Publications - by year


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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 ]

Diet dominates host genotype in shaping the murine gut microbiota
Carmody RN, Gerber GK, Luevano JM, Jr., Gatti DM, Somes L, Svenson KL and Turnbaugh PJ.
Cell Host & Microbe. 2015;17(1):72-84. PMCID: PMC4297240.

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 ]

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 ]


PRDM9 binding organizes hotspot nucleosomes and limits Holliday junction migration
Baker CL, Kajita S, Walker M, Petkov PM, Paigen K.
Genome Res. 2014 May;24(5):724-32. PMCID: PMC4009602.

Graph-regularized dual Lasso for robust eQTL mapping
Cheng W, Zhang X, Guo Z, Shi Y, Wang W.
Bioinformatics. 2014;30(12):i139-48. PMCID: PMC4058913. [ Full Text ]

Out of the bottleneck: the Diversity Outcross and Collaborative Cross mouse populations in behavioral genetics research
Chesler EJ.
Mamm Genome. 2014 Feb;25(1-2):3-11. PMCID: PMC3916706. [ Full Text ]

Cell-type-specific predictive network yields novel insights into mouse embryonic stem cell self-renewal and cell fate.
Dowell KG, Simons AK, Wang ZZ, Yun K, Hibbs MA.
PLoS One. 2013 8(2):e56810. doi: 10.1371/journal.pone.0056810. PMCID: PMC3585227. [ 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 ]

Merging of multi-string BWTs with applications
Holt J, McMillan L.
Bioinformatics. 2014;30(24):3524-31. PMCID: PMC4318930 [ Full Text ]

Identification of novel genes associated with renal tertiary lymphoid organ formation in aging mice
Huang Y, Caputo CR, Noordmans GA, Yazdani S, Monteiro LH, van den Born J, van Goor H, Heeringa P, Korstanje R and Hillebrands JL.
PloS One. 2014;9(3):e91850. PMCID: PMC3956762. [ Full Text ]

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 ]

FastHap: fast and accurate single individual haplotype reconstruction using fuzzy conflict graphs
Mazrouee S, Wang W.
Bioinformatics. 2014;30(17):i371-8. PMCID: PMC4147895 [ 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 ]

Using the Collaborative Cross to probe the immune system
Phillippi J, Xie Y, Miller DR, Bell TA, Zhang Z, Lenarcic AB, Aylor DL, Krovi SH, Threadgill DW, de Villena FP, Wang W, Valdar W, Frelinger JA.
Genes Immun. 2014 Jan;15(1):38-46. PMCID: PMC4004367. [ Full Text ]

Dissection of Complex Gene Expression Using the Combined Analysis of Pleiotropy and Epistasis
Philip VM, Tyler AL, Carter GW.
Pac Symp Biocomput. 2014:200-11. PubMed PMID: 24297548; PubMed Central PMCID: PMC3900022. [ Full Text ]

Rapid identification of major-effect genes using the collaborative cross
Ram R, Mehta M, Balmer L, Gatti DM, Morahan G.
Genetics. 2014;198(1):75-86. PMCID: PMC4174955 [ 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 ]

A genetic interaction network model of a complex neurological disease.
Tyler AL, McGarr TC, Beyer BJ, Frankel WN, Carter GW.
Genes, Brain, and Behavior. 2014;13(8):831-40. PMCID: PMC4241132 [ Full Text ]

RNA-Skim: a rapid method for RNA-Seq quantification at transcript level
Zhang Z, Wang W.
Bioinformatics. 2014;30(12):i283-i92. PMCID: PMC4058932[ Full Text ]


DNA binding specificities of the long zinc finger recombination protein PRDM9
Billings T, Parvanov ED, Baker CL, Walker M, Paigen K, Petkov PM.
Genome Biol. 2013 Apr 24;14(4):R35. PMCID: 23618393. [ Full Text ]

Genetic architecture of skewed X inactivation in the laboratory mouse
Calaway JD, Lenarcic AB, Didion JP, Wang JR, Searle JB, McMillan L, Valdar W, Pardo-Manuel de Villena F.
PLoS Genetics. 2013 9(10):e1003853. PMCID: PMC3789830. [ Full Text ]

Inferring gene function and network organization in Drosophila signaling by combined analysis of pleiotropy and epistasis
Carter GW.
G3 (Bethesda). 2013 Mar 18. pii: g3.113.005710v1. doi: 10.1534/g3.113.005710. PMCID: PMC3656728 [ Full Text ]

Deconstructing Mus gemischus: advances in understanding ancestry, structure, and variation in the genome of the laboratory mouse
Didion JP, de Villena FP.
Mamm Genome. 2013 Feb;24(1-2):1-20. doi: 10.1007/s00335-012-9441-z. PMCID: PMC4034049. [ Full Text ]

Cell-type-specific predictive network yields novel insights into mouse embryonic stem cell self-renewal and cell fate.
Dowell KG, Simons AK, Wang ZZ, Yun K, Hibbs MA.
PLoS One. 2013 8(2):e56810. doi: 10.1371/journal.pone.0056810. PMCID: PMC3585227. [ Full Text ]

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. doi: 10.1371/journal.ppat.1003196. PMCID: PMC3585141 [ Full Text ]

DNA damage induces targeted, genome-wide variation of poly(A) sites in budding yeast
Graber JH, Nazeer FI, Yeh PC, Kuehner JN, Borikar S, Hoskinson D, Moore CL.
Genome Res. 2013 Oct;23(10):1690-703. PMCID: PMC3787265. [ 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. PMCID: PMC3709837. [ Full Text ]

Students as collaborators in systems biology research
McClatchy S, McGann D, Gotwals R, Baskett A, Churchill G.
2013. IBI* series winner. Science. 2013 May 31;340(6136):1061-2. doi: 10.1126/science.1229906. PMCID: PMC4088332. [ Full Text ]

Genetic analysis of mesangial matrix expansion in aging mice and identification of Far2 as a candidate gene
Noordmans GA, Caputo CR, Huang Y, Sheehan SM, Bulthuis M, Heeringa P, Hillebrands JL, van Goor H, Korstanje R.
J Am Soc Nephrol. 2013 Dec;24(12):1995-2001. PMCID: PMC3839541. [ Full Text ]

CAPE: An R Package for Combined Analysis of Pleiotropy and Epistasis
Tyler AL, Lu W, Hendrick J, Philip V, Carter GW.
PLoS Computational Biology. 2013. 9(10): e1003270. PMCID: PMC3808451. [ Full Text ]

GeneScissors: a comprehensive approach to detecting and correcting spurious transcriptome inference owing to RNA-seq reads misalignment
Zhang Z, Huang S, Wang J, Zhang X, Pardo Manuel de Villena F, McMillan L, Wang W.
Bioinformatics. 2013 Jul 1;29(13):i291-9. PMCID: PMC3694649. [ Full Text ]


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 ]

Intronic parent-of-origin dependent differential methylation at the Actn1 gene is conserved in rodents but is not associated with imprinted expression
Calaway JD, Domínguez JI, Hanson ME, Cambranis EC, Pardo-Manuel de Villena F, de la Casa-Esperon E.
PLoS One. 2012;7(11):e48936. doi: 10.1371/journal.pone.0048936. PMCID: PMC3493592 [ Full Text ]

Predicting the effects of copy-number variation in double and triple mutant combinations
Carter GW, Hays M, Li S, Galitski T.
Pac Symp Biocomput. 2012:19-30. PMCID: PMC3334851 [ Full Text ]

Use of pleiotropy to model genetic interactions in a population
Carter GW, Hays M, Sherman A, Galitski T.
PLoS Genet. 2012;8(10):e1003010. doi: 10.1371/journal.pgen.1003010. PMCID: PMC3469415 [ Full Text ]

The Diversity Outbred Mouse Population
Churchill GA, Gatti DM, Munger SC, Svenson KL
Mamm Genome. 2012 Oct;23(9-10):713-8. doi: 10.1007/s00335-012-9414-2. PMCID: PMC3524832 [ 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 ]

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 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]

Clusters of ancestrally related genes that show paralogy in whole or in part are a major feature of the genomes of humans and other species
Walker MB, King BL, Paigen K.
PLoS One. 2012;7(4):e35274. PMCID: PMC3338513 [ Full Text ] [ datasets ]

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 ]

Comparative analysis and visualization of multiple collinear genomes
Wang JR, de Villena FP, McMillan L.
BMC Bioinformatics. 2012 Mar 21;13 Suppl 3:S13. PMCID: PMC3311102 [ Full Text ]

Status and access to the Collaborative Cross population
Welsh CE, Miller DR, Manly KF, Wang J, McMillan L, Morahan G, Mott R, Iraqi FA, Threadgill DW, de Villena FP.
Mamm Genome. 2012 Oct;23(9-10):706-12. doi: 10.1007/s00335-012-9410-6. PMCID: PMC3463789 [ Full Text ]

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 ]

HTreeQA: Using Semi-Perfect Phylogeny Trees in Quantitative Trait Loci Study on Genotype Data
Zhang Z, Zhang X, Wang W.
G3 (Bethesda). 2012 Feb;2(2):175-89. PMCID: PMC3284325 [ Full Text ]


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 ]

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 ]

The Collaborative Cross mice and their power to map host susceptibility to Aspergillus fumigates infection
Durrant C, Tayem H, Yalcin B, Osherov N, Pardo-Manuel de Villena F, Mott R, Iraqi FA.
Genome Res. 2011 Aug;21(8):1239-48. PMCID: PMC3149491. [ 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 [ 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 ]

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 [ 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 ]

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 ]


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 [ 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 ]

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 ]


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 ]


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 ]


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.


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 ]