| Characterization of ancient and modern genomes by SNP detection and phylogenomic and metagenomic analysis using PALEOMIX M Schubert, L Ermini, CD Sarkissian, H Jónsson, A Ginolhac, R Schaefer, ... Nature protocols 9 (5), 1056-1082, 2014 | 486 | 2014 |
| Reshaping of the maize transcriptome by domestication R Swanson-Wagner, R Briskine, R Schaefer, MB Hufford, J Ross-Ibarra, ... Proceedings of the National Academy of Sciences 109 (29), 11878-11883, 2012 | 165 | 2012 |
| Integrating coexpression networks with GWAS to prioritize causal genes in maize RJ Schaefer, JM Michno, J Jeffers, O Hoekenga, B Dilkes, I Baxter, ... The Plant Cell 30 (12), 2922-2942, 2018 | 140 | 2018 |
| Developing a 670k genotyping array to tag~ 2M SNPs across 24 horse breeds RJ Schaefer, M Schubert, E Bailey, DL Bannasch, E Barrey, GK Bar-Gal, ... BMC genomics 18, 1-18, 2017 | 119 | 2017 |
| Y chromosome uncovers the recent oriental origin of modern stallions B Wallner, N Palmieri, C Vogl, D Rigler, E Bozlak, T Druml, ... Current Biology 27 (13), 2029-2035. e5, 2017 | 89 | 2017 |
| Unraveling gene function in agricultural species using gene co-expression networks RJ Schaefer, JM Michno, CL Myers Biochimica et Biophysica Acta (BBA)-Gene Regulatory Mechanisms 1860 (1), 53-63, 2017 | 66 | 2017 |
| The horse Y chromosome as an informative marker for tracing sire lines S Felkel, C Vogl, D Rigler, V Dobretsberger, BP Chowdhary, O Distl, ... Scientific reports 9 (1), 6095, 2019 | 48 | 2019 |
| Genome-Wide Association Study Implicates Testis-Sperm Specific FKBP6 as a Susceptibility Locus for Impaired Acrosome Reaction in Stallions T Raudsepp, ME McCue, PJ Das, L Dobson, M Vishnoi, KL Fritz, ... PLoS genetics 8 (12), e1003139, 2012 | 45 | 2012 |
| Co-expression network analysis of duplicate genes in maize (Zea mays L.) reveals no subgenome bias L Li, R Briskine, R Schaefer, PS Schnable, CL Myers, LE Flagel, ... BMC genomics 17, 1-15, 2016 | 42 | 2016 |
| Genome-wide signatures of selection reveal genes associated with performance in American quarter horse subpopulations F Avila, JR Mickelson, RJ Schaefer, ME McCue Frontiers in Genetics 9, 249, 2018 | 34 | 2018 |
| Discovering functional modules across diverse maize transcriptomes using COB, the co-expression browser RJ Schaefer, R Briskine, NM Springer, CL Myers PloS one 9 (6), e99193, 2014 | 32 | 2014 |
| Evidence of Positive Selection for a Glycogen Synthase (GYS1) Mutation in Domestic Horse Populations AM McCoy, R Schaefer, JL Petersen, PL Morrell, MA Slamka, ... Journal of heredity 105 (2), 163-172, 2014 | 28 | 2014 |
| Robust remapping of equine SNP array coordinates to EquCab3 SK Beeson, RJ Schaefer, VC Mason, ME McCue Animal genetics 50 (1), 114, 2019 | 25 | 2019 |
| GWAS and coexpression network reveal ionomic variation in cultivated peanut H Zhang, ML Wang, R Schaefer, P Dang, T Jiang, C Chen Journal of agricultural and food chemistry 67 (43), 12026-12036, 2019 | 21 | 2019 |
| Equine genotyping arrays RJ Schaefer, ME McCue Veterinary Clinics of North America: Equine Practice 36 (2), 183-193, 2020 | 17 | 2020 |
| Genetic architecture of maize rind strength revealed by the analysis of divergently selected populations R Kumar, A Gyawali, GD Morrison, CA Saski, DJ Robertson, DD Cook, ... Plant and Cell Physiology 62 (7), 1199-1214, 2021 | 16 | 2021 |
| Genetic variation and the distribution of variant types in the horse SA Durward-Akhurst, RJ Schaefer, B Grantham, WK Carey, JR Mickelson, ... Frontiers in genetics 12, 758366, 2021 | 15 | 2021 |
| eQTL discovery and their association with severe equine asthma in European Warmblood horses VC Mason, RJ Schaefer, ME McCue, T Leeb, V Gerber BMC genomics 19, 1-15, 2018 | 13 | 2018 |
| Fine-mapping of 18q21. 1 locus identifies single nucleotide polymorphisms associated with nonsyndromic cleft lip with or without cleft palate AK Mitra, HAF Stessman, RJ Schaefer, W Wang, CL Myers, BG Van Ness, ... Frontiers in Genetics 7, 88, 2016 | 5 | 2016 |
| Functional contexts of adipose and gluteal muscle tissue gene co-expression networks in the domestic horse RJ Schaefer, J Cullen, J Manfredi, ME McCue Integrative and comparative biology 63 (1), 238-249, 2023 | 2 | 2023 |
