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Peer-reviewed, published articles

  1. Crouse WC, Kelada S, Valdar W (2020) Inferring the Allelic Series at QTL in Multiparental Populations Genetics In press/early online https://doi.org/10.1534/genetics.120.303393 [code]
  2. Keele GR*, Quach BC*, Israel JW, Chappell GA, Lewis L, Safi A, Simon JM, Cotney P, Crawford GE, Valdar W*, Rusyn I*, Furey TS* (2020) Integrative QTL analysis of gene expression and chromatin accessibility identifies multi-tissue patterns of genetic regulation. PLoS Genetics 16(1):e1008537 PMID:31961859
  3. Mosedale M*, Cai Y*, Eaddy JS, Corty RW, Nautiyal M, Watkins PB, Valdar W (2019) Identification of candidate risk factor genes for human idelalisib toxicity using a Collaborative Cross approach. Toxicological Sciences 172(2):265-278 PMID:31501888
  4. Keele GR*, Crouse WL*, Kelada SNP, Valdar W (2019) Determinants of QTL mapping power in the realized Collaborative Cross. G3: Genes, Genomes, Genetics 9(5):1707-1727 PMID:30914424 PMCID:PMC6505132
  5. Shorter JR*, Maurizio PL*, Bell TA, Shaw GD, Miller DR, Gooch TJ, Spence JS, McMillan L, Valdar W*, Pardo-Manuel de Villena F* (2019) A diallel of the mouse Collaborative Cross founders reveals strong strain-specific maternal effects on litter size. G3: Genes, Genomes, Genetics 9(5):1613-1622 PMID:30877080
  6. Corty RW, Valdar W (2018) vqtl: An R package for mean-variance QTL mapping. G3: Genes, Genomes, Genetics 8(12):3757-3766 PMID:30389795 PMC6288833
  7. Corty RW, Valdar W (2018) QTL mapping on a background of variance heterogeneity. G3: Genes, Genomes, Genetics 8(12):3767-3782 PMID:30389794 PMCID:PMC6288843
  8. Corty RW, Kumar V, Tarantino LM, Takahashi JS, Valdar W (2018) Mean-variance QTL mapping identifies novel QTL for circadian activity and exploratory behavior in mice. G3: Genes, Genomes, Genetics 8(12):3783-3790 PMID:30389793 PMCID:PMC6288835
  9. Oreper D, Schoenrock S, McMullan R, Ervin R, Farrington J, Miller D, Pardo-Manuel de Villena F, Valdar W*, Tarantino LM* (2018) Reciprocal F1 hybrids of two inbred mouse strains reveal parent-of-origin and perinatal diet effects on behavior and expression. G3: Genes, Genomes, Genetics 8(11):3447-3468 PMID:30171036 PMCID:PMC6222572
  10. Maurizio PL, Ferris MT, Keele GR, Miller DR, Shaw GD, Whitmore AC, West A, Morrison CR, Noll KE, Plante KS, Cockrell AS, Threadgill DW, Pardo-Manuel de Villena F, Baric RS, Heise MT, Valdar W (2018) Bayesian diallel analysis reveals Mx1-dependent and Mx1-independent effects on response to influenza A virus in mice. G3: Genes, Genomes, Genetics 8(2):427-445 PMID:29187420 PMCID:PMC5919740
  11. 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(2):411-426 PMID:29187420
  12. Keele GR, Prokop JW, He H, Holl K, Littrell J, Deal A, Francic S, Cui L, Gatti DM, Broman KW, Tschannen M, Tsaih S, Zagloul M, Kim Y, Baur B, Fox J, Robinson M, Levy S, Flister M, Mott R, Valdar W*, Solberg Woods LC* (2018) Genetic fine-mapping and identification of candidate genes and variants for adiposity traits in outbred rats. Obesity 26(1):213-222 PMID:29193816 PMCID:PMC5740008
  13. Schoenrock S, Oreper DG, McMullan R, Farrington J, Ervin R, Miller D, Pardo-Manuel de Villena F, Valdar W, Tarantino LM (2018) Perinatal nutrition interacts with genetic background to alter behavior in a parent-of-origin dependent manner in adult Collaborative Cross mice. Genes, Brain and Behavior 17(7):e12483 PMID:29125223
  14. Oreper DG*, Cai Y*, Tarantino LM, Pardo-Manual de Villena F, Valdar W (2017) Inbred Strain Variant Database (ISVdb): A repository for probabilistically informed sequence differences among the Collaborative Cross strains and their founders. G3: Genes, Genomes, Genetics 7(6):1623-1630 PMID:28592645 PMCID:PMC5473744
  15. Mosedale M*, Kim Y*, Brock WJ, Roth SE, Wiltshire T, Eaddy JS, Keele GR, Corty RW, Xie Y, Valdar W*, Watkins PB* (2017) Editors Highlight: Candidate Risk Factors and Mechanisms for Tolvaptan-Induced Liver Injury Are Identified Using a Collaborative Cross Approach. Toxicological Sciences 156(2):438-454 PMID:28115652 PMCID:6075566
  16. Schoenrock SA*, Oreper D*, Young N, Ervin RB, Bogue MA, Valdar W*, Tarantino LM* (2016) Ovariectomy results in inbred strain-specific increases in anxiety-like behavior in mice. Physiology and Behavior 167:404-412 PMID:27693591 [data]
  17. Xie Y, Liu Y, Valdar W (2016) Joint estimation of multiple dependent Gaussian graphical models with applications to mouse genomics. Biometrika 103(3):493-511 PMID:29038606 PMCID:PMC5640885 doi:10.1093/biomet/asw035
  18. Sabourin J, Valdar W, Nobel AB (2015) A permutation approach for selecting the penalty parameter in penalized model selection. Biometrics 71(4):1185-94. PMID:26243050 PMCID:PMC4314429
  19. Sabourin J, Nobel AB, Valdar W (2015) Fine-mapping additive and dominant SNP effects using group-LASSO and Fractional Resample Model Averaging Genetic Epidemiology 39(2):77-88 PMID:25417853 PMCID:PMC4314429
  20. Zhang Z, Wang W, Valdar W (2014) Bayesian modeling of haplotype effects in multiparent populations. Genetics 198:139-156 PMID:25236455 PMCID:PMC4174926
  21. Crowley JJ*, Kim Y*, Lenarcic AB*, Quackenbush CR, Barrick C, Adkins DE, Shaw GS, Miller DR, Pardo Manuel de Villena F, Sullivan PF, Valdar W (2014) Genetics of adverse reactions to haloperidol in a mouse diallel: A drug-placebo experiment and Bayesian causal analysis. Genetics 196(1):321-47 PMID:24240528 PMCID:PMC3872195
  22. Phillippi J*, Xie Y*, Miller DR, Bell TA, Zhang Z, Lenarcic AB, Aylor DL, Krovi SH, Threadgill DW, Pardo-Manuel de Villena F, Wang W, Valdar W*, Frelinger JA* (2014) Using the Collaborative Cross to probe the immune system. Genes and Immunity 15(1):38-46 PMID:24195963 PMCID:PMC4004367
  23. Calaway J, Lenarcic AB, Didion JP, Wang JR, Searle JB, McMillan L, Valdar W, Pardo-Manuel de Villena F (2013) Genetic architecture of skewed X inactivation in the laboratory mouse. PLoS Genetics 9(10):e1003853 PMID:24098153 PMCID:PMC3789830
  24. Solberg Woods LC, Holl KL, Oreper D, Xie Y, Tsaih S-W, Valdar W (2012) Fine-mapping diabetes-related traits, including insulin resistance, in heterogeneous stock rats. Physiological Genomics 44(21):1013-26 PMID:22947656 PMCID:PMC3524769
  25. Ronnegard L, Valdar W (2012) Recent developments in statistical methods for detecting genetic loci affecting phenotypic variability. BMC Genetics 13(1):63 PMID:22827487 PMCID:PMC3493319
  26. Valdar W*, Sabourin J*, Nobel A, Holmes C (2012) Reprioritizing genetic associations in hit regions using LASSO-based resample model averaging. Genetic Epidemiology 36(5):451-462 PMID:22549815 PMCID:PMC3470705
  27. Lenarcic AB, Svenson KL, Churchill GA, Valdar W (2012) A general Bayesian approach to analyzing diallel crosses of inbred strains. Genetics 190(2):413-435. PMID:22345610 PMCID:PMC3276624
  28. Ronnegard L, Valdar W (2011) Detecting major genetic loci controlling phenotypic variability in experimental crosses. Genetics 188:435-447. PMID:21467569 PMCID:PMC3122324
  29. Johnsen AK*, Valdar W*, Golden L, Ortiz-Lopez A, Hitzemann R, Flint J, Mathis D, Benoist C (2011) Genetics of arthritis severity: a genome-wide and species-wide dissection in HS mice. Arthritis & Rheumatism 63(9):2630-2640. PMID:21560115 PMCID:PMC3371645
  30. Aylor DL, Valdar W, Foulds-Mathes W, Buus RJ, Verdugo RA, Baric RS, Ferris MT, Frelinger JA, Heise M, Frieman MB, Gralinski LE, Bell TA, Didion JP, Hua K, Nehrenberg DL, Powell CL, Steigerwalt J, Xie Y, Kelada SNP, Collins FS, Yang IV, Schwartz DA, Branstetter LA, Chesler EJ, Miller DR, Spence J, Liu EY, McMillan L, Sarkar A, Wang J, Wang W, Zhang Q, Broman KW, Korstanje R, Durrant C, Mott R, Iraqi FA, Pomp D, Threadgill D, Pardo-Manuel de Villena F, Churchill GA (2011) Genetic analysis of complex traits in the emerging Collaborative Cross. Genome Research 21(8):1213-1222. PMID:21406540 PMCID:PMC3149489
  31. Solberg Woods L, Holl K, Tschannen M, Valdar W (2010) Fine-mapping a locus for glucose tolerance using heterogeneous stock rats. Physiological Genomics 41(1):102-8. PMID:20068026 PMCID:PMC2841497
  32. Valdar W, Holmes CC, Mott R, Flint J (2009) Mapping in structured populations by resample model averaging. Genetics 182(4):1263-77. PMID:19474203 PMCID:PMC2728864
  33. Kover PX, Valdar W, Trakalo J, Scarcelli N, Ehrenreich IM, Purugganan MD, Durrant C, Mott R (2009) A Multiparent Advanced Generation Inter-Cross to fine-map quantitative traits in Arabidopsis thaliana. PLoS Genetics 5(7):e1000551 PMID:19593375 PMCID:PMC2700969
  34. Bice P, Valdar W, Zhang L, Liu L, Lai D, Grahame N, Flint J, Li TK, Lumeng L, Foroud T (2009) Genomewide SNP Screen to Detect Quantitative Trait Loci for Alcohol Preference in the High Alcohol Preferring and Low Alcohol Preferring Mice. Alcohol Clin Exp Res 33(3):531-7. PMID:19120064 PMCID:PMC2867232
  35. Willis-Owen SAG, Valdar W (2009) Deciphering gene-environment interactions through mouse models of allergic asthma. Journal of Allergy and Clinical Immunology 123(1):14-23. PMID:18926561
  36. Taylor M, Valdar W, Flint J, Mott R (2007) Management, presentation and interpretation of genome scans using GSCANDB. Bioinformatics 15;23(12):1545-9 PMID:17400728
  37. Keays DA, Clark TG, Campbell TG, Broxholme J, Valdar W (2007) Estimating the number of coding mutations in genotypic and phenotypic driven N-ethyl-N-nitrosourea (ENU) screens: Revisited. Mammalian Genome 18(2):123-4 PMID:17347895
  38. Valdar W, Solberg LC, Gaugier D, Cookson WO, Rawlins JNP, Mott R, Flint J (2006) Genetic and environmental effects on complex traits in mice. Genetics 174(2):959-84. PMID:16888333 PMCID:PMC1602068
  39. Valdar W, Solberg LC, Gaugier D, Burnett S, Klenerman P, Cookson WO, Taylor M, Rawlins JNP, Mott R, Flint J (2006) Genome-wide genetic association of complex traits in outbred mice. Nature Genetics 38(8):879-87. PMID:16832355
  40. Solberg LC, Valdar W, Gauguier D, Nunez G, Taylor A, Hernandez P, Davidson S, Burns P, Cookson W, Deacon R, Rawlins span class=”pubjournal”P, Mott R, Flint J (2006) A protocol for high throughput phenotyping, suitable for quantitative trait analysis in mice. Mammalian Genome 17(2):129-46 PMID:16465593
  41. Valdar W, Mott R, Flint J (2006) Simulating the collaborative cross: power of QTL detection and mapping resolution in large sets of recombinant inbred strains of mice. Genetics 172(3):1783-97. PMID:16361245 PMCID:PMC1456308
  42. Flint J, Valdar W, Shifman S, Mott R (2005) Experimental strategies for mapping and cloning quantitative trait genes in rodents. Nature Reviews Genetics 6(4):271-286. PMID:15803197
  43. Valdar WSJ , Mott R, Flint J (2003) QTL fine-mapping with recombinant-inbred heterogeneous stocks and in-vitro heterogeneous stocks. Mammalian Genome 14(12):830-838. PMID:14724734
  44. Valdar WSJ (2002) Scoring residue conservation. Proteins: Structure, Function, and Genetics 43(2): 227-241. PMID:12112692 Errata
  45. Valdar WSJ, Thornton JM (2001) Conservation helps to identify biologically relevant crystal contacts. Journal of Molecular Biology 313(2):399-416. PMID:11800565 Errata
  46. Valdar WSJ, Thornton JM (2001) Protein-protein interfaces: analysis of amino acid conservation in homodimers. Proteins: Structure, Function, and Genetics 42(1):108-124. PMID:11093265