Brian S. Yandell Publications
(click on Yandell or journal title or visit www.stat.wisc.edu/$\sim$yandell/doc )

A. Papers published in, or accepted by, refereed journals

  1. Yandell BS (1982) Non-identifiability of lethality in the survival experiment with serial sacrifice. Mathematical Bioscience 62 : 1–6.
  2. Yandell BS (1983) Nonparametric inference for rates with censored survival data. Annals of Statistics 11 : 1119–1135.
  3. Nicot P, Rouse DI, Yandell BS (1984) Comparison of statistical methods for studying spatial patterns of soilborne plant pathogens in the field. Phytopathology 74 : 1399–1402.
  4. Bjerve S, Doksum KA, Yandell BS (1985) Uniform confidence bounds for nonparametric regression. Scandinavian J of Statistics 12 : 159–169.
  5. Schenkman DI, Berman DT, Yandell BS (1985) Effect of stage of lactation on transport of colloidal carbon or Staphylococcus aureus from the mammary gland lumen to lymph nodes in guinea pigs. J of Dairy Research 52 : 491–500.
  6. Barabás B, Csörgő M, Horváth L, Yandell BS (1986) Bootstrapped confidence bands for percentile lifetime. Annals of the Institute of Statistical Mathematics 38A : Tokyo, 429–438.
  7. O'Sullivan F, Yandell BS , Raynor WJ, Jr (1986) Automatic smoothing of regression functions in generalized linear models. J of the American Statistical Assocication 81 : 96–103.
  8. Romero-Andreas J, Bliss F, Yandell BS (1986) Bean Arcelin 1: Inheritance of a novel seed protein of Phaseolus vulgaris L. and its effect on seed composition. Theor Appl Genet 72 : 123–128.
  9. Taam W, Yandell BS (1986) Small sample power of Moran's I statistics for AR and MA models. J of Statistical Computation & Simulation 26 : 127–129. [ TR 769 , Dept. of Statistics, Univ. of Wisconsin-Madison.]
  10. Bates DM, Lindstrom MJ, Wahba G, Yandell BS (1987) GCVPACK Routines for Generalized Cross Validation. Communications in Statistics B16 : Algorithms Section, 263–297.
  11. Horváth L, Yandell BS (1987) Convergence rates for the bootstrapped product limit process. Annals of Statistics 15 : 1155–1173.
  12. Bewick TA, Binning LK, Yandell BS (1988) A degree day model for predicting the emergence of swamp dodder (Cuscuta gronovii Willd.) in cranberry (Vaccinium macrocarpon Ait.). J of the American Society of Horticultural Science 113 : 839–845.
  13. Chrisman NR, Yandell BS (1988) Effects of point error on area calculations: a statistical model. Surveying & Mapping 48: 241–246.
  14. Cox D, Koh E, Wahba G, Yandell BS (1988) Testing the (parametric) null model hypothesis in (semiparametric) partial and generalized spline models. Annals of Statistics 16 : 113–119.
  15. Horváth L, Yandell BS (1988) Asymptotics of conditional empirical processes. J of Multivariate Analysis 26 : 184–206.
  16. Luebke HJ, Scriber JM, Yandell BS (1988) Use of multivariate discriminant analysis of male wing morphometrics to delineate the Wisconsin hybrid zone for Papilio glaucus glaucus and P. g. canadensis. American Midland Naturalist 119 : 366–379.
  17. Yandell BS (1988) Block diagonal smoothing splines. Statistics & Probability Letters 6 : 331–334.
  18. Yandell BS (1988) Algorithms for multidimensional semiparametric GLM's. Communications in Statistics B17 : 295–312.
  19. Yandell BS , Hogg D (1988) Modeling insect natality using splines. Biometrics 44 : 385–395.
  20. Yandell BS , Horváth L (1988) Bootstrapped multi-dimensional product limit process. Australian J of Statistics 30 : 342–358.
  21. Yandell BS , Najar A, Wheeler R, Tibbitts TW (1988) Modelling the effects of light, carbon dioxide and temperature on the growth of potato. Crop Science 28 : 811–818.
  22. Hasegawa T, Horie T, Yandell BS (1991) Improvement of yielding ability in Japonica rice cultivars and its impact on regional yield increase in Kinki District, Japan. Agricultural Systems 35 : 173–187.
  23. Lathrop RG, Lillesand TM, Yandell BS (1991) Testing the utility of simple multi-date Thematic Mapper calibration algorithms for monitoring turbid inland waters. International J of Remote Sensing 12 : 2045–2063.
  24. Wang CS, Yandell BS , Rutledge JJ (1991) Bias of maximum likelihood estimators of intraclass correlation. Theor Appl Genet 82 : 421–424.
  25. Croxdale J, Smith J, Yandell BS , Johnson JB (1992) Stomatal patterning in Tradescantia: an evaluation of the cell lineage theory. Developmental Biology 149 158–167.
  26. Jeanne RL, Williams NM, Yandell BS (1992) Age polyethism and defense in a tropical social wasp. J of Insect Behavior 5 : 211–227.
  27. Price JI, Yandell BS , Porter WP (1992) Chemical effects on survival of avian cholera organisms in pondwater. J of Wildlife Management 56 : 274–278.
  28. Staniswallis JG, Yandell BS (1992) Locally adaptive smoothing splines. J of Statistical Computation & Simulation 43 : 45–53.
  29. Stieve SM, Stimart DP, Yandell BS (1992) Heritable tissue culture induced variation in Zinnia Marylandica. Euphytica 64 : 81–89.
  30. Wang CS, Yandell BS , Rutledge JJ (1992) The dilemma of negative analysis of variance estimators of intraclass correlation and its variants. Theor Appl Genet 85 : 79–88.
  31. Weigel KA, Gianola D, Yandell BS , Keown JF (1993) Identification of factors causing heterogeneous within-herd variance components using a structural model of variances. J of Dairy Science 76 : 1466–1478.
  32. Yandell BS (1993) Smoothing splines – a tutorial. The Statistician 42 : 317–319.
  33. Ferreira ME, Satagopan J, Yandell BS , Williams PH, Osborn TC (1995) Mapping loci controlling vernalization requirement and flowering time in Brassica napus. Theor Appl Genet 90 : 727–732.
  34. Jeanne RL, Graf CA, Yandell BS (1995) Non-size-based morphological castes in a social insect. Naturwissenschaften 82 : 296–298.
  35. Nichols SA, Yandell BS (1995) Habitat relationships for some Wisconsin lake plant associations. J of Freshwater Ecology 10 : 367–377.
  36. Scott TA, Shaver RD, Zepeda L, Yandell B , Smith TR (1995) Effects of rumen-inert fat on lactation, reproduction, and health in high-producing Holstein herds. J of Dairy Science 78 : 2435–2452.
  37. Teutonico RA, Ferreira ME, Satagopan JM, Yandell BS , Palta JP, Osborn TC (1995) Genetic analysis and mapping of genes controlling freezing tolerance in oilseed. Molecular Breeding 1 : 329–339.
  38. Satagopan JM, Yandell BS , Newton MA, Osborn TC (1996) Markov chain Monte Carlo approach to detect polygene loci for complex traits. Genetics 144 : 805–816. PMCID: PMC1207571
  39. Scott TA, Yandell BS , Shaver RD, Zepeda L, Smith TR (1996) Use of lactation curves in analysis of milk production data. J of Dairy Science 79 : 1885–1894.
  40. Tavoletti S, Bingham ET, Yandell BS , Veronesi F, Osborn TC (1996) Half tetrad analysis in alfalfa using multiple RFLP markers. Proceedings of the National Academy of Science USA 93 : 10918–10922. PMCID: PMC38258
  41. Qiu P, Yandell BS (1997) Jump detection in regression surfaces. J of Computational and Graphical Statistics 6 : 332–354.
  42. Qiu P, Yandell BS (1998) A local polynomial jump detection algorithm in nonparametric regression. Technometrics 40 : 141–152.
  43. Kidwell KK, Hartweck LM, Yandell BS , Crump PM, Brummer JE, Moutray J, Osborn TC (1999) Forage yields of alfalfa populations derived from parents selected on the basis of molecular marker diversity. Crop Science 39 : 223–227.
  44. Debaene JEP, Goldman IL, Yandell BS (1999) Postharvest flux and genotype x environment effects for onion-induced antiplatelet activity, pungency and soluble solids in long-day onion during postharvest cold storage. J Amer Soc Hort Sci 124 : 366–372.
  45. Tao H, Palta M, Yandell BS , Newton MA (1999) An estimation method for the semi-parametric mixed effects model. Biometrics 55 : 102–110.
  46. Vorperian HK, Kent RD, Gentry LR, Yandell BS (1999) Magnetic resonance imaging procedures to study the concurrent anatomic development of vocal tract structures. International J of Pediatric Otorhinolaryngology 49 : 197–206.
  47. RF Young and Yandell BS (1999) Top-down vs. bottom-up analyses of interlanguage data: a reply to Saito. Studies in Second Language Acquisition 21 : 477–488.
  48. Nadler ST, Stoehr JP, Schueler KL, Tanimoto G, Yandell BS , Attie AD (2000) The expression of adipogenic genes is decreased in obesity and Diabetes mellitus. Proceedings of the National Academy of Science USA 97 : 11371–11376. PMCID: PMC17207
  49. Stoehr JP, Nadler ST, Schueler KL, Rabaglia ME, Yandell BS , Metz SA, Attie AD (2000) Genetic obesity unmasks non-linear interactions between murine type 2 diabetes susceptibility loci. Diabetes 49 : 1946–1954.
  50. Ostermeier GC, Sargeant GA, Yandell BS , Evenson DP, Parrish JJ (2001) Relationship of bull fertility to sperm nuclear shape. J Androl 22 : 595–603.
  51. Ostermeier GC, Sargeant GA, Yandell BS , Parrish JJ (2001) Measurement of bovine sperm nuclear shape using Fourier harmonic amplitudes. J Androl 22 : 584–94.
  52. Zou F, Yandell BS , Fine JP (2001) Statistical issues in the analysis of quantitative traits in combined crosses Genetics 158 : 1339–1346. PMCID: PMC1461706
  53. Ewing B, Yandell BS , Barbieri JF, Luck RF, Forster LD (2002) Event-driven competing risks. Ecological Modelling 158 : 35–50.
  54. Rosa GJM, Yandell BS , Gianola D (2002) A Bayesian approach for constructing genetic maps when genotypes are miscoded. Genetics, Selection and Evolution 34 : 353–369.
  55. Kole C, Thorman CE, Karlsson BH, Palta JP, Gaffney P, Yandell BS , Osborn TC (2002) Comparative mapping of loci controlling winter survival and related traits in oilseed Brassica rapa and B. napus. Molecular Breeding 9 : 201–210.
  56. Ntambi JM, Miyazaki M, Stoehr JP, Lan H, Kendziorski CM, Yandell BS , Song Y, Cohen P, Friedman JM, Attie AD (2002) Loss of stearoyl-CoA desaturase-1 function protects mice against adiposiy. Proc. Nat. Acad. Sci. 99 : 11482-11486. PMCID: PMC123282
  57. Zou F, Fine JP, Yandell BS (2002) On empirical likelihood for a semiparametric mixture model. Biometrika 89 : 61–75.
  58. Lan H, Rabaglia ME, Stoehr JP, Nadler ST, Schueler KL, Zou F, Yandell BS , Attie AD (2003) Gene expression profiles of nondiabetic and diabetic obese mice suggest a role of hepatic lipogenic capacity in diabetes susceptibility. Diabetes 52 : 1–13.
  59. Lan H, Stoehr JP, Nadler ST, Schueler KL, Yandell BS , Attie AD (2003) Dimension Reduction for Mapping mRNA Abundance as Quantitative Traits. Genetics 164 : 1607–1614. PMCID: PMC1462655
  60. Zou F, Yandell BS , Fine JP (2003) Rank-based statistical methodologies for QTL mapping. Genetics 165 : 1599–1605. PMCID: PMC1462811
  61. Lan H, Rabaglia ME, Schueler KL, Mata C, Yandell BS , Attie AD (2004) Distinguishing co-variance from causality: a lesson from the protein disulfide isomerase mRNA abundance trait in diabetic mice. Diabetes 53 : 240-244.
  62. Stoehr JP, Byers JE, Clee SM, Lan H, Boronenkov I, Schueler KM, Yandell BS , Attie AD (2004) Identification of major quantitative trait loci controlling body weight variation in ob/ob mice. Diabetes 53 : 245–249.
  63. Fine JP, Zou F, Yandell BS (2004) Nonparametric estimation of mixture distributions with known mixture proportions. Biostatistics 5 : 501–513.
  64. Jin C, Lan H, Attie AD, Bulutuglo D, Churchill GA, Yandell BS (2004) Selective phenotyping for increased efficiency in genetic mapping studies. Genetics 168 : 2285–2293. PMCID: PMC1448737
  65. Spach KM, Pedersen LB, Nashold FE, Yandell BS , Kayo T, Prolla TA, Hayes CE (2004) Rapid gene expression changes in the central nervous system following 1,25-dihydroxyvitamin D3 administration to mice with experimental autoimmune encephalomyelitis suggest apoptosis induction as a disease resolution mechanism. Physiological Genomics 18 : 141–151.
  66. Vorperian HK, Kent RD, Lindstrom MJ, Kalina CM, Gentry LR, Yandell BS (2005) Development of vocal tract length during early childhood: A magnetic resonance imaging study. J Acoustical Soc Amer 117 : 338–350.
  67. Yi N, Yandell BS , Churchill GA, Allison DB, Eisen EJ, Pomp D (2005) Bayesian model selection for genome-wide epistatic QTL analysis. Genetics 170 : 1333–1344. PMCID: PMC1451197
  68. Clee SM, Yandell BS , Schueler KM, Rabaglia ME, Richards OC, Raines SM, Kabara EA, Klass DM, Mui ETK, Stapleton DS, Gray-Keller MP, Young MB, Stoehr JP, Lan H, Boronenkov I, Raess PW, Flowers MT, Attie AD (2006) Positional cloning of Sorcs1, a type 2 diabetes quantitative trait locus. Nat Genet 38 : 688-693. PMID: 16682971
  69. Guan Q, Zheng W, Tang S, Liu X, Zinkel R, Tsui KW, Yandell BS , Culbertson MR (2006) Impact of nonsense-mediated mRNA decay on the global expression profile of budding yeast. PLoS Genetics 2 : e203. PMCID: PMC1657058
  70. Lan H, Chen M, Flowers JB, Yandell BS , Stapleton DS, Mata CM, Mui ETK, Flowers MT, Schueler KL, Manly KF, Williams RW, Kendziorski C, Attie AD (2006) Combined expression trait correlations and expression quantitative trait locus mapping. PLoS Genetics 2 : e6. PMCID: PMC1331977
  71. Flowers J, Oler A, Nadler S, Choi Y, Schueler K, Yandell BS , Kendziorski C, Attie AD (2007) Abdominal obesity in BTBR male mice is associated with peripheral but not hepatic insulin resistance. AJP: Endocrinology and Metabolism 292 : E936–E945.
  72. Goodarzi MO, Lehman DM, Taylor KD, Guo X, Cui J, Quiñones MJ, Clee SM, Yandell BS , Blangero J, Hsueh WA, Attie AD, Stern MP, Rotter JI (2007) SORCS1: A novel human type 2 diabetes susceptibility gene suggested by the mouse. Diabetes 56 : 1922-1929.
  73. Jin C, Fine JP, Yandell BS (2007) A unified semiparametric framework for QTL analyses, with application to spike phenotypes. J Amer Statist Assoc 102 : 56–67.
  74. Simm C, Lahner B, Salt D, LeFurgey A, Ingram P, Yandell BS , Eide DJ (2007) The role of the yeast vacuole in zinc storage and intracellular zinc distribution. Eukaryotic Cell 6 : 1166–1177. PMCID: PMC1951117
  75. Stupar RM, Bhaskar PB, Yandell BS , Hart AL, Veilleux RE, Busse JS, Erhardt RJ, Buell CR, Jiang J (2007) Phenotypic and transcriptomic changes associated with potato autopolyploidization. Genetics 176 : 2055–2067. PMCID: PMC1950613
  76. Weber A, Clark R, Vaughn L, Sánchez-Gonzalez JdeJ, Yu J, Yandell BS , Bradbury P, Liu K, Doebley J (2007) Association genetics in Balsas teosinte (Zea mays ssp. parviglumis). Genetics 177 : 2349–2359. PMCID: PMC2219500
  77. Yandell BS (2007) Graphical data presentation, with emphasis on genetic data. Hort Sci 42 : 1047–1051.
  78. Yandell BS , Mehta T, Banerjee S, Shriner D, Venkataraman R, Moon JY, Neely WW, Wu H, von Smith R, Yi N (2007) R/qtlbim: QTL with Bayesian interval mapping in experimental crosses. Bioinformatics 23 : 641-643. PMID: 17237038
  79. Yi N, Banerjee S, Shriner D, Pomp D, Yandell BS (2007) Bayesian mapping of genome-wide interacting QTL for ordinal traits. Genetics 176 : 1855–1864. PMCID: PMC1931535
  80. Yi N, Shriner D, Banerjee S, Mehta T, Pomp D, Yandell BS (2007) Efficient strategies for Bayesian mapping of genome-wide interacting QTL. Genetics 176 : 1865–1877. PMCID: PMC1931520
  81. Banerjee S, Yandell BS , Yi N (2008) Bayesian QTL Mapping for Multiple Traits Genetics 179 : 2275–2289. PMCID: PMC2516097
  82. Chaibub Neto E, Ferrara C, Attie AD, Yandell BS (2008) Inferring causal phenotype networks from segregating populations. Genetics 179 : 1089–1100. PMCID: PMC2429862
  83. Dennison S, Haulena M, Williams DC, Dawson J, Yandell BS , Gulland FMD (2008) Determination of a safe sedative protocol for use in California sea lions (Zalophus californianus) with neurologic abnormalities undergoing electroencephalogram examination. J Zoo Wildlife Med 39 : 542–547. PMID: 19110694
  84. Dietz JA, Yan L, Chung LM, Yandell BS , Schlamp CL, Nickells RW (2008) Rgcs1, a dominant QTL that affects retinal ganglion cell death after optic nerve crush in mice. BMC Neuorsci 9 : 74. PMCID: PMC2518923
  85. Ferrara CT, Wang P, Chaibub Neto E, Stevens RD, Bain JR, Wenner BR, Ilkayeva OR, Keller MP, Blasiole DA, Kendziorski C, Yandell BS , Newgard CB, Attie AD (2008) Genetic networks of liver metabolism revealed by integration of metabolic and transcriptomic profiling. PLoS Genet 4 : e1000034. PMCID: PMC2265422
  86. Keller MP, Choi YJ, Wang P, Davis DB, Rabaglia ME, Oler AT, Stapleton DS, Argmann C, Schueler KL, Edwards S, Steinberg HA, Neto EC, Kleinhanz R, Turner S, Hellerstein MK, Schadt EE, Yandell BS , Kendziorski CM, Attie AD (2008) A gene expression network model of type 2 diabetes establishes a relationship between cell cycle regulation in islets and diabetes susceptibility. Genome Res 18 : 706–716. PMCID: PMC2336811
  87. Dennison SE, Adams WM, Johnson PJ, Yandell BS , Paul-Murphy JR (2009) Prognostic accuracy of the proventriculus: keel ratio in 48 psittacines with confirmed proventricular disease. Vet Radiol & Ultrasound 50 : 483–486. PMID: 19788031
  88. Just BJ, Santos CAF, Yandell BS , Simon PW (2009) Major QTL for carrot color are positionally associated with carotenoid biosynthetic genes and interact epistatically in a domesticated x wild carrot cross. Theor Appl Genet 119 : 1155–1169. PMID: 19657616
  89. Khatib H, Huang W, Wang X, Tran AH, Tontillo K, Bindrim AB, Schutzkus V, Monson RL, Yandel BS (2009) Single gene and gene interaction effects on fertility traits in cattle. J Dairy Sci 92 : 2238–2247. PMID: 19389983
  90. Manichaikul A, Moon JY, Sen S, Yandell BS , Broman KW (2009) A model selection approach for the identification of quantitative trait loci in experimental crosses. Genetics 181 : 1077–1086. PMCID: PMC2651044 [ TR 205 , Department of Biostatistics & Medical Informatics, UW-Madison.]
  91. Zhao E, Keller M, Rabaglia M, Oler A, Stapleton D, Schueler K, Chaibub Neto E, Moon JY, Wang P, Wang IM, Lum P, Ivanovska I, Greenawalt D, Tsang J, Choi YJ, Kleinhanz R, Shang J, Zhou YP, Howard A, Zhang B, Kendziorski C, Thornberry N, Yandell BS , Schadt EE, Attie AD (2009) Obesity and genetics regulate microRNAs in islets, liver and adipose of diabetic mice. Mammal Genome 20 : 476–485. PMCID: PMC2879069
  92. Chaibub Neto E, Keller MP, Attie AD, Yandell BS (2010) Causal Graphical Models in Systems Genetics: a unified framework for joint inference of causal network and genetic architecture for correlated phenotypes. Ann Appl Statist 4 : 320–339. PMCID: PMC3017382 [See TR 1146R , Department of Statistics, UW-Madison.]
  93. Chen K, Tian S, Yandell BS , Kaeppler SM, An YQC (2010) Loss-of-function of DELLA protein SLN1 activates GA signaling in barley aleurone. Acta Physiologiae Plantarum 32 : 789–800.
  94. Davis D, Lavine J, Suhonen J, Krautkramer K, Rabaglia M, Sperger J, Fernandez L, Yandell BS , Keller M, Wang IM, Schadt EE, Attie AD (2010) FoxM1 is upregulated by obesity and stimulates beta-cell proliferation. Molec Endocrin 24 : 1822–1834. PMCID: PMC2940473
  95. Dennison S, Drees R, Rylander H, Yandell B , Milovancev M, Pettigrew R, Schwarz T (2010) Evaluation of different computed tomographic techniques and myelography for the diagnosis of acute canine spinal disease. Vet Rad & Ultrasound 51 : 1-5. PMID: 20469546
  96. Dennison SE, Paul-Murphy JR, Yandell BS , Adams WM (2010) Effect of anesthesia, positioning and patient variables on the proventriculus:keel ratio of clinically healthy parrots. Vet Rad & Ultrasound 51 : 141–144. PMID: 20402397
  97. Huang W, Yandell BS , Khatib H (2010) Transcriptomic profiling of bovine IVF embryos revealed candidate genes and pathways involved in early embryonic death. BMC Genomics 11 : 23. PMCID: PMC2824717
  98. Lavine JA, Raess PW, Stapleton DS, Rabablia ME, Suhonen JI, Schueler KL, Koltes JE, Dawson JA, Yandell BS , Samuelson LC, Beinfeld MC, Davis DB, Hellerstein MK, Keller MP, Attie AD (2010) Cholecystokinin is upregulated in obese islets and expands beta-cell mass by increasing beta-cell survival. Endocrinology 151 : 3577–3588. PMCID: PMC2940525
  99. Zhong H, Beaulaurier J, Lum PY, Molony C, Yang X, MacNeil DJ, Weingarth DT, Zhang B, Greenawalt D, Dobrin R, Hao K, Woo S, Fabre-Suver C, Qian S, Tota BR, Keller MP, Kendziorski CM, Yandell BS , Castro V, Attie AD, Kaplan LM, Schadt EE (2010) Liver and adipose expression associated SNPs are enriched for association with Type 2 Diabetes. PLoS Genet 6 : e1000932. PMCID: PMC2865508
  100. Bhatnagar S, Oler AT, Rabaglia ME, Stapleton DS, Schueler KL, Truchan NA, Worzella SL, Stoehr JP, Clee SM, Yandell BS , Keller MP, Thurmond DC, Attie AD (2011) Positional cloning of a type 2 diabetes quantitative trait locus; Tomosyn-2, a negative regulator of insulin secretion. PLoS Genetics 7 : e1002323. PMID: 21998599
  101. Wang P, Dawson J, Keller MP, Yandell BS , Thornberry N, Zhang BB, Wang IM, Schadt EE, Attie AD, Kendziorski C (2011) A model selection approach for expression quantitative trait loci (eQTL) mapping. Genetics 187 : 611–621. PMCID: PMC3030500
  102. Calderon CI, Yandell BS , Havey MJ (2012) Genetic Mapping of Paternal Sorting of Mitochondria in Cucumber. Theor Appl Genet 125 : 11–18.
  103. Casellas J, Gularte RJ, Farber CR, Varona L, Mehrabian M, Schadt EE, Lusis AJ, Attie AD, Yandell BS , Medrano JF (2012) Genome scans for transmission ratio distortion regions in mice. Genetics 191 : 247–259. PMID: 21998599
  104. Chaibub Neto E, Keller MP, Broman AF, Attie AD, Jansen RC, Broman KW, Yandell BS (2012) Quantile-based permutation thresholds for QTL hotspots. Genetics 191 : 1355–1365. PMCID: PMC3416013
  105. Grimsrud PA, Carson JJ, Hubler SL, Hebert AS, Niemi NM, Bailey DJ, Jochem A, Stapleton DS, Keller MP, Westphall MS, Yandell BS , Attie AD, Coon JJ, Pagliarini DJ (2012) A quantitative map of the liver mitochondrial phosphoproteome reveals post-translational control of ketogenesis. Cell Metabolism 16 : 672–683. PMID: 22661325
  106. Tu Z, Keller MP, Zhang C, Rabaglia ME, Greenawalt DM, Yang X, Wang IM, Dai H, Bruss MD, Lum PY, Zhou YP, Kemp DM, Kendziorski C, Yandell BS , Attie AD, Schadt EE, Zhu J (2012) Integrative Analysis of a Cross-loci Regulation Network Identifies App as a Gene Regulating Insulin Secretion from Pancreatic Islets. PLoS Genetics 8 : e1003107.
  107. Wang CY, Stapleton DS, Schueler KL, Rabaglia ME, Oler AT, Keller MP, Kendziorski CM, Broman KW, Yandell BS , Schadt EE, Thornberry NA, Attie AD (2012) Tsc2, a positional candidate gene underlying a quantitative trait locus for hepatic steatosis. J Lipid Research 53 : 1493–1501.
  108. Chaibub Neto E, Broman AT, Keller MP, Attie AD, Zhang B, Zhu J, Yandell BS (2013) Modeling causality for pairs of phenotypes in system genetics. Genetics 193 : 1003–1013. [ March Highlights ] [Initially published as Chaibub Neto E, Keller MP, Broman AT, Attie AD, Yandell BS (2010) Causal model selection tests in systems genetics. TR 1157 , Department of Statistics, UW–Madison.]
  109. He X, Li Y, Pandey S, Yandell BS , Pathak M, Weng Y (2013) QTL Mapping of Powdery Mildew Resistance in WI 2757 Cucumber (Cucumis sativus L.). Theor Appl Genet 126 : 2149–2161.
  110. Dietz JA, Maes ME, Huang S, Yandell BS , Schlamp CL, Montgomery AD, Allingham RR, Hauser MA, Nickells RW (2014) Spink2 Modulates Apoptotic Susceptibility and Is a Candidate Gene in the Rgcs1 QTL That Affects Retinal Ganglion Cell Death after Optic Nerve Damage. PLoS ONE 9 : e93564.
  111. Broman KW, Keller MP, Broman AT, Kendziorski C, Yandell BS , Sen S, Attie AD (2015) Identifiation and correction of sample mix-ups in expression genetic data: A case study. G3 5 : 2177-2186.
  112. Tian J, Keller MP, Oler AT, Rabagalia ME, Schueler KL, Stapleton DS, Broman AT, Zhao W, Kendziorski C, Yandell BS , Hagenbuch B, Broman KW, Attie AD (2015) Identification of the bile acid transporter Slco1a6 as a candidate gene that broadly affects gene expression in mouse pancreatic islets. Genetics 201 : 1253-1262.
  113. Calderon CF, Yandell BS , Doebley JF (2016) Fine Mapping of a QTL Associated with Kernel Row Number on Chromosome 1 of Maize. PLoS ONE 0 : 000-000.
  114. Sinasac DS, Riordan JD, Spiezio SH, Yandell BS , Croniger CM, Nadeau JH (2016) Genetic control of obesity, glucose homeostasis, dyslipidemia, and fatty liver in a mouse model of diet-induced metabolic syndrome. Intl J Obesity 40 : 346-355. PMID: 26381349
  115. Tian J, Keller MP, Broman AT, Kendziorski C, Yandell BS , Attie AD, Broman KW (2016) The dissection of expression quantitative trait locus hotspots. Genetics 202 : 1-12.
  116. Keller MP, Paul PK, Rabaglia ME, Stapleton DS, Schueler KL, Broman AT, Ye SI, Leng N, Brandon CJ, Chaibub Neto E, Plaisier CL, Simonett SP, Kebede MA, Sheynkman GM, Klein MA, Baliga NS, Smith LM, Broman KW, Yandell BS , Kendziorski C, Attie AD (2016) The transcription factor Nfatc2 regulates beta-cell proliferation and genes associated with Type 2 Diabetes in mouse and human islets. PloS Genetics 12 : e1006466.
  117. Kreznar JH, Keller MP, Traeger LL, Rabaglia ME, Schueler KL, Stapleton DS, Zhao W, Vivas EI, Yandell BS , Broman AT, Hagenbuch B, Attie AD, Rey FE (2017) Host genotype and gut microbiome modulates insulin secretion and diet-induced metabolic phenotypes. Cell Report 18 : 1739-1730.
  118. Keller M, Gatti D, Schueler K, Rabaglia M, Stapleton D, Simecek P, Broman AT, Vincent M, Allen S, Bacher R, Kendziorski C, Broman KW, Yandell BS , Churchill GA, Attie AD (2018) Genetic drivers of pancreatic islet function Genetics 209: 335-356. PMID: 29567659 .
  119. Turner SD, Maurizio PL, Valdar W, Yandell BS , Simon PW (2018) Dissecting the Genetic Architecture of Shoot Growth in Carrot (Daucus carota L.) Using a Diallel Mating Design. G3: Genes, Genomes, Genetics 8 : 411-426.
  120. Broman KW, Gatti DM, Simecek P, Furlotte NA, Prins P, Sen S, Yandell BS , Gary A. Churchill GA (2019) R/qtl2: Software for Mapping Quantitative Trait Loci with High-Dimensional Data and Multi-parent Populations. Genetics 211: 495-502. PMCID: PMC6366910
  121. Keller MP, Rabaglia ME, Schueler KL, Stapleton DS, Gatti DM, Vincent M, Mitok KA, Wang Z, Ishimura T, Simonett SP, Emfinger CH, Das R, Beck T, Kendziorski C, Broman KW, Yandell BS , Churchill GA, Attie AD (2019) The Genetic Architecture of Insulin Secretion. J Clin Invest 130: 4419-4432. PMID: 31343992 .
  122. Kemis JH, Linke V, Barrett K, Boehm F, Traeger LL, Keller MP, Rabaglia ME, Schueler K, Stapleton DS, Gatti D, Churchill GA, Amador-Noguez D, Russell J, Yandell BS , Broman KW, Coon J, Attie AD, Rey FE (2019) Genetic determinants of gut microbiota composition and bile acid profiles in mice. PLOS Genetics 15: e1008073. PMID: 31465442 .
  123. Boehm FJ, Chesler EJ, Yandell BS , Broman KW, et al. (2019) Testing pleiotropy vs. separate QTL in multiparental populations. G3 9: 2317-2324.
  124. Boehm F, Yandell B , Broman KW (2019) qtl2pleio: Testing pleiotropy vs. separate QTL in multiparental populations. J Open Source Software 4: 1435.
  125. Gao S, Rao J, Kang Y, Liang Y, Kruse J, Dopfer D, Sethi AK, Reyes JFM, Yandell BS , Patz JA (2020) Association of Mobile Phone Location Data Indications of Travel and Stay-at-Home Mandates With COVID-19 Infection Rates in the US JAMA Netw Open 3: e2020485.
  126. Kruijer W, Behrouzi P, Bustos-Korts D, Rodriguez-Alvarez MX, Mahmoudi SM, Yandell B, Wit E, van Eeuwijk F (2020) Reconstruction of networks with direct and indirect genetic effects. Genetics 214 : 781-807.
  127. Currie DW, Moreno GK, Delahoy MJ, Pray IW, Jovaag A, Braun KM, Cole D, Shechter T, Fajardo GC, Griggs C, Yandell BS , Goldstein S, Bushman D, Segaloff H, Kelly GP, Pitts C, Lee C, Grande KM, Kita-Yarbro A, Grogan B, Mader S, Baggott J, Bateman AC, Westergaard RP, Tate JE, Friedrich TC, Kirking HL, O’Connor DH, Killerby ME (2021) Description of a University COVID-19 Outbreak and Interventions to Disrupt Transmission, Wisconsin, August - October, 2020. Emerging Infectious Diseases 27 : 2776–2785.
  128. Xie R, Wang X, Wang Y, Ye M, Zhao Y, Yandell BS, Gong S (2022) pH-Responsive Polymer Nanoparticles for Efficient Delivery of Cas9 Ribonucleoprotein With or Without Donor DNA. Advanced Materials 34 : e2110618.
  129. Aravamuthan S, Reyes JFM, Yandell BS, Döpfer D (2023) Real-Time Estimation and Forecasting of COVID-19 Cases and Hospitalizations in Wisconsin HERC Regions for Public Health Decision Making Processes. BMC Public Health 23 : 359.
  130. Gambardella JC, Schoephoerster W, Bondarenko V, Yandell BS, Emborg ME (2023) Expression of tau and phosphorylated tau in the brain of normal and hemiparkinsonian rhesus macaques. J Comparative Neruology 00: 000-000

B. Papers submitted to refereed journals

  1. Barzen JA, Lacy AE, Yandell BS (2019) Chemical deterrence on planted seeds promotes effective prevention of bird herbivory in agricultural landscapes. Conservation Science and Practice (in review).
  2. Emfinger CH, Clark LE, Yandell BS, Schueler KL, Simonett SP, Stapleton DS, Mitok KA, Merrins MJ, Keller MP, Attie AD (2023) Novel regulators of islet function identified from genetic variation in mouse islet Ca2+ oscillations. eLife (submitted). See also [*]Dryad Repository.
  3. Kent SP, Aravamuthan S, Yandell BS, Goldstein S (2021) Development and Performance of an Interactive Web-Based Decision Support Tool to Assess SARS-CoV-2 Screening Strategies (in prep.)

C. Published Monographs or Books

  1. Yandell BS (1981) Non-parametric inference for rates and densities with censored serial data. PhD Dissertation, Department of Statistics, University of California–Berkeley. Kjell A. Doksum, Advisor. UMI 8212159 .
  2. Yandell BS (1997) Practical Data Analysis for Designed Experiments. CRC/Chapman & Hall: London. ISBN 0-412-06341-7.

E. Invited Papers in Conference Proceedings and Book Chapters

  1. Doksum KA, Yandell BS (1982) Properties of regression estimates based on censored survival data. A Festschrift for Erich L. Lehmann , ed. by PJ Bickel, KA Doksum, JL Hodges, Jr, Wadsworth: Belmont, CA, 140–156. (refereed)
  2. Doksum KA, Yandell BS (1984) Tests for exponentiality. Handbook of Statistics 4, ch. 26, ed. by PR Krishnaiah and PK Sen, North Holland: Amsterdam, 579–611. (refereed)
  3. Green PJ, Yandell BS (1985) Semi-parametric generalized linear models. GLIM85: Proceedings of the International Conference on Generalized Linear Models, September 1985, Lecture Notes in Statistics 32, ed. by R Gilchrist, Springer-Verlag, 44–55.
  4. Ventura SJ, Lillesand TM, Lathrop RG Jr, Maclean GA, Yandell BS (1985) Thematic mapper crop spectral separability as determined by field radiometry. Proceedings of the 51st Annual Meeting, American Society of Photogrametry, Washington, DC, March 1985, 1, 404–413.
  5. Yandell BS (1985) Graphical analysis of proportional Poisson rates. Proceedings of the 17th Symposium on the Interface, Lexington, 17–19 March 1985, ed. by DM Allen, 283–287. [ TR 763 , Dept. of Statistics, Univ. of Wisconsin-Madison.]
  6. Yandell BS (1986) Graphical tests with censored data. Goodness-of-Fit, Debrecen, Hungary, June 1984, Colloquia Mathematica Societatis János Bolyai 45, ed. by Gy Michaletzky, 607–624.
  7. Yandell BS , Green PJ (1986) Semi-parametric generalized linear model diagnostics. Proceedings of the Statistical Computing Section, ASA, Joint Statistical Meetings, Chicago, 48–53.
  8. Yandell BS , Satagopan JM (1997) Mapping of QTLs associated with traits of agronomic importance. in Biodiversity, Genetics and Breeding of Plants – Current Techniques and their Applications, ed. by ME Ferreira and D Grattapaglia, SPI/EMBRAPA and Dalmo Catauli Giacometti Foundation in Support of Genetic Resources and Biotechnology, Brasılia, Brasil (in Portuguese). (invited; never published)
  9. Lin Y, Nadler ST, Lan H, Attie AD, Yandell BS (2003) Adaptive gene picking with microarray data: detecting important low abundance signals. in The Analysis of Gene Expression Data: Methods and Software , ed by G Parmigiani, ES Garrett, RA Irizarry, SL Zeger. Springer-Verlag.
  10. Zou F, Yandell BS , Fine JP (2007) Semiparametric and nonparametric gene mapping. In Advances in Statistical Modeling and Inference: Essays in honor of Kjell A. Doksum. Ed. by V Nair. World Scientific, pp. 387-404.
  11. Yandell BS , Bradbury P (2007) Computing strategies and software for gene mapping. Ch. 11, Principles & Practices of Plant Molecular Mapping & Breeding. Ed. by C Kole. Science Publishers, Inc., Enfield, New Hampshire, USA: 329–377.
  12. Moon JY, Chaibub Neto E, Deng X, Yandell BS (2011) Growing graphical models to infer causal phenotype networks. In Probabilistic Graphical Models Dedicated to Applications in Genetics. Sinoquet C, Mourad R, eds.
  13. Draper N, Johnson R, Stigler S, Tsui KW, Yandell B (2013) University of Wisconsin Department of Statistics . In Strength in Numbers: The Rising of Academic Statistics Departments in the US. Ed. by A Agresti, XL Meng. Springer, pp 525–536 .

F. Contributed Papers and Abstracts

  1. Yandell BS (1986) Algorithms for nonlinear generalized cross-validation. Proceedings of the 18th Symposium on the Interface, Fort Collins, 19–21 March 1986 , ed. by TJ Boardman, American Statistical Assocication, 450–455.
  2. Lathrop RG, Lillesand TM, Yandell BS (1987) An evaluation of thematic mapper data for forest cover mapping in northern Wisconsin. Proceedings of the 11th Pecora Symposium, Sioux Falls, 5–7 May 1987, 286–393.
  3. Taam W, Yandell BS (1989) The torus structure approximation for spatial autocovariances. Proceedings of the 21st Symposium on the Interface, March 1989, 579–585.
  4. Yandell BS (1991) Quantitative Trait Loci in Brassica rapa. Proceedings of the 23rd Symposium on the Interface, Seattle, April 1991, 258–261.
  5. Kidwell KK, Yandell BS, Crump PM, Osborn TC (1994) Estimating genetic diversity in multi-parent synthetics. Agronomy Abstracts, Crop Science Division C1: Crop Breeding, Genetics and Cytology, 125.
  6. Satagopan JM, Yandell BS, Newton MA, Osborn TC (1995) Simultaneous detection of multiple QTLs using Markov chain Monte Carlo. Plant Genome III abstract and poster.
  7. Qiu P, Yandell BS (1996) Discontinuity detection in regression surfaces. Contributed Paper Session, Joint Statistical Meetings, Chicago, IL.
  8. Satagopan JM, Yandell BS (1996) Estimating the number of quantitative trait loci via Bayesian model determination. Special Contributed Paper Session on Genetic Analysis of Quantitative Traits and Complex Diseases, Biometrics Section, Joint Statistical Meetings, Chicago, IL.
  9. Gaffney PJ, Yandell BS, Satagopan JM (1997) QTLCart-MCMC: Bayesian data exploration and inference module. Plant & Animal Genome V abstract and computer demo.
  10. Satagopan JM, Yandell BS (1998) Bayesian model determination for quantitative trait loci. TR, Department of Statistics, UW-Madison.
  11. Rosa GJM, Yandell BS, Gianola D (2001) A Bayesian approach for constructing genetic maps when genotypes are miscoded. J Anim Sci 79: 190.
  12. Vorperian HK, Kalina CM, Kent RD, Yandell BS , Gentry LR (2001) Vocal tract length development: MRI procedures. Acoustical Society of America, Chicago, IL, June. J Acoustical Soc Amer 109 : 2446.
  13. Shannon LM, Yandell BS, Galubitz J, Doebley JF (2012) Mapping domestication QTL in a Maize-Teosinte BC2S3 population using GBS data. Maize Meeting 2012.

G. Nonrefereed Publications Not Included Above

  1. Yandell BS (2006) My life as a statistical scientist. September Career Issue, Amstat News.

H. Departmental Technical Reports

Note: Technical Reports (TR) below without numbers are unpublished manuscripts. Those with numbers are in departmental series.

  1. Yandell BS (1979) Progressive multistage processes. TR, Dept of Statistics, UC–Berkeley.
  2. Nicot PC, Rouse DI, Yandell BS (1985) Spatial patterns of soilborne inoculum of Verticillium dahlia in four commercial potato fields of Central Wisconsin. TR, Dept of Plant Pathology, U Wisconsin–Madison.
  3. Yandell BS, Lindahl KQ Jr (1985) Computation of exact significance probabilities for generalized sum-of-scores tests: an algorithm and Pascal program. TR # 772, Dept of Statistics, U Wisconsin–Madison.
  4. Csörgő M, Csörgő C, Horváth L, Mason DM, Yandell BS (1986) Asymptotic theory of some bootstrapped empirical processes. TR, Laboratory for Research in Statistical Probability, Carleton U, Ottawa, Canada.
  5. Yandell BS (1987) Algortithms for mulidimensional semiparametric GLMs. TR 813, Dept of Statistics, U Wisconsin–Madison.
  6. Taam W, Yandell BS (1987) Approximate diagonalization of spatial covariance. TR 814, Dept of Statistics, U Wisconsin–Madison.
  7. Yandell BS , Green PJ (1987) Who owns phones: diagnosis using semi-parametric GLMs. TR, Dept of Statistics, U Wisconsin–Madison.
  8. Staniswalis JG, Yandell BS (1988) Locally adaptive smoothing splines. TR 828, Dept of Statistics, U Wisconsin–Madison.
  9. Reynolds PS, Yandell BS (1989) Time-series and intervention analysis of rodent body temperature data: implications for models of mammalian temperature regulation. TR, Dept of Zoology, U Wisconsin–Madison.
  10. Horváth L, Yandell BS , Sen A (1990) Convergence of kernel regression estimators. TR 869, Dept of Statistics, U Wisconsin–Madison.
  11. Yandell BS (1990) Bootstrapped spatial point processes. TR, Dept of Statistics, U Wisconsin–Madison.
  12. Yandell BS , Taylor CC, Ripley BD (1991) Ideas on Inference for Image Reconstructions. TR, Dept Statistics, U Wisconsin–Madison.
  13. Yandell BS, Scott EM, Buchanan D, Martin E (1991) Estimation and design considerations for the UK RIMNET. TR, Dept of Statistics, U Wisconsin–Madison.
  14. Borghi E, Yandell BS (2000) An approximation of the K-function for Strauss disc processes. TR 1018, March 2000, Statistics Department, UW-Madison.
  15. Borghi E, Yandell BS (2000) Methods for estimating the interaction parameter of Strauss disc processes. TR 1019, March 2000, Statistics Department, UW-Madison.
  16. Ewing B, Yandell BS , Barbieri JF, Luck RF (2001) Practical model building for quantitative population ethology with event-driven competing risks. TR 1034, Department of Statistics, UW-Madison (working paper).
  17. Ewing B, Yandell BS , Barbieri JF, Luck RF (2001) Quantitative population ethology. TR 1033, Department of Statistics, UW-Madison.
  18. Yandell BS , Kendziorski C, Lan H, Chaibub Neto E, Attie AD (2004) Inferring genetic architecture of complex biological processes. TR, Department of Statistics, UW-Madison.
  19. Chaibub Neto E, Keller MP, Attie AD, Yandell BS (2008) Causal Graphical Models in Systems Genetics: a unified framework for joint inference of causal network and genetic architecture for correlated phenotypes. TR 1146R , Department of Statistics, UW-Madison. [See 2010 Ann Appl Statist.]
  20. Manichaikul A, Moon JY, Sen S, Yandell BS , Broman KW (2008) A model selection approach for the identification of quantitative trait loci in experimental crosses. TR 205 , Department of Biostatistics and Medical Informatics, UW–Madison. [See 2009 Genetics.]

I. Published Discussions of Papers

  1. Yandell BS (1987) Discussion of Professor Jórgensen's paper on exponential dispersion models. J of the Royal Statistical Society B 49, 156–157.
  2. Taam W, Yandell BS (1989) Discussion of paper by Professors Haslett and Raftery. Applied Statistics 38 , 39–40.
  3. Clayton MK, Yandell BS (1990) Discussion of paper by Professors Cuzick and Edwards. J of the Royal Statistical Society B 52 , 100.
  4. Yandell BS , Jin C, Satagopan JM, Gaffney PJ (2002) Discussion of “A model selection approach for the identification of quantitative trait loci in experimental crosses” by Professors Broman and Speed. J of the Royal Statistical Society B 00, 000–000.

J. Book Manuscripts in Preparation

  1. Ewing B, Yandell BS , Barbieri JF, Luck RF, Forster LD, Quantitative Population Ethology.
  2. Yandell BS , Population Ethology: The Life and Work of Bland Ewing.
  3. Yi N, Yandell BS, Churchill GA, Bayesian Model Selection for Multiple QTL. To be published by Springer-Verlag.

K. Book Reviews

  1. Yandell BS (1989) Book review of Wegman and DePriest: Statistical Image Processing and Graphics. J of the American Statistical Association 84 , 338.
  2. Yandell BS (1989) Book review of Eubank: Spline Smoothing and Nonparametric Regression. Technometrics 31 , 380.
  3. Yandell BS (1990) Book review of Anselin: Spatial Econometrics. J of the American Statistical Association 85 , 905–906.
  4. Yandell BS (1996) Book review of Wand and Jones: Kernel Smoothing. Technometrics 38 , 210–211.
  5. Yandell BS (1997) Book review of Simonoff: Smoothing Methods in Statistics. Technometrics 39 , 338–339.
  6. Yandell BS (1998) Book review of Ryan: Modern Regression Methods. J of the American Statistical Association 93 , 837–838.

S. Software Releases

  1. GCVPACK: Routines for Generalized Cross Validation (free release in 1986; Bates, Lindstrom, Wahba, Yandell 1987)
  2. MCMC-QTL: Markov chain Monte Carlo inference for Quantitative Trait Loci. (free release in 1998; Satagopan, Yandell , Newton and Osborn 1996).
  3. RevJump-QTL: Bayesian model Determination of the Number of QTLs using Reversible Jump MCMC. (free release in 1999; Satagopan and Yandell 1998).
  4. Splus/QDA: Quality Data Attributes Analysis. (proprietary release in 1999; Yandell and Tragon Corporation).
  5. Practical Data Analsysis: library(pda) for Splus and R. (free release in 1997; revised in 2000; Yandell )
  6. Microarray Data Analysis: library(microarray) for R. (free release in 2001; Lin and Yandell 2001)
  7. Quantitative Population Ethology: library(ewing) for R. (free release in 2001; Ewing and Yandell 2001)
  8. Bmapqtl: Bayesian QTL mapping module for QTL Cartographer. (free release in 2001; Gaffney and Yandell 2001)
  9. library(bim): Bayesian interval mapping R package. (free release in 2002; Yandell )
  10. library(qtlbim): QTL Bayesian inteval mapping R package. (free release in 2006; Yandell and Yi)
  11. library(qdg): QTL-driven dependent graphs R package. (free release in 2008; Chaibub Neto and Yandell )
  12. library(qtlnet): Infer QTL genetic architecture and causal network for set of correlated traits R package. (free release in 2010; Chaibub Neto and Yandell )
  13. library(qtlview): Utilities to view QTL results on the web R package. (free release in 2010; Yandell )
  14. library(qtlhot): Inference for QTL hotspots R package. (free release in 2012; Chaibub Neto and Yandell )