| Year |
Citation |
Score |
| 2024 |
Ou S, Jiang N, Hirsch CN, Hufford MB. Response to Commentary: Accounting for diverse transposable element landscapes is key to developing and evaluating accurate de novo annotation strategies. Genome Biology. 25: 6. PMID 38169403 DOI: 10.1186/s13059-023-03119-0 |
0.7 |
|
| 2023 |
Sun S, Wang B, Li C, Xu G, Yang J, Hufford MB, Ross-Ibarra J, Wang H, Wang L. Unraveling prevalence and effects of deleterious mutations in maize elite lines across decades of modern breeding. Molecular Biology and Evolution. PMID 37494285 DOI: 10.1093/molbev/msad170 |
0.659 |
|
| 2023 |
Chen J, Wang Z, Tan K, Huang W, Shi J, Li T, Hu J, Wang K, Wang C, Xin B, Zhao H, Song W, Hufford MB, Schnable JC, Jin W, et al. A complete telomere-to-telomere assembly of the maize genome. Nature Genetics. PMID 37322109 DOI: 10.1038/s41588-023-01419-6 |
0.424 |
|
| 2023 |
Phillips AR, Seetharam AS, Albert PS, AuBuchon-Elder T, Birchler JA, Buckler ES, Gillespie LJ, Hufford MB, Llaca V, Romay MC, Soreng RJ, Kellogg EA, Ross-Ibarra J. A happy accident: a novel turfgrass reference genome. G3 (Bethesda, Md.). PMID 37002915 DOI: 10.1093/g3journal/jkad073 |
0.82 |
|
| 2022 |
Hu H, Crow T, Nojoomi S, Schulz AJ, Estévez-Palmas JM, Hufford MB, Flint-Garcia S, Sawers R, Rellan-Alvarez R, Ross-Ibarra J, Runcie DE. Allele-specific expression reveals multiple paths to highland adaptation in maize. Molecular Biology and Evolution. PMID 36327321 DOI: 10.1093/molbev/msac239 |
0.633 |
|
| 2022 |
Chen L, Luo J, Jin M, Yang N, Liu X, Peng Y, Li W, Phillips A, Cameron B, Bernal JS, Rellán-Álvarez R, Sawers RJH, Liu Q, Yin Y, Ye X, ... ... Hufford MB, et al. Genome sequencing reveals evidence of adaptive variation in the genus Zea. Nature Genetics. PMID 36266506 DOI: 10.1038/s41588-022-01184-y |
0.716 |
|
| 2022 |
Barnes AC, Rodríguez-Zapata F, Juárez-Núñez KA, Gates DJ, Janzen GM, Kur A, Wang L, Jensen SE, Estévez-Palmas JM, Crow TM, Kavi HS, Pil HD, Stokes RL, Knizner KT, Aguilar-Rangel MR, ... ... Hufford MB, et al. An adaptive teosinte introgression modulates phosphatidylcholine levels and is associated with maize flowering time. Proceedings of the National Academy of Sciences of the United States of America. 119: e2100036119. PMID 35771940 DOI: 10.1073/pnas.2100036119 |
0.66 |
|
| 2022 |
Ou S, Su W, Liao Y, Chougule K, Agda JRA, Hellinga AJ, Lugo CSB, Elliott TA, Ware D, Peterson T, Jiang N, Hirsch CN, Hufford MB. Author Correction: Benchmarking transposable element annotation methods for creation of a streamlined, comprehensive pipeline. Genome Biology. 23: 76. PMID 35260190 DOI: 10.1186/s13059-022-02645-7 |
0.683 |
|
| 2022 |
Perez-Limón S, Li M, Cintora-Martinez GC, Aguilar-Rangel MR, Salazar-Vidal MN, González-Segovia E, Blöcher-Juárez K, Guerrero-Zavala A, Barrales-Gamez B, Carcaño-Macias J, Costich DE, Nieto-Sotelo J, Martinez de la Vega O, Simpson J, Hufford MB, et al. A B73×Palomero Toluqueño mapping population reveals local adaptation in Mexican highland maize. G3 (Bethesda, Md.). PMID 35100386 DOI: 10.1093/g3journal/jkab447 |
0.685 |
|
| 2021 |
Seetharam AS, Yu Y, Bélanger S, Clark LG, Meyers BC, Kellogg EA, Hufford MB. The Genome and the Evolution of the Grasses. Frontiers in Plant Science. 12: 710383. PMID 34671369 DOI: 10.3389/fpls.2021.710383 |
0.407 |
|
| 2021 |
Hufford MB, Seetharam AS, Woodhouse MR, Chougule KM, Ou S, Liu J, Ricci WA, Guo T, Olson A, Qiu Y, Della Coletta R, Tittes S, Hudson AI, Marand AP, Wei S, et al. De novo assembly, annotation, and comparative analysis of 26 diverse maize genomes. Science (New York, N.Y.). 373: 655-662. PMID 34353948 DOI: 10.1126/science.abg5289 |
0.809 |
|
| 2021 |
Bornowski N, Michel KJ, Hamilton JP, Ou S, Seetharam AS, Jenkins J, Grimwood J, Plott C, Shu S, Talag J, Kennedy M, Hundley H, Singan VR, Barry K, Daum C, ... ... Hufford MB, et al. Genomic variation within the maize stiff-stalk heterotic germplasm pool. The Plant Genome. e20114. PMID 34275202 DOI: 10.1002/tpg2.20114 |
0.758 |
|
| 2021 |
Song B, Buckler ES, Wang H, Wu Y, Rees E, Kellogg EA, Gates DJ, Khaipho-Burch M, Bradbury PJ, Ross-Ibarra J, Hufford MB, Romay MC. Conserved noncoding sequences provide insights into regulatory sequence and loss of gene expression in maize. Genome Research. PMID 34045362 DOI: 10.1101/gr.266528.120 |
0.676 |
|
| 2021 |
Wang L, Josephs EB, Lee KM, Roberts LM, Rellán-Álvarez R, Ross-Ibarra J, Hufford MB. Molecular Parallelism Underlies Convergent Highland Adaptation of Maize Landraces. Molecular Biology and Evolution. PMID 33905497 DOI: 10.1093/molbev/msab119 |
0.65 |
|
| 2021 |
Su W, Ou S, Hufford MB, Peterson T. A Tutorial of EDTA: Extensive De Novo TE Annotator. Methods in Molecular Biology (Clifton, N.J.). 2250: 55-67. PMID 33900591 DOI: 10.1007/978-1-0716-1134-0_4 |
0.702 |
|
| 2021 |
Verzegnazzi AL, Dos Santos IG, Krause MD, Hufford M, Frei UK, Campbell J, Almeida VC, Zuffo LT, Boerman N, Lübberstedt T. Major locus for spontaneous haploid genome doubling detected by a case-control GWAS in exotic maize germplasm. Tag. Theoretical and Applied Genetics. Theoretische Und Angewandte Genetik. PMID 33543310 DOI: 10.1007/s00122-021-03780-8 |
0.404 |
|
| 2021 |
Della Coletta R, Qiu Y, Ou S, Hufford MB, Hirsch CN. How the pan-genome is changing crop genomics and improvement. Genome Biology. 22: 3. PMID 33397434 DOI: 10.1186/s13059-020-02224-8 |
0.763 |
|
| 2020 |
Liu J, Seetharam AS, Chougule K, Ou S, Swentowsky KW, Gent JI, Llaca V, Woodhouse MR, Manchanda N, Presting GG, Kudrna DA, Alabady M, Hirsch CN, Fengler KA, Ware D, ... ... Hufford MB, et al. Gapless assembly of maize chromosomes using long-read technologies. Genome Biology. 21: 121. PMID 32434565 DOI: 10.1186/S13059-020-02029-9 |
0.811 |
|
| 2020 |
Ou S, Liu J, Chougule KM, Fungtammasan A, Seetharam AS, Stein JC, Llaca V, Manchanda N, Gilbert AM, Wei S, Chin CS, Hufnagel DE, Pedersen S, Snodgrass SJ, Fengler K, ... ... Hufford MB, et al. Effect of sequence depth and length in long-read assembly of the maize inbred NC358. Nature Communications. 11: 2288. PMID 32385271 DOI: 10.1038/S41467-020-16037-7 |
0.811 |
|
| 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, ... ... Hufford MB, et al. Genome-wide selection and genetic improvement during modern maize breeding. Nature Genetics. PMID 32341525 DOI: 10.1038/S41588-020-0616-3 |
0.744 |
|
| 2020 |
Manchanda N, Portwood JL, Woodhouse MR, Seetharam AS, Lawrence-Dill CJ, Andorf CM, Hufford MB. GenomeQC: a quality assessment tool for genome assemblies and gene structure annotations. Bmc Genomics. 21: 193. PMID 32122303 DOI: 10.1186/S12864-020-6568-2 |
0.473 |
|
| 2019 |
Ou S, Su W, Liao Y, Chougule K, Agda JRA, Hellinga AJ, Lugo CSB, Elliott TA, Ware D, Peterson T, Jiang N, Hirsch CN, Hufford MB. Benchmarking transposable element annotation methods for creation of a streamlined, comprehensive pipeline. Genome Biology. 20: 275. PMID 31843001 DOI: 10.1186/S13059-019-1905-Y |
0.772 |
|
| 2019 |
Coffman SM, Hufford MB, Andorf CM, Lübberstedt T. Haplotype structure in commercial maize breeding programs in relation to key founder lines. Tag. Theoretical and Applied Genetics. Theoretische Und Angewandte Genetik. PMID 31749017 DOI: 10.1007/S00122-019-03486-Y |
0.418 |
|
| 2019 |
Woodhouse MR, Hufford MB. Parallelism and convergence in post-domestication adaptation in cereal grasses. Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences. 374: 20180245. PMID 31154975 DOI: 10.1098/rstb.2018.0245 |
0.413 |
|
| 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 |
0.637 |
|
| 2019 |
Hufford MB, Berny Mier Y Teran JC, Gepts P. Crop Biodiversity: An Unfinished Magnum Opus of Nature. Annual Review of Plant Biology. 70: 727-751. PMID 31035827 DOI: 10.1146/Annurev-Arplant-042817-040240 |
0.785 |
|
| 2019 |
Andorf C, Beavis WD, Hufford M, Smith S, Suza WP, Wang K, Woodhouse M, Yu J, Lübberstedt T. Technological advances in maize breeding: past, present and future. Tag. Theoretical and Applied Genetics. Theoretische Und Angewandte Genetik. PMID 30798332 DOI: 10.1007/S00122-019-03306-3 |
0.493 |
|
| 2018 |
Janzen GM, Wang L, Hufford MB. The extent of adaptive wild introgression in crops. The New Phytologist. PMID 30368812 DOI: 10.1111/Nph.15457 |
0.417 |
|
| 2018 |
Snodgrass SJ, Hufford MB. Domestication Genomics: Untangling the Complex History of African Rice. Current Biology : Cb. 28: R786-R788. PMID 30040938 DOI: 10.1016/J.Cub.2018.05.072 |
0.473 |
|
| 2018 |
Aburto-Oropeza O, Johnson AF, Agha M, Allen EB, Allen MF, González JA, Arenas Moreno DM, Beas-Luna R, Butterfield S, Caetano G, Caselle JE, Gaytán GC, Castorani MC, Cat LA, Cavanaugh K, ... ... Hufford MB, et al. Harnessing cross-border resources to confront climate change Environmental Science & Policy. 87: 128-132. DOI: 10.1016/J.Envsci.2018.01.001 |
0.585 |
|
| 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 |
0.814 |
|
| 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 |
0.684 |
|
| 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 |
0.809 |
|
| 2016 |
Janzen GM, Hufford MB. Crop Domestication: A Sneak-Peek into the Midpoint of Maize Evolution. Current Biology : Cb. 26: R1240-R1242. PMID 27923135 DOI: 10.1016/J.Cub.2016.10.045 |
0.358 |
|
| 2016 |
Hufford MB. Comparative genomics provides insight into maize adaptation in temperate regions. Genome Biology. 17: 155. PMID 27411931 DOI: 10.1186/S13059-016-1020-2 |
0.419 |
|
| 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 |
0.823 |
|
| 2016 |
Sexton JP, Hufford MB, Bateman A, Lowry DB, Meimberg H, Strauss SY, Rice KJ. Climate structures genetic variation across a species' elevation range: a test of range limits hypotheses. Molecular Ecology. PMID 26756973 DOI: 10.1111/Mec.13528 |
0.43 |
|
| 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, ... ... Hufford MB, 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 |
0.662 |
|
| 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 |
0.815 |
|
| 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 |
0.784 |
|
| 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, ... ... Hufford MB, et al. Erratum: The origin and evolution of maize in the Southwestern United States Nature Plants. 1. DOI: 10.1038/Nplants.2015.7 |
0.579 |
|
| 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, ... ... Hufford MB, et al. The origin and evolution of maize in the Southwestern United States Nature Plants. 1. DOI: 10.1038/nplants.2014.3 |
0.514 |
|
| 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 |
0.784 |
|
| 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 |
0.848 |
|
| 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 |
0.781 |
|
| 2013 |
Hufford MB, Lubinksy P, Pyhäjärvi T, Devengenzo MT, Ellstrand NC, Ross-Ibarra J. Correction: The Genomic Signature of Crop-Wild Introgression in Maize Plos Genetics. 9. DOI: 10.1371/Annotation/2Eef7B5B-29B2-412F-8472-8Fd7F9Bd65Ab |
0.734 |
|
| 2012 |
Hufford MB, Martínez-Meyer E, Gaut BS, Eguiarte LE, Tenaillon MI. Inferences from the historical distribution of wild and domesticated maize provide ecological and evolutionary insight. Plos One. 7: e47659. PMID 23155371 DOI: 10.1371/Journal.Pone.0047659 |
0.604 |
|
| 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 |
0.812 |
|
| 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 |
0.84 |
|
| 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 |
0.668 |
|
| 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, et al. Comparative population genomics of maize domestication and improvement. Nature Genetics. 44: 808-11. PMID 22660546 DOI: 10.1038/Ng.2309 |
0.815 |
|
| 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, et al. Maize HapMap2 identifies extant variation from a genome in flux. Nature Genetics. 44: 803-7. PMID 22660545 DOI: 10.1038/Ng.2313 |
0.847 |
|
| 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 |
0.767 |
|
| 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 |
0.733 |
|
| 2009 |
Piñeyro-Nelson A, Van Heerwaarden J, Perales HR, Serratos-Hernández JA, Rangel A, Hufford MB, Gepts P, Garay-Arroyo A, Rivera-Bustamante R, Alvarez-Buylla ER. Transgenes in Mexican maize: molecular evidence and methodological considerations for GMO detection in landrace populations. Molecular Ecology. 18: 750-61. PMID 19143938 DOI: 10.1111/J.1365-294X.2008.03993.X |
0.763 |
|
| 2009 |
Piñeyro-Nelson A, Van Heerwaarden J, Perales HR, Serratos-HernÁndez JA, Rangel A, Hufford MB, Gepts P, Garay-Arroyo A, Rivera-Bustamante R, Álvarez-Buylla ER. Resolution of the Mexican transgene detection controversy: Error sources and scientific practice in commercial and ecological contexts Molecular Ecology. 18: 4145-4150. DOI: 10.1111/J.1365-294X.2009.04369.X |
0.724 |
|
| 2008 |
Pasquet RS, Peltier A, Hufford MB, Oudin E, Saulnier J, Paul L, Knudsen JT, Herren HR, Gepts P. Long-distance pollen flow assessment through evaluation of pollinator foraging range suggests transgene escape distances Proceedings of the National Academy of Sciences of the United States of America. 105: 13456-13461. PMID 18768793 DOI: 10.1073/Pnas.0806040105 |
0.603 |
|
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