Sequence-based characterization of structural variation in the mouse genome

Pindel: a pattern growth approach to detect break points of large deletions and medium sized insertions from paired-end short reads

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Origins and functional impact of copy number variation in the human genome

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22q11.21 Deletion Syndromes: A Review of Proximal, Central, and Distal Deletions and Their Associated Features

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

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BreakDancer: an algorithm for high-resolution mapping of genomic structural variation

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Copy number variation in human health, disease, and evolution

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Structural Variation in the Human Genome and its Role in Disease

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Population genomics of human gene expression

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Mapping copy number variation by population-scale genome sequencing

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An integrative genomics approach to infer causal associations between gene expression and disease

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

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Endogenous viruses: insights into viral evolution and impact on host biology

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Phenotypic impact of genomic structural variation: insights from and for human disease

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Dynamic landscape and regulation of RNA editing in mammals

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Spatial Organization of the Mouse Genome and Its Role in Recurrent Chromosomal Translocations

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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 Genetics of Transcription Factor DNA Binding Variation

Deplancke, B., Alpern, D., & Gardeux, V. (2016) · Cell · doi:10.1016/j.cell.2016.07.012 · Cited by 390

Copy number variation of individual cattle genomes using next-generation sequencingPreprint

Bickhart, D. M., Hou, Y., Schroeder, S., Alkan, C., Mf, C., Matukumalli, L. K., Song, J., Schnabel, R., Ventura, M., Taylor, J. F., et al. (2012) · Genome Research · doi:10.1101/gr.133967.111 · Cited by 317

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

Maximum likelihood inference of reticulate evolutionary histories

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Mismatch Repair Genes Mlh1 and Mlh3 Modify CAG Instability in Huntington's Disease Mice: Genome-Wide and Candidate Approaches

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Identification, Characterization, and Heritability of Murine Metastable Epialleles: Implications for Non-genetic Inheritance

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Genomes of the Mouse Collaborative Cross

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Endogenous Retroviruses and the Development of Cancer

Kassiotis, G. (2014) · The Journal of Immunology · doi:10.4049/jimmunol.1302972 · Cited by 202

Lactation and Neonatal Nutrition: Defining and Refining the Critical Questions

Neville, M. C., Anderson, S. M., McManaman, J. L., Badger, T. M., Bunik, M. E., Contractor, N., Crume, T., Dabelea, D., Donovan, S. M., Forman, N. A., et al. (2012) · Journal of Mammary Gland Biology and Neoplasia · doi:10.1007/s10911-012-9261-5 · Cited by 194

The genomic landscape shaped by selection on transposable elements across 18 mouse strains

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Creating reference gene annotation for the mouse C57BL6/J genome assembly

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A decade of structural variants: description, history and methods to detect structural variation

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Passenger Mutations Confound Interpretation of All Genetically Modified Congenic Mice

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Genome-Wide Mapping of Structural Variations Reveals a Copy Number Variant That Determines Reproductive Morphology in Cucumber

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Xenomic networks variability and adaptation traits in wood decaying fungi

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Mouse Phenome Database (MPD)

Maddatu, T. P., Grubb, S. C., Bult, C. J., & Bogue, M. A. (2011) · Nucleic Acids Research · doi:10.1093/nar/gkr1061 · Cited by 141

Individual differences in recovery from traumatic fear

Holmes, A., & Singewald, N. (2012) · Trends in Neurosciences · doi:10.1016/j.tins.2012.11.003 · Cited by 147

Genome-wide association of multiple complex traits in outbred mice by ultra-low-coverage sequencing

Nicod, J., Davies, R. W., Cai, N., Hassett, C., Goodstadt, L., Cosgrove, C., Yee, B. K., Lionikaite, V., McIntyre, R. E., Remme, C. A., et al. (2016) · Nature Genetics · doi:10.1038/ng.3595 · Cited by 133

An integrative probabilistic model for identification of structural variation in sequencing data

Sindi, S., Önal, S., Peng, L., Wu, H.-T., & Raphael, B. J. (2012) · Genome biology · doi:10.1186/gb-2012-13-3-r22 · Cited by 139

Dynamics of gene silencing during X inactivation using allele-specific RNA-seq

Marks, H., Kerstens, H. H. D., Barakat, T. S., Splinter, E., Dirks, R. A. M., van Mierlo, G., Joshi, O., Wang, S.-Y., Babak, T., Albers, C. A., et al. (2015) · Genome biology · doi:10.1186/s13059-015-0698-x · Cited by 127

The blessings and curses of C57BL/6 substrains in mouse genetic studies

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Substrains matter in phenotyping of C57BL/6 mice

Mekada, K., & Yoshiki, A. (2021) · EXPERIMENTAL ANIMALS · doi:10.1538/expanim.20-0158 · Cited by 131

A sheep pangenome reveals the spectrum of structural variations and their effects on tail phenotypesPreprint

Li, R., Gong, M., Zhang, X., Wang, F., Liu, Z., Zhang, L., Yang, Q., Xu, Y., Xu, M., Zhang, H., et al. (2023) · Genome Research · doi:10.1101/gr.277372.122 · Cited by 125

Diversity Outbred Mice Identify Population-Based Exposure Thresholds and Genetic Factors that Influence Benzene-Induced Genotoxicity

French, J. E., Gatti, D. M., Morgan, D. L., Kissling, G. E., Shockley, K. R., Knudsen, G. A., Shepard, K. G., Price, H. C., King, D., Witt, K. L., et al. (2014) · Environmental Health Perspectives · doi:10.1289/ehp.1408202 · Cited by 121

High‐precision genetic mapping of behavioral traits in the diversity outbred mouse population

Logan, R. W., Robledo, R. F., Recla, J. M., Philip, V. M., Bubier, J. A., Jay, J. J., Harwood, C., Wilcox, T. D., Gatti, D. M., Bult, C. J., et al. (2013) · Genes Brain & Behavior · doi:10.1111/gbb.12029 · Cited by 114

Genomic Variation and Its Impact on Gene Expression in Drosophila melanogaster

Massouras, A., Waszak, S. M., Albarca-Aguilera, M., Hens, K., Holcombe, W., Ayroles, J. F., Dermitzakis, E. T., Stone, E. A., Jensen, J. D., Mackay, T. F. C., et al. (2012) · PLoS Genetics · doi:10.1371/journal.pgen.1003055 · Cited by 113

Deep genome sequencing and variation analysis of 13 inbred mouse strains defines candidate phenotypic alleles, private variation and homozygous truncating mutations

Doran, A. G., Wong, K., Flint, J., Adams, D. J., Hunter, K. W., & Keane, T. M. (2016) · Genome Biology · doi:10.1186/s13059-016-1024-y · Cited by 101

Genome‐wide patterns of standing genetic variation in a marine population of three‐spined sticklebacks

Feulner, P. G. D., Chain, F. J. J., Panchal, M., Eizaguirre, C., Kalbe, M., Lenz, T. L., Mundry, M., Samonte, I. E., Stoll, M., Milinski, M., et al. (2012) · Molecular Ecology · doi:10.1111/j.1365-294x.2012.05680.x · Cited by 101

Ly6a Differential Expression in Blood–Brain Barrier Is Responsible for Strain Specific Central Nervous System Transduction Profile of AAV-PHP.B

Batista, A. R., King, O. D., Reardon, C. P., Davis, C., Shankaracharya, Philip, V. M., Gray‐Edwards, H. L., D, N. A. M., Lutz, C. M., Landers, J. E., et al. (2019) · Human Gene Therapy · doi:10.1089/hum.2019.186 · Cited by 98

Copy number variation of a gene cluster encoding endopolygalacturonase mediates flesh texture and stone adhesion in peach

Gu, C., Wang, L., Wang, W., Zhou, H., Ma, B., Zheng, H., Fang, T., Ogutu, C. O., Vimolmangkang, S., & Han, Y. (2016) · Journal of Experimental Botany · doi:10.1093/jxb/erw021 · Cited by 99

Genes, behavior and next‐generation RNA sequencing

Hitzemann, R., Bottomly, D., Darakjian, P., Walter, N., Iancu, O., Searles, R., Wilmot, B., & McWeeney, S. (2013) · Genes, Brain and Behavior · doi:10.1111/gbb.12007 · Cited by 88

Genome-wide patterns of copy number variation in the diversified chicken genomes using next-generation sequencing

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Genetic Analysis of Hematological Parameters in Incipient Lines of the Collaborative Cross

Kelada, S. N. P., Aylor, D. L., Peck, B. C. E., Ryan, J. F., Tavarez, U. L., Buus, R. J., Miller, D. R., Chesler, E. J., Threadgill, D. W., Churchill, G. A., et al. (2012) · G3 Genes Genomes Genetics · doi:10.1534/g3.111.001776 · Cited by 94

High-fat feeding rapidly induces obesity and lipid derangements in C57BL/6N mice

Sanger Mouse Genetics Project, Podrini, C., Cambridge, E. L., Lelliott, C. J., Carragher, D. M., Estabel, J., Gerdin, A.-K., Karp, N. A., Scudamore, C. L., Ramírez‐Solis, R., et al. (2013) · Mammalian Genome · doi:10.1007/s00335-013-9456-0 · Cited by 101

Emerging genetics of COPD

Berndt, A., Leme, A. S., & Shapiro, S. D. (2012) · EMBO Molecular Medicine · doi:10.1002/emmm.201100627 · Cited by 89

Fine mapping of copy number variations on two cattle genome assemblies using high density SNP array

Hou, Y., Bickhart, D. M., Hvinden, M. L., Li, C., Song, J., Boichard, D., Fritz, S., Eggen, A. A., DeNise, S. K., Wiggans, G. R., et al. (2012) · BMC Genomics · doi:10.1186/1471-2164-13-376 · Cited by 86

A Multi-Megabase Copy Number Gain Causes Maternal Transmission Ratio Distortion on Mouse Chromosome 2

Didion, J. P., Morgan, A. P., Clayshulte, A. M.-F., McMullan, R., Yadgary, L., Petkov, P. M., Bell, T. A., Gatti, D. M., Crowley, J. J., Hua, K., et al. (2015) · PLoS Genetics · doi:10.1371/journal.pgen.1004850 · Cited by 83

Mapping Genetic Contributions to Cardiac Pathology Induced by Beta-Adrenergic Stimulation in Mice

Rau, C. D., Wang, J., Avetisyan, R., Romay, M. C., Martin, L., Ren, S. V., Wang, Y., & Lusis, A. J. (2014) · Circulation Cardiovascular Genetics · doi:10.1161/circgenetics.113.000732 · Cited by 84

Modifier genes and the plasticity of genetic networks in mice

Hamilton, B. A., & Yu, B. D. (2012) · PLoS Genetics · doi:10.1371/journal.pgen.1002644 · Cited by 78

The Mouse Genomes Project: a repository of inbred laboratory mouse strain genomes

Adams, D. J., Doran, A., Lilue, J., & Keane, T. (2015) · Mammalian Genome · doi:10.1007/s00335-015-9579-6 · Cited by 81

Trace Amine-Associated Receptor 1 Regulation of Methamphetamine Intake and Related Traits

Harkness, J. H., Shi, X., Janowsky, A. J., & Phillips, T. J. (2015) · Neuropsychopharmacology · doi:10.1038/npp.2015.61 · Cited by 78

Sequencing and characterization of the FVB/NJ mouse genome

Wong, K., Bumpstead, S., van der Weyden, L., Reinholdt, L. G., Wilming, L. G., Adams, D. J., & Keane, T. (2012) · Genome biology · doi:10.1186/gb-2012-13-8-r72 · Cited by 75

Resolution of structural variation in diverse mouse genomes reveals chromatin remodeling due to transposable elements

Ferraj, A., Audano, P. A., Balachandran, P., Czechanski, A., Flores, J. I., Radecki, A. A., Mosur, V., Gordon, D., Walawalkar, I. A., Eichler, E. E., et al. (2023) · Cell Genomics · doi:10.1016/j.xgen.2023.100291 · Cited by 80

Variable Colonization after Reciprocal Fecal Microbiota Transfer between Mice with Low and High Richness Microbiota

Ericsson, A. C., Personett, A. R., Turner, G., Dorfmeyer, R. A., & Franklin, C. L. (2017) · Frontiers in Microbiology · doi:10.3389/fmicb.2017.00196 · Cited by 77

Cardiac-Specific Inducible and Conditional Gene Targeting in Mice

Doetschman, T., & Azhar, M. (2012) · Circulation Research · doi:10.1161/circresaha.112.265066 · Cited by 74

Cytoplasmic FMR1-Interacting Protein 2 Is a Major Genetic Factor Underlying Binge Eating

Kirkpatrick, S. L., Goldberg, L. R., Yazdani, N., Babbs, R. K., Wu, J., Reed, E. R., Jenkins, D. F., Bolgioni, A. F., Landaverde, K. I., Luttik, K. P., et al. (2017) · Biological Psychiatry · doi:10.1016/j.biopsych.2016.10.021 · Cited by 71

Genome-wide and parental allele-specific analysis of CTCF and cohesin DNA binding in mouse brain reveals a tissue-specific binding pattern and an association with imprinted differentially methylated regionsPreprint

Prickett, A. R., Barkas, N., McCole, R. B., Hughes, S., Amante, S. M., Schulz, R., & Oakey, R. J. (2013) · Genome Research · doi:10.1101/gr.150136.112 · Cited by 70

High-Resolution Sex-Specific Linkage Maps of the Mouse Reveal Polarized Distribution of Crossovers in Male Germline

Liu, E. Y., Morgan, A. P., Chesler, E. J., Wang, W., Churchill, G. A., & de Villena, F. P. (2014) · Genetics · doi:10.1534/genetics.114.161653 · Cited by 67

Resolving complex tandem repeats with long reads

Ummat, A., & Bashir, A. (2014) · Bioinformatics · doi:10.1093/bioinformatics/btu437 · Cited by 66

Copy number variation in the cattle genome

Liu, G. E., & Bickhart, D. M. (2012) · Functional & Integrative Genomics · doi:10.1007/s10142-012-0289-9 · Cited by 66

Going Forward with Genetics

Moresco, E. M. Y., Li, X., & Beutler, B. (2013) · American Journal Of Pathology · doi:10.1016/j.ajpath.2013.02.002 · Cited by 69

Genetic loci and metabolic states associated with murine epigenetic aging

Mozhui, K., Lu, A. T., Li, C. Z., Haghani, A., Sandoval-Sierra, J. V., Wu, Y., Williams, R. W., & Horvath, S. (2022) · eLife · doi:10.7554/elife.75244 · Cited by 58

Next-generation sequencing of experimental mouse strains

Yalcin, B., Adams, D. J., Flint, J., & Keane, T. (2012) · Mammalian Genome · doi:10.1007/s00335-012-9402-6 · Cited by 60

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

Didion, J. P., & de Villena, F. P. (2012) · Mammalian Genome · doi:10.1007/s00335-012-9441-z · Cited by 58

Conversion of random X-inactivation to imprinted X-inactivation by maternal PRC2

Harris, C. E., Cloutier, M., Trotter, M., Hinten, M., Gayen, S., Du, Z., Xie, W., & Kalantry, S. (2019) · eLife · doi:10.7554/elife.44258 · Cited by 55

High-Resolution Genetic Mapping in the Diversity Outbred Mouse Population Identifies Apobec1 as a Candidate Gene for Atherosclerosis

Smallwood, T. L., Gatti, D. M., Quizon, P., Weinstock, G. M., Jung, K.-C., Zhao, L., Hua, K., Pomp, D., & Bennett, B. J. (2014) · G3 Genes|Genomes|Genetics · doi:10.1534/g3.114.014704 · Cited by 54

Deleted copy number variation of Hanwoo and Holstein using next generation sequencing at the population level

Shin, D., Lee, H. J., Cho, S., Kim, H. J., Hwang, J. Y., Lee, C., Jeong, J., Yoon, D., & Kim, H. (2014) · BMC Genomics · doi:10.1186/1471-2164-15-240 · Cited by 52

The fine-scale architecture of structural variants in 17 mouse genomes

Yalcin, B., Wong, K., Bhomra, A., Goodson, M., Keane, T., Adams, D. J., & Flint, J. (2012) · Genome biology · doi:10.1186/gb-2012-13-3-r18 · Cited by 52

Epigenetic control of alternative mRNA processing at the imprinted Herc3/Nap1l5 locus

Cowley, M., Wood, A. J., Böhm, S., Schulz, R., & Oakey, R. J. (2012) · Nucleic Acids Research · doi:10.1093/nar/gks654 · Cited by 53

Mouse endogenous retroviruses can trigger premature transcriptional termination at a distancePreprint

Li, J., Akagi, K., Hu, Y., Trivett, A. L., Hlynialuk, C. J. W., Swing, D. A., Volfovsky, N., Morgan, T. C., Golubeva, Y. G., Stephens, R. M., et al. (2012) · Genome Research · doi:10.1101/gr.130740.111 · Cited by 52

Comparative Analysis of CNV Calling Algorithms: Literature Survey and a Case Study Using Bovine High-Density SNP Data

Xu, L., Hou, Y., Bickhart, D. M., Song, J., & Liu, G. E. (2013) · Microarrays · doi:10.3390/microarrays2030171 · Cited by 54

Genomic copy number variation in Mus musculus

Locke, M. E. O., Milojevic, M., Eitutis, S. T., Patel, N., Wishart, A. E., Daley, M., & Hill, K. A. (2015) · BMC Genomics · doi:10.1186/s12864-015-1713-z · Cited by 51

Associations of MYH3 gene copy number variations with transcriptional expression and growth traits in Chinese cattle

Xu, Y., Shi, T., Cai, H., Zhou, Y., Lan, X., Zhang, C., Lei, C., Qi, X., & Chen, H. (2013) · Gene · doi:10.1016/j.gene.2013.11.057 · Cited by 50

Hnrnph1 Is A Quantitative Trait Gene for Methamphetamine Sensitivity

Yazdani, N., Parker, C. C., Shen, Y., Reed, E. R., Guido, M. A., Kole, L. A., Kirkpatrick, S. L., Lim, J. E., Sokoloff, G., Cheng, R., et al. (2015) · PLoS Genetics · doi:10.1371/journal.pgen.1005713 · Cited by 46

Cytosolic Iron-Sulfur Assembly Is Evolutionarily Tuned by a Cancer-Amplified Ubiquitin Ligase

Weon, J. L., Yang, S. W., & Potts, P. R. (2017) · Molecular Cell · doi:10.1016/j.molcel.2017.11.010 · Cited by 49

Epistatic Networks Jointly Influence Phenotypes Related to Metabolic Disease and Gene Expression in Diversity Outbred Mice

Tyler, A. L., Ji, B., Gatti, D. M., Munger, S. C., Churchill, G. A., Svenson, K. L., & Carter, G. W. (2017) · Genetics · doi:10.1534/genetics.116.198051 · Cited by 52

Improving detection of copy-number variation by simultaneous bias correction and read-depth segmentation

Szatkiewicz, J., Wang, W., Sullivan, P. F., Wang, W. W., & Sun, W. (2012) · Nucleic Acids Research · doi:10.1093/nar/gks1363 · Cited by 47

Genome-Wide Association for Fear Conditioning in an Advanced Intercross Mouse Line

Parker, C. C., Sokoloff, G., Cheng, R., & Palmer, A. A. (2012) · Behavior Genetics · doi:10.1007/s10519-011-9524-8 · Cited by 49

Copy number variation in potato – an asexually propagated autotetraploid species

Iovene, M., Zhang, T., Lou, Q., Buell, C. R., & Jiang, J. (2013) · The Plant Journal · doi:10.1111/tpj.12200 · Cited by 51

Genetic Architecture of Skewed X Inactivation in the Laboratory Mouse

Calaway, J. D., Lenarcic, A., Didion, J. P., Wang, J., Searle, J. B., McMillan, L., Valdar, W. S. J., & de Villena, F. P. (2013) · PLoS Genetics · doi:10.1371/journal.pgen.1003853 · Cited by 45

The optimal mating distance resulting from heterosis and genetic incompatibility

Wei, X., & Zhang, J. (2018) · Science Advances · doi:10.1126/sciadv.aau5518 · Cited by 47

Immunity-related GTPase induces lipophagy to prevent excess hepatic lipid accumulation

Schwerbel, K., Kamitz, A., Krahmer, N., Hallahan, N., Jähnert, M., Gottmann, P., Lebek, S., Schallschmidt, T., Arends, D., Schumacher, F., et al. (2020) · Journal of Hepatology · doi:10.1016/j.jhep.2020.04.031 · Cited by 50

Copy number variations of MICAL-L2 shaping gene expression contribute to different phenotypes of cattle

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Structural variation during dog domestication: insights from gray wolf and dhole genomes

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