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Dynamic Patterns of Transcript Abundance of Transposable Element Families in Maize.

Anderson SN, Stitzer MC, Zhou P, Ross-Ibarra J, Hirsch CD, Springer NM.

G3 (Bethesda). 2019 Nov 5;9(11):3673-3682. doi: 10.1534/g3.119.400431.


Adaptive phenotypic divergence in an annual grass differs across biotic contexts.

O'Brien AM, Sawers RJH, Strauss SY, Ross-Ibarra J.

Evolution. 2019 Nov;73(11):2230-2246. doi: 10.1111/evo.13818. Epub 2019 Aug 26.


Transposable elements contribute to dynamic genome content in maize.

Anderson SN, Stitzer MC, Brohammer AB, Zhou P, Noshay JM, O'Connor CH, Hirsch CD, Ross-Ibarra J, Hirsch CN, Springer NM.

Plant J. 2019 Dec;100(5):1052-1065. doi: 10.1111/tpj.14489. Epub 2019 Sep 18.


Hybrid Decay: A Transgenerational Epigenetic Decline in Vigor and Viability Triggered in Backcross Populations of Teosinte with Maize.

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, Doebley JF.

Genetics. 2019 Sep;213(1):143-160. doi: 10.1534/genetics.119.302378. Epub 2019 Jul 18.


Characterization of introgression from the teosinte Zea mays ssp. mexicana to Mexican highland maize.

Gonzalez-Segovia E, Pérez-Limon S, Cíntora-Martínez GC, Guerrero-Zavala A, Janzen GM, Hufford MB, Ross-Ibarra J, Sawers RJH.

PeerJ. 2019 May 3;7:e6815. doi: 10.7717/peerj.6815. eCollection 2019.


Detecting Adaptive Differentiation in Structured Populations with Genomic Data and Common Gardens.

Josephs EB, Berg JJ, Ross-Ibarra J, Coop G.

Genetics. 2019 Mar;211(3):989-1004. doi: 10.1534/genetics.118.301786. Epub 2019 Jan 24.


Genetic architecture and selective sweeps after polygenic adaptation to distant trait optima.

Stetter MG, Thornton K, Ross-Ibarra J.

PLoS Genet. 2018 Nov 19;14(11):e1007794. doi: 10.1371/journal.pgen.1007794. eCollection 2018 Nov.


Evolutionary Responses to Conditionality in Species Interactions across Environmental Gradients.

O'Brien AM, Sawers RJH, Ross-Ibarra J, Strauss SY.

Am Nat. 2018 Dec;192(6):715-730. doi: 10.1086/700118. Epub 2018 Oct 31.


Maize domestication and gene interaction.

Stitzer MC, Ross-Ibarra J.

New Phytol. 2018 Oct;220(2):395-408. doi: 10.1111/nph.15350. Epub 2018 Jul 23. Review.


Parallel altitudinal clines reveal trends in adaptive evolution of genome size in Zea mays.

Bilinski P, Albert PS, Berg JJ, Birchler JA, Grote MN, Lorant A, Quezada J, Swarts K, Yang J, Ross-Ibarra J.

PLoS Genet. 2018 May 10;14(5):e1007162. doi: 10.1371/journal.pgen.1007162. eCollection 2018 May.


A Kinesin-14 Motor Activates Neocentromeres to Promote Meiotic Drive in Maize.

Dawe RK, Lowry EG, Gent JI, Stitzer MC, Swentowsky KW, Higgins DM, Ross-Ibarra J, Wallace JG, Kanizay LB, Alabady M, Qiu W, Tseng KF, Wang N, Gao Z, Birchler JA, Harkess AE, Hodges AL, Hiatt EN.

Cell. 2018 May 3;173(4):839-850.e18. doi: 10.1016/j.cell.2018.03.009. Epub 2018 Apr 5.


Adaptation in plant genomes: Bigger is different.

Mei W, Stetter MG, Gates DJ, Stitzer MC, Ross-Ibarra J.

Am J Bot. 2018 Jan;105(1):16-19. doi: 10.1002/ajb2.1002. Epub 2018 Feb 13. No abstract available.


Construction of the third-generation Zea mays haplotype map.

Bukowski R, Guo X, Lu Y, Zou C, He B, Rong Z, Wang B, Xu D, Yang B, Xie C, Fan L, Gao S, Xu X, Zhang G, Li Y, Jiao Y, Doebley JF, Ross-Ibarra J, Lorant A, Buffalo V, Romay MC, Buckler ES, Ware D, Lai J, Sun Q, Xu Y.

Gigascience. 2018 Apr 1;7(4):1-12. doi: 10.1093/gigascience/gix134.


The interplay of demography and selection during maize domestication and expansion.

Wang L, Beissinger TM, Lorant A, Ross-Ibarra C, Ross-Ibarra J, Hufford MB.

Genome Biol. 2017 Nov 13;18(1):215. doi: 10.1186/s13059-017-1346-4.


Incomplete dominance of deleterious alleles contributes substantially to trait variation and heterosis in maize.

Yang J, Mezmouk S, Baumgarten A, Buckler ES, Guill KE, McMullen MD, Mumm RH, Ross-Ibarra J.

PLoS Genet. 2017 Sep 27;13(9):e1007019. doi: 10.1371/journal.pgen.1007019. eCollection 2017 Sep.


How to make a domesticate.

Stetter MG, Gates DJ, Mei W, Ross-Ibarra J.

Curr Biol. 2017 Sep 11;27(17):R896-R900. doi: 10.1016/j.cub.2017.06.048.


The potential role of genetic assimilation during maize domestication.

Lorant A, Pedersen S, Holst I, Hufford MB, Winter K, Piperno D, Ross-Ibarra J.

PLoS One. 2017 Sep 8;12(9):e0184202. doi: 10.1371/journal.pone.0184202. eCollection 2017.


Allele specific expression analysis identifies regulatory variation associated with stress-related genes in the Mexican highland maize landrace Palomero Toluqueño.

Aguilar-Rangel MR, Chávez Montes RA, González-Segovia E, Ross-Ibarra J, Simpson JK, Sawers RJH.

PeerJ. 2017 Aug 23;5:e3737. doi: 10.7717/peerj.3737. eCollection 2017.


Advances and Limits of Using Population Genetics to Understand Local Adaptation: (Trends in Ecology & Evolution 29, 673-680; 2014).

Tiffin P, Ross-Ibarra J.

Trends Ecol Evol. 2017 Oct;32(10):801-802. doi: 10.1016/j.tree.2017.08.001. Epub 2017 Aug 17. No abstract available.


Genomic estimation of complex traits reveals ancient maize adaptation to temperate North America.

Swarts K, Gutaker RM, Benz B, Blake M, Bukowski R, Holland J, Kruse-Peeples M, Lepak N, Prim L, Romay MC, Ross-Ibarra J, Sanchez-Gonzalez JJ, Schmidt C, Schuenemann VJ, Krause J, Matson RG, Weigel D, Buckler ES, Burbano HA.

Science. 2017 Aug 4;357(6350):512-515. doi: 10.1126/science.aam9425.


Improved maize reference genome with single-molecule technologies.

Jiao Y, Peluso P, Shi J, Liang T, Stitzer MC, Wang B, Campbell MS, Stein JC, Wei X, Chin CS, Guill K, Regulski M, Kumari S, Olson A, Gent J, Schneider KL, Wolfgruber TK, May MR, Springer NM, Antoniou E, McCombie WR, Presting GG, McMullen M, Ross-Ibarra J, Dawe RK, Hastie A, Rank DR, Ware D.

Nature. 2017 Jun 22;546(7659):524-527. doi: 10.1038/nature22971. Epub 2017 Jun 12.


Genomic abundance is not predictive of tandem repeat localization in grass genomes.

Bilinski P, Han Y, Hufford MB, Lorant A, Zhang P, Estep MC, Jiang J, Ross-Ibarra J.

PLoS One. 2017 Jun 1;12(6):e0177896. doi: 10.1371/journal.pone.0177896. eCollection 2017.


Gene Fractionation and Function in the Ancient Subgenomes of Maize.

Renny-Byfield S, Rodgers-Melnick E, Ross-Ibarra J.

Mol Biol Evol. 2017 Aug 1;34(8):1825-1832. doi: 10.1093/molbev/msx121.


Genome Sequence of a 5,310-Year-Old Maize Cob Provides Insights into the Early Stages of Maize Domestication.

Ramos-Madrigal J, Smith BD, Moreno-Mayar JV, Gopalakrishnan S, Ross-Ibarra J, Gilbert MTP, Wales N.

Curr Biol. 2016 Dec 5;26(23):3195-3201. doi: 10.1016/j.cub.2016.09.036. Epub 2016 Nov 17.


Evolutionary Genomics of Peach and Almond Domestication.

Velasco D, Hough J, Aradhya M, Ross-Ibarra J.

G3 (Bethesda). 2016 Dec 7;6(12):3985-3993. doi: 10.1534/g3.116.032672.


angsd-wrapper: utilities for analysing next-generation sequencing data.

Durvasula A, Hoffman PJ, Kent TV, Liu C, Kono TJ, Morrell PL, Ross-Ibarra J.

Mol Ecol Resour. 2016 Nov;16(6):1449-1454. doi: 10.1111/1755-0998.12578. Epub 2016 Aug 29.


Recent demography drives changes in linked selection across the maize genome.

Beissinger TM, Wang L, Crosby K, Durvasula A, Hufford MB, Ross-Ibarra J.

Nat Plants. 2016 Jun 13;2:16084. doi: 10.1038/nplants.2016.84.


High Quality Maize Centromere 10 Sequence Reveals Evidence of Frequent Recombination Events.

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.

Front Plant Sci. 2016 Mar 23;7:308. doi: 10.3389/fpls.2016.00308. eCollection 2016.


Maize diversity associated with social origin and environmental variation in Southern Mexico.

Orozco-Ramírez Q, Ross-Ibarra J, Santacruz-Varela A, Brush S.

Heredity (Edinb). 2016 May;116(5):477-84. doi: 10.1038/hdy.2016.10. Epub 2016 Feb 24.


Seed filling in domesticated maize and rice depends on SWEET-mediated hexose transport.

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.

Nat Genet. 2015 Dec;47(12):1489-93. doi: 10.1038/ng.3422. Epub 2015 Nov 2.


Correction: Transposable Elements Contribute to Activation of Maize Genes in Response to Abiotic Stress.

Makarevitch I, Waters AJ, West PT, Stitzer M, Hirsch CN, Ross-Ibarra J, Springer NM.

PLoS Genet. 2015 Oct 9;11(10):e1005566. doi: 10.1371/journal.pgen.1005566. eCollection 2015 Oct. No abstract available.


The Genomic Impacts of Drift and Selection for Hybrid Performance in Maize.

Gerke JP, Edwards JW, Guill KE, Ross-Ibarra J, McMullen MD.

Genetics. 2015 Nov;201(3):1201-11. doi: 10.1534/genetics.115.182410. Epub 2015 Sep 18.


Independent Molecular Basis of Convergent Highland Adaptation in Maize.

Takuno S, Ralph P, Swarts K, Elshire RJ, Glaubitz JC, Buckler ES, Hufford MB, Ross-Ibarra J.

Genetics. 2015 Aug;200(4):1297-312. doi: 10.1534/genetics.115.178327. Epub 2015 Jun 15.


Natural variation in teosinte at the domestication locus teosinte branched1 (tb1).

Vann L, Kono T, Pyhäjärvi T, Hufford MB, Ross-Ibarra J.

PeerJ. 2015 Apr 16;3:e900. doi: 10.7717/peerj.900. eCollection 2015.


Genetic, evolutionary and plant breeding insights from the domestication of maize.

Hake S, Ross-Ibarra J.

Elife. 2015 Mar 25;4. doi: 10.7554/eLife.05861. Review.


Transposable elements contribute to activation of maize genes in response to abiotic stress.

Makarevitch I, Waters AJ, West PT, Stitzer M, Hirsch CN, Ross-Ibarra J, Springer NM.

PLoS Genet. 2015 Jan 8;11(1):e1004915. doi: 10.1371/journal.pgen.1004915. eCollection 2015 Jan. Erratum in: PLoS Genet. 2015 Oct;11(10):e1005566.


The origin and evolution of maize in the Southwestern United States.

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, Nielsen R, Hufford MB, Albrechtsen A, Ross-Ibarra J, Gilbert MT.

Nat Plants. 2015 Jan 8;1:14003. doi: 10.1038/nplants.2014.3.


Reply to Brush et al.: Wake-up call for crop conservation science.

Dyer GA, López-Feldman A, Yúnez-Naude A, Taylor JE, Ross-Ibarra J.

Proc Natl Acad Sci U S A. 2015 Jan 6;112(1):E2. doi: 10.1073/pnas.1422645112. Epub 2014 Dec 29. No abstract available.


Advances and limits of using population genetics to understand local adaptation.

Tiffin P, Ross-Ibarra J.

Trends Ecol Evol. 2014 Dec;29(12):673-80. doi: 10.1016/j.tree.2014.10.004. Epub 2014 Nov 1. Review. Erratum in: Trends Ecol Evol. 2017 Oct;32(10 ):801-802.


Diversity and evolution of centromere repeats in the maize genome.

Bilinski P, Distor K, Gutierrez-Lopez J, Mendoza GM, Shi J, Dawe RK, Ross-Ibarra J.

Chromosoma. 2015 Mar;124(1):57-65. doi: 10.1007/s00412-014-0483-8. Epub 2014 Sep 5.


The pattern and distribution of deleterious mutations in maize.

Mezmouk S, Ross-Ibarra J.

G3 (Bethesda). 2014 Jan 10;4(1):163-71. doi: 10.1534/g3.113.008870.


Comprehensive analysis of imprinted genes in maize reveals allelic variation for imprinting and limited conservation with other species.

Waters AJ, Bilinski P, Eichten SR, Vaughn MW, Ross-Ibarra J, Gehring M, Springer NM.

Proc Natl Acad Sci U S A. 2013 Nov 26;110(48):19639-44. doi: 10.1073/pnas.1309182110. Epub 2013 Nov 11.


Complex patterns of local adaptation in teosinte.

Pyhäjärvi T, Hufford MB, Mezmouk S, Ross-Ibarra J.

Genome Biol Evol. 2013;5(9):1594-609. doi: 10.1093/gbe/evt109.


From many, one: genetic control of prolificacy during maize domestication.

Wills DM, Whipple CJ, Takuno S, Kursel LE, Shannon LM, Ross-Ibarra J, Doebley JF.

PLoS Genet. 2013 Jun;9(6):e1003604. doi: 10.1371/journal.pgen.1003604. Epub 2013 Jun 27.


Agriculture: Feeding the future.

McCouch S, Baute GJ, Bradeen J, Bramel P, Bretting PK, Buckler E, Burke JM, Charest D, Cloutier S, Cole G, Dempewolf H, Dingkuhn M, Feuillet C, Gepts P, Grattapaglia D, Guarino L, Jackson S, Knapp S, Langridge P, Lawton-Rauh A, Lijua Q, Lusty C, Michael T, Myles S, Naito K, Nelson RL, Pontarollo R, Richards CM, Rieseberg L, Ross-Ibarra J, Rounsley S, Hamilton RS, Schurr U, Stein N, Tomooka N, van der Knaap E, van Tassel D, Toll J, Valls J, Varshney RK, Ward J, Waugh R, Wenzl P, Zamir D.

Nature. 2013 Jul 4;499(7456):23-4. doi: 10.1038/499023a. No abstract available.


The genomic signature of crop-wild introgression in maize.

Hufford MB, Lubinksy P, Pyhäjärvi T, Devengenzo MT, Ellstrand NC, Ross-Ibarra J.

PLoS Genet. 2013 May;9(5):e1003477. doi: 10.1371/journal.pgen.1003477. Epub 2013 May 9.


Diversity and abundance of the abnormal chromosome 10 meiotic drive complex in Zea mays.

Kanizay LB, Pyhäjärvi T, Lowry EG, Hufford MB, Peterson DG, Ross-Ibarra J, Dawe RK.

Heredity (Edinb). 2013 Jun;110(6):570-7. doi: 10.1038/hdy.2013.2. Epub 2013 Feb 27.


Comparative analysis of tandem repeats from hundreds of species reveals unique insights into centromere evolution.

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, Korf I, Chan SW.

Genome Biol. 2013 Jan 30;14(1):R10. doi: 10.1186/gb-2013-14-1-r10.


Teosinte as a model system for population and ecological genomics.

Hufford MB, Bilinski P, Pyhäjärvi T, Ross-Ibarra J.

Trends Genet. 2012 Dec;28(12):606-15. doi: 10.1016/j.tig.2012.08.004. Epub 2012 Sep 27. Review.


Historical genomics of North American maize.

van Heerwaarden J, Hufford MB, Ross-Ibarra J.

Proc Natl Acad Sci U S A. 2012 Jul 31;109(31):12420-5. doi: 10.1073/pnas.1209275109. Epub 2012 Jul 16.

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