J
John P. Hamilton
Researcher at Michigan State University
Publications - 81
Citations - 7375
John P. Hamilton is an academic researcher from Michigan State University. The author has contributed to research in topics: Genome & Gene. The author has an hindex of 35, co-authored 68 publications receiving 5774 citations. Previous affiliations of John P. Hamilton include Research Medical Center & Colorado State University.
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Journal ArticleDOI
Improvement of the Oryza sativa Nipponbare reference genome using next generation sequence and optical map data
Yoshihiro Kawahara,Melissa De La Bastide,John P. Hamilton,Hiroyuki Kanamori,W. Richard McCombie,Shu Ouyang,David C. Schwartz,Tsuyoshi Tanaka,Jianzhong Wu,Shiguo Zhou,Kevin L. Childs,Rebecca M. Davidson,Haining Lin,Haining Lin,Lina M. Quesada-Ocampo,Brieanne Vaillancourt,Hiroaki Sakai,Sung Shin Lee,Jungsok Kim,Hisataka Numa,Takeshi Itoh,C. Robin Buell,Takashi Matsumoto +22 more
TL;DR: A revised, error-corrected, and validated assembly of the Nipponbare cultivar of rice was generated using optical map data, re-sequencing data, and manual curation that will facilitate on-going and future research in rice.
Journal ArticleDOI
Comprehensive analysis of alternative splicing in rice and comparative analyses with Arabidopsis
TL;DR: Alternative splicing is widespread in both rice and Arabidopsis and these species share many common features, indicating that many isoforms will presumably have negative consequences for protein structure and function, suggesting that their biological role involves post-transcriptional regulation of gene expression.
Journal ArticleDOI
Genome sequence of the necrotrophic plant pathogen Pythium ultimum reveals original pathogenicity mechanisms and effector repertoire
C. André Lévesque,C. André Lévesque,H. Brouwer,Liliana M. Cano,John P. Hamilton,Carson Holt,Edgar Huitema,Sylvain Raffaele,Gregg P. Robideau,Gregg P. Robideau,Marco Thines,Joe Win,Marcelo M. Zerillo,Gordon W. Beakes,Jeffrey L. Boore,Dana A. Busam,Bernard Dumas,Steve Ferriera,Susan I. Fuerstenberg,Claire M. M. Gachon,Elodie Gaulin,Francine Govers,Laura J. Grenville-Briggs,Neil R. Horner,Jessica B. Hostetler,Rays H. Y. Jiang,Justin Johnson,Theerapong Krajaejun,Haining Lin,Harold J. G. Meijer,Barry Moore,Paul Morris,Vipaporn Phuntmart,Daniela Puiu,Jyoti Shetty,Jason E. Stajich,Sucheta Tripathy,Stephan Wawra,Pieter van West,Brett R Whitty,Pedro M. Coutinho,Bernard Henrissat,Frank N. Martin,Paul Thomas,Brett M. Tyler,Ronald P. de Vries,Sophien Kamoun,Mark Yandell,Ned Tisserat,C. Robin Buell +49 more
TL;DR: Access to the P. ultimum genome has revealed not only core pathogenic mechanisms within the oomycetes but also lineage-specific genes associated with the alternative virulence and lifestyles found within the pythiaceous lineages compared to the Peronosporaceae.
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Development of a large SNP genotyping array and generation of high-density genetic maps in tomato.
Sung Chur Sim,Gregor Durstewitz,Jörg Plieske,Ralf Wieseke,Martin W. Ganal,Allen Van Deynze,John P. Hamilton,C. Robin Buell,Mathilde Causse,Saranga Wijeratne,David M. Francis +10 more
TL;DR: An array for tomato with 8,784 Single Nucleotide Polymorphisms (SNPs) mainly discovered based on NGS-derived transcriptome sequences revealed that genomic regions with high recombination rates were consistent with the known distribution of euchromatin across the 12 chromosomes, while very low recombination Rates observed in the heterochromatic regions.
Journal ArticleDOI
Genome diversity of tuber-bearing Solanum uncovers complex evolutionary history and targets of domestication in the cultivated potato
Michael A. Hardigan,F. Parker E. Laimbeer,Linsey Newton,Emily Crisovan,John P. Hamilton,Brieanne Vaillancourt,Krystle Wiegert-Rininger,Joshua C. Wood,David S. Douches,Eva M. Farré,Richard E. Veilleux,C. Robin Buell +11 more
TL;DR: A historic role of wild Solanum species in the diversification of long-day–adapted tetraploid potatoes is uncovered, showing that extant natural populations represent an essential source of untapped adaptive potential.