Brian S Yandell

Summary

Affiliation: University of Wisconsin
Country: USA

Publications

  1. ncbi request reprint Distinguishing covariation from causation in diabetes: a lesson from the protein disulfide isomerase mRNA abundance trait
    Hong Lan
    Department of Biochemistry, University of Wisconsin, Madison, Wisconsin 53706, USA
    Diabetes 53:240-4. 2004
  2. ncbi request reprint R/qtlbim: QTL with Bayesian Interval Mapping in experimental crosses
    Brian S Yandell
    Department of Statistics, University of Wisconsin Madison, 1300 University Avenue, Madison, WI 53706, USA
    Bioinformatics 23:641-3. 2007
  3. pmc Quantile-based permutation thresholds for quantitative trait loci hotspots
    Elias Chaibub Neto
    Department of Computational Biology, Sage Bionetworks, Seattle, Washington 98109, USA
    Genetics 191:1355-65. 2012
  4. pmc Modeling causality for pairs of phenotypes in system genetics
    Elias Chaibub Neto
    Sage Bionetworks, Seattle, Washington 98109, USA
    Genetics 193:1003-13. 2013
  5. pmc Obesity and genetics regulate microRNAs in islets, liver, and adipose of diabetic mice
    Enpeng Zhao
    Biochemistry Department, University of Wisconsin, Madison, WI 53706, USA
    Mamm Genome 20:476-85. 2009
  6. pmc Tsc2, a positional candidate gene underlying a quantitative trait locus for hepatic steatosis
    Chen Yu Wang
    Department of Biochemistry, University of Wisconsin Madison, Madison, WI, USA
    J Lipid Res 53:1493-501. 2012
  7. pmc Cholecystokinin is up-regulated in obese mouse islets and expands beta-cell mass by increasing beta-cell survival
    Jeremy A Lavine
    Department of Biochemistry, University of Wisconsin, Madison, Wisconsin 53706, USA
    Endocrinology 151:3577-88. 2010
  8. pmc Positional cloning of a type 2 diabetes quantitative trait locus; tomosyn-2, a negative regulator of insulin secretion
    Sushant Bhatnagar
    Department of Biochemistry, University of Wisconsin Madison, Madison, Wisconsin, United States of America
    PLoS Genet 7:e1002323. 2011
  9. pmc A gene expression network model of type 2 diabetes links cell cycle regulation in islets with diabetes susceptibility
    Mark P Keller
    Department of Biochemistry, University of Wisconsin, Madison, Wisconsin 53076, USA
    Genome Res 18:706-16. 2008
  10. pmc Combined expression trait correlations and expression quantitative trait locus mapping
    Hong Lan
    Department of Biochemistry, University of Wisconsin, Madison, Wisconsin, USA
    PLoS Genet 2:e6. 2006

Collaborators

Detail Information

Publications42

  1. ncbi request reprint Distinguishing covariation from causation in diabetes: a lesson from the protein disulfide isomerase mRNA abundance trait
    Hong Lan
    Department of Biochemistry, University of Wisconsin, Madison, Wisconsin 53706, USA
    Diabetes 53:240-4. 2004
    ..Genetic analysis is a powerful tool for distinguishing covariation from causation in expression array studies of disease traits...
  2. ncbi request reprint R/qtlbim: QTL with Bayesian Interval Mapping in experimental crosses
    Brian S Yandell
    Department of Statistics, University of Wisconsin Madison, 1300 University Avenue, Madison, WI 53706, USA
    Bioinformatics 23:641-3. 2007
    ..Availability: The package is freely available from cran.r-project.org...
  3. pmc Quantile-based permutation thresholds for quantitative trait loci hotspots
    Elias Chaibub Neto
    Department of Computational Biology, Sage Bionetworks, Seattle, Washington 98109, USA
    Genetics 191:1355-65. 2012
    ..We assess and compare the performances of these three methods in simulations and we illustrate how our approach can effectively assess the significance of moderate and small hotspots with strong LOD scores in a yeast expression data set...
  4. pmc Modeling causality for pairs of phenotypes in system genetics
    Elias Chaibub Neto
    Sage Bionetworks, Seattle, Washington 98109, USA
    Genetics 193:1003-13. 2013
    ..In practice, this is a useful feature since follow-up studies tend to be time consuming and expensive and, hence, it is important for the experimentalist to have causal predictions with low false-positive rates...
  5. pmc Obesity and genetics regulate microRNAs in islets, liver, and adipose of diabetic mice
    Enpeng Zhao
    Biochemistry Department, University of Wisconsin, Madison, WI 53706, USA
    Mamm Genome 20:476-85. 2009
    ..Understanding the influence that obesity and genetics exert on the regulation of miRNA expression will reveal the role miRNAs play in the context of obesity-induced type 2 diabetes...
  6. pmc Tsc2, a positional candidate gene underlying a quantitative trait locus for hepatic steatosis
    Chen Yu Wang
    Department of Biochemistry, University of Wisconsin Madison, Madison, WI, USA
    J Lipid Res 53:1493-501. 2012
    ..This difference is due to a different affinity of binding to Tsc1, which affects the stability of Tsc2...
  7. pmc Cholecystokinin is up-regulated in obese mouse islets and expands beta-cell mass by increasing beta-cell survival
    Jeremy A Lavine
    Department of Biochemistry, University of Wisconsin, Madison, Wisconsin 53706, USA
    Endocrinology 151:3577-88. 2010
    ..In summary, CCK is up-regulated by islet cells during obesity and functions as a paracrine or autocrine factor to increase beta-cell survival and expand beta-cell mass to compensate for obesity-induced insulin resistance...
  8. pmc Positional cloning of a type 2 diabetes quantitative trait locus; tomosyn-2, a negative regulator of insulin secretion
    Sushant Bhatnagar
    Department of Biochemistry, University of Wisconsin Madison, Madison, Wisconsin, United States of America
    PLoS Genet 7:e1002323. 2011
    ..We conclude that tomosyn-2 is the major gene responsible for the T2D Chr 16 quantitative trait locus (QTL) we mapped in our mouse cross. Our findings suggest that tomosyn-2 is a key negative regulator of insulin secretion...
  9. pmc A gene expression network model of type 2 diabetes links cell cycle regulation in islets with diabetes susceptibility
    Mark P Keller
    Department of Biochemistry, University of Wisconsin, Madison, Wisconsin 53076, USA
    Genome Res 18:706-16. 2008
    ....
  10. pmc Combined expression trait correlations and expression quantitative trait locus mapping
    Hong Lan
    Department of Biochemistry, University of Wisconsin, Madison, Wisconsin, USA
    PLoS Genet 2:e6. 2006
    ..The combined analysis is more sensitive compared with linkage mapping alone...
  11. pmc Inferring causal phenotype networks from segregating populations
    Elias Chaibub Neto
    Department of Statistics, University of Wisconsin, Madison, Wisconsin 53706, USA
    Genetics 179:1089-100. 2008
    ..Finally, we illustrate our method with an example involving gene expression and metabolite traits from experimental crosses...
  12. pmc A model selection approach for expression quantitative trait loci (eQTL) mapping
    Ping Wang
    Department of Statistics, University of Wisconsin, Madison, Wisconsin 53726, USA
    Genetics 187:611-21. 2011
    ..Output can be used to identify groups of transcripts that are likely coregulated, as demonstrated in a study of diabetes in mouse...
  13. pmc FoxM1 is up-regulated by obesity and stimulates beta-cell proliferation
    Dawn Belt Davis
    Department of Medicine, University of Wisconsin, Madison, WI, USA
    Mol Endocrinol 24:1822-34. 2010
    ..Our data suggest that beta-cell proliferation occurs in adult obese humans in an attempt to expand beta-cell mass to compensate for insulin resistance, and that the FoxM1 transcriptional program plays a key role in this process...
  14. ncbi request reprint Abdominal obesity in BTBR male mice is associated with peripheral but not hepatic insulin resistance
    Jessica B Flowers
    Department of Nutritional Sciences, University of Wisconsin Madison, 433 Babcock Dr, Madison, WI 53706, USA
    Am J Physiol Endocrinol Metab 292:E936-45. 2007
    ..These studies reveal a genetic difference in body composition that correlates with large differences in peripheral insulin sensitivity...
  15. ncbi request reprint Identification of major quantitative trait loci controlling body weight variation in ob/ob mice
    Jonathan P Stoehr
    Department of Biochemistry, University of Wisconsin Madison, Madison, Wisconsin 53706, USA
    Diabetes 53:245-9. 2004
    ..Thus, the identification of these loci may provide important new insights into the pathogenesis of human obesity...
  16. pmc Selective phenotyping for increased efficiency in genetic mapping studies
    Chunfang Jin
    Department of Statistics, University of Wisconsin, Madison, Wisconsin 53706, USA
    Genetics 168:2285-93. 2004
    ..The substantial improvement introduced by selective phenotyping is particularly useful when phenotyping is difficult or costly and thus limits the sample size in a genetic mapping study...
  17. ncbi request reprint Positional cloning of Sorcs1, a type 2 diabetes quantitative trait locus
    Susanne M Clee
    Department of Biochemistry, University of Wisconsin Madison, Madison, Wisconsin 53706, USA
    Nat Genet 38:688-93. 2006
    ..Our identification of the Sorcs1 gene provides insight into the pathway underlying the pathophysiology of obesity-induced type 2 diabetes mellitus...
  18. doi request reprint Genetic mapping of paternal sorting of mitochondria in cucumber
    Claudia I Calderon
    Department of Horticulture, University of Wisconsin, Madison, WI 53706, USA
    Theor Appl Genet 125:11-8. 2012
    ....
  19. pmc Rgcs1, a dominant QTL that affects retinal ganglion cell death after optic nerve crush in mice
    Joel A Dietz
    Department of Ophthalmology and Visual Sciences, University of Wisconsin, Madison, WI, USA
    BMC Neurosci 9:74. 2008
    ..To assess this further, we bred and phenotyped a large population of F2 mice derived from a resistant inbred strain (DBA/2J) and a susceptible strain (BALB/cByJ)...
  20. doi request reprint Major QTL for carrot color are positionally associated with carotenoid biosynthetic genes and interact epistatically in a domesticated x wild carrot cross
    Brian J Just
    Plant Breeding and Plant Genetics Program, Department of Horticulture, University of Wisconsin, Madison, WI 53706, USA
    Theor Appl Genet 119:1155-69. 2009
    ..These two genes played a major role in carrot domestication and account for the significant role that modern carrot plays in vitamin A nutrition...
  21. ncbi request reprint Prognostic accuracy of the proventriculus: keel ratio for short-term survival in psittacines with proventricular disease
    Sophie E Dennison
    Department of Surgical Sciences, School of Veterinary Medicine, University of Wisconsin, Madison, WI 53706, USA
    Vet Radiol Ultrasound 50:483-6. 2009
    ..9). The proventriculus:keel ratio is a sensitive indicator of proventricular disease in parrots but is insensitive as a prognostic indicator...
  22. ncbi request reprint Development of vocal tract length during early childhood: a magnetic resonance imaging study
    Houri K Vorperian
    Waisman Center, University of Wisconsin Madison, Madison, Wisconsin 53705, USA
    J Acoust Soc Am 117:338-50. 2005
    ..Findings provide normative data that can be used for modeling the development of the vocal tract...
  23. pmc Determination of a sedative protocol for use in California sea lions (Zalophus californianus) with neurologic abnormalities undergoing electroencephalographic examination
    Sophie Dennison
    The Marine Mammal Center, 1065 Fort Cronkhite, Sausalito, California 94965, USA
    J Zoo Wildl Med 39:542-7. 2008
    ..Medetomidine alone at a dose rate of 0.07 mg/kg thus provides adequate and safe sedation in sea lions with neurologic signs undergoing EEG evaluation...
  24. pmc Major regulatory genes in maize contribute to standing variation in teosinte (Zea mays ssp. parviglumis)
    Allison Weber
    Laboratory of Genetics, University of Wisconsin, Madison 53706, USA
    Genetics 177:2349-59. 2007
    ..Our data suggest that major regulatory genes in maize do play a role in the natural variation for complex traits in teosinte and that some of the minor variants we identified may have been targets of selection during domestication...
  25. pmc Loss of stearoyl-CoA desaturase-1 function protects mice against adiposity
    James M Ntambi
    Department of Biochemistry, University of Wisconsin, Madison, WI 53706, USA
    Proc Natl Acad Sci U S A 99:11482-6. 2002
    ..These observations suggest that a consequence of SCD1 deficiency is an activation of lipid oxidation in addition to reduced triglyceride synthesis and storage...
  26. ncbi request reprint Gene expression analysis suggests that 1,25-dihydroxyvitamin D3 reverses experimental autoimmune encephalomyelitis by stimulating inflammatory cell apoptosis
    Karen M Spach
    Department of Nutritional Sciences, University of Wisconsin Madison, Madison, Wisconsin 53706, USA
    Physiol Genomics 18:141-51. 2004
    ..Together, these results suggest that sensitization of inflammatory cells to apoptotic signals may be one mechanism by which the 1,25-(OH)2D3 resolved EAE...
  27. pmc Dimension reduction for mapping mRNA abundance as quantitative traits
    Hong Lan
    Department of Biochemistry, University of Wisconsin, 433 Babcock Drive, Madison, WI 53706, USA
    Genetics 164:1607-14. 2003
    ..As a further statistical refinement, we show that principal component analysis also effectively reduced dimensions for mapping phenotypes composed of mRNA abundances...
  28. pmc Transcriptomic profiling of bovine IVF embryos revealed candidate genes and pathways involved in early embryonic development
    Wen Huang
    Department of Dairy Science, University of Wisconsin Madison, Madison, WI 53706, USA
    BMC Genomics 11:23. 2010
    ..The objective of this study was to identify genes differentially expressed between blastocysts and degenerative embryos at early stages of development...
  29. ncbi request reprint Nonparametric estimation of the effects of quantitative trait loci
    Jason P Fine
    Department of Statistics, University of Wisconsin, Madison, WI 53706, USA
    Biostatistics 5:501-13. 2004
    ..They have a closed form and their small and large sample properties are readily established. Their practical utility as numerical summaries which complement nonparametric tests is demonstrated on two recent genetics examples...
  30. pmc Phenotypic and transcriptomic changes associated with potato autopolyploidization
    Robert M Stupar
    Department of Horticulture, University of Wisconsin, Madison, WI 53706, USA
    Genetics 176:2055-67. 2007
    ..We demonstrated that there are few genes, if any, whose expression is linearly correlated with the ploidy and can be dramatically changed because of ploidy alteration...
  31. ncbi request reprint Gene expression profiles of nondiabetic and diabetic obese mice suggest a role of hepatic lipogenic capacity in diabetes susceptibility
    Hong Lan
    Department of Biochemistry, University of Wisconsin, 433 Babcock Drive, Madison, WI 53706, USA
    Diabetes 52:688-700. 2003
    ..We propose that increased hepatic lipogenic capacity protects the B6-ob/ob mice from the development of type 2 diabetes...
  32. pmc A quantitative map of the liver mitochondrial phosphoproteome reveals posttranslational control of ketogenesis
    Paul A Grimsrud
    Department of Biochemistry, University of Wisconsin Madison, Madison, WI 53706, USA
    Cell Metab 16:672-83. 2012
    ..Collectively, our work describes the plasticity of this organelle at high resolution and provides a framework for investigating the roles of proteome restructuring and reversible phosphorylation in mitochondrial adaptation...
  33. ncbi request reprint Effect of anesthesia, positioning, time, and feeding on the proventriculus: keel ratio of clinically healthy parrots
    Sophie E Dennison
    Department of Surgical Sciences, School of Veterinary Medicine, University of Wisconsin, 100 University Avenue, Madison, WI 53706, USA
    Vet Radiol Ultrasound 51:141-4. 2010
    ..Ratio fluctuations within the normal range between radiographs obtained on different dates may be observed in normal parrots...
  34. ncbi request reprint Evaluation of different computed tomography techniques and myelography for the diagnosis of acute canine myelopathy
    Sophie E Dennison
    Department of Surgical Sciences, School of Veterinary Medicine, University of Wisconsin Madison, 2015 Linden Drive, Madison, WI 53706, USA
    Vet Radiol Ultrasound 51:254-8. 2010
    ....
  35. pmc A Bayesian approach for constructing genetic maps when markers are miscoded
    Guilherme J M Rosa
    Department of Biostatistics, UNESP, Botucatu, SP, Brazil
    Genet Sel Evol 34:353-69. 2002
    ..The results suggest that unless there is strong reason to believe that genotypes are ascertained without error, the proposed approach provides more reliable inference on the genetic map...
  36. 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...
  37. pmc An efficient Bayesian model selection approach for interacting quantitative trait loci models with many effects
    Nengjun Yi
    Department of Biostatistics, Section on Statistical Genetics, University of Alabama, Birmingham, Alabama 35294 0022, USA
    Genetics 176:1865-77. 2007
    ..Our method has been implemented in the freely available package R/qtlbim (http://www.qtlbim.org) to facilitate the general usage of the Bayesian methodology for genomewide interacting QTL analysis...
  38. pmc Bayesian mapping of genomewide interacting quantitative trait loci for ordinal traits
    Nengjun Yi
    Section on Statistical Genetics, Department of Biostatistics, University of Alabama, Birmingham, Alabama 35294 0022, USA
    Genetics 176:1855-64. 2007
    ....
  39. pmc Bayesian quantitative trait loci mapping for multiple traits
    Samprit Banerjee
    Departments of Biostatistics, Section on Statistical Genetics, University of Alabama, Birmingham, AL 35294, USA
    Genetics 179:2275-89. 2008
    ..Our methods have been implemented in the freely available package R/qtlbim (http://www.qtlbim.org), which greatly facilitates the general usage of the Bayesian methodology for unraveling the genetic architecture of complex traits...
  40. pmc Genetic networks of liver metabolism revealed by integration of metabolic and transcriptional profiling
    Christine T Ferrara
    Sarah W Stedman Nutrition and Metabolism Center, Duke University Medical Center, Durham, North Carolina, United States of America
    PLoS Genet 4:e1000034. 2008
    ..Thus, the methods described here have the potential to reveal regulatory networks that contribute to chronic, complex, and highly prevalent diseases and conditions such as obesity and diabetes...
  41. pmc Rank-based statistical methodologies for quantitative trait locus mapping
    Fei Zou
    Department of Biostatistics, University of North Carolina, Chapel Hill, North Carolina 27599, USA
    Genetics 165:1599-605. 2003
    ..The results indicate that the nonparametric method is a competitive alternative to the existing parametric methodologies...
  42. ncbi request reprint SORCS1: a novel human type 2 diabetes susceptibility gene suggested by the mouse
    Mark O Goodarzi
    Cedars Sinai Medical Center, Division of Endocrinology, Diabetes, and Metabolism, 8700 Beverly Blvd, Becker B 131, Los Angeles, CA 90048, USA
    Diabetes 56:1922-9. 2007
    ..Thus, we sought to determine whether variation in the human SORCS1 gene was associated with diabetes-related traits...