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2012 2011 2010 2009 2008 2007 2006
2012
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. [Epub ahead of print] [ 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 ]
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 ]
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 Apr 3. [Epub ahead of print]
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 ]
Computation 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 [Available on 2013/2/1] [ 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
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 [Available on 2012/2/1] [ Full Text ] [ Highlight in Nature Reviews Genetics ] [ datasets ]
Patterns of recombination activity on mouse chromosome 11 revealed by high resolution mapping
Billings T, Sargent EE, Szatkiewicz JP, Leahy N, Kwak IY, Bektassova N, Walker M, Hassold T, Graber JH, Broman KW, Petkov PM.
PLoS One. 2010 Dec 8;5(12):e15340. PMCID: PMC2999565. [ Full Text ]
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 [Available on 2012/1/1] [ 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 ]
Architecture of energy balance traits in emerging lines of the Collaborative Cross
Mathes WF, Aylor DL, Miller DR, Churchill GA, Chesler EJ, de Villena FP, Threadgill DW, Pomp D.
Am J Physiol Endocrinol Metab. 2011 Jun;300(6):E1124-34. PMCID: PMC3118585 [Available on 2012/6/1] [ datasets ]
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 [Available on 2012/1/1] [ Full Text ] [ News Article ] [ datasets ]
2010
Functional genomics complements quantitative genetics in identifying disease-gene associations
Guan Y, Ackert-Bicknell CL, Kell B, Troyanskaya OG, Hibbs MA.
PLoS Comput Biol. 2010 Nov 11;6(11):e1000991. PMCID: PMC2978695. [ Full Text ] [ Supplemental Website ]
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 ] [ datasets 1 ] [ datasets 2 ]
Genetic architecture of voluntary exercise in an advanced intercross line of mice
Kelly SA, Nehrenberg DL, Peirce JL, Hua K, Steffy BM, Wiltshire T, Pardo-Manuel de Villena F, Garland T Jr, Pomp D.
Physiol Genomics. 2010 Jul 7;42(2):190-200. PMCID: PMC3032284 [ Full Text ]
Epistasis contributes to the genetic buffering of plasma HDL cholesterol in mice
Li RH, Churchill GA.
Physiol Genomics. 2010 Nov 29;42A(4):228-34. PMCID: PMC3008368 [Available on 2011/12/1] [ 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 [Available on 2011/12/1]
Efficient genome ancestry inference in complex pedigrees with inbreeding
Liu EY, Zhang Q, McMillan L, de Villena FP, Wang W.
Bioinformatics. 2010 Jun 15;26(12):i199-207. PMCID: PMC2881372. [ Full Text ]
Genomic mapping of social behavior traits in a F2 cross derived from mice selectively bred for high aggression
Nehrenberg DL, Wang S, Buus RJ, Perkins J, de Villena FP, Pomp D.
BMC Genet. 2010 Dec 31;11:113. PMCID: PMC3022667 [ Full Text ]
Mammalian recombination hot spots: properties, control and evolution
Paigen K, Petkov P.
Nat Rev Genet. 2010 Mar;11(3):221-33.
Prdm9 controls activation of mammalian recombination hotspots
Parvanov ED, Petkov PM, Paigen K.
Science. 2010 Feb 12;327(5967):835. PMCID: PMC2821451. [ Full Text ]
Coordinated expression domains in mammalian genomes
Woo YH, Walker M, Churchill GA.
PLoS One. 2010 Aug 18;5(8):e12158. PMCID: PMC2923606. [ Full Text ] [ datasets ]
2009
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 ] [ datasets 1 ] [ datasets 2 ]
An experimental assessment of in silico haplotype association mapping in laboratory mice
Burgess-Herbert SL, Tsaih SW, Stylianou IM, Walsh K, Cox AJ, Paigen B.
BMC Genet. 2009 Dec 9;10:81. PMCID: PMC2797012. [ Full Text ] [ datasets ]
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 ]
Parental origin of chromosomes influences crossover activity within the Kcnq1 transcriptionally imprinted domain of Mus musculus
Ng SH, Madeira R, Parvanov ED, Petros LM, Petkov PM, Paigen K.
BMC Mol Biol. 2009 May 13;10:43. PMCID: PMC2689222. [ Full Text ]
TreeQA: quantitative genome wide association mapping using local perfect phylogeny trees
Pan F, McMillan L, Pardo-Manuel De Villena F, Threadgill D, Wang W.
Pac Symp Biocomput. 2009:415-26. PMCID: PMC2739990. [ Full Text ]
Trans-regulation of mouse meiotic recombination hotspots by Rcr1
Parvanov ED, Ng SHS, Petkov PM, Paigen K.
PLoS Biol. 2009 Feb 17;7(2):e36. PMCID: PMC2642880. [ Full Text ]
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 ]
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 ]
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 ]
Inferring genome-wide mosaic structure
Zhang Q, Wang W, McMillan L, Pardo-Manuel De Villena F, Threadgill D.
Pac Symp Biocomput. 2009:150-61. PMCID: PMC2736068. [ Full Text ]
2008
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 ]
Position-dependent motif characterization using non-negative matrix factorization
Hutchins LN, Murphy SM, Singh P, Graber JH.
Bioinformatics. 2008 Dec 1;24(23):2684-90. PMCID: PMC2639279. [ Full Text ]
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 ]
A quantitative assay for crossover and noncrossover molecular events at individual recombination hotspots in both male and female gametes
Ng SH, Parvanov E, Petkov PM, Paigen K.
Genomics. 2008 Oct;92(4):204-9. PMCID: PMC2610674 [ Full Text ]
The recombinational anatomy of a mouse chromosome
Paigen K, Szatkiewicz JP, Sawyer K, Leahy N, Parvanov ED, Ng SH, Graber JH, Broman KW, Petkov PM.
PLoS Genet. 2008 Jul 11;4(7):e1000119. PMCID: PMC2440539 [ 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 ]
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.
Crossover interference underlies sex differences in recombination rates
Petkov PM, Broman KW, Szatkiewicz JP, Paigen K.
Trends Genet. 2007 Nov;23(11):539-42.
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 ]
The polymorphism architecture of mouse genetic resources elucidated using genome-wide resequencing data: implications for QTL discovery and systems genetics
Roberts A, Pardo-Manuel de Villena F, Wang W, McMillan L, Threadgill DW.
Mamm Genome. 2007 Jul;18(6-7):473-81. PMCID: PMC1998888 [ Full Text ]
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 ]
Three male germline-specific aldolase A isozymes are generated by alternative splicing and retrotransposition
Vemuganti SA, Bell TA, Scarlett CO, Parker CE, de Villena FP, O'Brien DA.
Dev Biol. 2007 Sep 1;309(1):18-31. NIHMSID30168.
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
The genetics of gene expression
Churchill GA.
Mamm Genome. 2006 Jun;17(6):465.
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.
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 ]
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