Eric H Lyons

Interests

Teaching

Comparative genomics, genome evolution, applied cyberinfrastructure for life sciences

Research

Comparative genomics, genome evolution, applied cyberinfrastructure for life sciences

Courses

Scholarly Contributions

Books

• Pessarakli, M. (2014). Handbook of plant and crop physiology. CRC Press.

Chapters

• Lyons, E., & Tang, H. (2014). Syntenic Sequence Conservation Between and Within Papaya Genes. In Genetics and Genomics of Papaya(pp 205--224). Springer New York.
• Tang, H., Zhang, X., Tong, C., Chalhoub, B., Liu, S., & Lyons, E. (2018). From Alpha-Duplication to Triplication and Sextuplication. In The Brassica napus Genome(pp 99--109). Springer, Cham.
• Lyons, E., Castelletti, S., Pedersen, B., Lisch, D., & Freeling, M. (2009). Maize GEvo: A Comparative DNA Sequence Alignment Visualization and Research Tool. In Handbook of Maize(pp 341--351). Springer, New York, NY.

Journals/Publications

• Tuggle, C. K., Clarke, J. L., Murdoch, B. M., Lyons, E., Scott, N. M., Benev{s}, B., Campbell, J. D., Chung, H., Daigle, C. L., Das, C. S., & others, . (2024). Current challenges and future of agricultural genomes to phenomes in the USA. Genome Biology, 25(1), 8.
• Gonzalez, E. M., Zarei, A., Hendler, N., Simmons, T., Zarei, A., Demieville, J., Strand, R., Rozzi, B., Calleja, S., Ellingson, H., & others, . (2023). PhytoOracle: Scalable, modular phenomics data processing pipelines. Frontiers in Plant Science, 14, 1112973.
• Swetnam, T. L., Antin, P. B., Bartelme, R., Bucksch, A., Camhy, D., Chism, G., Choi, I., Cooksey, A. M., Cosi, M., Cowen, C., & others, . (2023). CyVerse: Cyberinfrastructure for Open Science. bioRxiv, 2023--06.
• Tuggle, C. K., Scott, N., Clarke, J., Murdoch, B. M., Dekkers, J. C., Ertl, D., Lawrence-Dill, C. J., Lyons, E., & Schnable, P. S. (2023). 175 Building the Tools to Solve the Genome to Phenome Puzzle in Agriculture. Journal of Animal Science, 101(Supplement_2), 25--26.
• Tuggle, C. K., Scott, N., Clarke, J., Murdoch, B. M., Dekkers, J. C., Ertl, D., Lyons, E., Lawrence-Dill, C. J., & Schnable, P. S. (2023). 72 The AG2pi Vision for Resources in Agricultural Genomics and Phenomics: How Asas Can Contribute. Journal of Animal Science, 101(Supplement_3), 50--51.
• Ch'avez, M., Haber, A., Pardo, J., Powell, R. F., Divisetty, U. K., Silva, A. T., Hern'andez-Hern'andez, T., Silveira, V., Tang, H., Lyons, E., & others, . (2022). A comparative genomics examination of desiccation tolerance and sensitivity in two sister grass species. Proceedings of the National Academy of Sciences, 119(5), e2118886119.
• Clarke, J., Dekkers, J., Ertl, D., Lawrence-Dill, C., Lyons, E., Murdoch, B. M., Scott, N. M., Tuggle, C. K., & Schnable, P. (2022). Community Perspectives: Genome to Phenome in Agricultural Sciences.
• Clarke, J., Dekkers, J., Ertl, D., Lawrence-Dill, C., Lyons, E., Murdoch, B. M., Scott, N. M., Tuggle, C. K., & Schnable, P. (2022). Community Perspectives: Genome to Phenome in Agricultural Sciences. OSF Preprints.
• Ehsani, M. R., Zarei, A., Gupta, H. V., Barnard, K., Lyons, E., & Behrangi, A. (2022). NowCasting-Nets: Representation Learning to Mitigate Latency Gap of Satellite Precipitation Products Using Convolutional and Recurrent Neural Networks. IEEE Transactions on Geoscience and Remote Sensing, 60, 1--21.
• Hao, Y., Fleming, J., Petterson, J., Lyons, E., Edger, P. P., Pires, J. C., Thorne, J. L., & Conant, G. C. (2022). Convergent evolution of polyploid genomes from across the eukaryotic tree of life. G3, 12(6), jkac094.
• Kramer, M. C., Kim, H. J., Palos, K. R., Garcia, B. A., Lyons, E., Beilstein, M. A., Nelson, A. D., & Gregory, B. D. (2022). A conserved long intergenic non-coding RNA containing snoRNA sequences, lncCOBRA1, affects Arabidopsis germination and development. Frontiers in Plant Science, 1703.
• Lawrence-Dill, C. J., Allscheid, R. L., Boaitey, A., Bauman, T., Buckler, I., Clarke, J. L., Cullis, C., Dekkers, J., Dorius, C. J., Dorius, S. F., & others, . (2022). Ten simple rules to ruin a collaborative environment. PLoS computational biology, 18(4), e1009957.
• Palos, K., Nelson, D., Yu, L., Brock, J. R., Railey, C. E., Wu, H. L., Sokolowska, E., Skirycz, A., Hsu, P. Y., Gregory, B. D., & others, . (2022). Identification and functional annotation of long intergenic non-coding RNAs in Brassicaceae. The Plant Cell, 34(9), 3233--3260.
• Stephan, T., Burgess, S. M., Cheng, H., Danko, C. G., Gill, C. A., Jarvis, E. D., Koepfli, K., Koltes, J. E., Lyons, E., Ronald, P., & others, . (2022). Darwinian genomics and diversity in the tree of life. Proceedings of the National Academy of Sciences, 119(4), e2115644119.
• Stephan, T., Burgess, S. M., Cheng, H., Danko, C. G., Gill, C. A., Jarvis, E. D., Koepfli, K., Koltes, J. E., Lyons, E., Ronald, P., & others, . (2022). Darwinian genomics and diversity in the tree of life. Proceedings of the National Academy of Sciences, 119(4).
• Tuggle, C. K., Clarke, J., Dekkers, J., Ertl, D., Lawrence-Dill, C. J., Lyons, E., Murdoch, B. M., Scott, N. M., & Schnable, P. S. (2022). The Agricultural Genome to Phenome Initiative (AG2PI): creating a shared vision across crop and livestock research communities. Genome Biology.
• Varshney, R. K., Roorkiwal, M., Sun, S., Bajaj, P., Chitikineni, A., Thudi, M., Singh, N. P., Du, X., Upadhyaya, H. D., Khan, A. W., & others, . (2022). A chickpea genetic variation map based on the sequencing of 3,366 genomes (vol 599, pg 622, 2021). NATURE, 604(7905), E12--E12.
• Zarei, A., Gonzalez, E., Merchant, N., Pauli, D., Lyons, E., & Barnard, K. (2022). MegaStitch: Robust Large-Scale Image Stitching. IEEE Transactions on Geoscience and Remote Sensing, 60, 1--9.
• Cosi, M., Forstedt, J. J., Gonzalez, E., Xu, Z., Peri, S., Tuteja, R., Blumberg, K., Campbell, T., Merchant, N., & Lyons, E. (2021). StarBLAST: a scalable BLAST+ solution for the classroom. Journal of Open Source Education, 4(38), 102.
• Hao, Y., Fleming, J., Petterson, J., Lyons, E., Edger, P. P., Pires, C., Thorne, J. L., & Conant, G. C. (2021). Convergent evolution of polyploid genomes from across the eukaryotic tree of life. bioRxiv.
• Hao, Y., Mabry, M. E., Edger, P. P., Freeling, M., Zheng, C., Jin, L., VanBuren, R., Colle, M., An, H., Abrahams, R. S., & others, . (2021). The contributions from the progenitor genomes of the mesopolyploid Brassiceae are evolutionarily distinct but functionally compatible. Genome research, 31(5), 799--810.
• Hua, X., Berkowitz, N. D., Willmann, M. R., Yu, X., Lyons, E., & Gregory, B. D. (2021). Global Analysis of RNA-Dependent RNA Polymerase-Dependent Small RNAs Reveals New Substrates and Functions for These Proteins and SGS3 in Arabidopsis. Non-coding RNA, 7(2), 28.
• Kramer, M. C., Kim, H. J., Palos, K. R., Garcia, B. A., Lyons, E., Beilstein, M. A., Nelson, A. D., & Gregory, B. D. (2021). A conserved long intergenic non-coding RNA containing snoRNA sequences, lncCOBRA1, affects Arabidopsis germination and development. bioRxiv.
• Palos, K. R., Dittrich, A., Brock, J. R., Wu, L., Sokolowska, E., Skirycz, A., Hsu, P. Y., Lyons, E., Beilstein, M., Nelson, A. D., & others, . (2021). Identification and Functional Annotation of Long Intergenic Non-coding RNAs in the Brassicaceae. bioRxiv.
• Sahneh, F., Balk, M. A., Kisley, M., Chan, C., Fox, M., Nord, B., Lyons, E., Swetnam, T., Huppenkothen, D., Sutherland, W., & others, . (2021). Ten simple rules to cultivate transdisciplinary collaboration in data science. PLoS computational biology. doi:10.1371/journal.pcbi.1008879
• Varshney, R. K., Roorkiwal, M., Sun, S., Bajaj, P., Chitikineni, A., Thudi, M., Singh, N. P., Du, X., Upadhyaya, H. D., Khan, A. W., & others, . (2021). A chickpea genetic variation map based on the sequencing of 3,366 genomes. Nature, 599(7886), 622--627.
• Yu, X., Willmann, M. R., Vandivier, L. E., Trefely, S., Kramer, M. C., Shapiro, J., Guo, R., Lyons, E., Snyder, N. W., & Gregory, B. D. (2021). Messenger RNA 5′ NAD+ capping is a dynamic regulatory epitranscriptome mark that is required for proper response to abscisic acid in Arabidopsis. Developmental Cell, 56(1), 125--140.
• Zarei, A., Gonzalez, E., Merchant, N., Pauli, D., Lyons, E., & Barnard, K. (2022). MegaStitch: Robust Large Scale Image Stitching. IEEE Transactions on Geoscience and Remote Sensing, 1. doi:10.1109/TGRS.2022.3141907
• Henkhaus, N., Bartlett, M., Gang, D., Grumet, R., Jordon-Thaden, I., Lorence, A., Lyons, E., Miller, S., Murray, S., Nelson, A., & others, . (2020). Plant science decadal vision 2020--2030: Reimagining the potential of plants for a healthy and sustainable future. Plant direct, 4(8), e00252.
• Lyons, E. H., & Oxnam, M. G. (2020). Ten simple rules for organizing a data science workshop. PLOS Computational Biology.
• Peri, S., Roberts, S., Kreko, I. R., McHan, L. B., Naron, A., Ram, A., Murphy, R. L., Lyons, E., Gregory, B. D., Devisetty, U. K., & others, . (2020). 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.
• Ponsero, A., Bartelme, R., Oliveira, A. G., Bigelow, A., Tuteja, R., Ellingson, H., Swetnam, T., Merchant, N., Oxnam, M., & Lyons, E. (2020). Ten simple rules for organizing a data science workshop.
• Albert, V. A., Barbazuk, W. B., Der, J. P., Leebens-Mack, J., Ma, H., Palmer, J. D., Rounsley, S., Sankoff, D., Schuster, S. C., Soltis, D. E., & others, . (2013). The Amborella Genome and the Evolution of Flowering Plants. Science, 342(6165), 1241089.
• Brodt, A., Acharya, C. B., Lyons, E., & Cole, G. S. (2019). Data from: Origin and evolution of the octoploid strawberry genome.
• Castillo, A. I., Nelson, A. D., & Lyons, E. (2019). Tail wags the dog? Functional gene classes driving genome-wide GC content in Plasmodium spp.. Genome biology and evolution, 11(2), 497--507.
• Chen, E. C., Najar, C. F., Zheng, C., Brandts, A., Lyons, E., Tang, H., Carretero-Paulet, L., Albert, V. A., & Sankoff, D. (2013). The dynamics of functional classes of plant genes in rediploidized ancient polyploids. BMC Bioinformatics, 14(Suppl 15), S19.
• Edger, P. P., Poorten, T. J., VanBuren, R., Hardigan, M. A., Colle, M., McKain, M. R., Smith, R. D., Teresi, S. J., Nelson, A. D., Wai, C. M., & others, . (2019). Origin and evolution of the octoploid strawberry genome. Nature genetics, 51(3), 541--547.
• McCarthy, F. M., Pendarvis, K., Cooksey, A. M., Gresham, C. R., Bomhoff, M., Davey, S., Lyons, E., Sonstegard, T. S., Bridges, S. M., & Burgess, S. C. (2019). Chickspress: a resource for chicken gene expression. Database, 2019.
• McCarthy, F., & Lyons, E. (2013). From data to function: Functional modeling of poultry genomics data. Poultry science, 92(9), 2519--2529.
• Anderson, S. J., Kramer, M. C., Gosai, S. J., Yu, X., Vandivier, L. E., Nelson, A. D., Anderson, Z. D., Beilstein, M. A., Fray, R. G., Lyons, E., & others, . (2018). N6-Methyladenosine Inhibits Local Ribonucleolytic Cleavage to Stabilize mRNAs in Arabidopsis. Cell reports, 25(5), 1146--1157.
• Castillo, A. I., Nelson, A. D., Haug-Baltzell, A. K., & Lyons, E. (2018). A tutorial of diverse genome analysis tools found in the CoGe web-platform using Plasmodium spp. as a model. Database, 2018.
• Emery, M., Willis, M., Hao, Y., Barry, K., Oakgrove, K., Peng, Y. i., Schmutz, J., Lyons, E., Pires, J. C., Edger, P. P., & others, . (2018). 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(3), e1007267.
• François-Moutal, L., Jahanbakhsh, S., Nelson, A. D., Ray, D., Scott, D. D., Hennefarth, M. R., Moutal, A., Perez-Miller, S., Ambrose, A. J., Al-Shamari, A., & others, . (2018). A Chemical Biology Approach to Model Pontocerebellar Hypoplasia Type 1B (PCH1B). ACS chemical biology, 13(10), 3000--3010.
• Hao, Y., Washburn, J. D., Rosenthal, J., Nielsen, B., Lyons, E., Edger, P. P., Pires, J. C., & Conant, G. C. (2018). Patterns of population variation in two paleopolyploid eudicot lineages suggest that dosage-based selection on homeologs is long-lived. Genome biology and evolution, 10(3), 999--1011.
• Lyons, E., Lent, H., Hahn-Powell, G., Haug-Baltzell, A., Davey, S., & Surdeanu, M. (2018). Science Citation Knowledge Extractor. Frontiers in Research Metrics and Analytics, 3, 35.
• Nelson, A. D., Haug-Baltzell, A. K., Davey, S., Gregory, B. D., Lyons, E., & Hancock, J. (2018). EPIC-CoGe: managing and analyzing genomic data. Bioinformatics, 1, 3.
• Sankoff, D., Zheng, C., Zhang, Y., Meidanis, J., Lyons, E., & Tang, H. (2018). Models for similarity distributions of syntenic homologs and applications to phylogenomics. IEEE/ACM transactions on computational biology and bioinformatics.
• Varshney, R. K., Shi, C., Thudi, M., Mariac, C., Wallace, J., Qi, P., Zhang, H. e., Zhao, Y., Wang, X., Rathore, A., & others, . (2018). Erratum: Pearl millet genome sequence provides a resource to improve agronomic traits in arid environments. Nature Biotechnology, 36(4), 368.
• Foley, S. W., Gosai, S. J., Wang, D., Selamoglu, N., Sollitti, A. C., K\"oster, T., Steffen, A., Lyons, E., Daldal, F., Garcia, B. A., & others, . (2017). A global view of RNA-protein interactions identifies post-transcriptional regulators of root hair cell fate. Developmental cell, 41(2), 204--220.
• Grover, J. W., Bomhoff, M., Davey, S., Gregory, B. D., Mosher, R. A., & Lyons, E. (2017). CoGe LoadExp+: A web-based suite that integrates next-generation sequencing data analysis workflows and visualization. Plant Direct, 1(2).
• Haug-Baltzell, A., Stephens, S. A., Davey, S., Scheidegger, C. E., & Lyons, E. (2017). SynMap2 and SynMap3D: web-based whole-genome synteny browsers. Bioinformatics, 33(14), 2197--2198.
• Joyce, B. L., Haug-Baltzell, A. K., Hulvey, J. P., McCarthy, F., Devisetty, U. K., & Lyons, E. (2017). Leveraging CyVerse Resources for De Novo Comparative Transcriptomics of Underserved (Non-model) Organisms. Journal of visualized experiments: JoVE.
• Joyce, B. L., Haug-Baltzell, A., Davey, S., Bomhoff, M., Schnable, J. C., & Lyons, E. (2017). FractBias: A graphical tool for assessing fractionation bias following polyploidy. Bioinformatics, 33(4), 552--554.
• Joyce, B., Baltzell, A., Bomhoff, M., & Lyons, E. (2017). Comparative Genomics Using CoGe, Hook, Line, and Sinker. Bioinformatics in Aquaculture: Principles and Methods, 461--487.
• Joyce, B., Baltzell, A., McCarthy, F., Bomhoff, M., & Lyons, E. (2017). iAnimal: Cyberinfrastructure to Support Data-driven Science. Bioinformatics in Aquaculture: Principles and Methods, 527--545.
• Luo, M., Gu, Y. Q., Puiu, D., Wang, H., Twardziok, S. O., Deal, K. R., Huo, N., Zhu, T., Wang, L. e., Wang, Y. i., & others, . (2017). Genome sequence of the progenitor of the wheat D genome Aegilops tauschii. Nature, 551(7681).
• Nelson, A. D., Devisetty, U. K., Palos, K., Haug-Baltzell, A. K., Lyons, E., & Beilstein, M. A. (2017). Evolinc: A tool for the identification and evolutionary comparison of long intergenic non-coding RNAs. Frontiers in genetics, 8, 52.
• Nelson, A. D., Forsythe, E. S., Devisetty, U. K., Meldrum, A. M., Haug-Baltzell, A. K., Lyons, E. H., & Beilstein, M. A. (2015). A Genomic and Transcriptomic Analysis of Factors Driving lincRNA Diversification: Lessons from Plants. Plant Cell.
• Varshney, R. K., Shi, C., Thudi, M., Mariac, C., Wallace, J., Qi, P., Zhang, H. e., Zhao, Y., Wang, X., Rathore, A., & others, . (2017). Pearl millet genome sequence provides a resource to improve agronomic traits in arid environments. Nature biotechnology, 35(10), 969.
• Wu, Y., Sheehan, P. D., Males, J. R., Close, L. M., Morzinski, K. M., Teske, J. K., Haug-Baltzell, A., Merchant, N., & Lyons, E. (2017). An ALMA and MagAO study of the substellar companion GQ Lup B. The Astrophysical Journal, 836(2), 223.
• Xu, S., Brockm\"oller, T., Navarro-Quezada, A., Kuhl, H., Gase, K., Ling, Z., Zhou, W., Kreitzer, C., Stanke, M., Tang, H., & others, . (2017). Wild tobacco genomes reveal the evolution of nicotine biosynthesis. Proceedings of the National Academy of Sciences, 114(23), 6133--6138.
• Bombarely, A., Moser, M., Amrad, A., Bao, M., Bapaume, L., Barry, C. S., Bliek, M., Boersma, M. R., Borghi, L., Bruggmann, R., & others, . (2016). Insight into the evolution of the Solanaceae from the parental genomes of Petunia hybrida. Nature plants, 2, 16074.
• Devisetty, U. K., Kennedy, K., Sarando, P., Merchant, N., & Lyons, E. (2016). Bringing your tools to CyVerse Discovery Environment using Docker. F1000Research, 5.
• Koltes, J., Reecy, J., Lyons, E., McCarthy, F., Vaughn, M., Carson, J., Fritz-Waters, E., & Williams, J. (2016). P1039 Bioinformatics resources for animal genomics using CyVerse cyberinfrastructure.. Journal of Animal Science, 94(7supplement4), 33--34.
• Merchant, N., Lyons, E., Goff, S., Vaughn, M., Ware, D., Micklos, D., & Antin, P. (2016). The iPlant Collaborative: Cyberinfrastructure for Enabling Data to Discovery for the Life Sciences.. PLoS biology, 14, e1002342--e1002342.
• Nelson, A. D., Forsythe, E. S., Devisetty, U. K., Clausen, D. S., Haug-Batzell, A. K., Meldrum, A. M., Frank, M. R., Lyons, E., & Beilstein, M. A. (2016). A genomic analysis of factors driving lincRNA diversification: lessons from plants. G3: Genes| Genomes| Genetics, 6(9), 2881--2891.
• VanBuren, R., Bryant, D., Bushakra, J. M., Vining, K. J., Edger, P. P., Rowley, E. R., Priest, H. D., Michael, T. P., Lyons, E., Filichkin, S. A., & others, . (2016). The genome of black raspberry (Rubus occidentalis). The Plant Journal, 87(6), 535--547.
• Haug-Baltzell, A., Jarvis, E. D., McCarthy, F. M., & Lyons, E. (2015). 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.
• Ming, R., VanBuren, R., Wai, C. M., Tang, H., Schatz, M. C., Bowers, J. E., Lyons, E., Wang, M., Chen, J., Biggers, E., & others, . (2015). The pineapple genome and the evolution of CAM photosynthesis. Nature genetics, 47(12), 1435--1442.
• Tang, H., Bomhoff, M. D., Briones, E., Zhang, L., Schnable, J. C., & Lyons, E. (2015). Genome Biology and Evolution Advance Access published November 11, 2015 doi: 10.1093/gbe/evv219.
• Tang, H., Bomhoff, M. D., Briones, E., Zhang, L., Schnable, J. C., & Lyons, E. (2015). SynFind: compiling syntenic regions across any set of genomes on demand. Genome biology and evolution, 7, 3286--3298.
• Tang, H., Lyons, E., & Town, C. D. (2015). Optical mapping in plant comparative genomics. GigaScience, 4(1), s13742--015.
• Tang, H., Zhang, X., Miao, C., Zhang, J., Ming, R., Schnable, J. C., Schnable, P. S., Lyons, E., & Lu, J. (2015). ALLMAPS: robust scaffold ordering based on multiple maps. Genome biology, 16, 3.
• VanBuren, R., Bryant, D., Edger, P. P., Tang, H., Burgess, D., Challabathula, D., Spittle, K., Hall, R., Gu, J., Lyons, E., & others, . (2015). Single-molecule sequencing of the desiccation-tolerant grass Oropetium thomaeum. Nature, 527(7579), 508--511.
• Cannarozzi, G., Plaza-Wüthrich, S., Esfeld, K., Larti, S., Wilson, Y. S., Girma, D., de Castro, E., Chanyalew, S., Blösch, R., Farinelli, L., Lyons, E., Schneider, M., Falquet, L., Kuhlemeier, C., Assefa, K., & Tadele, Z. (2014). Genome and transcriptome sequencing identifies breeding targets in the orphan crop tef (Eragrostis tef). BMC genomics, 15, 581.
  More info

  Tef (Eragrostis tef), an indigenous cereal critical to food security in the Horn of Africa, is rich in minerals and protein, resistant to many biotic and abiotic stresses and safe for diabetics as well as sufferers of immune reactions to wheat gluten. We present the genome of tef, the first species in the grass subfamily Chloridoideae and the first allotetraploid assembled de novo. We sequenced the tef genome for marker-assisted breeding, to shed light on the molecular mechanisms conferring tef's desirable nutritional and agronomic properties, and to make its genome publicly available as a community resource.
• Chalhoub, B., Denoeud, F., Liu, S., Parkin, I. A., Tang, H., Wang, X., Chiquet, J., Belcram, H., Tong, C., Samans, B., & others, . (2014). Early allopolyploid evolution in the post-Neolithic Brassica napus oilseed genome. Science, 345, 950--953.
• Chalhoub, B., Denoeud, F., Liu, S., Parkin, I. A., Tang, H., Wang, X., Chiquet, J., Belcram, H., Tong, C., Samans, B., & others, . (2014). Early allopolyploid evolution in the post-Neolithic Brassica napus oilseed genome. science, 345(6199), 950--953.
• Chalhoub, B., Denoeud, F., Liu, S., Parkin, I. A., Tang, H., Wang, X., Chiquet, J., Belcram, H., Tong, C., Samans, B., Corréa, M., Da Silva, C., Just, J., Falentin, C., Koh, C. S., Le Clainche, I., Bernard, M., Bento, P., Noel, B., , Labadie, K., et al. (2014). Plant genetics. Early allopolyploid evolution in the post-Neolithic Brassica napus oilseed genome. Science (New York, N.Y.), 345(6199), 950-3.
  More info

  Oilseed rape (Brassica napus L.) was formed ~7500 years ago by hybridization between B. rapa and B. oleracea, followed by chromosome doubling, a process known as allopolyploidy. Together with more ancient polyploidizations, this conferred an aggregate 72× genome multiplication since the origin of angiosperms and high gene content. We examined the B. napus genome and the consequences of its recent duplication. The constituent An and Cn subgenomes are engaged in subtle structural, functional, and epigenetic cross-talk, with abundant homeologous exchanges. Incipient gene loss and expression divergence have begun. Selection in B. napus oilseed types has accelerated the loss of glucosinolate genes, while preserving expansion of oil biosynthesis genes. These processes provide insights into allopolyploid evolution and its relationship with crop domestication and improvement.
• Green, R. E., Braun, E. L., Armstrong, J., Earl, D., Nguyen, N., Hickey, G., Vandewege, M. W., John, J. A., Capella-Guti{\'e}rrez, S., Castoe, T. A., & others, . (2014). Three crocodilian genomes reveal ancestral patterns of evolution among archosaurs. Science, 346, 1254449.
• Green, R. E., Braun, E. L., Armstrong, J., Earl, D., Nguyen, N., Hickey, G., Vandewege, M. W., John, J., Capella-Guti\'errez, S., Castoe, T. A., & others, . (2014). Three crocodilian genomes reveal ancestral patterns of evolution among archosaurs. Science, 346(6215).
• Jaratlerdsiri, W., Deakin, J., Godinez, R. M., Shan, X., Peterson, D. G., Marthey, S., Lyons, E., McCarthy, F. M., Isberg, S. R., Higgins, D. P., & others, . (2014). Comparative genome analyses reveal distinct structure in the saltwater crocodile MHC. PloS one, 9, e114631.
• Tang, H., Lyons, E., & Schnable, J. C. (2014). Early History of the Angiosperms. Advances in Botanical Research, 69, 195-222.
  More info

  Abstract: The flowering plants, also known as the angiosperms, are the most diverse group of plants. The basal flowering plant lineages diverged at very early stage in flowering plant evolution, followed by rapid diversification of the magnoliids, the eudicots and the monocots. Genomic comparisons within and across plant lineages help identify the critical events that occurred during the evolution of major groups of flowering plants. In this chapter, we first review the basic concepts and analytic methods for studying ancient polyploidy-a prominent feature during plant evolution. We then highlight recent progress on the dating of deep polyploidies in the eudicot and monocot lineage, respectively. With a clear knowledge of genomic history, we can effectively compare the eudicot genomes to monocot genomes, which promise to bridge functional equivalence between genes of the two well-studied groups. Finally, we deduce the composition and structure of the 'ancestral genome' on the basis of the arrangements of genes in the extant species. The in silico reconstruction of the ancestral genome provides an integrated framework under which conservation of modern plant genomes can be systematically studied. © 2014 Elsevier Ltd.
• Zhang, G., Li, C., Li, Q., Li, B., Larkin, D. M., Lee, C., Storz, J. F., Antunes, A., Greenwold, M. J., Meredith, R. W., & others, . (2014). Comparative genomics reveals insights into avian genome evolution and adaptation. Science, 346(6215), 1311--1320.
• Zheng, C., Kononenko, A., Leebens-Mack, J., Lyons, E., & Sankoff, D. (2014). Gene families as soft cliques with backbones: Amborella contrasted with other flowering plants. BMC genomics, 15(Suppl 6), S8.
  More info

  Chaining is a major problem in constructing gene families.
• Hofberger, J. A., Lyons, E., Edger, P. P., Chris Pires, J., & Eric Schranz, M. (2013). Whole genome and tandem duplicate retention facilitated glucosinolate pathway diversification in the mustard family. Genome biology and evolution, 5(11).
  More info

  Plants share a common history of successive whole-genome duplication (WGD) events retaining genomic patterns of duplicate gene copies (ohnologs) organized in conserved syntenic blocks. Duplication was often proposed to affect the origin of novel traits during evolution. However, genetic evidence linking WGD to pathway diversification is scarce. We show that WGD and tandem duplication (TD) accelerated genetic versatility of plant secondary metabolism, exemplified with the glucosinolate (GS) pathway in the mustard family. GS biosynthesis is a well-studied trait, employing at least 52 biosynthetic and regulatory genes in the model plant Arabidopsis. In a phylogenomics approach, we identified 67 GS loci in Aethionema arabicum of the tribe Aethionemae, sister group to all mustard family members. All but one of the Arabidopsis GS gene families evolved orthologs in Aethionema and all but one of the orthologous sequence pairs exhibit synteny. The 45% fraction of duplicates among all protein-coding genes in Arabidopsis was increased to 95% and 97% for Arabidopsis and Aethionema GS pathway inventory, respectively. Compared with the 22% average for all protein-coding genes in Arabidopsis, 52% and 56% of Aethionema and Arabidopsis GS loci align to ohnolog copies dating back to the last common WGD event. Although 15% of all Arabidopsis genes are organized in tandem arrays, 45% and 48% of GS loci in Arabidopsis and Aethionema descend from TD, respectively. We describe a sequential combination of TD and WGD events driving gene family extension, thereby expanding the evolutionary playground for functional diversification and thus potential novelty and success.
• Ibarra-Laclette, E., Lyons, E., Hernández-Guzmán, G., Pérez-Torres, C. A., Carretero-Paulet, L., Chang, T., Lan, T., Welch, A. J., Juárez, M. J., Simpson, J., Fernández-Cortés, A., Arteaga-Vázquez, M., Góngora-Castillo, E., Acevedo-Hernández, G., Schuster, S. C., Himmelbauer, H., Minoche, A. E., Xu, S., Lynch, M., , Oropeza-Aburto, A., et al. (2013). Architecture and evolution of a minute plant genome. Nature, 498(7452).
  More info

  It has been argued that the evolution of plant genome size is principally unidirectional and increasing owing to the varied action of whole-genome duplications (WGDs) and mobile element proliferation. However, extreme genome size reductions have been reported in the angiosperm family tree. Here we report the sequence of the 82-megabase genome of the carnivorous bladderwort plant Utricularia gibba. Despite its tiny size, the U. gibba genome accommodates a typical number of genes for a plant, with the main difference from other plant genomes arising from a drastic reduction in non-genic DNA. Unexpectedly, we identified at least three rounds of WGD in U. gibba since common ancestry with tomato (Solanum) and grape (Vitis). The compressed architecture of the U. gibba genome indicates that a small fraction of intergenic DNA, with few or no active retrotransposons, is sufficient to regulate and integrate all the processes required for the development and reproduction of a complex organism.
• Ming, R., Vanburen, R., Liu, Y., Yang, M., Han, Y., Li, L., Zhang, Q., Kim, M., Schatz, M. C., Campbell, M., & others, . (2013). Nelumbo nucifera [data set].
• Ming, R., Vanburen, R., Liu, Y., Yang, M., Han, Y., Li, L., Zhang, Q., Kim, M., Schatz, M. C., Campbell, M., Li, J., Bowers, J. E., Tang, H., Lyons, E., Ferguson, A. A., Narzisi, G., Nelson, D. R., Blaby-Haas, C. E., Gschwend, A. R., , Jiao, Y., et al. (2013). Genome of the long-living sacred lotus (Nelumbo nucifera Gaertn.). Genome biology, 14(5).
  More info

  Sacred lotus is a basal eudicot with agricultural, medicinal, cultural and religious importance. It was domesticated in Asia about 7,000 years ago, and cultivated for its rhizomes and seeds as a food crop. It is particularly noted for its 1,300-year seed longevity and exceptional water repellency, known as the lotus effect. The latter property is due to the nanoscopic closely packed protuberances of its self-cleaning leaf surface, which have been adapted for the manufacture of a self-cleaning industrial paint, Lotusan.
• Tang, H., Lyons, E., & Schnable, J. C. (2013). Early History of the Angiosperms. Genomes of Herbaceous Land Plants, 69, 195.
• Vaughn, M., Goff, S. A., McKay, S., Lyons, E., Stapleton, A. E., Gessler, D., Matasci, N., Wang, L., Lenards, A., Muir, A., & others, . (2013). Matthew Vaughn. The Sienna Miller Handbook-Everything you need to know about Sienna Miller, 155.
• Zheng, C., Chen, E., Albert, V. A., Lyons, E., & Sankoff, D. (2013). Ancient eudicot hexaploidy meets ancestral eurosid gene order. BMC genomics, 14 Suppl 7, S3.
  More info

  A hexaploidization event over 125 Mya underlies the evolutionary lineage of the majority of flowering plants, including very many species of agricultural importance. Half of these belong to the rosid subgrouping, containing severals whose genome sequences have been published. Although most duplicate and triplicate genes have been lost in all descendants, clear traces of the original chromosome triples can be discerned, their internal contiguity highly conserved in some genomes and very fragmented in others. To understand the particular evolutionary patterns of plant genomes, there is a need to systematically survey the fate of the subgenomes of polyploids, including the retention of a small proportion of the duplicate and triplicate genes and the reconstruction of putative ancestral intermediates between the original hexaploid and modern species, in this case the ancestor of the eurosid clade.
• Consortium, I. (2012). Taking the next step: building an Arabidopsis information portal. The Plant Cell, 24(6), 2248--2256.
• D'Hont, A., Denoeud, F., Aury, J., Baurens, F., Carreel, F., Garsmeur, O., Noel, B., Bocs, S., Droc, G., Rouard, M., Da Silva, C., Jabbari, K., Cardi, C., Poulain, J., Souquet, M., Labadie, K., Jourda, C., Lengellé, J., Rodier-Goud, M., , Alberti, A., et al. (2012). The banana (Musa acuminata) genome and the evolution of monocotyledonous plants. Nature, 488(7410), 213-7.
  More info

  Bananas (Musa spp.), including dessert and cooking types, are giant perennial monocotyledonous herbs of the order Zingiberales, a sister group to the well-studied Poales, which include cereals. Bananas are vital for food security in many tropical and subtropical countries and the most popular fruit in industrialized countries. The Musa domestication process started some 7,000 years ago in Southeast Asia. It involved hybridizations between diverse species and subspecies, fostered by human migrations, and selection of diploid and triploid seedless, parthenocarpic hybrids thereafter widely dispersed by vegetative propagation. Half of the current production relies on somaclones derived from a single triploid genotype (Cavendish). Pests and diseases have gradually become adapted, representing an imminent danger for global banana production. Here we describe the draft sequence of the 523-megabase genome of a Musa acuminata doubled-haploid genotype, providing a crucial stepping-stone for genetic improvement of banana. We detected three rounds of whole-genome duplications in the Musa lineage, independently of those previously described in the Poales lineage and the one we detected in the Arecales lineage. This first monocotyledon high-continuity whole-genome sequence reported outside Poales represents an essential bridge for comparative genome analysis in plants. As such, it clarifies commelinid-monocotyledon phylogenetic relationships, reveals Poaceae-specific features and has led to the discovery of conserved non-coding sequences predating monocotyledon-eudicotyledon divergence.
• Dodson, K. L., Tardif, F., Jordan, K. S., & Lyons, E. M. (2012). Maintaining Turfgrass Coverage Under High Traffic Conditions.
• Holbrook, S., Finley, J. K., Lyons, E. L., & Herman, T. G. (2012). Loss of syd-1 from R7 neurons disrupts two distinct phases of presynaptic development. The Journal of neuroscience : the official journal of the Society for Neuroscience, 32(50), 18101-11.
  More info

  Genetic analyses in both worm and fly have identified the RhoGAP-like protein Syd-1 as a key positive regulator of presynaptic assembly. In worm, loss of syd-1 can be fully rescued by overexpressing wild-type Liprin-α, suggesting that the primary function of Syd-1 in this process is to recruit Liprin-α. We show that loss of syd-1 from Drosophila R7 photoreceptors causes two morphological defects that occur at distinct developmental time points. First, syd-1 mutant R7 axons often fail to form terminal boutons in their normal M6 target layer. Later, those mutant axons that do contact M6 often project thin extensions beyond it. We find that the earlier defect coincides with a failure to localize synaptic vesicles, suggesting that it reflects a failure in presynaptic assembly. We then analyze the relationship between syd-1 and Liprin-α in R7s. We find that loss of Liprin-α causes a stronger early R7 defect and provide a possible explanation for this disparity: we show that Liprin-α promotes Kinesin-3/Unc-104/Imac-mediated axon transport independently of Syd-1 and that Kinesin-3/Unc-104/Imac is required for normal R7 bouton formation. Unlike loss of syd-1, loss of Liprin-α does not cause late R7 extensions. We show that overexpressing Liprin-α partly rescues the early but not the late syd-1 mutant R7 defect. We therefore conclude that the two defects are caused by distinct molecular mechanisms. We find that Trio overexpression rescues both syd-1 defects and that trio and syd-1 have similar loss- and gain-of-function phenotypes, suggesting that the primary function of Syd-1 in R7s may be to promote Trio activity.
• Reneker, J., Lyons, E., Conant, G. C., Pires, J. C., Freeling, M., Shyu, C., & Korkin, D. (2012). Long identical multispecies elements in plant and animal genomes. Proceedings of the National Academy of Sciences of the United States of America, 109(19), E1183-91.
  More info

  Ultraconserved elements (UCEs) are DNA sequences that are 100% identical (no base substitutions, insertions, or deletions) and located in syntenic positions in at least two genomes. Although hundreds of UCEs have been found in animal genomes, little is known about the incidence of ultraconservation in plant genomes. Using an alignment-free information-retrieval approach, we have comprehensively identified all long identical multispecies elements (LIMEs), which include both syntenic and nonsyntenic regions, of at least 100 identical base pairs shared by at least two genomes. Among six animal genomes, we found the previously known syntenic UCEs as well as previously undescribed nonsyntenic elements. In contrast, among six plant genomes, we only found nonsyntenic LIMEs. LIMEs can also be classified as either simple (repetitive) or complex (nonrepetitive), they may occur in multiple copies in a genome, and they are often spread across multiple chromosomes. Although complex LIMEs were found in both animal and plant genomes, they differed significantly in their composition and copy number. Further analyses of plant LIMEs revealed their functional diversity, encompassing elements found near rRNA and enzyme-coding genes, as well as those found in transposons and noncoding DNA. We conclude that despite the common presence of LIMEs in both animal and plant lineages, the evolutionary processes involved in the creation and maintenance of these elements differ in the two groups and are likely attributable to several mechanisms, including transfer of genetic material from organellar to nuclear genomes, de novo sequence manufacturing, and purifying selection.
• Schnable, J. C., & Lyons, E. (2012). Comparative genomics with maize and other grasses: from genes to genomes!. Maydica, 56(2).
• Schnable, J. C., Freeling, M., & Lyons, E. (2012). Genome-wide analysis of syntenic gene deletion in the grasses. Genome biology and evolution, 4(3), 265-77.
  More info

  The grasses, Poaceae, are one of the largest and most successful angiosperm families. Like many radiations of flowering plants, the divergence of the major grass lineages was preceded by a whole-genome duplication (WGD), although these events are not rare for flowering plants. By combining identification of syntenic gene blocks with measures of gene pair divergence and different frequencies of ancient gene loss, we have separated the two subgenomes present in modern grasses. Reciprocal loss of duplicated genes or genomic regions has been hypothesized to reproductively isolate populations and, thus, speciation. However, in contrast to previous studies in yeast and teleost fishes, we found very little evidence of reciprocal loss of homeologous genes between the grasses, suggesting that post-WGD gene loss may not be the cause of the grass radiation. The sets of homeologous and orthologous genes and predicted locations of deleted genes identified in this study, as well as links to the CoGe comparative genomics web platform for analyzing pan-grass syntenic regions, are provided along with this paper as a resource for the grass genetics community.
• Tang, H., & Lyons, E. (2012). The evolution of genome structure. Int J Evol 1, 1, 2.
• Tang, H., & Lyons, E. (2012). Unleashing the genome of brassica rapa. Frontiers in plant science, 3, 172.
  More info

  The completion and release of the Brassica rapa genome is of great benefit to researchers of the Brassicas, Arabidopsis, and genome evolution. While its lineage is closely related to the model organism Arabidopsis thaliana, the Brassicas experienced a whole genome triplication subsequent to their divergence. This event contemporaneously created three copies of its ancestral genome, which had diploidized through the process of homeologous gene loss known as fractionation. By the fractionation of homeologous gene content and genetic regulatory binding sites, Brassica's genome is well placed to use comparative genomic techniques to identify syntenic regions, homeologous gene duplications, and putative regulatory sequences. Here, we use the comparative genomics platform CoGe to perform several different genomic analyses with which to study structural changes of its genome and dynamics of various genetic elements. Starting with whole genome comparisons, the Brassica paleohexaploidy is characterized, syntenic regions with A. thaliana are identified, and the TOC1 gene in the circadian rhythm pathway from A. thaliana is used to find duplicated orthologs in B. rapa. These TOC1 genes are further analyzed to identify conserved non-coding sequences that contain cis-acting regulatory elements and promoter sequences previously implicated in circadian rhythmicity. Each "cookbook style" analysis includes a step-by-step walk-through with links to CoGe to quickly reproduce each step of the analytical process.
• Zheng, C., Albert, V. A., Lyons, E., & Sankoff, D. (2012). Ancient angiosperm hexaploidy meets ancestral eudicot gene order. 2012 IEEE 2nd International Conference on Computational Advances in Bio and Medical Sciences, ICCABS 2012.
  More info

  Abstract: We propose a protocol for reconstructing and analyzing the post-polyploidization ancestor of a set of genomes. Our method, applied to the post-hexaploid ancestor of six core eudicot flowering plants, reconstructs ancestral gene order, based on orthologs obtained for each pair of data genomes, harmonized into disjoint ortholog sets for multiple genomes. © 2012 IEEE.
• Banks, J. A., Nishiyama, T., Hasebe, M., Bowman, J. L., Gribskov, M., dePamphilis, C., Albert, V. A., Aono, N., Aoyama, T., Ambrose, B. A., Ashton, N. W., Axtell, M. J., Barker, E., Barker, M. S., Bennetzen, J. L., Bonawitz, N. D., Chapple, C., Cheng, C., Correa, L. G., , Dacre, M., et al. (2011). The Selaginella genome identifies genetic changes associated with the evolution of vascular plants. Science (New York, N.Y.), 332(6032), 960-3.
  More info

  Vascular plants appeared ~410 million years ago, then diverged into several lineages of which only two survive: the euphyllophytes (ferns and seed plants) and the lycophytes. We report here the genome sequence of the lycophyte Selaginella moellendorffii (Selaginella), the first nonseed vascular plant genome reported. By comparing gene content in evolutionarily diverse taxa, we found that the transition from a gametophyte- to a sporophyte-dominated life cycle required far fewer new genes than the transition from a nonseed vascular to a flowering plant, whereas secondary metabolic genes expanded extensively and in parallel in the lycophyte and angiosperm lineages. Selaginella differs in posttranscriptional gene regulation, including small RNA regulation of repetitive elements, an absence of the trans-acting small interfering RNA pathway, and extensive RNA editing of organellar genes.
• Dodson, K., Lyons, E., Jordan, K., & Tardif, F. (2011). Is Overseeding With Supina Bluegrass a Viable Option?.
• Goff, S. A., Vaughn, M., McKay, S., Lyons, E., Stapleton, A. E., Gessler, D., Matasci, N., Wang, L., Hanlon, M., Lenards, A., Muir, A., Merchant, N., Lowry, S., Mock, S., Helmke, M., Kubach, A., Narro, M., Hopkins, N., Micklos, D., , Hilgert, U., et al. (2011). The iPlant Collaborative: Cyberinfrastructure for Plant Biology. Frontiers in plant science, 2, 34.
  More info

  The iPlant Collaborative (iPlant) is a United States National Science Foundation (NSF) funded project that aims to create an innovative, comprehensive, and foundational cyberinfrastructure in support of plant biology research (PSCIC, 2006). iPlant is developing cyberinfrastructure that uniquely enables scientists throughout the diverse fields that comprise plant biology to address Grand Challenges in new ways, to stimulate and facilitate cross-disciplinary research, to promote biology and computer science research interactions, and to train the next generation of scientists on the use of cyberinfrastructure in research and education. Meeting humanity's projected demands for agricultural and forest products and the expectation that natural ecosystems be managed sustainably will require synergies from the application of information technologies. The iPlant cyberinfrastructure design is based on an unprecedented period of research community input, and leverages developments in high-performance computing, data storage, and cyberinfrastructure for the physical sciences. iPlant is an open-source project with application programming interfaces that allow the community to extend the infrastructure to meet its needs. iPlant is sponsoring community-driven workshops addressing specific scientific questions via analysis tool integration and hypothesis testing. These workshops teach researchers how to add bioinformatics tools and/or datasets into the iPlant cyberinfrastructure enabling plant scientists to perform complex analyses on large datasets without the need to master the command-line or high-performance computational services.
• Lawrence, C. J. (2011). MaizeGDB--Past, Present, and Future. Maydica, 56(1).
• Lyons, E., Freeling, M., Kustu, S., & Inwood, W. (2011). Using genomic sequencing for classical genetics in E. coli K12. PloS one, 6(2), e16717.
  More info

  We here develop computational methods to facilitate use of 454 whole genome shotgun sequencing to identify mutations in Escherichia coli K12. We had Roche sequence eight related strains derived as spontaneous mutants in a background without a whole genome sequence. They provided difference tables based on assembling each genome to reference strain E. coli MG1655 (NC_000913). Due to the evolutionary distance to MG1655, these contained a large number of both false negatives and positives. By manual analysis of the dataset, we detected all the known mutations (24 at nine locations) and identified and genetically confirmed new mutations necessary and sufficient for the phenotypes we had selected in four strains. We then had Roche assemble contigs de novo, which we further assembled to full-length pseudomolecules based on synteny with MG1655. This hybrid method facilitated detection of insertion mutations and allowed annotation from MG1655. After removing one genome with less than the optimal 20- to 30-fold sequence coverage, we identified 544 putative polymorphisms that included all of the known and selected mutations apart from insertions. Finally, we detected seven new mutations in a total of only 41 candidates by comparing single genomes to composite data for the remaining six and using a ranking system to penalize homopolymer sequencing and misassembly errors. An additional benefit of the analysis is a table of differences between MG1655 and a physiologically robust E. coli wild-type strain NCM3722. Both projects were greatly facilitated by use of comparative genomics tools in the CoGe software package (http://genomevolution.org/).
• Tang, H., Lyons, E., Pedersen, B., Schnable, J. C., Paterson, A. H., & Freeling, M. (2011). Screening synteny blocks in pairwise genome comparisons through integer programming. BMC Bioinformatics, 12.
  More info

  PMID: 21501495;PMCID: PMC3088904;Abstract: Background: It is difficult to accurately interpret chromosomal correspondences such as true orthology and paralogy due to significant divergence of genomes from a common ancestor. Analyses are particularly problematic among lineages that have repeatedly experienced whole genome duplication (WGD) events. To compare multiple "subgenomes" derived from genome duplications, we need to relax the traditional requirements of "one-to-one" syntenic matchings of genomic regions in order to reflect "one-to-many" or more generally "many-to-many" matchings. However this relaxation may result in the identification of synteny blocks that are derived from ancient shared WGDs that are not of interest. For many downstream analyses, we need to eliminate weak, low scoring alignments from pairwise genome comparisons. Our goal is to objectively select subset of synteny blocks whose total scores are maximized while respecting the duplication history of the genomes in comparison. We call this "quota-based" screening of synteny blocks in order to appropriately fill a quota of syntenic relationships within one genome or between two genomes having WGD events.Results: We have formulated the synteny block screening as an optimization problem known as "Binary Integer Programming" (BIP), which is solved using existing linear programming solvers. The computer program QUOTA-ALIGN performs this task by creating a clear objective function that maximizes the compatible set of synteny blocks under given constraints on overlaps and depths (corresponding to the duplication history in respective genomes). Such a procedure is useful for any pairwise synteny alignments, but is most useful in lineages affected by multiple WGDs, like plants or fish lineages. For example, there should be a 1:2 ploidy relationship between genome A and B if genome B had an independent WGD subsequent to the divergence of the two genomes. We show through simulations and real examples using plant genomes in the rosid superorder that the quota-based screening can eliminate ambiguous synteny blocks and focus on specific genomic evolutionary events, like the divergence of lineages (in cross-species comparisons) and the most recent WGD (in self comparisons).Conclusions: The QUOTA-ALIGN algorithm screens a set of synteny blocks to retain only those compatible with a user specified ploidy relationship between two genomes. These blocks, in turn, may be used for additional downstream analyses such as identifying true orthologous regions in interspecific comparisons. There are two major contributions of QUOTA-ALIGN: 1) reducing the block screening task to a BIP problem, which is novel; 2) providing an efficient software pipeline starting from all-against-all BLAST to the screened synteny blocks with dot plot visualizations. Python codes and full documentations are publicly available http://github.com/tanghaibao/quota-alignment. QUOTA-ALIGN program is also integrated as a major component in SynMap http://genomevolution.com/CoGe/SynMap.pl, offering easier access to thousands of genomes for non-programmers. © 2011 Tang et al; licensee BioMed Central Ltd.
• Kane, J., Freeling, M., & Lyons, E. (2010). The evolution of a high copy gene array in Arabidopsis. Journal of molecular evolution, 70(6), 531-44.
  More info

  Local gene duplication is a prominent mechanism of gene copy number expansion. Elucidating the mechanisms by which local duplicates arise is necessary in understanding the evolution of genomes and their host organisms. Chromosome one of Arabidopsis thaliana contains an 81-gene array subdivided into 27 triplet units (t-units), with each t-unit containing three pre-transfer RNA genes. We utilized phylogenetic tree reconstructions and comparative genomics to order the events leading to the array's formation, and propose a model using unequal crossing-over as the primary mechanism of array formation. The model is supported by additional phylogenetic information from intergenic spacer sequences separating each t-unit, comparative analysis to an orthologous array of 12 t-units in the sister taxa Arabidopsis lyrata, and additional modeling using a stochastic simulation of orthologous array divergence. Lastly, comparative phylogenetic analysis demonstrates that the two orthologous t-unit arrays undergo concerted evolution within each taxa and are likely fluctuating in copy number under neutral evolutionary drift. These findings hold larger implications for future research concerning gene and genome evolution.
• Woodhouse, M. R., Schnable, J. C., Pedersen, B. S., Lyons, E., Lisch, D., Subramaniam, S., & Freeling, M. (2010). Following tetraploidy in maize, a short deletion mechanism removed genes preferentially from one of the two homologs. PLoS biology, 8(6), e1000409.
  More info

  Previous work in Arabidopsis showed that after an ancient tetraploidy event, genes were preferentially removed from one of the two homologs, a process known as fractionation. The mechanism of fractionation is unknown. We sought to determine whether such preferential, or biased, fractionation exists in maize and, if so, whether a specific mechanism could be implicated in this process. We studied the process of fractionation using two recently sequenced grass species: sorghum and maize. The maize lineage has experienced a tetraploidy since its divergence from sorghum approximately 12 million years ago, and fragments of many knocked-out genes retain enough sequence similarity to be easily identifiable. Using sorghum exons as the query sequence, we studied the fate of both orthologous genes in maize following the maize tetraploidy. We show that genes are predominantly lost, not relocated, and that single-gene loss by deletion is the rule. Based on comparisons with orthologous sorghum and rice genes, we also infer that the sequences present before the deletion events were flanked by short direct repeats, a signature of intra-chromosomal recombination. Evidence of this deletion mechanism is found 2.3 times more frequently on one of the maize homologs, consistent with earlier observations of biased fractionation. The over-fractionated homolog is also a greater than 3-fold better target for transposon removal, but does not have an observably higher synonymous base substitution rate, nor could we find differentially placed methylation domains. We conclude that fractionation is indeed biased in maize and that intra-chromosomal or possibly a similar illegitimate recombination is the primary mechanism by which fractionation occurs. The mechanism of intra-chromosomal recombination explains the observed bias in both gene and transposon loss in the maize lineage. The existence of fractionation bias demonstrates that the frequency of deletion is modulated. Among the evolutionary benefits of this deletion/fractionation mechanism is bulk DNA removal and the generation of novel combinations of regulatory sequences and coding regions.
• Paterson, A. H., Bowers, J. E., 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., Bharti, A. K., Chapman, J., Feltus, F. A., Gowik, U., , Grigoriev, I. V., et al. (2009). The Sorghum bicolor genome and the diversification of grasses. Nature, 457(7229), 551-6.
  More info

  Sorghum, an African grass related to sugar cane and maize, is grown for food, feed, fibre and fuel. We present an initial analysis of the approximately 730-megabase Sorghum bicolor (L.) Moench genome, placing approximately 98% of genes in their chromosomal context using whole-genome shotgun sequence validated by genetic, physical and syntenic information. Genetic recombination is largely confined to about one-third of the sorghum genome with gene order and density similar to those of rice. Retrotransposon accumulation in recombinationally recalcitrant heterochromatin explains the approximately 75% larger genome size of sorghum compared with rice. Although gene and repetitive DNA distributions have been preserved since palaeopolyploidization approximately 70 million years ago, most duplicated gene sets lost one member before the sorghum-rice divergence. Concerted evolution makes one duplicated chromosomal segment appear to be only a few million years old. About 24% of genes are grass-specific and 7% are sorghum-specific. Recent gene and microRNA duplications may contribute to sorghum's drought tolerance.
• Freeling, M., Lyons, E., Pedersen, B., Alam, M., Ming, R., & Lisch, D. (2008). Many or most genes in Arabidopsis transposed after the origin of the order Brassicales. Genome Research, 18(12), 1924-1937.
  More info

  PMID: 18836034;PMCID: PMC2593585;Abstract: Previous to this work, typical genes were thought to move from one position to another infrequently. On the contrary, we now estimate that between one-fourth and three-fourths of the genes in Arabidopsis transposed in the Brassicales. We used the CoGe comparative genomics system to perform and visualize multiple orthologous chromosomal alignments. Using this tool, we found large differences between different categories of genes. Ten of the gene families examined, including genes in most transcription factor families, exhibited a median frequency of 5% transposed genes. In contrast, other gene families were composed largely of transposed genes: NB-LRR disease-resistance genes, genes encoding MADS-box and B3 transcription factors, and genes encoding F-box proteins. A unique method involving transposition-rich regions of genome allowed us to obtain an indirect estimate of the positional stability of the average gene. The observed differences between gene families raise important questions concerning the causes and consequences of gene transposition. ©2008 by Cold Spring Harbor Laboratory Press.
• Lyons, E., & Freeling, M. (2008). How to usefully compare homologous plant genes and chromosomes as DNA sequences. The Plant Journal, 53(4), 661--673.
• Lyons, E., Pedersen, B., Kane, J., & Freeling, M. (2008). The value of nonmodel genomes and an example using SynMap within CoGe to dissect the hexaploidy that predates the rosids. Tropical Plant Biology, 1(3), 181--190.
• Lyons, E., Pedersen, B., Kane, J., Alam, M., Ming, R., Tang, H., Wang, X., Bowers, J., Paterson, A., Lisch, D., & Freeling, M. (2008). Finding and comparing syntenic regions among Arabidopsis and the outgroups papaya, poplar, and grape: CoGe with rosids. Plant Physiology, 148(4), 1772-1781.
  More info

  PMID: 18952863;PMCID: PMC2593677;Abstract: In addition to the genomes of Arabidopsis (Arabidopsis thaliana) and poplar (Populus trichocarpa), two near-complete rosid genome sequences, grape (Vitis vinifera) and papaya (Carica papaya), have been recently released. The phylogenetic relationship among these four genomes and the placement of their three independent, fractionated tetraploidies sum to a powerful comparative genomic system. CoGe, a platform of multiple whole or near-complete genome sequences, provides an integrative Web-based system to find and align syntenic chromosomal regions and visualize the output in an intuitive and interactive manner. CoGe has been customized to specifically support comparisons among the rosids. Crucial facts and definitions are presented to clearly describe the sorts of biological questions that might be answered in part using CoGe, including patterns of DNA conservation, accuracy of annotation, transposability of individual genes, subfunctionalization and/or fractionation of syntenic gene sets, and conserved noncoding sequence content. This précis of an online tutorial, CoGe with Rosids (http://tinyurl.com/4a23pk), presents sample results graphically. © 2008 American Society of Plant Biologists.
• Ming, R., Hou, S., Feng, Y., Qingyi, Y. u., Dionne-Laporte, A., Saw, J. H., Senin, P., Wang, W., Ly, B. V., L., K., Salzberg, S. L., Feng, L., Jones, M. R., Skelton, R. L., Murray, J. E., Chen, C., Qian, W., Shen, J., Peng, D. u., , Eustice, M., et al. (2008). The draft genome of the transgenic tropical fruit tree papaya (Carica papaya Linnaeus). Nature, 452(7190), 991-996.
  More info

  PMID: 18432245;PMCID: PMC2836516;Abstract: Papaya, a fruit crop cultivated in tropical and subtropical regions, is known for its nutritional benefits and medicinal applications. Here we report a 3× draft genome sequence of 'SunUp' papaya, the first commercial virus-resistant transgenic fruit tree to be sequenced. The papaya genome is three times the size of the Arabidopsis genome, but contains fewer genes, including significantly fewer disease-resistance gene analogues. Comparison of the five sequenced genomes suggests a minimal angiosperm gene set of 13,311. A lack of recent genome duplication, atypical of other angiosperm genomes sequenced so far, may account for the smaller papaya gene number in most functional groups. Nonetheless, striking amplifications in gene number within particular functional groups suggest roles in the evolution of tree-like habit, deposition and remobilization of starch reserves, attraction of seed dispersal agents, and adaptation to tropical daylengths. Transgenesis at three locations is closely associated with chloroplast insertions into the nuclear genome, and with topoisomerase I recognition sites. Papaya offers numerous advantages as a system for fruit-tree functional genomics, and this draft genome sequence provides the foundation for revealing the basis of Carica's distinguishing morpho-physiological, medicinal and nutritional properties. ©2008 Nature Publishing Group.
• Freeling, M., Rapaka, L., Lyons, E., Pedersen, B., & Thomas, B. C. (2007). G-boxes, bigfoot genes, and environmental response: Characterization of intragenomic conserved noncoding sequences in Arabidopsis. Plant Cell, 19(5), 1441-1457.
  More info

  PMID: 17496117;PMCID: PMC1913728;Abstract: A tetraploidy left Arabidopsis thaliana with 6358 pairs of homoeologs that, when aligned, generated 14,944 intragenomic conserved noncoding sequences (CNSs). Our previous work assembled these phylogenetic footprints into a database. We show that known transcription factor (TF) binding motifs, including the G-box, are overrepresented in these CNSs. A total of 254 genes spanning long lengths of CNS-rich chromosomes (Bigfoot) dominate this database. Therefore, we made subdatabases: one containing Bigfoot genes and the other containing genes with three to five CNSs (Smallfoot). Bigfoot genes are generally TFs that respond to signals, with their modal CNS positioned 3.1 kb 5′ from the ATG. Smallfoot genes encode components of signal transduction machinery, the cytoskeleton, or involve transcription. We queried each subdatabase with each possible 7-nucleotide sequence. Among hundreds of hits, most were purified from CNSs, and almost all of those significantly enriched in CNSs had no experimental history. The 7-mers in CNSs are not 5′- to 3′-oriented in Bigfoot genes but are often oriented in Smallfoot genes. CNSs with one G-box tend to have two G-boxes. CNSs were shared with the homoeolog only and with no other gene, suggesting that binding site turnover impedes detection. Bigfoot genes may function in adaptation to environmental change. © 2007 American Society of Plant Biologists.
• Thomas, B. C., Rapaka, L., Lyons, E., Pedersen, B., & Freeling, M. (2007). Arabidopsis intragenomic conserved noncoding sequence. Proceedings of the National Academy of Sciences of the United States of America, 104(9), 3348-3353.
  More info

  PMID: 17301222;PMCID: PMC1805546;Abstract: After the most recent tetraploidy in the Arabidopsis lineage, most gene pairs lost one, but not both, of their duplicates. We manually inspected the 3,179 retained gene pairs and their surrounding gene space still present in the genome using a custom-made viewer application. The display of these pairs allowed us to define intragenic conserved noncoding sequences (CNSs), identify exon annotation errors, and discover potentially new genes. Using a strict algorithm to sort high-scoring pair sequences from the bl2seq data, we created a database of 14,944 intragenomic Arabidopsis CNSs. The mean CNS length is 31 bp, ranging from 15 to 285 bp. There are ≈1.7 CNSs associated with a typical gene, and Arabidopsis CNSs are found in all areas around exons, most frequently in the 5′ upstream region. Gene ontology classifications related to transcription, regulation, or "response to..." external or endogenous stimuli, especially hormones, tend to be significantly overrepresented among genes containing a large number of CNSs, whereas protein localization, transport, and metabolism are common among genes with no CNSs. There is a 1.5% overlap between these CNSs and the 218,982 putative RNAs in the Arabidopsis Small RNA Project database, allowing for two mismatches. These CNSs provide a unique set of noncoding sequences enriched for function. CMS function is implied by evolutionary conservation and independently supported because CNS-richness predicts regulatory gene ontology categories. © 2007 by The National Academy of Sciences of the USA.
• Thomas, B. C., Rapaka, L., Lyons, E., Pedersen, B., & Freeling, M. (2007). Arabidopsis intragenomic conserved noncoding sequence. Proceedings of the National Academy of Sciences, 104(9), 3348--3353.
• Leung, S., Holbrook, A., King, B., Lu, H., Evans, V., Miyamoto, N., Mallari, C., Harvey, S., Davey, D., Elena, H. o., Li, W., Parkinson, J., Horuk, R., Jaroch, S., Berger, M., Skuballa, W., West, C., Pulk, R., Phillips, G., , Bryant, J., et al. (2005). Differential inhibition of inducible T cell cytokine secretion by potent iron chelators. Journal of Biomolecular Screening, 10(2), 157-167.
  More info

  PMID: 15799959;Abstract: Effector functions and proliferation of T helper (Th) cells are influenced by cytokines in the environment. Th1 cells respond to a synergistic effect of interleukin-12 (IL-12) and interleukin-18 (IL-18) to secrete interferon-gamma (IFN-γ). In contrast, Th2 cells respond to interleukin-4 (IL-4) to secrete IL-4, interleukin-13 (IL-13), interleukin-5 (IL-5), and interleukin-10 (IL-10). The authors were interested in identifying nonpeptide inhibitors of the Th1 response selective for the IL-12/IL-18-mediated secretion of IFN-γ while leaving the IL-4-mediated Th2 cytokine secretion relatively intact. The authors established a screening protocol using human peripheral blood mononuclear cells (PBMCs) and identified the hydrazino anthranilate compound 1 as a potent inhibitor of IL-12/IL-18-mediated IFN-γ secretion from CD3′ cells with an IC50 around 200 nM. The inhibitor was specific because it had virtually no effect on IL-4-mediated IL-13 release from the same population of cells. Further work established that compound 1 was a potent intracellular iron chelator that inhibited both IL-12/IL-18- and IL-4-mediated T cell proliferation. Iron chelation affects multiple cellular pathways in T cells. Thus, the IL-12/IL-18-mediated proliferation and IFN-γ secretion are very sensitive to intracellular iron concentration. However, the IL-4-mediated IL-13 secretion does not correlate with proliferation and is partially resistant to potent iron chelation. © 2005 The Society for Biomolecular Screening.
• Frank, D. N., Spiegelman, G. B., Davis, W., Wagner, E., Lyons, E., & Pace, N. R. (2003). Culture-independent molecular analysis of microbial constituents of the healthy human outer ear. Journal of Clinical Microbiology, 41(1), 295-303.
  More info

  PMID: 12517864;PMCID: PMC149572;Abstract: Molecular-phylogenetic sequence analyses have provided a new perspective on microbial communities by allowing the detection and identification of constituent microorganisms in the absence of cultivation. In this study we used broad-specificity amplification of ribosomal DNA (rDNA) genes to survey organisms present in the human outer ear canal. Samples were obtained from 24 individuals, including members of three extended families, in order to survey the resident microbiota and to examine microbial population structures in individuals related by familial or household associations. To examine the stability of the microbial populations, one individual was sampled four times and another twice over a 14-month period. We found that a distinct set of microbial types was present in the majority of the subjects sampled. The two most prevalent rDNA sequence types that were identified in multiple individuals corresponded closely to those of Alloiococcus otitis and Corynebacterium otitidis, commonly thought to be associated exclusively with infections of the middle ear. Our results suggest, therefore, that the outer ear canal may serve as a reservoir for normally commensal microbes that can contribute to pathogenesis upon introduction into the middle ear. Alternatively, culture analyses of diseases of the middle ear may have been confounded by these contaminating commensal organisms.
• Washburn, J. O., Lyons, E. H., Haas-Stapleton, E. J., & Volkman, L. E. (1999). Multiple nucleocapsid packaging of Autographa californica nucleopolyhedrovirus accelerates the onset of systemic infection in Trichoplusia ni. Journal of Virology, 73(1), 411-416.
  More info

  PMID: 9847346;PMCID: PMC103847;Abstract: Among the nucleopolyhedroviruses (Baculoviridae), the occlusion-derived virus (ODV), which initiates infection in host insects, may contain only a single nucleocapsid per virion (the SNPVs) or one to many nucleocapsids per virion (the MNPVs), but the significance of this difference is unclear. To gain insight into the biological relevance of these different packaging strategies, we compared pathogenesis induced by ODV fractions enriched for multiple nucleocapsids (ODV-M) or single nucleocapsids (ODV-S) of Autographa californica multicapsid nucleopolyhedrovirus (AcMNPV) containing a β- galactosidase reporter gene. In time course experiments wherein newly molted fourth-instar Trichoplusia ni were challenged with doses of ODV-S or ODV-M that yielded the same final mortality (~70%), we characterized viral foci as either being restricted to the midgut or involving tracheal cells (the secondary target tissue, indicative of systemic infection). We found that while the timing of primary infection by ODV-S and ODV-M was similar, ODV-S established significantly more primary midgut cell loci than ODV-M, but ODV- M infected tracheal cells at twice the rate of ODV-S. The more efficient establishment of tracheal infections by ODV-M decreased the probability that infections were lost by midgut cell sloughing, explaining why higher numbers of primary infections established by ODV-S within larvae were needed to achieve the same final mortality. These results showed that the multiple nucleocapsid packaging strategy of AcMNPV accelerates the onset of irreversible systemic infections and may indicate why MNPVs have wider individual host ranges than SNPVs.

Proceedings Publications

• Kramer, M., Palos, K. R., Nelson, A., Lyons, E., Beilstein, M. A., & Gregory, B. D. (2020). Elucidating the Function of a Novel Long Non-Coding RNA during Arabidopsis development. In Plant and Animal Genome XXVIII Conference (January 11-15, 2020).
• Lyons, E. (2020). CyVerse 2020. In Plant and Animal Genome XXVIII Conference (January 11-15, 2020).
• Conant, G. C., Emery, M. L., Willis, M. M., Hao, Y., Barry, K. W., Oakgrove, K., Peng, Y. i., Schmutz, J., Lyons, E., Pires, J. C., & others, . (2019). Hybrid Conflict, Biased Gene Losses and Developmental Innovation: The Continuing Impact of Ancient Polyploidies on Genome Structure and Function. In Plant and Animal Genome XXVII Conference (January 12-16, 2019).
• Devisetty, U., Castillo-Siri, A., Palos, K. R., Bedre, R., Mandadi, K., Lyons, E., Beilstein, M. A., & Nelson, A. (2019). Comparative Genomic and Transcriptomic Analyses of Functionally Characterized Arabidopsis lncRNAs Reveals Conservation in Unexpected Places. In Plant and Animal Genome XXVII Conference (January 12-16, 2019).
• Lyons, E. (2014). EPIC CoGe: demonstration. In Plant and Animal Genome XXII Conference.
• Lyons, E. (2014). Syntenic Analysis of Banana's Paleopolyploidy Events. In Plant and Animal Genome XXII Conference.
• Hart, M., Jah, M. K., Gaylor, D., Butcher, E., Ten Eyck, B., Corral, E. L., Furfaro, R., Lyons, E. H., Merchant, N. C., Surdeanu, M., Walls, R., & Weiner, B. J. (2016, May). A New Approach to Space Domain Awareness at the University of Arizona. In NATO Symposium on "Considerations for Space and Space-Enabled Capabilities in NATO Coalition Operations".
• Haug-Baltzell, A., Males, J. R., Morzinski, K. M., Wu, Y., Merchant, N., Lyons, E., & Close, L. M. (2016). High-contrast imaging in the cloud with klipReduce and Findr. In SPIE Astronomical Telescopes+ Instrumentation.
• Haug-Baltzell, A., Males, J. R., Morzinski, K. M., Wu, Y., Merchant, N., Lyons, E., & Close, L. M. (2016). High-contrast imaging in the cloud with klipReduce and Findr. In Software and Cyberinfrastructure for Astronomy IV, 9913.
• Hubbard, A. H., Treible, W. R., Bomhoff, M. D., Davis, R., Lyons, E., & Schmidt, C. J. (2016). fRNAkenseq: a Powered-by-iPlant RNA Sequencing Analysis Platform. In INTEGRATIVE AND COMPARATIVE BIOLOGY, 56.
• Lyons, E. (2016). Introduction to CoGe. In Plant and Animal Genome XXIV Conference.
• Sankoff, D., Zheng, C., Lyons, E., & Tang, H. (2016). The Trees in the Peaks. In International Conference on Algorithms for Computational Biology.
• Swetnam, T., Pelletier, J., Rasmussen, C., Callahan, N., Merchant, N., Lyons, E., Rynge, M., Liu, Y., Nandigam, V., & Crosby, C. (2016). Scaling GIS analysis tasks from the desktop to the cloud utilizing contemporary distributed computing and data management approaches: A case study of project-based learning and cyberinfrastructure concepts. In Proceedings of the XSEDE16 Conference on Diversity, Big Data, and Science at Scale.
• This, D., Dufayard, J. F., Bocs, S., Larivi\`ere, D., & Couvin, D. (2016). Comparative genomics of gene families in relation with metabolic pathway for gene candidates highlighting.
• Etemadpour, R., Murray, P., Bomhoff, M., Lyons, E., & Forbes, A. G. (2015). Designing and Evaluating Scientific Workflows for Big Data Interactions. In Big Data Visual Analytics (BDVA), 2015.
• Swetnam, T. L., Pelletier, J. D., Merchant, N., Callahan, N., & Lyons, E. (2015). Scaling Critical Zone analysis tasks from desktop to the cloud utilizing contemporary distributed computing and data management approaches: A case study for project based learning of Cyberinfrastructure concepts. In AGU Fall Meeting Abstracts, 2015.
• Lyons, E., Bomhoff, M., Li, F., & Gregory, B. D. (2014). EPIC-CoGe: Functional and diversity comparative genomics. In Plant and Animal Genome XXII Conference.
• Zheng, C., Albert, V. A., Lyons, E., & Sankoff, D. (2012). Ancient angiosperm hexaploidy meets gene order reconstruction of the eudicot ancestor. In Second IEEE International Conference on Computational Advances in Bio and Medical Sciences (ICCABS).
• Zheng, C., Swenson, K., Lyons, E., & Sankoff, D. (2011). OMG! Orthologs in multiple genomes--competing graph-theoretical formulations. In International workshop on algorithms in bioinformatics.

Presentations

• Lyons, E. H. (2022, Sept). CyVerse. Aliance for Science. Webinar: Cornell.
• Lyons, E. H. (2018, February). Teaching students to use supercomputers for phonemics. Phenome 2018. Tucson, AZ: American Society of Plant Biologists.
• Lyons, E. H. (2018, January). Challenges and Opportunities in Plant Science Data Management “Scaling CoGe”. Plant and Animal Genome Conference. San Diego, CA.
  More info

  CoGe was first publicly launched 9 years ago and contained four genomes from two species – two version of Arabidopsis thaliana and two version of Oryza sativa with a few tools for analyzing and comparing genomes. Today it has grown to manage over 33,000 genomes from nearly 18,000 organisms. Its data management system stores over 1.5 billion structural annotations, 2.5 billion feature names, and over 3.1 billion genomic locations. Recently, CoGe has deployed several data processing pipelines to let users easily use fastq to do transcriptomics, identify variants, quantify epigenomic marks, and a variety of other functional and diversity data. These pipelines automatically add these data to CoGe for more detailed functional analyses of genomes. Of particular note, CoGe’s development team has always been small, averaging one full time employee (max of two). To achieve this growth and sustainability, several design decisions and choices were made during the development of CoGe. This talk will discuss those choices and the lessons learn in developing and maintaining one of the world’s most popular and open platforms for comparative genomics.
• Lyons, E. H. (2018, January). Cyberinfrastructure, Community Development, Capacity Building. Plant and Animal Genome Confernece. San Diego, CA: US National Plant Genome Initiative: the Next 20 years..
  More info

  US National Plant Genome Initiative: the Next 20 years.
• Lyons, E. H. (2018, May). Current advances in cyberinfrastructure for plant science research. CBGP Workshop Frontiers in Plant Biology. Madrid, Spain: Centro de Biotecnología y Genómica de Plantas (CBGP, UPM-INIA) Universidad Politécnica de Madrid (UPM) - Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA).
• Lyons, E. H. (2018, October). Data Science @ University of Arizona. TRIPODS Seminar Series. Tucson, AZ: University of Arizona.
  More info

  Demand for data science education is high at universities, with undergraduates, graduate students, postdocs, researchers, professors, and other professionals wanting to learn how to manage and analyze various datasets. This demand falls into two general categories, just-in-time training and traditional curricula. Just-in-time training meets the demands for researchers with immediate needs. They often have data in hand and need training in such areas as basic program, statistics with R, and data visualization packages. Universities meet this need by offering workshops lasting a couple of hours to a couple of weeks. While often useful for solving a particular problem, these workshops often lack breadth. On the other hand, students are more interested in developing skills that will allow them to get jobs in the future, and are seeking course work to provide both breadth and depth. While there are many programs and courses targeting upper division undergraduates and graduate students, there is a lack of courses at the lower undergraduate level. Pioneering undergraduate education in data science, UC Berkeley created a freshman level data science course, Data 8, to meet the demands of their students. In the three years it has been offered, the course has scaled to be taken by 1300 students a semester, led to a new College of Data Science (the first new college at UC Berkeley in nearly 100 years), and has resulted in over 25 new courses being offered across many departments including neuroscience, business, economics, ethics, history, law, computer science, and mathematics. This seminar will provide a detailed overview of Data 8 including its curricula, technology, and impact it has had at UC Berkeley. Both UC Berkeley and the University Arizona are the leading tier one public research universities in their respective states, with similar administrative structure, student population, and academic and research programs.
• Lyons, E. H. (2018, Septempter). Cyberinfrastructure for life science research. Seminar speaker for LANGEBIO (Mexico). Irapuato, Mexico: The National Laboratory of Genomics for Biodiversity LANGEBIO, Cinvestav.
• Grover, J. W., Bomhoff, M., Davey, S., Gregory, B. D., Mosher, R. A., & Lyons, E. H. (2017, January). User-Friendly Whole Genome DNA Methylation Analysis With FlowGE. Plant and Animal Genomes Conference XXV, Invited seminar. San Diego, CA, USA.
• Lyons, E. H. (2017, Mar 30, 2017). Cyberinfrastructure for Life Science Research. Iowa State University Plant Sciences Seminar. Iowa State University: Iowa State University.
• Beilstein, M. A., & Lyons, E. H. (2016, January). Evolution of Plant lincRNAs. Plant and Animal Genomes. San Diego, CA, USA: Scherago International.
• Nelson, A. D., Forsythe, E. S., Lyons, E. H., & Beilstein, M. A. (2015, September). Identification of long non-coding RNAs using a comparative genomic approach: lessons from Brassicaceae. Plant Genome Evolution. Amsterdam, Netherlands: Current Opinion Conferences - Elsevier.
• Lyons, E. H. (2012, January). Cyberinfrastructure, iPlant, and CoGe. Institute on Science for Global PolicyInstitute on Science for Global Policy.
• Lyons, E. H. (2012, November). What can you do with your genome?. Bi-annual meeting for the Collage of Agriculture and Life Sciences. Tucson, AZ: Collage of Agriculture and Life Sciences.

Others

• Tuggle, C. K., Clarke, J., Dekkers, J. C., Ertl, D., Lawrence-Dill, C. J., Lyons, E., Murdoch, B. M., Scott, N. M., & Schnable, P. S. (2022). The Agricultural Genome to Phenome Initiative (AG2PI): creating a shared vision across crop and livestock research communities.
• Lyons, E., Bomhoff, M. D., Oliver, S. L., & Lenards, A. J. (2014). Comparative Genomics of Grass Genomes using CoGe.
• Pivniouk, V., Rosenbaum, D., Pivniouk, O., Herrell, A., Miller, S., Sprissler, R., Lyons, E., & Vercelli, D. (2014). DNA methylation profiles at the human Th2 locus in BAC transgenic mice point to novel putative regulatory elements (IRM6P. 720).
• Lyons, E. H. (2008, Dec). CoGe, a new kind of comparative genomics platform: Insights into the evolution of plant genomes. Lyon's PhD Dissertation. https://www.amazon.ca/Coge-Kind-Comparative-Genomics-Platform/dp/1244000973