Gary A Churchill

Summary

Affiliation: The Jackson Laboratory
Country: USA

Publications

  1. pmc Discovery of novel variants in genotyping arrays improves genotype retention and reduces ascertainment bias
    John P Didion
    Department of Genetics, University of North Carolina at Chapel Hill, 27599 7264, USA
    BMC Genomics 13:34. 2012
  2. pmc Statistical tests for differential expression in cDNA microarray experiments
    Xiangqin Cui
    The Jackson Laboratory, 600 Main Street, Bar Harbor, Maine 04609, USA
    Genome Biol 4:210. 2003
  3. ncbi request reprint Bayesian restoration of a hidden Markov chain with applications to DNA sequencing
    G A Churchill
    The Jackson Laboratory, Bar Harbor, Maine 04609 1500, USA
    J Comput Biol 6:261-77. 1999
  4. ncbi request reprint Fundamentals of experimental design for cDNA microarrays
    Gary A Churchill
    The Jackson Laboratory, 600 Main Street, Bar Harbor, ME 04609, USA
    Nat Genet 32:490-5. 2002
  5. ncbi request reprint The Collaborative Cross, a community resource for the genetic analysis of complex traits
    Gary A Churchill
    The Jackson Laboratory, 600 Main Street Bar Harbor, Maine 04609, USA
    Nat Genet 36:1133-7. 2004
  6. ncbi request reprint QTL mapping for genetic determinants of lipoprotein cholesterol levels in combined crosses of inbred mouse strains
    Henning Wittenburg
    The Jackson Laboratory, Bar Harbor, ME, USA
    J Lipid Res 47:1780-90. 2006
  7. ncbi request reprint Quantitative trait loci that determine lipoprotein cholesterol levels in an intercross of 129S1/SvImJ and CAST/Ei inbred mice
    Malcolm A Lyons
    The Jackson Laboratory, Bar Harbor, Maine 04609, USA
    Physiol Genomics 17:60-8. 2004
  8. ncbi request reprint Quantitative trait locus mapping of genes that regulate phospholipid transfer activity in SM/J and NZB/BlNJ inbred mice
    Ron Korstanje
    The Jackson Laboratory, Bar Harbor, ME, USA
    Arterioscler Thromb Vasc Biol 24:155-60. 2004
  9. ncbi request reprint Association of a lithogenic Abcg5/Abcg8 allele on Chromosome 17 (Lith9) with cholesterol gallstone formation in PERA/EiJ mice
    Henning Wittenburg
    The Jackson Laboratory, 600 Main Street, Bar Harbor, Maine 04609, USA
    Mamm Genome 16:495-504. 2005
  10. ncbi request reprint Genetic contributors to lipoprotein cholesterol levels in an intercross of 129S1/SvImJ and RIIIS/J inbred mice
    Malcolm A Lyons
    The Jackson Laboratory, Bar Harbor, Maine 04609, USA
    Physiol Genomics 17:114-21. 2004

Detail Information

Publications96

  1. pmc Discovery of novel variants in genotyping arrays improves genotype retention and reduces ascertainment bias
    John P Didion
    Department of Genetics, University of North Carolina at Chapel Hill, 27599 7264, USA
    BMC Genomics 13:34. 2012
    ..Data for SNP probes that do not conform to the expected pattern of clustering are often discarded, contributing to ascertainment bias and resulting in lost information - as much as 50% in a recent genome-wide association study in dogs...
  2. pmc Statistical tests for differential expression in cDNA microarray experiments
    Xiangqin Cui
    The Jackson Laboratory, 600 Main Street, Bar Harbor, Maine 04609, USA
    Genome Biol 4:210. 2003
    ..With more than two conditions, analysis of variance (ANOVA) can be used, and the mixed ANOVA model is a general and powerful approach for microarray experiments with multiple factors and/or several sources of variation...
  3. ncbi request reprint Bayesian restoration of a hidden Markov chain with applications to DNA sequencing
    G A Churchill
    The Jackson Laboratory, Bar Harbor, Maine 04609 1500, USA
    J Comput Biol 6:261-77. 1999
    ..In conclusion, we discuss certain interesting aspects of biological sequence alignments that become accessible through the Bayesian approach to HMM restoration...
  4. ncbi request reprint Fundamentals of experimental design for cDNA microarrays
    Gary A Churchill
    The Jackson Laboratory, 600 Main Street, Bar Harbor, ME 04609, USA
    Nat Genet 32:490-5. 2002
    ..The discussion focuses on two-color spotted cDNA microarrays, but many of the same issues apply to single-color gene-expression assays as well...
  5. ncbi request reprint The Collaborative Cross, a community resource for the genetic analysis of complex traits
    Gary A Churchill
    The Jackson Laboratory, 600 Main Street Bar Harbor, Maine 04609, USA
    Nat Genet 36:1133-7. 2004
    ..The Collaborative Cross will provide a common reference panel specifically designed for the integrative analysis of complex systems and will change the way we approach human health and disease...
  6. ncbi request reprint QTL mapping for genetic determinants of lipoprotein cholesterol levels in combined crosses of inbred mouse strains
    Henning Wittenburg
    The Jackson Laboratory, Bar Harbor, ME, USA
    J Lipid Res 47:1780-90. 2006
    ....
  7. ncbi request reprint Quantitative trait loci that determine lipoprotein cholesterol levels in an intercross of 129S1/SvImJ and CAST/Ei inbred mice
    Malcolm A Lyons
    The Jackson Laboratory, Bar Harbor, Maine 04609, USA
    Physiol Genomics 17:60-8. 2004
    ..Our analysis furthers the knowledge of the genetic control of lipoprotein levels and points to the importance of Hdlq10, which was detected repeatedly in multiple studies...
  8. ncbi request reprint Quantitative trait locus mapping of genes that regulate phospholipid transfer activity in SM/J and NZB/BlNJ inbred mice
    Ron Korstanje
    The Jackson Laboratory, Bar Harbor, ME, USA
    Arterioscler Thromb Vasc Biol 24:155-60. 2004
    ..We performed quantitative trait locus (QTL) analysis to identify genomic loci regulating PLTP activity in mice...
  9. ncbi request reprint Association of a lithogenic Abcg5/Abcg8 allele on Chromosome 17 (Lith9) with cholesterol gallstone formation in PERA/EiJ mice
    Henning Wittenburg
    The Jackson Laboratory, 600 Main Street, Bar Harbor, Maine 04609, USA
    Mamm Genome 16:495-504. 2005
    ..Significantly higher mRNA expression of Abcg5 and Abcg8 in strain PERA compared with strains I/Ln and DBA/2 further substantiated that the PERA allele of Abcg5/Abcg8 was responsible for lithogenicity underlying Lith9...
  10. ncbi request reprint Genetic contributors to lipoprotein cholesterol levels in an intercross of 129S1/SvImJ and RIIIS/J inbred mice
    Malcolm A Lyons
    The Jackson Laboratory, Bar Harbor, Maine 04609, USA
    Physiol Genomics 17:114-21. 2004
    ..Overall, we detected eight QTLs for lipoprotein cholesterol concentrations on Chrs 1, 9, 12, and 17 (each two per chromosome), including a new QTL for non-HDL cholesterol, Nhdlq3, on Chr 17...
  11. ncbi request reprint New quantitative trait loci that contribute to cholesterol gallstone formation detected in an intercross of CAST/Ei and 129S1/SvImJ inbred mice
    Malcolm A Lyons
    Jackson Laboratory, Bar Harbor, Maine 04609, USA
    Physiol Genomics 14:225-39. 2003
    ..Our work continues to demonstrate the genetic complexity and to elucidate the pathophysiology of cholesterol gallstone formation. It should facilitate the development of new approaches for treating this common human disorder...
  12. pmc Applying gene expression, proteomics and single-nucleotide polymorphism analysis for complex trait gene identification
    Ioannis M Stylianou
    The Jackson Laboratory, Bar Harbor, Maine 04609, USA
    Genetics 178:1795-805. 2008
    ..We conclude that all three approaches are important and that focusing on a single approach such as mRNA expression may fail to identify a QTL gene...
  13. pmc Quantitative trait loci for BMD in an SM/J by NZB/BlNJ intercross population and identification of Trps1 as a probable candidate gene
    Naoki Ishimori
    The Jackson Laboratory, Bar Harbor, Maine 04609, USA
    J Bone Miner Res 23:1529-37. 2008
    ..This study shows the power of statistical modeling to resolve linked QTLs and the use of haplotype analysis in narrowing the list of candidates...
  14. ncbi request reprint Lith6: a new QTL for cholesterol gallstones from an intercross of CAST/Ei and DBA/2J inbred mouse strains
    Malcolm A Lyons
    The Jackson Laboratory, Bar Harbor, ME 04609, USA
    J Lipid Res 44:1763-71. 2003
    ....
  15. pmc Four additional mouse crosses improve the lipid QTL landscape and identify Lipg as a QTL gene
    Zhiguang Su
    The Jackson Laboratory, Bar Harbor, ME 04609, USA
    J Lipid Res 50:2083-94. 2009
    ..The data from these crosses further increase the ability to perform haplotype analyses that can lead to the identification of causal lipid genes...
  16. pmc Strain-specific effects of rosiglitazone on bone mass, body composition, and serum insulin-like growth factor-I
    Cheryl L Ackert-Bicknell
    The Jackson Laboratory, Bar Harbor, Maine 04609, USA
    Endocrinology 150:1330-40. 2009
    ..The divergent skeletal responses to rosiglitazone in this study suggest the existence of a strong genetic background effect...
  17. ncbi request reprint Single and interacting QTLs for cholesterol gallstones revealed in an intercross between mouse strains NZB and SM
    Malcolm A Lyons
    The Jackson Laboratory, Bar Harbor, Maine 04609, USA
    Mamm Genome 16:152-63. 2005
    ..The QTLs identified herein largely contributed to gallstone formation rather than gallstone severity. Cloning the genes underlying these murine QTLs should facilitate prediction and cloning of the orthologous human genes...
  18. pmc Effects of atherogenic diet on hepatic gene expression across mouse strains
    Keith R Shockley
    The Jackson Laboratory, Bar Harbor, Maine 04605, USA
    Physiol Genomics 39:172-82. 2009
    ..The gene expression data and phenotype data have been made publicly available as an online tool for exploring the effects of atherogenic diet in inbred mouse strains (http://cgd-array.jax.org/DietStrainSurvey)...
  19. ncbi request reprint Genetic analysis of albuminuria in a cross between C57BL/6J and DBA/2J mice
    Susan Sheehan
    The Jackson Laboratory, Bar Harbor, Maine, USA
    Am J Physiol Renal Physiol 293:F1649-56. 2007
    ..These results support the continued use of multiple cross-mapping and cross-species comparisons to further our understanding of the genetic basis of kidney disease...
  20. ncbi request reprint Quantitative trait loci analysis for plasma HDL-cholesterol concentrations and atherosclerosis susceptibility between inbred mouse strains C57BL/6J and 129S1/SvImJ
    Naoki Ishimori
    The Jackson Laboratory, Bar Harbor, ME 04609, USA
    Arterioscler Thromb Vasc Biol 24:161-6. 2004
    ..To identify loci controlling these traits, we performed quantitative trait loci (QTL) analysis...
  21. ncbi request reprint FXR and ABCG5/ABCG8 as determinants of cholesterol gallstone formation from quantitative trait locus mapping in mice
    Henning Wittenburg
    The Jackson Laboratory, Bar Harbor, Maine, USA
    Gastroenterology 125:868-81. 2003
    ..Cholesterol gallstone formation is a complex genetic trait. To identify additional cholesterol gallstone susceptibility loci, we performed a quantitative trait locus analysis using an intercross of PERA/Ei and I/LnJ inbred strains of mice...
  22. pmc Structural model analysis of multiple quantitative traits
    Renhua Li
    The Jackson Laboratory, Bar Harbor, Maine, USA
    PLoS Genet 2:e114. 2006
    ..The identification of causal networks sheds light on the nature of genetic heterogeneity and pleiotropy in complex genetic systems...
  23. ncbi request reprint Quantitative trait loci that determine plasma lipids and obesity in C57BL/6J and 129S1/SvImJ inbred mice
    Naoki Ishimori
    The Jackson Laboratory, Bar Harbor, ME, USA
    J Lipid Res 45:1624-32. 2004
    ..0) interacting with Obq18 (chromosome 9, cM 65). Knowing the genes for these QTL will enhance our understanding of obesity and lipid metabolism...
  24. pmc A Bayesian framework for inference of the genotype-phenotype map for segregating populations
    Rachael S Hageman
    The Jackson Laboratory, Bar Harbor, Maine 04609, USA
    Genetics 187:1163-70. 2011
    ..We applied our method to kidney gene expression data from an MRL/MpJ × SM/J intercross population and predicted a previously uncharacterized feedback loop in the local renin-angiotensin system...
  25. ncbi request reprint Quantitative trait loci for baseline erythroid traits
    Luanne L Peters
    The Jackson Laboratory, 600 Main Street, Bar Harbor, Maine 04609, USA
    Mamm Genome 17:298-309. 2006
    ..These analyses emphasize the genetic complexity underlying the regulation of erythroid peripheral blood traits in normal populations and suggest that genes not previously recognized as significantly impacting normal erythropoiesis exist...
  26. ncbi request reprint Multiple trait measurements in 43 inbred mouse strains capture the phenotypic diversity characteristic of human populations
    Karen L Svenson
    The Jackson Laboratory, 600 Main St, Bar Harbor, ME 04609, USA
    J Appl Physiol 102:2369-78. 2007
    ..Data generated by this effort builds on the value of inbred mouse strains as a powerful tool for biomedical research...
  27. pmc Using advanced intercross lines for high-resolution mapping of HDL cholesterol quantitative trait loci
    Xiaosong Wang
    The Jackson Laboratory, Bar Harbor, Maine 04609, USA
    Genome Res 13:1654-64. 2003
    ..All the major HDL QTLs in our study had homologous counterparts in humans, implying that their underlying genes regulate HDL in humans...
  28. pmc Pla2g12b and Hpn are genes identified by mouse ENU mutagenesis that affect HDL cholesterol
    Aleksandra Aljakna
    The Jackson Laboratory, Bar Harbor, Maine, United States of America
    PLoS ONE 7:e43139. 2012
    ..These new mutant mouse models are valuable tools to further study the role of these genes, their affect on HDL cholesterol levels, and metabolism...
  29. ncbi request reprint Quantitative trait loci for baseline white blood cell count, platelet count, and mean platelet volume
    Luanne L Peters
    The Jackson Laboratory, 600 Main Street, Bar Harbor, Maine 04609, USA
    Mamm Genome 16:749-63. 2005
    ..These analyses underscore the genetic complexity underlying these traits in normal populations and provide the basis for future studies to identify novel genes involved in the regulation of mammalian hematopoiesis...
  30. ncbi request reprint Locating Ath8, a locus for murine atherosclerosis susceptibility and testing several of its candidate genes in mice and humans
    Ron Korstanje
    The Jackson Laboratory, 600 Main Street, Bar Harbor, ME 04609, USA
    Atherosclerosis 177:443-50. 2004
    ..We found a significant association between ANGPTL3 and atherosclerotic lesions (P < 0.05) in human. These results suggest that Angptl3 is involved in atherosclerosis susceptibility in both mouse and human...
  31. pmc Mouse BMD quantitative trait loci show improved concordance with human genome-wide association loci when recalculated on a new, common mouse genetic map
    Cheryl L Ackert-Bicknell
    The Jackson Laboratory, Bar Harbor, ME 04609, USA
    J Bone Miner Res 25:1808-20. 2010
    ..We believe that this is an opportune time for a renewed effort by the genetics community to identify the causal variants regulating BMD using a synergistic mouse-human approach...
  32. pmc CGDSNPdb: a database resource for error-checked and imputed mouse SNPs
    Lucie N Hutchins
    Center for Genome Dynamics, The Jackson Laboratory, 600 Main Street, Bar Harbor, ME 04609, USA
    Database (Oxford) 2010:baq008. 2010
    ..CGDSNPdb is accessible online through either a web-based query tool or a MySQL public login. Database URL: http://cgd.jax.org/cgdsnpdb/..
  33. pmc High-fat diet leads to tissue-specific changes reflecting risk factors for diseases in DBA/2J mice
    Rachael S Hageman
    The Jackson Laboratory, Bar Harbor, Maine, USA
    Physiol Genomics 42:55-66. 2010
    ..Gluteal adipose tissue had the highest mass gain but was sluggish in its metabolism. In HFD conditions, BAT functioned largely like WAT in its role as a depot for excess energy, whereas WAT played a role in thermogenesis...
  34. doi request reprint Relationships of dietary fat, body composition, and bone mineral density in inbred mouse strain panels
    Renhua Li
    The Jackson Laboratory, Bar Harbor, Maine 04609, USA
    Physiol Genomics 33:26-32. 2008
    ..Sex has no net effect on areal BMD, but after accounting for body mass difference females have higher areal BMD. Leptin is affected by relative fat mass and has no net effect on areal BMD. IGF-I has a direct effect on areal BMD...
  35. ncbi request reprint Quantitative trait loci that determine BMD in C57BL/6J and 129S1/SvImJ inbred mice
    Naoki Ishimori
    The Jackson Laboratory, Bar Harbor, Maine 04609, USA
    J Bone Miner Res 21:105-12. 2006
    ..To identify loci controlling BMD, we conducted a QTL analysis in a (B6 x 129) F2 population of mice. We report on additional QTLs and also narrow one QTL by combining the data from multiple crosses and through haplotype analysis...
  36. pmc A customized and versatile high-density genotyping array for the mouse
    Hyuna Yang
    The Jackson Laboratory, Bar Harbor, Maine, USA
    Nat Methods 6:663-6. 2009
    ..The array opens the door to the characterization of genetic diversity, copy-number variation, allele-specific gene expression and DNA methylation, and will extend the successes of human genome-wide association studies to the mouse...
  37. pmc PPARG by dietary fat interaction influences bone mass in mice and humans
    Cheryl L Ackert-Bicknell
    The Jackson Laboratory, Bar Harbor, Maine 04609, USA
    J Bone Miner Res 23:1398-408. 2008
    ..These findings suggest that dietary fat has a significant influence on BMD that is dependent on the alleles present for the PPARG gene...
  38. ncbi request reprint Quantitative trait mapping in a diallel cross of recombinant inbred lines
    Shirng Wern Tsaih
    The Jackson Laboratory, 600 Maine St, Bar Harbor, Maine 04609, USA
    Mamm Genome 16:344-55. 2005
    ..This involves the use of a partial RIX population derived from a large RI panel in which the available information is maximized by minimizing correlations among RIX progeny...
  39. ncbi request reprint Genetic analysis of blood pressure in C3H/HeJ and SWR/J mice
    Keith DiPetrillo
    The Jackson Laboratory, Bar Harbor, Maine 04609, USA
    Physiol Genomics 17:215-20. 2004
    ..3-cM region where the high allele strains shared a common haplotype. Bpq8 is concordant with known QTL in both rat and human, suggesting that the causal gene underlying Bpq8 may be conserved as a disease gene in human hypertension...
  40. ncbi request reprint Identification of quantitative trait loci that modify the severity of hereditary spherocytosis in wan, a new mouse model of band-3 deficiency
    Luanne L Peters
    The Jackson Laboratory, Bar Harbor, ME 04609, USA
    Blood 103:3233-40. 2004
    ..The peak LOD score was obtained with a marker for Spnb1 encoding erythroid beta-spectrin, an obvious candidate gene...
  41. pmc An imputed genotype resource for the laboratory mouse
    Jin P Szatkiewicz
    The Jackson Laboratory, 600 Main Street, Bar Harbor, Maine 04609, USA
    Mamm Genome 19:199-208. 2008
    ..We anticipate that this resource will continue to evolve as new genotype data become available for laboratory mouse strains. The data are available for bulk download or query at http://cgd.jax.org /...
  42. pmc A new standard genetic map for the laboratory mouse
    Allison Cox
    The Jackson Laboratory, 600 Main Street, Bar Harbor, Maine 04609, USA
    Genetics 182:1335-44. 2009
    ..We demonstrate that utilization of the revised genetic map improves QTL mapping, partially due to the resolution of previously undetected errors in marker ordering along the chromosome...
  43. pmc Aging in inbred strains of mice: study design and interim report on median lifespans and circulating IGF1 levels
    Rong Yuan
    The Jackson Aging Center at The Jackson Laboratory, Bar Harbor, ME 04609, USA
    Aging Cell 8:277-87. 2009
    ..53, P < 0.01). These results support the hypothesis that the IGF1 pathway plays a key role in regulating longevity in mice and indicates that common genetic mechanisms may exist for regulating IGF1 levels and lifespan...
  44. pmc Identification of genetic determinants of IGF-1 levels and longevity among mouse inbred strains
    Magalie S Leduc
    The Jackson Laboratory, Bar Harbor, ME 04609, USA
    Aging Cell 9:823-36. 2010
    ..05) than strains with haplotype 2 or 3. Bioinformatic analysis, combined with sequencing and expression studies, showed that Igf1 is the most likely QTL gene, but that other genes may also play a role in this strong QTL...
  45. ncbi request reprint The mouse as a model for human biology: a resource guide for complex trait analysis
    Luanne L Peters
    The Jackson Laboratory, 600 Main Street, Bar Harbor, Maine 04609, USA
    Nat Rev Genet 8:58-69. 2007
    ..This review summarizes those resources and provides practical guidelines for their use, particularly in the analysis of quantitative traits...
  46. pmc Sequence variation at multiple loci influences red cell hemoglobin concentration
    Luanne L Peters
    The Jackson Laboratory, Bar Harbor, ME, USA
    Blood 116:e139-49. 2010
    ..85 versus 7.13. Thus, as shown in human erythrocytes, positively charged Hbs are associated with cell dehydration and increased CHCM in mouse erythrocytes...
  47. pmc Combining data from multiple inbred line crosses improves the power and resolution of quantitative trait loci mapping
    Renhua Li
    The Jackson Laboratory, Bar Harbor, Maine 04609, USA
    Genetics 169:1699-709. 2005
    ..Moreover, combined-cross analysis can establish the allelic states of a QTL among a set of parental lines, thus providing critical information for narrowing QTL regions by haplotype analysis...
  48. ncbi request reprint Quantitative trait locus mapping of genes that regulate HDL cholesterol in SM/J and NZB/B1NJ inbred mice
    Wendy A Pitman
    The Jackson Laboratory, 600 Main Street, Bar Harbor, Maine 04609, USA
    Physiol Genomics 9:93-102. 2002
    ..With these QTL, we have identified chromosomal regions that affect lipoprotein profiles in these strains...
  49. pmc Using bioinformatics and systems genetics to dissect HDL-cholesterol genetics in an MRL/MpJ x SM/J intercross
    Magalie S Leduc
    The Jackson Laboratory, Bar Harbor, ME, USA
    J Lipid Res 53:1163-75. 2012
    ..We conclude that integrating systems genetics to a more-traditional genetics approach improves the power of complex trait gene identification...
  50. pmc High-resolution genetic mapping using the Mouse Diversity outbred population
    Karen L Svenson
    The Jackson Laboratory, Bar Harbor, Maine 04609, USA
    Genetics 190:437-47. 2012
    ....
  51. ncbi request reprint Gonadal sex reversal in mutant Dax1 XY mice: a failure to upregulate Sox9 in pre-Sertoli cells
    Gerrit J Bouma
    The Jackson Laboratory, Bar Harbor, ME 04609, USA
    Development 132:3045-54. 2005
    ....
  52. pmc Randomization in laboratory procedure is key to obtaining reproducible microarray results
    Hyuna Yang
    The Jackson Laboratory, Bar Harbor, ME, USA
    PLoS ONE 3:e3724. 2008
    ....
  53. pmc Importance of randomization in microarray experimental designs with Illumina platforms
    Ricardo A Verdugo
    The Jackson Laboratory, Bar Harbor, ME 04609, USA
    Nucleic Acids Res 37:5610-8. 2009
    ..We conclude that lack of randomization cannot be corrected by normalization or by analytical methods. Proper randomization is essential for successful microarray experiments...
  54. pmc PPARgamma2 nuclear receptor controls multiple regulatory pathways of osteoblast differentiation from marrow mesenchymal stem cells
    Keith R Shockley
    The Jackson Laboratory, 600 Main Street, Bar Harbor, Maine 04609, USA
    J Cell Biochem 106:232-46. 2009
    ....
  55. ncbi request reprint Quantitative trait loci that determine lipoprotein cholesterol levels in DBA/2J and CAST/Ei inbred mice
    Malcolm A Lyons
    The Jackson Laboratory, Bar Harbor, ME 04609, USA
    J Lipid Res 44:953-67. 2003
    ....
  56. ncbi request reprint Quantitative trait locus analysis for obesity reveals multiple networks of interacting loci
    Ioannis M Stylianou
    The Jackson Laboratory, 600 Main Street, Bar Harbor, Maine 04609, USA
    Mamm Genome 17:22-36. 2006
    ..Haplotype patterns and a literature-driven approach were used to generate hypotheses regarding the identity of the genes and pathways underlying the QTL...
  57. pmc Stochastic variation of transcript abundance in C57BL/6J mice
    PETER T VEDELL
    The Jackson Laboratory, Bar Harbor, Maine 04609, USA
    BMC Genomics 12:167. 2011
    ..Between-mouse variance reflects differences in transcript abundance between genetically identical mice...
  58. ncbi request reprint Interacting QTLs for cholesterol gallstones and gallbladder mucin in AKR and SWR strains of mice
    Henning Wittenburg
    Jackson Laboratory, Bar Harbor, Maine 04609, USA
    Physiol Genomics 8:67-77. 2002
    ..According to standard nomenclature, the gallstone QTL on chromosome 9 is named Lith5...
  59. pmc The Diversity Outbred mouse population
    Gary A Churchill
    The Jackson Laboratory, 600 Main Street, Bar Harbor, ME 04609, USA
    Mamm Genome 23:713-8. 2012
    ..We anticipate a flood of new results to follow as our community begins to adopt and utilize these new genetic resource populations...
  60. pmc Subspecific origin and haplotype diversity in the laboratory mouse
    Hyuna Yang
    The Jackson Laboratory, Bar Harbor, Maine, USA
    Nat Genet 43:648-55. 2011
    ..The subspecific origin, haplotype diversity and identity by descent maps can be visualized using the Mouse Phylogeny Viewer (see URLs)...
  61. pmc Genetic background modifies inner ear and eye phenotypes of jag1 heterozygous mice
    Amy E Kiernan
    The Jackson Laboratory, Bar Harbor, Maine 04609, USA
    Genetics 177:307-11. 2007
    ..Genome scans of N2 backcross mice identified a significant modifier locus on chromosome 7, as well as a suggestive locus on chromosome 14. We also analyzed modifiers of an eye defect in Jag1del1 heterozygous mice from this same cross...
  62. pmc Uncovering genes and regulatory pathways related to urinary albumin excretion
    Rachael S Hageman
    The Jackson Laboratory, 600 Main Street, Bar Harbor, ME 04609, USA
    J Am Soc Nephrol 22:73-81. 2011
    ..This combined approach provides valuable insights into the causes and consequences of renal disease...
  63. ncbi request reprint Patterns and mechanisms of genome organization in the mouse
    Joel H Graber
    The Jackson Laboratory, Bar Harbor, Maine 04609, USA
    J Exp Zool A Comp Exp Biol 305:683-8. 2006
    ..The strong conservation of gene order among mammals suggests that the domains and networks we find likely characterize all mammals, and possibly beyond...
  64. ncbi request reprint Distal Chr 4 harbors a genetic locus (Gct1) fundamental for spontaneous ovarian granulosa cell tumorigenesis in a mouse model
    Ann M Dorward
    The Jackson Laboratory, Bar Harbor, Maine, USA
    Cancer Res 65:1259-64. 2005
    ..Our data substantiate the evidence that Gct1 on Chr 4 is a fundamental oncogene for granulosa cell tumorigenesis in mice and has identified additional interacting autosomal loci that support tumor development...
  65. ncbi request reprint Improved statistical tests for differential gene expression by shrinking variance components estimates
    Xiangqin Cui
    The Jackson Laboratory, Bar Harbor, Maine 04609, USA
    Biostatistics 6:59-75. 2005
    ..Thus FS provides a powerful and robust approach to test differential expression of genes that utilizes information not available in individual gene testing approaches and does not suffer from biases of the pooled variance approach...
  66. pmc Evidence of a large-scale functional organization of mammalian chromosomes
    Petko M Petkov
    The Jackson Laboratory, Bar Harbor, Maine, USA
    PLoS Genet 1:e33. 2005
    ..Given the strong conservation of gene order among mammals, the domains and networks we find in mice probably characterize all mammals, including humans...
  67. ncbi request reprint Gene expression analysis of mouse chromosome substitution strains
    Keith R Shockley
    The Jackson Laboratory, 600 Main Street, Bar Harbor, ME 04609, USA
    Mamm Genome 17:598-614. 2006
    ..Transcriptional profiling of chromosome substitution strains reveals a complex genetic architecture of transcriptional regulation...
  68. ncbi request reprint Recombinant inbred strain panels: a tool for systems genetics
    Gary A Churchill
    The Jackson Laboratory, Bar Harbor, Maine, USA
    Physiol Genomics 31:174-5. 2007
  69. ncbi request reprint On the subspecific origin of the laboratory mouse
    Hyuna Yang
    The Jackson Laboratory, Bar Harbor, Maine 04609, USA
    Nat Genet 39:1100-7. 2007
    ....
  70. ncbi request reprint Using ANOVA to analyze microarray data
    Gary A Churchill
    The Jackson Laboratory, Bar Harbor, ME, USA
    Biotechniques 37:173-5, 177. 2004
    ..We apply statistical tests to ensure that we are not just making up stories based on seeing patterns where there may be none...
  71. pmc Coordinated expression domains in mammalian genomes
    Yong H Woo
    The Jackson Laboratory, Center for Genome Dynamics, Bar Harbor, Maine, United States of America
    PLoS ONE 5:e12158. 2010
    ..Genes showing similar expression (coexpression) patterns are often clustered along the genome. The goal of this study is to characterize coexpression clustering in mammalian genomes and to investigate the underlying mechanisms...
  72. pmc Proteotypic classification of spontaneous and transgenic mammary neoplasms
    Igor Mikaelian
    The Jackson Laboratory, Bar Harbor, Maine, USA
    Breast Cancer Res 6:R668-79. 2004
    ....
  73. ncbi request reprint A collaborative database of inbred mouse strain characteristics
    Stephen C Grubb
    The Jackson Laboratory, Bar Harbor, ME 04609, USA
    Bioinformatics 20:2857-9. 2004
    ..The current focus is on a set of 40 inbred strains. The MPD as of February 2004 contains approximately 500 phenotypic parameters relevant to human health, voluntarily contributed by several dozen investigators and laboratories...
  74. ncbi request reprint QTL associated with blood pressure, heart rate, and heart weight in CBA/CaJ and BALB/cJ mice
    Fumihiro Sugiyama
    The Jackson Laboratory, Bar Harbor, Maine 04609, USA
    Physiol Genomics 10:5-12. 2002
    ..Identification of the genes for these QTL should lead to a better understanding of the causes of essential hypertension...
  75. ncbi request reprint The genetics of gene expression
    Gary A Churchill
    The Jackson Laboratory, Bar Harbor, Maine, USA
    Mamm Genome 17:465. 2006
  76. pmc The X chromosome in quantitative trait locus mapping
    Karl W Broman
    Department of Biostatistics, Johns Hopkins University, Baltimore, MD 21205, USA
    Genetics 174:2151-8. 2006
    ..We found suggestive evidence of linkage to the X chromosome, which would be viewed as strong evidence of linkage if the X chromosome was treated as an autosome. Our methods have been implemented in the package R/qtl...
  77. ncbi request reprint Genetic analysis of the stress-responsive adrenocortical axis
    Leah C Solberg
    Department of Psychiatry and Behavioral Science, Northwestern University Feinberg School of Medicine, Chicago, USA
    Physiol Genomics 27:362-9. 2006
    ..This analysis confirms that three separate traits regulated by the HPA axis are controlled by multiple, but mainly nonoverlapping, QTLs...
  78. pmc Test- and behavior-specific genetic factors affect WKY hypoactivity in tests of emotionality
    Amber E Baum
    Department of Psychiatry and Behavioral Science, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA
    Behav Brain Res 169:220-30. 2006
    ..However, in both contexts, other loci had greater effects on the behavior. Our results imply that environmental context's effects on decision-making vary depending on the category of behavior...
  79. ncbi request reprint 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
    Jon E Wergedal
    Musculoskeletal Disease Center, J L Pettis Memorial VA Medical Center, Loma Linda, CA 92357, USA
    J Bone Miner Res 21:1256-66. 2006
    ..Genetic analysis of an NZB/B1NJ x RF/J cross has identified QTLs for femur mechanical, geometric, and densitometric phenotypes. Most mechanical QTLs were associated with geometric QTLs, strongly suggesting common genetic regulation...
  80. ncbi request reprint Interacting genetic loci cause airway hyperresponsiveness
    Kate G Ackerman
    Division of Genetics, Brigham and Women s Hospital and Harvard Medical School, Boston, Massachusetts, USA
    Physiol Genomics 21:105-11. 2005
    ....
  81. ncbi request reprint Kinesin family member 12 is a candidate polycystic kidney disease modifier in the cpk mouse
    Michal Mrug
    Department of Medicine, University of Alabama at Birmingham, 740 Kaul Human Genetics Building, 720 20th Street South, Birmingham, AL 35294, USA
    J Am Soc Nephrol 16:905-16. 2005
    ..Therefore, the positional candidate gene, Kif12, fulfills the major criteria for QTL gene discovery established by the Complex Trait Consortium, and, thus, it is proposed that Kif12 is a cpk modifier gene...
  82. pmc Quantitative trait locus study design from an information perspective
    Saunak Sen
    Department of Epidemiology and Biostatistics, University of California, San Francisco, 94143, USA
    Genetics 170:447-64. 2005
    ..Software for performing power calculations for backcross and F(2) intercross incorporating selective genotyping and marker spacing is available from http://www.biostat.ucsf.edu/sen...
  83. ncbi request reprint Quantitative trait loci for femoral and lumbar vertebral bone mineral density in C57BL/6J and C3h/HeJ inbred strains of mice. (2001)
    Wesley G Beamer
    J Bone Miner Res 20:1701-12; discussion 1700. 2005
  84. ncbi request reprint Mapping quantitative trait loci for vertebral trabecular bone volume fraction and microarchitecture in mice
    Mary L Bouxsein
    Orthopedic Biomechanics Laboratory, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, Massachusetts 02215, USA
    J Bone Miner Res 19:587-99. 2004
    ..Ultimately, identification of genes that regulate trabecular bone traits may yield important information regarding mechanisms that regulate mechanical integrity of the skeleton...
  85. pmc R/qtlDesign: inbred line cross experimental design
    Saunak Sen
    Department of Epidemiology and Biostatistics, University of California San Francisco, San Francisco, California 94143, USA
    Mamm Genome 18:87-93. 2007
    ..We give examples of software usage in real-life settings. The software is available at http://www.biostat.ucsf.edu/sen/software.html ...
  86. pmc Bayesian model selection for genome-wide epistatic quantitative trait loci analysis
    Nengjun Yi
    Department of Biostatistics, University of Alabama, Birmingham 35294, USA
    Genetics 170:1333-44. 2005
    ..We illustrate the proposed method by detecting new epistatic QTL for obesity in a backcross of CAST/Ei mice onto M16i...
  87. ncbi request reprint Modifier locus for exencephaly in Cecr2 mutant mice is syntenic to the 10q25.3 region associated with neural tube defects in humans
    Courtney E Davidson
    Department of Biological Sciences, University of Alberta, Edmonton, Alberta, Canada
    Physiol Genomics 31:244-51. 2007
    ....
  88. ncbi request reprint X-linked and lineage-dependent inheritance of coping responses to stress
    Nasim Ahmadiyeh
    Department of Psychiatry and Behavioral Sciences, Northwestern University Feinberg School of Medicine, 303 E Chicago Ave, Ward 9 190 Chicago, Illinois 60611, USA
    Mamm Genome 14:748-57. 2003
    ....
  89. ncbi request reprint Genetic variation in Glp1r expression influences the rate of gastric emptying in mice
    K Ganesh Kumar
    Division of Experimental Obesity, Pennington Biomedical Research Center, Louisiana State University, 6400 Perkins Road, Baton Rouge, LA 70808 4124, USA
    Am J Physiol Regul Integr Comp Physiol 294:R362-71. 2008
    ..CAST-17 mice. Moreover, congenic mice displayed an impaired gastric emptying response to exendin-(9-39). These results suggest that genetic variation in Glp1r contributes to the strain differences in gastric emptying rate...
  90. pmc Sex- and lineage-specific inheritance of depression-like behavior in the rat
    Leah C Solberg
    Department of Psychiatry and Behavioral Science, Northwestern University Feinberg School of Medicine, 303 E Chicago Avenue, Chicago, Illinois 60611, USA
    Mamm Genome 15:648-62. 2004
    ..The presence of these loci across species suggests that these QTL may represent universal genetic factors contributing to mood disorders...
  91. ncbi request reprint Quantitative trait loci associated with blood pressure of metabolic syndrome in the progeny of NZO/HILtJxC3H/HeJ intercrosses
    Eri Nishihara
    Laboratory Animal Resource Center, University of Tsukuba, 1 1 1 Tennodai, Tsukuba, 305 8575, Japan
    Mamm Genome 18:573-83. 2007
    ..These results enhance our understanding of complicated genetic factors of hypertension in metabolic diseases...
  92. ncbi request reprint R/qtl: QTL mapping in experimental crosses
    Karl W Broman
    Department of Biostatistics, Johns Hopkins University, 615 N Wolfe St, Baltimore, MD 21205, USA
    Bioinformatics 19:889-90. 2003
    ....
  93. pmc Evidence of a large-scale functional organization of Mammalian chromosomes
    Petko M Petkov
    PLoS Biol 5:e127; author reply e128. 2007
  94. ncbi request reprint Sequential quantitative trait locus mapping in experimental crosses
    Jaya M Satagopan
    Memorial Sloan Kettering Cancer Center, USA
    Stat Appl Genet Mol Biol 6:Article12. 2007
    ..We examine settings under which the two-stage analytic approach provides sufficient power to detect the putative QTLs...
  95. ncbi request reprint Genetics of colitis susceptibility in IL-10-deficient mice: backcross versus F2 results contrasted by principal component analysis
    Michael Mahler
    Institute for Laboratory Animal Science and Central Animal Facility, Medical School Hannover, Germany
    Genomics 80:274-82. 2002
    ..These findings show the complexity of inheritance underlying susceptibility to colitis and illustrate why detection of human inflammatory bowel disease loci has proven to be so difficult...
  96. ncbi request reprint QTL analysis of self-selected macronutrient diet intake: fat, carbohydrate, and total kilocalories
    Brenda K Smith Richards
    Pennington Biomedical Research Center, Baton Rouge, Louisiana 70808 4124, USA
    Physiol Genomics 11:205-17. 2002
    ..These results provide new insight into the genetic basis of naturally occurring variation in nutrient intake phenotypes...