Literature

General

• Broman KW.
  A generic hidden Markov model for multiparent populations
  G3 2022 Feb 4;12(2):jkab396. doi: 10.1093/g3journal/jkab396.
  PMID: 34791211
  
  
• Saul MC et al
  High-Diversity Mouse Populations for Complex Traits
  Trends in Genetics. 2019 May 24;35(7):501-514. doi: 10.1016/j.tig.2019.04.003. Epub ahead of print.
  PMID: 31133439
   
• Klein AD
  Modeling diseases in multiple mouse strains for precision medicine studies
  Physiol Genomics. 2017 Mar 1;49(3):177-179. doi: 10.1152/physiolgenomics.00123.2016. Epub 2017 Jan 27.
  PMID: 28130429

• Williams RW & Williams EG
  Resources for systems genetics 
  Methods Mol Biol. 2017;1488:3-29. doi: 10.1007/978-1-4939-6427-7_1
  PMID: 27933518

Diversity Outbred

• Hackett JB, et al.
  A diversity outbred F1 mouse model identifies host-intrinsic genetic regulators of response to immune checkpoint inhibitors
  Oncoimmunology. 2022 Apr 20;11(1):2064958. doi: 10.1080/2162402X.2022.2064958.
  PMID: 35481286
  
  
• Bogue MA et al
  Collaborative Cross and Diversity Outbred data resources in the Mouse Phenome Database
  Mamm Genome. 2015; 26(9-10): 511–520. doi: 10.1007/s00335-015-9595-6
  PMID: 26286858 PMCID: PMC4602074

• Chesler EJ et al
  Diversity Outbred mice at 21: Maintaining allelic variation in the face of selection
  G3 (Bethesda). 2016 Dec 7;6(12):3893-3902. doi: 10.1534/g3.116.035527
  PMID: 27694113 PMCID: PMC5144960

• Churchill GA et al
  The Diversity Outbred mouse population
  Mamm Genome. 2012 Oct; 23(9-10): 713–718.  doi: 10.1007/s00335-012-9414-2
  PMID: 22892839 PMCID: PMC3524832

• Keller MP et al
  Genetic Drivers of Pancreatic Islet Function
  Genetics. 2018 May;209(1):335-356. doi: 10.1534/genetics.118.300864. Epub 2018 Mar 22
  PMID: 29567659 PMCID: PMC5937189 

• Mayeux et al
  Silicosis and Silica-Induced Autoimmunity in the Diversity Outbred Mouse
  Front Immunol. 2018 Apr 26;9:874. doi: 10.3389/fimmu.2018.00874. eCollection 2018.
  PMID: 29755467 PMCID: PMC5932595

• Schmidt CW
  Diversity Outbred: a new generation of mouse model
  Environ Health Perspect. 2015 Mar;123(3):A64-7. doi: 10.1289/ehp.123-A64.
  PMID: 25730842 PMCID: PMC4348734

• Shorter JR et al
  Quantitative trait mapping in Diversity Outbred mice identifies two genomic regions associated with heart size
  Mamm Genome. 2018 Feb;29(1-2):80-89. doi: 10.1007/s00335-017-9730-7. Epub 2017 Dec 26.
  PMID: 29279960

• Winter et al
  Mapping Complex Traits in a Diversity Outbred F1 Mouse Population Identifies Germline Modifiers of Metastasis in Human Prostate Cancer
  Cell Syst. 2017 Jan 25;4(1):31-45.e6. doi: 10.1016/j.cels.2016.10.018. Epub 2016 Dec 1.
  PMID: 27916600 PMCID: PMC5269474

Collaborative Cross

• Chesler EJ et al
  The Collaborative Cross at Oak Ridge National Laboratory: developing a powerful resource for systems genetics
  Mamm Genome. 2008 Jun; 19(6): 382–389. doi: 10.1007/s00335-008-9135-8
  PMID: 18716833 PMCID: PMC2745091

• Churchill GA et al
  The Collaborative Cross, a community resource for the genetic analysis of complex traits
  Nat Genet. 2004 Nov;36(11):1133-7. doi: 10.1038/ng1104-1133
  PMID: 15514660

• Graham JB et al
  Genetic diversity in the Collaborative Cross model recapitulates human West Nile virus disease outcomes
  MBio. 2015 May 5;6(3):e00493-15. doi: 10.1128/mBio.00493-15.
  PMID: 25944860 PMCID: PMC4436067

• Josset L et al
  Annotation of long non-coding RNAs expressed in Collaborative Cross founder mice in response to respiratory virus infection reveals a new class of interferon-stimulated transcripts
  RNA Biol. 2014;11(7):875-90. doi: 10.4161/rna.29442. Epub 2014 Jun 12.
  PMID: 24922324 PMCID: PMC4179962

• Levy R et al
  Collaborative Cross mice in a genetic association study reveal new candidate genes for bone microarchitecture
  BMC Genomics. 2015 Nov 26;16:1013. doi: 10.1186/s12864-015-2213-x.
  PMID: 26611327 PMCID: PMC4661944

• Smith CM et al
  Tuberculosis susceptibility and vaccine protection are independently controlled by host genotype
  MBio. 2016 Sep 20;7(5). pii: e01516-16. doi: 10.1128/mBio.01516-16.
  PMID: 27651361 PMCID: PMC5030360

• Srivastava A et al
  Genomes of the mouse Collaborative Cross
  Genetics. 2017 Jun;206(2):537-556. doi: 10.1534/genetics.116.198838.
  PMID: 28592495 PMCID: PMC5499171

• Threadgill DW & Churchill GA
  Ten years of the Collaborative Cross
  Genetics. 2012 Feb; 190(2): 291–294. doi:  10.1534/genetics.111.138032
  PMID: 22345604 PMCID: PMC3276648

• Venkatratnam A et al
  Collaborative Cross mouse population enables refinements to characterization of the variability in toxicokinetics of trichloroethylene and provides genetic evidence for the role of PPAR pathway in Its oxidative metabolism
  Toxicol Sci. 2017 Jul 1;158(1):48-62. doi: 10.1093/toxsci/kfx065.
  PMID: 28369613

BXD

• Andreux PA et al
  Systems genetics of metabolism: the use of the BXD murine reference panel for multiscalar integration of traits
  Cell. 2012 Sep 14; 150(6): 1287–1299. doi: 10.1016/j.cell.2012.08.012
  PMID: 22939713 PMCID: PMC3604687

• Kannan S et al
  Systems genetics analysis of a recombinant inbred mouse cell culture panel reveals Wnt pathway member Lrp6 as a regulator of adult hippocampal precursor cell proliferation
  Stem Cells. 2016 Mar;34(3):674-84. doi: 10.1002/stem.2313.
  PMID: 26840599

• King R et al
  Genomic locus modulating IOP in the BXD mouse strains
  G3 (Bethesda). 2018 May 4;8(5):1571-1578. doi: 10.1534/g3.118.200190.
  PMID: 29496776 PMCID: PMC5940149

• Li H et al
  An integrated systems genetics and omics toolkit to probe gene function
  Cell Syst. 2018 Jan 24;6(1):90-102.e4. doi: 10.1016/j.cels.2017.10.016. Epub 2017 Nov 30.
  PMID: 29199021

• Neuner SM et al
  Systems genetics identifies Hp1bp3 as a novel modulator of cognitive aging
  Neurobiol Aging. 2016 Oct;46:58-67. doi: 10.1016/j.neurobiolaging.2016.06.008. Epub 2016 Jun 17.
  PMID: 27460150 PMCID: PMC5018442

• Philip VM et al
  High-throughput behavioral phenotyping in the expanded panel of BXD recombinant inbred strains
  Genes Brain Behav. 2010 Mar 1;9(2):129-59. doi: 10.1111/j.1601-183X.2009.00540.x. Epub 2009 Sep 22.
  PMID: 19958391 PMCID: PMC2855868

• Wang X et al
  Joint mouse-human phenome-wide association to test gene function and disease risk
  Nat Commun. 2016 Feb 2;7:10464. doi: 10.1038/ncomms10464.
  PMID: 26833085 PMCID: PMC4740880