Yandell's Papers in Statistical Genomics

• Microarray Gene Expression Profiling
• Quantitative Trait Loci (QTL)
• Related Theoretical Work
• Applications in Statistical Genomics

Microarray Gene Expression Profiling

• Chaibub Neto E, Ferrara C, Attie AD, Yandell BS (2008) Inferring causal phenotype networks from segregating populations. Genetics 179 : 1089-1100.
• 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.
• 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.
• 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.
• 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.
• 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.
• Yandell BS (2002) A graphical investigation of some microarray experiments. ASBMB/ABRF Symposium, Experimental Biology 2002, New Orleans, LA. [Talk]
• Lin Y, Nadler ST, Attie AD, Yandell BS (2002) Mining for low-abundance transcripts in microarray data. ENAR/IMS Invited Session on Statistical Applications with Microarray Data. ENAR 2002, Arlington, VA. [Talk]

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  Quantitative Trait Loci (QTL)

• Manichaikul A, Moon JY, Sen S, Yandell BS , Broman KW, A model selection approach for the identification of quantitative trait loci in experimental crosses. Genetics (submitted).
• Banerjee S, Yandell BS , Yi N (2008) Bayesian QTL Mapping for Multiple Traits Genetics 179 : 2275-2289.
• Chaibub Neto E, Ferrara C, Attie AD, Yandell BS (2008) Inferring causal phenotype networks from segregating populations. Genetics 179 : 1089-1100.
• 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.
• 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.
• Yandell BS (2007) Graphical data presentation, with emphasis on genetic data. Hort Sci 42 : 1047-1051.
• 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.
• 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.
• 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.
• 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.
• 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.
• 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.
• 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.
• 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.
• Zou F, Yandell BS , Fine JP (2003) Rank-based statistical methodologies for QTL mapping. Genetics 165 : 1599-1605.
• Zou F, Fine JP, Yandell BS (2002) On empirical likelihood for a semiparametric mixture model. Biometrika 89 : 61-75.
• Zou F, Yandell BS , Fine JP (2001) Statistical issues in the analysis of quantitative traits in combined crosses Genetics 158 : 1339-1346.
• 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.
• 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. [Software]
• 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. [Software]

Related Theoretical Work

• Tao H, Palta M, Yandell BS , Newton MA (1999) An estimation method for the semi-parametric mixed effects model. Biometrics 55 , 102-110.
• 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.
• Wang CS, Yandell BS, Rutledge JJ (1992) The dilemma of negative analysis of variance estimators of intraclass correlation and its variants. Theoretical & Applied Genetics 85 , 79-88.
• Wang CS, Yandell BS, Rutledge JJ (1991) Bias of maximum likelihood estimators of intraclass correlation. Theoretical & Applied Genetics 82 , 421-424.

Applications in Statistical Genomics

• 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.
• 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.
• 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.
• 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.
• 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.
• 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.
• 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.
• 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.
• 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.
• 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.
• 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.
• 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.
• 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.
• 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.
• Jeanne RL, Graf CA, Yandell BS (1995) Non-size-based morphological castes in a social insect. Naturwissenschaften 82, 296-298.
• Ferreira ME, Satagopan J, Yandell BS, Williams PH, Osborn TC (1995) Mapping loci controlling vernalization requirement and flowering time in Brassica napus. Theoretical & Applied Genetics 90 , 727-732.
• Stieve SM, Stimart DP, Yandell BS (1992) Heritable tissue culture induced variation in Zinnia Marylandica. Euphytica 64 , 81-89.
• Jeanne RL, Williams NM, Yandell BS (1992) Age polyethism and defense in a tropical social wasp. J of Insect Behavior 5, 211-227.
• 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.
• 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. Theoretical & Applied Genetics 72 , 123-128.