Papers - by year

 2015  2014  2013  2012  2011  2010  2009   2008   2007   2006  2005  2004  2003  2002  2001  2000  1999  1998  1997  1996  1995 1994  1993  1992  1991  1990  1989  1986  1985

2015

PRDM9 drives evolutionary erosion of hotspots in Mus musculus through haplotype-specific initiation of meiotic recombination
Baker CL, Kajita S, Walker M, Saxl RL, Raghupathy N, Choi K, Petkov PM and Paigen K.
PLoS Genetics. 2015;11(1):e1004916. PMCID: PMC4287450 [ Full Text ]

Sensitivity to hepatotoxicity due to epigallocatechin gallate is affected by genetic background in diversity outbred mice
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.
Food Chem Toxicol 2015;76:19-26. PMCID: PMC4324012 [ Full Text ]

A multi-megabase copy number gain causes maternal transmission ratio distortion on mouse chromosome 2
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.
PLoS genetics. 2015;11(2):e1004850. PMCID: PMC4334553 [ Full Text ]

Diversity Outbred Mice Identify Population Based Exposure Thresholds and Genetic Factors that Influence Benzene-Induced Genotoxicity
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.
Env. Health Persp., 2015;123(3):237-45. [ Full Text ]

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

2014

Accessing Data Resources in the Mouse Phenome Database for Genetic Analysis of Murine Life Span and Health Span
Bogue MA, Peters LL, Paigen B, Korstanje R, Yuan R, Ackert-Bicknell C, Grubb SC, Churchill GA, Chesler EJ. J Gerontol A Biol Sci Med Sci. 2014. [ Full Text ]

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

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

Quantitative trait locus mapping methods for diversity outbred mice
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.
G3. 2014;4(9):1623-33. PMCID: PMC4169154. [ Full Text ] [ datasets ]

Integrative genetic analysis of allergic inflammation in the murine lung
Kelada SN, Carpenter DE, Aylor DL, Chines P, Rutledge H, Chesler EJ, Churchill GA, Pardo-Manuel de Villena F, Schwartz DA and Collins FS.
American Journal of Respiratory Cell and Molecular Biology. 2014;51(3):436-45. PMCID: PMC4189492.

High-Resolution Sex-Specific Linkage Maps of the Mouse Reveal Polarized Distribution of Crossovers in Male Germline
Liu EY, Morgan AP, Chesler EJ, Wang W, Churchill GA, Pardo-Manuel de Villena F.
Genetics. 2014 Feb 27. doi: 10.1534/genetics.114.161653. PMCID: PMC4012503. [ Full Text ]

RNA-seq alignment to individualized genomes improves transcript abundance estimates in multiparent populations
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.
Genetics. 2014;198(1):59-73. PMCID: PMC4174954 [ Full Text ]

Precise genetic mapping and integrative bioinformatics in Diversity Outbred mice reveals Hydin as a novel pain gene
Recla JM, Robledo RF, Gatti DM, Bult CJ, Churchill GA, Chesler EJ.
Mamm Genome. 2014 Jun;25(5-6):211-22. PMCID: PMC4032469. [ Full Text ]

Genetic regulation of Zfp30, CXCL1, and neutrophilic inflammation in murine lung
Rutledge H, Aylor DL, Carpenter DE, Peck BC, Chines P, Ostrowski LE, Chesler EJ, Churchill GA, de Villena FP and Kelada SN.
Genetics. 2014;198(2):735-45. PMCID: PMC4196624 [ Full Text ]

Spontaneous voiding by mice reveals strain-specific lower urinary tract function to be a quantitative genetic trait
Yu W, Ackert-Bicknell C, Larigakis JD, MacIver B, Steers WD, Churchill GA, Hill WG, Zeidel, ML.
Am J Physiol Renal Physiol. 2014 Jun 1;306(11):F1296-307. PMCID: PMC4042106[ Full Text ]

Genetic Regulation of Female Sexual Maturation and Longevity Through Circulating IGF1
Yuan R, Gatti DM, Krier R, Malay E, Schultz D, Peters LL, Churchill GA, Harrison, DE, Paigen B.
J Gerontol A Biol Sci Med Sci 2014 July 28.[ Full Text ]

2013

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.

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. PMCID: PMC3585141 [ Full Text ]

Integration of Mouse and Human Genome-Wide Association Data Identifies KCNIP4 as an Asthma Gene
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.
PLoS One. 2013;8(2):e56179. doi: 10.1371/journal.pone.0056179. PMCID: PMC3572953 [ Full Text ]

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.

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 ]

2012

Pla2g12b and Hpn Are Genes Identified by Mouse ENU Mutagenesis That Affect HDL Cholesterol
Aljakna A, Choi S, Savage H, Hageman Blair R, Gu T, Svenson KL, Churchill GA, Hibbs M, Korstanje R.
PLoS One. 2012;7(8):e43139. PMCID: PMC3422231 [ Full Text ]

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 ]

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 ]

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 ]

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 ]

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]

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 ]

Discovery of blood transcriptomic markers for depression in animal models and pilot validation in subjects with early-onset major depression
Pajer K, Andrus BM, Gardner W, Lourie A, Strange B, Campo J, Bridge J, Blizinsky K, Dennis K, Vedell P, Churchill GA, Redei EE.
Transl Psychiatry. 2012 Apr 17;2:e101. doi: 10.1038/tp.2012.26. PMCID: PMC3337072 [ 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 ]

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 ]

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 ]

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 ]

2011

The future of model organisms in human disease research
Aitman TJ, Boone C, Churchill GA, Hengartner MO, Mackay TFC, Stemple DL.
Nat Rev Genet. 2011 Jul 18;12(8):575-82. doi: 10.1038/nrg3047.

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 ]

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 ]

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 ]

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 ]

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 ]

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 ]

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.

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 ]

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 ]

2010

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

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 ]

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 ]

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 ]

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 ]

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 ]

Critical reasoning on causal inference in genome-wide linkage and association studies
Li Y, Tesson BM, Churchill GA, Jansen RC.
Trends Genet. 2010 Dec;26(12):493-8. PMCID: PMC2991400 [ Full Text ]

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 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 ]

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 ]

2009

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)]

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 ]

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 ]

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 ]

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 ]

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 ]

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. PMCID: PMC2942088 [ Full Text ]

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 ]

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 ]

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 ]

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

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 ]

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 ]

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 ]

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 ]

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

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 ]

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 ]

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 ]

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 ]

2008

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 ]

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 ]

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 ]

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 ]

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 ]

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 ]

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.

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 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 ]

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 ]

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 ]

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 ]

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 ]

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 ]

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 ]

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 ]

2007

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

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 ]

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 ]

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 ]

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 ]

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 ]

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.

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 ]

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

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 ]

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 ]

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 ]

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 ]

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.

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

2006

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 ]

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 ]

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 ]

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.

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 ]

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 ]

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.

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. 2006 Mar;7(2):184. [ datasets ]

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

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 ]

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 ]

2005

Interacting genetic loci cause airway hyperresponsiveness
Ackerman KG, Huang H, Grasemann H, Puma C, Singer JB, Hill AE, Lander E, Nadeau JH, Churchill GA, Drazen JM, Beier DR.
Physiol Genomics. 2005 Mar 21;21(1):105-11. [ Full Text ] [ datasets ]

Lineage is an epigenetic modifier of QTL influencing behavioral coping with stress
Ahmadiyeh N, Churchill GA, Solberg LC, Baum AE, Shimomura K, Takahashi JS, Redei EE.
Behav Genet. 2005 Mar;35(2):189-98. [ datasets ]

Quantitative trait loci associated with elevated thyroid-stimulating hormone in the Wistar-Kyoto rat
Baum AE, Solberg LC, Kopp P, Ahmadiyeh N, Churchill G, Takahashi JS, Jameson JL, Redei EE.
Endocrinology. 2005 Feb;146(2):870-8. [ Full Text ] [ datasets ]

Quantitative trait loci for femoral and lumbar vertebral bone mineral density in C57BL/6J and C3h/HeJ inbred strains of mice. (2001).
Beamer WG, Shultz KL, Donahue LR, Churchill GA, Sen S, Wergedal JR, Baylink DJ, Rosen CJ.
J Bone Miner Res. 2005 Sep;20(9):1701-12; discussion 1700.

Gonadal sex reversal in mutant Dax1 XY mice: a failure to upregulate Sox9 in pre-Sertoli cells
Bouma GJ, Albrecht KH, Washburn LL, Recknagel AK, Churchill GA, Eicher EM.
Development. 2005 Jul;132(13):3045-54. [ Full Text ] [ datasets ]

Improved statistical tests for differential gene expression by shrinking variance components estimates
Cui X, Hwang JT, Qiu J, Blades NJ, Churchill GA.
Biostatistics. 2005 Jan;6(1):59-75. [ Full Text ]

Distal Chr 4 harbors a genetic locus (Gct1) fundamental for spontaneous ovarian granulosa cell tumorigenesis in a mouse model
Dorward AM, Shultz KL, Horton LG, Li R, Churchill GA, Beamer WG.
Cancer Res. 2005 Feb 15;65(4):1259-64. [ Full Text ] [ datasets ]

Combining data from multiple inbred line crosses improves the power and resolution of quantitative trait loci mapping
Li R, Lyons MA, Wittenburg H, Paigen B, Churchill GA.
Genetics. 2005 Mar;169(3):1699-709. PMCID: PMC1449540. [ Full Text ] [ datasets 1 ] [ datasets 2 ] [ datasets 3 ] [ datasets 4 ]

Single and interacting QTLs for cholesterol gallstones revealed in an intercross between mouse strains NZB and SM
Lyons MA, Korstanje R, Li R, Sheehan SM, Walsh KA, Rollins JA, Carey MC, Paigen B, Churchill GA.
Mamm Genome. 2005 Mar;16(3):152-63.

Kinesin family member 12 is a candidate polycystic kidney disease modifier in the cpk mouse
Mrug M, Li R, Cui X, Schoeb TR, Churchill GA, Guay-Woodford LM.
J Am Soc Nephrol. 2005 Apr;16(4):905-16. [ Full Text ] [ datasets ]

Quantitative trait loci for baseline white blood cell count, platelet count, and mean platelet volume
Peters LL, Zhang W, Lambert AJ, Brugnara C, Churchill GA, Platt OS.
Mamm Genome. 2005 Oct;16(10):749-63.

Evidence of a large-scale functional organization of mammalian chromosomes
Petkov PM, Graber JH, Churchill GA, DiPetrillo K, King BL, Paigen K.
PLoS Genet. 2005 Sep;1(3):e33. PMCID: PMC1201368 [ Full Text ] [ datasets ]

Conditioning the genome identifies additional diabetes resistance loci in Type I 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 ]

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

Quantitative trait mapping in a diallel cross of recombinant inbred lines
Tsaih SW, Lu L, Airey DC, Williams RW, Churchill GA.
Mamm Genome. 2005 May;16(5):344-55. [ datasets ]

Association of a lithogenic Abcg5/Abcg8 allele on Chromosome 17 (Lith9) with cholesterol gallstone formation in PERA/EiJ mice
Wittenburg H, Lyons MA, Li R, Kurtz U, Mossner J, Churchill GA, Carey MC, Paigen B.
Mamm Genome. 2005 Jul;16(7):495-504. [ datasets ]

Experimental design for three-color and four-color gene expression microarrays
Woo Y, Krueger W, Kaur A, Churchill G.
Bioinformatics. 2005 Jun;21 Suppl 1:i459-67. [ Full Text ] [ datasets ]

Bayesian model selection for genome-wide epistatic quantitative trait loci analysis
Yi N, Yandell BS, Churchill GA, Allison DB, Eisen EJ, Pomp D.
Genetics. 2005 Jul;170(3):1333-44. PMCID: PMC1451197. [ Full Text ] [ datasets ]

2004

Mapping quantitative trait loci for vertebral trabecular bone volume fraction and microarchitecture in mice
Bouxsein ML, Uchiyama T, Rosen CJ, Shultz KL, Donahue LR, Turner CH, Sen S, Churchill GA, Muller R, Beamer WG.
J Bone Miner Res. 2004 Apr;19(4):587-99. [ datasets ]

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

The Collaborative Cross, a community resource for the genetic analysis of complex traits
Complex Trait Consortium.
Nat Genet. 2004 Nov;36(11):1133-7.

Genetic analysis of blood pressure in C3H/HeJ and SWR/J mice
DiPetrillo K, Tsaih SW, Sheehan S, Johns C, Kelmenson P, Gavras H, Churchill GA, Paigen B.
Physiol Genomics. 2004 Apr 13;17(2):215-20. [ datasets ]

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

Quantitative trait loci analysis for plasma HDL-cholesterol concentrations and atherosclerosis susceptibility between inbred mouse strains C57BL/6J and 129S1/SvIm
Ishimori N, Li R, Kelmenson PM, Korstanje R, Walsh KA, Churchill GA, Forsman-Semb K, Paigen B.
J. Arterioscler Thromb Vasc Biol 2004 Jan;24(1):161-6. [ Full Text ] [ datasets ]

Quantitative trait loci that determine plasma lipids and obesity in C57BL/6J and 129S1/SvImJ inbred mice
Ishimori N, Li R, Kelmenson PM, Korstanje R, Walsh KA, Churchill GA, Forsman-Semb K, Paigen B.
J Lipid Res 2004 Sep;45(9):1624-1632. [ Full Text ] [ datasets ]

Selective phenotyping for increased efficiency in genetic mapping studies
Jin C, Lan H, Attie AD, Churchill GA, Bulutuglo D, Yandell BS.
Genetics. 2004 Dec;168(4):2285-93. PMCID: PMC1448737. [ Full Text ]

Quantitative trait locus mapping of genes that regulate phospholipid transfer activity in SM/J and NZB/BlNJ inbred mice
Korstanje R, Albers JJ, Wolfbauer G, Li R, Tu AY, Churchill GA, Paigen BJ.
Arterioscler Thromb Vasc Biol. 2004 Jan;24(1):155-60. [ Full Text ]

Locating Ath8, a locus for murine atherosclerosis susceptibility and testing several of its candidate genes in mice and humans
Korstanje R, Eriksson P, Samnegard A, Olsson PG, Forsman-Semb K, Sen S, Churchill GA, Rollins J, Harris S, Hamsten A, Paigen B.
Atherosclerosis. 2004 Dec;177(2):443-50.

Influence of sex and diet on quantitative trait loci for HDL cholesterol levels in an SM/J by NZB/BlNJ intercross population
Korstanje R, Li R, Howard T, Kelmenson P, Marshall J, Paigen B, Churchill G.
J Lipid Res. 2004 May;45(5):881-8. [ Full Text ]

Exploration of low-dose estrogen effects: identification of No Observed Transcriptional Effect Level (NOTEL)
Lobenhofer EK, Cui X, Bennett L, Cable PL, Merrick BA, Churchill GA, Afshari CA.
Toxicol Pathol. 2004 Jul-Aug;32(4):482-92. [ datasets ]

Genetic contributors to lipoprotein cholesterol levels in an intercross of 129S1/SvImJ and RIIIS/J inbred mice
Lyons MA, Korstanje R, Li R, Walsh KA, Churchill GA, Carey MC, Paigen B.
Physiol Genomics. 2004 Apr 13;17(2):114-21. [ datasets ]

Quantitative trait loci that determine lipoprotein cholesterol levels in an intercross of 129S1/SvImJ and CAST/Ei inbred mice
Lyons MA, Wittenburg H, Li R, Walsh KA, Korstanje R, Churchill GA, Carey MC, Paigen B.
Physiol Genomics. 2004 Mar 12;17(1):60-8. [ datasets ]

Proteotypic classification of spontaneous and transgenic mammary neoplasms
Mikaelian I, Blades N, Churchill GA, Fancher K, Knowles BB, Eppig JT, Sundberg JP.
Breast Cancer Res. 2004;6(6):R668-79. PMCID: PMC1064077. [ Full Text ]

Identification of quantitative trait loci that modify the severity of hereditary spherocytosis in wan, a new mouse model of band-3 deficiency
Peters LL, Swearingen RA, Andersen SG, Gwynn B, Lambert AJ, Li R, Lux SE, Churchill GA.
Blood. 2004 Apr 15;103(8):3233-40. [ Full Text ] [ datasets ]

Sex- and lineage-specific inheritance of depression-like behavior in the rat
Solberg LC, Baum AE, Ahmadiyeh N, Shimomura K, Li R, Turek FW, Churchill GA, Takahashi JS, Redei EE.
Mamm Genome. 2004 Aug;15(8):648-62. [ datasets ]

A comparison of cDNA, oligonucleotide, and Affymetrix GeneChip gene expression microarray platforms
Woo Y, Affourtit J, Daigle S, Viale A, Johnson K, Naggert J, Churchill G.
J Biomol Tech 2004 Dec;15:276-284. PMCID: PMC2291701. [ Full Text ] [ datasets ]

2003

X-linked and lineage-dependent inheritance of coping responses to stress
Ahmadiyeh N, Churchill GA, Shimomura K, Solberg LC, Takahashi JS, Redei EE.
Mamm Genome. 2003 Nov;14(11):748-57. [ datasets ]

Genetic modulation of tau phosphorylation in the mouse
Brich J, Shie FS, Howell BW, Li R, Tus K, Wakeland EK, Jin LW, Mumby M, Churchill G, Herz J, Cooper JA.
J Neurosci. 2003 Jan 1;23(1):187-92. [ Full Text ] [ datasets ]

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

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

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

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

Quantitative trait loci that determine lipoprotein cholesterol levels in DBA/2J and CAST/Ei inbred mice
Lyons MA, Wittenburg H, Li R, Walsh KA, Churchill GA, Carey MC, Paigen B.
J Lipid Res. 2003 May;44(5):953-67. [ Full Text ] [ datasets ]

New quantitative trait loci that contribute to cholesterol gallstone formation detected in an intercross of CAST/Ei and 129S1/SvImJ inbred mice
Lyons MA, Wittenburg H, Li R, Walsh KA, Leonard MR, Churchill GA, Carey MC, Paigen B.
Physiol Genomics. 2003 Aug 15;14(3):225-39. [ datasets ]

Lith6: a new QTL for cholesterol gallstones from an intercross of CAST/Ei and DBA/2J inbred mouse strains
Lyons MA, Wittenburg H, Li R, Walsh KA, Leonard MR, Korstanje R, Churchill GA, Carey MC, Paigen B.
J Lipid Res. 2003 Sep;44(9):1763-71. [ Full Text ] [ datasets ]

Genetic analysis of resistance to Type-1 Diabetes in ALR/Lt mice, a NOD-related strain with defenses against autoimmune-mediated diabetogenic stress
Mathews CE, Graser RT, Bagley RJ, Caldwell JW, Li R, Churchill GA, Serreze DV, Leiter EH.
Immunogenetics. 2003 Oct;55(7):491-6. [ datasets ]

Pleiotropy, homeostasis, and functional networks based on assays of cardiovascular traits in genetically randomized populations
Nadeau JH, Burrage LC, Restivo J, Pao YH, Churchill G, Hoit BD.
Genome Res. 2003 Sep;13(9):2082-91. PMCID: PMC403692. [ Full Text ] [ datasets ]

Major locus on mouse chromosome 17 and minor locus on chromosome 9 are linked with alopecia areata in C3H/HeJ mice
Sundberg JP, Boggess D, Silva KA, McElwee KJ, King LE, Li R, Churchill G, Cox GA.
J Invest Dermatol. 2003 May;120(5):771-5. [ Full Text ] [ datasets ]

Using advanced intercross lines for high-resolution mapping of HDL cholesterol quantitative trait loci
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.
Genome Res. 2003 Jul;13(7):1654-64. PMCID: PMC403739. [ Full Text ] [ datasets 1 ] [ datasets 2 ]

FXR and ABCG5/ABCG8 as determinants of cholesterol gallstone formation from quantitative trait locus mapping in mice
Wittenburg H, Lyons MA, Li R, Churchill GA, Carey MC, Paigen B.
Gastroenterology. 2003 Sep;125(3):868-81. [ datasets ]

2002

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
Bouxsein ML, Rosen CJ, Turner CH, Ackert CL, Shultz KL, Donahue LR, Churchill G, Adamo ML, Powell DR, Turner RT, Muller R, Beamer WG.
J Bone Miner Res. 2002 Apr;17(4):570-9.

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

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

Statistical analysis of a gene expression microarray experiment with replication
Kerr MK, Afsharie CA, Bennett L, Bushel P, Martinez J, Walker N, Churchill GA.
Statistica Sinica 2002;12:203-218. [ Full Text ] [ datasets ]

Genetics of colitis susceptibility in IL-10-deficient mice: backcross versus F2 results contrasted by principal component analysis
Mahler M, Most C, Schmidtke S, Sundberg JP, Li R, Hedrich HJ, Churchill GA.
Genomics. 2002 Sep;80(3):274-82. [ datasets 1 ] [ datasets 2 ]

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

Quantitative trait locus mapping of genes that regulate HDL cholesterol in SM/J and NZB/B1NJ inbred mice
Pitman WA, Korstanje R, Churchill GA, Nicodeme E, Albers JJ, Cheung MC, Staton MA, Sampson SS, Harris S, Paigen B.
Physiol Genomics. 2002;9(2):93-102. [ Full Text ] [ datasets ]

QTL analysis of self-selected macronutrient diet intake: fat, carbohydrate, and total kilocalories
Smith Richards BK, Belton BN, Poole AC, Mancuso JJ, Churchill GA, Li R, Volaufova J, Zuberi A, York B.
Physiol Genomics. 2002 Dec 3;11(3):205-17. [ Full Text ] [ datasets ]

QTL associated with blood pressure, heart rate, and heart weight in CBA/CaJ and BALB/cJ mice
Sugiyama F, Churchill GA, Li R, Libby LJ, Carver T, Yagami K, John SW, Paigen B.
Physiol Genomics. 2002 Jul 12;10(1):5-12. [ datasets ]

Interacting QTLs for cholesterol gallstones and gallbladder mucin in AKR and SWR strains of mice
Wittenburg H, Lammert F, Wang DQ, Churchill GA, Li R, Bouchard G, Carey MC, Paigen B.
Physiol Genomics. 2002 Feb 11;8(1):67-77. [ datasets ]

2001

Quantitative trait loci for femoral and lumbar vertebral bone mineral density in C57BL/6J and C3H/HeJ inbred strains of mice
Beamer WG, Shultz KL, Donahue LR, Churchill GA, Sen S, Wergedal JR, Baylink DJ, Rosen CJ.
J Bone Miner Res. 2001 Jul;16(7):1195-206. [ datasets ]

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

A major quantitative trait locus on chromosome 3 controls colitis severity in IL-10-deficient mice
Farmer MA, Sundberg JP, Bristol IJ, Churchill GA, Li R, Elson CO, Leiter EH.
Proc Natl Acad Sci U S A 2001 Nov 20;98:13820-13825. PMCID: PMC61125. [ Full Text ] [ datasets ]

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

Bootstrapping cluster analysis: assessing the reliability of conclusions from microarray experiments
Kerr MK, Churchill GA.
Proc Natl Acad Sci U S A 2001 Jul 31;98:8961-8965. PMCID: PMC55356. [ Full Text ]

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

Genetic analysis of a new mouse model for non-insulin-dependent diabetes
Kim JH, Sen S, Avery CS, Simpson E, Chandler P, Nishina PM, Churchill GA, Naggert JK.
Genomics. 2001 Jun 15;74(3):273-86. [ datasets ]

The impact of reduced frequency of cage changes on the health of mice housed in ventilated cages
Reeb-Whitaker CK, Paigen B, Beamer WG, Bronson RT, Churchill GA, Schweitzer IB, Myers DD.
Lab Anim. 2001 Jan;35(1):58-73. [ Full Text ]

A statistical framework for quantitative trait mapping
Sen S, Churchill GA.
Genetics. 2001 Sep;159(1):371-87. PMCID: PMC1461799 [ Full Text ] [ datasets ]

Genome-wide epistatic interaction analysis reveals complex genetic determinants of circadian behavior in mice
Shimomura K, Low-Zeddies SS, King DP, Steeves TDL, Whiteley A, Kushla J, Zemenides PD, Lin A, Vitaterna MH, Churchill GA, Takahashi JS.
Genome Res. 2001 Jun;11(6):959-80. [ Full Text ] [ datasets ]

Concordance of murine quantitative trait loci for salt-induced hypertension with rat and human loci
Sugiyama F, Churchill GA, Higgins DC, Johns C, Makaritsis KP, Gavras H, Paigen B.
Genomics. 2001 Jan 1;71(1):70-7. [ datasets ]

2000

Genetic control of susceptibility to UV-induced immunosuppression by interacting quantitative trait loci
Clemens KE, Churchill G, Bhatt N, Richardson K, Noonan FP.
Genes Immun. 2000;1(4):251-9. [ Full Text ] [ datasets ]

Quantitative trait loci modulate renal cystic disease severity in the mouse bpk model
Guay-Woodford LM, Wright CJ, Walz G, Churchill GA.
J Am Soc Nephrol. 2000 Jul;11(7):1253-60. [ Full Text ] [ datasets ]

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

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

A new method for characterizing replacement rate variation in molecular sequences. Application of the Fourier and wavelet models to Drosophila and mammalian proteins
Morozov P, Sitnikova T, Churchill G, Ayala FJ, Rzhetsky A.
Genetics. 2000 Jan;154(1):381-95. PMCID: PMC1460898. [ Full Text ]

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

Mapping quantitative trait loci for serum insulin-like growth factor-1 levels in mice
Rosen CJ, Churchill GA, Donahue LR, Shultz KL, Burgess JK, Powell DR, Beamer WG.
Bone. 2000 Oct;27(4):521-8. [ datasets ]

The information content of a character under a Markov model of evolution
Shpak M, Churchill GA.
Mol Phylogenet Evol. 2000 Nov;17(2):231-43.

1999

Quantitative trait loci for bone density in C57BL/6J and CAST/EiJ inbred mice
Beamer WG, Shultz KL, Churchill GA, Frankel WN, Baylink DJ, Rosen CJ, Donahue LR.
Mamm Genome. 1999 Nov;10(11):1043-9. [ datasets ]

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

Bayesian restoration of a hidden Markov chain with applications to DNA sequencing
Churchill GA, Lazareva B.
J Comput Biol. 1999 Summer;6(2):261-77.

Genetic analysis of susceptibility to dextran sulfate sodium-induced colitis in mice
Mahler M, Bristol IJ, Sundberg JP, Churchill GA, Birkenmeier EH, Elson CO, Leiter EH.
Genomics. 1999 Jan 15;55(2):147-56.

Statistical aspects of genetic mapping in autopolyploids
Ripol MI, Churchill GA, da Silva JAG, Sorrells M.
Gene. 1999 Jul 22;235(1-2):31-41.

The role of subjectivity in reconstructing ancestral character states: A Bayesian approach to unknown rates, states and transformation asymmetries
Schultz TR, Churchill GA.
Syst Biol 1999;48:651-664.

Genetic modifiers of polycystic kidney disease in intersubspecific KAT2J mutants
Upadhya P, Churchill G, Birkenmeier EH, Barker JE, Frankel WN.
Genomics. 1999 Jun 1;58(2):129-37.

1998

Multigenic and imprinting control of ovarian granulosa cell tumorigenesis in mice
Beamer WG, Shultz KL, Tennent BJ, Nadeau JH, Churchill GA, Eicher EM.
Cancer Res. 1998 Aug 15;58(16):3694-9. [ Full Text ]

Identification of quantitative trait loci associated with acylsugar accumulation using intraspecific populations of the wild tomato, Lycopersicon pennellii
Blauth SL, Churchill GA, Mutschler MA.
Theor Appl Genet 1998 Mar;96(3-4):458-467.

1997

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

1996

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

A hidden Markov model approach to variation among sites in rate of evolution
Felsenstein J, Churchill GA.
Mol Biol Evol. 1996 Jan;13(1):93-104. [ Full Text ]

Biases in amino acid replacement matrices and alignment scores due to rate heterogeneity
Kelly C, Churchill GA.
J Comput Biol. 1996 Summer;3(2):307-18.

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

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

1995

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

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

1994

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

1993

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

Pooled-sampling makes high-resolution mapping practical with DNA markers
Churchill GA, Giovannoni JJ, Tanksley SD.
Proc Natl Acad Sci U S A. 1993 Jan 1;90(1):16-20. PMCID: PMC45590. [ Full Text ]

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

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

1992

Hidden Markov chains and the analysis of genome structure
Churchill GA.
Comput Chem 1992;16:107-115.

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

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

1991

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

1990

The distribution of restriction enzyme sites in Escherichia coli
Churchill GA, Daniels DL, Waterman MS.
Nucleic Acids Res. 1990 Feb 11;18(3):589-97. PMCID: PMC333466. [ Full Text ]

1989

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

Stable maintenance of a 35-base-pair yeast mitochondrial genome
Fangman WL, Henly JW, Churchill G, Brewer BJ.
Mol Cell Biol. 1989 May;9(5):1917-21. PMCID: PMC362982. [ Full Text ]

1986

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

1985

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