#Indicates member from the lab.
Transposition, duplication, and divergence of the telomerase RNA underlies the Mimulus telomere evolution
#Kumawat S, Martinez I, Logeswaran D, Chen H, Coughlan J, Chen J, Yuan YW, Sobel J, Choi JY
bioRxiv 2023
Nascent transcription and the associated cis-regulatory landscape in rice
Choi JY, Platts AE, Johary A, Purugganan MD, Joly-Lopez Z
bioRxiv 2022
No end in sight: Mysteries of the telomeric variation in plants
#Kumawat S and Choi JY
American Journal of Botany. 110:e16244 (2023)
Signatures of selection underpinning rapid coral adaptation to the world’s warmest reefs
Smith EG, Hazzouri KM, Choi JY, Delaney P, Al-Kharafi M, Howells EJ, Aranda M, Burt JA
Science Advances. 8:eabl7287 (2022)
Ancestral polymorphisms shape the adaptive radiation of Metrosideros across the Hawaiian Islands
Choi JY, Dai X, Alam O, Peng JZ, Rughani P, Hickey S, Harrington E, Juul S, Ayroles J, Purugganan MD, Stacy E
Proceedings of the National Academy of Sciences. 118:e2023801118 (2021)
Natural variation in plant telomere length is associated with flowering time
Choi JY, Abdulkina LR, Yin J, Chastukhina IB, Lovell JT, Agabekian IA, Young PG, Razzaque S, Shippen DE, Juenger TE, Shakirov EV, and Purugganan MD
The Plant Cell. 33:1118-1134 (2021)
Nanopore-based genome assembly and the evolutionary genomics of basmati rice
Choi JY , Lye ZN, Groen SC, Dai X, Rughani P, Zaaijer S, Harrington ED, Juul S, Purugganan MD
Genome Biology. 21:21 (2020)
Divergent selection and primary gene flow shape incipient speciation of a riparian tree on Hawaii Island
Choi JY, Purugganan MD, and Stacy EA
Molecular Biology and Evolution. 37:695-710 (2020)
The complex geography of domestication of the African rice Oryza glaberrima
Choi JY, Zaidem M, Gutaker R, Dorph K, Singh RK, Purugganan MD
PloS Genetics. 15:e1007414 (2019)
Evolutionary rate covariation analysis of E-cadherin identifies Raskol as regulator of cell adhesion and actin dynamics in Drosophila
Raza Q, Choi JY, Li Y, O’Dowd RM, Watkins SC, Hong Y, Clark NL, and Kwiatkowski AV
PloS Genetics. 15:e1007720 (2019)
The bracteatus pineapple genome and domestication of clonally propagated crops
Chen L-Y, VanBuren R, Paris M, Zhou H, Zhang X, Wai CM, Yan H, Chen S, Alonge M, Ramakrishnan S, et al. 2019
Nature Genetics 51:1549–1558 (2019) [Jae Young Choi is 22nd on author list]
Multiple Origin but Single Domestication Led to Oryza sativa
Choi JY and Purugganan MD
G3: Genes, Genomes, Genetics. 8:797-803 (2018)
Evolutionary epigenomics of retrotransposon-mediated methylation spreading in rice
Choi JY and Purugganan MD
Molecular Biology and Evolution. 35:365-382 (2018)
The rice paradox: Multiple origins but single domestication in Asian rice
Choi JY, Platts AE, Fuller DQ, Hsing YI, Wing RA, and Purugganan MD
Molecular Biology and Evolution. 34:969-979 (2017)
Study was recognized as MBE emerging classiscs 2022
Domestication history and geographical adaptation inferred from a SNP map of African rice
Meyer RS, Choi JY, Sanches M, Plessis A, Flowers JM, Amas J, Dorph K, Barretto A, Gross B, Fuller DQ, Bimpong IK, Ndjiondjop MN, Hazzouri KM, Gregorio GB, and Purugganan MD. 2016
Nature Genetics. 48:1083–1088
Recent and Long-Term Selection Across Synonymous Sites in Drosophila ananassae
Choi JY and Aquadro CF. 2016
Journal of Molecular Evolution. 83:50-60
Molecular evolution of Drosophila germline stem cell and neural stem cell regulating genes
Choi JY and Aquadro CF. 2015
Genome Biology and Evolution. 7 (11): 3097-3114
Population genomic analysis of the infectious and integrated Wolbachia pipientis genomes in Drosophila ananassae
Choi JY, Bubnell J, and Aquadro CF. 2015
Genome Biology and Evolution. 7:2362-2382
The coevolutionary period of Wolbachia piepientis infecting Drosophila ananassae and its impact on the evolution of the host germline stem cell regulating genes
Choi JY and Aquadro CF. 2014
Molecular Biology and Evolution. 31:2457-2471
Natural selection shapes nucleotide polymorphism across the genome of the nematode Caenorhabditis briggsae
Cutter AD and Choi JY. 2010
Genome Research. 20:1103-1111