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Correction to: Quantitative trait mapping in Diversity Outbred mice identifies two genomic regions associated with heart size.

Shorter JR, Huang W, Beak JY, Hua K, Gatti DM, de Villena FP, Pomp D, Jensen BC.

Mamm Genome. 2019 Feb;30(1-2):42. doi: 10.1007/s00335-018-9789-9.


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.


CC002/Unc females are mouse models of exercise-induced paradoxical fat response.

McMullan RC, Ferris MT, Bell TA, Menachery VD, Baric RS, Hua K, Pomp D, Smith-Ryan AE, de Villena FP.

Physiol Rep. 2018 Jun;6(12):e13716. doi: 10.14814/phy2.13716.


Quantitative trait mapping in Diversity Outbred mice identifies two genomic regions associated with heart size.

Shorter JR, Huang W, Beak JY, Hua K, Gatti DM, de Villena FP, Pomp D, Jensen BC.

Mamm Genome. 2018 Feb;29(1-2):80-89. doi: 10.1007/s00335-017-9730-7. Epub 2017 Dec 26. Erratum in: Mamm Genome. 2018 Dec 4;:.


Oas1b-dependent Immune Transcriptional Profiles of West Nile Virus Infection in the Collaborative Cross.

Green R, Wilkins C, Thomas S, Sekine A, Hendrick DM, Voss K, Ireton RC, Mooney M, Go JT, Choonoo G, Jeng S, de Villena FP, Ferris MT, McWeeney S, Gale M Jr.

G3 (Bethesda). 2017 Jun 7;7(6):1665-1682. doi: 10.1534/g3.117.041624.


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.


Structural Variation Shapes the Landscape of Recombination in Mouse.

Morgan AP, Gatti DM, Najarian ML, Keane TM, Galante RJ, Pack AI, Mott R, Churchill GA, de Villena FP.

Genetics. 2017 Jun;206(2):603-619. doi: 10.1534/genetics.116.197988.


Genomes of the Mouse Collaborative Cross.

Srivastava A, Morgan AP, Najarian ML, Sarsani VK, Sigmon JS, Shorter JR, Kashfeen A, McMullan RC, Williams LH, Giusti-Rodríguez P, Ferris MT, Sullivan P, Hock P, Miller DR, Bell TA, McMillan L, Churchill GA, de Villena FP.

Genetics. 2017 Jun;206(2):537-556. doi: 10.1534/genetics.116.198838.


Comparative genomic evidence for the involvement of schizophrenia risk genes in antipsychotic effects.

Kim Y, Giusti-Rodriguez P, Crowley JJ, Bryois J, Nonneman RJ, Ryan AK, Quackenbush CR, Iglesias-Ussel MD, Lee PH, Sun W, de Villena FP, Sullivan PF.

Mol Psychiatry. 2018 Mar;23(3):708-712. doi: 10.1038/mp.2017.111. Epub 2017 May 30.


Prevention of tumorigenesis in mice by exercise is dependent on strain background and timing relative to carcinogen exposure.

Kelly SA, Zhao L, Jung KC, Hua K, Threadgill DW, Kim Y, de Villena FP, Pomp D.

Sci Rep. 2017 Feb 22;7:43086. doi: 10.1038/srep43086.


Identifying protective host gene expression signatures within the spleen during West Nile virus infection in the collaborative cross model.

Green R, Wilkins C, Thomas S, Sekine A, Ireton RC, Ferris MT, Hendrick DM, Voss K, de Villena FP, Baric R, Heise M, Gale M Jr.

Genom Data. 2016 Oct 14;10:114-117. eCollection 2016 Dec.


Whole Genome Sequence of Two Wild-Derived Mus musculus domesticus Inbred Strains, LEWES/EiJ and ZALENDE/EiJ, with Different Diploid Numbers.

Morgan AP, Didion JP, Doran AG, Holt JM, McMillan L, Keane TM, de Villena FP.

G3 (Bethesda). 2016 Dec 7;6(12):4211-4216. doi: 10.1534/g3.116.034751.


The Evolutionary Fates of a Large Segmental Duplication in Mouse.

Morgan AP, Holt JM, McMullan RC, Bell TA, Clayshulte AM, Didion JP, Yadgary L, Thybert D, Odom DT, Flicek P, McMillan L, de Villena FP.

Genetics. 2016 Sep;204(1):267-85. doi: 10.1534/genetics.116.191007. Epub 2016 Jul 2.


IsoDOT Detects Differential RNA-isoform Expression/Usage with respect to a Categorical or Continuous Covariate with High Sensitivity and Specificity.

Sun W, Liu Y, Crowley JJ, Chen TH, Zhou H, Chu H, Huang S, Kuan PF, Li Y, Miller DR, Shaw GD, Wu Y, Zhabotynsky V, McMillan L, Zou F, Sullivan PF, de Villena FP.

J Am Stat Assoc. 2015;110(511):975-986. Epub 2015 Nov 7.


The Founder Strains of the Collaborative Cross Express a Complex Combination of Advantageous and Deleterious Traits for Male Reproduction.

Odet F, Pan W, Bell TA, Goodson SG, Stevans AM, Yun Z, Aylor DL, Kao CY, McMillan L, de Villena FP, O'Brien DA.

G3 (Bethesda). 2015 Oct 19;5(12):2671-83. doi: 10.1534/g3.115.020172. Erratum in: G3 (Bethesda). 2016 Mar;6(3):767.


Identification of microRNAs associated with allergic airway disease using a genetically diverse mouse population.

Rutledge H, Baran-Gale J, de Villena FP, Chesler EJ, Churchill GA, Sethupathy P, Kelada SN.

BMC Genomics. 2015 Aug 25;16:633. doi: 10.1186/s12864-015-1732-9.


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.


Host genetic diversity enables Ebola hemorrhagic fever pathogenesis and resistance.

Rasmussen AL, Okumura A, Ferris MT, Green R, Feldmann F, Kelly SM, Scott DP, Safronetz D, Haddock E, LaCasse R, Thomas MJ, Sova P, Carter VS, Weiss JM, Miller DR, Shaw GD, Korth MJ, Heise MT, Baric RS, de Villena FP, Feldmann H, Katze MG.

Science. 2014 Nov 21;346(6212):987-91. doi: 10.1126/science.1259595. Epub 2014 Oct 30.


SNP array profiling of mouse cell lines identifies their strains of origin and reveals cross-contamination and widespread aneuploidy.

Didion JP, Buus RJ, Naghashfar Z, Threadgill DW, Morse HC 3rd, de Villena FP.

BMC Genomics. 2014 Oct 3;15:847. doi: 10.1186/1471-2164-15-847.


Genetic regulation of Zfp30, CXCL1, and neutrophilic inflammation in murine lung.

Rutledge H, Aylor DL, Carpenter DE, Peck BC, Chines P, Ostrowski LE, Chesler EJ, Churchill GA, de Villena FP, Kelada SN.

Genetics. 2014 Oct;198(2):735-45. doi: 10.1534/genetics.114.168138. Epub 2014 Aug 11.


The Collaborative Cross as a resource for modeling human disease: CC011/Unc, a new mouse model for spontaneous colitis.

Rogala AR, Morgan AP, Christensen AM, Gooch TJ, Bell TA, Miller DR, Godfrey VL, de Villena FP.

Mamm Genome. 2014 Apr;25(3-4):95-108. doi: 10.1007/s00335-013-9499-2. Epub 2014 Feb 1.


C57BL/6N mutation in cytoplasmic FMRP interacting protein 2 regulates cocaine response.

Kumar V, Kim K, Joseph C, Kourrich S, Yoo SH, Huang HC, Vitaterna MH, de Villena FP, Churchill G, Bonci A, Takahashi JS.

Science. 2013 Dec 20;342(6165):1508-12. doi: 10.1126/science.1245503.


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.


Genetically determined severity of anti-myeloperoxidase glomerulonephritis.

Xiao H, Ciavatta D, Aylor DL, Hu P, de Villena FP, Falk RJ, Jennette JC.

Am J Pathol. 2013 Apr;182(4):1219-26. doi: 10.1016/j.ajpath.2012.12.006. Epub 2013 Feb 4.


Effect of the myostatin locus on muscle mass and intramuscular fat content in a cross between mouse lines selected for hypermuscularity.

Kärst S, Strucken EM, Schmitt AO, Weyrich A, de Villena FP, Yang H, Brockmann GA.

BMC Genomics. 2013 Jan 16;14:16. doi: 10.1186/1471-2164-14-16.


Deconstructing Mus gemischus: advances in understanding ancestry, structure, and variation in the genome of the laboratory mouse.

Didion JP, de Villena FP.

Mamm Genome. 2013 Feb;24(1-2):1-20. doi: 10.1007/s00335-012-9441-z. Epub 2012 Dec 9. Review.


Status and access to the Collaborative Cross population.

Welsh CE, Miller DR, Manly KF, Wang J, McMillan L, Morahan G, Mott R, Iraqi FA, Threadgill DW, de Villena FP.

Mamm Genome. 2012 Oct;23(9-10):706-12. doi: 10.1007/s00335-012-9410-6. Epub 2012 Jul 31. Erratum in: Mamm Genome. 2014 Apr;25(3-4):192.


Comparative analysis and visualization of multiple collinear genomes.

Wang JR, de Villena FP, McMillan L.

BMC Bioinformatics. 2012 Mar 21;13 Suppl 3:S13. doi: 10.1186/1471-2105-13-S3-S13.


Expression quantitative trait Loci for extreme host response to influenza a in pre-collaborative cross mice.

Bottomly D, Ferris MT, Aicher LD, Rosenzweig E, Whitmore A, Aylor DL, Haagmans BL, Gralinski LE, Bradel-Tretheway BG, Bryan JT, Threadgill DW, de Villena FP, Baric RS, Katze MG, Heise M, McWeeney SK.

G3 (Bethesda). 2012 Feb;2(2):213-21. doi: 10.1534/g3.111.001800. Epub 2012 Feb 1.


Imputation of single-nucleotide polymorphisms in inbred mice using local phylogeny.

Wang JR, de Villena FP, Lawson HA, Cheverud JM, Churchill GA, McMillan L.

Genetics. 2012 Feb;190(2):449-58. doi: 10.1534/genetics.111.132381.


Discovery of novel variants in genotyping arrays improves genotype retention and reduces ascertainment bias.

Didion JP, Yang H, Sheppard K, Fu CP, McMillan L, de Villena FP, Churchill GA.

BMC Genomics. 2012 Jan 19;13:34. doi: 10.1186/1471-2164-13-34.


Genome-wide association mapping of loci for antipsychotic-induced extrapyramidal symptoms in mice.

Crowley JJ, Kim Y, Szatkiewicz JP, Pratt AL, Quackenbush CR, Adkins DE, van den Oord E, Bogue MA, Yang H, Wang W, Threadgill DW, de Villena FP, McLeod HL, Sullivan PF.

Mamm Genome. 2012 Jun;23(5-6):322-35. doi: 10.1007/s00335-011-9385-8. Epub 2011 Dec 30.


Dynamic Visualization and Comparative Analysis of Multiple Collinear Genomic Data.

Wang J, de Villena FP, McMillan L.

ACM BCB. 2011 Aug;2011:335-339. doi: 10.1145/2147805.2147846.


Genetic determinants for intramuscular fat content and water-holding capacity in mice selected for high muscle mass.

Kärst S, Cheng R, Schmitt AO, Yang H, de Villena FP, Palmer AA, Brockmann GA.

Mamm Genome. 2011 Oct;22(9-10):530-43. doi: 10.1007/s00335-011-9342-6. Epub 2011 Jul 6.


Identification of quantitative trait loci influencing skeletal architecture in mice: emergence of Cdh11 as a primary candidate gene regulating femoral morphology.

Farber CR, Kelly SA, Baruch E, Yu D, Hua K, Nehrenberg DL, de Villena FP, Buus RJ, Garland T Jr, Pomp D.

J Bone Miner Res. 2011 Sep;26(9):2174-83. doi: 10.1002/jbmr.436.


Subspecific origin and haplotype diversity in the laboratory mouse.

Yang H, Wang JR, Didion JP, Buus RJ, Bell TA, Welsh CE, Bonhomme F, Yu AH, Nachman MW, Pialek J, Tucker P, Boursot P, McMillan L, Churchill GA, de Villena FP.

Nat Genet. 2011 May 29;43(7):648-55. doi: 10.1038/ng.847.


Collaborative Cross mice and their power to map host susceptibility to Aspergillus fumigatus infection.

Durrant C, Tayem H, Yalcin B, Cleak J, Goodstadt L, de Villena FP, Mott R, Iraqi FA.

Genome Res. 2011 Aug;21(8):1239-48. doi: 10.1101/gr.118786.110. Epub 2011 Apr 14.


The FaceBase Consortium: a comprehensive program to facilitate craniofacial research.

Hochheiser H, Aronow BJ, Artinger K, Beaty TH, Brinkley JF, Chai Y, Clouthier D, Cunningham ML, Dixon M, Donahue LR, Fraser SE, Hallgrimsson B, Iwata J, Klein O, Marazita ML, Murray JC, Murray S, de Villena FP, Postlethwait J, Potter S, Shapiro L, Spritz R, Visel A, Weinberg SM, Trainor PA.

Dev Biol. 2011 Jul 15;355(2):175-82. doi: 10.1016/j.ydbio.2011.02.033. Epub 2011 Mar 31.


Architecture of energy balance traits in emerging lines of the Collaborative Cross.

Mathes WF, Aylor DL, Miller DR, Churchill GA, Chesler EJ, de Villena FP, Threadgill DW, Pomp D.

Am J Physiol Endocrinol Metab. 2011 Jun;300(6):E1124-34. doi: 10.1152/ajpendo.00707.2010. Epub 2011 Mar 22.


The collaborative cross: a recombinant inbred mouse population for the systems genetic era.

Threadgill DW, Miller DR, Churchill GA, de Villena FP.

ILAR J. 2011;52(1):24-31. Review.


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.


Genomic mapping of social behavior traits in a F2 cross derived from mice selectively bred for high aggression.

Nehrenberg DL, Wang S, Buus RJ, Perkins J, de Villena FP, Pomp D.

BMC Genet. 2010 Dec 31;11:113. doi: 10.1186/1471-2156-11-113.


Genetic mapping and developmental timing of transmission ratio distortion in a mouse interspecific backcross.

Eversley CD, Clark T, Xie Y, Steigerwalt J, Bell TA, de Villena FP, Threadgill DW.

BMC Genet. 2010 Nov 3;11:98. doi: 10.1186/1471-2156-11-98.


Genome-wide compatible SNP intervals and their properties.

Wang J, de Villena FP, Moore KJ, Wang W, Zhang Q, McMillan L.

ACM Int Conf Bioinform Comput Biol (2010). 2010 Aug;2010:43-52. doi: 10.1145/1854776.1854788.


CGDSNPdb: a database resource for error-checked and imputed mouse SNPs.

Hutchins LN, Ding Y, Szatkiewicz JP, Von Smith R, Yang H, de Villena FP, Churchill GA, Graber JH.

Database (Oxford). 2010 Jul 6;2010:baq008. doi: 10.1093/database/baq008.


Efficient genome ancestry inference in complex pedigrees with inbreeding.

Liu EY, Zhang Q, McMillan L, de Villena FP, Wang W.

Bioinformatics. 2010 Jun 15;26(12):i199-207. doi: 10.1093/bioinformatics/btq187.


Frequent and recent retrotransposition of orthologous genes plays a role in the evolution of sperm glycolytic enzymes.

Vemuganti SA, de Villena FP, O'Brien DA.

BMC Genomics. 2010 May 6;11:285. doi: 10.1186/1471-2164-11-285.


A customized and versatile high-density genotyping array for the mouse.

Yang H, Ding Y, Hutchins LN, Szatkiewicz J, Bell TA, Paigen BJ, Graber JH, de Villena FP, Churchill GA.

Nat Methods. 2009 Sep;6(9):663-6. doi: 10.1038/nmeth.1359. Epub 2009 Aug 9.


Simulating association studies: a data-based resampling method for candidate regions or whole genome scans.

Wright FA, Huang H, Guan X, Gamiel K, Jeffries C, Barry WT, de Villena FP, Sullivan PF, Wilhelmsen KC, Zou F.

Bioinformatics. 2007 Oct 1;23(19):2581-8. Epub 2007 Sep 4.


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