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Eric Harold Lyons - Publications

Plant Sciences University of Arizona, Tucson, AZ 

39 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
2019 McCarthy FM, Pendarvis K, Cooksey AM, Gresham CR, Bomhoff M, Davey S, Lyons E, Sonstegard TS, Bridges SM, Burgess SC. Chickspress: a resource for chicken gene expression. Database : the Journal of Biological Databases and Curation. 2019. PMID 31210271 DOI: 10.1093/database/baz058  0.32
2019 Edger PP, Poorten TJ, VanBuren R, Hardigan MA, Colle M, McKain MR, Smith RD, Teresi SJ, Nelson ADL, Wai CM, Alger EI, Bird KA, Yocca AE, Pumplin N, Ou S, ... ... Lyons E, et al. Author Correction: Origin and evolution of the octoploid strawberry genome. Nature Genetics. PMID 30842601 DOI: 10.1038/s41588-019-0380-4  1
2019 Edger PP, Poorten TJ, VanBuren R, Hardigan MA, Colle M, McKain MR, Smith RD, Teresi SJ, Nelson ADL, Wai CM, Alger EI, Bird KA, Yocca AE, Pumplin N, Ou S, ... ... Lyons E, et al. Origin and evolution of the octoploid strawberry genome. Nature Genetics. PMID 30804557 DOI: 10.1038/s41588-019-0356-4  1
2018 Hao Y, Washburn JD, Rosenthal J, Nielsen B, Lyons E, Edger PP, Pires JC, Conant GC. Patterns of Population Variation in Two Paleopolyploid Eudicot Lineages Suggest That Dosage-Based Selection on Homeologs Is Long-Lived. Genome Biology and Evolution. 10: 999-1011. PMID 29617811 DOI: 10.1093/gbe/evy061  1
2018 Emery M, Willis MMS, Hao Y, Barry K, Oakgrove K, Peng Y, Schmutz J, Lyons E, Pires JC, Edger PP, Conant GC. Preferential retention of genes from one parental genome after polyploidy illustrates the nature and scope of the genomic conflicts induced by hybridization. Plos Genetics. 14: e1007267. PMID 29590103 DOI: 10.1371/journal.pgen.1007267  1
2018 Nelson ADL, Haug-Baltzell AK, Davey S, Gregory BD, Lyons E. EPIC-CoGe: Managing and Analyzing Genomic Data. Bioinformatics (Oxford, England). PMID 29474529 DOI: 10.1093/bioinformatics/bty106  0.32
2017 Varshney RK, Shi C, Thudi M, Mariac C, Wallace J, Qi P, Zhang H, Zhao Y, Wang X, Rathore A, Srivastava RK, Chitikineni A, Fan G, Bajaj P, Punnuri S, ... ... Lyons E, et al. Pearl millet genome sequence provides a resource to improve agronomic traits in arid environments. Nature Biotechnology. PMID 28922347 DOI: 10.1038/nbt.3943  1
2017 Xu S, Brockmöller T, Navarro-Quezada A, Kuhl H, Gase K, Ling Z, Zhou W, Kreitzer C, Stanke M, Tang H, Lyons E, Pandey P, Pandey SP, Timmermann B, Gaquerel E, et al. Wild tobacco genomes reveal the evolution of nicotine biosynthesis. Proceedings of the National Academy of Sciences of the United States of America. PMID 28536194 DOI: 10.1073/pnas.1700073114  1
2017 Joyce BL, Haug-Baltzell AK, Hulvey JP, McCarthy F, Devisetty UK, Lyons E. Leveraging CyVerse Resources for De Novo Comparative Transcriptomics of Underserved (Non-model) Organisms. Journal of Visualized Experiments : Jove. PMID 28518075 DOI: 10.3791/55009  0.32
2017 Haug-Baltzell A, Stephens S, Davey S, Scheidegger C, Lyons E. SynMap2 & SynMap3D: Web-based whole-genome synteny browsers. Bioinformatics (Oxford, England). PMID 28334338 DOI: 10.1093/bioinformatics/btx144  0.32
2016 Joyce BL, Haug-Baltzell A, Davey S, Bomhoff M, Schnable JC, Lyons E. FractBias: a graphical tool for assessing fractionation bias following polyploidy. Bioinformatics (Oxford, England). PMID 27794557 DOI: 10.1093/bioinformatics/btw666  1
2016 Bombarely A, Moser M, Amrad A, Bao M, Bapaume L, Barry CS, Bliek M, Boersma MR, Borghi L, Bruggmann R, Bucher M, D'Agostino N, Davies K, Druege U, Dudareva N, ... ... Lyons E, et al. Insight into the evolution of the Solanaceae from the parental genomes of Petunia hybrida. Nature Plants. 2: 16074. PMID 27255838 DOI: 10.1038/nplants.2016.74  1
2016 VanBuren R, Bryant D, Bushakra JM, Vining KJ, Edger PP, Rowley ER, Priest HD, Michael TP, Lyons E, Filichkin SA, Dossett M, Finn CE, Bassil NV, Mockler TC. The genome of black raspberry (Rubus occidentalis). The Plant Journal : For Cell and Molecular Biology. PMID 27228578 DOI: 10.1111/tpj.13215  1
2015 Tang H, Bomhoff MD, Briones E, Zhang L, Schnable JC, Lyons E. SynFind: compiling syntenic regions across any set of genomes on demand. Genome Biology and Evolution. PMID 26560340 DOI: 10.1093/gbe/evv219  1
2015 VanBuren R, Bryant D, Edger PP, Tang H, Burgess D, Challabathula D, Spittle K, Hall R, Gu J, Lyons E, Freeling M, Bartels D, Ten Hallers B, Hastie A, Michael TP, et al. Single-molecule sequencing of the desiccation-tolerant grass Oropetium thomaeum. Nature. 527: 508-11. PMID 26560029 DOI: 10.1038/nature15714  1
2015 Ming R, VanBuren R, Wai CM, Tang H, Schatz MC, Bowers JE, Lyons E, Wang ML, Chen J, Biggers E, Zhang J, Huang L, Zhang L, Miao W, Zhang J, et al. The pineapple genome and the evolution of CAM photosynthesis. Nature Genetics. 47: 1435-42. PMID 26523774 DOI: 10.1038/ng.3435  1
2015 Haug-Baltzell A, Jarvis ED, McCarthy FM, Lyons E. Identification of dopamine receptors across the extant avian family tree and analysis with other clades uncovers a polyploid expansion among vertebrates. Frontiers in Neuroscience. 9: 361. PMID 26500483 DOI: 10.3389/fnins.2015.00361  0.32
2015 Tang H, Lyons E, Town CD. Optical mapping in plant comparative genomics. Gigascience. 4: 3. PMID 25699175 DOI: 10.1186/s13742-015-0044-y  1
2015 Tang H, Zhang X, Miao C, Zhang J, Ming R, Schnable JC, Schnable PS, Lyons E, Lu J. ALLMAPS: robust scaffold ordering based on multiple maps. Genome Biology. 16: 3. PMID 25583564 DOI: 10.1186/s13059-014-0573-1  1
2014 Chalhoub B, Denoeud F, Liu S, Parkin IA, Tang H, Wang X, Chiquet J, Belcram H, Tong C, Samans B, Corréa M, Da Silva C, Just J, Falentin C, Koh CS, ... ... Lyons E, et al. Plant genetics. Early allopolyploid evolution in the post-Neolithic Brassica napus oilseed genome. Science (New York, N.Y.). 345: 950-3. PMID 25146293 DOI: 10.1126/science.1253435  1
2013 Chen EC, Buen Abad Najar C, Zheng C, Brandts A, Lyons E, Tang H, Carretero-Paulet L, Albert VA, Sankoff D. The dynamics of functional classes of plant genes in rediploidized ancient polyploids. Bmc Bioinformatics. 14: S19. PMID 24564814 DOI: 10.1186/1471-2105-14-S15-S19  1
2013 Hofberger JA, Lyons E, Edger PP, Chris Pires J, Eric Schranz M. Whole genome and tandem duplicate retention facilitated glucosinolate pathway diversification in the mustard family. Genome Biology and Evolution. 5: 2155-73. PMID 24171911 DOI: 10.1093/gbe/evt162  0.36
2013 Ibarra-Laclette E, Lyons E, Hernández-Guzmán G, Pérez-Torres CA, Carretero-Paulet L, Chang TH, Lan T, Welch AJ, Juárez MJ, Simpson J, Fernández-Cortés A, Arteaga-Vázquez M, Góngora-Castillo E, Acevedo-Hernández G, Schuster SC, et al. Architecture and evolution of a minute plant genome. Nature. 498: 94-8. PMID 23665961 DOI: 10.1038/nature12132  1
2013 Ming R, VanBuren R, Liu Y, Yang M, Han Y, Li LT, Zhang Q, Kim MJ, Schatz MC, Campbell M, Li J, Bowers JE, Tang H, Lyons E, Ferguson AA, et al. Genome of the long-living sacred lotus (Nelumbo nucifera Gaertn.). Genome Biology. 14: R41. PMID 23663246 DOI: 10.1186/gb-2013-14-5-r41  1
2012 Tang H, Lyons E. Unleashing the genome of brassica rapa. Frontiers in Plant Science. 3: 172. PMID 22866056 DOI: 10.3389/fpls.2012.00172  1
2012 D'Hont A, Denoeud F, Aury JM, Baurens FC, Carreel F, Garsmeur O, Noel B, Bocs S, Droc G, Rouard M, Da Silva C, Jabbari K, Cardi C, Poulain J, Souquet M, ... ... Lyons E, et al. The banana (Musa acuminata) genome and the evolution of monocotyledonous plants. Nature. 488: 213-7. PMID 22801500 DOI: 10.1038/nature11241  1
2012 Reneker J, Lyons E, Conant GC, Pires JC, Freeling M, Shyu CR, Korkin D. Long identical multispecies elements in plant and animal genomes. Proceedings of the National Academy of Sciences of the United States of America. 109: E1183-91. PMID 22496592 DOI: 10.1073/pnas.1121356109  1
2012 Schnable JC, Freeling M, Lyons E. Genome-wide analysis of syntenic gene deletion in the grasses. Genome Biology and Evolution. 4: 265-77. PMID 22275519 DOI: 10.1093/gbe/evs009  1
2011 Tang H, Lyons E, Pedersen B, Schnable JC, Paterson AH, Freeling M. Screening synteny blocks in pairwise genome comparisons through integer programming. Bmc Bioinformatics. 12: 102. PMID 21501495 DOI: 10.1186/1471-2105-12-102  1
2011 Lyons E, Freeling M, Kustu S, Inwood W. Using genomic sequencing for classical genetics in E. coli K12. Plos One. 6: e16717. PMID 21364914 DOI: 10.1371/journal.pone.0016717  1
2010 Woodhouse MR, Schnable JC, Pedersen BS, Lyons E, Lisch D, Subramaniam S, Freeling M. Following tetraploidy in maize, a short deletion mechanism removed genes preferentially from one of the two homologs. Plos Biology. 8: e1000409. PMID 20613864 DOI: 10.1371/journal.pbio.1000409  1
2010 Kane J, Freeling M, Lyons E. The evolution of a high copy gene array in Arabidopsis. Journal of Molecular Evolution. 70: 531-44. PMID 20495794 DOI: 10.1007/s00239-010-9350-2  1
2009 Paterson AH, Bowers JE, Bruggmann R, Dubchak I, Grimwood J, Gundlach H, Haberer G, Hellsten U, Mitros T, Poliakov A, Schmutz J, Spannagl M, Tang H, Wang X, Wicker T, ... ... Lyons E, et al. The Sorghum bicolor genome and the diversification of grasses. Nature. 457: 551-6. PMID 19189423 DOI: 10.1038/nature07723  1
2008 Lyons E, Pedersen B, Kane J, Alam M, Ming R, Tang H, Wang X, Bowers J, Paterson A, Lisch D, Freeling M. Finding and comparing syntenic regions among Arabidopsis and the outgroups papaya, poplar, and grape: CoGe with rosids. Plant Physiology. 148: 1772-81. PMID 18952863 DOI: 10.1104/pp.108.124867  1
2008 Freeling M, Lyons E, Pedersen B, Alam M, Ming R, Lisch D. Many or most genes in Arabidopsis transposed after the origin of the order Brassicales. Genome Research. 18: 1924-37. PMID 18836034 DOI: 10.1101/gr.081026.108  1
2008 Ming R, Hou S, Feng Y, Yu Q, Dionne-Laporte A, Saw JH, Senin P, Wang W, Ly BV, Lewis KL, Salzberg SL, Feng L, Jones MR, Skelton RL, Murray JE, ... ... Lyons E, et al. The draft genome of the transgenic tropical fruit tree papaya (Carica papaya Linnaeus). Nature. 452: 991-6. PMID 18432245 DOI: 10.1038/nature06856  1
2008 Lyons E, Freeling M. How to usefully compare homologous plant genes and chromosomes as DNA sequences. The Plant Journal : For Cell and Molecular Biology. 53: 661-73. PMID 18269575 DOI: 10.1111/j.1365-313X.2007.03326.x  1
2007 Freeling M, Rapaka L, Lyons E, Pedersen B, Thomas BC. G-boxes, bigfoot genes, and environmental response: characterization of intragenomic conserved noncoding sequences in Arabidopsis. The Plant Cell. 19: 1441-57. PMID 17496117 DOI: 10.1105/tpc.107.050419  1
2007 Thomas BC, Rapaka L, Lyons E, Pedersen B, Freeling M. Arabidopsis intragenomic conserved noncoding sequence. Proceedings of the National Academy of Sciences of the United States of America. 104: 3348-53. PMID 17301222 DOI: 10.1073/pnas.0611574104  1
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