Yeisoo Yu, Ph.D. - Publications

Affiliations: 
2000 Clemson University, Clemson, SC, United States 
Area:
Genetics, Molecular Biology

94 high-probability publications. We are testing a new system for linking publications to authors. You can help! If you notice any inaccuracies, please sign in and mark papers as correct or incorrect matches. If you identify any major omissions or other inaccuracies in the publication list, please let us know.

Year Citation  Score
2021 Kang SH, Pandey RP, Lee CM, Sim JS, Jeong JT, Choi BS, Jung M, Ginzburg D, Zhao K, Won SY, Oh TJ, Yu Y, Kim NH, Lee OR, Lee TH, et al. Author Correction: Genome-enabled discovery of anthraquinone biosynthesis in Senna tora. Nature Communications. 12: 1665. PMID 33686081 DOI: 10.1038/s41467-021-21987-7  0.504
2020 Kang SH, Pandey RP, Lee CM, Sim JS, Jeong JT, Choi BS, Jung M, Ginzburg D, Zhao K, Won SY, Oh TJ, Yu Y, Kim NH, Lee OR, Lee TH, et al. Genome-enabled discovery of anthraquinone biosynthesis in Senna tora. Nature Communications. 11: 5875. PMID 33208749 DOI: 10.1038/s41467-020-19681-1  0.468
2020 Shim J, Han J, Shin N, Lee J, Sung J, Yu Y, Lee S, Ahn KH, Chin JH. Complete Chloroplast Genome of a Milk Thistle (Silybum marianum) Acc. ‘912036’ Plant Breeding and Biotechnology. 8: 439-444. DOI: 10.9787/pbb.2020.8.4.439  0.528
2019 Zhang L, Ren Y, Yang T, Li G, Chen J, Gschwend AR, Yu Y, Hou G, Zi J, Zhou R, Wen B, Zhang J, Chougule K, Wang M, Copetti D, et al. Rapid evolution of protein diversity by de novo origination in Oryza. Nature Ecology & Evolution. PMID 30858588 DOI: 10.1038/S41559-019-0822-5  0.711
2018 Stein JC, Yu Y, Copetti D, Zwickl DJ, Zhang L, Zhang C, Chougule K, Gao D, Iwata A, Goicoechea JL, Wei S, Wang J, Liao Y, Wang M, Jacquemin J, et al. Publisher Correction: Genomes of 13 domesticated and wild rice relatives highlight genetic conservation, turnover and innovation across the genus Oryza. Nature Genetics. PMID 30291357 DOI: 10.1038/S41588-018-0261-2  0.607
2018 Kim JA, Roy NS, Lee IH, Choi AY, Choi BS, Yu YS, Park NI, Park KC, Kim S, Yang HS, Choi IY. Genome-wide transcriptome profiling of the medicinal plant Zanthoxylum planispinum using a single-molecule direct RNA sequencing approach. Genomics. PMID 30003944 DOI: 10.1016/J.Ygeno.2018.06.004  0.509
2018 Kim CK, Seol YJ, Perumal S, Lee J, Waminal NE, Jayakodi M, Lee SC, Jin S, Choi BS, Yu Y, Ko HC, Choi JW, Ryu KY, Sohn SH, Parkin I, et al. Re-exploration of U's Triangle Brassica Species Based on Chloroplast Genomes and 45S nrDNA Sequences. Scientific Reports. 8: 7353. PMID 29743507 DOI: 10.1038/S41598-018-25585-4  0.617
2018 Kim NH, Jayakodi M, Lee SC, Choi BS, Jang W, Lee J, Kim HH, Waminal NE, Lakshmanan M, Van Nguyen B, Lee YS, Park HS, Koo HJ, Park JY, Perumal S, ... ... Yu Y, et al. Genome and evolution of the shade-requiring medicinal herb Panax ginseng. Plant Biotechnology Journal. PMID 29604169 DOI: 10.1111/Pbi.12926  0.726
2018 Stein JC, Yu Y, Copetti D, Zwickl DJ, Zhang L, Zhang C, Chougule K, Gao D, Iwata A, Goicoechea JL, Wei S, Wang J, Liao Y, Wang M, Jacquemin J, et al. Genomes of 13 domesticated and wild rice relatives highlight genetic conservation, turnover and innovation across the genus Oryza. Nature Genetics. PMID 29358651 DOI: 10.1038/S41588-018-0040-0  0.692
2018 Kim M, Yu Y, Kang K, Cho Y. Gene expression and SNP identification related to leaf angle traits using a genome-wide association study in rice (Oryza sativaL.) Journal of Plant Biotechnology. 45: 17-29. DOI: 10.5010/JPB.2018.45.1.017  0.413
2018 Bhatia D, Wing RA, Yu Y, Chougule K, Kudrna D, Lee S, Rang A, Singh K. Genotyping by sequencing of rice interspecific backcross inbred lines identifies QTLs for grain weight and grain length Euphytica. 214. DOI: 10.1007/S10681-018-2119-1  0.57
2017 Yu Y, Lee HO, Chin JH, Park HY, Yoo SC. The complete chloroplast genome sequence of -type variety Nagina-22 (Poaceae). Mitochondrial Dna. Part B, Resources. 2: 819-820. PMID 33473995 DOI: 10.1080/23802359.2017.1407710  0.64
2017 Lee CR, Wang B, Mojica JP, Mandáková T, Prasad KVSK, Luis Goicoechea J, Perera N, Hellsten U, Hundley HN, Johnson J, Grimwood J, Barry K, Fairclough S, Jenkins JW, Yu Y, et al. Publisher correction: Young inversion with multiple linked QTLs under selection in a hybrid zone. Nature Ecology & Evolution. 1: 1585. PMID 29185503 DOI: 10.1038/S41559-017-0310-8  0.506
2017 Lee CR, Wang B, Mojica JP, Mandáková T, Prasad KVSK, Goicoechea JL, Perera N, Hellsten U, Hundley HN, Johnson J, Grimwood J, Barry K, Fairclough S, Jenkins JW, Yu Y, et al. Young inversion with multiple linked QTLs under selection in a hybrid zone. Nature Ecology & Evolution. 1: 119. PMID 28812690 DOI: 10.1038/S41559-017-0119  0.624
2017 Lee J, Joh HJ, Kim N, Lee S, Jang W, Choi BS, Yu Y, Yang T. High-Throughput Development of Polymorphic Simple Sequence Repeat Markers Using Two Whole Genome Sequence Data in Peucedanum japonicum Plant Breeding and Biotechnology. 5: 134-142. DOI: 10.9787/Pbb.2017.5.2.134  0.592
2017 Lee C, Wang B, Mojica JP, Mandáková T, Prasad KVSK, Goicoechea JL, Perera N, Hellsten U, Hundley HN, Johnson J, Grimwood J, Barry K, Fairclough S, Jenkins JW, Yu Y, et al. Erratum: Young inversion with multiple linked QTLs under selection in a hybrid zone Nature Ecology & Evolution. 1. DOI: 10.1038/s41559-017-0166  0.448
2016 Zhang J, Chen LL, Sun S, Kudrna D, Copetti D, Li W, Mu T, Jiao WB, Xing F, Lee S, Talag J, Song JM, Du B, Xie W, Luo M, ... ... Yu Y, et al. Building two indica rice reference genomes with PacBio long-read and Illumina paired-end sequencing data. Scientific Data. 3: 160076. PMID 27622467 DOI: 10.1038/Sdata.2016.76  0.736
2016 Wicker T, Yu Y, Haberer G, Mayer KF, Marri PR, Rounsley S, Chen M, Zuccolo A, Panaud O, Wing RA, Roffler S. DNA transposon activity is associated with increased mutation rates in genes of rice and other grasses. Nature Communications. 7: 12790. PMID 27599761 DOI: 10.1038/Ncomms12790  0.658
2016 Zhang J, Chen LL, Xing F, Kudrna DA, Yao W, Copetti D, Mu T, Li W, Song JM, Xie W, Lee S, Talag J, Shao L, An Y, Zhang CL, ... ... Yu Y, et al. Extensive sequence divergence between the reference genomes of two elite indica rice varieties Zhenshan 97 and Minghui 63. Proceedings of the National Academy of Sciences of the United States of America. PMID 27535938 DOI: 10.1073/Pnas.1611012113  0.775
2016 Cho KS, Cheon KS, Hong SY, Cho JH, Im JS, Mekapogu M, Yu YS, Park TH. Complete chloroplast genome sequences of Solanum commersonii and its application to chloroplast genotype in somatic hybrids with Solanum tuberosum. Plant Cell Reports. PMID 27417695 DOI: 10.1007/s00299-016-2022-y  0.538
2016 Zhang J, Kudrna D, Mu T, Li W, Copetti D, Yu Y, Goicoechea JL, Lei Y, Wing RA. Genome Puzzle Master (GPM) - An integrated pipeline for building and editing pseudomolecules from fragmented sequences. Bioinformatics (Oxford, England). PMID 27318200 DOI: 10.1093/Bioinformatics/Btw370  0.736
2016 Chen X, Li H, Pandey MK, Yang Q, Wang X, Garg V, Li H, Chi X, Doddamani D, Hong Y, Upadhyaya H, Guo H, Khan AW, Zhu F, Zhang X, ... ... Yu Y, et al. Draft genome of the peanut A-genome progenitor (Arachis duranensis) provides insights into geocarpy, oil biosynthesis, and allergens. Proceedings of the National Academy of Sciences of the United States of America. PMID 27247390 DOI: 10.1073/Pnas.1600899113  0.557
2016 Wang J, Yu Y, Tao F, Zhang J, Copetti D, Kudrna D, Talag J, Lee S, Wing RA, Fan C. DNA methylation changes facilitated evolution of genes derived from Mutator-like transposable elements. Genome Biology. 17: 92. PMID 27154274 DOI: 10.1186/S13059-016-0954-8  0.705
2015 Lee J, Izzah NK, Choi BS, Joh HJ, Lee SC, Perumal S, Seo J, Ahn K, Jo EJ, Choi GJ, Nou IS, Yu Y, Yang TJ. Genotyping-by-sequencing map permits identification of clubroot resistance QTLs and revision of the reference genome assembly in cabbage (Brassica oleracea L.). Dna Research : An International Journal For Rapid Publication of Reports On Genes and Genomes. PMID 26622061 DOI: 10.1093/Dnares/Dsv034  0.562
2015 Kim K, Lee SC, Lee J, Yu Y, Yang K, Choi BS, Koh HJ, Waminal NE, Choi HI, Kim NH, Jang W, Park HS, Lee J, Lee HO, Joh HJ, et al. Complete chloroplast and ribosomal sequences for 30 accessions elucidate evolution of Oryza AA genome species. Scientific Reports. 5: 15655. PMID 26506948 DOI: 10.1038/Srep15655  0.722
2015 Kim NR, Kim K, Lee SC, Lee JH, Cho SH, Yu Y, Kim YD, Yang TJ. The complete chloroplast genomes of two Wisteria species, W. floribunda and W. sinensis (Fabaceae). Mitochondrial Dna. 1-2. PMID 26465833 DOI: 10.3109/19401736.2015.1089497  0.677
2015 Zhang Y, Zhang S, Liu H, Fu B, Li L, Xie M, Song Y, Li X, Cai J, Wan W, Kui L, Huang H, Lyu J, Dong Y, Wang W, ... ... Yu Y, et al. Genome and comparative transcriptomics of African wild rice Oryza longistaminata provide insights into molecular mechanism of rhizomatousness and self-incompatibility. Molecular Plant. PMID 26358679 DOI: 10.1016/J.Molp.2015.08.006  0.64
2015 Lee J, Izzah NK, Jayakodi M, Perumal S, Joh HJ, Lee HJ, Lee SC, Park JY, Yang KW, Nou IS, Seo J, Yoo J, Suh Y, Ahn K, Lee JH, ... ... Yu Y, et al. Genome-wide SNP identification and QTL mapping for black rot resistance in cabbage. Bmc Plant Biology. 15: 32. PMID 25644124 DOI: 10.1186/S12870-015-0424-6  0.583
2015 Park D, Jung JW, Choi BS, Jayakodi M, Lee J, Lim J, Yu Y, Choi YS, Lee ML, Park Y, Choi IY, Yang TJ, Edwards OR, Nah G, Kwon HW. Uncovering the novel characteristics of Asian honey bee, Apis cerana, by whole genome sequencing. Bmc Genomics. 16: 1. PMID 25553907 DOI: 10.1186/1471-2164-16-1  0.622
2014 Wang M, Yu Y, Haberer G, Marri PR, Fan C, Goicoechea JL, Zuccolo A, Song X, Kudrna D, Ammiraju JS, Cossu RM, Maldonado C, Chen J, Lee S, Sisneros N, et al. The genome sequence of African rice (Oryza glaberrima) and evidence for independent domestication. Nature Genetics. 46: 982-8. PMID 25064006 DOI: 10.1038/Ng.3044  0.691
2014 Schmutz J, McClean PE, Mamidi S, Wu GA, Cannon SB, Grimwood J, Jenkins J, Shu S, Song Q, Chavarro C, Torres-Torres M, Geffroy V, Moghaddam SM, Gao D, Abernathy B, ... ... Yu Y, et al. A reference genome for common bean and genome-wide analysis of dual domestications. Nature Genetics. 46: 707-13. PMID 24908249 DOI: 10.1038/Ng.3008  0.766
2014 Kim S, Park M, Yeom SI, Kim YM, Lee JM, Lee HA, Seo E, Choi J, Cheong K, Kim KT, Jung K, Lee GW, Oh SK, Bae C, Kim SB, ... ... Yu Y, et al. Genome sequence of the hot pepper provides insights into the evolution of pungency in Capsicum species. Nature Genetics. 46: 270-8. PMID 24441736 DOI: 10.1038/Ng.2877  0.682
2014 Jacquemin J, Ammiraju JS, Haberer G, Billheimer DD, Yu Y, Liu LC, Rivera LF, Mayer K, Chen M, Wing RA. Fifteen million years of evolution in the Oryza genus shows extensive gene family expansion. Molecular Plant. 7: 642-56. PMID 24214894 DOI: 10.1093/Mp/Sst149  0.647
2013 Wang XQ, Yu Y, Li W, Guo HL, Lin ZX, Zhang XL. Association analysis of yield and fiber quality traits in Gossypium barbadense with SSRs and SRAPs. Genetics and Molecular Research : Gmr. 12: 3353-62. PMID 24065676 DOI: 10.4238/2013.September.4.1  0.316
2013 Koo HJ, McDowell ET, Ma X, Greer KA, Kapteyn J, Xie Z, Descour A, Kim H, Yu Y, Kudrna D, Wing RA, Soderlund CA, Gang DR. Ginger and turmeric expressed sequence tags identify signature genes for rhizome identity and development and the biosynthesis of curcuminoids, gingerols and terpenoids. Bmc Plant Biology. 13: 27. PMID 23410187 DOI: 10.1186/1471-2229-13-27  0.559
2013 Ortiz M, Neilson JW, Nelson WM, Legatzki A, Byrne A, Yu Y, Wing RA, Soderlund CA, Pryor BM, Pierson LS, Maier RM. Profiling bacterial diversity and taxonomic composition on speleothem surfaces in Kartchner Caverns, AZ. Microbial Ecology. 65: 371-83. PMID 23224253 DOI: 10.1007/S00248-012-0143-6  0.541
2012 Ha J, Abernathy B, Nelson W, Grant D, Wu X, Nguyen HT, Stacey G, Yu Y, Wing RA, Shoemaker RC, Jackson SA. Integration of the Draft Sequence and Physical Map as a Framework for Genomic Research in Soybean (Glycine max (L.) Merr.) and Wild Soybean (Glycine soja Sieb. and Zucc.). G3 (Bethesda, Md.). 2: 321-9. PMID 22413085 DOI: 10.1534/G3.111.001834  0.747
2012 Mo YJ, Kim KY, Shin WC, Lee GM, Ko JC, Nam JK, Kim BK, Ko JK, Yu Y, Yang TJ. Characterization of Imcrop, a Mutator-like MITE family in the rice genome Genes & Genomics. 34: 189-198. DOI: 10.1007/S13258-011-0193-Z  0.631
2011 Zuccolo A, Bowers JE, Estill JC, Xiong Z, Luo M, Sebastian A, Goicoechea JL, Collura K, Yu Y, Jiao Y, Duarte J, Tang H, Ayyampalayam S, Rounsley S, Kudrna D, et al. A physical map for the Amborella trichopoda genome sheds light on the evolution of angiosperm genome structure. Genome Biology. 12: R48. PMID 21619600 DOI: 10.1186/Gb-2011-12-5-R48  0.762
2011 Tian Z, Yu Y, Lin F, Yu Y, Sanmiguel PJ, Wing RA, McCouch SR, Ma J, Jackson SA. Exceptional lability of a genomic complex in rice and its close relatives revealed by interspecific and intraspecific comparison and population analysis. Bmc Genomics. 12: 142. PMID 21385395 DOI: 10.1186/1471-2164-12-142  0.735
2011 Song X, Goicoechea JL, Ammiraju JS, Luo M, He R, Lin J, Lee SJ, Sisneros N, Watts T, Kudrna DA, Golser W, Ashley E, Collura K, Braidotti M, Yu Y, et al. The 19 genomes of Drosophila: a BAC library resource for genus-wide and genome-scale comparative evolutionary research. Genetics. 187: 1023-30. PMID 21321134 DOI: 10.1534/Genetics.111.126540  0.773
2010 Febrer M, Goicoechea JL, Wright J, McKenzie N, Song X, Lin J, Collura K, Wissotski M, Yu Y, Ammiraju JS, Wolny E, Idziak D, Betekhtin A, Kudrna D, Hasterok R, et al. An integrated physical, genetic and cytogenetic map of Brachypodium distachyon, a model system for grass research. Plos One. 5: e13461. PMID 20976139 DOI: 10.1371/Journal.Pone.0013461  0.729
2010 Hurwitz BL, Kudrna D, Yu Y, Sebastian A, Zuccolo A, Jackson SA, Ware D, Wing RA, Stein L. Rice structural variation: a comparative analysis of structural variation between rice and three of its closest relatives in the genus Oryza. The Plant Journal : For Cell and Molecular Biology. 63: 990-1003. PMID 20626650 DOI: 10.1111/J.1365-313X.2010.04293.X  0.75
2010 Lin L, Pierce GJ, Bowers JE, Estill JC, Compton RO, Rainville LK, Kim C, Lemke C, Rong J, Tang H, Wang X, Braidotti M, Chen AH, Chicola K, Collura K, ... ... Yu Y, et al. A draft physical map of a D-genome cotton species (Gossypium raimondii). Bmc Genomics. 11: 395. PMID 20569427 DOI: 10.1186/1471-2164-11-395  0.749
2010 Sanyal A, Ammiraju JS, Lu F, Yu Y, Rambo T, Currie J, Kollura K, Kim HR, Chen J, Ma J, San Miguel P, Mingsheng C, Wing RA, Jackson SA. Orthologous comparisons of the Hd1 region across genera reveal Hd1 gene lability within diploid Oryza species and disruptions to microsynteny in Sorghum. Molecular Biology and Evolution. 27: 2487-506. PMID 20522726 DOI: 10.1093/Molbev/Msq133  0.639
2010 Ammiraju JS, Fan C, Yu Y, Song X, Cranston KA, Pontaroli AC, Lu F, Sanyal A, Jiang N, Rambo T, Currie J, Collura K, Talag J, Bennetzen JL, Chen M, et al. Spatio-temporal patterns of genome evolution in allotetraploid species of the genus Oryza. The Plant Journal : For Cell and Molecular Biology. 63: 430-42. PMID 20487382 DOI: 10.1111/J.1365-313X.2010.04251.X  0.714
2010 Dai L, Wu J, Li X, Wang X, Liu X, Jantasuriyarat C, Kudrna D, Yu Y, Wing RA, Han B, Zhou B, Wang GL. Genomic structure and evolution of the Pi2/9 locus in wild rice species. Tag. Theoretical and Applied Genetics. Theoretische Und Angewandte Genetik. 121: 295-309. PMID 20229250 DOI: 10.1007/S00122-010-1310-0  0.731
2010 Schmutz J, Cannon SB, Schlueter J, Ma J, Mitros T, Nelson W, Hyten DL, Song Q, Thelen JJ, Cheng J, Xu D, Hellsten U, May GD, Yu Y, Sakurai T, et al. Genome sequence of the palaeopolyploid soybean. Nature. 463: 178-83. PMID 20075913 DOI: 10.1038/Nature08670  0.781
2010 Ammiraju JSS, Song X, Luo M, Sisneros N, Angelova A, Kudrna D, Kim H, Yu Y, Goicoechea JL, Lorieux M, Kurata N, Brar D, Ware D, Jackson S, Wing RA. The Oryza BAC resource: A genus-wide and genome scale tool for exploring rice genome evolution and leveraging useful genetic diversity from wild relatives Breeding Science. 60: 536-543. DOI: 10.1270/Jsbbs.60.536  0.756
2010 Schmutz J, Cannon SB, Schlueter J, Ma J, Mitros T, Nelson W, Hyten DL, Song Q, Thelen JJ, Cheng J, Xu D, Hellsten U, May GD, Yu Y, Sakurai T, et al. Erratum: Genome sequence of the palaeopolyploid soybean Nature. 465: 120-120. DOI: 10.1038/Nature08957  0.729
2010 Goicoechea JL, Ammiraju JSS, Marri PR, Chen M, Jackson S, Yu Y, Rounsley S, Wing RA. The future of rice genomics: Sequencing the collective Oryza genome Rice. 3: 89-97. DOI: 10.1007/S12284-010-9052-9  0.78
2010 Zuccolo A, Sebastian A, Yu Y, Jackson S, Rounsley S, Billheimer D, Wing RA. Assessing the extent of substitution rate variation of retrotransposon Long Terminal Repeat sequences in Oryza sativa and Oryza glaberrima Rice. 3: 242-250. DOI: 10.1007/S12284-010-9046-7  0.657
2009 Schnable PS, Ware D, Fulton RS, Stein JC, Wei F, Pasternak S, Liang C, Zhang J, Fulton L, Graves TA, Minx P, Reily AD, Courtney L, Kruchowski SS, Tomlinson C, ... ... Yu Y, et al. The B73 maize genome: complexity, diversity, and dynamics. Science (New York, N.Y.). 326: 1112-5. PMID 19965430 DOI: 10.1126/Science.1178534  0.755
2009 Soderlund C, Descour A, Kudrna D, Bomhoff M, Boyd L, Currie J, Angelova A, Collura K, Wissotski M, Ashley E, Morrow D, Fernandes J, Walbot V, Yu Y. Sequencing, mapping, and analysis of 27,455 maize full-length cDNAs. Plos Genetics. 5: e1000740. PMID 19936069 DOI: 10.1371/Journal.Pgen.1000740  0.574
2009 Wei F, Stein JC, Liang C, Zhang J, Fulton RS, Baucom RS, De Paoli E, Zhou S, Yang L, Han Y, Pasternak S, Narechania A, Zhang L, Yeh CT, Ying K, ... ... Yu Y, et al. Detailed analysis of a contiguous 22-Mb region of the maize genome. Plos Genetics. 5: e1000728. PMID 19936048 DOI: 10.1371/Journal.Pgen.1000728  0.776
2009 Gao D, Gill N, Kim HR, Walling JG, Zhang W, Fan C, Yu Y, Ma J, SanMiguel P, Jiang N, Cheng Z, Wing RA, Jiang J, Jackson SA. A lineage-specific centromere retrotransposon in Oryza brachyantha. The Plant Journal : For Cell and Molecular Biology. 60: 820-31. PMID 19702667 DOI: 10.1111/J.1365-313X.2009.04005.X  0.726
2009 Nah G, Pagliarulo CL, Mohr PG, Luo M, Sisneros N, Yu Y, Collura K, Currie J, Goicoechea JL, Wing RA, Schumaker KS. Comparative sequence analysis of the SALT OVERLY SENSITIVE1 orthologous region in Thellungiella halophila and Arabidopsis thaliana. Genomics. 94: 196-203. PMID 19481598 DOI: 10.1016/J.Ygeno.2009.05.007  0.706
2009 Degnan PH, Yu Y, Sisneros N, Wing RA, Moran NA. Hamiltonella defensa, genome evolution of protective bacterial endosymbiont from pathogenic ancestors. Proceedings of the National Academy of Sciences of the United States of America. 106: 9063-8. PMID 19451630 DOI: 10.1073/Pnas.0900194106  0.687
2009 Zhang H, DiBaise JK, Zuccolo A, Kudrna D, Braidotti M, Yu Y, Parameswaran P, Crowell MD, Wing R, Rittmann BE, Krajmalnik-Brown R. Human gut microbiota in obesity and after gastric bypass. Proceedings of the National Academy of Sciences of the United States of America. 106: 2365-70. PMID 19164560 DOI: 10.1073/Pnas.0812600106  0.49
2009 Wing R, Kim H, Goicoechea J, Yu Y, Kudrna D, Zuccolo A, Jetty SA, Luo M, Nelson W, Soderlund C, San Miguel P, Gill N, Walling J, Jackson S, Hurwitz B, et al. The Oryza map alignment project (OMAP): a new resource for comparative genomics studies within Oryza International Rice Research Notes. 31. DOI: 10.3860/irrn.v31i2.1142  0.636
2009 Rounsley S, Marri PR, Yu Y, He R, Sisneros N, Goicoechea JL, Lee SJ, Angelova A, Kudrna D, Luo M, Affourtit J, Desany B, Knight J, Niazi F, Egholm M, et al. De novo next generation sequencing of plant genomes Rice. 2: 35-43. DOI: 10.1007/S12284-009-9025-Z  0.727
2008 Fan C, Zhang Y, Yu Y, Rounsley S, Long M, Wing RA. The subtelomere of Oryza sativa chromosome 3 short arm as a hot bed of new gene origination in rice. Molecular Plant. 1: 839-50. PMID 19825586 DOI: 10.1093/Mp/Ssn050  0.688
2008 Ammiraju JS, Lu F, Sanyal A, Yu Y, Song X, Jiang N, Pontaroli AC, Rambo T, Currie J, Collura K, Talag J, Fan C, Goicoechea JL, Zuccolo A, Chen J, et al. Dynamic evolution of oryza genomes is revealed by comparative genomic analysis of a genus-wide vertical data set. The Plant Cell. 20: 3191-209. PMID 19098269 DOI: 10.1105/Tpc.108.063727  0.775
2008 Grover CE, Yu Y, Wing RA, Paterson AH, Wendel JF. A phylogenetic analysis of indel dynamics in the cotton genus. Molecular Biology and Evolution. 25: 1415-28. PMID 18400789 DOI: 10.1093/Molbev/Msn085  0.755
2008 Shoemaker RC, Grant D, Olson T, Warren WC, Wing R, Yu Y, Kim H, Cregan P, Joseph B, Futrell-Griggs M, Nelson W, Davito J, Walker J, Wallis J, Kremitski C, et al. Microsatellite discovery from BAC end sequences and genetic mapping to anchor the soybean physical and genetic maps. Genome / National Research Council Canada = Gã©Nome / Conseil National De Recherches Canada. 51: 294-302. PMID 18356965 DOI: 10.1139/G08-010  0.572
2008 Kim H, Hurwitz B, Yu Y, Collura K, Gill N, SanMiguel P, Mullikin JC, Maher C, Nelson W, Wissotski M, Braidotti M, Kudrna D, Goicoechea JL, Stein L, Ware D, et al. Construction, alignment and analysis of twelve framework physical maps that represent the ten genome types of the genus Oryza. Genome Biology. 9: R45. PMID 18304353 DOI: 10.1186/Gb-2008-9-2-R45  0.752
2008 Schlueter JA, Goicoechea JL, Collura K, Gill N, Lin J, Yu Y, Kudrna D, Zuccolo A, Vallejos CE, Muñoz-Torres M, Blair MW, Tohme J, Tomkins J, McClean P, Wing RA, et al. BAC-end Sequence Analysis and a Draft Physical Map of the Common Bean (Phaseolus vulgaris L.) Genome Tropical Plant Biology. 1: 40-48. DOI: 10.1007/S12042-007-9003-9  0.751
2007 Ammiraju JS, Zuccolo A, Yu Y, Song X, Piegu B, Chevalier F, Walling JG, Ma J, Talag J, Brar DS, SanMiguel PJ, Jiang N, Jackson SA, Panaud O, Wing RA. Evolutionary dynamics of an ancient retrotransposon family provides insights into evolution of genome size in the genus Oryza. The Plant Journal : For Cell and Molecular Biology. 52: 342-51. PMID 17764506 DOI: 10.1111/J.1365-313X.2007.03242.X  0.729
2007 Zuccolo A, Sebastian A, Talag J, Yu Y, Kim H, Collura K, Kudrna D, Wing RA. Transposable element distribution, abundance and role in genome size variation in the genus Oryza. Bmc Evolutionary Biology. 7: 152. PMID 17727727 DOI: 10.1186/1471-2148-7-152  0.712
2007 Itoh T, Tanaka T, Barrero RA, Yamasaki C, Fujii Y, Hilton PB, Antonio BA, Aono H, Apweiler R, Bruskiewich R, Bureau T, Burr F, Costa de Oliveira A, Fuks G, ... ... Yu Y, et al. Curated genome annotation of Oryza sativa ssp. japonica and comparative genome analysis with Arabidopsis thaliana. Genome Research. 17: 175-83. PMID 17210932 DOI: 10.1101/Gr.5509507  0.712
2007 Wing RA, Kim H, Goicoechea JL, Yu Y, Kudrna D, Zuccolo A, Ammiraju JSS, Luo M, Nelson W, Ma J, Sanmiguel P, Hurwitz B, Ware D, Brar D, Mackill D, et al. The oryza map alignment project (OMAP): A new resource for comparative genome studies within oryza Rice Functional Genomics: Challenges, Progress and Prospects. 395-409. DOI: 10.3860/Irrn.V31I2.1142  0.672
2006 Udall JA, Swanson JM, Haller K, Rapp RA, Sparks ME, Hatfield J, Yu Y, Wu Y, Dowd C, Arpat AB, Sickler BA, Wilkins TA, Guo JY, Chen XY, Scheffler J, et al. A global assembly of cotton ESTs. Genome Research. 16: 441-50. PMID 16478941 DOI: 10.1101/Gr.4602906  0.74
2006 Ammiraju JS, Luo M, Goicoechea JL, Wang W, Kudrna D, Mueller C, Talag J, Kim H, Sisneros NB, Blackmon B, Fang E, Tomkins JB, Brar D, MacKill D, McCouch S, ... ... Yu Y, et al. The Oryza bacterial artificial chromosome library resource: construction and analysis of 12 deep-coverage large-insert BAC libraries that represent the 10 genome types of the genus Oryza. Genome Research. 16: 140-7. PMID 16344555 DOI: 10.1101/Gr.3766306  0.782
2006 Luo M, Yu Y, Kim H, Kudrna D, Itoh Y, Agate RJ, Melamed E, Goicoechea JL, Talag J, Mueller C, Wang W, Currie J, Sisneros NB, Wing RA, Arnold AP. Utilization of a zebra finch BAC library to determine the structure of an avian androgen receptor genomic region. Genomics. 87: 181-90. PMID 16321505 DOI: 10.1016/J.Ygeno.2005.09.005  0.761
2006 Yu Y, Santat LA, Choi S. Bioinformatics Packages for Sequence Analysis Applied Mycology and Biotechnology. 6: 143-160. DOI: 10.1016/S1874-5334(06)80009-2  0.594
2006 Luo M, Yu Y, Kim H, Kudrna D, Itoh Y, Agate RJ, Melamed E, Goicoechea JL, Talag J, Mueller C, Wang W, Currie J, Sisneros NB, Wing RA, Arnold AP. Erratum to “Utilization of a zebra finch BAC library to determine the structure of an avian androgen receptor genomic region” [Genomics 87 (2006) 181–190] Genomics. 87: 678-679. DOI: 10.1016/J.Ygeno.2006.01.008  0.701
2005 Wing RA, Ammiraju JS, Luo M, Kim H, Yu Y, Kudrna D, Goicoechea JL, Wang W, Nelson W, Rao K, Brar D, Mackill DJ, Han B, Soderlund C, Stein L, et al. The oryza map alignment project: the golden path to unlocking the genetic potential of wild rice species. Plant Molecular Biology. 59: 53-62. PMID 16217601 DOI: 10.1007/S11103-004-6237-X  0.705
2005 Ammiraju JS, Yu Y, Luo M, Kudrna D, Kim H, Goicoechea JL, Katayose Y, Matsumoto T, Wu J, Sasaki T, Wing RA. Random sheared fosmid library as a new genomic tool to accelerate complete finishing of rice (Oryza sativa spp. Nipponbare) genome sequence: sequencing of gap-specific fosmid clones uncovers new euchromatic portions of the genome. Tag. Theoretical and Applied Genetics. Theoretische Und Angewandte Genetik. 111: 1596-607. PMID 16200416 DOI: 10.1007/S00122-005-0091-3  0.789
2005 Buell CR, Yuan Q, Ouyang S, Liu J, Zhu W, Wang A, Maiti R, Haas B, Wortman J, Pertea M, Jones KM, Kim M, Overton L, Tsitrin T, Fadrosh D, ... ... Yu Y, et al. Sequence, annotation, and analysis of synteny between rice chromosome 3 and diverged grass species. Genome Research. 15: 1284-91. PMID 16109971 DOI: 10.1101/Gr.3869505  0.721
2005 Yang TJ, Lee S, Chang SB, Yu Y, de Jong H, Wing RA. In-depth sequence analysis of the tomato chromosome 12 centromeric region: identification of a large CAA block and characterization of pericentromere retrotranposons. Chromosoma. 114: 103-17. PMID 15965704 DOI: 10.1007/S00412-005-0342-8  0.687
2005 Yang TJ, Yu Y, Chang SB, de Jong H, Oh CS, Ahn SN, Fang E, Wing RA. Toward closing rice telomere gaps: mapping and sequence characterization of rice subtelomere regions. Tag. Theoretical and Applied Genetics. Theoretische Und Angewandte Genetik. 111: 467-78. PMID 15965650 DOI: 10.1007/S00122-005-2034-4  0.712
2005 Jantasuriyarat C, Gowda M, Haller K, Hatfield J, Lu G, Stahlberg E, Zhou B, Li H, Kim H, Yu Y, Dean RA, Wing RA, Soderlund C, Wang GL. Large-scale identification of expressed sequence tags involved in rice and rice blast fungus interaction. Plant Physiology. 138: 105-15. PMID 15888683 DOI: 10.1104/Pp.104.055624  0.691
2005 Horn R, Lecouls AC, Callahan A, Dandekar A, Garay L, McCord P, Howad W, Chan H, Verde I, Main D, Jung S, Georgi L, Forrest S, Mook J, Zhebentyayeva T, ... Yu Y, et al. Candidate gene database and transcript map for peach, a model species for fruit trees. Tag. Theoretical and Applied Genetics. Theoretische Und Angewandte Genetik. 110: 1419-28. PMID 15846479 DOI: 10.1007/S00122-005-1968-X  0.7
2005 Choisne N, Demange N, Orjeda G, Samain S, D'Hont A, Cattolico L, Pelletier E, Couloux A, Segurens B, Wincker P, Scarpelli C, Weissenbach J, Salanoubat M, Singh NK, Mohapatra T, ... ... Yu Y, et al. The sequence of rice chromosomes 11 and 12, rich in disease resistance genes and recent gene duplications Bmc Biology. 3. DOI: 10.1186/1741-7007-3-20  0.714
2005 Yu Y, Wing RA. Whole genome sequencing: Methodology and progress in cereals Cereal Genomics. 385-423. DOI: 10.1007/1-4020-2359-6_13  0.728
2004 Messing J, Bharti AK, Karlowski WM, Gundlach H, Kim HR, Yu Y, Wei F, Fuks G, Soderlund CA, Mayer KF, Wing RA. Sequence composition and genome organization of maize. Proceedings of the National Academy of Sciences of the United States of America. 101: 14349-54. PMID 15388850 DOI: 10.1073/Pnas.0406163101  0.775
2003 Yu Y, Rambo T, Currie J, Saski C, Kim HR, Collura K, Thompson S, Simmons J, Yang TJ, Nah G, Patel AJ, Thurmond S, Henry D, Oates R, Palmer M, et al. In-depth view of structure, activity, and evolution of rice chromosome 10 Science. 300: 1566-1569. PMID 12791992 DOI: 10.1126/Science.1083523  0.715
2003 Yang TJ, Yu Y, Nah G, Atkins M, Lee S, Frisch DA, Wing RA. Construction and utility of 10-kb libraries for efficient clone-gap closure for rice genome sequencing. Tag. Theoretical and Applied Genetics. Theoretische Und Angewandte Genetik. 107: 652-60. PMID 12783166 DOI: 10.1007/S00122-003-1302-4  0.763
2002 Goff SA, Ricke D, Lan TH, Presting G, Wang R, Dunn M, Glazebrook J, Sessions A, Oeller P, Varma H, Hadley D, Hutchison D, Martin C, Katagiri F, Lange BM, ... ... Yu Y, et al. A draft sequence of the rice genome (Oryza sativa L. ssp. japonica). Science (New York, N.Y.). 296: 92-100. PMID 11935018 DOI: 10.1126/science.1068275  0.76
2002 Chen M, Presting G, Barbazuk WB, Goicoechea JL, Blackmon B, Fang G, Kim H, Frisch D, Yu Y, Sun S, Higingbottom S, Phimphilai J, Phimphilai D, Thurmond S, Gaudette B, et al. An integrated physical and genetic map of the rice genome. The Plant Cell. 14: 537-45. PMID 11910002 DOI: 10.1105/Tpc.010485  0.766
2001 Presting GG, Budiman MA, Wood T, Yu Y, Kim HR, Goicoechea JL, Fang E, Blackman B, Jiang J, Woo SS, Dean RA, Frisch D, Wing RA. A framework for sequencing the rice genome. Novartis Foundation Symposium. 236: 13-24; discussion 24. PMID 11387975 DOI: 10.1002/9780470515778.Ch3  0.775
2000 Mao L, Wood TC, Yu Y, Budiman MA, Tomkins J, Woo S, Sasinowski M, Presting G, Frisch D, Goff S, Dean RA, Wing RA. Rice transposable elements: a survey of 73,000 sequence-tagged-connectors. Genome Research. 10: 982-90. PMID 10899147 DOI: 10.1101/Gr.10.7.982  0.759
2000 Yu Y, Tomkins JP, Waugh R, Frisch DA, Kudrna D, Kleinhofs A, Brueggeman RS, Muehlbauer GJ, Wise RP, Wing RA. A bacterial artificial chromosome library for barley (Hordeum vulgare L.) and the identification of clones containing putative resistance genes Theoretical and Applied Genetics. 101: 1093-1099. DOI: 10.1007/S001220051584  0.68
1999 Tomkins JP, Yu Y, Miller-Smith H, Frisch DA, Woo SS, Wing RA. A bacterial artificial chromosome library for sugarcane. Tag. Theoretical and Applied Genetics. Theoretische Und Angewandte Genetik. 99: 419-24. PMID 22665173 DOI: 10.1007/S001220051252  0.695
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