Saint Louis University *graduate student **undergraduate student / Allison's Google Scholar Page
Preprints and manuscripts in review/revision
Migicovsky Z, Swift JF, Helget Z, Klein LL, Ly A, Maimaitiyiming M, Woodhouse K, Fennell A, Kwasniewski M, Miller AJ, Chitwood DH, Cousins P. Grapevine leaf size influences vine canopy temperature. In revision. https://www.biorxiv.org/content/10.1101/2022.07.07.499216v1.
Risano** AM, Bergh E, Sandoval M, Selby** S, Sherrod S, Ciotir C, Herron* S, Rubin MJ, Miller AJ. Herbaria as a resource for evaluating trait variation and covariation in perennial crop candidate species. In revision.
Swift* JF, Migicovsky Z, Trello GE, Miller AJ. Grapevine bacterial communities across the Central Valley of California. In revision. https://www.biorxiv.org/content/10.1101/2023.07.01.547327v1.
Williams* BR, Edwards CE, Miller AJ. Epigenomic patterns reflect grafting and irrigation in the grapevine clone ‘Chambourcin’. https://www.biorxiv.org/content/10.1101/2020.09.09.290072v1.
2023
Williams* B, Miller A, Edwards, C. 2022. How do threatened plant species with low genetic diversity respond to environmental stress? Insights from comparative conservation epigenomics and phenotypic plasticity. Accpeted pending minor revisions.
Patel S, Harris ZN, Londo JP, Miller AJ, Fennel AF. 2023. Genome assembly of the hybrid grapevine ‘Chambourcin.’ Gigabyte. https://doi.org/10.46471/gigabyte.84
DeHaan LR, Anderson JA, Bajgain P, Basche A, Cattani DJ, Crain J, Crews TE, David C, Duchene O, Gutknecht J, Hayes RC, Hu F, Jungers JM, Knudsen S, Kong W, Larson S, Lundquist P-O, luo Guangbin, Miller AJ, Nabukalu P, Newell MT, Olsson L, Palmgren M, Paterson AH, Picasso VD, Poland JA, Sacks EJ, Wang S, Westerbergh A. 2023. Discussion: Prioritize perennial grain development for sustainable food production and environmental benefits. Science of the Total Environment 895: 15 October 2023, 164975. https://doi.org/10.1016/j.scitotenv.2023.164975.
To access: https://www.sciencedirect.com/science/article/pii/S0048969723035982?dgcid=coauthor
Karabulut E, Kerkoç K, Aci M, Al M, Aydin M, Barriball S, Braley J, Casetta E, Craine E, Diaz-Garcia L, Hershberer J, Meyering B, Miller AJ, Rubin MJ, Tesdell O, Van Tassel D, Schlautman Sakiroglu M. 2023. Sainfoin (Onobrychis sp.) crop ontology: supporting germplasm characterization and international research collaborations. Frontiers in Plant Science. 2023:14. https://doi.org/10.3389/fpls.2023.1177406
Interdisciplinary Plant Science Consortium. 2023. Inclusive collaboration across plant physiology and genomics: Now is the Time! In press. Plant Direct 7(5): e493. https://doi.org/10.1002/pld3.493
Harris* ZN, JE Pratt, LG Kovacs, LL Klein, MT Kwasniewski, JP Londo, A Wu, AJ Miller. 2023. Differential modulation of scion gene expression in grapevines is driven by rootstock and environment interaction. BMC Plant Biology 23:211. https://doi.org/10.1186/s12870-023-04223-w.
2022
Carley C, Chen G, Das KK, Delory BM, Simitrova A, Ding Y, Geoge AP, Greeley LA, Han Q, Hendriks P-W, Hernandez-Soriano MC, Li M, Ng LJP, Mau L, Mesa-Marin J, Miller A, Rae A, Schmidt J, Thies A, Topp CN, Wacker TS, Wang P, Wang X, Xie L, Zheng C. 2022. Root biology never sleeps. New Phytologist 235:2149–2154.
Harris* ZN, Pratt** JE, Bhakta N, Frawley E, Klein LL, Kwasniewski MT, Migicovsky Z, Miller AJ. 2022. Temporal and environmental factors interact with rootstock genotype to shape leaf elemental composition in grafted grapevines. Plant Direct. DOI: 10.1002/pld3.440. https://www.biorxiv.org/content/10.1101/2022.02.28.482393v1
Khoury CK, Brush S, Costich D, Curry HA, de Haan S, Englels JMM, Guarino L, Hoban S, Mercer K, Miller AJ, Nabhan GP, Perales HR, Richards C, Riggins C, Thormann I. 2022. Crop genetic erosion: understanding and responding to loss of crop diversity. New Phytologist. https://doi.org/10.1111/nph.17733
Linan* AG, Lowry II PP, Miller AJ, Schatz GE, Sevathian JC, Edwards CE. 2022. Interspecific hybridization and island colonization history, not rarity, most strongly affect the genetic diversity in Diospyros, a clade of Mascarene-Endemic Trees. Journal of Heredity 113 (3), 336-352
Migicovksy Z, Swift* JF, Helget Z, Klein LL, Ly A, Maimaitiyiming M, Woodhouse A, Fennell A, Kwasniewski M, Miller AJ, Cousins P, Chitwood DH. 2022. Increases in vein length compensate for leaf area lost to lobing in grapevine. American Journal of Botany. DOI: 10.1002/ajb2.16033. https://www.biorxiv.org/content/10.1101/2022.03.15.484490v1.
Van Tassel D, DeHaan L, Diaz-Garcia L, Rubin M, Schlautman B, Turner K, Miller A. Reimagining crop domestication in the era of high throughput phenomics. Current Opinion in Plant Biology 65, 102150. https://doi.org/10.1016/j.pbi.2021.102150
2021
Harris* ZA, Klein LL, Awale M, Swift J, Migicovsky Z, Bhakta N, Frawley E, Chitwood DH, Fennell A, Kovacs LG, Kwasniewski M, Londo JP, Ma Q and Miller AJ. Root system influence on high dimensional leaf phenotypes over the grapevine growing season. GigaScience. https://doi.org/10.1093/gigascience/giab087
Griffiths M, Delory B, Jawahir V, Wong K, Bagnall GC, Dowd T, Nusinow D, Miller A, Topp C. Optimization of root traits to provide enhanced ecosystem services in agricultural systems: a focus on cover crops. Plant, Cell and Environment. https://doi.org/10.1111/pce.14247
Herron* SA, Rubin MJ, Albrecht MA, Long QG, Sandoval MC, Miller AJ. Seed and growth trait patterns in wild annual and herbaceous perennial species of Lathyrus, Phaseolus, and Vicia (Fabaceae). American Journal of Botany. https://doi.org/10.1002/ajb2.1773
Swift* JF, Hall ME, Kwasniewski MT, Miller AJ. Rootstock genotype impacts microbiome diversity and composition across the root and shoot system of grafted grapevines. Microorganisms 9(1): 92. https://doi.org/10.3390/microorganisms9010092
Linan*, A., P. Lowry, A. Miller G. Schatz, J.-C. Sevathian, C. Edwards. RAD-seq reveals patterns of diversification, hybridization, and the accumulation of reproductive isolation in a clade of partially sympatric, tropical island trees. Molecular Ecology 30 (18), 4520-4537.
2020
Maimaitiyiming M, Sagan V, Sidike P, Maimaitijiang M, Miller AJ, Kwasniewski M. 2020. Leveraging very high spatial resolution hyperspectral and thermal UAV imageries for characterizing diurnal grapevine physiology. Accepted. International Journal of Applied Earth Observation and Geoinformation.
Herron* SA, Rubin MJ, Ciotir EC, Crews TE, Van Tassel DL, Miller AJ. 2020 Seed size, germination, and vegetative allocation in first-year annual and herbaceous perennial crops and their wild relatives in Lupinus and Phaseolus (Fabaceae). Frontiers Plant Science. https://doi.org/10.3389/fpls.2020.00034
Frawley ES, Micke**B, Ciotir C, Rubin MJ, Miller AJ. 2020. An ethnobotanical study of the genus Elymus. Economic Botany. 74, 159–177. https://doi.org/10.1007/s12231-020-09494-0
Khoury CK, Greene SL, Krishnan S, Miller AJ, Moreau T, Williams KA, Rodriguez-Bonilla L, Spurrier CS, Zalapa J, Nabhan GP. 2020. Toward integrated conservation of North America’s Crop Wild Relatives. Natural Areas Journal 40(1): 96-100.
2019
Migicovsky, Z., E. Warschefsky, L. Klein, A. J. Miller. 2019. Using Living Germplasm Collections to Understand, Improve, and Conserve Woody Perennials. Crop Science. https://doi.org/10.2135/cropsci2019.05.0353
Li M, Klein L, Duncan K, Jiang N, Chitwood DH, Londo J, Miller A, Topp C. Characterizing grapevine (Vitis spp.) inflorescence architecture using X-ray imaging: implications for understanding cluster density. Journal of Experimental Botany 70(21): 6261-6276. https://doi.org/10.1093/jxb/erz394
Gaut, BS, Miller AJ, Seymour DK. 2019. Living with two genomes: Grafting and its Implications for Plant Genome-to-
Genome Interactions, Phenotypic Variation and Evolution. Annual Reviews in Genetics. doi: 10.1146/annurev-genet-112618-043545.
Khoury CK, Greene SL, Krishnan S, Miller AJ, Moreau T. 2019. A Road Map for Conservation, Use, and Public Engagement around North America’s Crop Wild Relatives and Wild Utilized Plants. In press. Crop Science. 59:1–6 (2019).
Khoury CK, Kantar M, Barber E, Kisel Y, Ricciardi V, Klirs C, Kucera L, Mehrabi Z, Johnson N, Klabin S, Valiño A, Nowakoski K, Bartomeus I, Ramankutty N, Miller A, Schipanski M, Gore MA, Novy A. 2019. Science – graphic art partnerships to increase research impact. Commmunications Biology 2(295).
Linan*, A., Lowry, Miller, A.J., P., Schatz, G. and Edwards C.E. 2019. Ebony and the Mascarenes: the evolutionary relationships and biogeography of Diospyros L. (Ebenaceae) in the western Indian Ocean. Botanical Journal of the Linnean Society. 190(4): 359 – 373.
Schier* HE, Eliot KA, Herron* SA, Landfried LK, Migicovsy Z, Rubin MJ, Miller AJ. 2019. Comparative analysis of perennial and annual Phaseolus seed nutrient concentrations. Sustainability 11(10): 2787https://www.biorxiv.org/content/10.1101/612010v1
Migicovsky, Z., Harris*, Z.N., Klein. L.L, Li, M., McDermaid, A., Chitwood, D.H., Fennell, A., Kovacs, L.G., Kwasniewski, M., Londo, J.P., Ma, Q., Miller, A.J. 2019. Rootstock effects on scion phenotypes in a ‘Chambourcin’ experimental vineyard. Horticulture Research 6: 64 https://www.nature.com/articles/s41438-019-0146-2
Ciotir, C., Applequist, W., Crews, T.E., Cristea, N., DeHaan L.R., Frawley, E., Herron*, S., Magill, R., Miller, J., Roskov, Y., Schlautman, B., Solomon, J., Townesmith, A., Van Tassel, D., Zarucchi, J., Miller, A.J. 2019. Building a botanical foundation for the ecological intensification of agriculture: global inventory of wild, perennial herbaceous Fabaceae species. 2019. Plants, People, Planet. DOI: 10.1002/ppp3.37. https://nph.onlinelibrary.wiley.com/doi/abs/10.1002/ppp3.37.
Monier, B., A. McDermaid, J. Zhao, A. Miller, A. Fennell, and Q. Ma. 2019. IRIS-EDA: interactive RNA-seq data interpretation using Shiny for differentially gene expression analysis. PLoS Computational Biology. DOI: https://doi.org/10.1101/283341.
2018
Li, M., An, H., Angelovici, R., Bagaza, C. Batushansky, A., Clark, L., Coneva, V., Donoghue, M., Edwards, E., Fajardo, D. Fang, H., Frank, M., Gallaher, T., Gebken, S., Hill, T. Jansky, S., Kaur, B., Klahs, P. Klein, L. Kuraparthy, V., Londo, J., Migicovsky, Z., Miller, A., Mohn, R., Myles, S., Otoni, W., Pires, C.J., Riffer, E., Schmerler, S., Spriggs, E., Topp, C., Van Deynze, A., Zhang, K., Zhu, L., Zink, B.M., Chitwood, D.H. 2018. Topological data analysis as a morphometric method: using persistent homology to demarcate a leaf morphospace. Frontiers in Plant Science 9: 553.
Schlautman, B., S. Barribal, C. Ciotir, S. Herron*, and A. J. Miller. 2018. Perennial Grain Legume Domestication Phase I: Criteria for Candidate Species Selection. Sustainability. 10, 730; doi:10.3390/su10030730
Klein*, L.K., Miller, A.J., Ciotir, E.C., S. Uribe-Convers, Londo, J.P. 2018. High-throughput sequencing data clarify evolutionary relationships among North American Vitis species and improve identification in USDA Vitis germplasm collections. American Journal of Botany 105(2): 215 – 226.
2017
Klein* L, Caito** M, Chapnick** C, Kitchen** C, O’Hanlon** R, Chitwood D, and A Miller. 2017. Digital morphometrics of two North American grapevines: assessing leaf variation within and among individuals, and among species (Vitaceae). Frontiers in Plant Science. doi: 10.3389/fpls.2017.00373.
2016
Walters SA, Bernhardt P, Joseph** M, and Miller AJ. 2016. Compatible and Self-Incompatible Flowering Systems in Horseradish. Plant Breeding. DOI: 10.1111/pbr.12413.
McAllister* CA and Miller AJ. 2016. SNP discovery via genotyping-by-sequencing for assessment of population genetic structure and recurrent polyploidization in big bluestem (Andropogon gerardii). American Journal of Botany 103(7): 1314-1325.
Migicovsky, Z., Sawler, J., Money, D., Eibach, R., Miller, A.J., Luby, J.J., Jamieson, A.R., Velasco, D., von Kintzel, S., Warner, J., Wührer, W., Brown, P.J., and Myles, S. 2016. Genomic ancestry estimation quantifies use of wild species in grape breeding. BMC Genomics 17(1)
Miller AJ and BL Gross. 2016. Report from the International Plant and Animal Genome Meeting. Invited Letter to the Editor for American Journal of Botany 103(6): 982 – 985. .
Callen* ST, Klein* LL, and Miller AJ. 2016. Climatic niche characterization of 13 North American Vitis species. American Journal of Enology and Viticulture 67: 339-349.
DeHaan L, VanTassel D, Anderson J, Asselin S. Barnes R, Baute G, Cattani G, Culman S, Dorn K, Hulke B, Kantar M, Larson S, Marks M, Miller A, Poland J, Ravetta D, Rude E, Ryan M, Wyse D, and Zhang X. 2016. A pipeline strategy for crop domestication. Crop Science 56: 917 – 930.
Warschefsky E, Klein* L, Frank M, Chitwood D, Londo J, von Wettberg E, and Miller AJ. 2016. Rootstocks: diversity, domestication, and impacts on shoot phenotypes. Trends in Plant Science 21(5): 418-437. DOI: http://dx.doi.org/10.1016/j.tplants.2015.11.008.
Maimaitiyiming* M, Miller AJ, and Wulamu A. 2016. Discriminating spectral signatures among and within two closely related grapevine species. Photogrammetric Engineering and Remote Sensing 82(1): 51-62. DOI: 10.14358/PERS.82.2.51
Chitwood DH, Klein* LL, O'Hanlon** R, Chacko** S, Greg** M, Kitchen** C, Miller AJ, and Londo JP 2016. Leaves as composites of latent developmental and evolutionary shapes. New Phytologist 210: 343-355. doi:10.1111/nph.13754.
2015
Miller AJ, Novy A., Glover J, Maul J, Kellogg EA, Raven P and Wyse Jackson P. 2015. Expanding the role of botanical gardens in the future of food. Nature Plants 1:15078.
Pap D, Londo J, Miller AJ, and Kovacs L. 2015. Population structure of Vitis rupestris, an important but vanishing resource for grape breeding. American Journal of Enology and Viticulture 66:403-410 doi:10.5344/ajev.2015.15012.
Callen* ST and Miller AJ. 2015. Signatures of niche conservatism and niche shift in the North American kudzu (Pueraria montana) invasion). Diversity and Distributions 21(8): 853-863. DOI: 10.1111/ddi.12341.
Pell SK, Mitchell JD, and Miller AJ. 2015. Anacardiaceae. In Flora of North America.
McAllister* C, Blaine R, Kron P, Bennett B, Garrett H, Kidson J, Matzenbacher B, Glotzbach A, and Miller AJ. 2015. Environmental correlates of cytotype distribution in Andropogon gerardii. American Journal of Botany 102(1): 92 – 102.
2014
Gross BL, Kellogg EA, and Miller AJ. 2014. Speaking of food: connecting basic and applied science. American Journal of Botany 101: 1597 – 1600.
Gross BL and Miller AJ. 2014. From field to table: perspectives and potential for perennial fruit domestication. Proceedings from the Perennial Crop Workshop, Food and Agriculture Organization.
Hancock J, and Miller AJ. 2014. Crop Plants: Evolution. Encyclopedia of Life Sciences. John Wiley and Sons. DOI: 10.1002/9780470015902.a0003360.pub2.
Albrecht MA, Broecker** JA, Romero-Hernandez* C, and Miller AJ. 2014. Conservation genetics of edaphic endemics in naturally isolated habitats: a case study with Geocarpon minimum (Caryophyllaceae). Journal of the Torrey Botanical Society 141(1): 1-13.
2013
Miller AJ, Matasci N, Schwaninger H, Aradhya M, Prins B, Zhong G-Y, Simon C, Buckler E, and Myles S. 2013. Vitis phylogenomics: hybridization intensities from a SNP array outperform genotype calls. PLOS ONE 8(11): e78680.
2012 and earlier
Miller AJ. 2012. Out of the cold- how big and how old? Genetic fingerprinting reveals how long-lived individuals withstand climatic oscillations in the arctic-alpine. Molecular Ecology 21(5): 1036-7.
Miller AJ. 2011. Wealth of Crop Relatives: Genomic and Breeding Resources. Spondias purpurea and its sympatric wild relatives in Mesoamerica. Chittaranjan Kole, Editor. Springer-Verlag, Berlin, Germany.
Miller AJ and Gross BL. 2011. Forest to Field: Perennial fruit crop domestication. American Journal of Botany 98(9): 1389-1414.
Grauke LJ, Mendoza-Herrera MA, Miller AJ, and Wood BW. 2011. Geographic patterns of genetic variation in native pecan populations (Carya illinoinensis). Tree Genetics and Genomes 7:917-932.
Pell S, Mitchell JD, Miller AJ, and Lobova TA. 2011. Anacardiaceae. The Families and Genera of Vascular Plants. K. Kubitzki, ed. Springer-Verlag, Heidelberg, Germany.
Gunn BF, Aradhya M, Salick J, Miller A, Yongping Y, Lin L, and Xian H. 2010. Genetic variation in walnuts (Juglans sigillata Dode and J. regia L., Juglandaceae): species distinctions, human impacts, and agrobiodiversity conservation in Yunnan, China. American Journal of Botany 97(4): 660-671.
Sampliner* DS and Miller AJ. 2009. Ethnobotany of horseradish: reproductive biology and local uses of Armoracia species (Brassicaceae) in their native ranges. Economic Botany 63(3): 303-313.
Miller AJ. 2008. Characterization of the Spondias purpurea lineage in Mesoamerica based on nuclear and chloroplast sequence data. Journal of the Torrey Botanical Society. 135(4): 463-474.
Miller AJ. 2007. Crop Plants: Evolution. Encyclopedia of Life Sciences. John Wiley and Sons.
Yi T, Miller AJ, and Wen J. 2007. The phylogeny of Rhus (Ancardiaceae) based on sequences of nuclear NIA-i3 intron and chloroplast trnC-D suggests reticulate evolution. Systematic Botany 32(2): 379-391.
Miller AJ and Knouft JH. 2006. GIS-based characterization of the wild and cultivated niches of a Mesoamerican fruit tree, Spondias purpurea (Anacardiaceae). American Journal of Botany 93(12): 1757-1767.
Miller AJ and Schaal BA. 2006. Domestication and the distribution of genetic variation in wild and cultivated populations of the Mesoamerican fruit tree Spondias purpurea L. (Anacardiaceae). Molecular Ecology 15: 1467-1480.
Miller AJ and Schaal BA. 2005. Domestication of a Mesoamerican cultivated fruit tree. Proceedings of the National Academy of Science 102 (36): 12801-12806.
Yi T, Miller AJ and Wen J. 2004. Phylogenetic and biogeographic diversification of Rhus (Anacardiaceae) in the Northern Hemisphere. Molecular Phylogenetics and Evolution 33 (3): 861-879.
Miller AJ, Wen J, and Young DA. 2001. Systematics of Rhus: Phylogenetic and biogeographic inferences based on ITS sequence data. International Journal of Plant Sciences 162(6): 1401-1407.
Kiss JZ, Guisinger MM, Miller AJ. 1997. What is the threshold amount of starch necessary for full gravitropic sensitivity? Advances in Space Research 21: 1197-1202.
Kiss JZ, Guisinger MM, Miller AJ, and Stackhouse KS. 1997. Reduced gravitropism in hypocotyls of starch-deficient mutants of Arabidopsis. Plant and Cell Physiology 38(5): 518-525.
Migicovsky Z, Swift JF, Helget Z, Klein LL, Ly A, Maimaitiyiming M, Woodhouse K, Fennell A, Kwasniewski M, Miller AJ, Chitwood DH, Cousins P. Grapevine leaf size influences vine canopy temperature. In revision. https://www.biorxiv.org/content/10.1101/2022.07.07.499216v1.
Risano** AM, Bergh E, Sandoval M, Selby** S, Sherrod S, Ciotir C, Herron* S, Rubin MJ, Miller AJ. Herbaria as a resource for evaluating trait variation and covariation in perennial crop candidate species. In revision.
Swift* JF, Migicovsky Z, Trello GE, Miller AJ. Grapevine bacterial communities across the Central Valley of California. In revision. https://www.biorxiv.org/content/10.1101/2023.07.01.547327v1.
Williams* BR, Edwards CE, Miller AJ. Epigenomic patterns reflect grafting and irrigation in the grapevine clone ‘Chambourcin’. https://www.biorxiv.org/content/10.1101/2020.09.09.290072v1.
2023
Williams* B, Miller A, Edwards, C. 2022. How do threatened plant species with low genetic diversity respond to environmental stress? Insights from comparative conservation epigenomics and phenotypic plasticity. Accpeted pending minor revisions.
Patel S, Harris ZN, Londo JP, Miller AJ, Fennel AF. 2023. Genome assembly of the hybrid grapevine ‘Chambourcin.’ Gigabyte. https://doi.org/10.46471/gigabyte.84
DeHaan LR, Anderson JA, Bajgain P, Basche A, Cattani DJ, Crain J, Crews TE, David C, Duchene O, Gutknecht J, Hayes RC, Hu F, Jungers JM, Knudsen S, Kong W, Larson S, Lundquist P-O, luo Guangbin, Miller AJ, Nabukalu P, Newell MT, Olsson L, Palmgren M, Paterson AH, Picasso VD, Poland JA, Sacks EJ, Wang S, Westerbergh A. 2023. Discussion: Prioritize perennial grain development for sustainable food production and environmental benefits. Science of the Total Environment 895: 15 October 2023, 164975. https://doi.org/10.1016/j.scitotenv.2023.164975.
To access: https://www.sciencedirect.com/science/article/pii/S0048969723035982?dgcid=coauthor
Karabulut E, Kerkoç K, Aci M, Al M, Aydin M, Barriball S, Braley J, Casetta E, Craine E, Diaz-Garcia L, Hershberer J, Meyering B, Miller AJ, Rubin MJ, Tesdell O, Van Tassel D, Schlautman Sakiroglu M. 2023. Sainfoin (Onobrychis sp.) crop ontology: supporting germplasm characterization and international research collaborations. Frontiers in Plant Science. 2023:14. https://doi.org/10.3389/fpls.2023.1177406
Interdisciplinary Plant Science Consortium. 2023. Inclusive collaboration across plant physiology and genomics: Now is the Time! In press. Plant Direct 7(5): e493. https://doi.org/10.1002/pld3.493
Harris* ZN, JE Pratt, LG Kovacs, LL Klein, MT Kwasniewski, JP Londo, A Wu, AJ Miller. 2023. Differential modulation of scion gene expression in grapevines is driven by rootstock and environment interaction. BMC Plant Biology 23:211. https://doi.org/10.1186/s12870-023-04223-w.
2022
Carley C, Chen G, Das KK, Delory BM, Simitrova A, Ding Y, Geoge AP, Greeley LA, Han Q, Hendriks P-W, Hernandez-Soriano MC, Li M, Ng LJP, Mau L, Mesa-Marin J, Miller A, Rae A, Schmidt J, Thies A, Topp CN, Wacker TS, Wang P, Wang X, Xie L, Zheng C. 2022. Root biology never sleeps. New Phytologist 235:2149–2154.
Harris* ZN, Pratt** JE, Bhakta N, Frawley E, Klein LL, Kwasniewski MT, Migicovsky Z, Miller AJ. 2022. Temporal and environmental factors interact with rootstock genotype to shape leaf elemental composition in grafted grapevines. Plant Direct. DOI: 10.1002/pld3.440. https://www.biorxiv.org/content/10.1101/2022.02.28.482393v1
Khoury CK, Brush S, Costich D, Curry HA, de Haan S, Englels JMM, Guarino L, Hoban S, Mercer K, Miller AJ, Nabhan GP, Perales HR, Richards C, Riggins C, Thormann I. 2022. Crop genetic erosion: understanding and responding to loss of crop diversity. New Phytologist. https://doi.org/10.1111/nph.17733
Linan* AG, Lowry II PP, Miller AJ, Schatz GE, Sevathian JC, Edwards CE. 2022. Interspecific hybridization and island colonization history, not rarity, most strongly affect the genetic diversity in Diospyros, a clade of Mascarene-Endemic Trees. Journal of Heredity 113 (3), 336-352
Migicovksy Z, Swift* JF, Helget Z, Klein LL, Ly A, Maimaitiyiming M, Woodhouse A, Fennell A, Kwasniewski M, Miller AJ, Cousins P, Chitwood DH. 2022. Increases in vein length compensate for leaf area lost to lobing in grapevine. American Journal of Botany. DOI: 10.1002/ajb2.16033. https://www.biorxiv.org/content/10.1101/2022.03.15.484490v1.
Van Tassel D, DeHaan L, Diaz-Garcia L, Rubin M, Schlautman B, Turner K, Miller A. Reimagining crop domestication in the era of high throughput phenomics. Current Opinion in Plant Biology 65, 102150. https://doi.org/10.1016/j.pbi.2021.102150
2021
Harris* ZA, Klein LL, Awale M, Swift J, Migicovsky Z, Bhakta N, Frawley E, Chitwood DH, Fennell A, Kovacs LG, Kwasniewski M, Londo JP, Ma Q and Miller AJ. Root system influence on high dimensional leaf phenotypes over the grapevine growing season. GigaScience. https://doi.org/10.1093/gigascience/giab087
Griffiths M, Delory B, Jawahir V, Wong K, Bagnall GC, Dowd T, Nusinow D, Miller A, Topp C. Optimization of root traits to provide enhanced ecosystem services in agricultural systems: a focus on cover crops. Plant, Cell and Environment. https://doi.org/10.1111/pce.14247
Herron* SA, Rubin MJ, Albrecht MA, Long QG, Sandoval MC, Miller AJ. Seed and growth trait patterns in wild annual and herbaceous perennial species of Lathyrus, Phaseolus, and Vicia (Fabaceae). American Journal of Botany. https://doi.org/10.1002/ajb2.1773
Swift* JF, Hall ME, Kwasniewski MT, Miller AJ. Rootstock genotype impacts microbiome diversity and composition across the root and shoot system of grafted grapevines. Microorganisms 9(1): 92. https://doi.org/10.3390/microorganisms9010092
Linan*, A., P. Lowry, A. Miller G. Schatz, J.-C. Sevathian, C. Edwards. RAD-seq reveals patterns of diversification, hybridization, and the accumulation of reproductive isolation in a clade of partially sympatric, tropical island trees. Molecular Ecology 30 (18), 4520-4537.
2020
Maimaitiyiming M, Sagan V, Sidike P, Maimaitijiang M, Miller AJ, Kwasniewski M. 2020. Leveraging very high spatial resolution hyperspectral and thermal UAV imageries for characterizing diurnal grapevine physiology. Accepted. International Journal of Applied Earth Observation and Geoinformation.
Herron* SA, Rubin MJ, Ciotir EC, Crews TE, Van Tassel DL, Miller AJ. 2020 Seed size, germination, and vegetative allocation in first-year annual and herbaceous perennial crops and their wild relatives in Lupinus and Phaseolus (Fabaceae). Frontiers Plant Science. https://doi.org/10.3389/fpls.2020.00034
Frawley ES, Micke**B, Ciotir C, Rubin MJ, Miller AJ. 2020. An ethnobotanical study of the genus Elymus. Economic Botany. 74, 159–177. https://doi.org/10.1007/s12231-020-09494-0
Khoury CK, Greene SL, Krishnan S, Miller AJ, Moreau T, Williams KA, Rodriguez-Bonilla L, Spurrier CS, Zalapa J, Nabhan GP. 2020. Toward integrated conservation of North America’s Crop Wild Relatives. Natural Areas Journal 40(1): 96-100.
2019
Migicovsky, Z., E. Warschefsky, L. Klein, A. J. Miller. 2019. Using Living Germplasm Collections to Understand, Improve, and Conserve Woody Perennials. Crop Science. https://doi.org/10.2135/cropsci2019.05.0353
Li M, Klein L, Duncan K, Jiang N, Chitwood DH, Londo J, Miller A, Topp C. Characterizing grapevine (Vitis spp.) inflorescence architecture using X-ray imaging: implications for understanding cluster density. Journal of Experimental Botany 70(21): 6261-6276. https://doi.org/10.1093/jxb/erz394
Gaut, BS, Miller AJ, Seymour DK. 2019. Living with two genomes: Grafting and its Implications for Plant Genome-to-
Genome Interactions, Phenotypic Variation and Evolution. Annual Reviews in Genetics. doi: 10.1146/annurev-genet-112618-043545.
Khoury CK, Greene SL, Krishnan S, Miller AJ, Moreau T. 2019. A Road Map for Conservation, Use, and Public Engagement around North America’s Crop Wild Relatives and Wild Utilized Plants. In press. Crop Science. 59:1–6 (2019).
Khoury CK, Kantar M, Barber E, Kisel Y, Ricciardi V, Klirs C, Kucera L, Mehrabi Z, Johnson N, Klabin S, Valiño A, Nowakoski K, Bartomeus I, Ramankutty N, Miller A, Schipanski M, Gore MA, Novy A. 2019. Science – graphic art partnerships to increase research impact. Commmunications Biology 2(295).
Linan*, A., Lowry, Miller, A.J., P., Schatz, G. and Edwards C.E. 2019. Ebony and the Mascarenes: the evolutionary relationships and biogeography of Diospyros L. (Ebenaceae) in the western Indian Ocean. Botanical Journal of the Linnean Society. 190(4): 359 – 373.
Schier* HE, Eliot KA, Herron* SA, Landfried LK, Migicovsy Z, Rubin MJ, Miller AJ. 2019. Comparative analysis of perennial and annual Phaseolus seed nutrient concentrations. Sustainability 11(10): 2787https://www.biorxiv.org/content/10.1101/612010v1
Migicovsky, Z., Harris*, Z.N., Klein. L.L, Li, M., McDermaid, A., Chitwood, D.H., Fennell, A., Kovacs, L.G., Kwasniewski, M., Londo, J.P., Ma, Q., Miller, A.J. 2019. Rootstock effects on scion phenotypes in a ‘Chambourcin’ experimental vineyard. Horticulture Research 6: 64 https://www.nature.com/articles/s41438-019-0146-2
Ciotir, C., Applequist, W., Crews, T.E., Cristea, N., DeHaan L.R., Frawley, E., Herron*, S., Magill, R., Miller, J., Roskov, Y., Schlautman, B., Solomon, J., Townesmith, A., Van Tassel, D., Zarucchi, J., Miller, A.J. 2019. Building a botanical foundation for the ecological intensification of agriculture: global inventory of wild, perennial herbaceous Fabaceae species. 2019. Plants, People, Planet. DOI: 10.1002/ppp3.37. https://nph.onlinelibrary.wiley.com/doi/abs/10.1002/ppp3.37.
Monier, B., A. McDermaid, J. Zhao, A. Miller, A. Fennell, and Q. Ma. 2019. IRIS-EDA: interactive RNA-seq data interpretation using Shiny for differentially gene expression analysis. PLoS Computational Biology. DOI: https://doi.org/10.1101/283341.
2018
Li, M., An, H., Angelovici, R., Bagaza, C. Batushansky, A., Clark, L., Coneva, V., Donoghue, M., Edwards, E., Fajardo, D. Fang, H., Frank, M., Gallaher, T., Gebken, S., Hill, T. Jansky, S., Kaur, B., Klahs, P. Klein, L. Kuraparthy, V., Londo, J., Migicovsky, Z., Miller, A., Mohn, R., Myles, S., Otoni, W., Pires, C.J., Riffer, E., Schmerler, S., Spriggs, E., Topp, C., Van Deynze, A., Zhang, K., Zhu, L., Zink, B.M., Chitwood, D.H. 2018. Topological data analysis as a morphometric method: using persistent homology to demarcate a leaf morphospace. Frontiers in Plant Science 9: 553.
Schlautman, B., S. Barribal, C. Ciotir, S. Herron*, and A. J. Miller. 2018. Perennial Grain Legume Domestication Phase I: Criteria for Candidate Species Selection. Sustainability. 10, 730; doi:10.3390/su10030730
Klein*, L.K., Miller, A.J., Ciotir, E.C., S. Uribe-Convers, Londo, J.P. 2018. High-throughput sequencing data clarify evolutionary relationships among North American Vitis species and improve identification in USDA Vitis germplasm collections. American Journal of Botany 105(2): 215 – 226.
2017
Klein* L, Caito** M, Chapnick** C, Kitchen** C, O’Hanlon** R, Chitwood D, and A Miller. 2017. Digital morphometrics of two North American grapevines: assessing leaf variation within and among individuals, and among species (Vitaceae). Frontiers in Plant Science. doi: 10.3389/fpls.2017.00373.
2016
Walters SA, Bernhardt P, Joseph** M, and Miller AJ. 2016. Compatible and Self-Incompatible Flowering Systems in Horseradish. Plant Breeding. DOI: 10.1111/pbr.12413.
McAllister* CA and Miller AJ. 2016. SNP discovery via genotyping-by-sequencing for assessment of population genetic structure and recurrent polyploidization in big bluestem (Andropogon gerardii). American Journal of Botany 103(7): 1314-1325.
Migicovsky, Z., Sawler, J., Money, D., Eibach, R., Miller, A.J., Luby, J.J., Jamieson, A.R., Velasco, D., von Kintzel, S., Warner, J., Wührer, W., Brown, P.J., and Myles, S. 2016. Genomic ancestry estimation quantifies use of wild species in grape breeding. BMC Genomics 17(1)
Miller AJ and BL Gross. 2016. Report from the International Plant and Animal Genome Meeting. Invited Letter to the Editor for American Journal of Botany 103(6): 982 – 985. .
Callen* ST, Klein* LL, and Miller AJ. 2016. Climatic niche characterization of 13 North American Vitis species. American Journal of Enology and Viticulture 67: 339-349.
DeHaan L, VanTassel D, Anderson J, Asselin S. Barnes R, Baute G, Cattani G, Culman S, Dorn K, Hulke B, Kantar M, Larson S, Marks M, Miller A, Poland J, Ravetta D, Rude E, Ryan M, Wyse D, and Zhang X. 2016. A pipeline strategy for crop domestication. Crop Science 56: 917 – 930.
Warschefsky E, Klein* L, Frank M, Chitwood D, Londo J, von Wettberg E, and Miller AJ. 2016. Rootstocks: diversity, domestication, and impacts on shoot phenotypes. Trends in Plant Science 21(5): 418-437. DOI: http://dx.doi.org/10.1016/j.tplants.2015.11.008.
Maimaitiyiming* M, Miller AJ, and Wulamu A. 2016. Discriminating spectral signatures among and within two closely related grapevine species. Photogrammetric Engineering and Remote Sensing 82(1): 51-62. DOI: 10.14358/PERS.82.2.51
Chitwood DH, Klein* LL, O'Hanlon** R, Chacko** S, Greg** M, Kitchen** C, Miller AJ, and Londo JP 2016. Leaves as composites of latent developmental and evolutionary shapes. New Phytologist 210: 343-355. doi:10.1111/nph.13754.
2015
Miller AJ, Novy A., Glover J, Maul J, Kellogg EA, Raven P and Wyse Jackson P. 2015. Expanding the role of botanical gardens in the future of food. Nature Plants 1:15078.
- related Nature Plants editorial: More than naming of parts.
Pap D, Londo J, Miller AJ, and Kovacs L. 2015. Population structure of Vitis rupestris, an important but vanishing resource for grape breeding. American Journal of Enology and Viticulture 66:403-410 doi:10.5344/ajev.2015.15012.
Callen* ST and Miller AJ. 2015. Signatures of niche conservatism and niche shift in the North American kudzu (Pueraria montana) invasion). Diversity and Distributions 21(8): 853-863. DOI: 10.1111/ddi.12341.
Pell SK, Mitchell JD, and Miller AJ. 2015. Anacardiaceae. In Flora of North America.
McAllister* C, Blaine R, Kron P, Bennett B, Garrett H, Kidson J, Matzenbacher B, Glotzbach A, and Miller AJ. 2015. Environmental correlates of cytotype distribution in Andropogon gerardii. American Journal of Botany 102(1): 92 – 102.
2014
Gross BL, Kellogg EA, and Miller AJ. 2014. Speaking of food: connecting basic and applied science. American Journal of Botany 101: 1597 – 1600.
- Coverage in Current Biology: Plant Science called up to provide food security.
- Eureka alert: Building a bridge from basic botany to applied agriculture.
Gross BL and Miller AJ. 2014. From field to table: perspectives and potential for perennial fruit domestication. Proceedings from the Perennial Crop Workshop, Food and Agriculture Organization.
Hancock J, and Miller AJ. 2014. Crop Plants: Evolution. Encyclopedia of Life Sciences. John Wiley and Sons. DOI: 10.1002/9780470015902.a0003360.pub2.
Albrecht MA, Broecker** JA, Romero-Hernandez* C, and Miller AJ. 2014. Conservation genetics of edaphic endemics in naturally isolated habitats: a case study with Geocarpon minimum (Caryophyllaceae). Journal of the Torrey Botanical Society 141(1): 1-13.
2013
Miller AJ, Matasci N, Schwaninger H, Aradhya M, Prins B, Zhong G-Y, Simon C, Buckler E, and Myles S. 2013. Vitis phylogenomics: hybridization intensities from a SNP array outperform genotype calls. PLOS ONE 8(11): e78680.
2012 and earlier
Miller AJ. 2012. Out of the cold- how big and how old? Genetic fingerprinting reveals how long-lived individuals withstand climatic oscillations in the arctic-alpine. Molecular Ecology 21(5): 1036-7.
Miller AJ. 2011. Wealth of Crop Relatives: Genomic and Breeding Resources. Spondias purpurea and its sympatric wild relatives in Mesoamerica. Chittaranjan Kole, Editor. Springer-Verlag, Berlin, Germany.
Miller AJ and Gross BL. 2011. Forest to Field: Perennial fruit crop domestication. American Journal of Botany 98(9): 1389-1414.
Grauke LJ, Mendoza-Herrera MA, Miller AJ, and Wood BW. 2011. Geographic patterns of genetic variation in native pecan populations (Carya illinoinensis). Tree Genetics and Genomes 7:917-932.
Pell S, Mitchell JD, Miller AJ, and Lobova TA. 2011. Anacardiaceae. The Families and Genera of Vascular Plants. K. Kubitzki, ed. Springer-Verlag, Heidelberg, Germany.
Gunn BF, Aradhya M, Salick J, Miller A, Yongping Y, Lin L, and Xian H. 2010. Genetic variation in walnuts (Juglans sigillata Dode and J. regia L., Juglandaceae): species distinctions, human impacts, and agrobiodiversity conservation in Yunnan, China. American Journal of Botany 97(4): 660-671.
Sampliner* DS and Miller AJ. 2009. Ethnobotany of horseradish: reproductive biology and local uses of Armoracia species (Brassicaceae) in their native ranges. Economic Botany 63(3): 303-313.
Miller AJ. 2008. Characterization of the Spondias purpurea lineage in Mesoamerica based on nuclear and chloroplast sequence data. Journal of the Torrey Botanical Society. 135(4): 463-474.
Miller AJ. 2007. Crop Plants: Evolution. Encyclopedia of Life Sciences. John Wiley and Sons.
Yi T, Miller AJ, and Wen J. 2007. The phylogeny of Rhus (Ancardiaceae) based on sequences of nuclear NIA-i3 intron and chloroplast trnC-D suggests reticulate evolution. Systematic Botany 32(2): 379-391.
Miller AJ and Knouft JH. 2006. GIS-based characterization of the wild and cultivated niches of a Mesoamerican fruit tree, Spondias purpurea (Anacardiaceae). American Journal of Botany 93(12): 1757-1767.
Miller AJ and Schaal BA. 2006. Domestication and the distribution of genetic variation in wild and cultivated populations of the Mesoamerican fruit tree Spondias purpurea L. (Anacardiaceae). Molecular Ecology 15: 1467-1480.
Miller AJ and Schaal BA. 2005. Domestication of a Mesoamerican cultivated fruit tree. Proceedings of the National Academy of Science 102 (36): 12801-12806.
Yi T, Miller AJ and Wen J. 2004. Phylogenetic and biogeographic diversification of Rhus (Anacardiaceae) in the Northern Hemisphere. Molecular Phylogenetics and Evolution 33 (3): 861-879.
Miller AJ, Wen J, and Young DA. 2001. Systematics of Rhus: Phylogenetic and biogeographic inferences based on ITS sequence data. International Journal of Plant Sciences 162(6): 1401-1407.
Kiss JZ, Guisinger MM, Miller AJ. 1997. What is the threshold amount of starch necessary for full gravitropic sensitivity? Advances in Space Research 21: 1197-1202.
Kiss JZ, Guisinger MM, Miller AJ, and Stackhouse KS. 1997. Reduced gravitropism in hypocotyls of starch-deficient mutants of Arabidopsis. Plant and Cell Physiology 38(5): 518-525.