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Eric Harold Lyons - Publications

Plant Sciences University of Arizona, Tucson, AZ 

67 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
2022 Palos K, Nelson Dittrich AC, Yu L, Brock JR, Railey CE, Wu HL, Sokolowska E, Skirycz A, Hsu PY, Gregory BD, Lyons E, Beilstein MA, Nelson ADL. Identification and functional annotation of long intergenic non-coding RNAs in Brassicaceae. The Plant Cell. PMID 35666179 DOI: 10.1093/plcell/koac166  0.321
2022 Hao Y, Fleming J, Petterson J, Lyons E, Edger PP, Pires JC, Thorne JL, Conant GC. Convergent evolution of polyploid genomes from across the eukaryotic tree of life. G3 (Bethesda, Md.). PMID 35451464 DOI: 10.1093/g3journal/jkac094  0.744
2022 Varshney RK, Roorkiwal M, Sun S, Bajaj P, Chitikineni A, Thudi M, Singh NP, Du X, Upadhyaya HD, Khan AW, Wang Y, Garg V, Fan G, Cowling WA, Crossa J, ... ... Lyons E, et al. Author Correction: A chickpea genetic variation map based on the sequencing of 3,366 genomes. Nature. PMID 35338354 DOI: 10.1038/s41586-022-04660-x  0.612
2022 Chávez Montes RA, Haber A, Pardo J, Powell RF, Divisetty UK, Silva AT, Hernández-Hernández T, Silveira V, Tang H, Lyons E, Herrera Estrella LR, VanBuren R, Oliver MJ. A comparative genomics examination of desiccation tolerance and sensitivity in two sister grass species. Proceedings of the National Academy of Sciences of the United States of America. 119. PMID 35082155 DOI: 10.1073/pnas.2118886119  0.345
2022 Stephan T, Burgess SM, Cheng H, Danko CG, Gill CA, Jarvis ED, Koepfli KP, Koltes JE, Lyons E, Ronald P, Ryder OA, Schriml LM, Soltis P, VandeWoude S, Zhou H, et al. Darwinian genomics and diversity in the tree of life. Proceedings of the National Academy of Sciences of the United States of America. 119. PMID 35042807 DOI: 10.1073/pnas.2115644119  0.509
2022 Tuggle CK, Clarke J, Dekkers JCM, Ertl D, Lawrence-Dill CJ, Lyons E, Murdoch BM, Scott NM, Schnable PS. The Agricultural Genome to Phenome Initiative (AG2PI): creating a shared vision across crop and livestock research communities. Genome Biology. 23: 3. PMID 34980221 DOI: 10.1186/s13059-021-02570-1  0.335
2021 Varshney RK, Roorkiwal M, Sun S, Bajaj P, Chitikineni A, Thudi M, Singh NP, Du X, Upadhyaya HD, Khan AW, Wang Y, Garg V, Fan G, Cowling WA, Crossa J, ... ... Lyons E, et al. A chickpea genetic variation map based on the sequencing of 3,366 genomes. Nature. PMID 34759320 DOI: 10.1038/s41586-021-04066-1  0.71
2021 Hao Y, Mabry ME, Edger PP, Freeling M, Zheng C, Jin L, VanBuren R, Colle M, An H, Abrahams RS, Washburn JD, Qi X, Barry K, Daum C, Shu S, ... ... Lyons E, et al. The contributions from the progenitor genomes of the mesopolyploid Brassiceae are evolutionarily distinct but functionally compatible. Genome Research. PMID 33863805 DOI: 10.1101/gr.270033.120  0.818
2019 Peri S, Roberts S, Kreko IR, McHan LB, Naron A, Ram A, Murphy RL, Lyons E, Gregory BD, Devisetty UK, Nelson ADL. Read Mapping and Transcript Assembly: A Scalable and High-Throughput Workflow for the Processing and Analysis of Ribonucleic Acid Sequencing Data. Frontiers in Genetics. 10: 1361. PMID 32038716 DOI: 10.3389/Fgene.2019.01361  0.322
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  0.451
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  0.716
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  0.794
2019 Castillo AI, Nelson ADL, Lyons E. Tail wags the dog? Functional gene classes driving genome-wide GC content in Plasmodium spp. Genome Biology and Evolution. PMID 30689842 DOI: 10.1093/Gbe/Evz015  0.535
2018 Sankoff D, Zheng C, Zhang Y, Meidanis J, Lyons E, Tang H. Models for Similarity Distributions of Syntenic Homologs and Applications to Phylogenomics. Ieee/Acm Transactions On Computational Biology and Bioinformatics. PMID 30072336 DOI: 10.1109/Tcbb.2018.2849377  0.571
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  0.735
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  0.784
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  0.571
2018 Castillo AI, Nelson ADL, Haug-Baltzell AK, Lyons E. A tutorial of diverse genome analysis tools found in the CoGe web-platform usingPlasmodiumspp. as a model Database. 2018. DOI: 10.1093/Database/Bay030  0.611
2017 Grover JW, Bomhoff M, Davey S, Gregory BD, Mosher RA, Lyons E. CoGe LoadExp+: A web-based suite that integrates next-generation sequencing data analysis workflows and visualization. Plant Direct. 1. PMID 31240274 DOI: 10.1002/pld3.8  0.439
2017 Luo MC, Gu YQ, Puiu D, Wang H, Twardziok SO, Deal KR, Huo N, Zhu T, Wang L, Wang Y, McGuire PE, Liu S, Long H, Ramasamy RK, Rodriguez JC, ... ... Lyons E, et al. Genome sequence of the progenitor of the wheat D genome Aegilops tauschii. Nature. PMID 29143815 DOI: 10.1038/Nature24486  0.75
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  0.791
2017 Nelson ADL, Devisetty UK, Palos K, Haug-Baltzell AK, Lyons E, Beilstein MA. Evolinc: A Tool for the Identification and Evolutionary Comparison of Long Intergenic Non-coding RNAs. Frontiers in Genetics. 8: 52. PMID 28536600 DOI: 10.3389/Fgene.2017.00052  0.489
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  0.483
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  0.445
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  0.542
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  0.771
2016 Nelson AD, Forsythe ES, Devisetty UK, Clausen DS, Haug-Batzell AK, Meldrum AM, Frank MR, Lyons E, Beilstein MA. A Genomic Analysis of Factors Driving lincRNA Diversification: Lessons from Plants. G3 (Bethesda, Md.). PMID 27440919 DOI: 10.1534/G3.116.030338  0.658
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  0.789
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  0.774
2016 Koltes JE, Reecy JM, Lyons E, McCarthy F, Vaughn MW, Carson JP, Fritz-Waters E, Williams J. P1039 Bioinformatics resources for animal genomics using CyVerse cyberinfrastructure. Journal of Animal Science. 94: 33-34. DOI: 10.2527/Jas2016.94Supplement433A  0.478
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  0.789
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  0.818
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  0.809
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  0.356
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  0.445
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  0.652
2014 Zheng C, Kononenko A, Leebens-Mack J, Lyons E, Sankoff D. Gene families as soft cliques with backbones: Amborella contrasted with other flowering plants. Bmc Genomics. 15: S8. PMID 25572777 DOI: 10.1186/1471-2164-15-S6-S8  0.367
2014 Green RE, Braun EL, Armstrong J, Earl D, Nguyen N, Hickey G, Vandewege MW, St John JA, Capella-Gutiérrez S, Castoe TA, Kern C, Fujita MK, Opazo JC, Jurka J, Kojima KK, ... ... Lyons E, et al. Three crocodilian genomes reveal ancestral patterns of evolution among archosaurs. Science (New York, N.Y.). 346: 1254449. PMID 25504731 DOI: 10.1126/Science.1254449  0.626
2014 Jaratlerdsiri W, Deakin J, Godinez RM, Shan X, Peterson DG, Marthey S, Lyons E, McCarthy FM, Isberg SR, Higgins DP, Chong AY, John JS, Glenn TC, Ray DA, Gongora J. Comparative genome analyses reveal distinct structure in the saltwater crocodile MHC. Plos One. 9: e114631. PMID 25503521 DOI: 10.1371/Journal.Pone.0114631  0.488
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  0.768
2014 Cannarozzi G, Plaza-Wüthrich S, Esfeld K, Larti S, Wilson YS, Girma D, de Castro E, Chanyalew S, Blösch R, Farinelli L, Lyons E, Schneider M, Falquet L, Kuhlemeier C, Assefa K, et al. Genome and transcriptome sequencing identifies breeding targets in the orphan crop tef (Eragrostis tef). Bmc Genomics. 15: 581. PMID 25007843 DOI: 10.1186/1471-2164-15-581  0.614
2014 Chalhoub B, Denoeud F, Liu S, Parkin IAP, Tang H, Wang X, Chiquet J, Belcram H, Tong C, Samans B, Corréa M, Silva CD, Just J, Falentin C, Koh CS, ... ... Lyons E, et al. Erratum: Early allopolyploid evolution in the post-Neolithic Brassica napus oilseed genome (Science (2014) 345:6199 (950-953)) Science. 345. DOI: 10.1126/Science.1260782  0.535
2014 Tang H, Lyons E, Schnable JC. Early History of the Angiosperms Advances in Botanical Research. 69: 195-222. DOI: 10.1016/B978-0-12-417163-3.00008-1  0.724
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  0.535
2013 Zheng C, Chen E, Albert VA, Lyons E, Sankoff D. Ancient eudicot hexaploidy meets ancestral eurosid gene order. Bmc Genomics. 14: S3. PMID 24564362 DOI: 10.1186/1471-2164-14-S7-S3  0.675
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  0.768
2013 McCarthy FM, Lyons E. From data to function: Functional modeling of poultry genomics data Poultry Science. 92: 2519-2529. PMID 23960137 DOI: 10.3382/Ps.2012-02808  0.451
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  0.606
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  0.339
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  0.688
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  0.741
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  0.746
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  0.818
2011 Banks JA, Nishiyama T, Hasebe M, Bowman JL, Gribskov M, dePamphilis C, Albert VA, Aono N, Aoyama T, Ambrose BA, Ashton NW, Axtell MJ, Barker E, Barker MS, Bennetzen JL, ... ... Lyons E, et al. The Selaginella genome identifies genetic changes associated with the evolution of vascular plants. Science (New York, N.Y.). 332: 960-3. PMID 21551031 DOI: 10.1126/Science.1203810  0.694
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  0.804
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  0.675
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  0.802
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  0.719
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  0.78
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  0.836
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  0.787
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  0.78
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  0.73
2008 Lyons E, Pedersen B, Kane J, Freeling M. The Value of Nonmodel Genomes and an Example Using SynMap Within CoGe to Dissect the Hexaploidy that Predates the Rosids Tropical Plant Biology. 1: 181-190. DOI: 10.1007/S12042-008-9017-Y  0.752
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  0.681
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  0.722
2003 Frank DN, Spiegelman GB, Davis W, Wagner E, Lyons E, Pace NR. Culture-independent molecular analysis of microbial constituents of the healthy human outer ear. Journal of Clinical Microbiology. 41: 295-303. PMID 12517864 DOI: 10.1128/Jcm.41.1.295-303.2003  0.347
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