The Collaborative Cross, a community resource for the genetic analysis of complex traits

Mouse genomic variation and its effect on phenotypes and gene regulation.

Keane, T. M., Goodstadt, L., Danecek, P., White, M. A., Wong, K., Yalcin, B., Heger, A., Agam, A., Slater, G., Goodson, M., et al. (2011) · Nature · doi:10.1038/nature10413 · Cited by 1,580

Individuality in gut microbiota composition is a complex polygenic trait shaped by multiple environmental and host genetic factors

Benson, A. K., Kelly, S. A., Legge, R., Ma, F., Low, S. J., Kim, J., Zhang, M., Oh, P. L., Nehrenberg, D., Hua, K., et al. (2010) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1007028107 · Cited by 1,314

Association mapping: critical considerations shift from genotyping to experimental design

Myles, S., Peiffer, J., Brown, P. J., Ersoz, E. S., Zhang, Z., Costich, D. E., & Buckler, E. S. (2009) · The Plant Cell · doi:10.1105/tpc.109.068437 · Cited by 857

Complex trait analysis of gene expression uncovers polygenic and pleiotropic networks that modulate nervous system function

Chesler, E. J., Lu, L., Shou, S., Qu, Y., Gu, J., Wang, J., Hsu, H. C., Mountz, J. D., Baldwin, N. E., Langston, M. A., et al. (2005) · Nature Genetics · doi:10.1038/ng1518 · Cited by 719

Preclinical Mouse Cancer Models: A Maze of Opportunities and Challenges

Day, C.-P., Merlino, G., & Van Dyke, T. (2015) · Cell · doi:10.1016/j.cell.2015.08.068 · Cited by 676

A comparative phenotypic and genomic analysis of C57BL/6J and C57BL/6N mouse strains

Simon, M. M., Greenaway, S., White, J. K., Fuchs, H., Gailus-Durner, V., Wells, S., Sorg, T., Wong, K., Bedu, E., Cartwright, E. J., et al. (2013) · Genome Biology · doi:10.1186/gb-2013-14-7-r82 · Cited by 507

The Genome Architecture of the Collaborative Cross Mouse Genetic Reference Population

Collaborative Cross Consortium (2012) · Genetics · doi:10.1534/genetics.111.132639 · Cited by 480

The mouse ascending: perspectives for human-disease models

Rosenthal, N., & Brown, S. (2007) · Nature Cell Biology · doi:10.1038/ncb437 · Cited by 442

Defining the consequences of genetic variation on a proteome-wide scale

Chick, J. M., Munger, S. C., Simecek, P., Huttlin, E. L., Choi, K., Gatti, D. M., Raghupathy, N., Svenson, K. L., Churchill, G. A., & Gygi, S. P. (2016) · Nature · doi:10.1038/nature18270 · Cited by 361

Genetic analysis of complex traits in the emerging Collaborative Cross

Aylor, D. L., Valdar, W., Foulds-Mathes, W., Buus, R. J., Verdugo, R. A., Baric, R. S., Ferris, M. T., Frelinger, J. A., Heise, M., Frieman, M. B., et al. (2011) · Genome Research · doi:10.1101/gr.111310.110 · Cited by 328

Animal Models of Zika Virus Infection, Pathogenesis, and Immunity

Morrison, T. E., & Diamond, M. S. (2017) · Journal of Virology · doi:10.1128/jvi.00009-17 · Cited by 275

Sixteen diverse laboratory mouse reference genomes define strain-specific haplotypes and novel functional loci

Lilue, J., Doran, A. G., Fiddes, I. T., Abrudan, M., Armstrong, J., Bennett, R., Chow, W., Collins, J., Collins, S., Czechanski, A., et al. (2018) · Nature Genetics · doi:10.1038/s41588-018-0223-8 · Cited by 267

The polymorphic prelude to Bateson–Dobzhansky–Muller incompatibilities

Cutter, A. D. (2012) · Trends in Ecology & Evolution · doi:10.1016/j.tree.2011.11.004 · Cited by 220

Reproducibility and replicability of rodent phenotyping in preclinical studies

Kafkafi, N., Agassi, J., Chesler, E. J., Crabbe, J. C., Crusio, W. E., Eilam, D., Gerlai, R., Golani, I., Gomez-Marin, A., Heller, R., et al. (2018) · Neuroscience & Biobehavioral Reviews · doi:10.1016/j.neubiorev.2018.01.003 · Cited by 215

Host genotype and gut microbiome modulate insulin secretion and diet-induced metabolic phenotypes

Kreznar, J. H., Keller, M. P., Traeger, L. L., Rabaglia, M. E., Schueler, K. L., Stapleton, D. S., Zhao, W., Vivas, E. I., Yandell, B. S., Broman, A. T., et al. (2017) · Cell Reports · doi:10.1016/j.celrep.2017.01.062 · Cited by 177

Genetic analysis in the Collaborative Cross breeding population

Philip, V. M., Sokoloff, G., Ackert-Bicknell, C. L., Striz, M., Branstetter, L., Beckmann, M. A., Spence, J. S., Jackson, B. L., Galloway, L. D., Barker, P., et al. (2011) · Genome Research · doi:10.1101/gr.113886.110 · Cited by 168

A platform for experimental precision medicine: The extended BXD mouse family

Ashbrook, D. G., Arends, D., Prins, P., Mulligan, M. K., Roy, S., Williams, E. G., Lutz, C. M., Valenzuela, A., Bohl, C. J., Ingels, J. F., et al. (2021) · Cell Systems · doi:10.1016/j.cels.2020.12.002 · Cited by 171

Current issues in mouse genome engineering

Glaser, S., Anastassiadis, K., & Stewart, A. F. (2005) · Nature Genetics · doi:10.1038/ng1668 · Cited by 160

Mouse models of ageing and their relevance to disease

Kõks, S., Dogan, S., Tuna, B. G., González-Navarro, H., Potter, P., & Vandenbroucke, R. E. (2016) · Mechanisms of Ageing and Development · doi:10.1016/j.mad.2016.10.001 · Cited by 125

Genetics of behavioural domains across the neuropsychiatric spectrum; of mice and men

Kas, M. J. H., Fernandes, C., Schalkwyk, L. C., & Collier, D. A. (2007) · Molecular Psychiatry · doi:10.1038/sj.mp.4001979 · Cited by 122

Genetic contributions to behavioural diversity at the gene-environment interface

Bendesky, A., & Bargmann, C. I. (2011) · Nature Reviews Genetics · doi:10.1038/nrg3065 · Cited by 103

Gene-to-phenotype models and complex trait genetics

Cooper, M., Podlich, D. W., & Smith, O. S. (2005) · Australian Journal of Agricultural Research · doi:10.1071/ar05154 · Cited by 104

Fine mapping in 94 inbred mouse strains using a high-density haplotype resource

Kirby, A., Kang, H. M., Wade, C. M., Cotsapas, C., Kostem, E., Han, B., Furlotte, N., Kang, E. Y., Rivas, M., Bogue, M. A., et al. (2010) · Genetics · doi:10.1534/genetics.110.115014 · Cited by 102

Translational approaches to understanding resilience to Alzheimer’s disease

Neuner, S. M., Telpoukhovskaia, M., Menon, V., O’Connell, K. M. S., Hohman, T. J., & Kaczorowski, C. C. (2022) · Trends in Neurosciences · doi:10.1016/j.tins.2022.02.005 · Cited by 68

Inbred or Outbred? Genetic Diversity in Laboratory Rodent Colonies

Brekke, T. D., Steele, K. A., & Mulley, J. F. (2018) · G3 Genes|Genomes|Genetics · doi:10.1534/g3.117.300495 · Cited by 67

Technical approaches for mouse models of human disease

Justice, M. J., Siracusa, L. D., & Stewart, A. F. (2011) · Disease Models & Mechanisms · doi:10.1242/dmm.000901 · Cited by 66

Cosplicing network analysis of mammalian brain RNA-Seq data utilizing WGCNA and Mantel correlations

Iancu, O. D., Colville, A., Oberbeck, D., Darakjian, P., McWeeney, S. K., & Hitzemann, R. (2015) · Frontiers in Genetics · doi:10.3389/fgene.2015.00174 · Cited by 57

Joint Estimates of Quantitative Trait Locus Effect and Frequency Using Synthetic Recombinant Populations of Drosophila melanogaster

Macdonald, S. J., & Long, A. D. (2007) · Genetics · doi:10.1534/genetics.106.069641 · Cited by 61

Mouse phenogenomics: the fast track to “systems metabolism

Argmann, C. A., Chambon, P., & Auwerx, J. (2005) · Cell Metabolism · doi:10.1016/j.cmet.2005.11.002 · Cited by 51

Mouse population genetics phenocopies heterogeneity of human Chd8 haploinsufficiency

Tabbaa, M., Knoll, A., & Levitt, P. (2023) · Neuron · doi:10.1016/j.neuron.2023.01.009 · Cited by 45

Diverse CD8 T Cell Responses to Viral Infection Revealed by the Collaborative Cross

Martin, M. D., Sompallae, R., Winborn, C. S., Harty, J. T., & Badovinac, V. P. (2020) · Cell Reports · doi:10.1016/j.celrep.2020.03.072 · Cited by 21

Introduction to Sequencing the Brain Transcriptome

Hitzemann, R., Darakjian, P., Walter, N., Dan Iancu, O., Searles, R., & McWeeney, S. (2014) · International Review of Neurobiology · doi:10.1016/b978-0-12-801105-8.00001-1 · Cited by 20

Genome-wide association for testis weight in the diversity outbred mouse population

Yuan, J. T., Gatti, D. M., Philip, V. M., Kasparek, S., Kreuzman, A. M., Mansky, B., Sharif, K., Taterra, D., Taylor, W. M., Thomas, M., et al. (2018) · Mammalian Genome · doi:10.1007/s00335-018-9745-8 · Cited by 15

Network analysis identifies strain-dependent response to tau and tau seeding-associated genes

Acri, D. J., You, Y., Tate, M. D., Karahan, H., Martinez, P., McCord, B., Sharify, A. D., John, S., Kim, B., Dabin, L. C., et al. (2023) · Journal of Experimental Medicine · doi:10.1084/jem.20230180 · Cited by 3

Genetic mapping in collaborative cross mouse strains identifies loci that affect initial sensitivity to cocaine

(2025) · doi:10.1007/s00213-025-06901-z · Cited by 1