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Determinants of QTL Mapping Power in the Realized Collaborative Cross.

Keele GR, Crouse WL, Kelada SNP, Valdar W.

G3 (Bethesda). 2019 May 7;9(5):1707-1727. doi: 10.1534/g3.119.400194.


A Diallel of the Mouse Collaborative Cross Founders Reveals Strong Strain-Specific Maternal Effects on Litter Size.

Shorter JR, Maurizio PL, Bell TA, Shaw GD, Miller DR, Gooch TJ, Spence JS, McMillan L, Valdar W, Pardo-Manuel de Villena F.

G3 (Bethesda). 2019 May 7;9(5):1613-1622. doi: 10.1534/g3.118.200847.


vqtl: An R Package for Mean-Variance QTL Mapping.

Corty RW, Valdar W.

G3 (Bethesda). 2018 Dec 10;8(12):3757-3766. doi: 10.1534/g3.118.200642.


QTL Mapping on a Background of Variance Heterogeneity.

Corty RW, Valdar W.

G3 (Bethesda). 2018 Dec 10;8(12):3767-3782. doi: 10.1534/g3.118.200790.


Mean-Variance QTL Mapping Identifies Novel QTL for Circadian Activity and Exploratory Behavior in Mice.

Corty RW, Kumar V, Tarantino LM, Takahashi JS, Valdar W.

G3 (Bethesda). 2018 Dec 10;8(12):3783-3790. doi: 10.1534/g3.118.200194.


Impact of vitamin D depletion during development on mouse sperm DNA methylation.

Xue J, Gharaibeh RZ, Pietryk EW, Brouwer C, Tarantino LM, Valdar W, Ideraabdullah FY.

Epigenetics. 2018;13(9):959-974. doi: 10.1080/15592294.2018.1526027. Epub 2018 Oct 21.


Reciprocal F1 Hybrids of Two Inbred Mouse Strains Reveal Parent-of-Origin and Perinatal Diet Effects on Behavior and Expression.

Oreper D, Schoenrock SA, McMullan R, Ervin R, Farrington J, Miller DR, de Villena FP, Valdar W, Tarantino LM.

G3 (Bethesda). 2018 Nov 6;8(11):3447-3468. doi: 10.1534/g3.118.200135.


Reproducibility and replicability of rodent phenotyping in preclinical studies.

Kafkafi N, Agassi J, Chesler EJ, Crabbe JC, Crusio WE, Eilam D, Gerlai R, Golani I, Gomez-Marin A, Heller R, Iraqi F, Jaljuli I, Karp NA, Morgan H, Nicholson G, Pfaff DW, Richter SH, Stark PB, Stiedl O, Stodden V, Tarantino LM, Tucci V, Valdar W, Williams RW, Würbel H, Benjamini Y.

Neurosci Biobehav Rev. 2018 Apr;87:218-232. doi: 10.1016/j.neubiorev.2018.01.003. Epub 2018 Jan 31. Review.


Genetic Fine-Mapping and Identification of Candidate Genes and Variants for Adiposity Traits in Outbred Rats.

Keele GR, Prokop JW, He H, Holl K, Littrell J, Deal A, Francic S, Cui L, Gatti DM, Broman KW, Tschannen M, Tsaih SW, Zagloul M, Kim Y, Baur B, Fox J, Robinson M, Levy S, Flister MJ, Mott R, Valdar W, Solberg Woods LC.

Obesity (Silver Spring). 2018 Jan;26(1):213-222. doi: 10.1002/oby.22075. Epub 2017 Nov 28.


Bayesian Diallel Analysis Reveals Mx1-Dependent and Mx1-Independent Effects on Response to Influenza A Virus in Mice.

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.

G3 (Bethesda). 2018 Feb 2;8(2):427-445. doi: 10.1534/g3.117.300438.


Dissecting the Genetic Architecture of Shoot Growth in Carrot (Daucus carota L.) Using a Diallel Mating Design.

Turner SD, Maurizio PL, Valdar W, Yandell BS, Simon PW.

G3 (Bethesda). 2018 Feb 2;8(2):411-426. doi: 10.1534/g3.117.300235.


Perinatal nutrition interacts with genetic background to alter behavior in a parent-of-origin-dependent manner in adult Collaborative Cross mice.

Schoenrock SA, Oreper D, Farrington J, McMullan RC, Ervin R, Miller DR, Pardo-Manuel de Villena F, Valdar W, Tarantino LM.

Genes Brain Behav. 2018 Sep;17(7):e12438. doi: 10.1111/gbb.12438. Epub 2017 Dec 13.


Joint Estimation of Multiple Dependent Gaussian Graphical Models with Applications to Mouse Genomics.

Xie Y, Liu Y, Valdar W.

Biometrika. 2016 Sep;103(3):493-511. doi: 10.1093/biomet/asw035.


Inbred Strain Variant Database (ISVdb): A Repository for Probabilistically Informed Sequence Differences Among the Collaborative Cross Strains and Their Founders.

Oreper D, Cai Y, Tarantino LM, de Villena FP, Valdar W.

G3 (Bethesda). 2017 Jun 7;7(6):1623-1630. doi: 10.1534/g3.117.041491.


Editor's Highlight: Candidate Risk Factors and Mechanisms for Tolvaptan-Induced Liver Injury Are Identified Using a Collaborative Cross Approach.

Mosedale M, Kim Y, Brock WJ, Roth SE, Wiltshire T, Eaddy JS, Keele GR, Corty RW, Xie Y, Valdar W, Watkins PB.

Toxicol Sci. 2017 Apr 1;156(2):438-454. doi: 10.1093/toxsci/kfw269.


Maternal vitamin D depletion alters DNA methylation at imprinted loci in multiple generations.

Xue J, Schoenrock SA, Valdar W, Tarantino LM, Ideraabdullah FY.

Clin Epigenetics. 2016 Oct 12;8:107. eCollection 2016.


Ovariectomy results in inbred strain-specific increases in anxiety-like behavior in mice.

Schoenrock SA, Oreper D, Young N, Ervin RB, Bogue MA, Valdar W, Tarantino LM.

Physiol Behav. 2016 Dec 1;167:404-412. doi: 10.1016/j.physbeh.2016.09.026. Epub 2016 Sep 29.


Genome Wide Identification of SARS-CoV Susceptibility Loci Using the Collaborative Cross.

Gralinski LE, Ferris MT, Aylor DL, Whitmore AC, Green R, Frieman MB, Deming D, Menachery VD, Miller DR, Buus RJ, Bell TA, Churchill GA, Threadgill DW, Katze MG, McMillan L, Valdar W, Heise MT, Pardo-Manuel de Villena F, Baric RS.

PLoS Genet. 2015 Oct 9;11(10):e1005504. doi: 10.1371/journal.pgen.1005504. eCollection 2015 Oct.


Genome- and exome-wide association study of serum lipoprotein (a) in the Jackson Heart Study.

Li J, Lange LA, Sabourin J, Duan Q, Valdar W, Willis MS, Li Y, Wilson JG, Lange EM.

J Hum Genet. 2015 Dec;60(12):755-61. doi: 10.1038/jhg.2015.107. Epub 2015 Sep 17.


Plasma Levels of Soluble Interleukin-2 Receptor α: Associations With Clinical Cardiovascular Events and Genome-Wide Association Scan.

Durda P, Sabourin J, Lange EM, Nalls MA, Mychaleckyj JC, Jenny NS, Li J, Walston J, Harris TB, Psaty BM, Valdar W, Liu Y, Cushman M, Reiner AP, Tracy RP, Lange LA.

Arterioscler Thromb Vasc Biol. 2015 Oct;35(10):2246-53. doi: 10.1161/ATVBAHA.115.305289. Epub 2015 Aug 20.


A permutation approach for selecting the penalty parameter in penalized model selection.

Sabourin JA, Valdar W, Nobel AB.

Biometrics. 2015 Dec;71(4):1185-94. doi: 10.1111/biom.12359. Epub 2015 Aug 3.


Corrigendum: analyses of allele-specific gene expression in highly divergent mouse crosses identifies pervasive allelic imbalance.

Crowley JJ, Zhabotynsky V, Sun W, Huang S, Pakatci IK, Kim Y, Wang JR, Morgan AP, Calaway JD, Aylor DL, Yun Z, Bell TA, Buus RJ, Calaway ME, Didion JP, Gooch TJ, Hansen SD, Robinson NN, Shaw GD, Spence JS, Quackenbush CR, Barrick CJ, Nonneman RJ, Kim K, Xenakis J, Xie Y, Valdar W, Lenarcic AB, Wang W, Welsh CE, Fu CP, Zhang Z, Holt J, Guo Z, Threadgill DW, Tarantino LM, Miller DR, Zou F, McMillan L, Sullivan PF, de Villena FP.

Nat Genet. 2015 Jun;47(6):690. doi: 10.1038/ng0615-690a. No abstract available.


Analyses of allele-specific gene expression in highly divergent mouse crosses identifies pervasive allelic imbalance.

Crowley JJ, Zhabotynsky V, Sun W, Huang S, Pakatci IK, Kim Y, Wang JR, Morgan AP, Calaway JD, Aylor DL, Yun Z, Bell TA, Buus RJ, Calaway ME, Didion JP, Gooch TJ, Hansen SD, Robinson NN, Shaw GD, Spence JS, Quackenbush CR, Barrick CJ, Nonneman RJ, Kim K, Xenakis J, Xie Y, Valdar W, Lenarcic AB, Wang W, Welsh CE, Fu CP, Zhang Z, Holt J, Guo Z, Threadgill DW, Tarantino LM, Miller DR, Zou F, McMillan L, Sullivan PF, Pardo-Manuel de Villena F.

Nat Genet. 2015 Apr;47(4):353-60. doi: 10.1038/ng.3222. Epub 2015 Mar 2. Erratum in: Nat Genet. 2015 Jun;47(6):690.


Fine-mapping additive and dominant SNP effects using group-LASSO and fractional resample model averaging.

Sabourin J, Nobel AB, Valdar W.

Genet Epidemiol. 2015 Feb;39(2):77-88. doi: 10.1002/gepi.21869. Epub 2014 Nov 21.


Quantitative trait locus mapping methods for diversity outbred mice.

Gatti DM, Svenson KL, Shabalin A, Wu LY, Valdar W, Simecek P, Goodwin N, Cheng R, Pomp D, Palmer A, Chesler EJ, Broman KW, Churchill GA.

G3 (Bethesda). 2014 Sep 18;4(9):1623-33. doi: 10.1534/g3.114.013748.


Bayesian modeling of haplotype effects in multiparent populations.

Zhang Z, Wang W, Valdar W.

Genetics. 2014 Sep;198(1):139-56. doi: 10.1534/genetics.114.166249.


Midregional pro-adrenomedullin plasma concentrations are blunted in severe preeclampsia.

Matson BC, Corty RW, Karpinich NO, Murtha AP, Valdar W, Grotegut CA, Caron KM.

Placenta. 2014 Sep;35(9):780-3. doi: 10.1016/j.placenta.2014.07.003. Epub 2014 Jul 10.


Quantitative trait loci for energy balance traits in an advanced intercross line derived from mice divergently selected for heat loss.

Leamy LJ, Elo K, Nielsen MK, Thorn SR, Valdar W, Pomp D.

PeerJ. 2014 May 27;2:e392. doi: 10.7717/peerj.392. eCollection 2014.


Genetics of adverse reactions to haloperidol in a mouse diallel: a drug-placebo experiment and Bayesian causal analysis.

Crowley JJ, Kim Y, Lenarcic AB, Quackenbush CR, Barrick CJ, Adkins DE, Shaw GS, Miller DR, de Villena FP, Sullivan PF, Valdar W.

Genetics. 2014 Jan;196(1):321-47. doi: 10.1534/genetics.113.156901. Epub 2013 Nov 15.


Using the emerging Collaborative Cross to probe the immune system.

Phillippi J, Xie Y, Miller DR, Bell TA, Zhang Z, Lenarcic AB, Aylor DL, Krovi SH, Threadgill DW, de Villena FP, Wang W, Valdar W, Frelinger JA.

Genes Immun. 2014 Jan;15(1):38-46. doi: 10.1038/gene.2013.59. Epub 2013 Nov 7.


Genetic architecture of skewed X inactivation in the laboratory mouse.

Calaway JD, Lenarcic AB, Didion JP, Wang JR, Searle JB, McMillan L, Valdar W, Pardo-Manuel de Villena F.

PLoS Genet. 2013;9(10):e1003853. doi: 10.1371/journal.pgen.1003853. Epub 2013 Oct 3.


Modeling host genetic regulation of influenza pathogenesis in the collaborative cross.

Ferris MT, Aylor DL, Bottomly D, Whitmore AC, Aicher LD, Bell TA, Bradel-Tretheway B, Bryan JT, Buus RJ, Gralinski LE, Haagmans BL, McMillan L, Miller DR, Rosenzweig E, Valdar W, Wang J, Churchill GA, Threadgill DW, McWeeney SK, Katze MG, Pardo-Manuel de Villena F, Baric RS, Heise MT.

PLoS Pathog. 2013 Feb;9(2):e1003196. doi: 10.1371/journal.ppat.1003196. Epub 2013 Feb 28.


Fine-mapping diabetes-related traits, including insulin resistance, in heterogeneous stock rats.

Solberg Woods LC, Holl KL, Oreper D, Xie Y, Tsaih SW, Valdar W.

Physiol Genomics. 2012 Nov 1;44(21):1013-26. doi: 10.1152/physiolgenomics.00040.2012. Epub 2012 Sep 4.


Recent developments in statistical methods for detecting genetic loci affecting phenotypic variability.

Rönnegård L, Valdar W.

BMC Genet. 2012 Jul 24;13:63. doi: 10.1186/1471-2156-13-63.


Reprioritizing genetic associations in hit regions using LASSO-based resample model averaging.

Valdar W, Sabourin J, Nobel A, Holmes CC.

Genet Epidemiol. 2012 Jul;36(5):451-62. doi: 10.1002/gepi.21639. Epub 2012 Apr 30.


Genome-wide association mapping of quantitative traits in outbred mice.

Zhang W, Korstanje R, Thaisz J, Staedtler F, Harttman N, Xu L, Feng M, Yanas L, Yang H, Valdar W, Churchill GA, Dipetrillo K.

G3 (Bethesda). 2012 Feb;2(2):167-74. doi: 10.1534/g3.111.001792. Epub 2012 Feb 1.


High-resolution genetic mapping using the Mouse Diversity outbred population.

Svenson KL, Gatti DM, Valdar W, Welsh CE, Cheng R, Chesler EJ, Palmer AA, McMillan L, Churchill GA.

Genetics. 2012 Feb;190(2):437-47. doi: 10.1534/genetics.111.132597.


A general Bayesian approach to analyzing diallel crosses of inbred strains.

Lenarcic AB, Svenson KL, Churchill GA, Valdar W.

Genetics. 2012 Feb;190(2):413-35. doi: 10.1534/genetics.111.132563.


High-resolution mapping of a complex disease, a model for rheumatoid arthritis, using heterogeneous stock mice.

Ahlqvist E, Ekman D, Lindvall T, Popovic M, Förster M, Hultqvist M, Klaczkowska D, Teneva I, Johannesson M, Flint J, Valdar W, Nandakumar KS, Holmdahl R.

Hum Mol Genet. 2011 Aug 1;20(15):3031-41. doi: 10.1093/hmg/ddr206. Epub 2011 May 12.


Genome-wide and species-wide dissection of the genetics of arthritis severity in heterogeneous stock mice.

Johnsen AK, Valdar W, Golden L, Ortiz-Lopez A, Hitzemann R, Flint J, Mathis D, Benoist C.

Arthritis Rheum. 2011 Sep;63(9):2630-40. doi: 10.1002/art.30425.


Detecting major genetic loci controlling phenotypic variability in experimental crosses.

Rönnegård L, Valdar W.

Genetics. 2011 Jun;188(2):435-47. doi: 10.1534/genetics.111.127068. Epub 2011 Apr 5.


Genetic analysis of complex traits in the emerging Collaborative Cross.

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 JD, Hua K, Nehrenberg DL, Powell CL, Steigerwalt J, Xie Y, Kelada SN, 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, de Villena FP, Churchill GA.

Genome Res. 2011 Aug;21(8):1213-22. doi: 10.1101/gr.111310.110. Epub 2011 Mar 15.


Fine-mapping a locus for glucose tolerance using heterogeneous stock rats.

Solberg Woods LC, Holl K, Tschannen M, Valdar W.

Physiol Genomics. 2010 Mar 3;41(1):102-8. doi: 10.1152/physiolgenomics.00178.2009. Epub 2010 Jan 12.


A Multiparent Advanced Generation Inter-Cross to fine-map quantitative traits in Arabidopsis thaliana.

Kover PX, Valdar W, Trakalo J, Scarcelli N, Ehrenreich IM, Purugganan MD, Durrant C, Mott R.

PLoS Genet. 2009 Jul;5(7):e1000551. doi: 10.1371/journal.pgen.1000551. Epub 2009 Jul 10.


Mapping in structured populations by resample model averaging.

Valdar W, Holmes CC, Mott R, Flint J.

Genetics. 2009 Aug;182(4):1263-77. doi: 10.1534/genetics.109.100727. Epub 2009 May 27.


Unlearned anxiety predicts learned fear: a comparison among heterogeneous rats and the Roman rat strains.

López-Aumatell R, Vicens-Costa E, Guitart-Masip M, Martínez-Membrives E, Valdar W, Johannesson M, Cañete T, Blázquez G, Driscoll P, Flint J, Tobeña A, Fernández-Teruel A.

Behav Brain Res. 2009 Aug 24;202(1):92-101. doi: 10.1016/j.bbr.2009.03.024. Epub 2009 Mar 28.


High resolution mapping of expression QTLs in heterogeneous stock mice in multiple tissues.

Huang GJ, Shifman S, Valdar W, Johannesson M, Yalcin B, Taylor MS, Taylor JM, Mott R, Flint J.

Genome Res. 2009 Jun;19(6):1133-40. doi: 10.1101/gr.088120.108. Epub 2009 Apr 17.


Association of infectious mononucleosis with multiple sclerosis. A population-based study.

Ramagopalan SV, Valdar W, Dyment DA, DeLuca GC, Yee IM, Giovannoni G, Ebers GC, Sadovnick AD; Canadian Collaborative Study Group.

Neuroepidemiology. 2009;32(4):257-62. doi: 10.1159/000201564. Epub 2009 Feb 11.


Age of puberty and the risk of multiple sclerosis: a population based study.

Ramagopalan SV, Valdar W, Criscuoli M, DeLuca GC, Dyment DA, Orton SM, Yee IM, Ebers GC, Sadovnick AD; Canadian Collaborative Study Group.

Eur J Neurol. 2009 Mar;16(3):342-7. doi: 10.1111/j.1468-1331.2008.02431.x.


Genomewide SNP screen to detect quantitative trait loci for alcohol preference in the high alcohol preferring and low alcohol preferring mice.

Bice P, Valdar W, Zhang L, Liu L, Lai D, Grahame N, Flint J, Li TK, Lumeng L, Foroud T.

Alcohol Clin Exp Res. 2009 Mar;33(3):531-7. doi: 10.1111/j.1530-0277.2008.00866.x. Epub 2008 Dec 19.

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