mpMap2.bib

@article{Mackay2014,
author = {Mackay, Ian J. and Bansept-Basler, Pauline and Barber, Toby and Bentley, Alison R. and Cockram, James and Gosman, Nick and Greenland, Andy J. and Horsnell, Richard and Howells, Rhian and O’Sullivan, Donal M. and Rose, Gemma A. and Howell, Phil J.}, 
title = {An Eight-Parent Multiparent Advanced Generation Inter-Cross Population for Winter-Sown Wheat: Creation, Properties, and Validation},
volume = {4}, 
number = {9}, 
pages = {1603-1610}, 
year = {2014}, 
journal = {G3: Genes|Genomes|Genetics} 
}

@article {Huang2012,
author = {Huang, Bevan E. and George, Andrew W. and Forrest, Kerrie L. and Kilian, Andrzej and Hayden, Matthew J. and Morell, Matthew K. and Cavanagh, Colin R.},
title = {A multiparent advanced generation inter-cross population for genetic analysis in wheat},
journal = {Plant Biotechnology Journal},
volume = {10},
number = {7},
publisher = {Blackwell Publishing Ltd},
pages = {826--839},
keywords = {linkage, wheat, QTL mapping, LD, four-way, RIL},
year = {2012}
}

@article{Churchill2004,
Author = {Churchill, G and Airey, DC and Allayee, H and Angel, JM and Attie, AD
   and Beatty, J and Beavis, WD and Belknap, JK and Bennett, B and
   Berrettini, W and Bleich, A and Bogue, M and Broman, KW and Buck, KJ and
   Buckler, E and Burmeister, M and Chesler, EJ and Cheverud, JM and
   Clapcote, S and Cook, MN and Cox, RD and Crabbe, JC and Crusio, WE and
   Darvasi, A and Deschnepper, CF and Doerge, RW and Farber, CR and Forejt,
   J and Gaile, D and Garlow, SJ and Geiger, H and Gershenfeld, H and
   Gordon, T and Gu, J and Gu, WK and de Haan, G and Hayes, NL and Heller,
   C and Himmelbauer, H and Hitzemann, R and Hunter, K and Hsu, HC and
   Iraqi, FA and Ivandic, B and Jacob, HJ and Jansen, RC and Jjepsen, KJ
   and Johnson, DK and Johnson, TE and Kempermann, G and Kendziorski, C and
   Kotb, M and Kooy, RF and Llamas, B and Lammert, F and Lassalle, JM and
   Lowenstein, PR and Lu, L and Lusiss, A and Manly, KF and Marcucio, R and
   Matthews, D and Medrano, JF and Miller, DR and Mittleman, G and Mock, BA
   and Mogil, JS and Montagutelli, X and Morahan, G and Morris, DG and
   Mott, R and Nadeau, JH and Nagase, H and Nowakowski, RS and O'Hara, BF
   and Osadchuk, AV and Page, GP and Paigen, B and Paigen, K and Palmer, AA
   and Pan, HJ and Peltonen-Palotie, L and Peirce, J and Pomp, D and
   Pravenec, M and Prows, DR and Qi, ZH and Reeves, RH and Roder, J and
   Rosen, GD and Schadt, EE and Schalkwyk, LC and Seltzer, Z and Shimomura,
   K and Shou, SM and Sillanpaa, MJ and Siracusa, LD and Snoeck, HW and
   Spearow, JL and Svenson, K and Tarantino, LM and Threadgill, D and Toth,
   LA and Valdar, W and de Villena, FPM and Warden, C and Whatley, S and
   Williams, RW and Wiltshire, T and Yi, NJ and Zhang, DB and Zhang, M and
   Zou, F and Complex Trait Consortium},
Title = {{The Collaborative Cross, a community resource for the genetic analysis
   of complex traits}},
Journal = {{Nature Genetics}},
Year = {{2004}},
Volume = {{36}},
Number = {{11}},
Pages = {{1133-1137}},
Publisher = {{Nature Publishing Group}},
}

@article {Pascual2015,
author = {Pascual, Laura and Desplat, Nelly and Huang, Bevan E. and Desgroux, Aurore and Bruguier, Laure and Bouchet, Jean-Paul and Le, Quang H. and Chauchard, Betty and Verschave, Philippe and Causse, Mathilde},
title = {Potential of a tomato MAGIC population to decipher the genetic control of quantitative traits and detect causal variants in the resequencing era},
journal = {Plant Biotechnology Journal},
volume = {13},
number = {4},
pages = {565--577},
keywords = {multiparental population, Solanum lycopersicum, resequencing, QTL, SNP},
year = {2015}
}

@article{Kover2009,
    author = {Kover, Paula X. AND Valdar, William AND Trakalo, Joseph AND Scarcelli, Nora AND Ehrenreich, Ian M. AND Purugganan, Michael D. AND Durrant, Caroline AND Mott, Richard},
    journal = {PLoS Genetics},
    publisher = {Public Library of Science},
    title = {A Multiparent Advanced Generation Inter-Cross to Fine-Map Quantitative Traits in Arabidopsis thaliana},
    year = {2009},
    month = {07},
    volume = {5},
    number = {7}
}        

@article {Teuscher2007,
  author = {Teuscher, Friedrich and Broman, Karl W.},
  title = {Haplotype Probabilities for Multiple-Strain Recombinant Inbred Lines},
  volume = {175},
  number = {3},
  pages = {1267--1274},
  year = {2007},
  publisher = {Genetics},
  abstract = {Recombinant inbred lines (RIL) derived from multiple inbred strains can serve as a powerful resource for the genetic dissection of complex traits. The use of such multiple-strain RIL requires a detailed knowledge of the haplotype structure in such lines. Broman (2005) derived the two- and three-point haplotype probabilities for 2n-way RIL; the former required hefty computation to infer the symbolic results, and the latter were strictly numerical. We describe a simpler approach for the calculation of these probabilities, which allowed us to derive the symbolic form of the three-point haplotype probabilities. We also extend the two-point results for the case of additional generations of intermating, including the case of 2n-way intermated recombinant inbred populations (IRIP).},
  journal = {Genetics}
}

@article{Sannemann2015,
  title={Multi-parent advanced generation inter-cross in barley: high-resolution quantitative trait locus mapping for flowering time as a proof of concept},
  author={Sannemann, Wiebke and Huang, Bevan Emma and Mathew, Boby and L{\'e}on, Jens},
  journal={Molecular Breeding},
  volume={35},
  number={3},
  pages={1--16},
  year={2015},
  publisher={Springer}
}
@article {Broman2012a,
  author = {Broman, Karl W.},
  title = {Genotype Probabilities at Intermediate Generations in the Construction of Recombinant Inbred Lines},
  volume = {190},
  number = {2},
  pages = {403--412},
  year = {2012},
  doi = {10.1534/genetics.111.132647},
  publisher = {Genetics},
  journal = {Genetics}
}

@article{Broman2012b,
author = {Broman, Karl W.}, 
title = {Haplotype Probabilities in Advanced Intercross Populations},
volume = {2}, 
number = {2}, 
pages = {199-202}, 
year = {2012}, 
journal = {G3: Genes|Genomes|Genetics} 
}

@article {Broman2005,
  author = {Broman, Karl W.},
  title = {The Genomes of Recombinant Inbred Lines},
  volume = {169},
  number = {2},
  pages = {1133--1146},
  year = {2005},
  doi = {10.1534/genetics.104.035212},
  publisher = {Genetics},
  journal = {Genetics}
}

@Article{Shah2014,
author="Shah, Rohan
and Cavanagh, Colin R.
and Huang, B. Emma",
title="Computationally efficient map construction in the presence of segregation distortion",
journal="Theoretical and Applied Genetics",
year="2014",
volume="127",
number="12",
pages="2585--2597"
}

@book{Brusco2005,
  author = {Brusco, Michael J. and Stahl, Stephanie},
  doi = {10.1007/0-387-28810-4},
  url = {http://dx.doi.org/10.1007/0-387-28810-4},
  year  = {2005},
  publisher = {Springer-Verlag},
  title = {Branch-and-Bound Applications in Combinatorial Data Analysis}
}

@article{Hahsler2008,
   author = {Michael Hahsler and Kurt Hornik and Christian Buchta},
   title = {Getting Things in Order: An Introduction to the R Package seriation},
   journal = {Journal of Statistical Software},
   volume = {25},
   number = {1},
   year = {2008},
   pages = {1--34},
   url = {https://www.jstatsoft.org/index.php/jss/article/view/v025i03}
}

@Manual{nnls,
    title = {nnls: The Lawson-Hanson algorithm for non-negative least squares (NNLS)},
    author = {Katharine M. Mullen and Ivo H. M. {van Stokkum}},
    year = {2012},
    note = {R package version 1.4},
    url = {https://CRAN.R-project.org/package=nnls},
}