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Jeffrey Ross-Ibarra, PhD - Publications

Affiliations: 
Plant Sciences University of California, Davis, Davis, CA 
Area:
plant population genetics, crop evolution
Website:
http://www.rilab.org/

75 high-probability publications. We are testing a new system for linking publications to authors. You can help! If you notice any inaccuracies, please sign in and mark papers as correct or incorrect matches. If you identify any major omissions or other inaccuracies in the publication list, please let us know.

Year Citation  Score
2021 Muyle A, Ross-Ibarra J, Seymour DK, Gaut BS. Gene body methylation is under selection in Arabidopsis thaliana. Genetics. PMID 33871638 DOI: 10.1093/genetics/iyab061  1
2020 Xu G, Lyu J, Li Q, Liu H, Wang D, Zhang M, Springer NM, Ross-Ibarra J, Yang J. Evolutionary and functional genomics of DNA methylation in maize domestication and improvement. Nature Communications. 11: 5539. PMID 33139747 DOI: 10.1038/s41467-020-19333-4  0.6
2020 Zeitler L, Ross-Ibarra J, Stetter MG. Selective Loss of Diversity in Doubled-Haploid Lines from European Maize Landraces. G3 (Bethesda, Md.). PMID 32467127 DOI: 10.1534/G3.120.401196  0.36
2020 Wang B, Lin Z, Li X, Zhao Y, Zhao B, Wu G, Ma X, Wang H, Xie Y, Li Q, Song G, Kong D, Zheng Z, Wei H, Shen R, ... ... Ross-Ibarra J, et al. Genome-wide selection and genetic improvement during modern maize breeding. Nature Genetics. PMID 32341525 DOI: 10.1038/S41588-020-0616-3  1
2020 Torres R, Stetter MG, Hernandez RD, Ross-Ibarra J. The Temporal Dynamics of Background Selection in Non-equilibrium Populations. Genetics. PMID 32071195 DOI: 10.1534/Genetics.119.302892  0.36
2019 Xue W, Anderson SN, Wang X, Yang L, Crisp PA, Li Q, Noshay J, Albert PS, Birchler JA, Bilinski P, Stitzer MC, Ross-Ibarra J, Flint-Garcia S, Chen X, Springer NM, et al. Hybrid Decay: A Transgenerational Epigenetic Decline in Vigor and Viability Triggered in Backcross Populations of Teosinte with Maize. Genetics. PMID 31320409 DOI: 10.1534/Genetics.119.302378  0.68
2019 Gonzalez-Segovia E, Pérez-Limon S, Cíntora-Martínez GC, Guerrero-Zavala A, Janzen GM, Hufford MB, Ross-Ibarra J, Sawers RJH. Characterization of introgression from the teosinte ssp. to Mexican highland maize. Peerj. 7: e6815. PMID 31110920 DOI: 10.7717/Peerj.6815  1
2018 Stetter MG, Thornton K, Ross-Ibarra J. Genetic architecture and selective sweeps after polygenic adaptation to distant trait optima. Plos Genetics. 14: e1007794. PMID 30452452 DOI: 10.1371/Journal.Pgen.1007794  0.36
2018 Bilinski P, Albert PS, Berg JJ, Birchler JA, Grote MN, Lorant A, Quezada J, Swarts K, Yang J, Ross-Ibarra J. Parallel altitudinal clines reveal trends in adaptive evolution of genome size in Zea mays. Plos Genetics. 14: e1007162. PMID 29746459 DOI: 10.1371/Journal.Pgen.1007162  0.68
2017 Wang L, Beissinger TM, Lorant A, Ross-Ibarra C, Ross-Ibarra J, Hufford MB. The interplay of demography and selection during maize domestication and expansion. Genome Biology. 18: 215. PMID 29132403 DOI: 10.1186/S13059-017-1346-4  1
2017 Yang J, Mezmouk S, Baumgarten A, Buckler ES, Guill KE, McMullen MD, Mumm RH, Ross-Ibarra J. Incomplete dominance of deleterious alleles contributes substantially to trait variation and heterosis in maize. Plos Genetics. 13: e1007019. PMID 28953891 DOI: 10.1371/Journal.Pgen.1007019  0.68
2017 Stetter MG, Gates DJ, Mei W, Ross-Ibarra J. How to make a domesticate. Current Biology : Cb. 27: R896-R900. PMID 28898661 DOI: 10.1016/J.Cub.2017.06.048  0.36
2017 Lorant A, Pedersen S, Holst I, Hufford MB, Winter K, Piperno D, Ross-Ibarra J. The potential role of genetic assimilation during maize domestication. Plos One. 12: e0184202. PMID 28886108 DOI: 10.1371/Journal.Pone.0184202  1
2017 Tiffin P, Ross-Ibarra J. Advances and Limits of Using Population Genetics to Understand Local Adaptation: (Trends in Ecology & Evolution 29, 673-680; 2014). Trends in Ecology & Evolution. PMID 28823588 DOI: 10.1016/J.Tree.2017.08.001  1
2017 Bilinski P, Han Y, Hufford MB, Lorant A, Zhang P, Estep MC, Jiang J, Ross-Ibarra J. Genomic abundance is not predictive of tandem repeat localization in grass genomes. Plos One. 12: e0177896. PMID 28570674 DOI: 10.1371/Journal.Pone.0177896  1
2016 Beissinger TM, Wang L, Crosby K, Durvasula A, Hufford MB, Ross-Ibarra J. Recent demography drives changes in linked selection across the maize genome. Nature Plants. 2: 16084. PMID 27294617 DOI: 10.1038/Nplants.2016.84  1
2016 Wolfgruber TK, Nakashima MM, Schneider KL, Sharma A, Xie Z, Albert PS, Xu R, Bilinski P, Dawe RK, Ross-Ibarra J, Birchler JA, Presting GG. High Quality Maize Centromere 10 Sequence Reveals Evidence of Frequent Recombination Events. Frontiers in Plant Science. 7: 308. PMID 27047500 DOI: 10.3389/Fpls.2016.00308  1
2016 Orozco-Ramírez Q, Ross-Ibarra J, Santacruz-Varela A, Brush S. Maize diversity associated with social origin and environmental variation in Southern Mexico. Heredity. 116: 477-84. PMID 26905463 DOI: 10.1038/Hdy.2016.10  1
2015 da Fonseca RR, Smith BD, Wales N, Cappellini E, Skoglund P, Fumagalli M, Samaniego JA, Carøe C, Ávila-Arcos MC, Hufnagel DE, Korneliussen TS, Vieira FG, Jakobsson M, Arriaza B, Willerslev E, ... ... Ross-Ibarra J, et al. The origin and evolution of maize in the Southwestern United States. Nature Plants. 1: 14003. PMID 27246050 DOI: 10.1038/Nplants.2014.3  1
2015 Sosso D, Luo D, Li QB, Sasse J, Yang J, Gendrot G, Suzuki M, Koch KE, McCarty DR, Chourey PS, Rogowsky PM, Ross-Ibarra J, Yang B, Frommer WB. Seed filling in domesticated maize and rice depends on SWEET-mediated hexose transport. Nature Genetics. PMID 26523777 DOI: 10.1038/Ng.3422  1
2015 Makarevitch I, Waters AJ, West PT, Stitzer M, Hirsch CN, Ross-Ibarra J, Springer NM. Correction: Transposable Elements Contribute to Activation of Maize Genes in Response to Abiotic Stress. Plos Genetics. 11: e1005566. PMID 26452261 DOI: 10.1371/Journal.Pgen.1005566  1
2015 Gerke JP, Edwards JW, Guill KE, Ross-Ibarra J, McMullen MD. The Genomic Impacts of Drift and Selection for Hybrid Performance in Maize. Genetics. PMID 26385980 DOI: 10.1534/Genetics.115.182410  1
2015 Takuno S, Ralph P, Swarts K, Elshire RJ, Glaubitz JC, Buckler ES, Hufford MB, Ross-Ibarra J. Independent Molecular Basis of Convergent Highland Adaptation in Maize. Genetics. PMID 26078279 DOI: 10.1534/Genetics.115.178327  1
2015 Vann L, Kono T, Pyhäjärvi T, Hufford MB, Ross-Ibarra J. Natural variation in teosinte at the domestication locus teosinte branched1 (tb1). Peerj. 3: e900. PMID 25909039 DOI: 10.7717/Peerj.900  1
2015 Hake S, Ross-Ibarra J. Genetic, evolutionary and plant breeding insights from the domestication of maize. Elife. 4. PMID 25807085 DOI: 10.7554/Elife.05861  1
2015 Makarevitch I, Waters AJ, West PT, Stitzer M, Hirsch CN, Ross-Ibarra J, Springer NM. Transposable elements contribute to activation of maize genes in response to abiotic stress. Plos Genetics. 11: e1004915. PMID 25569788 DOI: 10.1371/Journal.Pgen.1004915  1
2015 Dyer GA, López-Feldman A, Yúnez-Naude A, Taylor JE, Ross-Ibarra J. Reply to Brush et al.: Wake-up call for crop conservation science. Proceedings of the National Academy of Sciences of the United States of America. 112: E2. PMID 25548196 DOI: 10.1073/Pnas.1422645112  1
2015 Bilinski P, Distor K, Gutierrez-Lopez J, Mendoza GM, Shi J, Dawe RK, Ross-Ibarra J. Diversity and evolution of centromere repeats in the maize genome. Chromosoma. 124: 57-65. PMID 25190528 DOI: 10.1007/S00412-014-0483-8  1
2015 Da Fonseca RR, Smith BD, Wales N, Cappellini E, Skoglund P, Fumagalli M, Samaniego JA, Carøe C, Ávila-Arcos MC, Hufnagel DE, Korneliussen TS, Vieira FG, Jakobsson M, Arriaza B, Willerslev E, ... ... Ross-Ibarra J, et al. The origin and evolution of maize in the Southwestern United States Nature Plants. 1. DOI: 10.1038/nplants.2014.3  1
2014 Tiffin P, Ross-Ibarra J. Advances and limits of using population genetics to understand local adaptation. Trends in Ecology & Evolution. 29: 673-80. PMID 25454508 DOI: 10.1016/J.Tree.2014.10.004  1
2014 Mezmouk S, Ross-Ibarra J. The pattern and distribution of deleterious mutations in maize. G3 (Bethesda, Md.). 4: 163-71. PMID 24281428 DOI: 10.1534/G3.113.008870  1
2013 Waters AJ, Bilinski P, Eichten SR, Vaughn MW, Ross-Ibarra J, Gehring M, Springer NM. Comprehensive analysis of imprinted genes in maize reveals allelic variation for imprinting and limited conservation with other species. Proceedings of the National Academy of Sciences of the United States of America. 110: 19639-44. PMID 24218619 DOI: 10.1073/Pnas.1309182110  1
2013 Pyhäjärvi T, Hufford MB, Mezmouk S, Ross-Ibarra J. Complex patterns of local adaptation in teosinte. Genome Biology and Evolution. 5: 1594-609. PMID 23902747 DOI: 10.1093/Gbe/Evt109  1
2013 Wills DM, Whipple CJ, Takuno S, Kursel LE, Shannon LM, Ross-Ibarra J, Doebley JF. From many, one: genetic control of prolificacy during maize domestication. Plos Genetics. 9: e1003604. PMID 23825971 DOI: 10.1371/Journal.Pgen.1003604  1
2013 Hufford MB, Lubinksy P, Pyhäjärvi T, Devengenzo MT, Ellstrand NC, Ross-Ibarra J. The genomic signature of crop-wild introgression in maize. Plos Genetics. 9: e1003477. PMID 23671421 DOI: 10.1371/Journal.Pgen.1003477  1
2013 Kanizay LB, Pyhäjärvi T, Lowry EG, Hufford MB, Peterson DG, Ross-Ibarra J, Dawe RK. Diversity and abundance of the abnormal chromosome 10 meiotic drive complex in Zea mays. Heredity. 110: 570-7. PMID 23443059 DOI: 10.1038/Hdy.2013.2  1
2013 Melters DP, Bradnam KR, Young HA, Telis N, May MR, Ruby JG, Sebra R, Peluso P, Eid J, Rank D, Garcia JF, DeRisi JL, Smith T, Tobias C, Ross-Ibarra J, et al. Comparative analysis of tandem repeats from hundreds of species reveals unique insights into centromere evolution. Genome Biology. 14: R10. PMID 23363705 DOI: 10.1186/Gb-2013-14-1-R10  1
2013 Provance MC, García-Ruiz I, Thommes C, Ross-Ibarra J. Population genetics and ethnobotany of cultivated Diospyros riojae Gómez Pompa (Ebenaceae), an endangered fruit crop from Mexico Genetic Resources and Crop Evolution. 60: 2171-2182. DOI: 10.1007/S10722-013-0015-Z  1
2012 Hufford MB, Bilinski P, Pyhäjärvi T, Ross-Ibarra J. Teosinte as a model system for population and ecological genomics. Trends in Genetics : Tig. 28: 606-15. PMID 23021022 DOI: 10.1016/J.Tig.2012.08.004  1
2012 van Heerwaarden J, Hufford MB, Ross-Ibarra J. Historical genomics of North American maize. Proceedings of the National Academy of Sciences of the United States of America. 109: 12420-5. PMID 22802642 DOI: 10.1073/Pnas.1209275109  1
2012 Swanson-Wagner R, Briskine R, Schaefer R, Hufford MB, Ross-Ibarra J, Myers CL, Tiffin P, Springer NM. Reshaping of the maize transcriptome by domestication. Proceedings of the National Academy of Sciences of the United States of America. 109: 11878-83. PMID 22753482 DOI: 10.1073/Pnas.1201961109  1
2012 Hufford MB, Xu X, van Heerwaarden J, Pyhäjärvi T, Chia JM, Cartwright RA, Elshire RJ, Glaubitz JC, Guill KE, Kaeppler SM, Lai J, Morrell PL, Shannon LM, Song C, Springer NM, ... ... Ross-Ibarra J, et al. Comparative population genomics of maize domestication and improvement. Nature Genetics. 44: 808-11. PMID 22660546 DOI: 10.1038/Ng.2309  1
2012 Chia JM, Song C, Bradbury PJ, Costich D, de Leon N, Doebley J, Elshire RJ, Gaut B, Geller L, Glaubitz JC, Gore M, Guill KE, Holland J, Hufford MB, Lai J, ... ... Ross-Ibarra J, et al. Maize HapMap2 identifies extant variation from a genome in flux. Nature Genetics. 44: 803-7. PMID 22660545 DOI: 10.1038/Ng.2313  1
2012 Fang Z, Pyhäjärvi T, Weber AL, Dawe RK, Glaubitz JC, González Jde J, Ross-Ibarra C, Doebley J, Morrell PL, Ross-Ibarra J. Megabase-scale inversion polymorphism in the wild ancestor of maize. Genetics. 191: 883-94. PMID 22542971 DOI: 10.1534/Genetics.112.138578  1
2012 Cook JP, McMullen MD, Holland JB, Tian F, Bradbury P, Ross-Ibarra J, Buckler ES, Flint-Garcia SA. Genetic architecture of maize kernel composition in the nested association mapping and inbred association panels. Plant Physiology. 158: 824-34. PMID 22135431 DOI: 10.1104/Pp.111.185033  1
2012 Muñoz-Diez C, Vitte C, Ross-Ibarra J, Gaut BS, Tenaillon MI. Using nextgen sequencing to investigate genome size variation and transposable element content Topics in Current Genetics. 24: 41-58. DOI: 10.1007/978-3-642-31842-9-3  1
2012 Muñoz-Diez C, Vitte C, Ross-Ibarra J, Gaut BS, Tenaillon MI. Using nextgen sequencing to investigate genome size variation and transposable element content Topics in Current Genetics. 24: 41-58. DOI: 10.1007/978-3-642-31842-9-3  1
2011 Morrell PL, Buckler ES, Ross-Ibarra J. Crop genomics: advances and applications. Nature Reviews. Genetics. 13: 85-96. PMID 22207165 DOI: 10.1038/Nrg3097  1
2011 Studer A, Zhao Q, Ross-Ibarra J, Doebley J. Identification of a functional transposon insertion in the maize domestication gene tb1. Nature Genetics. 43: 1160-3. PMID 21946354 DOI: 10.1038/Ng.942  1
2011 Tenaillon MI, Hufford MB, Gaut BS, Ross-Ibarra J. Genome size and transposable element content as determined by high-throughput sequencing in maize and Zea luxurians. Genome Biology and Evolution. 3: 219-29. PMID 21296765 DOI: 10.1093/Gbe/Evr008  1
2011 van Heerwaarden J, Doebley J, Briggs WH, Glaubitz JC, Goodman MM, de Jesus Sanchez Gonzalez J, Ross-Ibarra J. Genetic signals of origin, spread, and introgression in a large sample of maize landraces. Proceedings of the National Academy of Sciences of the United States of America. 108: 1088-92. PMID 21189301 DOI: 10.1073/Pnas.1013011108  1
2011 Hufford MB, Gepts P, Ross-Ibarra J. Influence of cryptic population structure on observed mating patterns in the wild progenitor of maize (Zea mays ssp. parviglumis). Molecular Ecology. 20: 46-55. PMID 21070423 DOI: 10.1111/J.1365-294X.2010.04924.X  1
2010 Eckert AJ, van Heerwaarden J, Wegrzyn JL, Nelson CD, Ross-Ibarra J, González-Martínez SC, Neale DB. Patterns of population structure and environmental associations to aridity across the range of loblolly pine (Pinus taeda L., Pinaceae). Genetics. 185: 969-82. PMID 20439779 DOI: 10.1534/Genetics.110.115543  1
2010 Shi J, Wolf SE, Burke JM, Presting GG, Ross-Ibarra J, Dawe RK. Widespread gene conversion in centromere cores. Plos Biology. 8: e1000327. PMID 20231874 DOI: 10.1371/Journal.Pbio.1000327  1
2010 Van Heerwaarden J, Ross-Ibarra J, Doebley J, Glaubitz JC, González Jde J, Gaut BS, Eguiarte LE. Fine scale genetic structure in the wild ancestor of maize (Zea mays ssp. parviglumis). Molecular Ecology. 19: 1162-73. PMID 20163543 DOI: 10.1111/J.1365-294X.2010.04559.X  1
2010 Whitney KD, Baack EJ, Hamrick JL, Godt MJ, Barringer BC, Bennett MD, Eckert CG, Goodwillie C, Kalisz S, Leitch IJ, Ross-Ibarra J. A role for nonadaptive processes in plant genome size evolution? Evolution; International Journal of Organic Evolution. 64: 2097-109. PMID 20148953 DOI: 10.1111/J.1558-5646.2010.00967.X  1
2010 Hollister JD, Ross-Ibarra J, Gaut BS. Indel-associated mutation rate varies with mating system in flowering plants. Molecular Biology and Evolution. 27: 409-16. PMID 19825943 DOI: 10.1093/Molbev/Msp249  1
2010 van Heerwaarden J, van Eeuwijk FA, Ross-Ibarra J. Genetic diversity in a crop metapopulation. Heredity. 104: 28-39. PMID 19738636 DOI: 10.1038/Hdy.2009.110  1
2010 Fuchs EJ, Ross-Ibarra J, Barrantes G. Reproductive biology of macleania rupestris (ericaceae), a pollen-limited neotropical cloud-forest species in Costa Rica Journal of Tropical Ecology. 26: 351-354. DOI: 10.1017/S0266467410000064  1
2009 May MR, Provance MC, Sanders AC, Ellstrand NC, Ross-Ibarra J. A Pleistocene clone of Palmer's oak persisting in Southern California. Plos One. 4: e8346. PMID 20041136 DOI: 10.1371/Journal.Pone.0008346  1
2009 Gore MA, Chia JM, Elshire RJ, Sun Q, Ersoz ES, Hurwitz BL, Peiffer JA, McMullen MD, Grills GS, Ross-Ibarra J, Ware DH, Buckler ES. A first-generation haplotype map of maize. Science (New York, N.Y.). 326: 1115-7. PMID 19965431 DOI: 10.1126/Science.1177837  1
2009 Zhang LB, Zhu Q, Wu ZQ, Ross-Ibarra J, Gaut BS, Ge S, Sang T. Selection on grain shattering genes and rates of rice domestication. The New Phytologist. 184: 708-20. PMID 19674325 DOI: 10.1111/J.1469-8137.2009.02984.X  1
2009 Ross-Ibarra J, Tenaillon M, Gaut BS. Historical divergence and gene flow in the genus Zea. Genetics. 181: 1399-413. PMID 19153259 DOI: 10.1534/Genetics.108.097238  1
2008 Ross-Ibarra J, Gaut BS. Multiple domestications do not appear monophyletic. Proceedings of the National Academy of Sciences of the United States of America. 105: E105; author reply E. PMID 19057016 DOI: 10.1073/Pnas.0809042105  1
2008 Lockton S, Ross-Ibarra J, Gaut BS. Demography and weak selection drive patterns of transposable element diversity in natural populations of Arabidopsis lyrata. Proceedings of the National Academy of Sciences of the United States of America. 105: 13965-70. PMID 18772373 DOI: 10.1073/Pnas.0804671105  1
2008 Ross-Ibarra J, Wright SI, Foxe JP, Kawabe A, DeRose-Wilson L, Gos G, Charlesworth D, Gaut BS. Patterns of polymorphism and demographic history in natural populations of Arabidopsis lyrata. Plos One. 3: e2411. PMID 18545707 DOI: 10.1371/Journal.Pone.0002411  1
2008 Gaut BS, Ross-Ibarra J. Selection on major components of angiosperm genomes. Science (New York, N.Y.). 320: 484-6. PMID 18436777 DOI: 10.1126/Science.1153586  1
2007 Ross-Ibarra J, Morrell PL, Gaut BS. Plant domestication, a unique opportunity to identify the genetic basis of adaptation. Proceedings of the National Academy of Sciences of the United States of America. 104: 8641-8. PMID 17494757 DOI: 10.1073/Pnas.0700643104  1
2007 Ross-Ibarra J. Genome size and recombination in angiosperms: a second look. Journal of Evolutionary Biology. 20: 800-6. PMID 17305845 DOI: 10.1111/J.1420-9101.2006.01275.X  1
2006 Wares JP, Barber PH, Ross-Ibarra J, Sotka EE, Toonen RJ. Mitochondrial DNA and population size. Science (New York, N.Y.). 314: 1388-90; author repl. PMID 17144000 DOI: 10.1126/science.314.5804.1388  1
2005 Ross-Ibarra J. Quantitative trait loci and the study of plant domestication. Genetica. 123: 197-204. PMID 15881692 DOI: 10.1007/S10709-004-2744-6  1
2004 Ross-Ibarra J. The evolution of recombination under domestication: a test of two hypotheses. The American Naturalist. 163: 105-12. PMID 14767840 DOI: 10.1086/380606  1
2003 Ross-Ibarra J. Origin and domestication of the chaya (Cnidoscolus aconitifolius Mill I. M. Johnst): The Mayan spinach | Origen y domesticación de la chaya (Cnidoscolus aconitifolius Mill I. M. Johnst): La espinaca Maya Mexican Studies - Estudios Mexicanos. 19: 287-302. DOI: 10.1525/msem.2003.19.2.287  1
2002 Ross-Ibarra J, Molina-Cruz A. The ethnobotany of chaya (Cnidoscolus aconitifolius ssp. aconitifolius Breckon): A nutritious Maya vegetable Economic Botany. 56: 350-365. DOI: 10.1663/0013-0001(2002)056[0350:Teocca]2.0.Co;2  1
2001 Neel MC, Ross-Ibarra J, Ellstrand NC. Implications of mating patterns for conservation of the endangered plant Eriogonum ovalifolium var. vineum (Polygonaceae). American Journal of Botany. 88: 1214-22. PMID 11454621 DOI: 10.2307/3558332  1
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