterol levels in an MRL/MpJ x SM/J intercross
Leduc MS, Blair RH, Verdugo RA, Tsaih SW, Walsh K, Churchill GA, Paigen B.
J Lipid Res. 2012 Jun;53(6):1163-75. PMCID: PMC3351823 [Available on 2013/6/1]

Identification of genetic determinants of IGF-1 levels and longevity among mouse inbred strains
Leduc MS, Hageman RS, Meng Q, Verdugo RA, Tsaih SW, Churchill GA, Paigen B, Yuan R.
Aging Cell. 2010 Oct;9(5):823-36. doi: 10.1111/j.1474-9726.2010.00612.x. PMCID: PMC3025299 [ Full Text ] [ datasets ]

Integration of QTL and bioinformatic tools to identify candidate genes for triglycerides in mice
Leduc MS, Hageman RS, Verdugo RA, Tsaih SW, Walsh K, Churchill GA, Paigen B.
J Lipid Res. 2011 Sep;52(9):1672-82. PMCID: PMC3151687 [ Full Text ]

NOD x 129.H2g7 Backcross Delineates 129S1/SvImJ-Derived Genomic Regions Modulating Type 1 Diabetes (T1D) Development In Mice
Leiter EH, Reifsnyder PC, Wallace R, Li R, King B, Churchill GC.
Diabetes. 2009 Jul;58(7):1700-3. PMCID: PMC2699846 [ Full Text ] [ datasets ]

Epistasis contributes to the genetic buffering of plasma HDL cholesterol in mice
Li R, Churchill GA.
Physiol Genomics. 2010 Nov 29;42A(4):228-34. PMCID: PMC3008368 [ Full Text ] [ datasets ]

Quantitative trait loci associated with blood pressure of metabolic syndrome in the progeny of NZO/HILtJ x C3H/HeJ intercrosses
Nishihara E, Tsaih SW, Tsukahara C, Langley S, Sheehan S, Dipetrillo K, Kunita S, Yagami K, Churchill GA, Paigen B, Sugiyama F.
Mamm Genome. 2007 Aug;18(8):573-83. [ datasets ]

Quantitative trait loci for baseline erythroid traits
Peters LL, Lambert AJ, Zhang W, Churchill GA, Brugnara C, Platt OS.
Mamm Genome. 2006 Apr;17(4):298-309.

Sequence variation at multiple loci influences red cell hemoglobin concentration
Peters LL, Shavit JA, Lambert AJ, Tsaih SW, Li Q, Su Z, Leduc MS, Paigen B, Churchill GA, Ginsburg D, Brugnara C.
Blood. 2010 Dec 16;116(25):e139-49. PMCID: PMC3031420 [ Full Text ]

Genetic influence on immune phenotype revealed strain-specific variations in peripheral blood lineages
Petkova SB, Yuan R, Tsaih SW, Schott W, Roopenian DC, Paigen B.
Physiol Genomics. 2008 Aug 15;34(3):304-14. PMCID: PMC2519960 [ Full Text ] [ datasets ]

Conditioning the genome identifies additional diabetes resistance loci in Type 1 diabetes-resistant NOR/Lt mice
Reifsnyder PC, Li R, Silveira PA, Churchill G, Serreze DV, Leiter EH.
Genes Immun. 2005 Sep;6(6):528-38. [ datasets ]

A Cmv2 QTL on chromosome X affects MCMV resistance in New Zealand male mice
Rodriguez MR, Lundgren A, Sabastian P, Li Q, Churchill G, Brown MG.
Mamm Genome. 2009 Jul;20(7):414-23. PMCID: PMC2767104 [ Full Text ] [ datasets ]

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

Genetic analysis of albuminuria in a cross between C57BL/6J and DBA/2J mice
Sheehan S, Tsaih SW, King BL, Stanton C, Churchill GA, Paigen B, DiPetrillo K.
Am J Physiol Renal Physiol 2007 Nov;293(5):F1649-56. [ Full Text ] [ datasets ]

Genetic analysis of the stress-responsive adrenocortical axis
Solberg LC, Baum AE, Ahmadiyeh N, Shimomura K, Li R, Turek FW, Takahashi JS, Churchill GA, Redei EE.
Physiol Genomics. 2006 Nov 27;27(3):362-9. [ Full Text ]

Identification of genetic loci involved in diabetes using a rat model of depression
Solberg Woods LC, Ahmadiyeh N, Baum A, Shimomura K, Li Q, Steiner DF, Turek FW, Takahashi JS, Churchill GA, Redei EE.
Mamm Genome. 2009 Aug;20(8):486-97. PMCID: PMC2775460 [ Full Text ] [ datasets ]

Applying gene expression, proteomics and single-nucleotide polymorphism analysis for complex trait gene identification
Stylianou IM, Affourtit JP, Shockley KR, Wilpan RY, Abdi FA, Bhardwaj S, Rollins J, Churchill GA, Paigen B.
Genetics. 2008 Mar;178(3):1795-805. PMCID: PMC2278051 [ Full Text ] [ datasets ]

Quantitative trait locus analysis for obesity reveals multiple networks of interacting loci
Stylianou IM, Korstanje R, Li R, Sheehan S, Paigen B, Churchill GA.
Mamm Genome. 2006 Jan;17(1):22-36.

Complex genetic architecture revealed by analysis of high-density lipoprotein cholesterol in chromosome substitution strains and f2 crosses
Stylianou IM, Tsaih SW, Dipetrillo K, Ishimori N, Li R, Paigen B, Churchill G.
Genetics. 2006 Oct;174(2):999-1007. PMCID: PMC1602087 [ Full Text ] [ datasets 1 ] [ datasets 2 ] [ datasets 3 ] [ datasets 4 ]

Four additional mouse crosses improve the lipid QTL landscape and identify Lipg as a QTL gene
Su Z, Ishimori N, Chen Y, Leiter EH, Churchill GA, Paigen B, Stylianou IM.
J Lipid Res. 2009 Oct;50(10):2083-94. PMCID: PMC2739753 [ Full Text ] [ datasets 1 ] [ datasets 2 ]

Candidate genes for obesity revealed from a C57BL/6J x 129S1/SvImJ intercross
Su Z, Korstanje R, Tsaih SW, Paigen B.
Int J Obes (Lond). 2008 Jul;32(7):1180-9. PMCID: PMC2782629 [ Full Text ]

Candidate genes for plasma triglyceride, FFA, and glucose revealed from an intercross between inbred mouse strains NZB/B1NJ and NZW/LacJ
Su Z, Tsaih SW, Szatkiewicz J, Shen Y, Paigen B.
J Lipid Res. 2008 Jul;49(7):1500-10. PMCID: PMC2431102 [ Full Text ]

Genetic basis of HDL variation in 129/SvImJ and C57BL/6J mice: importance of testing candidate genes in targeted mutant mice
Su Z, Wang X, Tsaih SW, Zhang A, Cox A, Sheehan S, Paigen B.
J Lipid Res. 2009 Jan;50(1):116-25. PMCID: PMC2602865 [ Full Text ]

High-Resolution Genetic Mapping Using the Mouse Diversity Outbred Population
Svenson KL, Gatti DM, Valdar W, Welsh CE, Cheng R, Chesler EJ, Palmer AA, McMillan L, Churchill GA.
Genetics. 2012 Feb;190(2):437-47. PMCID: PMC3276626 [Available on 2013/2/1] [ datasets ]

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

Genetic analysis of albuminuria in aging mice and concordance with loci for human diabetic nephropathy found in a genome-wide association scan
Tsaih SW, Pezzolesi MG, Yuan R, Warram JH, Krolewski AS, Korstanje R.
Kidney Int. 2010 Feb;77(3):201-10. PMCID: PMC2807478 [ Full Text ] [ Commentary ] [ datasets ]

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
Wergedal JE, Ackert-Bicknell CL, Tsaih S-W, Sheng M H-C, Li R, Mohan S, Beamer WG, Churchill GA, Baylink DJ.
J Bone Miner Res. 2006 Aug;21(8):1256-66. [ datasets ]

QTL mapping for genetic determinants of lipoprotein cholesterol levels in combined crosses of inbred mouse strains
Wittenburg H, Lyons MA, Li R, Kurtz U, Wang X, Mossner J, Churchill GA, Carey MC, Paigen B.
J Lipid Res. 2006 Aug;47(8):1780-90. [ Full Text ] [ datasets 1 ] [ datasets 2 ]

Genetic influence on electrocardiogram time intervals and heart rate in aging mice
Xing S, Tsaih SW, Yuan R, Svenson KL, Jorgenson LM, So M, Paigen BJ, Korstanje R.
Am J Physiol Heart Circ Physiol. 2009 Jun;296(6):H1907-13.PMCID: PMC2716104 [ Full Text ] [ datasets ]

Aging in inbred strains of mice: study design and interim report on median lifespans and circulating IGF1 levels
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 Cell. 2009 June; 8(3):277-87. PMCID: PMC2768517 [ Full Text ] [ datasets 1 ] [ datasets 2 ]

Genome-Wide Association Mapping of Quantitative Traits in Outbred Mice
Zhang W, Korstanje R, Thaisz J, Staedtler F, Harttman N, Xu L, Feng M, Yanas L, Yang H, Valdar W, Churchill GA, DiPetrillo K.
G3 (Bethesda). 2012 Feb;2(2):167-74. PMCID: PMC3284324 [ Full Text ] [ datasets ]

Graphical Modeling

Genetic factors contributing to obesity and body weight can act through mechanisms affecting muscle weight, fat weight, or both
Brockmann GA, Tsaih SW, Neuschl C, Churchill GA, Li R.
Physiol Genomics 2009 Jan 8;36(2):114-126. PMCID: PMC2636925 [ Full Text ] [ dataset 1 ] [ dataset 2 ]

Relationships of dietary fat, body composition, and bone mineral density in inbred mouse strain panels
Li R, Svenson KL, Donahue LR, Peters LL, Churchill GA.
Physiol Genomics. 2008 Mar 14;33(1):26-32. [ Full Text ] [ datasets ]

Structural model analysis of multiple quantitative traits
Li R, Tsaih SW, Shockley K, Stylianou IM, Wergedal J, Paigen B, Churchill GA.
PLoS Genet. 2006 Jul;2(7):e114. PMCID: PMC1513264. [ Full Text ] [ datasets ]

Collaborative Cross and other Mouse Resources

Genetic analysis of complex traits in the emerging collaborative cross
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.
Genome Res. 2011 Aug;21(8):1223-38. PMCID: PMC3149489 [ Full Text ] [ Highlight in Nature Reviews Genetics ] [ datasets ]

The Collaborative Cross at Oak Ridge National Laboratory: developing a powerful resource for systems genetics
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.
Mamm Genome. 2008 Jun;19(6):382-9. PMCID: PMC2745091 [ Full Text ]

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

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

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

Modeling host genetic regulation of influenza pathogenesis in the collaborative cross
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.
PLoS Pathog. 2013 Feb;9(2):e1003196. [ Full Text ]

The Collaborative Cross, developing a resource for mammalian systems genetics: a status report of the Wellcome Trust cohort
Iraqi FA, Churchill G, Mott R.
Mamm Genome. 2008 Jun;19(6):379-81

Genetic Analysis of Hematologic Parameters in Incipient Lines of the Collaborative Cross
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.
G3 (Bethesda). 2012 Feb;2(2):157-65. PMCID: PMC3284323 [ Full Text ] [ datasets ]

A General Bayesian Approach to Analyzing Diallel Crosses of Inbred Strains
Lenarcic AB, Svenson KL, Churchill GA, Valdar W.
Genetics. 2012 Feb;190(2):413-35. PMCID: PMC3276624 [ Full Text ] [ datasets ] [ software ]

High-precision genetic mapping of behavioral traits in the diversity outbred mouse population
Logan RW, Robledo RF, Recla JM, Philip VM, Bubier JA, Jay JJ, Harwood C, Wilcox T, Gatti DM, Bult CJ, Churchill GA, Chesler EJ.
Genes Brain Behav. 2013 Feb 21. doi: 10.1111/gbb.12029.

Architecture of energy balance traits in emerging lines of the Collaborative Cross
Mathes WF, Aylor DL, Miller DR, Churchill GA, Chesler EJ, Pardo Manuel de Villena F, Threadgill DW, Pomp D.
Am J Physiol Endocrinol Metab. 2011 Jun;300(6):E1124-34. PMCID: PMC3118585 [ Full Text ] [ datasets ]

The mouse as a model for human biology: a resource guide for complex trait analysis
Peters LL, Robledo RF, Bult CJ, Churchill GA, Paigen BJ, Svenson KL.
Nat Rev Genet. 2007 Jan;8(1):58-69.

Genetic analysis in the Collaborative Cross breeding population
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.
Genome Res. 2011 Aug;21(8):1223-38. PMCID: PMC3149490 [ Full Text ] [ datasets ]

High-Resolution Genetic Mapping Using the Mouse Diversity Outbred Population
Svenson KL, Gatti DM, Valdar W, Welsh CE, Cheng R, Chesler EJ, Palmer AA, McMillan L, Churchill GA.
Genetics. 2012 Feb;190(2):437-47. PMCID: PMC3276626 [ Full Text ] [ datasets ]

Genetic analysis of albuminuria in Collaborative Cross and multiple mouse intercross populations
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.
Am J Physiol Renal Physiol. 2012 Oct;303(7):F972-81. PMCID: PMC3469684 [Available on 2013/10/1]

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

The collaborative cross: a recombinant inbred mouse population for the systems genetic era
Threadgill DW, Pardo-Manuel de Villena F, Miller DR, Miller DR, Churchill GA.
ILAR J. 2011 Feb 8;52(1):24-31.

Imputation of single-nucleotide polymorphisms in inbred mice using local phylogeny
Wang JR, Pardo-Manuel de Villena F, Lawson HA, Cheverud JM, Churchill GA, McMillan L.
Genetics. 2012 Feb;190(2):449-58. PMCID: PMC3276610 [ Full Text ] [ datasets ] [ software ]

Center for Genome Dynamics

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

Discovery of novel variants in genotyping arrays improves genotype retention and reduces ascertainment bias
Didion JP, Yang H, Sheppard K, Fu CP, McMillan L, Pardo-Manuel de Villena F, Churchill GA
BMC Genomics. 2012 Jan 19;13(1):34. PMCID: PMC3305361 [ Full Text ] [ software ] [ datasets 1 ] [ datasets 2 ]

Patterns and mechanisms of genome organization in the mouse
Graber JH, Churchill GA, Dipetrillo KJ, King BL, Petkov PM, Paigen K.
J Exp Zoolog A Comp Exp Biol. 2006 Sep 1;305(9):683-8.

CGDSNPdb: a database resource for error-checked and imputed mouse SNPs
Hutchins LN, Ding Y, Szatkiewicz JP, Smith RV, Yang H, de Villena FP, Churchill GA, Graber JH.
Database (Oxford). 2010 Jul 6;2010:baq008. Print 2010. PMCID: PMC2911843 [ Full Text ] [ database ]

Students as collaborators in systems biology research
McClatchy S, McGann D, Gotwals R, Baskett A, Churchill G.
Science. 2013 May 31;340(6136):1061-2. doi: 10.1126/science.1229906. [ Full Text ]

Evidence of a large-scale functional organization of mammalian chromosomes
Petkov PM, Graber JH, Churchill GA, DiPetrillo K, King BL, Paigen K.
PLoS Biol. 2007 May;5(5):e127; author reply e128. PMCID: PMC1868061 [ Full Text ]

Adaptive evolution and effective population size in wild house mice
Phifer-Rixey M, Bonhomme F, Boursot P, Churchill GA, Piálek J, Tucker P, Nachman M.
Mol Biol Evol. 2012 Oct;29(10):2949-55. PMCID: PMC3457769 [Available on 2013/10/1] [ datasets ]

Independent Studies in Computational Biology
Smith R, McGann D, Gotwals R, Symonds R, Hageman R, Vedell P, Churchill G.
NCSSSMST Journal. Fall 2009:10-16. [ Full Text ]

Multiple trait measurements in 43 inbred mouse strains capture the phenotypic diversity characteristic of human populations
Svenson KL, Von Smith R, Magnani PA, Suetin HR, Paigen B, Naggert JK, Li R, Churchill GA, Peters LL.
J Appl Physiol. 2007 Jun;102(6):2369-78. [ Full Text ] [ datasets ]

An imputed genotype resource for the laboratory mouse
Szatkiewicz JP, Beane GL, Ding Y, Hutchins L, Pardo-Manuel de Villena F, Churchill GA.
Mamm Genome. 2008 Mar;19(3):199-208. PMCID: PMC2725522. [ Full Text ] [ datasets ]

On the subspecific origin of the laboratory mouse
Yang H, Bell TA, Churchill GA, Pardo-Manuel de Villena F.
Nat Genet. 2007 Sep;39(9):1100-7.

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

Subspecific origin and haplotype diversity in the laboratory mouse
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.
Nat Genet. 2011 May 29;43(7):648-55. PMCID: PMC3125408 [ Full Text ] [ News Article ] [ datasets ]

Software Development

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

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